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: 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 +       F AR+SA +++Y Y I  +++  AL
Sbjct: 66  TSSKIPTDKFPLALNSVL--PGDISIKDAVEAPLDFSARYSARQKTYKYLIYNKKSRPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +      I 
Sbjct: 124 LRNYAYYYPYQLDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFENECIA 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY   V 
Sbjct: 184 IYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTKAGKTLPPWGLYLVDVV 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|163857158|ref|YP_001631456.1| tRNA pseudouridine synthase A [Bordetella petrii DSM 12804]
 gi|229557953|sp|A9IRL0|TRUA_BORPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|163260886|emb|CAP43188.1| pseudouridylate synthase I [Bordetella petrii]
          Length = 268

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/249 (36%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---VTGEIVVVHGAGRTDSGVHA 57
           M R  + + Y+GS + GWQ Q +  ++Q ++E A+     + G +  V  AGRTD+GVHA
Sbjct: 1   MPRMALGLAYDGSSWQGWQTQPHRQTVQDTLEAALARFAGIDGSLPTV-CAGRTDTGVHA 59

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV H D   E       + +NA+L  S  I++     V   FHARFSA  R+YLY + 
Sbjct: 60  AMQVVHLDTRLERRAESWVRGVNAFLPPS--IAVQWAQPVPDDFHARFSARSRTYLYLLW 117

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +    L  GRA    + LD + MR AA  L+G HDF++FRS  CQA  P+RT+   D+
Sbjct: 118 RGRVRPPLWAGRAGWCFQPLDVQAMRQAASALLGEHDFSSFRSSQCQARHPVRTLHRLDI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +   + A +FLH  +R+ +G+L  +G G+     +   L A+DR+   P    +
Sbjct: 178 DERGPFLVFTLRANAFLHHMVRNLMGALLQIGQGRQPVAWMPAVLAARDRRLAAPTFAAD 237

Query: 238 GLYFDSVEY 246
           GLY  ++EY
Sbjct: 238 GLYLSAIEY 246


>gi|302038272|ref|YP_003798594.1| tRNA pseudouridine synthase A [Candidatus Nitrospira defluvii]
 gi|300606336|emb|CBK42669.1| tRNA pseudouridine synthase A [Candidatus Nitrospira defluvii]
          Length = 253

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 139/252 (55%), Gaps = 12/252 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + +++EY+G+ Y GWQRQ N  +IQ ++E+A+  +    + + GAGRTD+GVHA  Q
Sbjct: 1   MTTFKLVLEYDGTQYAGWQRQPNAPTIQAAVEEALAAIAQTRLTIIGAGRTDAGVHAFGQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           VA F        REW+     +ALNA+L     IS L++  V   FHAR+SA  + Y Y 
Sbjct: 61  VASFRTDRGLSQREWL-----RALNAHLPAD--ISALSVKAVPDHFHARYSANGKLYEYH 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++ R     L + RAW++ K LD   M  AA +L G HDF++F +      +P   +   
Sbjct: 114 LMNRSERAPLLRERAWMLYKPLDFAAMTEAAAYLTGSHDFSSFETAPTDNENPQCRLQRA 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D+   G+LI +   A  FL   +RS VG+L  VG GK T+ D+   L A+ R   G  AP
Sbjct: 174 DLRRQGDLIILSFYADRFLKQMVRSMVGTLVEVGQGKRTAADMRTVLAARARAAAGRTAP 233

Query: 236 PEGLYFDSVEYS 247
             GLY   V+Y+
Sbjct: 234 AHGLYLVRVDYT 245


>gi|268590477|ref|ZP_06124698.1| tRNA pseudouridine synthase A [Providencia rettgeri DSM 1131]
 gi|291314156|gb|EFE54609.1| tRNA pseudouridine synthase A [Providencia rettgeri DSM 1131]
          Length = 271

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 134/247 (54%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + R  + IEYNGS YFGWQRQ+   S+QG +E+A+  +  E + V  AGRTD+GVHA  Q
Sbjct: 7   LYRIALGIEYNGSRYFGWQRQQEVKSVQGCLEEALSKIAAEPISVFCAGRTDAGVHATGQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-R 119
           V HF+              N +L     I++     V ++FHARFSA  R Y Y I   R
Sbjct: 67  VVHFETSAIRKEAAWTMGANTHL--PPDIAVRWCKPVAEEFHARFSATARRYRYVIFNHR 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L  G        LD + M  AAQ L+G  DFT+FR++ CQ+ SP R + H +V+ 
Sbjct: 125 YRPAILSSGVTHF-HYPLDEKRMHEAAQALLGERDFTSFRAVQCQSKSPWRNVMHVNVSR 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + + + A +F+H  +R+ VGSL  +G G      +   L+ +DR +    A  EGL
Sbjct: 184 HGHYVVVDIKANAFVHHMVRNIVGSLLEIGCGNQNIDWMAHLLELKDRTKAAATAKAEGL 243

Query: 240 YFDSVEY 246
           Y  SV+Y
Sbjct: 244 YLVSVDY 250


>gi|52078642|ref|YP_077433.1| tRNA pseudouridine synthase A [Bacillus licheniformis ATCC 14580]
 gi|52784004|ref|YP_089833.1| tRNA pseudouridine synthase A [Bacillus licheniformis ATCC 14580]
 gi|319649083|ref|ZP_08003291.1| tRNA pseudouridine synthase A [Bacillus sp. BT1B_CT2]
 gi|62901269|sp|Q65P74|TRUA_BACLD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52001853|gb|AAU21795.1| pseudouridylate synthase I [Bacillus licheniformis ATCC 14580]
 gi|52346506|gb|AAU39140.1| TruA [Bacillus licheniformis ATCC 14580]
 gi|317388783|gb|EFV69602.1| tRNA pseudouridine synthase A [Bacillus sp. BT1B_CT2]
          Length = 247

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/248 (36%), Positives = 136/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  ++G+Q Q    +IQ  +EKA+  +    E + V  +GRTDSGVHA+ 
Sbjct: 1   MRMKCTISYDGHLFYGYQVQPGQRTIQDELEKALQTLHKAKERIPVVSSGRTDSGVHAVG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD            ALNA L   D IS+     V+ QFHARFSA R+ Y Y I   
Sbjct: 61  QTIHFDSPLSIPEAKWPYALNALL--PDDISVRKAEAVNDQFHARFSAKRKEYRYMIYRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+ +P  LD E ++ A+++LVG HDFT+F +   +    +RT+   + + 
Sbjct: 119 RHPDVFKRYYAYHVPYDLDMEKVKEASRYLVGTHDFTSFCATKTEVKDKVRTVHELEWSD 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +++R+V   FL+  +R   G+L  VG GK++  D+EK + A++R   G  AP  GL
Sbjct: 179 TGDGLQMRIVGSGFLYNMVRIIAGTLLDVGTGKFSPGDIEKMILAKNRDAAGRTAPAHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 239 YLWRVIYD 246


>gi|312622107|ref|YP_004023720.1| tRNA pseudouridine synthase a [Caldicellulosiruptor kronotskyensis
           2002]
 gi|312202574|gb|ADQ45901.1| tRNA pseudouridine synthase A [Caldicellulosiruptor kronotskyensis
           2002]
          Length = 244

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 134/245 (54%), 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   + I D I       V   F AR+SA +++Y Y I  +++
Sbjct: 66  TSSKIPTDKFPLALNSVLPGDISIKDAIE------VPLDFSARYSARQKTYKYLIYNKKS 119

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL +  A+  P  LD + M+   ++ +G +DF +F S   +A + IR + +  +    
Sbjct: 120 RPALLRNYAYYYPYQLDVDAMQRTCEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFEN 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY 
Sbjct: 180 ECIAIYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTKAGKTLPPWGLYL 239

Query: 242 DSVEY 246
             V Y
Sbjct: 240 VDVVY 244


>gi|330966232|gb|EGH66492.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 274

 Score =  156 bits (395), 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-------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|158319577|ref|YP_001512084.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
 gi|158139776|gb|ABW18088.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
          Length = 248

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 136/247 (55%), Gaps = 5/247 (2%)

Query: 2   IRYCMI-IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  MI IEY+GS Y GWQ Q N  +IQ  I KA+  + G+ VV+HG+GRTD+GVHA  Q
Sbjct: 1   MRNIMIEIEYDGSNYSGWQVQPNAITIQEEIMKALKKLEGKDVVIHGSGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA F L+   +PV  L  A+N+ L     I+I++   V   FHAR+SAI + Y+Y I   
Sbjct: 61  VATF-LMERNIPVERLPLAMNSNL--PKDITIIDAKEVPMDFHARYSAIGKRYIYHIYES 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   A+ +  ++ I   LD   M  A++ L+G HDF  F S        +RTI   +  S
Sbjct: 118 RYRSAILRNYSYHINYKLDRSKMMEASKLLIGTHDFRGFMSNGSSVEDTVRTIKSLEFKS 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I + +    FL+  +R   G+L  +G G      +EK L+ +DR   G  APP+GL
Sbjct: 178 DGENIYMIIEGDGFLYNMVRIITGTLVQIGAGNKPLEQIEKILKTKDRSLAGHTAPPQGL 237

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 238 FLDKVFY 244


>gi|22125494|ref|NP_668917.1| tRNA pseudouridine synthase A [Yersinia pestis KIM 10]
 gi|45442187|ref|NP_993726.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Microtus str.
           91001]
 gi|108808073|ref|YP_651989.1| tRNA pseudouridine synthase A [Yersinia pestis Antiqua]
 gi|108812343|ref|YP_648110.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|145599273|ref|YP_001163349.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides F]
 gi|162419146|ref|YP_001604969.1| tRNA pseudouridine synthase A [Yersinia pestis Angola]
 gi|165925379|ref|ZP_02221211.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165937079|ref|ZP_02225644.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166008316|ref|ZP_02229214.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166214223|ref|ZP_02240258.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167398935|ref|ZP_02304459.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167421195|ref|ZP_02312948.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167424547|ref|ZP_02316300.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167469280|ref|ZP_02333984.1| tRNA pseudouridine synthase A [Yersinia pestis FV-1]
 gi|170023770|ref|YP_001720275.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis YPIII]
 gi|229838336|ref|ZP_04458495.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229895366|ref|ZP_04510539.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides A]
 gi|229898902|ref|ZP_04514047.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229902698|ref|ZP_04517815.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|270490127|ref|ZP_06207201.1| tRNA pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294504649|ref|YP_003568711.1| tRNA pseudouridine synthase A [Yersinia pestis Z176003]
 gi|21958390|gb|AAM85168.1|AE013763_2 pseudouridylate synthase I [Yersinia pestis KIM 10]
 gi|45437051|gb|AAS62603.1| pseudouridylate synthase I [Yersinia pestis biovar Microtus str.
           91001]
 gi|108775991|gb|ABG18510.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|108779986|gb|ABG14044.1| tRNA pseudouridine synthase A [Yersinia pestis Antiqua]
 gi|145210969|gb|ABP40376.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides F]
 gi|162351961|gb|ABX85909.1| tRNA pseudouridine synthase A [Yersinia pestis Angola]
 gi|165914942|gb|EDR33554.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165922986|gb|EDR40137.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165992698|gb|EDR44999.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166204579|gb|EDR49059.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166960684|gb|EDR56705.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167051439|gb|EDR62847.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167056429|gb|EDR66198.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169750304|gb|ACA67822.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis YPIII]
 gi|229680145|gb|EEO76244.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|229688450|gb|EEO80521.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229694702|gb|EEO84749.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229701674|gb|EEO89700.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides A]
 gi|262362710|gb|ACY59431.1| tRNA pseudouridine synthase A [Yersinia pestis D106004]
 gi|270338631|gb|EFA49408.1| tRNA pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294355108|gb|ADE65449.1| tRNA pseudouridine synthase A [Yersinia pestis Z176003]
 gi|320014566|gb|ADV98137.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 293

 Score =  156 bits (394), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 30  LKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQV 89

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + R 
Sbjct: 90  VHFVTSAVRKDAAWTMGVNSHLPAD--IAVRWVKTVDNDFHARFSATARRYRYIIFSHRY 147

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   
Sbjct: 148 RPAILAQGVTHCY-MPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRH 206

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY
Sbjct: 207 GAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLY 266

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 267 LVSVDY 272


>gi|68249766|ref|YP_248878.1| tRNA pseudouridine synthase A [Haemophilus influenzae 86-028NP]
 gi|81335806|sp|Q4QL79|TRUA_HAEI8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|68057965|gb|AAX88218.1| tRNA pseudouridine synthase A [Haemophilus influenzae 86-028NP]
          Length = 269

 Score =  156 bits (394), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|163790163|ref|ZP_02184597.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
 gi|159874654|gb|EDP68724.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
          Length = 279

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 88/253 (34%), Positives = 143/253 (56%), Gaps = 15/253 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
           IRY MII+Y+G+ + G+Q Q N  ++QG I+KA+ ++T G  +++HG+GRTDSGVHA  Q
Sbjct: 4   IRYKMIIQYDGTHFAGFQIQPNDRTVQGEIQKALKIMTKGLEIIIHGSGRTDSGVHAKGQ 63

Query: 61  VAHFDLVREWVPVILC-----KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD      P++L      +ALN+    +D + +  ++IVD  FHAR++   + Y YR
Sbjct: 64  VIHFDY-----PILLPVENMQRALNSL--TTDELFVEKVAIVDTNFHARYNTSGKKYQYR 116

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +     P   ++      P  +D E ++ A + L G HDF++F + +    + +RT+   
Sbjct: 117 VDLNAIPNPFKRLYTLHHPYPIDMEKLQNALKDLEGEHDFSSFCASNSGRENKVRTVYEA 176

Query: 176 DV--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            V  + F N +        FL+  +R FVG+L  + +G   + ++++ L  +DR E GP 
Sbjct: 177 SVVKDIFNNELIFTFSGNGFLYNMVRIFVGTLLQIANGLRPADEIKRLLAVKDRNEAGPT 236

Query: 234 APPEGLYFDSVEY 246
           A P+GLY   V Y
Sbjct: 237 AKPQGLYLMEVYY 249


>gi|302187262|ref|ZP_07263935.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. syringae
           642]
          Length = 274

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), 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  VHFDTQAERTMKAWV-------MGANINLPHDVSVTWARVMPAAFHARFKAIARRYRYVI 120

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA+ LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEFLVGTHDFSAFRAGQCQAKSPVKQLHHL 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|319897314|ref|YP_004135510.1| tRNA pseudouridine synthase a [Haemophilus influenzae F3031]
 gi|317432819|emb|CBY81184.1| tRNA pseudouridine synthase A [Haemophilus influenzae F3031]
          Length = 269

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|197285647|ref|YP_002151519.1| tRNA pseudouridine synthase A [Proteus mirabilis HI4320]
 gi|194683134|emb|CAR43721.1| tRNA pseudouridine synthase A [Proteus mirabilis HI4320]
          Length = 281

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 18  LKIALGIEYDGSHYYGWQRQNEVRSVQERLEKALSQVANEPISVFCAGRTDAGVHATGQV 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+             +N +L     I++  +  V   FHARFSA  R Y Y I   R 
Sbjct: 78  VHFETTAHRKDAAWTMGVNTHLP--QDIAVRWVKTVANDFHARFSATARRYRYVIFNHRY 135

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +
Sbjct: 136 RPAILSSGVTHF-HYPLDAQRMHQAAQCLLGENDFTSFRAVQCQSRTPWRNVMHVNVSRY 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + + + A +F+H  +R+ VGSL  +G G    T + + L  +DR +    A   GLY
Sbjct: 195 GDYVVVDIKANAFVHHMVRNIVGSLLEIGCGNQAITWMAELLALKDRTKAAATAKANGLY 254

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 255 LVSVDY 260


>gi|262366637|gb|ACY63194.1| tRNA pseudouridine synthase A [Yersinia pestis D182038]
          Length = 293

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 30  LKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQV 89

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + R 
Sbjct: 90  VHFVTSAVRKDAAWTMGVNSHLPAD--IAVRWVKTVDNDFHARFSATARRYRYIIFSHRY 147

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   
Sbjct: 148 RPAILAQGVTHCY-MPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRH 206

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY
Sbjct: 207 GAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLY 266

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 267 LVSVDY 272


>gi|16273533|ref|NP_439786.1| tRNA pseudouridine synthase A [Haemophilus influenzae Rd KW20]
 gi|260580419|ref|ZP_05848248.1| tRNA pseudouridine synthase A [Haemophilus influenzae RdAW]
 gi|1174804|sp|P45291|TRUA_HAEIN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1574492|gb|AAC23291.1| pseudouridylate synthase I (truA) [Haemophilus influenzae Rd KW20]
 gi|260093096|gb|EEW77030.1| tRNA pseudouridine synthase A [Haemophilus influenzae RdAW]
          Length = 269

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGTGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|51596937|ref|YP_071128.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186896018|ref|YP_001873130.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis PB1/+]
 gi|51590219|emb|CAH21856.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186699044|gb|ACC89673.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis PB1/+]
          Length = 299

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 36  LKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQV 95

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + R 
Sbjct: 96  VHFVTSAVRKDAAWTMGVNSHLPAD--IAVRWVKTVDNDFHARFSATARRYRYIIFSHRY 153

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   
Sbjct: 154 RPAILAQGVTHCY-MPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRH 212

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY
Sbjct: 213 GAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLY 272

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 273 LVSVDY 278


>gi|266620223|ref|ZP_06113158.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
 gi|288868186|gb|EFD00485.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
          Length = 354

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q NG +I+  + +A+  +  E V V GA RTDSGVHA   
Sbjct: 1   MKRIKLIVAYDGTNYCGWQIQNNGRTIEEVLNEALTALLHEKVAVIGASRTDSGVHAEGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C ALN   ++ + I +L    V   +H R     ++Y YRI+ R+
Sbjct: 61  VAVFDTENRMPADKICFALNQ--RLPEDIRVLKSEEVPLTWHPRKCNCVKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +  A+     LD E M+ AA++LVG HDFT+F +   QA   +RTI   DV   
Sbjct: 119 IEVPTLRLYAYFCYYPLDVEKMKQAAEYLVGEHDFTSFCAPRTQAEDMVRTIYSLDVGKT 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IRV    FL+  +R   G+L  VG G W    +E+ L A+ R   GP A   GL 
Sbjct: 179 GDMITIRVSGSGFLYNMVRIIAGTLMKVGLGVWPPEHVEEILDARSRAAAGPTAVARGLT 238

Query: 241 FDSVE 245
             S+E
Sbjct: 239 LISLE 243


>gi|165976323|ref|YP_001651916.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|307250146|ref|ZP_07532106.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307256957|ref|ZP_07538734.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|238687566|sp|B0BPI7|TRUA_ACTPJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|165876424|gb|ABY69472.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|306857811|gb|EFM89907.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306864532|gb|EFM96438.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 262

 Score =  156 bits (394), Expect = 3e-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-------NKLRSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPW 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|260589149|ref|ZP_05855062.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|331082565|ref|ZP_08331690.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
 gi|260540569|gb|EEX21138.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|330400543|gb|EGG80173.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 245

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG ++Q  + + +   TGE +   GA RTD+GVHAL  
Sbjct: 1   MKRVKLTVAYDGTNYCGWQVQPNGITVQEVLNQCLSEFTGENIETIGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN   ++ + I I     VD  FH R+   +++Y YRI+  +
Sbjct: 61  VAVFDTEMRMPGDKFSFALNQ--RLPEDIRIQKSEEVDADFHPRYVKSQKTYEYRILNCR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+  +      LD + M+ AA +L+G HDF +F     Q  + +RT+    +   
Sbjct: 119 FPIPTERFYSHFTYIPLDVDKMKEAASYLIGEHDFKSFCGTGAQVKTTVRTVKEIQIEKS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I IR+    FL+  +R   G+L  +G G +    +++ L+A+DRK+ GP AP  GL 
Sbjct: 179 GDRITIRITGEGFLYNMVRIIAGTLMDIGGGLYPPEKMKEILEAKDRKKAGPTAPARGLT 238

Query: 241 FDSVEY 246
              ++Y
Sbjct: 239 LMKIQY 244


>gi|134301921|ref|YP_001121890.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|166228700|sp|A4IXW8|TRUA_FRATW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|134049698|gb|ABO46769.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis WY96-3418]
          Length = 258

 Score =  155 bits (393), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q S+EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQESLEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


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

 Score =  155 bits (393), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 137/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   S+QG +E+A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 16  MKIALGIEYDGSRYYGWQRQQEVKSVQGCLEEALSKVADEPISVFCAGRTDAGVHATGQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+   +         +N +L     I++  +  VD+ FHARFSA  R Y Y I   R 
Sbjct: 76  VHFETSVQRKDAAWTMGVNVHL--PPDIAVRWVKTVDEGFHARFSATARRYRYIIFNHRY 133

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD + M  AAQ ++G +DFT+FR++ CQ+ +P R + H +VN +
Sbjct: 134 RPAVLANGVTHF-HYPLDEKRMHQAAQCILGENDFTSFRAVQCQSKTPWRNVMHINVNRY 192

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I + A +F+H  +R+  GSL  +G G      + + L  +DR +    A   GLY
Sbjct: 193 GHYVVIDIKANAFVHHMVRNIAGSLMEIGCGNQDINWMAQLLALKDRAKAAATAKAAGLY 252

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 253 LVAVDY 258


>gi|227356152|ref|ZP_03840541.1| tRNA pseudouridine synthase A [Proteus mirabilis ATCC 29906]
 gi|227163616|gb|EEI48532.1| tRNA pseudouridine synthase A [Proteus mirabilis ATCC 29906]
          Length = 289

 Score =  155 bits (393), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 26  LKIALGIEYDGSHYYGWQRQNEVRSVQERLEKALSQVANEPISVFCAGRTDAGVHATGQV 85

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+             +N +L     I++  +  V   FHARFSA  R Y Y I   R 
Sbjct: 86  VHFETTAHRKDAAWTMGVNTHLP--QDIAVRWVKTVANDFHARFSATARRYRYVIFNHRY 143

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +
Sbjct: 144 RPAILSSGVTHF-HYPLDAQRMHQAAQCLLGENDFTSFRAVQCQSRTPWRNVMHVNVSRY 202

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + + + A +F+H  +R+ VGSL  +G G    T + + L  +DR +    A   GLY
Sbjct: 203 GDYVVVDIKANAFVHHMVRNIVGSLLEIGCGNQAITWMAELLALKDRTKAAATAKANGLY 262

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 263 LVSVDY 268


>gi|260582150|ref|ZP_05849944.1| tRNA pseudouridine synthase A [Haemophilus influenzae NT127]
 gi|260094782|gb|EEW78676.1| tRNA pseudouridine synthase A [Haemophilus influenzae NT127]
          Length = 269

 Score =  155 bits (393), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRQEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|160881752|ref|YP_001560720.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
 gi|160430418|gb|ABX43981.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
          Length = 245

 Score =  155 bits (393), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q N  +I+G + + +  +  E +V+ GA RTD+GVHA   
Sbjct: 1   MKRVLLKVAYDGTNYCGWQVQPNAKTIEGVLNECLTKLLKEEIVIIGASRTDAGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         L  ALNA+L   + I I     V+  FH R+   R++Y YRI    
Sbjct: 61  VAVFDTNSRIPAEKLSYALNAHL--PEDIVIQASMEVESDFHPRYCDTRKTYEYRIYNAT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL   +  A  +   LD E MR AA +L+G HDF +F S + Q     RTI    +   
Sbjct: 119 FPLPTNRRYAHFVYYDLDLEAMRKAASYLIGEHDFVSFCSANTQVKDTTRTIYDIQIEKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI IR+    FL+  +R   G+L  VG  +W    + +AL  +DR+  GP AP +GL 
Sbjct: 179 RELIVIRIKGNGFLYNMVRIIAGTLIQVGTHQWEPERVLEALTKKDRQAAGPTAPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LVEIEY 244


>gi|325276985|ref|ZP_08142659.1| tRNA pseudouridine synthase A [Pseudomonas sp. TJI-51]
 gi|324097881|gb|EGB96053.1| tRNA pseudouridine synthase A [Pseudomonas sp. TJI-51]
          Length = 286

 Score =  155 bits (393), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 96/251 (38%), Positives = 130/251 (51%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ +G  S+Q ++E+A+  V  E + V  AGRTD+GVH   QV
Sbjct: 20  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPIAVVCAGRTDAGVHGCGQV 79

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R W        +     +   IS++    +   FHARF A  R Y Y I
Sbjct: 80  VHFDTRAVRDERAWT-------MGTNFNLPHDISVVWSQPMPADFHARFKACARRYRYVI 132

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 P  L +   W   + LD E M  AAQ L+G HDF+ FR+  CQA SPI+ I H 
Sbjct: 133 YNDPIRPAHLAEEVTW-NHRPLDVERMAQAAQSLLGTHDFSAFRASQCQAKSPIKHIYHL 191

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + V A +FLH  +R+  G L  +G G+   +   + L+ +DR+E G  A 
Sbjct: 192 RVTRHGQMIVLDVRATAFLHHMVRNIAGVLMAIGSGERPVSWAREVLEGRDRREGGVTAH 251

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 252 PYGLYLVQVEY 262


>gi|90410767|ref|ZP_01218782.1| tRNA pseudouridine synthase A [Photobacterium profundum 3TCK]
 gi|90328398|gb|EAS44696.1| tRNA pseudouridine synthase A [Photobacterium profundum 3TCK]
          Length = 261

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGAKYCGWQRQVDVDSVQERLEKALSHIANKPIAVFCAGRTDTGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +   V     +NA+L     IS+   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDVDVDRQMVAWTIGVNAHL--PRDISVRWATPVSDDFHARFSATARRYRYIIYNNAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ+LVG HDFT+ R+  CQ+ SP R + H +V+  G
Sbjct: 119 RPAIFGIGVSHYHGHLDEKKMHEAAQYLVGEHDFTSVRASQCQSRSPWRAMKHVNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+ T   ++  L+ +DR+  G  A   GLY 
Sbjct: 179 DFVIIDIKANAFVHHMVRNIAGSLIRVGRGQETPEWMKWVLEQKDRRVAGETAKAAGLYL 238

Query: 242 DSVEY 246
            +V+Y
Sbjct: 239 VAVDY 243


>gi|32491058|ref|NP_871312.1| hypothetical protein WGLp309 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|31340463|sp|Q8D2P5|TRUA_WIGBR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|25166265|dbj|BAC24455.1| truA [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 264

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 90/241 (37%), Positives = 139/241 (57%), Gaps = 6/241 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--D 65
           I Y G+ Y GWQ QKN  SIQ  +E A+F  +GE + ++ AGRTD+ VHAL QV HF  D
Sbjct: 8   ISYQGNNYCGWQSQKNIISIQEYVELALFKFSGEKIKIYCAGRTDAKVHALLQVVHFYTD 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           + R +   IL   +N+YL     ISI+ +  V   FHAR+SAI + YLY I    +   +
Sbjct: 68  IKRSYRQWIL--GVNSYLPYD--ISIMWVIKVHNNFHARYSAIAKKYLYLIHNNISRSGI 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   + +  SL+  +M+ AAQ L+G+HDF++F+   CQ+ +  R I +  +N +   I 
Sbjct: 124 FRKYCFNVFISLNINDMKKAAQKLIGKHDFSSFKGSECQSKTTYRVIYYIRINKYKEYIF 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + + A SFL+  +R+ +G+L  +G GK +   + + L  ++ K     A P+GLY  +V 
Sbjct: 184 VEIKANSFLNHMMRNIIGNLIEIGKGKKSKEWMSELLFLKNNKFSIFSADPKGLYLSNVY 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|149365240|ref|ZP_01887275.1| tRNA pseudouridine synthase A [Yersinia pestis CA88-4125]
 gi|153950548|ref|YP_001400399.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
 gi|218929838|ref|YP_002347713.1| tRNA pseudouridine synthase A [Yersinia pestis CO92]
 gi|25009503|sp|Q8ZD27|TRUA_YERPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901277|sp|Q668W9|TRUA_YERPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166991167|sp|A7FGM1|TRUA_YERP3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|115348449|emb|CAL21385.1| tRNA pseudouridine synthase A [Yersinia pestis CO92]
 gi|149291653|gb|EDM41727.1| tRNA pseudouridine synthase A [Yersinia pestis CA88-4125]
 gi|152962043|gb|ABS49504.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
          Length = 264

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + R 
Sbjct: 61  VHFVTSAVRKDAAWTMGVNSHLPAD--IAVRWVKTVDNDFHARFSATARRYRYIIFSHRY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   
Sbjct: 119 RPAILAQGVTHCY-MPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY
Sbjct: 178 GAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLY 237

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 238 LVSVDY 243


>gi|146282143|ref|YP_001172296.1| tRNA pseudouridine synthase A [Pseudomonas stutzeri A1501]
 gi|145570348|gb|ABP79454.1| tRNA-pseudouridine synthase I [Pseudomonas stutzeri A1501]
          Length = 286

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 102/252 (40%), Positives = 135/252 (53%), Gaps = 16/252 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           R  + +EY GS Y G+QRQ+ G  SIQ S+E A+  V G   V +  AGRTD+ VHA  Q
Sbjct: 19  RIALGVEYKGSRYRGFQRQRAGVPSIQESLENALTRVAGGHPVTLSCAGRTDALVHASGQ 78

Query: 61  VAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD   E     WV       + A + +   IS+     +   F ARFSA+ R Y Y 
Sbjct: 79  VVHFDTPVERSMHAWV-------MGANMNLPPDISVTWAKKMPPHFDARFSAMARRYRYV 131

Query: 116 IITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I   Q  P  + +   W   + LD E MR AA  LVG HDF+ FR+  CQA SPI+TI H
Sbjct: 132 IYNDQIRPAHMAEEVTWNH-RPLDIERMRAAAAALVGTHDFSAFRARQCQAKSPIKTIHH 190

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++  FG LI I V A +FLH  +R+F G L  +G G+       + L+++ R+  G  A
Sbjct: 191 LELLQFGRLIVIDVRANAFLHHMVRNFAGVLMTIGAGERPVEWAAQVLESRVRRTGGVTA 250

Query: 235 PPEGLYFDSVEY 246
            P GLY   V+Y
Sbjct: 251 HPYGLYLVEVDY 262


>gi|319776538|ref|YP_004139026.1| tRNA pseudouridine synthase A [Haemophilus influenzae F3047]
 gi|329124048|ref|ZP_08252595.1| tRNA pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
 gi|317451129|emb|CBY87362.1| tRNA pseudouridine synthase A [Haemophilus influenzae F3047]
 gi|327467473|gb|EGF12971.1| tRNA pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
          Length = 269

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHRAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|296315347|ref|ZP_06865288.1| tRNA pseudouridine synthase A [Neisseria polysaccharea ATCC 43768]
 gi|296837693|gb|EFH21631.1| tRNA pseudouridine synthase A [Neisseria polysaccharea ATCC 43768]
          Length = 267

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 129/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 10  RWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGEAVSTIVAGRTDTGVHATAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           +  NA L   + I++L+       FHARF A  R Y Y + +   
Sbjct: 70  VHFDTAARRPAQAWIRGTNAVLP--EGIAVLHARQTAPGFHARFDAYGRHYRYLLESSPV 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   G
Sbjct: 128 RSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQAG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 188 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSALIQERSRLKAPPTFMPDGLYL 247

Query: 242 DSVEY 246
             V+Y
Sbjct: 248 TGVDY 252


>gi|262198313|ref|YP_003269522.1| tRNA pseudouridine synthase A [Haliangium ochraceum DSM 14365]
 gi|262081660|gb|ACY17629.1| tRNA pseudouridine synthase A [Haliangium ochraceum DSM 14365]
          Length = 264

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 128/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+G  GWQRQ N  ++Q  +E A+  + G  V + GA RTD+GVHAL QVAHF 
Sbjct: 9   LVLEYDGTGLSGWQRQNNAPTVQAHVEDALSSMLGRAVQIVGASRTDAGVHALGQVAHFR 68

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P    + LN   K+   I+++  + V   FHARF +  + Y Y + TR A   L
Sbjct: 69  TGSSIPPHGFLRGLNG--KLPPAIAVVACAEVRADFHARFDSRGKHYRYALHTRAARAPL 126

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFGNLI 184
            + RAW  P+ LD   M  AAQ ++G  DF  FR+  C A +  R +D   ++    +LI
Sbjct: 127 LRERAWHCPRPLDLAAMERAAQAMLGERDFQAFRASGCTAKTSRRRVDRVALSRPAADLI 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I V   +FL   +R   G+L  VG G+  + ++   L ++DR   G  AP  GL    V
Sbjct: 187 HIDVYGNAFLRNMVRIMAGTLVDVGLGRLAADEISSILDSRDRTCAGRTAPAHGLTLVEV 246

Query: 245 EY 246
            Y
Sbjct: 247 FY 248


>gi|299138466|ref|ZP_07031645.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX8]
 gi|298599712|gb|EFI55871.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX8]
          Length = 271

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 142/270 (52%), Gaps = 26/270 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + + Y+G+ + GWQ Q    ++QGS+  A+  VTGE V+  G+GRTDSGVHAL Q
Sbjct: 1   MNHWKLTLSYDGTLFHGWQVQPELPTVQGSLALALKYVTGESVLPQGSGRTDSGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F L     P  L +ALN  L  S  I IL   +VD+ FHAR SA R++Y YRI  R+
Sbjct: 61  VTSFALETSIPPANLQRALNRALPPS--IRILTAELVDESFHARHSARRKTYEYRIFERR 118

Query: 121 APLALEK--GRAWLIPKSLDC------ENMRIAAQHLVGRHDFTTF------RSIHCQAS 166
              +  +     +L P + DC      E M+ A+++L G HDFT+F      R +  + S
Sbjct: 119 TAASPSERICSPFLAPYAWDCRWQLAIEPMQEASKYLCGTHDFTSFAASDPERGLREEES 178

Query: 167 ----------SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                     +P++T+          L+  RV    FLH  +R+ VG+L  VG G     
Sbjct: 179 DDANGKAHGPNPVKTLLQAGWAHEDGLLVYRVTGSGFLHHMVRNIVGTLADVGRGSLAVD 238

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++ + L A++R   GP AP  GL+  SVEY
Sbjct: 239 EIPRILAARNRTAAGPTAPACGLFLHSVEY 268


>gi|170720741|ref|YP_001748429.1| tRNA pseudouridine synthase A [Pseudomonas putida W619]
 gi|169758744|gb|ACA72060.1| tRNA pseudouridine synthase A [Pseudomonas putida W619]
          Length = 284

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 96/251 (38%), Positives = 130/251 (51%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  S+Q ++E+A+  V  E + V  AGRTD+GVH   Q+
Sbjct: 18  RIALGVEYKGSRYRGWQRQASGVPSVQQALEQALSKVANEPITVVCAGRTDAGVHGCGQI 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R W        L     +   IS++    +   FHARF A  R Y Y I
Sbjct: 78  VHFDTRANRDERAWT-------LGTNFNLPHDISVVWSRPMPADFHARFKATARRYRYVI 130

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 P  L +   W   + LD E M  AAQ L+G HDF+ FR+  CQA SPI+ I H 
Sbjct: 131 YNDPIRPAHLAEEVTW-NHRPLDVERMADAAQFLLGTHDFSAFRASQCQAKSPIKHIHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + V A +FLH  +R+  G L  +G G+  +    + L+ ++R+E G  A 
Sbjct: 190 RVTRHGQMIVLDVRATAFLHHMVRNIAGVLMTIGAGERPAGWAREVLEGRNRREGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVQVEY 260


>gi|325265188|ref|ZP_08131914.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
 gi|324029592|gb|EGB90881.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
          Length = 263

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + K +  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLTVAYDGTNYCGWQIQPNGITIEEILNKKLSRLTGEEIRVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  L  ALN   ++ + I I+    V   +H R+    ++Y Y I+  +
Sbjct: 61  VAVFDTETTIPPDRLAYALNQ--RMPEDIVIVKSEEVPADWHPRYCDTVKTYEYLILNAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   + +   LD + MR AA +L G HDF +F ++       +RTI   D+   
Sbjct: 119 IPDPTRRLTTYFVSYDLDLQKMRRAAGYLSGEHDFASFCNVRTNVEDTVRTIYELDILEN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I IR+    FL+  +R  VG+L  VG G +T   ++  L+A+DR+  G  APP GL 
Sbjct: 179 GEEITIRIRGNGFLYNMVRIIVGTLLRVGRGFYTPEQVKDILEAKDRQAAGVTAPPHGLR 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LIGIEY 244


>gi|323143617|ref|ZP_08078294.1| tRNA pseudouridine synthase A [Succinatimonas hippei YIT 12066]
 gi|322416680|gb|EFY07337.1| tRNA pseudouridine synthase A [Succinatimonas hippei YIT 12066]
          Length = 261

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 137/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY G  Y G+QRQ N  ++QG +EKA+ ++  E V +  AGRTD+GV+A  QV
Sbjct: 1   MRVALGVEYEGWNYAGFQRQPNAVTVQGELEKALSIIADEPVSLVCAGRTDAGVNATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII-TRQ 120
            H D+ ++     L    N   K+   I+I    IV + FHARFSA  R Y Y I  T  
Sbjct: 61  IHIDITKDRSEKALLLGTNT--KLPSDIAITWAKIVSEDFHARFSARARRYRYIIQNTMH 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L KG + +     D E M+ AA+ L+G HDF +F+    Q+SS  R + + +++  
Sbjct: 119 RPGVLNKGVS-VYHGDYDIELMQKAAKILIGEHDFASFKGADEQSSSTFRCVHYIEISRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   + A +FL+  +R+ VGSL LVG    ++   E+A +A++R   GP A P+GLY
Sbjct: 178 GPFIVFDIAANAFLNHMVRNIVGSLLLVGSKVKSTAWFEEAFKARNRDAAGPTAHPDGLY 237

Query: 241 FDSVEY 246
              V Y
Sbjct: 238 LVDVTY 243


>gi|145633047|ref|ZP_01788779.1| tRNA pseudouridine synthase A [Haemophilus influenzae 3655]
 gi|144986273|gb|EDJ92852.1| tRNA pseudouridine synthase A [Haemophilus influenzae 3655]
          Length = 269

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|145639258|ref|ZP_01794864.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittII]
 gi|145271561|gb|EDK11472.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittII]
 gi|309751137|gb|ADO81121.1| tRNA pseudouridine synthase A [Haemophilus influenzae R2866]
          Length = 269

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPNKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|145637534|ref|ZP_01793192.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittHH]
 gi|145269340|gb|EDK09285.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittHH]
          Length = 269

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|308050321|ref|YP_003913887.1| tRNA pseudouridine synthase A [Ferrimonas balearica DSM 9799]
 gi|307632511|gb|ADN76813.1| tRNA pseudouridine synthase A [Ferrimonas balearica DSM 9799]
          Length = 263

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 98/247 (39%), Positives = 126/247 (51%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G GYFGWQRQ+    +Q  +E AI  V    V V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGHGYFGWQRQREVVGVQERLEAAIAKVANHPVEVACAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HFD   +  P      LNA L   D I++     V   FHARFSA  R Y Y I   R 
Sbjct: 61  VHFDAQFDRRPAAWTLGLNANL--PDGIAVRWAQPVSDDFHARFSATARRYRYIIFNNRL 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD   M  A Q L+G +DF+ FR+I CQ+ +P R I H  V   
Sbjct: 119 RPGILRHGVSHYH-HPLDEALMHQAGQQLLGENDFSAFRAIQCQSRTPWRNIHHLRVTRQ 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G      + + L+ +DR      A  EGLY
Sbjct: 178 GQYVIIDIKANAFVHHMVRNIAGSLMEVGMGNRPVEWIAELLEGKDRNLAAATAKAEGLY 237

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 238 LVEVDYP 244


>gi|145630935|ref|ZP_01786711.1| tRNA pseudouridine synthase A [Haemophilus influenzae R3021]
 gi|144983402|gb|EDJ90878.1| tRNA pseudouridine synthase A [Haemophilus influenzae R3021]
          Length = 269

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVYHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|52425230|ref|YP_088367.1| tRNA pseudouridine synthase A [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307282|gb|AAU37782.1| TruA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 270

 Score =  155 bits (392), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/258 (36%), Positives = 132/258 (51%), Gaps = 26/258 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +++  + IEYNG  YFGWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   Q
Sbjct: 7   IMKIALGIEYNGKNYFGWQRQEKVHSVQAELEKALSFVANEKIEVFCAGRTDSGVHGTGQ 66

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+       + W       A      + D I++     V   FHARFSA  R Y Y 
Sbjct: 67  VVHFETNAIRPEKAW-------AFGTNANLPDDIAVRWAKEVPDDFHARFSATARRYRYV 119

Query: 116 IITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
                  L   K R+ ++P         LD   M+ A + L+G +DF++FR+  CQ+++P
Sbjct: 120 -------LYCNKLRSAILPYGITHTHLDLDEHKMQEAGRFLLGENDFSSFRAAQCQSNTP 172

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            R I H +V   GN + + + A +F+H  +R+ VGSL  VG G      +E  L  ++RK
Sbjct: 173 WRNIHHLNVIRRGNFVIVDIKANAFVHHMVRNIVGSLMEVGCGNQPPEWIEWLLAQKNRK 232

Query: 229 ECGPLAPPEGLYFDSVEY 246
              P A  EGLY   V Y
Sbjct: 233 LAAPTAKAEGLYLVQVTY 250


>gi|261401977|ref|ZP_05988102.1| tRNA pseudouridine synthase A [Neisseria lactamica ATCC 23970]
 gi|269207832|gb|EEZ74287.1| tRNA pseudouridine synthase A [Neisseria lactamica ATCC 23970]
          Length = 267

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 129/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 10  RWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGESVATTVAGRTDTGVHATAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           +  NA L   + I++L+       FHARF A  R Y Y + +   
Sbjct: 70  VHFDTAARRPAQAWIRGTNAALP--EGIAVLHARQTSPGFHARFDAYGRHYRYLLESSPV 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   G
Sbjct: 128 RSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQTG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY 
Sbjct: 188 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSTLIRERSRLKAPPTFMPDGLYL 247

Query: 242 DSVEY 246
             V+Y
Sbjct: 248 TGVDY 252


>gi|42559741|sp|Q7MB17|TRUA_PHOLL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 264

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 91/240 (37%), Positives = 134/240 (55%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ+   S+QG +E+A+  V  E + V  AGRTD+GVHA  QV HF+  
Sbjct: 7   IEYDGSRYYGWQRQQEVKSVQGCLEEALSKVADEPISVFCAGRTDAGVHATGQVVHFETS 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +N +L     I++  +  VD+ FHARFSA  R Y Y I   R  P  L 
Sbjct: 67  VQRKDAAWTMGVNVHL--PPDIAVRWVKTVDEGFHARFSATARRYRYIIFNHRYRPAVLA 124

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G        LD + M  AAQ ++G +DFT+FR++ CQ+ +P R + H +VN +G+ + I
Sbjct: 125 NGVTHF-HYPLDEKRMHQAAQCILGENDFTSFRAVQCQSKTPWRNVMHINVNRYGHYVVI 183

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+  GSL  +G G      + + L  +DR +    A   GLY  +V+Y
Sbjct: 184 DIKANAFVHHMVRNIAGSLMEIGCGNQDINWMAQLLALKDRAKAAATAKAAGLYLVAVDY 243


>gi|148828368|ref|YP_001293121.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittGG]
 gi|166228702|sp|A5UIY2|TRUA_HAEIG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148719610|gb|ABR00738.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittGG]
          Length = 269

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAIRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|145627788|ref|ZP_01783589.1| tRNA pseudouridine synthase A [Haemophilus influenzae 22.1-21]
 gi|144979563|gb|EDJ89222.1| tRNA pseudouridine synthase A [Haemophilus influenzae 22.1-21]
          Length = 269

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHEAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|54309813|ref|YP_130833.1| tRNA pseudouridine synthase A [Photobacterium profundum SS9]
 gi|51316618|sp|Q6LNU5|TRUA_PHOPR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46914251|emb|CAG21031.1| Putative tRNA pseudouridine synthase A [Photobacterium profundum
           SS9]
          Length = 261

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGAKYCGWQRQVDVDSVQERLEKALSHIANKPIAVFCAGRTDTGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +   V     +NA+L     IS+   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDVDVDRQMVAWTIGVNAHL--PRDISVRWATQVSDDFHARFSATARRYRYIIYNSAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ+LVG HDFT+ R+  CQ+ SP R + H +V+  G
Sbjct: 119 RPAIFGVGVSHYHGHLDEKKMHEAAQYLVGEHDFTSVRASQCQSRSPWRAMKHVNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+ T   ++  L+ +DR+  G  A   GLY 
Sbjct: 179 DFVIIDIKANAFVHHMVRNIAGSLIRVGRGQETPEWMKWVLEQKDRRVAGETAKAAGLYL 238

Query: 242 DSVEY 246
            +V+Y
Sbjct: 239 VAVDY 243


>gi|301170402|emb|CBW30008.1| pseudouridylate synthase I [Haemophilus influenzae 10810]
          Length = 269

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 130/245 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDTEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|237808326|ref|YP_002892766.1| tRNA pseudouridine synthase A [Tolumonas auensis DSM 9187]
 gi|259550489|sp|C4LF13|TRUA_TOLAT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|237500587|gb|ACQ93180.1| tRNA pseudouridine synthase A [Tolumonas auensis DSM 9187]
          Length = 261

 Score =  155 bits (392), Expect = 5e-36,   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  +E A+  V    V +  AGRTD+GV+A  QV
Sbjct: 1   MRIALGIEYFGADYYGWQRQREVNSVQQELETALSRVANHPVEIQCAGRTDAGVNATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +NA  ++ D I++    +VD  FHARFSA  R Y Y I     
Sbjct: 61  IHFDTTANRQMSAWTLGINA--QLPDDIAVRWAHVVDDNFHARFSATARRYRYIIYNEPL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L KG +      L+ + M  A Q L+G  DFT+FR+  CQ+++P R I    V+  
Sbjct: 119 RPGILAKGVSHYY-HPLNADQMNEAGQLLLGERDFTSFRAAQCQSNTPFRNIMSLSVHRA 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + + + A +FLH  +R+ +GSL LVG G+     + + L A+DR   G  A  EGLY
Sbjct: 178 GSYVILDIQANAFLHHMVRNIMGSLLLVGTGEKPKEWIGEILDAKDRTVSGATAKAEGLY 237

Query: 241 FDSVEY 246
              V Y
Sbjct: 238 LVDVTY 243


>gi|118497491|ref|YP_898541.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida U112]
 gi|195536184|ref|ZP_03079191.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
 gi|254372827|ref|ZP_04988316.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|166228699|sp|A0Q6C2|TRUA_FRATN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|118423397|gb|ABK89787.1| tRNA pseudouridine synthase A [Francisella novicida U112]
 gi|151570554|gb|EDN36208.1| tRNA pseudouridine synthase A [Francisella novicida GA99-3549]
 gi|194372661|gb|EDX27372.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
          Length = 258

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGRNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    E       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSDAERPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|300903709|ref|ZP_07121624.1| tRNA pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300404291|gb|EFJ87829.1| tRNA pseudouridine synthase A [Escherichia coli MS 84-1]
          Length = 270

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 94/241 (39%), Positives = 130/241 (53%), Gaps = 4/241 (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 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTRAAATAKAEGLYLVAVDY 252

Query: 247 S 247
            
Sbjct: 253 P 253


>gi|332678185|gb|AEE87314.1| tRNA pseudouridine synthase A [Francisella cf. novicida Fx1]
          Length = 258

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    E       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IINFYSDAERPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|74317934|ref|YP_315674.1| tRNA pseudouridine synthase A [Thiobacillus denitrificans ATCC
           25259]
 gi|123759044|sp|Q3SHL7|TRUA_THIDA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|74057429|gb|AAZ97869.1| tRNA pseudouridine synthase [Thiobacillus denitrificans ATCC 25259]
          Length = 260

 Score =  155 bits (391), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 83/246 (33%), Positives = 123/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + +EY G G+ GWQ Q     +Q ++EKA+  + GE + V  AGRTD+GVHA  Q
Sbjct: 1   MMRIAVGLEYRGVGFCGWQSQPQACGVQDAVEKAVSAIAGEAITVTAAGRTDTGVHAALQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD           + +N++L     +++L    VD +FHARF+A  R Y Y ++   
Sbjct: 61  IVHFDTTSVRPLTAWVRGVNSHLPAG--VAVLWAREVDAEFHARFAAFERGYRYVLLNHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  G      + LD   M  AA  L+GRHDF+ FR+  CQA SP++ +    +   
Sbjct: 119 VRPGLNAGLVGWHHRPLDVACMNRAASPLIGRHDFSAFRAAECQARSPVKELRRALIERR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +     A  FLH  +R+ +G L  +G G      L + L  +DR    P     GLY
Sbjct: 179 GDYLLCDFRADGFLHHMVRNLMGCLVQIGAGGRPPEWLHEVLAGRDRTRAAPTFEAAGLY 238

Query: 241 FDSVEY 246
              + Y
Sbjct: 239 LTHIRY 244


>gi|119475872|ref|ZP_01616224.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2143]
 gi|119450499|gb|EAW31733.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2143]
          Length = 288

 Score =  155 bits (391), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 132/247 (53%), Gaps = 6/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+GS Y GWQ Q+    +++Q ++EKA+  V    V+V  AGRTD+GVHA  Q
Sbjct: 27  RVALCVSYDGSAYHGWQSQRKPQVATVQETLEKALSSVANANVIVQCAGRTDTGVHASHQ 86

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD           +  N  L  S  I+I     V  +F+ARFSA  R Y Y I+ R 
Sbjct: 87  IVHFDSPSARGEKAWVRGGNTNLPSS--IAIQWAKPVSAKFNARFSATARRYRYVILNRP 144

Query: 121 APLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           A  A L  G  W     LD  +M  AAQ LVG  DFT++R+  CQ+ +P+R I   DV+ 
Sbjct: 145 ARSAILSAGVTWQR-YPLDEISMHEAAQALVGELDFTSYRAAACQSKTPMRNIHRVDVSR 203

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ I + A +FLH  +R+  G L  +G G   +   E+ L A+DR      APP GL
Sbjct: 204 QGDLVIIDIQANAFLHHMVRNIAGVLMAIGTGAKPTVWAEEVLLAKDRSVAAATAPPHGL 263

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 264 YLIGVTY 270


>gi|327480383|gb|AEA83693.1| tRNA pseudouridine synthase A [Pseudomonas stutzeri DSM 4166]
          Length = 275

 Score =  155 bits (391), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 102/252 (40%), Positives = 135/252 (53%), Gaps = 16/252 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           R  + +EY GS Y G+QRQ+ G  SIQ S+E A+  V G   V +  AGRTD+ VHA  Q
Sbjct: 8   RIALGVEYKGSRYRGFQRQRAGVPSIQESLENALTRVAGGHPVTLSCAGRTDALVHASGQ 67

Query: 61  VAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD   E     WV       + A + +   IS+     +   F ARFSA+ R Y Y 
Sbjct: 68  VVHFDTPVERSMHAWV-------MGANMNLPPDISVTWAKKMPPHFDARFSAMARRYRYV 120

Query: 116 IITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I   Q  P  + +   W   + LD E MR AA  LVG HDF+ FR+  CQA SPI+TI H
Sbjct: 121 IYNDQIRPAHMAEEVTWNH-RPLDIERMRAAAAALVGTHDFSAFRARQCQAKSPIKTIHH 179

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++  FG LI I V A +FLH  +R+F G L  +G G+       + L+++ R+  G  A
Sbjct: 180 LELLQFGRLIVIDVRANAFLHHMVRNFAGVLMTIGAGERPVEWAAQVLESRVRRTGGVTA 239

Query: 235 PPEGLYFDSVEY 246
            P GLY   V+Y
Sbjct: 240 HPYGLYLVEVDY 251


>gi|205372037|ref|ZP_03224854.1| tRNA pseudouridine synthase A [Bacillus coahuilensis m4-4]
          Length = 251

 Score =  155 bits (391), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 143/254 (56%), Gaps = 16/254 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R    ++Y+G+ Y G+Q Q N  +IQG IEK +  + G+ + +  +GRTD+GVHA+ Q
Sbjct: 4   MRRIKCTVQYDGTWYAGYQVQPNSKTIQGEIEKVLEKIHGKPIRISASGRTDAGVHAIGQ 63

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD      V +W+P+      N+  ++ + I ++++  V   FH+RF +I + Y Y+
Sbjct: 64  VFHFDTDTKFPVEKWLPI-----FNS--QLPNDIVVIHVEEVAGSFHSRFGSIEKEYRYK 116

Query: 116 II--TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           +     ++P  +    A+ +P SL  + M  A+++L+G HDFT+F S   +    +RTI 
Sbjct: 117 VYRAPHKSPFLIH--HAYHVPHSLSVQKMEEASRYLLGTHDFTSFCSAKTEVEDKVRTIF 174

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              +    N++   +V   FL+  +R  +G L  VG GK    ++++ L+A+DR+  G  
Sbjct: 175 TISIEEEENMLTFSLVGNGFLYNMVRIIIGVLIEVGQGKRAPIEVKEILEAKDRRAGGKT 234

Query: 234 APPEGLYFDSVEYS 247
           AP +GLY   V+YS
Sbjct: 235 APAQGLYLYRVKYS 248


>gi|160935852|ref|ZP_02083227.1| hypothetical protein CLOBOL_00746 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441596|gb|EDP19306.1| hypothetical protein CLOBOL_00746 [Clostridium bolteae ATCC
           BAA-613]
          Length = 248

 Score =  155 bits (391), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 86/241 (35%), Positives = 129/241 (53%), Gaps = 3/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G+ Y GWQ+Q N   +IQG +E  +  + G  V VHG+GRTD+GVHA  QVA+F L
Sbjct: 7   LSYDGTRYDGWQKQGNTDRTIQGKLEAVLEKLEGSPVEVHGSGRTDAGVHAESQVANFHL 66

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            +   P  + + +N YL   + I++    ++ ++FH+R +A+R++Y Y+I T       E
Sbjct: 67  AKNMTPDEIMRYMNRYL--PEDIAVTRACVMPERFHSRLNALRKTYRYQIETAPKKNVFE 124

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +   + + + LD   M  AA  L G HD+ +F        S IRTI+       G+ I I
Sbjct: 125 RYYYYGLGQDLDVGKMEQAAAILTGTHDYKSFCGNKKMKKSTIRTIESICFYRMGSRIHI 184

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                 FL   +R   G+L  VG GK    ++   L+A DR   G  APPEGL+ + VEY
Sbjct: 185 SFTGNGFLQQMVRILSGTLIEVGTGKRKPEEMAAILEAGDRSMAGFTAPPEGLFLEKVEY 244

Query: 247 S 247
            
Sbjct: 245 G 245


>gi|187779482|ref|ZP_02995955.1| hypothetical protein CLOSPO_03078 [Clostridium sporogenes ATCC
           15579]
 gi|187773107|gb|EDU36909.1| hypothetical protein CLOSPO_03078 [Clostridium sporogenes ATCC
           15579]
          Length = 246

 Score =  155 bits (391), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), 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 + + G+GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIGSGRTDAGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTNFQGSTNEILNYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ +P++LD E M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHVPQTLDIEAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++I  +   FLH  IR   G+L  +G    +  +++  L+A+DR++    AP +GL
Sbjct: 179 KDGYVDIVYLGSGFLHKMIRILTGTLIEIGLHNLSPMNVKTILEAEDRRKASSTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV Y
Sbjct: 239 FMTSVTY 245


>gi|145635070|ref|ZP_01790776.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittAA]
 gi|145267678|gb|EDK07676.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittAA]
          Length = 269

 Score =  155 bits (391), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EK++  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKSLSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVVY 243


>gi|312127288|ref|YP_003992162.1| tRNA pseudouridine synthase a [Caldicellulosiruptor hydrothermalis
           108]
 gi|311777307|gb|ADQ06793.1| tRNA pseudouridine synthase A [Caldicellulosiruptor hydrothermalis
           108]
          Length = 244

 Score =  155 bits (391), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 89/241 (36%), Positives = 133/241 (55%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ YFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q A+F 
Sbjct: 6   LTIEYDGTEYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQKANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +        ALN+ L     ISI +   V   F AR+SA +++Y Y I  + +  AL
Sbjct: 66  TSSKIPTDKFPLALNSVL--PGDISIKDAVEVPLNFSARYSAKQKTYKYLIYNKNSRPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +      I 
Sbjct: 124 LRNYAYYYPYQLDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNSYLTFENECIA 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY   V 
Sbjct: 184 IYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTKAGKTLPPWGLYLVDVV 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|258545708|ref|ZP_05705942.1| tRNA pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
 gi|258519078|gb|EEV87937.1| tRNA pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
          Length = 265

 Score =  155 bits (391), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 128/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           RY + +EY+G+ Y GWQRQ    ++IQ  +E A+  V    V    AGRTD+GVHA  QV
Sbjct: 4   RYAVGLEYDGTHYAGWQRQPFFAATIQEQLECALSQVAAHPVETTCAGRTDAGVHATAQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N YL     I +  +  V  +FHAR+SA  R Y Y I  R  
Sbjct: 64  IHFDTGAARSDFAWLAGANRYLPAD--IRLQWIRAVPAEFHARYSARERHYRYLIRHRAQ 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P AL   R     KSLD   M  AAQ L+G HDF+ FR+  CQA SP R I   DV    
Sbjct: 122 PSALWARRCHWHKKSLDAAAMHSAAQALIGEHDFSAFRAAECQAKSPWRFIRSIDVRERH 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + +   +FLH  +R+ VG+L  VGDG+  +    + L ++DR+  G  AP +GLYF
Sbjct: 182 GWIAVDICGNAFLHHMVRNIVGTLLAVGDGRRDTAWPGEVLASRDRRCAGVTAPAQGLYF 241

Query: 242 DSVEY 246
             V Y
Sbjct: 242 HGVAY 246


>gi|62901272|sp|Q65TC8|TRUA_MANSM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 263

 Score =  154 bits (390), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 94/257 (36%), Positives = 131/257 (50%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  YFGWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYNGKNYFGWQRQEKVHSVQAELEKALSFVANEKIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+       + W       A      + D I++     V   FHARFSA  R Y Y  
Sbjct: 61  VHFETNAIRPEKAW-------AFGTNANLPDDIAVRWAKEVPDDFHARFSATARRYRYV- 112

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                 L   K R+ ++P         LD   M+ A + L+G +DF++FR+  CQ+++P 
Sbjct: 113 ------LYCNKLRSAILPYGITHTHLDLDEHKMQEAGRFLLGENDFSSFRAAQCQSNTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R I H +V   GN + + + A +F+H  +R+ VGSL  VG G      +E  L  ++RK 
Sbjct: 167 RNIHHLNVIRRGNFVIVDIKANAFVHHMVRNIVGSLMEVGCGNQPPEWIEWLLAQKNRKL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 227 AAPTAKAEGLYLVQVTY 243


>gi|311694720|gb|ADP97593.1| tRNA pseudouridine synthase A [marine bacterium HP15]
          Length = 302

 Score =  154 bits (390), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 129/250 (51%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +  EY+G G+ GWQ QK+G  S++  +  A+  V    V +  AGRTD+GVHA  Q+
Sbjct: 18  RVALAFEYDGRGFHGWQLQKSGVRSVEAELTAAVAKVANHAVDLVCAGRTDAGVHASYQI 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AHFD      +R WV       +     + D IS+         FHARFSA  R Y Y I
Sbjct: 78  AHFDTPSVRNLRSWV-------MGINTALPDDISVHWAGNGVGDFHARFSATYRRYRYII 130

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   +++G+     + LD + M  AAQ L G HDF++FR+  CQ+ +PIR ++   
Sbjct: 131 YNHPVRPGIQRGQVSWTFRPLDADRMHRAAQALAGEHDFSSFRAAGCQSRTPIRFLERIS 190

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V    + + I V A +FLH  +R+  G+L  VG GK     + + L A+DR   G  APP
Sbjct: 191 VTRKRDFVVIDVQANAFLHHMVRNIAGALMAVGSGKQRPEWIHEILVARDRTAAGVTAPP 250

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 251 HGLYLVDVGY 260


>gi|295698698|ref|YP_003603353.1| tRNA pseudouridine synthase A [Candidatus Riesia pediculicola USDA]
 gi|291157129|gb|ADD79574.1| tRNA pseudouridine synthase A [Candidatus Riesia pediculicola USDA]
          Length = 255

 Score =  154 bits (390), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 139/247 (56%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + I+Y+GS Y GWQ+QKNG  SIQ  +E ++  +T E +  +  GRTDSGVHA  QV
Sbjct: 4   RVALGIQYDGSRYHGWQKQKNGLDSIQKRLESSLKKLTDEDIKTYCGGRTDSGVHAFGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+  +    V+    +N +L     IS+L +  V  +FHARFSAI R Y Y I  ++ 
Sbjct: 64  VHFETYKIRKDVVWVSGVNHFL--PKDISVLWVKPVSHRFHARFSAISRHYRYLIFNKEI 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSF 180
             A+ +     I K LD ++M  AAQ L+G +D  +F S   ++  S  R I + +V  F
Sbjct: 122 RPAIFRSNVLHISKKLDYKDMNKAAQCLLGENDLISFISFDRRSFRSTKRNIRYINVKRF 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + + I +VA SF +  +R+ VGSL  VG GK  +  ++K +  +DR + GP    +GLY
Sbjct: 182 DSYVIIDIVANSFAYNMVRNIVGSLIEVGLGKKGTEWIKKLIDLKDRTKSGPKVHSKGLY 241

Query: 241 FDSVEYS 247
              + YS
Sbjct: 242 LMHINYS 248


>gi|322514646|ref|ZP_08067676.1| tRNA pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
 gi|322119437|gb|EFX91539.1| tRNA pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
          Length = 289

 Score =  154 bits (390), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 95/257 (36%), Positives = 135/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    V    AGRTDSGVH   QV
Sbjct: 28  MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSVVANAPVEAFCAGRTDSGVHGTGQV 87

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      ++ W     C   NA L   + I++     V + FHARFSA  R Y Y I
Sbjct: 88  VHFETETVRPLQSW-----CFGTNANL--PNDIAVKWAVEVSEDFHARFSATARRYRYII 140

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                     K R+ ++PK        LD + M  A Q L+G +DF++FR+  C++ +P 
Sbjct: 141 FN-------NKLRSAILPKGVSHYHHELDHQKMHEAGQFLLGENDFSSFRAAKCESHTPW 193

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R I H +V+  GN I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR  
Sbjct: 194 RNIHHLNVSRLGNYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTL 253

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 254 AAPTAKAEGLYLVDVHY 270


>gi|325678788|ref|ZP_08158386.1| tRNA pseudouridine synthase A [Ruminococcus albus 8]
 gi|324109292|gb|EGC03510.1| tRNA pseudouridine synthase A [Ruminococcus albus 8]
          Length = 250

 Score =  154 bits (390), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 127/247 (51%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + + Y+GSGY GWQRQ N  ++Q  +E AIF +TGE VVV G  RTD+GVHA   
Sbjct: 1   MRNFKVTLAYDGSGYHGWQRQSNALAVQEVVENAIFKLTGEKVVVQGCSRTDAGVHARMY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V   +L     P  +   LN++L   D IS++     +  FHAR+    + Y Y +   +
Sbjct: 61  VLSMELESTITPRGIQLGLNSWL--PDDISVIGCEECEAGFHARYHCKGKEYEYIVHNSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 K  A+     +D   +  AA+  VG HDF  F S  C     +RTI  FDV   
Sbjct: 119 IKDPFLKNTAFRNTYPIDEVLLDKAAKDYVGEHDFKAFCSTACDKEITVRTIYRFDVRRE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+   V    FL+  +R  VG+L  + +GK  +  + + ++++DR + G   PP+GLY
Sbjct: 179 GELVIFTVAGNGFLYNMVRIMVGTLLFINEGKIAADAIPRIIESKDRTKAGKTVPPQGLY 238

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 239 LNKVYYD 245


>gi|171463727|ref|YP_001797840.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|226708657|sp|B1XV49|TRUA_POLNS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171193265|gb|ACB44226.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 276

 Score =  154 bits (390), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 93/255 (36%), Positives = 141/255 (55%), Gaps = 12/255 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG------AGRTDSGV 55
           +R  + ++Y+GS Y GWQ Q N +++Q  +EKAI    GE   V        AGRTD+GV
Sbjct: 1   MRIALGLQYDGSPYSGWQTQVNHNTVQNELEKAISAFVGEQACVVKPINTITAGRTDTGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HAL QV HFD   E       + +N++L  S +I I     V ++F ARFSA  R Y+Y 
Sbjct: 61  HALGQVVHFDTNVEREDFSWVRGVNSFL--SSSIVINWAKPVSEEFCARFSAYEREYIYA 118

Query: 116 IITR--QAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           +     ++P+A  +    ++P S   D E M+ +A+ L+G HDF++FRS  CQ+ +PI+T
Sbjct: 119 LHAGPCRSPMAHSRAGYLMLPPSQWFDIEAMQKSAECLIGEHDFSSFRSSECQSKTPIKT 178

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           I   ++ S    +  R+   +FLH  IR+ VG    +G GK TS  + + L A++R+   
Sbjct: 179 IYLIEIISKQPWLYFRIRGNAFLHHMIRNLVGCFLQIGQGKQTSQWMAEVLAAKNRQIAA 238

Query: 232 PLAPPEGLYFDSVEY 246
           P    +GLY   + Y
Sbjct: 239 PTFMADGLYLAKITY 253


>gi|260856362|ref|YP_003230253.1| pseudouridylate synthase I [Escherichia coli O26:H11 str. 11368]
 gi|257755011|dbj|BAI26513.1| pseudouridylate synthase I [Escherichia coli O26:H11 str. 11368]
 gi|323156469|gb|EFZ42624.1| tRNA pseudouridine synthase A [Escherichia coli EPECa14]
          Length = 270

 Score =  154 bits (390), Expect = 9e-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  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 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTRAAATAKAEGLYLVAVDY 252


>gi|306825673|ref|ZP_07459012.1| tRNA pseudouridine synthase A [Streptococcus sp. oral taxon 071
           str. 73H25AP]
 gi|304432034|gb|EFM35011.1| tRNA pseudouridine synthase A [Streptococcus sp. oral taxon 071
           str. 73H25AP]
          Length = 261

 Score =  154 bits (390), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 134/251 (53%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  L  G  + VHGAGRTDSGVHAL 
Sbjct: 13  MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGHAITVHGAGRTDSGVHALG 72

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL+ +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 73  QVIHFDLLYQMDEEKLRFALDT--QSPEDIDVISMELVADDFHCRYAKHSKTYEF-IVDR 129

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFD 176
             P   + +  A   P  LD E M++A + L G HDFT F +        +RTI   +  
Sbjct: 130 GRPKNPMRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTSVEDKVRTITEANLT 189

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 190 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 249

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 250 NGLYLKEIRYE 260


>gi|254514517|ref|ZP_05126578.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR5-3]
 gi|219676760|gb|EED33125.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR5-3]
          Length = 272

 Score =  154 bits (390), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 93/252 (36%), Positives = 136/252 (53%), Gaps = 15/252 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           R  + IEY+GS Y GWQ Q       ++Q  +E A+  +    V V  AGRTD+GVHA  
Sbjct: 7   RVALKIEYDGSAYSGWQSQPQLPKVRTVQTEVEVALSKIANSPVRVFCAGRTDTGVHAAA 66

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           Q  HFD      ++ W+ V     L   ++++D +S      V + FHAR SA+ R Y Y
Sbjct: 67  QWLHFDAPCDRSLKAWI-VGANAQLPLDVRLTDGLS------VAEDFHARHSAVARQYDY 119

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I   + P AL   R   + + LD   MR + Q L+G  DF+ FR+  CQ+++P+R ++ 
Sbjct: 120 LIANTRTPSALLANRMVWVRQPLDANLMRCSLQALLGEQDFSAFRAASCQSTTPMRFMES 179

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G++I+IRVVA +FLH  +R+ VGS   VG  +  +  L + L  +DR +    A
Sbjct: 180 TQVFRRGDIIQIRVVANAFLHHMVRNIVGSCLQVGLCEQPAGWLGELLAGRDRTQAAATA 239

Query: 235 PPEGLYFDSVEY 246
           PP+GLY   V Y
Sbjct: 240 PPQGLYLTGVRY 251


>gi|56708110|ref|YP_170006.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670581|ref|YP_667138.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|224457202|ref|ZP_03665675.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370594|ref|ZP_04986599.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254874909|ref|ZP_05247619.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|62901197|sp|Q5NG36|TRUA_FRATT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123169371|sp|Q14HI8|TRUA_FRAT1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56604602|emb|CAG45654.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320914|emb|CAL09037.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|151568837|gb|EDN34491.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254840908|gb|EET19344.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159310|gb|ADA78701.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 258

 Score =  154 bits (390), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|262375036|ref|ZP_06068270.1| tRNA pseudouridine synthase A [Acinetobacter lwoffii SH145]
 gi|262310049|gb|EEY91178.1| tRNA pseudouridine synthase A [Acinetobacter lwoffii SH145]
          Length = 265

 Score =  154 bits (390), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 134/252 (53%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + IE+ G  Y GWQ Q+ G +S+Q +IEK +  V  + + +HGAGRTD+GVHA  
Sbjct: 1   MQRFAVGIEFCGMHYRGWQTQQPGVASVQETIEKVLSKVADQPISLHGAGRTDAGVHATN 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+  + C +     ++   ISI  +  +D  FHARF A  R Y Y
Sbjct: 61  MVAHFDTDAVRSERGWL--MGCNS-----QLPKDISIQWIKEMDHSFHARFKAQARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   +   LD E M  AA+   G H+F +FR+  CQ++ P+R + H
Sbjct: 114 VVYNHPVRPALLHKQVTHVYAPLDVEQMIYAAKKFEGTHNFESFRAAACQSNQPVRHVSH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G + +  ++    A+DRK  G  A
Sbjct: 174 CRLIQHGQYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYAADHIDNIFAAEDRKAAGVTA 233

Query: 235 PPEGLYFDSVEY 246
           P +GLYF   +Y
Sbjct: 234 PADGLYFIHADY 245


>gi|297623065|ref|YP_003704499.1| tRNA pseudouridine synthase A [Truepera radiovictrix DSM 17093]
 gi|297164245|gb|ADI13956.1| tRNA pseudouridine synthase A [Truepera radiovictrix DSM 17093]
          Length = 260

 Score =  154 bits (389), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 90/255 (35%), Positives = 137/255 (53%), Gaps = 13/255 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R  + +E++G+ +FGWQ Q   +    ++QG +E A+  + G     H AGRTD+GVH
Sbjct: 1   MRRIKLTLEFDGTDFFGWQVQAGAAHPVRTVQGVLEAALATLPGARPKAHAAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           AL  VAH+D   + +PV  +  ALNA  ++   + +L+   V + F A+FS   R YLYR
Sbjct: 61  ALAMVAHYD-TDDRIPVAKVPAALNA--RLPPDVRVLHAEEVPRSFEAQFSCCYRRYLYR 117

Query: 116 ---IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
              +   +A  ALE+ R   +P +LD E M+ AA    G  DF    +   + +  +RT+
Sbjct: 118 MRLLRASRAGSALERRRVLFVPGALDLEAMQRAAPRFEGTRDFAALATQESRTT--VRTV 175

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
               + + G  + + + A  FL   +R+ VG+L  VG+GK    D+   L A+DR+  GP
Sbjct: 176 YRCRLGAAGPDLTLDIAADGFLRNMVRAVVGTLLWVGEGKLAPEDVSALLAARDRRRAGP 235

Query: 233 LAPPEGLYFDSVEYS 247
            APP GLYF    Y 
Sbjct: 236 NAPPHGLYFAEAGYE 250


>gi|254374311|ref|ZP_04989793.1| tRNA pseudouridine synthase A [Francisella novicida GA99-3548]
 gi|151572031|gb|EDN37685.1| tRNA pseudouridine synthase A [Francisella novicida GA99-3548]
          Length = 258

 Score =  154 bits (389), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PKDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|153874369|ref|ZP_02002618.1| tRNA pseudouridine synthase A [Beggiatoa sp. PS]
 gi|152069168|gb|EDN67383.1| tRNA pseudouridine synthase A [Beggiatoa sp. PS]
          Length = 272

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 100/255 (39%), Positives = 133/255 (52%), Gaps = 22/255 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ +FGWQ Q +  S+QG +E A+  V    V V  AGRTD+GVHA+ QV
Sbjct: 1   MRIALGVEYNGANFFGWQFQPHARSVQGEVEIALSKVANHPVKVICAGRTDTGVHAIGQV 60

Query: 62  AHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            H D+      R WV        N+ L I   +S+L    VD  FHARFSA  R Y Y I
Sbjct: 61  IHADVTVQRSTRSWV-----LGTNSNLPID--VSMLWAQSVDNNFHARFSAQARHYRYII 113

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           + R   P  L K   W   + L+ E M+IA  +L+G HDF        +  +PIRTI   
Sbjct: 114 LNRPTRPALLTKQVTWE-RRILEVERMQIAGNYLIGTHDFHLIVPFPVKQKTPIRTISRL 172

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG----KWTSTDLEKALQAQDRKECG 231
            V+   + + I + A +FLH  +R+  G L  +G G    KW  T LE    AQDR   G
Sbjct: 173 MVSRMDDRVIIDISANAFLHHMVRNIAGVLITIGAGEKRPKWADTVLE----AQDRTMGG 228

Query: 232 PLAPPEGLYFDSVEY 246
             AP  GLYF  ++Y
Sbjct: 229 ITAPAAGLYFCGIDY 243


>gi|253577209|ref|ZP_04854529.1| tRNA pseudouridine synthase A [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251843453|gb|EES71481.1| tRNA pseudouridine synthase A [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 261

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 96/263 (36%), Positives = 138/263 (52%), Gaps = 26/263 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    M + Y+G+ YFG+Q Q  G+++Q  IE AI  +TGE V +HG+GRTD+GVHA +Q
Sbjct: 1   MRNLLMTVSYDGTNYFGFQTQPGGNTVQDHIEGAIRQLTGETVKIHGSGRTDAGVHARQQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
             HF       V  W     C ALNA  ++   I +L    V   FH+R SA R++Y Y 
Sbjct: 61  PFHFHTDSRIPVERW-----CLALNA--RLPSDIRVLTAREVPLTFHSRHSAKRKTYRYT 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I T + P   ++   +  P  L+ + M+ +  +LVG HDFT+F S      S +RTI  +
Sbjct: 114 INTNRFPDVFQRNYQFHHPGQLNVDAMQASLPYLVGTHDFTSFASRQSTKLSHVRTI--Y 171

Query: 176 D----VNSFGN--------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           D    V+S           ++   V    FL   +R  VG+L  +G+GK T   ++  L+
Sbjct: 172 DARIVVDSLAKIPGTTGQGIVHFYVTGSGFLQHMVRIIVGTLIEIGEGKRTPESIQAILE 231

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A+DR   GP A  +GL   SVEY
Sbjct: 232 AKDRTAAGPTAESKGLMLWSVEY 254


>gi|172056172|ref|YP_001812632.1| tRNA pseudouridine synthase A [Exiguobacterium sibiricum 255-15]
 gi|229470753|sp|B1YH83|TRUA_EXIS2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171988693|gb|ACB59615.1| tRNA pseudouridine synthase A [Exiguobacterium sibiricum 255-15]
          Length = 249

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 131/246 (53%), Gaps = 4/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+   I+Y+G+ Y G+Q Q NG +IQ  +EK +  +    V V G+GRTD+ VHA  Q
Sbjct: 1   MRRFKCTIQYDGTDYSGYQVQPNGLTIQEVLEKTLGRMHKHPVKVIGSGRTDARVHAQGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P  + KALN  L   D I + +   V   F AR+  + + Y Y    R+
Sbjct: 61  VIHFDTELSIAPASMVKALNTLL--PDDIRVRDCKEVASDFEARYDVVGKEYRY--FVRR 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A  + ++ LIP SLD   +R+   HLVG HDF++F     +  + +RTI   ++   
Sbjct: 117 TENAFRRHQSVLIPYSLDVAQIRLGLAHLVGTHDFSSFCVAKTETDNRVRTIYEAELIEQ 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +  R     FL+ QIR  VG+L  VG G++   D+++ L+A+DR   G  APP GLY
Sbjct: 177 GEELIFRFQGSGFLYNQIRIMVGTLLDVGRGRFAPDDIKRMLEAKDRNVAGVTAPPHGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LWEVFY 242


>gi|149377425|ref|ZP_01895168.1| tRNA pseudouridine synthase A [Marinobacter algicola DG893]
 gi|149358266|gb|EDM46745.1| tRNA pseudouridine synthase A [Marinobacter algicola DG893]
          Length = 298

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 128/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +  EY+G G+ GWQ QK+G  S+QG + +A+  V    V +  AGRTD+GVHA  Q+
Sbjct: 18  RVAIAFEYDGRGFHGWQYQKSGVRSVQGELTQAVSKVADHPVELVCAGRTDAGVHASYQI 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+      P      +N  L     +      + D  FHARFSA  R Y Y I     
Sbjct: 78  AHFETPSVRNPRSWVMGINTSLPQDIAVHWAGNGVDD--FHARFSATYRRYRYVIYNHAV 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  G+     + LD   M  AAQ L G HDF++FR+  CQ+ SPIR ++  +V   G
Sbjct: 136 RPGILHGQVSWTFRPLDEALMHQAAQFLCGEHDFSSFRAAGCQSRSPIRFLEAIEVTRKG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I V A +FLH  +R+  G+L  VG GK     + + L+A+DR   G  APP GLY 
Sbjct: 196 DFVVIDVQANAFLHHMVRNIAGALMSVGTGKQRPEWIREILEARDRTVAGVTAPPHGLYL 255

Query: 242 DSVEY 246
             V Y
Sbjct: 256 VDVGY 260


>gi|328951883|ref|YP_004369217.1| tRNA pseudouridine synthase A [Desulfobacca acetoxidans DSM 11109]
 gi|328452207|gb|AEB08036.1| tRNA pseudouridine synthase A [Desulfobacca acetoxidans DSM 11109]
          Length = 267

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 137/245 (55%), Gaps = 7/245 (2%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           C+ +EY+G+ Y GWQRQ N  +IQ  +E  +  +TG+++ +H +GRTD+GVHAL QVAHF
Sbjct: 26  CLTLEYDGTAYHGWQRQANALTIQEVVETCLARLTGQVIRLHSSGRTDAGVHALGQVAHF 85

Query: 65  DLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            L    +P+    + LN+ L     ++IL +      FHAR+SA  ++Y YRI+ R    
Sbjct: 86  -LTTSSLPLSAFREGLNSLLP--RDLAILKVCDAPAGFHARYSATAKTYEYRILNRPVRS 142

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVNSFG 181
            +     W + + LD   +R AA +++G  DF  F++      +  R +    ++    G
Sbjct: 143 PVHCNYCWWLARPLDQGLLRQAAGYILGEQDFAAFQASGGSVKTTTRKVMAASWEEKPGG 202

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I  ++ A  FL   +R+ VG++  VG GK +  DL++ L A+DR++ GP AP  GLY 
Sbjct: 203 WRI-FQITANGFLRGMVRALVGTMVEVGWGKRSPGDLKRLLAARDRRQAGPTAPAAGLYL 261

Query: 242 DSVEY 246
             V Y
Sbjct: 262 VEVRY 266


>gi|253689176|ref|YP_003018366.1| tRNA pseudouridine synthase A [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251755754|gb|ACT13830.1| tRNA pseudouridine synthase A [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 283

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), 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  LKIALGIEYDGSQYYGWQRQSDVASVQACLEKALSKVADEPIEVFCAGRTDAGVHGTGQV 82

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +NA L     I++  +  V++ FHARFSA  R Y Y I   R 
Sbjct: 83  VHFTTQAIRKDAAWTMGVNANL--PPDIAVRWVKTVEEDFHARFSATARRYRYVIYNHRY 140

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD + M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   
Sbjct: 141 RPAVLSHGMTHFY-HPLDVDRMERAGQCLLGENDFTSFRAVQCQSRTPWRYVNHLKVTRH 199

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY
Sbjct: 200 GDYIVVDIKANAFVHHMVRNIVGSLMEVGCGNRPESWIAELLAAKDRTLAAATARAEGLY 259

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 260 LVAVDY 265


>gi|225025215|ref|ZP_03714407.1| hypothetical protein EIKCOROL_02112 [Eikenella corrodens ATCC
           23834]
 gi|224941973|gb|EEG23182.1| hypothetical protein EIKCOROL_02112 [Eikenella corrodens ATCC
           23834]
          Length = 269

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + + Y+GS +FGWQ+Q +G +++Q ++E A+  +  E + V  AGRTD+GVHA  QV
Sbjct: 8   RRALFVSYDGSRFFGWQKQADGIATVQSALEAALSELAQERISVVTAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA L   + +++  +  V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDSAARRPDQAWVRGVNALLP--EGVAVWRVQDVAPEFHARFDACGRRYRYLLQSAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L  GRA     +LD   MR AA  LVG HDF++FR+  CQA SP++T+    +    
Sbjct: 126 RSPLLVGRAGWTHYALDMAAMRQAAALLVGEHDFSSFRAAECQAKSPVKTLYRVALCGTP 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ +     +FLH  +R+ +G+L  VG GK +       L A+ RK   P   P+GLY 
Sbjct: 186 ELMAVDFHGNAFLHHMVRNLMGALVYVGCGKLSVDGFAGLLAARSRKLAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             ++Y
Sbjct: 246 TGIDY 250


>gi|313669058|ref|YP_004049342.1| tRNA pseudouridine synthase [Neisseria lactamica ST-640]
 gi|313006520|emb|CBN87984.1| tRNA pseudouridine synthase [Neisseria lactamica 020-06]
          Length = 267

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 129/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 10  RWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGEAVSTIVAGRTDTGVHATAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           +  NA L   + I++L+       FHARF A  R Y Y + +   
Sbjct: 70  VHFDTAARRPAQAWIRGTNAALP--EGIAVLHARQTAPGFHARFDAYGRHYRYLLESSPV 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   G
Sbjct: 128 RSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQTG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY 
Sbjct: 188 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSALIRERSRLKAPPTFMPDGLYL 247

Query: 242 DSVEY 246
             V+Y
Sbjct: 248 TGVDY 252


>gi|148986314|ref|ZP_01819186.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP3-BS71]
 gi|147921782|gb|EDK72913.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP3-BS71]
 gi|301800423|emb|CBW33056.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae OXC141]
          Length = 249

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 86/250 (34%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+++ VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQVITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFTVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|85860424|ref|YP_462626.1| tRNA pseudouridine synthase A [Syntrophus aciditrophicus SB]
 gi|85723515|gb|ABC78458.1| tRNA pseudouridine synthase A [Syntrophus aciditrophicus SB]
          Length = 328

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 133/246 (54%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++Y + +EY+G+GY GWQ QKN  SIQG++ +    + G  V + GAGRTD+GVHAL QV
Sbjct: 65  VKYRLTLEYDGTGYSGWQMQKNAKSIQGTLLRVAEDLLGGPVDIQGAGRTDAGVHALAQV 124

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH +  R   P  L + LN  L  S  I+IL +      FHAR SA  RSYLY I   + 
Sbjct: 125 AHLETTRRMPPRKLLEGLNDALPSS--INILRVEEAPPLFHARHSAQLRSYLYVISGHRT 182

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT-IDHFDVNSF 180
             A  K   W I   L+ + M+ A++   G HDF++F        +P R  ++  ++++ 
Sbjct: 183 --AFGKRYVWWIRDHLELKKMQAASRLFAGFHDFSSFADKRMDKQAPTRVKVEATELHAS 240

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI  RV    FL   +R  VG +  VG  K   +D+ + L++   +     APP GLY
Sbjct: 241 GDLIFFRVTGSHFLWKMVRRMVGVMVEVGREKLDISDVRQMLKSYSPEPARLTAPPSGLY 300

Query: 241 FDSVEY 246
            + V Y
Sbjct: 301 LERVLY 306


>gi|225377724|ref|ZP_03754945.1| hypothetical protein ROSEINA2194_03375 [Roseburia inulinivorans DSM
           16841]
 gi|225210401|gb|EEG92755.1| hypothetical protein ROSEINA2194_03375 [Roseburia inulinivorans DSM
           16841]
          Length = 245

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQ Q + G +IQG IE  +  + G  V V G+GRTD+GVHA  
Sbjct: 1   MNNYKITIQYDGTRYKGWQGQNSTGLTIQGKIEAVLGQMAGHAVEVIGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F +   +    +   LN YL   D I+++ +  VD++FH+R++A +++Y Y I   
Sbjct: 61  QVANFHIEEHFTEGKILSYLNHYL--PDDIAVIAVEQVDERFHSRYAAKKKTYRYHIHMG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     E+   +   K+LD E M+ AA +L+G HDFT+F        + +RTI   +   
Sbjct: 119 EISDVFERKYEYQYEKTLDVERMKEAASYLIGTHDFTSFCGNKKMKKTAVRTIYEINFTK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN + I      FL   +R   G+L  VGDG+    +L + L++++R+  G  AP  GL
Sbjct: 179 KGNDLWIDYRGNGFLQNMVRILTGTLIEVGDGRRAPEELPQILESKNRENAGYTAPACGL 238

Query: 240 YFDSVEY 246
               V Y
Sbjct: 239 MLMEVHY 245


>gi|309378319|emb|CBX23065.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 267

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 129/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 10  RWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGEAVSTIVAGRTDTGVHATAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           +  NA L   + I++L+       FHARF A  R Y Y + +   
Sbjct: 70  VHFDTAARRPAQAWIRGTNAALP--EGIAVLHARQTAPGFHARFDAYGRHYRYLLESSPV 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   G
Sbjct: 128 RSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQTG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY 
Sbjct: 188 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSTLIRERSRLKAPPTFMPDGLYL 247

Query: 242 DSVEY 246
             V+Y
Sbjct: 248 TGVDY 252


>gi|120609904|ref|YP_969582.1| tRNA pseudouridine synthase A [Acidovorax citrulli AAC00-1]
 gi|166228672|sp|A1TLH0|TRUA_ACIAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120588368|gb|ABM31808.1| tRNA pseudouridine synthase A [Acidovorax citrulli AAC00-1]
          Length = 278

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/258 (33%), Positives = 127/258 (49%), Gaps = 20/258 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNGS Y GWQ Q  G+++Q  +E A+       V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGSAYRGWQSQPGGATVQDRLEAALARFATHEVSTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E  P    +  N +L     I++     V + FH+R SA  R Y Y ++    
Sbjct: 61  VHFDTPLERTPFSWVRGTNTFLPPD--IAVQWARPVPEAFHSRASATARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +  +LD + MR AA+HL+G HDFT+FR+  CQA SP++T+   ++   G
Sbjct: 119 RPSVEAGRVGWVFHALDGDAMRAAARHLLGEHDFTSFRASACQAKSPVKTLRRIEITQRG 178

Query: 182 N------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                                       +FLH  +R+ +G L  VG G+  +  +   LQ
Sbjct: 179 TGGVPAGQAPGDRGDVPTCYWRFEFEGNAFLHHMVRNIMGCLVAVGQGQHPADWMHAVLQ 238

Query: 224 AQDRKECGPLAPPEGLYF 241
           A+ R    P   P+GLYF
Sbjct: 239 ARSRDAAAPTFSPDGLYF 256


>gi|326203861|ref|ZP_08193723.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
 gi|325985959|gb|EGD46793.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
          Length = 245

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/248 (37%), Positives = 133/248 (53%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +IIEY+G+ Y GWQ QKN  ++Q +++KAI  + GE V V G  RTD GVHA  Q
Sbjct: 1   MRKIKIIIEYDGTNYHGWQVQKNAKTVQETVQKAISKLLGEGVGVTGCSRTDVGVHAYGQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAHF L    +P      A+N  L   D I I +   V ++FHAR+S   + Y Y I   
Sbjct: 61  VAHF-LTDSQIPGDKFSYAINNLL--PDDIVIKHSEEVSEEFHARYSTKGKKYRYLIYNA 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A+ + R+  +   LD E M+ AA++ +G HDF  F++   Q  S +R I   +V+ 
Sbjct: 118 PHPSAIMRNRSCHVRPVLDIEQMKKAARYFIGEHDFAAFQATGGQVRSTVREIYSMEVSG 177

Query: 180 F-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N+I I V    FL+  +R   G+L  VG GK   +++   +   DR + G  AP +G
Sbjct: 178 KEDNMIYIEVSGNGFLYNMVRIIAGTLIYVGMGKLQESEIPGIIAGLDRTKSGKTAPAQG 237

Query: 239 LYFDSVEY 246
           LY   + Y
Sbjct: 238 LYLMEIYY 245


>gi|208779289|ref|ZP_03246635.1| tRNA pseudouridine synthase A [Francisella novicida FTG]
 gi|208745089|gb|EDZ91387.1| tRNA pseudouridine synthase A [Francisella novicida FTG]
          Length = 258

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    E       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSDAERPLSAWQRGVNALL--PQDIKILAVQQVDNDFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD   M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIYKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|254369374|ref|ZP_04985386.1| hypothetical protein FTAG_00346 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157122324|gb|EDO66464.1| hypothetical protein FTAG_00346 [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 258

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 132/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           + +F     + P+    + +NA L     I IL +  VD  F++RF+AI R+Y Y I   
Sbjct: 61  IVNF-YSNAYRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNS 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +   
Sbjct: 118 ATSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GL
Sbjct: 178 QGSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGL 237

Query: 240 YFDSVEY 246
           YF  VEY
Sbjct: 238 YFVGVEY 244


>gi|307706977|ref|ZP_07643775.1| tRNA pseudouridine synthase A [Streptococcus mitis SK321]
 gi|307617638|gb|EFN96807.1| tRNA pseudouridine synthase A [Streptococcus mitis SK321]
          Length = 249

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVVSIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLR 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     +E  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIELILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|90416037|ref|ZP_01223970.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2207]
 gi|90332411|gb|EAS47608.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2207]
          Length = 285

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 138/250 (55%), Gaps = 14/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY  ++ Y+GS + G+Q+QK+  S+Q  +E+A+  V    ++V  AGRTD+ VHA  QV 
Sbjct: 26  RYAAVVSYDGSAFCGFQKQKHSPSVQQELERALSSVANAEIIVSCAGRTDTAVHASYQVI 85

Query: 63  HFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD       R WV     K  N+  ++ D+I++L    V++ FHARFSA  R+Y Y I 
Sbjct: 86  HFDTQALRTGRNWV-----KGSNS--QLPDSIALLWADEVNETFHARFSATSRTYRYVIH 138

Query: 118 TRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  A P  L +G  W + K L+   M+ A Q+L+G  DF+ FR   CQ+ SP R I    
Sbjct: 139 SAPARPAILSQGVTW-VRKPLNTAAMQEACQYLLGEQDFSAFRGAGCQSLSPNRNITSAK 197

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G LI   V A +F+   +R+ +GSL  VG G+     + + ++ +DR +    A P
Sbjct: 198 IIQAGELIVFEVTANAFVLHMVRNIIGSLMEVGFGRRDPGWIGQLIKGRDRTKSAATASP 257

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 258 KGLYLVQVGY 267


>gi|54114177|gb|AAV29722.1| NT02FT0202 [synthetic construct]
          Length = 258

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MI Y + I Y G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MINYLLQIGYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|296136763|ref|YP_003644005.1| tRNA pseudouridine synthase A [Thiomonas intermedia K12]
 gi|295796885|gb|ADG31675.1| tRNA pseudouridine synthase A [Thiomonas intermedia K12]
          Length = 257

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 88/241 (36%), Positives = 129/241 (53%), Gaps = 1/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M + Y G+ Y GWQ Q  G  +Q  +E+A     G       AGRTD+GVHAL QV H D
Sbjct: 1   MGLSYGGTSYCGWQSQPGGCGVQDFLERAFAQFLGVPTRTICAGRTDAGVHALGQVVHLD 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P    + +NA+L   D       + + + F AR SA +R Y Y +       AL
Sbjct: 61  TPLQREPSSWVRGVNAFLP-RDMAVQWARTDLPQTFDARRSAYQRRYRYVLRNHPVRPAL 119

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           +  RA    + LD + +R AAQ L+G HDF+ FRS  CQA SP++T+   ++  +G+ + 
Sbjct: 120 DHARAGWTHRPLDLDLLRAAAQCLLGEHDFSAFRSSECQALSPVKTLHAIEIARYGHTLV 179

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             + A +FLH  +R+ VGSL  VG+G    + L + L ++DR+   P   P+GLYF   +
Sbjct: 180 FDLRANAFLHHMVRNIVGSLLAVGNGSKPVSWLAEVLASRDRRLAAPTFMPDGLYFLGPD 239

Query: 246 Y 246
           Y
Sbjct: 240 Y 240


>gi|307709543|ref|ZP_07645997.1| tRNA pseudouridine synthase A [Streptococcus mitis SK564]
 gi|307619674|gb|EFN98796.1| tRNA pseudouridine synthase A [Streptococcus mitis SK564]
          Length = 249

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLAYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLR 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|311105424|ref|YP_003978277.1| tRNA pseudouridine synthase A [Achromobacter xylosoxidans A8]
 gi|310760113|gb|ADP15562.1| tRNA pseudouridine synthase A [Achromobacter xylosoxidans A8]
          Length = 269

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/253 (35%), Positives = 136/253 (53%), Gaps = 14/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +  ++Q ++E A+  F      V    AGRTD+GVH  
Sbjct: 1   MSRVALGLAYDGSAWQGWQTQPHRQTVQDTLEAALGSFCGVKGPVATICAGRTDTGVHGA 60

Query: 59  RQVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            QV H D      +  WV     + +NA+L  S  IS+     V  +FHARFSA  R+Y+
Sbjct: 61  MQVVHLDTELDRRMESWV-----RGVNAFLPSS--ISVQWAQPVSDEFHARFSARARTYV 113

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y +   +   AL  GRA    + LD + MR AA  L+G HDF++FRS  CQA  P+R + 
Sbjct: 114 YLLWRGRVRPALWAGRAGWCFQPLDVDAMRTAANALLGEHDFSSFRSSQCQAKHPVRHLY 173

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             D++  G  +   + A +FLH  +R+ +G+L  +G G+     + + L  +DRK   P 
Sbjct: 174 RLDIDERGPFLVFTLKANAFLHHMVRNIMGALLQIGQGREPVDWMAQLLSWRDRKLGAPT 233

Query: 234 APPEGLYFDSVEY 246
             P+GLY  +++Y
Sbjct: 234 FAPDGLYLSAIDY 246


>gi|319942390|ref|ZP_08016704.1| pseudouridylate synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804078|gb|EFW00986.1| pseudouridylate synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 269

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 128/239 (53%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY G+ + GWQ Q +  S+Q ++E A+       + V  AGRTD+GVHA  QV  F  V
Sbjct: 15  IEYRGTAFNGWQVQPDHPSVQAALEAALSQFADHPISVICAGRTDTGVHATHQVVSFTSV 74

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                    + +NA L   +++++  +  VD++FHARFSA  R+Y Y I        L +
Sbjct: 75  ARRPSAGWIRGVNAILP--ESVAVRWMREVDEKFHARFSARSRTYEYWIWNDPVRSPLFE 132

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
           G A  + + LD   M+  A  L+G HDFT+FR+  CQA +P+RTI    +   G L+ +R
Sbjct: 133 GSAGWVFRPLDEALMQRGATALIGEHDFTSFRASECQAKTPVRTISELKIVRRGALVGVR 192

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A +FL   +R+ VG+L  VG G+     + + L A+ R    P   P GLY   V Y
Sbjct: 193 ITANAFLQHMVRNIVGALIYVGTGRERPEWIAEVLAAKSRDAAAPTFSPAGLYLTGVGY 251


>gi|153007028|ref|YP_001381353.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. Fw109-5]
 gi|152030601|gb|ABS28369.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. Fw109-5]
          Length = 245

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 85/242 (35%), Positives = 130/242 (53%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +  E   V  AGRTD+GVHA  QV  F 
Sbjct: 6   LVLEYDGTRYVGWQVQPNGPSIQAEVERALATLHKEPRRVTAAGRTDAGVHARGQVVSFP 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             R        K +NA L   D +++   S+    F AR SA  + Y Y +   +    L
Sbjct: 66  EARPLPLAAYVKGMNALL--PDEVAVRAASVEPDGFDARRSARGKRYRYVLENLETRAPL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSFGNLI 184
            + +AW +  +LD   MR A++HL+GR DF  F++  C     +R +   DV       +
Sbjct: 124 SRLQAWQLFGALDVGAMREASRHLLGRQDFAAFQAADCACDHAVREVHRLDVLGEPSGRV 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E+ V A +F+   +R+FVG+L  VG G+  + D+   + ++DR   G  APP+GL+ + V
Sbjct: 184 ELVVEATAFVKHMVRNFVGTLVEVGKGRRRAEDMPALVASRDRTRAGRTAPPQGLFLEEV 243

Query: 245 EY 246
            Y
Sbjct: 244 FY 245


>gi|269468479|gb|EEZ80140.1| pseudouridylate synthase [uncultured SUP05 cluster bacterium]
          Length = 247

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 136/246 (55%), Gaps = 13/246 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK+G  ++Q  +E+A+  V    V V  +GRTD+GVHAL Q
Sbjct: 1   MKLALGVEYLGTNFHGWQLQKSGIRTVQQVVEQALSSVADHPVRVFCSGRTDAGVHALEQ 60

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+       + WV       L   + +   ++      V+  FHARF A  R Y Y+
Sbjct: 61  VIHFETTAKREDKAWV-------LGGNVNLPFDVNFKWAKQVNDDFHARFDAHARQYHYK 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I       A++        ++LD + M  AA+ L+G HDF++FR   CQA SPI+T++  
Sbjct: 114 IHNTPVRSAVKHAYTLWESRTLDIKLMNQAAECLIGEHDFSSFRGSLCQAKSPIKTVEFI 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   GN I + + A +FLH  +R+ VG+L  VG G+  S  ++  L A+DRK+ G  A 
Sbjct: 174 RLTQSGNGILLDIKANAFLHHMVRNIVGTLIKVGKGEQDSAWVKTVLDAKDRKQAGVTAE 233

Query: 236 PEGLYF 241
           P+GLYF
Sbjct: 234 PQGLYF 239


>gi|104780847|ref|YP_607345.1| tRNA pseudouridine synthase A [Pseudomonas entomophila L48]
 gi|95109834|emb|CAK14539.1| tRNA-pseudouridine synthase I [Pseudomonas entomophila L48]
          Length = 284

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 97/253 (38%), Positives = 132/253 (52%), Gaps = 19/253 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  S+Q ++E+A+  V  E + V  AGRTD+GVH   Q+
Sbjct: 18  RIALGVEYKGSRYRGWQRQASGVPSVQQALEQALSTVANEPITVVCAGRTDAGVHGCGQI 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R W        L     +   IS++  + +   FHARF A  R Y Y I
Sbjct: 78  VHFDTRAVRDERAWT-------LGTNFNLPHDISVVWSAPMPAHFHARFKATARRYRYVI 130

Query: 117 IT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
                R A LA E    W   + LD   M  AA++L+G HDF+ FR+  CQA SPI+ I 
Sbjct: 131 YNDPIRPAHLAEEV--TW-NHRPLDVTRMAEAARYLLGTHDFSAFRASQCQAKSPIKHIH 187

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           H  V   G +I + V A +FLH  +R+  G L  +G G+       + L+ ++R+E G  
Sbjct: 188 HLRVTRHGQMIVLDVRATAFLHHMVRNIAGVLMTIGAGERPVEWAREVLEGRNRREGGVT 247

Query: 234 APPEGLYFDSVEY 246
           A P GLY   VEY
Sbjct: 248 AHPYGLYLVQVEY 260


>gi|160894208|ref|ZP_02074986.1| hypothetical protein CLOL250_01762 [Clostridium sp. L2-50]
 gi|156864241|gb|EDO57672.1| hypothetical protein CLOL250_01762 [Clostridium sp. L2-50]
          Length = 273

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 132/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y  +I Y+G+ Y GW+ +K+  +IQG IE  + L+ GE V ++GAGRTD+GVHA   
Sbjct: 25  MQNYRFLIAYDGTRYHGWEHKKDVVTIQGKIESVLSLMAGEEVRINGAGRTDAGVHARAM 84

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA   +  +  P  +   +N YL   D I IL ++   ++FHARF+A  + Y Y I   +
Sbjct: 85  VASGPVPTDKTPEEIRDYMNHYL--PDDICILEVTPAAERFHARFNAKGKHYRYTIYRGR 142

Query: 121 APLALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                ++   W + +  ++DCE MR AA +LVG HDF +F        S +R +   D+ 
Sbjct: 143 LKPVFDRKYVWTLDEGETIDCERMRKAAAYLVGEHDFKSFCGNKQMKKSTVRKLFAIDIK 202

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + +      FL   +R   G+L  VG G+     +E+ L  + R+  GP APP+G
Sbjct: 203 EDGDYVILDFYGAGFLQNMVRILTGTLVEVGAGRMEPAYMEEVLTGRCRQLAGPTAPPQG 262

Query: 239 LYFDSVEYS 247
           L    V+Y 
Sbjct: 263 LCLMQVDYE 271


>gi|313891575|ref|ZP_07825185.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
 gi|313120034|gb|EFR43216.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
          Length = 244

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y MIIEY+G+ Y GWQ+QK+   ++QG IEKA   VTGE V + GAGRTDSGVHA  Q
Sbjct: 1   MNYKMIIEYDGTRYEGWQKQKHSDETLQGKIEKAFEKVTGENVQIIGAGRTDSGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +  L  +     L   LN  L   D I I   + V+++FH+RF A  + Y Y +    
Sbjct: 61  VVNVHLPYDLNAENLKNELNEIL--PDDIYIKQCTEVEEKFHSRFHAKSKIYEYNLRIGS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +K   W   K L  E M+ AA+ L G HDFT F +      S +RT+   ++++ 
Sbjct: 119 NKDVFQKRFIWQFAKPLCIEKMKRAAEILQGTHDFTAFCNNKNFKKSAVRTVYSIEISTS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ +R     FL   IR  VG+L  VG+ K  +  L   L+++ R   G  APP+GL 
Sbjct: 179 NDILHLRFCGDGFLQGMIRIMVGTLVEVGENKRDADSLYDVLKSKQRSNAGFTAPPQGLT 238

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 239 LISVQY 244


>gi|331266815|ref|YP_004326445.1| tRNA pseudouridine synthase A [Streptococcus oralis Uo5]
 gi|326683487|emb|CBZ01105.1| tRNA pseudouridine synthase A [Streptococcus oralis Uo5]
          Length = 249

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/251 (36%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++ + IV   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVILIEIVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   L +  A   P  LD E M++A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPLRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLS 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNDRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|167032538|ref|YP_001667769.1| tRNA pseudouridine synthase A [Pseudomonas putida GB-1]
 gi|166859026|gb|ABY97433.1| tRNA pseudouridine synthase A [Pseudomonas putida GB-1]
          Length = 286

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 130/251 (51%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ +G  S+Q ++E+A+  V  E + V  AGRTD+GVH   Q+
Sbjct: 20  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPISVICAGRTDAGVHGCGQI 79

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R W        +     +   IS++    +   FHARF A  R Y Y I
Sbjct: 80  VHFDTRAVRDERAWT-------MGTNFNLPHDISVVWSQPMPADFHARFKACARRYRYVI 132

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 P  L +   W   + LD E M  AAQ L+G HDF+ FR+  CQA SPI+ I H 
Sbjct: 133 YNDPIRPAHLAEEVTW-NHRPLDVERMAEAAQFLLGTHDFSAFRASQCQAKSPIKHIYHL 191

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + V A +FLH  +R+  G L  +G G+   T   + L+ ++R+E G  A 
Sbjct: 192 RVTRHGQMIVLDVRATAFLHHMVRNIAGVLMAIGAGERPVTWAREVLEGRNRREGGVTAH 251

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 252 PYGLYLVQVEY 262


>gi|298373324|ref|ZP_06983313.1| tRNA pseudouridine synthase A [Bacteroidetes oral taxon 274 str.
           F0058]
 gi|298274376|gb|EFI15928.1| tRNA pseudouridine synthase A [Bacteroidetes oral taxon 274 str.
           F0058]
          Length = 247

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 135/245 (55%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I YNG+ Y GWQ Q N  ++Q ++ +A+ +V G  V + GAGRTD+GVHA    
Sbjct: 1   MRYFIYIAYNGTNYHGWQIQPNAVTVQETVGQAMSVVLGSNVEITGAGRTDTGVHARTMT 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFDL +      L K LN+ L     I++  +  V  + HARFSA+ R+Y Y +   + 
Sbjct: 61  AHFDLTKRIDEANLVKRLNSLLPAD--IAVYKIVEVIPEAHARFSAMSRTYEYLLYLDKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +G A+   + LD E M IAA  +    DFT+F  +H    +   T+   + +   
Sbjct: 119 PFL--RGLAYRHYRDLDFEKMNIAANKMRDYTDFTSFAKLHTDTRTNNCTVSKAEWHKQD 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N+    +VA  FL   +R+ VG+L LVG+G+ T  D  + ++A+DR++ G     +GLY 
Sbjct: 177 NIWIFTIVADRFLRDMVRATVGTLILVGEGRITVDDFCRIIEAKDRQKAGQSIDAQGLYL 236

Query: 242 DSVEY 246
             ++Y
Sbjct: 237 TDIQY 241


>gi|322374222|ref|ZP_08048755.1| tRNA pseudouridine synthase A [Streptococcus sp. C150]
 gi|321276927|gb|EFX53999.1| tRNA pseudouridine synthase A [Streptococcus sp. C150]
          Length = 248

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 88/249 (35%), Positives = 135/249 (54%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+QRQ +  SIQ  IEK +  L +G  VVVHGAGRTD+GVHA  
Sbjct: 1   MVRYKAIISYDGTLFSGFQRQPDARSIQEEIEKTLLRLNSGTPVVVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V + FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEDFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  L    M+ AA+ LVG HDFT F +      + +RTI      +
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAKDLVGTHDFTGFTASGTSVENKVRTITQARVSI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L++ DR   GP A   
Sbjct: 179 DEKTGFYVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPISQVKTVLESCDRNLAGPTASGN 238

Query: 238 GLYFDSVEY 246
           GLY   ++Y
Sbjct: 239 GLYLKEIKY 247


>gi|254673733|emb|CBA09384.1| tRNA pseudouridine synthase A [Neisseria meningitidis alpha275]
          Length = 266

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 133/247 (53%), Gaps = 6/247 (2%)

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--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HFD   VR     I  + +    K    + +L+   V  +FHARF A  R Y Y + + 
Sbjct: 68  VHFDTTAVRPQQAWIRGRKMPTCPK---ALPVLHARQVALEFHARFDAYGRHYRYLLESS 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L K RA      LD   MR AA +L+G  DF++FR+  CQA SPI+TI   ++  
Sbjct: 125 PVRSPLLKNRAGWTHLKLDIGPMRQAATYLIGEQDFSSFRAAECQAKSPIKTIYRANLTQ 184

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GL
Sbjct: 185 SAGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGL 244

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 245 YLTGVDY 251


>gi|126667385|ref|ZP_01738357.1| tRNA pseudouridine synthase A [Marinobacter sp. ELB17]
 gi|126628141|gb|EAZ98766.1| tRNA pseudouridine synthase A [Marinobacter sp. ELB17]
          Length = 303

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 132/250 (52%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  ++ EY+G  + GWQ+QK+G  ++Q  + KA   V    V +  AGRTD+GVHA  Q+
Sbjct: 18  RVALVFEYDGREFHGWQQQKSGIRAVQQQLAKAASKVADHDVELVCAGRTDAGVHASYQL 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      +R WV       +N  L     IS+         FHARFSA+ R Y Y I
Sbjct: 78  VHFDTPSLRTMRSWV-----MGINTALPFD--ISVRWAGQCQGDFHARFSAVYRRYRYII 130

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   +++G+     + L+ ENM  AAQ LVG HDF+ FR+  CQ+ SPIR +    
Sbjct: 131 YNNPVRPGIQRGQVSWNFRPLNAENMHQAAQALVGEHDFSAFRAAGCQSHSPIRFLQSIS 190

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ + I V A +FLH  +R+  G+L  VG  +     + + L  +DR++ G  APP
Sbjct: 191 VTRKGDYLVIDVQANAFLHHMVRNIAGALMAVGCQEQAPDWIGQILATKDRRQAGVTAPP 250

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 251 DGLYLVDVGY 260


>gi|255067233|ref|ZP_05319088.1| tRNA pseudouridine synthase A [Neisseria sicca ATCC 29256]
 gi|255048601|gb|EET44065.1| tRNA pseudouridine synthase A [Neisseria sicca ATCC 29256]
          Length = 272

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 135/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q  +E A+  + GE +    AGRTD+GVHA  QV
Sbjct: 15  RWALTLSYDGSRFYGWQKQADGLPTVQTVLESALSQIAGETIRTIVAGRTDTGVHATAQV 74

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NAYL   + +++L    V   FHARF A  R Y Y + +   
Sbjct: 75  VHFDTQVARPEQAWVRGVNAYLP--EGVAVLFAQQVAPHFHARFDAYGRRYRYLLESSPV 132

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +G+       LD E M+ AA  L G HDF++FR++ CQA SP++T+    ++   
Sbjct: 133 RSPILQGKVGWTHLKLDPEKMQQAALLLEGEHDFSSFRAVECQAKSPVKTLYSAKISGTP 192

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +++ +   +FLH  +R+ +G+L  VG G+ + +  +  ++ + R +  P   P+GLY 
Sbjct: 193 QFLKLDLHGNAFLHHMVRNIMGALVYVGSGRLSISGFQDLIEERSRLKAPPTFMPDGLYL 252

Query: 242 DSVEY 246
             V+Y
Sbjct: 253 TGVDY 257


>gi|290475958|ref|YP_003468853.1| pseudouridylate synthase I [Xenorhabdus bovienii SS-2004]
 gi|289175286|emb|CBJ82089.1| pseudouridylate synthase I [Xenorhabdus bovienii SS-2004]
          Length = 279

 Score =  153 bits (386), Expect = 2e-35,   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  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 16  VKIALGIEYDGSRYYGWQRQQEVKSVQECLEKALSKVADEPISVFCAGRTDAGVHATGQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF    +         +N++L     I++  +  VD +FHARFSA  R Y Y I   R 
Sbjct: 76  VHFKTSAQRKDAAWTMGVNSHL--PPDIAVRWVKTVDDEFHARFSATARRYRYIIFNHRY 133

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD   M  AAQ L+G +DFT+FR++ CQ++SP R + H +V+  
Sbjct: 134 RPAVLAQGVTHF-HYLLDERKMHEAAQSLLGENDFTSFRAVQCQSNSPWRNMMHINVSRH 192

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + + + A +F+H  +R+ VGSL  +G        + + L  +DR +    A  EGLY
Sbjct: 193 GHYVVVDIKANAFVHHMVRNIVGSLLEIGCSNQDIGWMAELLALKDRTKAAATAKAEGLY 252

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 253 LVAVDY 258


>gi|255321215|ref|ZP_05362381.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SK82]
 gi|262380100|ref|ZP_06073255.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SH164]
 gi|255301769|gb|EET81020.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SK82]
 gi|262298294|gb|EEY86208.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SH164]
          Length = 265

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 134/252 (53%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G  Y GWQ Q+ G  S+Q ++E+ +  +  E +++HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFCGIRYRGWQTQQAGVPSVQETLERVLSKIADEKIILHGAGRTDAGVHATN 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + +  ++   I++  L  + + FHARF A  R Y Y
Sbjct: 61  MVAHFDTHAIRTERGWM-------MGSNSQLPKDIALQWLQPMGEDFHARFKACARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I       AL   +   + + LD E M+ AA+   G H+F +FR+  CQ++ PIR + H
Sbjct: 114 VIYNAPYRPALLHKQVTHVYQQLDIEKMKKAAKKFRGVHNFESFRAAACQSNQPIRDVTH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++   G  + + + A  FLH  +R+ VG L  VG G +    ++    A+DR+  G  A
Sbjct: 174 CELFEHGRYLVLDIQANGFLHHMVRNIVGCLLEVGQGMYDIGHIDSIFAAEDRRAAGMTA 233

Query: 235 PPEGLYFDSVEY 246
           P +GLYF    Y
Sbjct: 234 PADGLYFIQAYY 245


>gi|317492661|ref|ZP_07951088.1| tRNA pseudouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919411|gb|EFV40743.1| tRNA pseudouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 285

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 89/239 (37%), Positives = 128/239 (53%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y GWQRQ +  S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV HF+  
Sbjct: 31  IEYDGSQYAGWQRQSDAPSVQECLEKALSKVACEPITVSCAGRTDAGVHATGQVVHFETH 90

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                      +N ++     I++  +  V + FHARFSA  R Y Y I   +   A+ +
Sbjct: 91  VARKDAAWTMGVNTHMP--KDIAVRWVKSVSEDFHARFSATARRYRYVIYNHRYRQAVLQ 148

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
                    LD E M  A Q L+G +DFT+FR+  CQ+ +P R + H  V   G+ + + 
Sbjct: 149 NGLTHFYHHLDAERMERAGQALLGENDFTSFRASQCQSRTPWRNVSHLKVTRLGDYVIVD 208

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A +F+H  +R+ VGSL  +G G    + + + L A+DRK     A   GLY  SV+Y
Sbjct: 209 IKANAFVHHMVRNIVGSLMEIGCGNQPESWMAELLAAKDRKLAAATAKAAGLYLVSVDY 267


>gi|266623132|ref|ZP_06116067.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
 gi|288865107|gb|EFC97405.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
          Length = 404

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 84/244 (34%), Positives = 135/244 (55%), Gaps = 3/244 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y ++++Y+GS Y GWQ+Q N G++IQG +E  +  +TG  V VHG+GRTD+GVHAL Q A
Sbjct: 159 YKIVLQYDGSRYDGWQKQGNTGNTIQGKLEGILLKLTGRPVEVHGSGRTDAGVHALAQTA 218

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F          +    N YL   + I++L++  V  +FH+R +A++++YLYRI      
Sbjct: 219 NFHADTGMTEDQIRAYFNQYL--PEDIAVLSVEKVQDKFHSRLNAVQKTYLYRIEMGPKK 276

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   + + K L  + M+ AA  ++G HDF +F        S +RTI    +   G 
Sbjct: 277 DVFERKYCYGLGKQLSADRMKEAAACVLGEHDFKSFCGNKKMKKSTVRTISDITIEKEGT 336

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + IR     FL+  +R   G+L  +G  + +  ++++ L   DR+  G  APPEGL+ +
Sbjct: 337 KLLIRYTGNGFLYHMVRILTGTLIEIGLEERSPQEMKEILLKLDRQAAGFTAPPEGLFLE 396

Query: 243 SVEY 246
            V Y
Sbjct: 397 RVMY 400


>gi|89256403|ref|YP_513765.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314847|ref|YP_763570.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica OSU18]
 gi|167010425|ref|ZP_02275356.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367741|ref|ZP_04983762.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica 257]
 gi|122325138|sp|Q0BLV1|TRUA_FRATO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122999741|sp|Q2A3D7|TRUA_FRATH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|89144234|emb|CAJ79507.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129746|gb|ABI82933.1| tRNA-pseudouridine synthase I [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253552|gb|EBA52646.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica 257]
          Length = 258

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 132/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSLSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           + +F     + P+    + +NA L     I IL +  VD  F++RF+AI R+Y Y I   
Sbjct: 61  IVNF-YSNAYRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNS 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +   
Sbjct: 118 ATSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GL
Sbjct: 178 QGSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGL 237

Query: 240 YFDSVEY 246
           YF  VEY
Sbjct: 238 YFVGVEY 244


>gi|329121886|ref|ZP_08250501.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
 gi|327467824|gb|EGF13316.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
          Length = 244

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 95/246 (38%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y MIIEY+G+ Y GWQ+QK+   ++QG IEKA   VTGE V + GAGRTDSGVHA  Q
Sbjct: 1   MNYKMIIEYDGTRYEGWQKQKHSDETLQGKIEKAFEKVTGENVQIIGAGRTDSGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+  L  +     L   LN  L   D I I     V+++FH+RF A  + Y Y +    
Sbjct: 61  VANVHLPYDLNAENLKNELNEIL--PDDIYIKQCIEVEEKFHSRFHAKSKIYEYNLRIGS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +K   W   K L  E M+ AA+ L G HDFT F +      S +RT+   ++++ 
Sbjct: 119 NKDVFQKRFIWQFAKPLCIEKMKRAAEILQGTHDFTAFCNNKHFKKSAVRTVYSIEISTS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ +R     FL   IR  VG+L  VG+ K  +  L   L+++ R   G  APP+GL 
Sbjct: 179 NDILHLRFCGDGFLQGMIRIMVGTLVEVGENKRDADSLYDVLKSKQRSNAGFTAPPQGLT 238

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 239 LISVQY 244


>gi|228477786|ref|ZP_04062414.1| tRNA pseudouridine synthase A [Streptococcus salivarius SK126]
 gi|228250478|gb|EEK09692.1| tRNA pseudouridine synthase A [Streptococcus salivarius SK126]
          Length = 248

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 134/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  +EK +  L +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEELEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I ++++ +V ++FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDVVSIELVSEEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L    M+ AA+ LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAKDLVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L+++DR   GP A   
Sbjct: 179 DEKTGFYIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESRDRNLAGPTAAGN 238

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 239 GLYLKEIRY 247


>gi|322377359|ref|ZP_08051850.1| tRNA pseudouridine synthase A [Streptococcus sp. M334]
 gi|321281559|gb|EFX58568.1| tRNA pseudouridine synthase A [Streptococcus sp. M334]
          Length = 249

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVLHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMSRYYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLK 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|302873576|ref|YP_003842209.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|307688243|ref|ZP_07630689.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|302576433|gb|ADL50445.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
          Length = 245

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 82/249 (32%), Positives = 136/249 (54%), Gaps = 7/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G  Y GWQ+   +  +IQ  +EK +  +  E V V G+GRTD+GVHA +
Sbjct: 1   MNNYKLTIQYDGKNYRGWQKLSDSDKTIQSKLEKVLSTLVDEEVNVIGSGRTDAGVHARK 60

Query: 60  QVAHFDLVRE--WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           Q+A+F   ++  W  V+     + Y  + + I + +   VD++FHAR++A ++ Y YRI 
Sbjct: 61  QIANFHTEKDLKWKDVLK----HCYTYLPEDIVVKSCDKVDEKFHARYNAKKKIYTYRIC 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                 A E+  ++L+ K L+ + M  A+++ +G HDF +F S+  +  S +R I    +
Sbjct: 117 NSAFGDAFERKYSYLVDKKLNIDKMLAASKYFIGIHDFKSFTSMKSKKKSTVREIYDISI 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+++EI  +   FLH  IR   G+L  VG GK    ++   +   +R + G  AP  
Sbjct: 177 NCIGDMVEITYIGEGFLHNMIRILTGTLIEVGLGKMKIDEIPTIMDGLERSDAGFTAPAH 236

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 237 GLFLVDVIY 245


>gi|187776609|ref|ZP_02993082.1| hypothetical protein CLOSPO_00123 [Clostridium sporogenes ATCC
           15579]
 gi|187775268|gb|EDU39070.1| hypothetical protein CLOSPO_00123 [Clostridium sporogenes ATCC
           15579]
          Length = 246

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 80/241 (33%), Positives = 134/241 (55%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EK I  +T E V + GA RTDSGVHA   + +F 
Sbjct: 8   LEYDGTNYCGWQKQKNEKFITLQGTLEKVISNITKEKVEITGASRTDSGVHAKGYMCNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P  L + +N  L     I +L+   V  +FH+RF +  ++Y Y I+ +  P+A+
Sbjct: 68  TNSRIPPENLQRVINNNL--PPDIVVLSSEEVSSEFHSRFCSKGKTYEYTILNKSEPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     LD + M+IA+++ +G HDF+ F++      + +RTI  F++N  G+LI+
Sbjct: 126 GRNYVFHFKYKLDIDKMKIASKYFIGTHDFSAFQTKGSSVKTSVRTISKFEINKSGDLIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  K     +E  ++++DR++ G   P  GL    V 
Sbjct: 186 FIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIEYVIKSKDRRKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|326316049|ref|YP_004233721.1| tRNA pseudouridine synthase A [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323372885|gb|ADX45154.1| tRNA pseudouridine synthase A [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 278

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 86/258 (33%), Positives = 128/258 (49%), Gaps = 20/258 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNGS Y GWQ Q  G+++Q  +E A+       V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGSAYRGWQSQPGGATVQDRLEAALARFATHEVSTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   + +P    +  N +L     I++     V + FH+R SA  R Y Y ++    
Sbjct: 61  VHFDTPLDRMPFSWVRGTNTFLPPD--IAVQWARPVPEAFHSRASATARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +  +LD + MR AA+HL+G HDFT+FR+  CQA SP++T+   ++   G
Sbjct: 119 RPSVESGRVGWVFHALDGDAMRAAARHLLGEHDFTSFRASACQAKSPVKTLRRIEITQRG 178

Query: 182 N------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                                       +FLH  +R+ +G L  VG G+  +  +   LQ
Sbjct: 179 TGGVPAGQASGDRGDVPTCYWRFEFEGNAFLHHMVRNIMGCLVAVGQGQHPADWMHAVLQ 238

Query: 224 AQDRKECGPLAPPEGLYF 241
           A+ R    P   P+GLYF
Sbjct: 239 ARSRDAAAPTFSPDGLYF 256


>gi|240144416|ref|ZP_04743017.1| tRNA pseudouridine synthase A [Roseburia intestinalis L1-82]
 gi|257203524|gb|EEV01809.1| tRNA pseudouridine synthase A [Roseburia intestinalis L1-82]
          Length = 294

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 86/245 (35%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  MI+ Y+G+ Y GWQ Q NG +I+  + K +  + GE +VV GA RTDSGVH+L  +
Sbjct: 48  MRVKMIVAYDGTNYKGWQVQPNGITIEEVLNKNLSNLLGEQIVVSGASRTDSGVHSLGNI 107

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FD         +  ALN   ++ + I +     V+  +H R+   R++Y YRI+ R  
Sbjct: 108 AVFDTNTRMPADKIAFALNQ--RLPEDIVVQGSCEVEDGWHPRYQNSRKTYEYRILNRTF 165

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
            +   +   +     LD E M+ AA +L G HDF +F +I  Q  + +RTI   DV   G
Sbjct: 166 RMPTRRLDTYFYHYPLDVEKMKKAASYLEGEHDFKSFCAIGAQVKTTVRTIYACDVEKEG 225

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IRV    FL+  +R   G+L  VG G      ++  L  +DR   GP AP  GL  
Sbjct: 226 DIITIRVTGNGFLYNMVRIIAGTLVQVGGGAIKPEAVKGILAKKDRSAAGPTAPAHGLTM 285

Query: 242 DSVEY 246
             +E+
Sbjct: 286 MGIEF 290


>gi|187931655|ref|YP_001891639.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|238691562|sp|B2SGK2|TRUA_FRATM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|187712564|gb|ACD30861.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 258

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+ +DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEVKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|222100131|ref|YP_002534699.1| tRNA pseudouridine synthase A [Thermotoga neapolitana DSM 4359]
 gi|254764873|sp|B9K8Q0|TRUA_THENN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221572521|gb|ACM23333.1| tRNA pseudouridine synthase A [Thermotoga neapolitana DSM 4359]
          Length = 245

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 133/246 (54%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   I+EY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MRRVAAIVEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+   + +     K A+NA L   D + +  +  V K FH RF   +R Y Y I T 
Sbjct: 61  LIAFNCPNDRMTTEDIKNAMNANL--PDDVYVKKVFEVPKNFHPRFDVKKRIYHYFIHTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  AW  P  LD E MR AA++L G HDFT+F++       P+RTI    + S
Sbjct: 119 REKNVFLRKYAWWFPYELDLEAMRKAAKYLEGTHDFTSFKT-GSDERDPVRTIYRIRILS 177

Query: 180 FG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            G ++I IRV  RSFL   +R+ V +L  VG  +W    L++ L+A+DR      AP  G
Sbjct: 178 LGKDMILIRVEGRSFLRRMVRNIVAALVKVGLRQWEPEKLKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|315169224|gb|EFU13241.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1341]
 gi|315171531|gb|EFU15548.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1342]
          Length = 277

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 37  LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 96

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 97  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 154

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 155 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKNKKSTTRTIEKITIERNGEML 214

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 215 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 274

Query: 245 EY 246
            Y
Sbjct: 275 YY 276


>gi|52841533|ref|YP_095332.1| tRNA pseudouridine synthase A [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|54297221|ref|YP_123590.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Paris]
 gi|148358844|ref|YP_001250051.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Corby]
 gi|296106890|ref|YP_003618590.1| tRNA pseudouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
 gi|62901237|sp|Q5X5Q4|TRUA_LEGPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901247|sp|Q5ZVY6|TRUA_LEGPH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228736|sp|A5IBF5|TRUA_LEGPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52628644|gb|AAU27385.1| tRNA pseudouridine synthase A [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|53751006|emb|CAH12417.1| tRNA-pseudouridine synthase I [Legionella pneumophila str. Paris]
 gi|148280617|gb|ABQ54705.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Corby]
 gi|295648791|gb|ADG24638.1| tRNA pseudouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
          Length = 262

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 87/250 (34%), Positives = 135/250 (54%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    +IQ ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVVEYDGSQYHGWQAQTGLHTIQQAVEFALSKVADSSISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSI-----VDKQFHARFSAIRRSYLYRI 116
            HFD  ++       +++ A++  ++T    ++ +     + + FHAR+SA+ R Y Y I
Sbjct: 61  IHFDCEKD-------RSIRAWIHGANTFLPKDICVKWGKEMPENFHARYSAVSRRYRYVI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G      + LD   M+   Q L+G +DFT+FRS+ CQ+++P+R I    
Sbjct: 114 YNGAIRPGLLRGNVTWQYRQLDHRLMQQGGQCLLGENDFTSFRSVECQSNTPMRNIHQLQ 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+L+ + + A +FLH  +R+  G L  VG GK     ++  L A+DRK     AP 
Sbjct: 174 VTRHGDLVVLDITANAFLHHMVRNIAGVLIAVGSGKHPVGWVKDVLNAKDRKLGAETAPS 233

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 234 YGLYLVQVTY 243


>gi|262374120|ref|ZP_06067397.1| tRNA pseudouridine synthase A [Acinetobacter junii SH205]
 gi|262311131|gb|EEY92218.1| tRNA pseudouridine synthase A [Acinetobacter junii SH205]
          Length = 265

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 131/247 (53%), Gaps = 13/247 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G+ Y GWQ Q+ G  S+Q +IEK +  +    V++H AGRTD+GVHA  
Sbjct: 1   MQRYAIGIEFCGTQYRGWQTQQAGVVSVQETIEKVLSKIADHPVILHAAGRTDAGVHATN 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + A  ++   ISI  +  +D+ FHARF A+ R Y Y
Sbjct: 61  MVAHFDTTAIRPERGWL-------MGANSQLPKDISIQWIKCMDENFHARFKAMARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   + + LD + M  AA    G H+F +FR+  CQ++ P+R + H
Sbjct: 114 LVYNAPTRPALLHKQVTHLYQELDVQKMIKAAAKFEGTHNFESFRAAACQSNQPVRHVKH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DR+  G  A
Sbjct: 174 CRLFEHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRRAAGITA 233

Query: 235 PPEGLYF 241
           P +GLYF
Sbjct: 234 PADGLYF 240


>gi|15903494|ref|NP_359044.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae R6]
 gi|116516785|ref|YP_816881.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae D39]
 gi|148988650|ref|ZP_01820083.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP6-BS73]
 gi|149004327|ref|ZP_01829087.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS69]
 gi|169833383|ref|YP_001694996.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182684548|ref|YP_001836295.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CGSP14]
 gi|221232354|ref|YP_002511507.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae ATCC
           700669]
 gi|225855038|ref|YP_002736550.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae JJA]
 gi|237649225|ref|ZP_04523477.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CCRI 1974]
 gi|237822076|ref|ZP_04597921.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CCRI
           1974M2]
 gi|307127806|ref|YP_003879837.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 670-6B]
 gi|38258775|sp|Q8CWQ1|TRUA_STRR6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122278273|sp|Q04JF7|TRUA_STRP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238688376|sp|B1ID11|TRUA_STRPI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238691180|sp|B2IRB1|TRUA_STRPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764868|sp|B8ZM12|TRUA_STRPJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764870|sp|C1CFH9|TRUA_STRZJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|15459107|gb|AAL00255.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae R6]
 gi|116077361|gb|ABJ55081.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae D39]
 gi|147757704|gb|EDK64720.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS69]
 gi|147925851|gb|EDK76926.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP6-BS73]
 gi|168995885|gb|ACA36497.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182629882|gb|ACB90830.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CGSP14]
 gi|220674815|emb|CAR69389.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae ATCC
           700669]
 gi|225723432|gb|ACO19285.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae JJA]
 gi|306484868|gb|ADM91737.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 670-6B]
 gi|332072765|gb|EGI83246.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA17545]
 gi|332200155|gb|EGJ14228.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA47368]
          Length = 249

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLI 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|291279383|ref|YP_003496218.1| tRNA pseudouridine synthase A [Deferribacter desulfuricans SSM1]
 gi|290754085|dbj|BAI80462.1| tRNA pseudouridine synthase A [Deferribacter desulfuricans SSM1]
          Length = 244

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +   ++EY+G+ +FGWQRQK+  ++QG IE A+  +    + + G+GRTD+GVHA+ Q
Sbjct: 1   MYKKKCVVEYDGTYFFGWQRQKDLRTVQGVIEAALSKIYKSSINIVGSGRTDTGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF   R      +   LN+ L   + + I ++  VD  FHA+ SAI ++Y+Y+I   Q
Sbjct: 61  VFHFVSERYLENRSVLLGLNSVL--PEDVVIKHVEDVDLSFHAQKSAISKTYIYKIYNYQ 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL + RAW I  ++D + +    +   G  DF+          +P+RTI++      
Sbjct: 119 IRSALFRNRAWWIRDNIDVDLLNEYLKFFKGEKDFSAMCLKRSVPENPVRTINYIFAKRD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I + A  FLH  +R+ VG++  +     +   +E+ L+++DRK  G  APP+GLY
Sbjct: 179 GDFINIEINANGFLHNMVRNIVGTVIDLYSDNSSPEKIEEILKSKDRKNAGRTAPPQGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LKEVFY 244


>gi|255974352|ref|ZP_05424938.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|257088141|ref|ZP_05582502.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
 gi|307278161|ref|ZP_07559243.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|255967224|gb|EET97846.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|256996171|gb|EEU83473.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
 gi|306505150|gb|EFM74338.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|315026898|gb|EFT38830.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2137]
          Length = 246

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKNKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|303240936|ref|ZP_07327447.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
 gi|302591522|gb|EFL61259.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
          Length = 245

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 89/244 (36%), Positives = 135/244 (55%), Gaps = 8/244 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ Y GWQ Q N  ++Q ++EKAI+ +TGE++ ++G+ RTD GVHA  QVA+F 
Sbjct: 6   LIIEYDGTNYHGWQSQSNAKTVQETVEKAIYGLTGEVININGSSRTDQGVHAYGQVANF- 64

Query: 66  LVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
             +  +P      ALN  L   + I I     V   FHAR+ A  + Y Y I     P A
Sbjct: 65  FTKSNIPHDRFSYALNRML--PEDIIIRKSEEVSMDFHARYCAKGKKYRYLIYNSSFPSA 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--SFGN 182
           + + R++ +  +LD ++M+ A     G HDF+ F++      + +RTI  FDVN     +
Sbjct: 123 IFRNRSYHVSHNLDMDSMKKAIPFFKGTHDFSAFKATGSSVKTSVRTI--FDVNLSRAED 180

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I   V    FL+  +R  VG+L  VG G+  + ++   +++ DRK  G  APP+GLY  
Sbjct: 181 NIWFEVSGDGFLYNMVRIMVGTLVDVGMGRIKAEEIPGIIESCDRKRAGRTAPPQGLYLV 240

Query: 243 SVEY 246
            V Y
Sbjct: 241 EVYY 244


>gi|291520511|emb|CBK75732.1| pseudouridylate synthase I [Butyrivibrio fibrisolvens 16/4]
          Length = 245

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 83/246 (33%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++ Y+GS Y GWQ Q NG +I+  + +A+  +  E + + GA RTD+GVH+L  V
Sbjct: 1   MRVMIVVAYDGSNYSGWQIQPNGVTIEQKLNEALTDLLQEPISIMGASRTDAGVHSLGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FD         +  ALN   ++ D I +     V+  FH R++A R++Y Y+I+ R+ 
Sbjct: 61  AVFDTNSRMPADKISFALNQ--RLPDDIVVQYSCQVEDDFHPRYAACRKTYEYKILNRKM 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   ++   +     LD E M  AA +L+G+HDFT+F S+  Q  S +RTI    V    
Sbjct: 119 PDPTKRKDTFHYYYDLDVEKMNEAAAYLIGQHDFTSFSSVKAQVKSRVRTIYTAKVYKED 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IR+    FL+  +R   G+L  VG G+     + +  + ++R+  GP AP  GL  
Sbjct: 179 DVIHIRLTGDGFLYNMVRIIAGTLIKVGAGEMEPMYMLEIFRGRNRELAGPTAPAHGLTM 238

Query: 242 DSVEYS 247
             +EY 
Sbjct: 239 IGIEYE 244


>gi|308172039|ref|YP_003918744.1| pseudouridylate synthase I [Bacillus amyloliquefaciens DSM 7]
 gi|307604903|emb|CBI41274.1| pseudouridylate synthase I [Bacillus amyloliquefaciens DSM 7]
 gi|328551849|gb|AEB22341.1| tRNA pseudouridine synthase A [Bacillus amyloliquefaciens TA208]
 gi|328910104|gb|AEB61700.1| pseudouridylate synthase I [Bacillus amyloliquefaciens LL3]
          Length = 247

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 87/248 (35%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  T   V V+ +GRTDS VHA  
Sbjct: 1   MRMKCTIAYDGHLFNGYQVQPGKRTVQSELEKALAVIHKTDGRVPVYSSGRTDSDVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAEKWPFALNALL--PDDIAVKTAEIADDGFHARFSAVQKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ + MR A++HL+G HDFT+F ++       +RTI   +   
Sbjct: 119 KHPDVFKRHYAYHFAYQLNVQKMREASRHLIGTHDFTSFCAVDTAVQDKVRTIYELEWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +++R+    FL+  +R   G+L   G GK++  D++  L+A+DR+  G  AP  GL
Sbjct: 179 TGDGLQMRITGNGFLYNMVRIIAGTLLDTGAGKFSPDDVKAMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  SV Y 
Sbjct: 239 YLWSVCYD 246


>gi|270293156|ref|ZP_06199367.1| tRNA pseudouridine synthase A [Streptococcus sp. M143]
 gi|270279135|gb|EFA24981.1| tRNA pseudouridine synthase A [Streptococcus sp. M143]
          Length = 249

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  L  G+ V VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAVTVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + I+ R
Sbjct: 61  QAIHFDLPYQMNEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+ A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVEQMQEAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLS 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDKTGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|281202734|gb|EFA76936.1| hypothetical protein PPL_09688 [Polysphondylium pallidum PN500]
          Length = 275

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 91/250 (36%), Positives = 134/250 (53%), Gaps = 32/250 (12%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL----------VREWVPVILC 76
           +Q  +E+++ +   + V + G+ RTD+GV+AL QVAHFD+          +    P ++ 
Sbjct: 10  VQQVLEESLEVFIRKKVRLVGSSRTDTGVNALHQVAHFDVDTRISKTGEEIDMMPPEVIT 69

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII----TRQAPLALEKGRAWL 132
            ALN  ++    + +++  IVD  FH+RFSA  R+YLYR++      QAP  L K R W 
Sbjct: 70  MALNQNVQ-GYPVRVISTEIVDDSFHSRFSAKSRTYLYRMLGGMHRNQAPFEL-KDRVWA 127

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN---------- 182
           +   LD   M+ AA  L GRH+F +FRS  CQA +P+RTI  F V    N          
Sbjct: 128 VTNQLDVPKMQEAATLLCGRHNFNSFRSSKCQADNPVRTISSFQVFDLPNPDIWQYNSAP 187

Query: 183 ------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 LI I V AR+FLH Q+R  V +L+ VG  + +   L++ + A+DR++  P APP
Sbjct: 188 LGVNPQLIGIEVKARAFLHNQVRIMVSTLERVGSHQMSLDQLQELIDAKDRQKAPPTAPP 247

Query: 237 EGLYFDSVEY 246
             L    V Y
Sbjct: 248 YPLTLTKVSY 257


>gi|110636905|ref|YP_677113.1| tRNA pseudouridine synthase A [Cytophaga hutchinsonii ATCC 33406]
 gi|110279586|gb|ABG57772.1| pseudouridylate synthase I [Cytophaga hutchinsonii ATCC 33406]
          Length = 248

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y G+ Y GWQ Q+N  ++QG ++KA+  V G  + + G+GRTD+GVHA  Q+
Sbjct: 1   MRYFLDISYRGANYHGWQIQENAVTVQGVLQKALSNVLGAKIDILGSGRTDTGVHASSQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D  +E +   L   +N YL     I I +  +V    HARF A+ R+Y+YRI   + 
Sbjct: 61  VHLDSPKE-IDAALIFRINGYL--PKDICIKSARLVQDDAHARFDALSRAYVYRITLVKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E G A+     ++ + M  AA  L+   DF +F  +H   ++   TI H      G
Sbjct: 118 PF--EIGLAYYFYPPIEIDRMNKAAAILLQYEDFESFSKVHTDVTNFNCTIFHAYWERNG 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +++   V A  FL   +R+ VG++  VG G+ +  D  + + A+DRK  G  APPE LY 
Sbjct: 176 DMLYFHVKANRFLRGMVRTLVGTMLEVGKGRMSLDDFVQIILAKDRKRAGISAPPEALYL 235

Query: 242 DSVEY 246
             VEY
Sbjct: 236 SEVEY 240


>gi|293364991|ref|ZP_06611708.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
 gi|307703239|ref|ZP_07640185.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
 gi|291316441|gb|EFE56877.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
 gi|307623314|gb|EFO02305.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
          Length = 249

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGFAFAGFQRQPHARSVQEEIEKTLTRLNKGQAIAVHGAGRTDSGVHALE 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+ A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLS 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|170703047|ref|ZP_02893873.1| tRNA pseudouridine synthase A [Burkholderia ambifaria IOP40-10]
 gi|170132039|gb|EDT00541.1| tRNA pseudouridine synthase A [Burkholderia ambifaria IOP40-10]
          Length = 270

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 92/249 (36%), Positives = 136/249 (54%), Gaps = 10/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHG--AGRTDSGVHA 57
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+    GE   V +H   AGRTD+GVH 
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDALERAL----GEFACVPLHTTVAGRTDTGVHG 56

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y + 
Sbjct: 57  LGQVVHFDTDLDRTDFSWVRGTNAFLP--STVSVQWAKPMPDTFHARFAAFERTYYYVLY 114

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV
Sbjct: 115 VHPVRSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDV 174

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DRK   P    +
Sbjct: 175 RRAGHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRKLAAPTFMAD 234

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 235 GLYLAHVGY 243


>gi|241668494|ref|ZP_04756072.1| tRNA pseudouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877028|ref|ZP_05249738.1| tRNA pseudouridine synthetase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843049|gb|EET21463.1| tRNA pseudouridine synthetase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 258

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  SIQ  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSIQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +       +  NA L     I IL++ +VD  F++RF+A  R+Y Y I    
Sbjct: 61  VVNFHSDADRNLSSWMRGTNALL--PQDIKILDIKVVDNDFNSRFTAKNRTYNYIIYNSL 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + L+ + M  A ++L+G  DFT+FRS  CQ+++P R I   +    
Sbjct: 119 ISSPIFAEHCLWENRQLNIDKMNQACKYLLGEQDFTSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+F+GSL  VG    +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNFIGSLLKVGLEFESPEWIKLVLEAKDRTKAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|149021302|ref|ZP_01835548.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP23-BS72]
 gi|168491513|ref|ZP_02715656.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC0288-04]
 gi|225861429|ref|YP_002742938.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298229625|ref|ZP_06963306.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae str. Canada
           MDR_19F]
 gi|298254115|ref|ZP_06977701.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae str. Canada
           MDR_19A]
 gi|298503335|ref|YP_003725275.1| tRNA-pseudouridine synthase I [Streptococcus pneumoniae
           TCH8431/19A]
 gi|254764872|sp|C1CSL6|TRUA_STRZT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|147930403|gb|EDK81387.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP23-BS72]
 gi|183574268|gb|EDT94796.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC0288-04]
 gi|225728219|gb|ACO24070.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298238930|gb|ADI70061.1| tRNA-pseudouridine synthase I [Streptococcus pneumoniae
           TCH8431/19A]
 gi|327389783|gb|EGE88128.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA04375]
 gi|332073932|gb|EGI84410.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA41301]
          Length = 249

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVAADFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLI 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|306829107|ref|ZP_07462297.1| tRNA pseudouridine synthase A [Streptococcus mitis ATCC 6249]
 gi|304428193|gb|EFM31283.1| tRNA pseudouridine synthase A [Streptococcus mitis ATCC 6249]
          Length = 249

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 91/251 (36%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++ + IV   FH R++   + Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVILIEIVADDFHCRYAKHSKIYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+IA + L G HDFT F +      + +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVENKVRTITEASLT 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMLVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|15901439|ref|NP_346043.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae TIGR4]
 gi|111656856|ref|ZP_01407696.1| hypothetical protein SpneT_02001886 [Streptococcus pneumoniae
           TIGR4]
 gi|149013277|ref|ZP_01834035.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP19-BS75]
 gi|168486863|ref|ZP_02711371.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1087-00]
 gi|225859353|ref|YP_002740863.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 70585]
 gi|303253960|ref|ZP_07340080.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS455]
 gi|303258528|ref|ZP_07344508.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP-BS293]
 gi|303262617|ref|ZP_07348557.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS292]
 gi|303263556|ref|ZP_07349478.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS397]
 gi|303267576|ref|ZP_07353421.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS457]
 gi|303269928|ref|ZP_07355667.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS458]
 gi|25453312|sp|Q97PL0|TRUA_STRPN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764867|sp|C1C8I7|TRUA_STRP7 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|14973090|gb|AAK75683.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae TIGR4]
 gi|147762942|gb|EDK69888.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP19-BS75]
 gi|183570198|gb|EDT90726.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1087-00]
 gi|225721425|gb|ACO17279.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 70585]
 gi|301794601|emb|CBW37047.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae INV104]
 gi|301802309|emb|CBW35063.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae INV200]
 gi|302599048|gb|EFL66074.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS455]
 gi|302636173|gb|EFL66668.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS292]
 gi|302640029|gb|EFL70484.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP-BS293]
 gi|302640531|gb|EFL70939.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS458]
 gi|302642899|gb|EFL73201.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS457]
 gi|302646594|gb|EFL76819.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS397]
          Length = 249

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 86/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFTVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|325955163|ref|YP_004238823.1| tRNA pseudouridine synthase A [Weeksella virosa DSM 16922]
 gi|323437781|gb|ADX68245.1| tRNA pseudouridine synthase A [Weeksella virosa DSM 16922]
          Length = 248

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 132/246 (53%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  YFGWQRQ    S+Q  IE  +  +  E + + GAGRTD+GVHA +  
Sbjct: 1   MRYFLELAYNGQNYFGWQRQPKQLSVQEKIEFCLSTLLREEINIVGAGRTDTGVHAKKMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD         + + LN++L   + IS+ ++  V  + HARF A++R+Y Y I T++ 
Sbjct: 61  AHFDFDGSLTDDFI-RRLNSFL--PEDISVTSIHCVAPEAHARFDAVKRTYHYHIYTQKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNSF 180
           P       +W I K LD E M  AA++L+ + DF +F  +H    + I T+   + +   
Sbjct: 118 PFTTTT--SWQIRKPLDIEKMNEAAKYLIKKADFGSFAKLHTDVKTNICTVYRAEWIQIE 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +     + A  FL   +R+ VG+L  VG GK T +D    +  +DRK     APP+GL+
Sbjct: 176 KDFFCFEITADRFLRNMVRAIVGTLVEVGLGKITPSDFNNIIDKKDRKFAAASAPPQGLF 235

Query: 241 FDSVEY 246
              V Y
Sbjct: 236 LVEVLY 241


>gi|322517723|ref|ZP_08070585.1| tRNA pseudouridine synthase A [Streptococcus vestibularis ATCC
           49124]
 gi|322123654|gb|EFX95247.1| tRNA pseudouridine synthase A [Streptococcus vestibularis ATCC
           49124]
          Length = 249

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 87/249 (34%), Positives = 132/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  +EK +  L +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEELEKTLLRLNSGTPVTVHGAGRTDAGVHAYE 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L++ DR   GP A   
Sbjct: 179 DEKTGFYIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESCDRNLAGPTAAGN 238

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 239 GLYLKEIRY 247


>gi|317403279|gb|EFV83796.1| pseudouridylate synthase I [Achromobacter xylosoxidans C54]
          Length = 268

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 86/243 (35%), Positives = 132/243 (54%), Gaps = 4/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           M + Y+GS + GWQ Q +  ++Q ++E A+  F    + V    AGRTD+GVH   QV H
Sbjct: 1   MGLAYDGSAWQGWQTQPHRQTVQDTLEAALAQFCGVTDAVPTICAGRTDTGVHGAMQVIH 60

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            D   +       + +NA+L  S  IS+     V   FHARFSA  R+Y+Y +   +   
Sbjct: 61  LDTTLDRRMESWVRGVNAFLPSS--ISVQWAKAVPDAFHARFSARARTYVYLLWRGRVRP 118

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           AL  GRA    + LD   MR AA  L+G HDF++FRS  CQA  P+R +   D++  G  
Sbjct: 119 ALWAGRAGWCYQPLDVGAMRAAANALLGEHDFSSFRSSQCQAKHPVRIMHRLDIDERGPF 178

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   + A +FLH  +R+ +G+L  +G G+ +   + + L  +DR+   P   P+GLY  +
Sbjct: 179 LVFTLRANAFLHHMVRNIMGALLQIGQGRESVDWMAQLLSWRDRRRGAPTFSPDGLYLSA 238

Query: 244 VEY 246
           ++Y
Sbjct: 239 IDY 241


>gi|160872663|ref|ZP_02062795.1| tRNA pseudouridine synthase A [Rickettsiella grylli]
 gi|159121462|gb|EDP46800.1| tRNA pseudouridine synthase A [Rickettsiella grylli]
          Length = 264

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 94/250 (37%), Positives = 128/250 (51%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R    I Y G  Y GWQ Q     IQ  +E+AI  V    V +  AGRTD GVHAL QV
Sbjct: 1   MRIAFGISYQGGAYHGWQSQTKLPCIQTYLERAISRVADHSVRLQCAGRTDKGVHALSQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       + W+        N+YL     I +  + +V+  FHARFSA+ R Y Y I
Sbjct: 61  VHFDTDVWRSKKSWL-----FGSNSYLP--PDIRVNWVQVVEDTFHARFSALARRYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             R    AL           L+ ++M  AAQ+LVG HDF++FR+  CQA+  +R I H  
Sbjct: 114 YNRHLKSALWNAYTSHCCYPLNEKDMHRAAQYLVGEHDFSSFRAASCQANHALREIQHIQ 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ + + + A +FLH  +R+    L L+G GK ++   ++ L AQ+RK     A P
Sbjct: 174 VKRHGDYVIMDIQANAFLHHMVRNISAVLMLIGQGKKSTLWAQEVLFAQNRKMADVTASP 233

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 234 TGLYLSHVIY 243


>gi|256618219|ref|ZP_05475065.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256597746|gb|EEU16922.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|315033638|gb|EFT45570.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0017]
          Length = 246

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILKQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKNKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|55820220|ref|YP_138662.1| tRNA pseudouridine synthase A [Streptococcus thermophilus LMG
           18311]
 gi|55822111|ref|YP_140552.1| tRNA pseudouridine synthase A [Streptococcus thermophilus CNRZ1066]
 gi|62901189|sp|Q5M1T6|TRUA_STRT1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901193|sp|Q5M6C9|TRUA_STRT2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|55736205|gb|AAV59847.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Streptococcus thermophilus LMG 18311]
 gi|55738096|gb|AAV61737.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Streptococcus thermophilus CNRZ1066]
          Length = 248

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 135/250 (54%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  IEK +  L +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEEIEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYSKHIKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V S
Sbjct: 119 RPKNPMMRNYAIHYPYPLSLALMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASV-S 177

Query: 180 FGNLIEIRVVARS---FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                   V A S   FL+ Q+R+ VG+L  +G+G+   + ++  L+++DR   GP    
Sbjct: 178 IDEKTGFYVFAFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESRDRNLAGPTVAG 237

Query: 237 EGLYFDSVEY 246
            GLY   + Y
Sbjct: 238 NGLYLKEIRY 247


>gi|15602502|ref|NP_245574.1| tRNA pseudouridine synthase A [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|13431946|sp|P57861|TRUA_PASMU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|12720912|gb|AAK02721.1| TruA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 264

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 95/252 (37%), Positives = 129/252 (51%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + I+YNG  Y GWQRQ+N +S+Q  +EKAI  V  +   +  AGRTDSGVHA  QV
Sbjct: 1   MKIALGIQYNGKNYCGWQRQENVASVQEQLEKAISFVANQPCQIFCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D IS+     V   FHARFSA  R Y Y       
Sbjct: 61  VHFETDAIRAEKAWSFGVNANL--PDDISVSWAKCVTDDFHARFSATARRYRY------- 111

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            L   K R+ ++P+        LD   M  A Q L+G  DF++FR+  CQ+ +P R + H
Sbjct: 112 ILYCNKLRSAILPEGVTHCHLDLDHHLMHQAGQALLGEQDFSSFRAAQCQSHTPFRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G  I + + A +F+H  +R+ VGSL  VG G      +   L  +DR+   P A
Sbjct: 172 LKVVRRGQYIIVDIQANAFVHHMVRNIVGSLIEVGAGHQPVEWIGWLLAQKDRRLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            PEGLY  +V Y
Sbjct: 232 KPEGLYLVNVSY 243


>gi|182418813|ref|ZP_02950078.1| tRNA pseudouridine synthase A [Clostridium butyricum 5521]
 gi|237666467|ref|ZP_04526452.1| tRNA pseudouridine synthase A [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377310|gb|EDT74871.1| tRNA pseudouridine synthase A [Clostridium butyricum 5521]
 gi|237657666|gb|EEP55221.1| tRNA pseudouridine synthase A [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 244

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/242 (35%), Positives = 134/242 (55%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IE++GS + GWQ+Q  G ++Q  IE+AIF  TGE ++++G+ RTDSGVHA   +A+F 
Sbjct: 6   LTIEFDGSEFCGWQKQPKGRTVQKVIEEAIFKATGEEIIINGSSRTDSGVHAKDMIANF- 64

Query: 66  LVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                +P     +ALN  +++   +SI+    V + FHAR+S+  ++Y Y II R   ++
Sbjct: 65  FTNSTIPGDKFREALN--VRLPKDVSIIRSEEVSEDFHARYSSKGKTYSYTIIHRYERVS 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                 +     LD +NMR A ++ +G HDF  F S      + +RTI    +   G  I
Sbjct: 123 FGHQYVYHWRHDLDIDNMREACKYFIGTHDFRAFMSPGSSIKTTVRTITDLHIEQNGEKI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I V A  FL+  +R  VG+L  VG+ K    D++  ++  +RK  G + PP GL  + V
Sbjct: 183 KIFVSADGFLYNMVRIIVGTLIKVGNKKLKPEDIQDIIREGNRKRAGMVVPPNGLVLEKV 242

Query: 245 EY 246
            Y
Sbjct: 243 FY 244


>gi|239814424|ref|YP_002943334.1| tRNA pseudouridine synthase A [Variovorax paradoxus S110]
 gi|259550491|sp|C5CSH0|TRUA_VARPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239801001|gb|ACS18068.1| tRNA pseudouridine synthase A [Variovorax paradoxus S110]
          Length = 270

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 131/246 (53%), Gaps = 10/246 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I YNG  Y GWQ Q++G ++Q  +E A+     + +    AGRTD+GVHAL QV
Sbjct: 1   MRLALGIRYNGQAYEGWQSQRSGRTVQDKLEAALAKFAAQPIGTLCAGRTDAGVHALMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E  P    +  N +L   D I++     V  +FH R SA+ R YLY  +  Q+
Sbjct: 61  VHFDTTVEREPFSWMRGTNRFLP--DDIAVQWAQPVPDEFHCRASALARRYLY--VLSQS 116

Query: 122 PL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           P+  +L+ GR       LD + MR AA  LVG+HDF++FR+  CQA SP++ +   ++  
Sbjct: 117 PVRPSLDSGRVGWSMHPLDGDAMRAAAALLVGKHDFSSFRASACQARSPVKDLRRIEITR 176

Query: 180 FGNLIEIR----VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            G+    R      A +FLH  IR+ +G L  +G G      + + L+A+ RK   P   
Sbjct: 177 VGSGDRCRWHFEFEADAFLHHMIRNLMGCLVRIGRGDERPEWITEVLEARSRKVAAPTFS 236

Query: 236 PEGLYF 241
             GLYF
Sbjct: 237 ANGLYF 242


>gi|148997657|ref|ZP_01825221.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP11-BS70]
 gi|168575203|ref|ZP_02721166.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae MLV-016]
 gi|194397044|ref|YP_002038227.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae G54]
 gi|307068239|ref|YP_003877205.1| pseudouridylate synthase [Streptococcus pneumoniae AP200]
 gi|238690845|sp|B5E6N8|TRUA_STRP4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|147756156|gb|EDK63198.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP11-BS70]
 gi|183578806|gb|EDT99334.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae MLV-016]
 gi|194356711|gb|ACF55159.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae G54]
 gi|306409776|gb|ADM85203.1| Pseudouridylate synthase [Streptococcus pneumoniae AP200]
 gi|332199640|gb|EGJ13715.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA41317]
          Length = 249

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-ILDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLI 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|88799996|ref|ZP_01115567.1| tRNA-pseudouridine synthase I [Reinekea sp. MED297]
 gi|88777274|gb|EAR08478.1| tRNA-pseudouridine synthase I [Reinekea sp. MED297]
          Length = 286

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 129/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ + GWQ QK+G S+IQ ++E AI  V  E V    AGRTD+GVHA  Q+
Sbjct: 15  RIVLCLEYKGTAFHGWQIQKSGVSTIQAALEAAIAKVADEPVSTIVAGRTDAGVHATNQI 74

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +         +N   ++ D IS+  ++ VD+ FHARFSA  R+Y + I     
Sbjct: 75  VHFDTRAQRSDYGWKMGING--RLPDDISVKWVTQVDEHFHARFSAQERAYRFIIHNNWV 132

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL           LD   M+ AA  L+G HDF++FR+  CQA SP+RT+    V  FG
Sbjct: 133 KSALLHEVTTWEQYELDVGLMQQAANRLLGTHDFSSFRAAECQAHSPVRTLRELTVARFG 192

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I+  A  FLH  +R+ VG +  +G G+         L  +DR+  G  A   GLYF
Sbjct: 193 EFIVIQARADGFLHHMVRNLVGVMLPIGRGRKPVDWASDVLNYKDRRRGGVTAKGNGLYF 252

Query: 242 DSVEYS 247
               Y+
Sbjct: 253 VRASYN 258


>gi|146307739|ref|YP_001188204.1| tRNA pseudouridine synthase A [Pseudomonas mendocina ymp]
 gi|145575940|gb|ABP85472.1| tRNA pseudouridine synthase A [Pseudomonas mendocina ymp]
          Length = 287

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 133/252 (52%), Gaps = 16/252 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           R  + +EY G+ Y G+QRQ  N +SIQG +E A+  V G E + +  AGRTD+ VHA  Q
Sbjct: 19  RIALGLEYKGARYRGFQRQAGNVASIQGCLESALSKVAGGEPINIMCAGRTDASVHASGQ 78

Query: 61  VAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD   E     W+       + A + + + IS+    ++   FHARFSA+ R Y Y 
Sbjct: 79  VVHFDTAVERPLHAWI-------MGANMNLPNDISVTWARVMPAHFHARFSAMARRYRYV 131

Query: 116 IITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I      P  + +   W   + LD   MR AA+ LVG HDF+ FR+  CQA SPI+T+ H
Sbjct: 132 IYNDPIRPAHMAEEVTW-NHRPLDVTRMREAARALVGTHDFSAFRATQCQAKSPIKTVHH 190

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G  I + + A +FLH  +R+  G L  +G G+       + L+  DR+  G  A
Sbjct: 191 LQVIEHGCFIVLDIRANAFLHHMVRNIAGVLMAIGAGERPVEWAREVLERADRRSGGVTA 250

Query: 235 PPEGLYFDSVEY 246
            P GLY   VEY
Sbjct: 251 HPYGLYLVQVEY 262


>gi|54294200|ref|YP_126615.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Lens]
 gi|62901233|sp|Q5WX34|TRUA_LEGPL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|53754032|emb|CAH15505.1| tRNA-pseudouridine synthase I [Legionella pneumophila str. Lens]
          Length = 262

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 131/250 (52%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    +IQ ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVVEYDGSQYHGWQAQTGLHTIQQAVEFALSKVADSSISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      +R W+        N++L     I +     + + FHAR+SA+ R Y Y I
Sbjct: 61  IHFDCEKDRSIRAWI-----HGANSFL--PKDICVKWGKEMPENFHARYSAVSRRYRYVI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G      + LD   M+   Q L+G +DFT+FRS+ CQ+++P+R I    
Sbjct: 114 YNGAIRPGLLRGNVTWQYRQLDHRLMQQGGQCLLGENDFTSFRSVECQSNTPMRNIHQLQ 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+L+ + + A +FLH  +R+  G L  VG GK     ++  L A+DRK     AP 
Sbjct: 174 VTRHGDLVVLDITANAFLHHMVRNIAGVLIAVGSGKHPVGWVKDVLNAKDRKLGAETAPS 233

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 234 YGLYLVQVTY 243


>gi|257083304|ref|ZP_05577665.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256991334|gb|EEU78636.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 246

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTNKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|164688053|ref|ZP_02212081.1| hypothetical protein CLOBAR_01698 [Clostridium bartlettii DSM
           16795]
 gi|164602466|gb|EDQ95931.1| hypothetical protein CLOBAR_01698 [Clostridium bartlettii DSM
           16795]
          Length = 245

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/242 (35%), Positives = 131/242 (54%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M++EY+GS + G+Q+ K N ++IQG +E  +  +  E + + G+GRTD GVHA  QV +F
Sbjct: 6   MVVEYDGSNFKGFQKLKDNENTIQGKLESVLSQMADENIEIIGSGRTDMGVHAYGQVVNF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + K L  YL    +I+I  +  VD +FH+R++A R+ YLY+I   + P  
Sbjct: 66  KTNSPLSLNKMHKYLYEYL--PQSIAIREIEEVDDRFHSRYNAKRKVYLYKIDNNEYPNP 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +     +PK +D + MR  A  LVG HDFT+F S   +  S +R I    +N    LI
Sbjct: 124 FNRKYTCHVPKKIDLDKMRAVADVLVGEHDFTSFCSSRSKKKSHVREIYSISINENNGLI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           EI V    FL+  +R   G+L   G  K T  +++  L+ +DR +    AP +GL+   V
Sbjct: 184 EIYVEGNGFLYNMVRIIAGTLIDAGHNKITPEEVKNLLELKDRSKSPETAPSKGLFLYRV 243

Query: 245 EY 246
           +Y
Sbjct: 244 KY 245


>gi|288554758|ref|YP_003426693.1| tRNA pseudouridine synthase A [Bacillus pseudofirmus OF4]
 gi|288545918|gb|ADC49801.1| tRNA pseudouridine synthase A [Bacillus pseudofirmus OF4]
          Length = 247

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 89/248 (35%), Positives = 134/248 (54%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R   II Y+G+ + G+Q Q N  ++Q  IE+A+  V  G+ V V  +GRTD+GVHA  
Sbjct: 1   MNRIACIISYDGTNFSGYQVQPNKRTVQLEIEQALKRVHKGQEVSVTASGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           KALNA L   D I +L+    +K FHAR+    + Y YR++  
Sbjct: 61  QVIHFDSPFRIPAAQWPKALNACL--PDDIRVLSAHYAEKDFHARYHTTGKEYRYRVLNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +     +  +LD + MR AA +L+G HDF+ F + +      +RT+   D+N 
Sbjct: 119 EDPDVFRRHHTAHVLYALDIDKMRQAAAYLIGTHDFSAFCAANTSVIDKVRTLYAVDINV 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +   +    FL+  +R  VG+L  VG GK T+  ++ AL+   R + G  APP+GL
Sbjct: 179 HEDELHFILRGNGFLYNMVRIIVGTLLEVGYGKRTAESVDTALRTCKRDDAGKTAPPQGL 238

Query: 240 YFDSVEYS 247
           Y  SV+Y+
Sbjct: 239 YLWSVQYN 246


>gi|322388332|ref|ZP_08061936.1| tRNA pseudouridine synthase A [Streptococcus infantis ATCC 700779]
 gi|321141004|gb|EFX36505.1| tRNA pseudouridine synthase A [Streptococcus infantis ATCC 700779]
          Length = 249

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + +HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTKLNKGQAITIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEVVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+ A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHYPYPLDVERMQKAVKKLEGTHDFTGFTAAGTSVEDKVRTITEASLR 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPIEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|296333145|ref|ZP_06875599.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305672848|ref|YP_003864519.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|296149761|gb|EFG90656.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305411091|gb|ADM36209.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           str. W23]
          Length = 247

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 87/248 (35%), Positives = 135/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  + + + V  +GRTDSGVHA  
Sbjct: 1   MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAEKWPYALNALL--PDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ +NMR AA+HL+G HDFT+F ++  +    +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFSYHLNVQNMREAAKHLLGTHDFTSFCAVKTEVQDKVRTIYELDWAE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK +  D++  L+A+DR+  G  AP  GL
Sbjct: 179 TDDGLQMRITGSGFLYNMVRIIAGTLLDAGIGKISPDDVKSMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLWNVFYD 246


>gi|326792573|ref|YP_004310394.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
 gi|326543337|gb|ADZ85196.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
          Length = 245

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 132/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +I+ Y+G+ Y G+ +Q N ++IQG+++ AI  +    V   GAGRTD GVHA  Q
Sbjct: 1   MKRFKLIVAYDGTNYNGFAKQPNATTIQGTLDVAIAKIVQHEVRTLGAGRTDRGVHAFAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              FD   +     L KA+N+ L     IS+ ++  V + FH RF A R++Y Y+I+  +
Sbjct: 61  CCVFDSDTKIPADRLAKAINSQLPAD--ISVKSVEEVSEDFHPRFGAKRKTYRYQILNAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    A L P  LD E M+ AA  ++G HDF  F +        +R I   DV   
Sbjct: 119 IRDPFLYKYALLYPYELDVERMQEAANEMIGEHDFACFCAAGSTVKDTVRIIYSIDVKKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ I V    FL+  +R  +G+L  V + K T   ++  +++++R+  GP  PP+GL 
Sbjct: 179 GDLVSIDVCGNGFLYNMVRIIIGTLLDVNENKITKDSIKTIIESKNRELAGPTVPPQGLT 238

Query: 241 FDSVEYS 247
             ++ Y+
Sbjct: 239 MLNIVYN 245


>gi|315612755|ref|ZP_07887666.1| tRNA pseudouridine synthase A [Streptococcus sanguinis ATCC 49296]
 gi|315314865|gb|EFU62906.1| tRNA pseudouridine synthase A [Streptococcus sanguinis ATCC 49296]
          Length = 274

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 26  MTRYKATISYDGFAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 85

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + I+ R
Sbjct: 86  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEF-IVDR 142

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M++A + L G HDFT F +        +RTI      
Sbjct: 143 GRPKNPMRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTSVEDKVRTITEARLS 202

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 203 VDETGQFLTFSFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILKKKDRQLAGPTAAP 262

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 263 NGLYLKEIRYE 273


>gi|315651854|ref|ZP_07904857.1| tRNA pseudouridine synthase A [Eubacterium saburreum DSM 3986]
 gi|315485856|gb|EFU76235.1| tRNA pseudouridine synthase A [Eubacterium saburreum DSM 3986]
          Length = 245

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ+Q NG +++  + +AI  +TGE + V GA RTDSGVHA   
Sbjct: 1   MRRIRLIVSYDGTNYCGWQKQPNGITVEEILNRAISKLTGEEIEVIGASRTDSGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            A+N   ++ D I I     V+  +H R +   ++Y YRI+ R+
Sbjct: 61  VAVFDTNVRMAADKFAFAINQ--RLPDDIRIQYSDEVESDWHPRKNDCIKTYTYRILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  A     +LD E MR A+ + +G HDFT+F S   QASSPIRT+   +V   
Sbjct: 119 IDIPTERLYAHFCYFNLDVEKMREASGYFIGTHDFTSFCSQKSQASSPIRTVFSLEVLQD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++I I V    FL+  IR   G+L  VG G +  + + + ++A++RK  G   P +GL 
Sbjct: 179 EDMITIVVRGDGFLYNMIRIIAGTLIKVGMGVYPPSHITEIMKAKERKFAGQTMPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LVEIEY 244


>gi|290968602|ref|ZP_06560140.1| tRNA pseudouridine synthase A [Megasphaera genomosp. type_1 str.
           28L]
 gi|290781255|gb|EFD93845.1| tRNA pseudouridine synthase A [Megasphaera genomosp. type_1 str.
           28L]
          Length = 264

 Score =  152 bits (383), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 86/244 (35%), Positives = 131/244 (53%), Gaps = 4/244 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           C+I+ Y+G+ + G+QRQ N SSIQ  IE+A+  +  E + V+GA RTD+GVHA  QV +F
Sbjct: 8   CLIVAYDGTDFHGFQRQTNASSIQQYIEEALTRIFQEPITVYGAARTDAGVHARGQVVNF 67

Query: 65  DLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
                 +PV  +  A+ AYL    TI++L    +   F  R     + Y YRI+ R  P 
Sbjct: 68  -YASGSIPVDKIPYAMKAYL--PPTIAVLQAREMASHFSVRHDNCGKHYCYRIVNRAVPD 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
             +   +W I K LD E MR  A  L+G HDF+ F   +    +PI+T+    +    + 
Sbjct: 125 PFQLRYSWFIRKPLDVEAMRQGANILLGTHDFSAFEGKNTTPMNPIKTMYAVQIQKNRDN 184

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +EI V+   FL+  +R+  G L  +G  ++T+    + L+  DRK+ G  AP  GL  + 
Sbjct: 185 VEIHVIGDGFLYHMVRNMAGGLADIGLHRFTTIHFRRILKGLDRKKLGATAPAGGLCLEE 244

Query: 244 VEYS 247
           V Y+
Sbjct: 245 VFYT 248


>gi|317055617|ref|YP_004104084.1| tRNA pseudouridine synthase A [Ruminococcus albus 7]
 gi|315447886|gb|ADU21450.1| tRNA pseudouridine synthase A [Ruminococcus albus 7]
          Length = 245

 Score =  152 bits (383), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 86/244 (35%), Positives = 126/244 (51%), Gaps = 6/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M + Y+GS Y GWQRQ N  ++Q  +E AIF +TGE VVV G  RTD+GVHA   V  F 
Sbjct: 1   MTLAYDGSNYHGWQRQSNALAVQEVVEDAIFKLTGENVVVQGCSRTDAGVHAREYVLSFG 60

Query: 66  LVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           L    +P I C+ +   L   + D IS++     D+ FHAR+    + Y Y +   +   
Sbjct: 61  L---ELP-INCRGIQLGLNSWLPDDISVIGCEEADEGFHARYMCKGKEYEYIVHNSRIKD 116

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
              +  A+     +D   +  AA++ VG HDF  F S  C     +R I  FDV   G+ 
Sbjct: 117 PFMRNTAFRNTYPIDEVLLDRAAKYFVGEHDFKAFCSTACDKEITVRKIYRFDVRREGDK 176

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   V    FL+  +R  VG+L  + +GK  +  + + L ++DRK+ G   PP+GLY + 
Sbjct: 177 VIFTVAGNGFLYNMVRIMVGTLLFINEGKIAADAIPRILDSKDRKKAGKTVPPQGLYLNK 236

Query: 244 VEYS 247
           V Y 
Sbjct: 237 VYYD 240


>gi|269213866|ref|ZP_05983015.2| tRNA pseudouridine synthase A [Neisseria cinerea ATCC 14685]
 gi|269145225|gb|EEZ71643.1| tRNA pseudouridine synthase A [Neisseria cinerea ATCC 14685]
          Length = 277

 Score =  152 bits (383), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 131/245 (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: 20  RWALTLSYDGSRFYGWQKQAGGVPTVQTALENALAQIAGEAVSTIVAGRTDTGVHATAQV 79

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA L   + I++L+      +FHARF A  R Y Y + +   
Sbjct: 80  VHFDTAAVRPAQAWIRGVNANLP--EGIAVLHAQQAAPEFHARFDAYGRHYRYLLESSPV 137

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K R       LD E MR AA  LVG  DF++FR+  CQA SP++TI   ++    
Sbjct: 138 RSPLLKHRVGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAECQAKSPVKTIYSAEIAYGR 197

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY 
Sbjct: 198 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVDGFAALIRERSRLKAPPTFMPDGLYL 257

Query: 242 DSVEY 246
             ++Y
Sbjct: 258 TGIDY 262


>gi|118444045|ref|YP_877232.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
 gi|118134501|gb|ABK61545.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
          Length = 246

 Score =  152 bits (383), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 139/242 (57%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++IEY+GS Y GWQ+QK+  +IQ  IE+AIF +T + + V+G  RTD+GVHA   VA+F 
Sbjct: 7   LVIEYDGSNYSGWQKQKHSMTIQQRIEEAIFDITKQKIEVNGCSRTDAGVHARNFVANFI 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +     P     A+N+  K+   I I N   V   FHARF +  + Y+Y I+ R+ P  +
Sbjct: 67  IDSSIPPEKFKYAMNS--KLPKDIVIKNSCEVPMDFHARFQSKGKKYVYTILNREEPPTI 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
           ++G  +   K LD + MR A+++ +G H+F +F +       S +RTI + DV    ++I
Sbjct: 125 DRGVVYHFNKKLDVDLMRSASKYFIGSHEFDSFYKKAGSSVKSTLRTIYYCDVTKVDDII 184

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I V+   FL+  +R   G+L  VG  +    D++  + A+DR++ G   PP+GL  + V
Sbjct: 185 KIIVIGEGFLYNMVRIIAGTLVEVGIARIKPEDIKNIILAKDREKAGRSLPPQGLCLEEV 244

Query: 245 EY 246
            Y
Sbjct: 245 LY 246


>gi|332201036|gb|EGJ15107.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA47901]
          Length = 249

 Score =  152 bits (383), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-ILDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLI 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|217077259|ref|YP_002334977.1| tRNA pseudouridine synthase A [Thermosipho africanus TCF52B]
 gi|226708660|sp|B7IHS2|TRUA_THEAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217037114|gb|ACJ75636.1| tRNA pseudouridine synthase A [Thermosipho africanus TCF52B]
          Length = 244

 Score =  152 bits (383), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 134/246 (54%), Gaps = 6/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +   Y+G+ +FG+Q Q N  ++QG +E A+  +  E +    AGRTD+GVHA  Q
Sbjct: 1   MKRFAIEFAYDGTKFFGYQGQPNVRTVQGDLEDALERIFKERIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA F+  +       +  ALNA L   D I +    +VDK F+ RF+A +R Y Y I T 
Sbjct: 61  VAAFNCPIERLTETDIKNALNANL--PDDIYVKKAWVVDKSFNPRFAATKRIYHYFISTN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  + + +   W     LD E MR AA  L G HDF++F+    +  +P+RTI    + +
Sbjct: 119 EKDVFM-RNYVWNFRYDLDIEAMRKAASFLEGEHDFSSFKKGKDE-KNPVRTIYRIRILT 176

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               LI IRV  RSFL + +R+ VGSL  VG G+W    + + L+ + R+E    APP G
Sbjct: 177 LKKGLILIRVEGRSFLRSMVRNIVGSLVRVGLGQWKPEKILEVLEKRSRQEAAGTAPPHG 236

Query: 239 LYFDSV 244
           LY   V
Sbjct: 237 LYLYKV 242


>gi|27904686|ref|NP_777812.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|29611884|sp|P59508|TRUA_BUCBP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|27904083|gb|AAO26917.1| tRNA pseudouridine synthase A (Pseudouridylate synthase I)
           (Pseudouridine synthase I) (Uracil hydrolyase) (PSU-I)
           [Buchnera aphidicola str. Bp (Baizongia pistaciae)]
          Length = 264

 Score =  151 bits (382), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 95/242 (39%), Positives = 129/242 (53%), Gaps = 6/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--D 65
           IEYNGS Y GWQ QK  SS+Q  +E A+ ++    V V  AGRTD+GVH+  QV HF   
Sbjct: 12  IEYNGSNYHGWQYQKFASSVQEKVELALSIIANHPVRVTCAGRTDAGVHSTGQVVHFCTS 71

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
            +R     IL    N YL     IS++    V   FHAR+SA+ R Y Y +       ++
Sbjct: 72  SIRNDQAWIL--GTNRYL--PKDISVIWKRDVPMHFHARYSALSRRYRYILYNNSCRSSI 127

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
                    + L+ E M  AAQ+L+G HDFTTFRS HCQ+ +P R I + +V     LI 
Sbjct: 128 FYQGLKFYHRILNVEKMNQAAQYLLGEHDFTTFRSSHCQSKTPFRKILYVNVFCINCLII 187

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I +VA SFL+  +R+ VG L  +G  K   T +   L+ ++R     +    GLY   V+
Sbjct: 188 IDIVANSFLYHMVRNIVGCLIEIGISKKKVTWIRDILKFKNRTSSTKIVESNGLYLVQVQ 247

Query: 246 YS 247
           YS
Sbjct: 248 YS 249


>gi|297582482|ref|YP_003698262.1| tRNA pseudouridine synthase A [Bacillus selenitireducens MLS10]
 gi|297140939|gb|ADH97696.1| tRNA pseudouridine synthase A [Bacillus selenitireducens MLS10]
          Length = 261

 Score =  151 bits (382), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 84/248 (33%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R  + IEY+GSG+ G+Q+Q N  ++QG +E+A+ ++   E      +GRTD+GVH +R
Sbjct: 1   MRRMLIRIEYDGSGFNGYQKQPNARTVQGELERALSVMHKAESWPCTSSGRTDTGVHGVR 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD            ALN+ L   D I +L    VD  FHAR+  + + Y YR+ T 
Sbjct: 61  QPVHFDSPLTIPDERWPMALNSLL--PDDIQVLGAMEVDASFHARYDTVGKVYRYRVDTA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P ++D E MR AA+HL G HDFT+  S        +RT+    +  
Sbjct: 119 KRQTVFRRSFAAHFPGNMDIEAMREAAKHLEGTHDFTSLSSPKTDVKDKVRTLFAVSLEE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +  ++      FL+  +R  +G+L  VG G W    +   ++ Q+R+  GP AP  GL
Sbjct: 179 REDGFDVVFAGSGFLYQMVRILMGTLIKVGSGDWPPDVIPAIIEKQERQAAGPTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y + V Y+
Sbjct: 239 YLEDVFYT 246


>gi|254248703|ref|ZP_04942023.1| Pseudouridylate synthase [Burkholderia cenocepacia PC184]
 gi|124875204|gb|EAY65194.1| Pseudouridylate synthase [Burkholderia cenocepacia PC184]
          Length = 271

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + I+Y+G+ + GWQ Q +G ++Q  +E A+       +    AGRTD+GVH L Q
Sbjct: 1   MMRIALGIQYDGAAFCGWQAQPHGKTVQNRLEHALAEFARVPLHTTVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       +  NA+L    T+S+     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTDLEREVFSWVRGTNAFLP--PTVSVQWAKPMPDTFHARFSAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   
Sbjct: 119 VRSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRA 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY
Sbjct: 179 GYFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LAHVGYP 245


>gi|196233677|ref|ZP_03132518.1| tRNA pseudouridine synthase A [Chthoniobacter flavus Ellin428]
 gi|196222347|gb|EDY16876.1| tRNA pseudouridine synthase A [Chthoniobacter flavus Ellin428]
          Length = 251

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 130/250 (52%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  M+I Y+G  + GWQ Q    ++Q  +E A     G  VVVHG+GRTD+GVHAL Q
Sbjct: 4   ILRLKMLIAYDGRPFRGWQSQATKDAVQDHMEAAFAKTIGGRVVVHGSGRTDAGVHALAQ 63

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +AH D+    + V   + ALN +L     I +L +S     FHARF A  + Y YR+   
Sbjct: 64  IAHADVPAARLEVSAWRGALNNFL--PPEIRVLRVSRAAPDFHARFHARGKIYTYRMWNA 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---RSIHCQASSPIRTIDHFD 176
                LE GRAW +P  LD + +R  AQ L G+HDF  F   R+    A   +RTI H  
Sbjct: 122 SYLHPLEIGRAWHMPSKLDLDILRQGAQMLEGKHDFAGFAANRAPGYAAEDTVRTIQHIC 181

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+L+ +R     FL+  +R   G+L     G+   T +++ L  +  K+    AP 
Sbjct: 182 LTRRGDLLNLRFEGNGFLYKMVRLLTGTLVRCAQGRAELTFIKELLAGKGAKKTSFAAPA 241

Query: 237 EGLYFDSVEY 246
           EGLY   V Y
Sbjct: 242 EGLYLTRVLY 251


>gi|153839728|ref|ZP_01992395.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
 gi|149746752|gb|EDM57740.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
          Length = 246

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 88/233 (37%), Positives = 123/233 (52%), Gaps = 2/233 (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 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           + + I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A
Sbjct: 179 DYVVIDIKANAFVHHMVRNITGSLIKVGRGEEKPEWIKWLLEAKDRKLAGATA 231


>gi|242239994|ref|YP_002988175.1| tRNA pseudouridine synthase A [Dickeya dadantii Ech703]
 gi|242132051|gb|ACS86353.1| tRNA pseudouridine synthase A [Dickeya dadantii Ech703]
          Length = 275

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 97/247 (39%), Positives = 136/247 (55%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 13  LKIALGIEYDGSRYYGWQRQAEVESVQECLEKALSNVANEPISVFCAGRTDAGVHATGQV 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +NA+L  SD I++  ++ VD+ FHARFSA  R Y Y I   R 
Sbjct: 73  VHFTTGAVRKDAAWTMGVNAHLP-SD-IAVRWVTTVDEAFHARFSATARRYRYVIYNHRY 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 RPAILSHGVTHYHLP--LDAARMERAGQCLLGENDFTSFRAVQCQSRTPWRNVKHLKVMR 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I + + A +F+H  +R+ VGSL  VG G      + + L A+DR      A  +GL
Sbjct: 189 HGAYIVVDIKANAFVHHMVRNIVGSLMEVGCGNQPEGWIAELLAAKDRTLAAATARADGL 248

Query: 240 YFDSVEY 246
           Y  +V+Y
Sbjct: 249 YLVAVDY 255


>gi|210623220|ref|ZP_03293659.1| hypothetical protein CLOHIR_01609 [Clostridium hiranonis DSM 13275]
 gi|210153757|gb|EEA84763.1| hypothetical protein CLOHIR_01609 [Clostridium hiranonis DSM 13275]
          Length = 243

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 134/242 (55%), Gaps = 5/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + ++YNG+ Y GWQ Q N   IQG+IE AI  +TGE V ++G+GRTD+GVHAL QVA+F 
Sbjct: 6   ITVQYNGANYCGWQEQPNSPGIQGNIEYAIKEITGEKVKINGSGRTDAGVHALGQVANFK 65

Query: 66  LVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +   +PV  +  ALN+  K+   ISI++   V+ +FHAR+SA  + Y Y +   +    
Sbjct: 66  -IESQIPVNRIPDALNS--KLPKDISIIDAEEVEDEFHARYSAKGKIYKYLVYNSRYRNP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           + K  ++ +   LD E M+  A+ L+G +DF  F S        +RTI    +    +LI
Sbjct: 123 ILKDISYQVKYDLDFEKMKKEAESLIGTYDFCGFMSSGSSVKDTVRTIKSVKIEKEDDLI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                   FL+  +R   G+L  +G G+ T + +E  +++QDR + G  AP   L+   V
Sbjct: 183 VFEFEGNGFLYNMVRILSGTLIDIGRGRITES-MEDIIKSQDRSKAGHTAPGHALFLKKV 241

Query: 245 EY 246
            Y
Sbjct: 242 FY 243


>gi|156502494|ref|YP_001428559.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|290953826|ref|ZP_06558447.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312837|ref|ZP_06803569.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|166228698|sp|A7NCA0|TRUA_FRATF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|156253097|gb|ABU61603.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 258

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 132/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSLSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           + +F     + P+    + +NA L     I IL +  V+  F++RF+AI R+Y Y I   
Sbjct: 61  IVNF-YSNAYRPLSAWQRGVNALL--PQDIKILAVQQVNNNFNSRFTAINRTYNYIIYNS 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +   
Sbjct: 118 ATSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GL
Sbjct: 178 QGSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGL 237

Query: 240 YFDSVEY 246
           YF  VEY
Sbjct: 238 YFVGVEY 244


>gi|326202743|ref|ZP_08192611.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
 gi|325987327|gb|EGD48155.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
          Length = 247

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 88/248 (35%), Positives = 137/248 (55%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y +I++Y+GS Y GWQ+ K+   SIQG IE  +  ++GE + V G GRTD+G HA  
Sbjct: 1   MKNYKIIVQYDGSKYKGWQKLKDSDLSIQGKIETVLSKMSGEEIQVIGCGRTDAGTHAEN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+F       P ++   L  +L     I + ++  VD++FHA+ +A  ++Y+Y I   
Sbjct: 61  YVANFHTNSRMSPKLILNHLYEFL--PQDIVVRSVEEVDERFHAQHNAKAKTYVYSITKG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++   + LD   M+ AA++L+G HDF +F S+   + S IRTI+  D+  
Sbjct: 119 KFRNVFNRKYSFHSEEKLDLVQMKNAAEYLIGTHDFQSFTSLKEGSKSTIRTINSLDIIE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +IEI +    FL    R  VG+L  VG  K  + D++K L  + R E  P+A P+GL
Sbjct: 179 NGMVIEIIINGNDFLLHMARLVVGALLEVGKNKIKAIDVQKILNEKKRTEAVPMAQPKGL 238

Query: 240 YFDSVEYS 247
               V+YS
Sbjct: 239 CLRDVKYS 246


>gi|148993376|ref|ZP_01822893.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP9-BS68]
 gi|168488681|ref|ZP_02712880.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP195]
 gi|147927931|gb|EDK78951.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP9-BS68]
 gi|183572616|gb|EDT93144.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP195]
 gi|332072441|gb|EGI82924.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA17570]
          Length = 249

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLI 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     +   L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIALILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|312277540|gb|ADQ62197.1| tRNA pseudouridine synthase A [Streptococcus thermophilus ND03]
          Length = 248

 Score =  151 bits (382), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 134/250 (53%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  IEK +  L +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEEIEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLSQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYSKHIKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V S
Sbjct: 119 RPKNPMMRNYAIHYPYPLSLALMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASV-S 177

Query: 180 FGNLIEIRVVARS---FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                   V A S   FL+ Q+R+ VG+L  +G+G+   +  +  L+++DR   GP    
Sbjct: 178 IDEKTGFYVFAFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQAKTVLESRDRNLAGPTVAG 237

Query: 237 EGLYFDSVEY 246
            GLY   + Y
Sbjct: 238 NGLYLKEIRY 247


>gi|312862611|ref|ZP_07722852.1| tRNA pseudouridine synthase A [Streptococcus vestibularis F0396]
 gi|311101871|gb|EFQ60073.1| tRNA pseudouridine synthase A [Streptococcus vestibularis F0396]
          Length = 249

 Score =  151 bits (382), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 87/249 (34%), Positives = 132/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  +EK +  L +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEELEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L++ DR   GP A   
Sbjct: 179 DEKTGFYIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESCDRNLAGPTAAGN 238

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 239 GLYLKEIRY 247


>gi|168493506|ref|ZP_02717649.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC3059-06]
 gi|183576362|gb|EDT96890.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC3059-06]
          Length = 249

 Score =  151 bits (381), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVLHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E MR A + L G HDFT F +        IRTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMREAIKKLEGTHDFTGFTASGTSVEDKIRTITEASLT 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEICYE 248


>gi|295093425|emb|CBK82516.1| pseudouridylate synthase I [Coprococcus sp. ART55/1]
          Length = 247

 Score =  151 bits (381), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 128/249 (51%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+ Y     Y+G+ Y GW+ + N  +++G IE  +  +    V +HGAGRTD+GVHA   
Sbjct: 1   MVNYRFTFSYDGTRYHGWESKTNADTVEGRIEAVLTRMVDAKVDIHGAGRTDAGVHARAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+  L  +  P  +   LN YL     I  L++++   +FHAR +A  + Y Y +    
Sbjct: 61  VANGRLETDKTPEEIKDYLNRYLPAD--ICALDVAVAGDRFHARLNATGKVYEYTLYVGA 118

Query: 121 APLALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                ++   W +P+  +LD + M+ AA +LVG+HDF +F   +    S +RTI   D+ 
Sbjct: 119 EKPVFDRNYVWCVPQGSALDVDVMKKAASYLVGKHDFRSFCGNNKMKKSTVRTIYDVDIV 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + +R     FL   +R   G+L  VG G  ++  + + +   DR+  GP APP G
Sbjct: 179 KEGDYVRMRFHGNGFLQNMVRILTGTLVEVGYGNMSAEHIPEIIAGMDRQLAGPTAPPHG 238

Query: 239 LYFDSVEYS 247
           L    VEY 
Sbjct: 239 LCLMKVEYD 247


>gi|328676060|gb|AEB28735.1| tRNA pseudouridine synthase A [Francisella cf. novicida 3523]
          Length = 258

 Score =  151 bits (381), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  SIQ  +EKA+  +    + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSIQAELEKALSKIANRNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +       +  NA L     I IL    V+  F++RF+AI R+Y Y I    
Sbjct: 61  VVNFHSDADRPLSAWQRGANALL--PHDIKILAAQEVNDDFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKLVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|325294776|ref|YP_004281290.1| tRNA pseudouridine synthase A [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325065224|gb|ADY73231.1| tRNA pseudouridine synthase A [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 250

 Score =  151 bits (381), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 89/243 (36%), Positives = 129/243 (53%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY G+ YFGWQ      +IQG I K +  +    V + GA RTD+GVHA  QVA+F 
Sbjct: 6   LTIEYLGTNYFGWQILPEKPTIQGEIIKVLERILQHPVKLTGASRTDAGVHAFGQVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             +E     L  ALN  L     I I+++  V  +F +R  A  + Y YRI  R+ P   
Sbjct: 66  TKKEIPLYKLQSALNGLL--PPDIKIISVEEVPLEFDSRRWAKGKRYRYRIFNRKVPSPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
           E  R+W +P  LD   M  A + L+G  DFT+F +S      +P+RT+D+ ++    + I
Sbjct: 124 EYKRSWFVPYQLDISLMEKAKEFLIGTFDFTSFSKSDRNVDINPVRTVDNIEIVKKESHI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +     RSFL   +R  V +L  VG GK    D+++  + ++RK    LAPP+GLY + V
Sbjct: 184 DFIFYGRSFLRHMVRIMVATLVEVGKGKLRPEDIKEIREKKNRKFAPFLAPPDGLYLEKV 243

Query: 245 EYS 247
            Y 
Sbjct: 244 YYD 246


>gi|149006661|ref|ZP_01830347.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP18-BS74]
 gi|147761576|gb|EDK68540.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP18-BS74]
          Length = 249

 Score =  151 bits (381), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFDGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLI 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     +   L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIALILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|294506655|ref|YP_003570713.1| tRNA pseudouridine synthase A [Salinibacter ruber M8]
 gi|294342983|emb|CBH23761.1| tRNA pseudouridine synthase A [Salinibacter ruber M8]
          Length = 265

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 131/250 (52%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  +IEY+G+ + GWQ Q    ++QG++E+A+  V G    V G+GRTD+GVHA  Q
Sbjct: 1   MPRYRFLIEYDGTDFHGWQIQPTVPTVQGALEEAVDTVVGTACRVAGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL     P  L  +LN      D +++  +      FHAR+ A RR Y Y + T+ 
Sbjct: 61  VAHVDLPETRDPYRLRGSLNGL--TPDAVAVRRVERAPDDFHARYDACRRRYHYHLHTQ- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF---DV 177
            P AL +     +    D   +R AA  L+GRH+F++F     +  + + T+ H    D 
Sbjct: 118 -PCALGRRARTPVRPVPDFGRIRAAAPDLLGRHNFSSFCLTQSETENRVCTLTHLRWVDE 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G    + VV   FLH  +R+ VG+L  +G  K  +  L   L A+DR+  GP  PPE
Sbjct: 177 ARRG-CWRVEVVGTRFLHGMVRALVGTLVEIGHEKRAADALPAVLAARDRRAAGPSMPPE 235

Query: 238 GLYFDSVEYS 247
           GL  ++V Y 
Sbjct: 236 GLVLEAVRYE 245


>gi|46931324|gb|AAT06466.1| At1g09800 [Arabidopsis thaliana]
          Length = 372

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 97/314 (30%), Positives = 153/314 (48%), Gaps = 70/314 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + G Q+Q    ++ G +++A     G+ V +  + RTD+GVHAL  V 
Sbjct: 56  RYLVAIEYIGTRFSGSQQQAKDRTVVGVLQEAFHKFIGQPVKIFCSSRTDAGVHALSNVC 115

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  R
Sbjct: 116 HVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQER 175

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR+++   PL+ LEK R W +P+ L+   M+ A + LVG HDF++FR+  CQA SP+
Sbjct: 176 TYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEACRVLVGSHDFSSFRAAGCQAKSPM 235

Query: 170 RTIDHFDV---------------------------------------------------- 177
           R++D  ++                                                    
Sbjct: 236 RSLDELNITEVPSTPYFPSITERTLSNLNNGDPLACSNQPKSETAGVTTNVGEVEGSTGG 295

Query: 178 NSFGNLIEIR---VVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           +SFG     R   V ARS  FL+ Q+R  VG+LK VG G+ T +D+E+ L+A+      P
Sbjct: 296 DSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAKP 355

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GLY   V Y
Sbjct: 356 MAPASGLYLARVRY 369


>gi|167627942|ref|YP_001678442.1| tRNA pseudouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|189029995|sp|B0U0B1|TRUA_FRAP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167597943|gb|ABZ87941.1| tRNA-pseudouridine synthase I [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 258

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  SIQ  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSIQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +       +  NA L     I IL++  VD  F++RF+A  R+Y Y I    
Sbjct: 61  VVNFHSDADRNLSSWMRGTNALL--PQGIKILDIKEVDNDFNSRFTATNRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + L+ + M  A ++L+G  DFT+FRS  CQ+++P R I   +    
Sbjct: 119 ISSPILAEHCLWENRQLNIDKMNQACKYLLGEQDFTSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+F+GSL  +G    +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNFIGSLLKIGLEFESPEWIKLVLEAKDRTKAAETAKAHGLY 238

Query: 241 FDSVEY 246
           F  VEY
Sbjct: 239 FVGVEY 244


>gi|42561874|ref|NP_172451.2| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|332190374|gb|AEE28495.1| tRNA pseudouridine synthase A [Arabidopsis thaliana]
          Length = 372

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 97/314 (30%), Positives = 153/314 (48%), Gaps = 70/314 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + G Q+Q    ++ G +++A     G+ V +  + RTD+GVHAL  V 
Sbjct: 56  RYLVAIEYIGTRFSGSQQQAKDRTVVGVLQEAFHKFIGQPVKIFCSSRTDAGVHALSNVC 115

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  R
Sbjct: 116 HVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQER 175

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR+++   PL+ LEK R W +P+ L+   M+ A + LVG HDF++FR+  CQA SP+
Sbjct: 176 TYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEACRVLVGSHDFSSFRAAGCQAKSPM 235

Query: 170 RTIDHFDV---------------------------------------------------- 177
           R++D  ++                                                    
Sbjct: 236 RSLDELNITEVPSTPYFPSITERTLSNLNNGDPLACSNQPKSETAGVTTNVGEVEGSTEG 295

Query: 178 NSFGNLIEIR---VVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           +SFG     R   V ARS  FL+ Q+R  VG+LK VG G+ T +D+E+ L+A+      P
Sbjct: 296 DSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAKP 355

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GLY   V Y
Sbjct: 356 MAPASGLYLARVRY 369


>gi|51971559|dbj|BAD44444.1| unnamed protein product [Arabidopsis thaliana]
 gi|51971573|dbj|BAD44451.1| unnamed protein product [Arabidopsis thaliana]
          Length = 368

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 97/314 (30%), Positives = 153/314 (48%), Gaps = 70/314 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + G Q+Q    ++ G +++A     G+ V +  + RTD+GVHAL  V 
Sbjct: 52  RYLVAIEYIGTRFSGSQQQAKDRTVVGVLQEAFHKFIGQPVKIFCSSRTDAGVHALSNVC 111

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  R
Sbjct: 112 HVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQER 171

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR+++   PL+ LEK R W +P+ L+   M+ A + LVG HDF++FR+  CQA SP+
Sbjct: 172 TYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEACRVLVGSHDFSSFRAAGCQAKSPM 231

Query: 170 RTIDHFDV---------------------------------------------------- 177
           R++D  ++                                                    
Sbjct: 232 RSLDELNITEVPSTPYFPSITERTLSNLNNGDPLACSNQPKSETAGVTTNVGEVEGSTGG 291

Query: 178 NSFGNLIEIR---VVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           +SFG     R   V ARS  FL+ Q+R  VG+LK VG G+ T +D+E+ L+A+      P
Sbjct: 292 DSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAKP 351

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GLY   V Y
Sbjct: 352 MAPASGLYLARVRY 365


>gi|331007056|ref|ZP_08330287.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC1989]
 gi|330419141|gb|EGG93576.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC1989]
          Length = 286

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + IEY G  + G+Q Q  +  ++Q ++E A+ LV  E + +  AGRTD+GVHA  
Sbjct: 24  MQRVALGIEYAGHVFHGFQSQPHDEKTVQSALENALSLVANEPIKLVCAGRTDAGVHATN 83

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+ HFD + +       +  NA  K+ D ++I     V   FH+RFSA  R+Y Y I   
Sbjct: 84  QIVHFDTLAKRKDTAWLRGANA--KLPDGVAIRWAQDVSCDFHSRFSAKHRTYRYVIYNS 141

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   AL K       +SLD + M  A+Q LVGRHDF  FR+  CQA++ IR + +  V+ 
Sbjct: 142 RTHSALLKNFVTWDRRSLDIDAMAEASQALVGRHDFNAFRASQCQANNAIRDMHYIKVHR 201

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I I V A +FL+  +R+ VG L  +  G+   +  ++ L+++DR+  G  A P+GL
Sbjct: 202 QNDFIVIEVQATAFLYHMVRNIVGVLSTIAAGEKPVSWAKEVLESKDRRCGGITASPDGL 261

Query: 240 YFDSVEY 246
           Y  +VEY
Sbjct: 262 YLVAVEY 268


>gi|268318033|ref|YP_003291752.1| tRNA pseudouridine synthase A [Rhodothermus marinus DSM 4252]
 gi|262335567|gb|ACY49364.1| tRNA pseudouridine synthase A [Rhodothermus marinus DSM 4252]
          Length = 252

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 98/253 (38%), Positives = 138/253 (54%), Gaps = 14/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y ++IEY+G+ + GWQ Q+NG SIQ ++E+A+ +V  E V V G+GRTD+GVHA  Q
Sbjct: 1   MPTYRLLIEYDGTDFSGWQIQRNGPSIQAALEEALAVVLRERVRVVGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF   R   P  L  +LN  L  S  I+I ++S+    FHAR+ A  R Y Y + T  
Sbjct: 61  VAHFRTDRPVDPERLQGSLNGLLPPS--IAIRSVSLAPDDFHARYDARWRRYHYYVAT-- 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT------IDH 174
            P ALE+   W +  + D E M  AA  L+G HDFTTF    C+  +  R       +  
Sbjct: 117 VPCALERHLRWYLRPAPDFERMNRAACDLLGTHDFTTF----CRTQTATRNRTCTVYLAR 172

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +  +         +VA  FLH  +R+ VG+L  +G G+     L + L A+DR+  GP A
Sbjct: 173 WVPDPRPGDWHFEIVADRFLHGMVRAIVGTLIEIGRGQRDIAALPELLAARDRRLAGPAA 232

Query: 235 PPEGLYFDSVEYS 247
           P  GL  ++V Y 
Sbjct: 233 PAHGLVLEAVGYE 245


>gi|148548973|ref|YP_001269075.1| tRNA pseudouridine synthase A [Pseudomonas putida F1]
 gi|148513031|gb|ABQ79891.1| tRNA pseudouridine synthase A [Pseudomonas putida F1]
          Length = 332

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 97/253 (38%), Positives = 131/253 (51%), Gaps = 19/253 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ +G  S+Q ++E+A+  V  E + V  AGRTD+GVH   QV
Sbjct: 66  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPISVVCAGRTDAGVHGCGQV 125

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R W        +     +   IS++    +   FHARF A  R Y Y I
Sbjct: 126 VHFDTRAVRDERAWT-------MGTNFNLPHDISVVWSRPMPADFHARFKACARRYRYVI 178

Query: 117 IT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
                R A LA E    W   + LD + M  AAQ L+G HDF+ FR+  CQA SPI+ I 
Sbjct: 179 YNDPIRPAHLAEEV--TWNH-RPLDVDRMAEAAQFLLGTHDFSAFRASQCQAKSPIKHIY 235

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           H  V   G +I + V A +FLH  +R+  G L  +G G+       + L+ ++R+E G  
Sbjct: 236 HLRVTRHGQMIVLDVRATAFLHHMVRNIAGVLMAIGAGERPVAWAREVLEGRNRREGGVT 295

Query: 234 APPEGLYFDSVEY 246
           A P GLY   VEY
Sbjct: 296 AHPYGLYLVQVEY 308


>gi|224542274|ref|ZP_03682813.1| hypothetical protein CATMIT_01449 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524816|gb|EEF93921.1| hypothetical protein CATMIT_01449 [Catenibacterium mitsuokai DSM
           15897]
          Length = 245

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   I+ Y+G+ ++GWQ Q +  ++Q  I+KAI+ +T E V +H +GRTD+GVHA+ QV
Sbjct: 1   MRIKCIVTYDGTHFYGWQIQPDKRTVQEEIQKAIYKITHEEVTIHSSGRTDAGVHAVGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+ +E       +ALN +L   D I I +  IVD+ FHAR+SA ++ Y Y + T+  
Sbjct: 61  FHFDINKEIPEKQWIRALNNFL--PDDIYIKDSFIVDESFHARYSAKKKEYRYLVSTKPY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +E+   +   +SLD E MR  A+  +G HDF +F  +       IR I+  D+    
Sbjct: 119 N-PIERLYVYQHNRSLDIEAMRECAKIFLGEHDFASF-CVFNGLGDTIRVIETIDIQEKD 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++ +R +   F    +R   G+L  VG    T   +E  L ++ +K+C   A PEGLY 
Sbjct: 177 GIVTMRFIGNGFRRYMVRLITGALIQVGSHWRTKEFVEDLLNSKGKKKCLFKAKPEGLYL 236

Query: 242 DSVEYS 247
             V Y 
Sbjct: 237 QEVYYE 242


>gi|254253654|ref|ZP_04946971.1| Pseudouridylate synthase [Burkholderia dolosa AUO158]
 gi|124898299|gb|EAY70142.1| Pseudouridylate synthase [Burkholderia dolosa AUO158]
          Length = 271

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L Q
Sbjct: 1   MMRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       +  NA+L  S  +++     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTDLDRADFSWVRGTNAFLPPS--VAVQWAKPMPDTFHARFSAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  +   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   
Sbjct: 119 VRSPMLAGRAGWVHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R  A +FLH  +R+ +G L  VG G++ +  +   L  +DR    P    +GLY
Sbjct: 179 GHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGRDRDLAAPTFMADGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAHVGY 244


>gi|255526720|ref|ZP_05393623.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
 gi|255509607|gb|EET85944.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
          Length = 249

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 133/246 (54%), Gaps = 7/246 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+I+Y+GS Y GWQ+Q +      S+IQ  IE  +  +TGE + V G GRTD+GVHA   
Sbjct: 6   MLIQYDGSRYKGWQKQNHKDNNSVSTIQDKIESVLSKMTGEDIQVVGCGRTDTGVHAENY 65

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F          + K L  +L   + I + +L    ++FHAR++A  ++YLY I   +
Sbjct: 66  VANFHTDSILTVEDMLKYLYEFL--PEDIVVKSLRDTSERFHARYNAKSKTYLYTINNNK 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A+ + ++L+   MR AA+ L G HDF +F S+     S +RTI++  +   
Sbjct: 124 FRNVFNRKYAYHVEENLNLSEMRDAAEVLTGTHDFQSFTSLKSNTKSTVRTINYISITEE 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +I I V   SFL   +R  VG+L  VG G    +D+EK L  + R E GP+A  +GL 
Sbjct: 184 HGMIGIEVNGNSFLLNMVRIIVGTLLDVGKGILKPSDVEKILYEKKRAEAGPMAAAKGLC 243

Query: 241 FDSVEY 246
              ++Y
Sbjct: 244 LKDIQY 249


>gi|332141777|ref|YP_004427515.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327551799|gb|AEA98517.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 264

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 128/251 (50%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+G+  +GWQRQ+   S+Q  +EKA+  V  E + V  AGRTD+GVHA  Q
Sbjct: 1   MGRIALGIEYDGAAVYGWQRQREVPSVQEHLEKALSTVANEPIEVQCAGRTDAGVHATGQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+       R W        L     + +++++     V   FHARFSA  R Y Y 
Sbjct: 61  VVHFNCDAPRSERAWT-------LGVNANLPNSVAVTWAKNVADDFHARFSATHRRYRYV 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I   +   A+       I + LD + M +AAQ L+G  DFT+FR+  CQ+ +P R + + 
Sbjct: 114 IHNAKMRPAILSSGVTHIHRELDEKKMHLAAQALLGEQDFTSFRAALCQSKTPFRNVTNV 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G  + I + A +FLH  +R+  G+L  +G G+     +   L  +DR +    A 
Sbjct: 174 GVYRQGRYVIIDIRANAFLHHMVRNITGALVEIGAGEQDVNWIAHLLSLKDRSKSAATAK 233

Query: 236 PEGLYFDSVEY 246
           P GLY   V Y
Sbjct: 234 PNGLYLVDVTY 244


>gi|223935594|ref|ZP_03627510.1| tRNA pseudouridine synthase A [bacterium Ellin514]
 gi|223895602|gb|EEF62047.1| tRNA pseudouridine synthase A [bacterium Ellin514]
          Length = 270

 Score =  150 bits (379), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 85/249 (34%), Positives = 137/249 (55%), Gaps = 6/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +++ + I Y+G  Y GWQ QK+G  +Q  +E+A+  +   +  +H + RTD+GVHA+  V
Sbjct: 4   LKFKLTIAYDGKNYSGWQVQKSGIGVQQRVEEALTKLFPSVGRIHSSSRTDTGVHAIGMV 63

Query: 62  AHFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           AH ++ +    +    L  A+NA+L   + I +++   V   FHARF A  + Y Y +  
Sbjct: 64  AHMEIPKAEFRMTSEKLALAINAHL--PEDIRVMSAQKVAADFHARFDAAGKQYRYFVWN 121

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDV 177
           + A   L + +AW +PK LD + MR AA+   G+HDF +F  S + +  S +RT+   D+
Sbjct: 122 QTAMNPLLREQAWQVPKELDLKAMRSAAKLFPGKHDFRSFAASRNYEVESTVRTLARCDI 181

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+L+   +    FL+   R  VG+L  VG GK  + D++K L+ +DR+  G  AP  
Sbjct: 182 KKSGSLLTFIIEGDGFLYKMCRGIVGTLVQVGQGKIAAADIKKILETRDRRVAGMTAPAH 241

Query: 238 GLYFDSVEY 246
           GL    V Y
Sbjct: 242 GLVLWKVFY 250


>gi|171321983|ref|ZP_02910866.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MEX-5]
 gi|171092713|gb|EDT37998.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MEX-5]
          Length = 270

 Score =  150 bits (379), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/249 (36%), Positives = 134/249 (53%), Gaps = 10/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--HG--AGRTDSGVHA 57
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+    GE   V  H   AGRTD+GVH 
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDALERAL----GEFACVPLHTTVAGRTDTGVHG 56

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y + 
Sbjct: 57  LGQVVHFDTDLDRTDFSWVRGTNAFLP--STVSVQWAKPMADTFHARFAAFERTYYYVLY 114

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV
Sbjct: 115 VHPVRSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDV 174

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +
Sbjct: 175 RRAGHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMAD 234

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 235 GLYLAHVGY 243


>gi|313499900|gb|ADR61266.1| TruA [Pseudomonas putida BIRD-1]
          Length = 284

 Score =  150 bits (379), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 94/251 (37%), Positives = 129/251 (51%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ +G  S+Q ++E+A+  V  E + V  AGRTD+GVH   QV
Sbjct: 18  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPISVICAGRTDAGVHGCGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R W        +     +   IS++    +   FHARF A  R Y Y I
Sbjct: 78  VHFDTRAVRDERAWT-------MGTNFNLPHDISVVWSRPMPADFHARFKACARRYRYVI 130

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 P  L +   W   + LD + M  AAQ L+G HDF+ FR+  CQA SPI+ I H 
Sbjct: 131 YNDPIRPAHLAEEVTW-NHRPLDVDRMAEAAQFLLGTHDFSAFRASQCQAKSPIKHIYHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + V A +FLH  +R+  G L  +G G+       + L+ ++R+E G  A 
Sbjct: 190 RVTRHGQMIVLDVRATAFLHHMVRNIAGVLMAIGAGERPVAWAREVLEGRNRREGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVQVEY 260


>gi|172062883|ref|YP_001810534.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MC40-6]
 gi|238692865|sp|B1Z1N7|TRUA_BURA4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171995400|gb|ACB66318.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MC40-6]
          Length = 270

 Score =  150 bits (379), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/249 (36%), Positives = 135/249 (54%), Gaps = 10/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHG--AGRTDSGVHA 57
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+    GE   V +H   AGRTD+GVH 
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDALERAL----GEFACVPLHTTVAGRTDTGVHG 56

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y + 
Sbjct: 57  LGQVVHFDTDLDRTDFSWVRGTNAFLP--STVSVQWAKPMPDTFHARFAAFERTYYYVLY 114

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV
Sbjct: 115 VHPVRSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDV 174

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +
Sbjct: 175 RRSGHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRTLAAPTFMAD 234

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 235 GLYLAHVGY 243


>gi|154483152|ref|ZP_02025600.1| hypothetical protein EUBVEN_00853 [Eubacterium ventriosum ATCC
           27560]
 gi|149735960|gb|EDM51846.1| hypothetical protein EUBVEN_00853 [Eubacterium ventriosum ATCC
           27560]
          Length = 246

 Score =  150 bits (379), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +II Y+G+ Y GWQ Q NG +++  + KA+  +  E + V GA RTDSGVHA+  
Sbjct: 1   MKRVRLIIAYDGTNYCGWQVQINGITVEEVLNKALKDLLNEEIAVIGASRTDSGVHAMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN   ++ + I I     V   +H R+    ++Y Y+I+ R+
Sbjct: 61  VAVFDTETRIPAEKISFALNQ--RLPNDIRIQKSDEVPLDWHPRYRDSTKTYEYKILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L++     +   LD + M+ AA+++VG HDF +F S   Q  S +RT+    VN  
Sbjct: 119 FPDPLQRFYTHFMYMPLDEQKMKEAAEYIVGEHDFASFCSAGSQVDSTVRTVYSLSVNKR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++I IR+    FL+  +R  VG+L  VG G +    +++ ++A+DR   GP AP  GL 
Sbjct: 179 DDVISIRITGNGFLYNMVRIIVGTLIKVGLGVYPPEHVKEIIEAKDRYVAGPKAPACGLT 238

Query: 241 FDSVEYS 247
              +EYS
Sbjct: 239 LVGIEYS 245


>gi|115358097|ref|YP_775235.1| tRNA pseudouridine synthase A [Burkholderia ambifaria AMMD]
 gi|122321799|sp|Q0BAC2|TRUA_BURCM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|115283385|gb|ABI88901.1| tRNA pseudouridine synthase A [Burkholderia ambifaria AMMD]
          Length = 270

 Score =  150 bits (379), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 90/249 (36%), Positives = 136/249 (54%), Gaps = 10/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHG--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+     + + FHARF+A  R+Y Y + 
Sbjct: 57  LGQVVHFDTDLDRTDFSWVRGTNAFLP--STVSVQWAKPMPETFHARFAAFERTYYYVLY 114

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV
Sbjct: 115 VHPVRSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDV 174

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +
Sbjct: 175 RRSGHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRTLAAPTFMAD 234

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 235 GLYLAHVGY 243


>gi|108758714|ref|YP_633269.1| tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
 gi|30913405|sp|Q93NE2|TRUA_MYXXA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|14517923|gb|AAK64428.1|AF377337_4 pseudouridine synthase TruA [Myxococcus xanthus]
 gi|108462594|gb|ABF87779.1| tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
          Length = 265

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + +EY G+ Y GWQ Q NG SIQ  +E  +  + G  V V  AGRTD+GVHA  Q
Sbjct: 1   MPRLKLTLEYEGTRYVGWQVQPNGPSIQSVLESGLERLLGARVSVASAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD  R          LN  L     +++++   V + F  R  +  + Y YR+  R+
Sbjct: 61  VACFDSPRVLPMKAYVMGLNGLL--PPDVAVVDAVEVAEDFDPRRWSRGKRYRYRVSNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
               L +   W +   LD E MR AA HL+GRHDF+ FR+  CQA   +R I    V  +
Sbjct: 119 TRSPLRRMTHWEVFAPLDVEAMRQAAAHLLGRHDFSAFRAADCQAKHAVREIRSLAVEGT 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   V   +FL   +R+  G+L  VG G+  ++ + + L +Q+RK  GP APP+GL
Sbjct: 179 SGDAVSFVVEGTAFLKHMVRNLAGTLVEVGKGRRPASWVAEVLASQERKRAGPTAPPQGL 238

Query: 240 YFDSVEY 246
             + V Y
Sbjct: 239 VLEEVFY 245


>gi|225857220|ref|YP_002738731.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae P1031]
 gi|254764871|sp|C1CLU3|TRUA_STRZP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225725422|gb|ACO21274.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae P1031]
          Length = 249

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQIDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
             P   + +  A   P  LD E M+IA + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLI 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     +   L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIALILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|206562845|ref|YP_002233608.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia J2315]
 gi|198038885|emb|CAR54847.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia J2315]
          Length = 271

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + I+Y+G+ + GWQ Q +G ++Q  +E A+       +    AGRTD+GVH L Q
Sbjct: 1   MMRIALGIQYDGAAFCGWQAQPHGKTVQDRLEHALAEFARVPLHTTVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       +  NA+L    T+S+     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELEREVFSWVRGTNAFLP--PTVSVQWAKPMPDTFHARFSAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  I   LD + MR AA +L+G HDF++FRS  CQ+ +P++ +   DV   
Sbjct: 119 VRSPMLAGRAGWIHTPLDDDAMRAAAAYLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRA 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY
Sbjct: 179 GHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAHVGY 244


>gi|309798794|ref|ZP_07693058.1| tRNA pseudouridine synthase A [Streptococcus infantis SK1302]
 gi|308117611|gb|EFO55023.1| tRNA pseudouridine synthase A [Streptococcus infantis SK1302]
          Length = 249

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IE  +  L  G+ + +HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEITLTKLNKGQAITIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M++A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHYPYPLDVERMQLAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLR 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPIEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|325282723|ref|YP_004255264.1| tRNA pseudouridine synthase A [Deinococcus proteolyticus MRP]
 gi|324314532|gb|ADY25647.1| tRNA pseudouridine synthase A [Deinococcus proteolyticus MRP]
          Length = 294

 Score =  150 bits (379), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 129/249 (51%), Gaps = 7/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + ++GS Y GWQ Q N  S+Q ++  A+  +  E      AGRTD+GVHAL   A
Sbjct: 32  RVLLTVAWDGSAYGGWQSQPNAPSVQDTLHAALNRLGLEAARPVAAGRTDAGVHALNMPA 91

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H DL    +P     AL    ++  ++++L+       FHARFS  +R YLY+I+   A 
Sbjct: 92  HVDLHAPRIPPERL-ALALARQLPRSVAVLSAQAAPAGFHARFSCTQRRYLYQILNAPAR 150

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS--- 179
             LE+GR+  +   LD   M  AAQHL+G HDF  F +   + +  +R +    V +   
Sbjct: 151 HPLEEGRSLWVRGQLDLSAMNAAAQHLIGLHDFAAFATKEDRQT--VRELQRLAVTASPL 208

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +G  + + VV  SFL   +R  VG+L  VG GK     + + L + DR++ G    P+G
Sbjct: 209 PYGQRVTLAVVGESFLRHMVRGLVGTLIAVGQGKLAPEAVAEILASGDRRQAGINVAPDG 268

Query: 239 LYFDSVEYS 247
           LYF    Y+
Sbjct: 269 LYFAGAGYA 277


>gi|33592579|ref|NP_880223.1| tRNA pseudouridine synthase A [Bordetella pertussis Tohama I]
 gi|42559761|sp|Q7U363|TRUA_BORPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33572225|emb|CAE41775.1| tRNA pseudouridine synthase A [Bordetella pertussis Tohama I]
 gi|332381997|gb|AEE66844.1| tRNA pseudouridine synthase A [Bordetella pertussis CS]
          Length = 270

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 93/248 (37%), Positives = 137/248 (55%), 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 GRVRPALWAGRAGWAFQPLDVPAMRAAARALLGEHDFSSFRSSQCQARHPVRTLHRLDID 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A +FLH  +R+ +G+L  VG G+     ++  L A+DR+   P   P+G
Sbjct: 179 ERGAFLVFTLRANAFLHHMVRNLIGALLQVGQGREPVAWMDALLCARDRRLGAPTFMPDG 238

Query: 239 LYFDSVEY 246
           LY  ++EY
Sbjct: 239 LYLSAIEY 246


>gi|307702068|ref|ZP_07639075.1| tRNA pseudouridine synthase A [Streptococcus mitis NCTC 12261]
 gi|307616555|gb|EFN95745.1| tRNA pseudouridine synthase A [Streptococcus mitis NCTC 12261]
          Length = 249

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQTHARSVQEEIEKTLTRLNKGKAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+ A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLR 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|33519947|ref|NP_878779.1| tRNA pseudouridine synthase A [Candidatus Blochmannia floridanus]
 gi|42559760|sp|Q7U356|TRUA_BLOFL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33504293|emb|CAD83185.1| tRNA pseudouridine synthase A [Candidatus Blochmannia floridanus]
          Length = 252

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 93/239 (38%), Positives = 129/239 (53%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           +EY+GS Y GWQ+QK  SSIQ  +E A+  V+ E ++V   GRTDSGVHAL Q+ HF+  
Sbjct: 8   VEYDGSMYCGWQKQKCVSSIQSCLEYALSKVSSESILVFCGGRTDSGVHALEQIVHFETQ 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
            +         +N +L   + I +  +S VD  FHARFSAI R Y Y I   +   A+  
Sbjct: 68  LKCSRSAWTLGVNCHLP--NDICVRWVSEVDNSFHARFSAISRRYCYFIYNNRIRSAVFC 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            R W   + LD   M  AAQ+L+G +DF+ FRS   Q+ S  R I H  V   G+ + I 
Sbjct: 126 KRVWSYSRFLDVNKMSKAAQYLLGENDFSVFRSSGSQSCSTNRNIYHLRVIRQGHYVVID 185

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A +FL+  +R+ VGSL  VG G    T + + L+          AP  GLY   ++Y
Sbjct: 186 IRANAFLYRMVRNIVGSLVEVGCGNKPVTWILELLKNYRGSLNRITAPASGLYLVEIKY 244


>gi|107026755|ref|YP_624266.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia AU 1054]
 gi|116692053|ref|YP_837586.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia HI2424]
 gi|170735954|ref|YP_001777214.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia MC0-3]
 gi|123370548|sp|Q1BM62|TRUA_BURCA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123464580|sp|A0AZ67|TRUA_BURCH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238688629|sp|B1K370|TRUA_BURCC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|105896129|gb|ABF79293.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia AU 1054]
 gi|116650053|gb|ABK10693.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia HI2424]
 gi|169818142|gb|ACA92724.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia MC0-3]
          Length = 270

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q  +E A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDRLEHALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       +  NA+L    T+S+     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTDLEREVFSWVRGTNAFLP--STVSVQWAKPMPDTFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY 
Sbjct: 179 HFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|257452870|ref|ZP_05618169.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|317059412|ref|ZP_07923897.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|313685088|gb|EFS21923.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
          Length = 251

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 128/245 (52%), Gaps = 9/245 (3%)

Query: 8   IEYNGSGYFGWQR---QKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHALRQV 61
           IEY G+ Y GWQR   ++   +IQG IE+ +   F +  E V V  +GRTD+GVHA  Q+
Sbjct: 10  IEYEGTRYLGWQRLGEKQREKTIQGKIEQVLARLFALNPEEVSVIASGRTDAGVHAKEQI 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+  L     P  + +  N YL   + I I +   V++ FH+RF A  + Y Y I + Q 
Sbjct: 70  ANVHLPSGKSPQEIEEYCNQYL--PEDIRIFHAHFVEELFHSRFHAKTKEYHYEI-SLQK 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +   W  P  LD E M+ ++Q+ +G HDF  F S+     S IR ID  ++    
Sbjct: 127 PSVFHRNVTWYCPMQLDIEKMKESSQYFLGEHDFIAFSSLKKTKKSTIRRIDRIEIQETE 186

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R V   FL   IR  VG+L  VG+GK T  D+    Q++ R++ G LAP +GL  
Sbjct: 187 SGLLFRFVGNGFLQNMIRILVGTLIEVGEGKKTKEDIISIFQSKTRQKAGFLAPAKGLTL 246

Query: 242 DSVEY 246
             V Y
Sbjct: 247 YKVYY 251


>gi|158320711|ref|YP_001513218.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
 gi|158140910|gb|ABW19222.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
          Length = 245

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 132/242 (54%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           ++IEY+GS Y GWQR K+   +IQG IEK +  +TG  V + G+GRTD+GVHA  Q+A+F
Sbjct: 6   LVIEYDGSRYDGWQRLKDSEQTIQGKIEKVLNEMTGSSVEIIGSGRTDAGVHAKNQIANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   +N YL     I +  +  V  +FH+R++A ++ Y Y +   + P A
Sbjct: 66  KTKSSMSIRDIHNYMNHYL--PQDIVVKEVKEVSDRFHSRYNAQKKKYTYYVWNHRIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            ++  ++  P++LD + M  AA  L+G HDF  F S+     S +RTI+   +    +++
Sbjct: 124 FQRKYSYYFPETLDLQRMEAAANQLLGTHDFIGFSSVKKAKKSTVRTIEEITIVQNNHML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E   +   FLH  IR  +G+L  +G  +   + +++   ++ R   G  AP +GL+ + V
Sbjct: 184 EFSFIGDGFLHNMIRILMGTLLEIGTREKDISCIDEIFTSKTRAMAGKTAPAQGLFLEEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|259502563|ref|ZP_05745465.1| tRNA pseudouridine synthase A [Lactobacillus antri DSM 16041]
 gi|259169515|gb|EEW54010.1| tRNA pseudouridine synthase A [Lactobacillus antri DSM 16041]
          Length = 256

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 90/253 (35%), Positives = 137/253 (54%), Gaps = 11/253 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           M RY +   Y+G+ + G+Q Q +  +++  ++ A+  +       V V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGANFSGFQIQPHKRTVEQVLKNAVNKIAKHPDPPVSVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD+  +     + KALN+ L +   I +     VD+ FHAR+SA R++Y YR+ 
Sbjct: 61  LNQVAHFDIPYQLSDEAMRKALNSLLPLD--ILVKKAERVDENFHARYSAHRKTYRYRVD 118

Query: 118 TRQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 P        + +P  +D E MR+AA+  +G HDFT+F +   QA S +RT++  
Sbjct: 119 QGDFVDPFKRNYTAHYKVP--VDIEKMRLAAKDFIGEHDFTSFVASGSQAKSNVRTVEKI 176

Query: 176 DVN--SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            VN     N +        FL+ QIR  V  L  VG G+   +D+++ L A+DR +    
Sbjct: 177 TVNRDPAQNEVVFEFTGNGFLYNQIRIMVAFLLEVGSGQRPVSDVKRVLAAKDRTQARMT 236

Query: 234 APPEGLYFDSVEY 246
           AP  GLY  SV+Y
Sbjct: 237 APASGLYLVSVDY 249


>gi|283796516|ref|ZP_06345669.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
 gi|291075930|gb|EFE13294.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
 gi|295092580|emb|CBK78687.1| pseudouridylate synthase I [Clostridium cf. saccharolyticum K10]
          Length = 368

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 131/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + +A+  +  E + V GA RTDSGVHA+  
Sbjct: 1   MKRIRLTVAYDGTNYCGWQLQPNGITIEEVLNRALSELLKEEIQVVGASRTDSGVHAMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD      P  +C ALN   ++ + + +     V   FH R +   ++Y Y+I+ R+
Sbjct: 61  IAVFDTESRIPPEKICFALNQ--RLPEDVRVQKSEEVPLTFHPRKANCVKTYEYKILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
             + L +         LD E MR AA  LVG HDF +F ++  QA   +RTI    V+  
Sbjct: 119 IDMPLNRLYCHFCYFDLDVEKMRRAAAFLVGEHDFKSFCTVRTQAEETVRTIYSLTVDRG 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IR+    FL+  +R   G+L  +G G W    +E+ L+A+DR   GP  P +GL
Sbjct: 179 ADDVIVIRISGSGFLYNMVRIITGTLVKIGMGVWPPEYMEEILEARDRAAAGPTIPAKGL 238

Query: 240 YFDSVEYS 247
              S+EY 
Sbjct: 239 TLVSMEYE 246


>gi|116627085|ref|YP_819704.1| tRNA pseudouridine synthase A [Streptococcus thermophilus LMD-9]
 gi|122268312|sp|Q03MR4|TRUA_STRTD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116100362|gb|ABJ65508.1| Pseudouridylate synthase [Streptococcus thermophilus LMD-9]
          Length = 248

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 134/250 (53%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  IEK +  L +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEEIEKTLLRLNSGIPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYSKHIKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V S
Sbjct: 119 RPKNPMMRNYAIHYPYPLSLALMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASV-S 177

Query: 180 FGNLIEIRVVARS---FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                   V A S   FL+ Q+R+ VG+L  +G+G+   +  +  L+++DR   GP    
Sbjct: 178 IDEKTGFYVFAFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQAKTVLESRDRNLAGPTVAG 237

Query: 237 EGLYFDSVEY 246
            GLY   + Y
Sbjct: 238 NGLYLKEIRY 247


>gi|239825725|ref|YP_002948349.1| tRNA pseudouridine synthase A [Geobacillus sp. WCH70]
 gi|259550397|sp|C5D3U9|TRUA_GEOSW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239806018|gb|ACS23083.1| tRNA pseudouridine synthase A [Geobacillus sp. WCH70]
          Length = 248

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 86/241 (35%), Positives = 128/241 (53%), Gaps = 3/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G+ +FG+Q Q    ++QG +E+ +  +  G+ + V  +GRTD+GVHA  QV HFD 
Sbjct: 9   LSYDGTHFFGYQIQPGKRTVQGELERVLEQMHKGKAIRVTASGRTDAGVHAYGQVIHFDT 68

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                P    KALNA  ++ D I I ++   D  FHARFSA  + Y Y++   Q      
Sbjct: 69  FLSLSPDQWKKALNA--QLPDDIVIKDVQEADPSFHARFSAKAKEYRYKVRIAQERDVFL 126

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +   +  P  LD E MR A + + G HDFT+F S        +RTI   D+    +L+E 
Sbjct: 127 RNYCYHYPYPLDMEAMRHALRLIEGTHDFTSFCSAKTDVDDRVRTIYKADMAMHDDLLEF 186

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             +   FL+  +R  VG++  VG GK +   +  A +A+DR+  G  APP+GLY   V Y
Sbjct: 187 CFIGNGFLYNMVRIIVGTILEVGQGKRSIDSISHAFEAKDRQFAGKTAPPQGLYLWKVYY 246

Query: 247 S 247
            
Sbjct: 247 D 247


>gi|289167524|ref|YP_003445793.1| tRNA pseudouridine synthase A [Streptococcus mitis B6]
 gi|288907091|emb|CBJ21925.1| tRNA pseudouridine synthase A [Streptococcus mitis B6]
          Length = 249

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 130/251 (51%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  E  + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKEQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYTKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E MR A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMREAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLT 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|332664422|ref|YP_004447210.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
 gi|332333236|gb|AEE50337.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
          Length = 256

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 137/247 (55%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M ++ + +EY+GS + GWQ Q++  SIQG + KA  +V   + V V+G+GRTD+GVHAL 
Sbjct: 1   MAKFKLTLEYDGSRFKGWQVQEDARSIQGQLIKAAKIVFETDKVEVYGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH  +  +    ++ + LN  L  +  I++L++  V  +FHAR  A+ RSY+Y+I  R
Sbjct: 61  QVAHLAVDTKMPVKMIRQKLNDQL--THDINVLSVDPVSDKFHARHDAVARSYVYQISRR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   A  K   W +   LD E M +AA HL+G HDF +F +      S    + H  V  
Sbjct: 119 RN--AFGKHFMWWVKDPLDVERMNVAAAHLIGMHDFKSFSNEKGTEKSSKVELQHLKVVE 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + + ++A  FL   +R  VGSL  VG G+      ++ L+   ++     APP GL
Sbjct: 177 KGDKVVVHIIASHFLWKMVRRVVGSLVEVGAGRLDPDKFKEWLEKPSQEPAKFTAPPAGL 236

Query: 240 YFDSVEY 246
           + + V +
Sbjct: 237 FLERVYF 243


>gi|290891783|ref|ZP_06554780.1| truA protein [Listeria monocytogenes FSL J2-071]
 gi|290558377|gb|EFD91894.1| truA protein [Listeria monocytogenes FSL J2-071]
          Length = 248

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 133/251 (52%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMNKGKTVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ KAL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEY 246
           P+GLY   V+Y
Sbjct: 237 PQGLYLWRVDY 247


>gi|294637213|ref|ZP_06715519.1| tRNA pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
 gi|291089602|gb|EFE22163.1| tRNA pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
          Length = 275

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 126/240 (52%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y GWQRQ+   S+Q  +E A+  V  E V V  AGRTD+GVHA  QV HF   
Sbjct: 21  IEYDGSRYAGWQRQQEVDSVQARLEAALSRVASEPVTVFCAGRTDAGVHATGQVVHFTTH 80

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA+L     I++  +  V   FHARFSA  R Y Y I   R  P  L+
Sbjct: 81  ASRQEGAWTMGVNAHLP--KDIAVRWVKAVSADFHARFSATARRYRYVIYNHRYRPAVLQ 138

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G        LD E M  A Q L+G +DF++FR+  CQ+ +P R + H  VN +G  + +
Sbjct: 139 SGVTHFY-HPLDAERMARAGQALLGENDFSSFRAAQCQSRTPWRNVSHLWVNRYGPYVVV 197

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG G      + + L A+DR      A   GLY  +V+Y
Sbjct: 198 DIKANAFVHHMVRNIVGSLLEVGCGNQPEGWIAELLAARDRTLAAATAKAAGLYLVAVDY 257


>gi|311070796|ref|YP_003975719.1| tRNA pseudouridine synthase A [Bacillus atrophaeus 1942]
 gi|310871313|gb|ADP34788.1| tRNA pseudouridine synthase A [Bacillus atrophaeus 1942]
          Length = 247

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 132/242 (54%), Gaps = 4/242 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQVAHFD 65
           I Y+G  + G+Q Q    ++Q  +EKA+ ++  + + V V  +GRTDSGVHA  QV HFD
Sbjct: 7   ISYDGHLFNGYQVQPGKRTVQAELEKALAILHKSEDKVPVISSGRTDSGVHAAGQVIHFD 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALNA L     I++      D  FHARFSAI++ Y Y + T + P   
Sbjct: 67  TPLSIPAERWPYALNALL--PGDIAVKTAEHADDGFHARFSAIKKEYRYFVYTEKHPDVF 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           ++  A+     L+ + MR A++HL+G HDFT+F S + +    +RTI   D     + ++
Sbjct: 125 KRHYAYHFSYRLNVQKMREASEHLIGTHDFTSFCSANTEVRDKVRTIYELDWTDTDDGLQ 184

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           +R+V   FL+  +R   G+L  VG GK+++ D++  L A+DR+  G  AP  GLY   V 
Sbjct: 185 MRIVGSGFLYNMVRIIAGTLLDVGTGKFSADDVKGMLDAKDREAAGRTAPGHGLYLWHVY 244

Query: 246 YS 247
           Y 
Sbjct: 245 YD 246


>gi|322392372|ref|ZP_08065833.1| tRNA pseudouridine synthase A [Streptococcus peroris ATCC 700780]
 gi|321144907|gb|EFX40307.1| tRNA pseudouridine synthase A [Streptococcus peroris ATCC 700780]
          Length = 249

 Score =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  +I Y+G  + G+QRQ +  S+Q  IEK +  L  G  V +HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAVISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGLGVTIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMEEEKLRFALDT--QSPEDIDVISVEIVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M+ A + L G HDFT F +        +RTI      
Sbjct: 118 GRPKNPMRRHYATHYPYPLDVERMQKAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLK 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPIEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|85713087|ref|ZP_01044122.1| tRNA pseudouridine synthase A [Idiomarina baltica OS145]
 gi|85693073|gb|EAQ31036.1| tRNA pseudouridine synthase A [Idiomarina baltica OS145]
          Length = 261

 Score =  149 bits (377), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 86/245 (35%), Positives = 127/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G  Y+GWQRQ+   S+Q  +E A+  V  + V    AGRTD+GVHA  QV
Sbjct: 1   MRIALGLEYDGRAYYGWQRQREVDSVQQRLENALSKVADQAVETVCAGRTDAGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +         +N++L     I++     VD  F ARFSA  R Y Y I     
Sbjct: 61  VHFDVSTQRRAAAWTLGVNSHLPPD--IAVRWAQPVDDSFSARFSATARRYRYIIANHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M+ A   L+G HDF+ FR+  CQ+ S  R I H +V+  G
Sbjct: 119 RPGIHSHGVSHYHHPLDVDAMQAATPALLGEHDFSAFRAAQCQSHSAHREITHLNVHRRG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +FLH  +R+ VGSL ++G  +   + L + L  +DR +    A P GLY 
Sbjct: 179 DFIIVDIKANAFLHHMVRNIVGSLIVIGRHQQDPSWLGELLAGKDRTKAAATAKPGGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VEVDY 243


>gi|297849290|ref|XP_002892526.1| hypothetical protein ARALYDRAFT_471082 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297338368|gb|EFH68785.1| hypothetical protein ARALYDRAFT_471082 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 373

 Score =  149 bits (377), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 97/314 (30%), Positives = 152/314 (48%), Gaps = 70/314 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + G Q+Q    ++ G ++ A     G+ V +  + RTD+GVHAL  V 
Sbjct: 57  RYLVAIEYIGTRFSGSQQQAKDRTVVGVLQDAFHKFIGQPVKIFCSSRTDAGVHALSNVC 116

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  R
Sbjct: 117 HVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQER 176

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR++    PL+ LEK R W +P+ L+  +M+ A + LVG HDF++FR+  CQA SP+
Sbjct: 177 TYFYRLLAGSDPLSILEKDRCWHVPEELNPRSMQEACRVLVGYHDFSSFRAAGCQAKSPM 236

Query: 170 RTIDHFDV---------------------------------------------------- 177
           R +D  ++                                                    
Sbjct: 237 RYLDELNITEVPSTPYFPSITERAWSNLNNGDPLACSSQPKSETAGVTTNVGEVEGSTDG 296

Query: 178 NSFGNLIEIR---VVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           +SFG     R   V ARS  FL+ Q+R  VG+LK VG G+ T +D+E+ L+A+      P
Sbjct: 297 DSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAKP 356

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GLY   V+Y
Sbjct: 357 MAPASGLYLARVKY 370


>gi|170289026|ref|YP_001739264.1| tRNA pseudouridine synthase A [Thermotoga sp. RQ2]
 gi|238688847|sp|B1LB83|TRUA_THESQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|170176529|gb|ACB09581.1| tRNA pseudouridine synthase A [Thermotoga sp. RQ2]
          Length = 245

 Score =  149 bits (377), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 131/246 (53%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+   + +     K A+NA L   D + +  +  V K FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIKNAMNANL--PDDVYVKEVFEVSKNFHPRFDVKKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR AA++L G HDFT+F++       P+RTI    +  
Sbjct: 119 KQKNVFLRKYVWWFPYELDLDAMRKAAKYLEGTHDFTSFKT-GSDERDPVRTIYRIRILR 177

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|297567108|ref|YP_003686080.1| tRNA pseudouridine synthase A [Meiothermus silvanus DSM 9946]
 gi|296851557|gb|ADH64572.1| tRNA pseudouridine synthase A [Meiothermus silvanus DSM 9946]
          Length = 259

 Score =  149 bits (377), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 96/257 (37%), Positives = 133/257 (51%), Gaps = 13/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + +E++G+ + G Q Q  G  ++Q ++E+A+  + G I  V  AGRTD+GVHAL 
Sbjct: 1   MRRIKLTVEFDGTHFAGLQTQAKGERTVQNTLEQALAQIPGAIPKVVAAGRTDAGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H+D +    P  +  ALN  L     +  L    V  +FHAR S   R+Y YRI+ R
Sbjct: 61  MPLHYDTLDPIPPEKIPLALNGLL--PPDLRALAAEEVAPEFHARKSCHWRAYRYRILNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---------RSIHCQASSPIR 170
           + P AL +  AW IP+ L+   MR A +HLVG HDF  F         R I+ +A   + 
Sbjct: 119 KTPSALLRHYAWWIPQQLNLVAMRHALEHLVGEHDFKAFAVKEKRPTVRRIY-RAHLTVL 177

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           T D          I +  V   FL  Q+RS VG+L  VG GK  S  L + L+   R + 
Sbjct: 178 TPDIAQDAKNEREIHLEFVGSGFLRGQVRSMVGTLVEVGLGKRDSQSLGELLRTGTRSQA 237

Query: 231 GPLAPPEGLYFDSVEYS 247
           GP APP+GLYF    Y+
Sbjct: 238 GPTAPPQGLYFVGAGYA 254


>gi|258592098|emb|CBE68403.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [NC10 bacterium 'Dutch
           sediment']
          Length = 263

 Score =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + IEY+G+ Y GWQ Q   ++IQG+++ A+  + G+ V V GAGRTD+GVHA  Q
Sbjct: 1   MTTFKLTIEYDGTDYHGWQVQPGMTTIQGTLQGAVARIVGKDVHVMGAGRTDAGVHAHGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA         P    +AL + L  SD I +  +  +D  FHA++SA  + Y Y ++TR 
Sbjct: 61  VASLRTEFHHPPDTFRRALTSVLP-SD-IVVTAVEEMDDDFHAQYSAQWKRYRYSLLTRP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P A+E+     +P  L  + M +AA  LVG HDF+ F++ H  A SP+RT+   +    
Sbjct: 119 YPSAIERRYTLFVPYPLQTDAMAVAAGSLVGTHDFSAFQAAHSSAESPVRTVLVAEFRQH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +   +VA  FL   IR  +G+L  +G G+     L    + +DR +      P GL 
Sbjct: 179 GDHLLFEIVADGFLRHMIRIIMGTLLDIGRGRLQVEALHIIREGRDRNQASKTISPHGLC 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LLEVGY 244


>gi|317131990|ref|YP_004091304.1| tRNA pseudouridine synthase A [Ethanoligenens harbinense YUAN-3]
 gi|315469969|gb|ADU26573.1| tRNA pseudouridine synthase A [Ethanoligenens harbinense YUAN-3]
          Length = 252

 Score =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 86/242 (35%), Positives = 123/242 (50%), Gaps = 2/242 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++ ++G+ Y GWQ QKNG ++Q  ++ A+  V      V G  RTD+GVHAL    +F 
Sbjct: 6   LLLRFDGAAYHGWQVQKNGVTVQEVLQNALETVLRHRPPVTGCSRTDAGVHALAYACNFR 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    L +ALNA L   D I++     V   FHAR+SA  + Y+YRI+   A    
Sbjct: 66  TEHTIPCQNLVRALNACL--PDDIAVFACREVPPDFHARYSAHEKEYVYRILNAPARDPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +GRA  +P  LD   M  AA+  +G HDF  FR+        +RT+ H  V   G+L+ 
Sbjct: 124 WRGRALHVPYPLDEAVMDKAARGFLGTHDFAGFRAAGSDVKDTVRTVFHSGVQRDGDLVL 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            RV A  FL+  +R  VG+L      K    D+   + ++DR   GP AP  GLY + V 
Sbjct: 184 FRVRADGFLYNMVRIMVGTLLYTAQDKLQPADILAVIDSRDRTAAGPTAPAHGLYLNRVF 243

Query: 246 YS 247
           Y 
Sbjct: 244 YD 245


>gi|306820983|ref|ZP_07454602.1| tRNA pseudouridine synthase A [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550924|gb|EFM38896.1| tRNA pseudouridine synthase A [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 245

 Score =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 88/241 (36%), Positives = 134/241 (55%), Gaps = 5/241 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ Y GWQRQKN  SIQ  IE AI L+  E + V  +GRTD+GVHAL Q+A+F   
Sbjct: 8   ISYDGTNYSGWQRQKNAISIQEKIEDAISLICNEEINVIASGRTDAGVHALSQIANFSTS 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                    KA+N   K+ D I IL+   VD+ F+ARFSA +++Y+Y I+ R+       
Sbjct: 68  SSIDAKKFAKAINT--KLPDDIRILSSKEVDEDFNARFSAKKKTYIYHILNREIKNPFWD 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFD-VNSFGNLIE 185
             +  I + LD E M+  +  L+G HDFT+F +       + I+TI   D V  + +++ 
Sbjct: 126 KYSMHINRKLDLELMKSNSNMLIGTHDFTSFYTYEENNPKNTIKTIYSSDIVKIYEDILT 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  +  + D+ + L  +DR + G  A  +GL+  +VE
Sbjct: 186 FSITGDGFLYNMVRIIVGTLIEIGLHQ-KNDDISQILMYKDRIKAGATAKAKGLFLKNVE 244

Query: 246 Y 246
           Y
Sbjct: 245 Y 245


>gi|168483521|ref|ZP_02708473.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1873-00]
 gi|172043050|gb|EDT51096.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1873-00]
          Length = 249

 Score =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYVFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVLHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E MR A + L G HDFT F +        IRTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMREAIKKLEGTHDFTGFTASGTSVEDKIRTITEASLT 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAP 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEICYE 248


>gi|221212470|ref|ZP_03585447.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD1]
 gi|221167569|gb|EEE00039.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD1]
          Length = 270

 Score =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G+++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGNTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFLP--PTVAVQWAKPMPDAFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLDGRAGWIHTPLDDDAMRAAAAHLLGEHDFSAFRSSECQSKTPVKHVYEIDIRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  +   L  +DR    P    +GLY 
Sbjct: 179 HFLHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGRDRNRAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|325913236|ref|ZP_08175605.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 60-B]
 gi|325477500|gb|EGC80643.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 60-B]
          Length = 260

 Score =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 136/249 (54%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD     +P   +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A+DR++    AP  G
Sbjct: 179 QHGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKDVEDVEKIILAKDRQKARNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>gi|168178866|ref|ZP_02613530.1| tRNA pseudouridine synthase A [Clostridium botulinum NCTC 2916]
 gi|226950899|ref|YP_002805990.1| tRNA pseudouridine synthase A [Clostridium botulinum A2 str. Kyoto]
 gi|182670055|gb|EDT82031.1| tRNA pseudouridine synthase A [Clostridium botulinum NCTC 2916]
 gi|226843785|gb|ACO86451.1| tRNA pseudouridine synthase A [Clostridium botulinum A2 str. Kyoto]
          Length = 246

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 134/241 (55%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA   + +F 
Sbjct: 8   LEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAKGYICNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++    P+A+
Sbjct: 68  TNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLNSSKPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N  G+ I+
Sbjct: 126 GRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEINKKGDFIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  K     ++  ++++DR++ G   P  GL    V 
Sbjct: 186 FIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIKYVIKSKDRRKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|225448126|ref|XP_002263416.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|297739525|emb|CBI29707.3| unnamed protein product [Vitis vinifera]
          Length = 380

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 97/315 (30%), Positives = 149/315 (47%), Gaps = 71/315 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G Q+Q N  ++ G++++A     G+ V +  + RTD+GVHAL  V 
Sbjct: 63  RYLVAVEYIGTRFSGSQQQLNCRTVAGALQEAFHKFIGQPVSIFCSSRTDAGVHALSNVC 122

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+ ++  + ++++  V   FHAR+ A  R
Sbjct: 123 HVDVERISKRKPGEVLPPHEPAVVRRAVNHFLQKNEGDVMVIDVRCVPPDFHARYKARER 182

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR+++   PL+  EK RAW +P+ LD   M+ A + LVG HDF++FR+  CQA SPI
Sbjct: 183 TYFYRLLSGPEPLSSFEKDRAWHVPEDLDLLAMQKACRVLVGCHDFSSFRAAGCQAKSPI 242

Query: 170 RTIDHFDV-------------------------------------------------NSF 180
           RT+D   V                                                 N  
Sbjct: 243 RTLDELCVSEVLPTPYFPSITERAQNNFTEENPLACSNNAEVPDSPSTANHDRLDGFNGA 302

Query: 181 GNLIEIRVVARSFLHT---------QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           G    +R   R FL T         Q+R  VG +K VG G  T +D+E+ L A+      
Sbjct: 303 GQGFGVRRRHRCFLVTARARSFLYHQVRLLVGVIKCVGTGDLTVSDVERILNAKTVTAAS 362

Query: 232 PLAPPEGLYFDSVEY 246
           P+AP  GLY  +V Y
Sbjct: 363 PMAPACGLYLGNVNY 377


>gi|241765867|ref|ZP_04763802.1| tRNA pseudouridine synthase A [Acidovorax delafieldii 2AN]
 gi|241364216|gb|EER59401.1| tRNA pseudouridine synthase A [Acidovorax delafieldii 2AN]
          Length = 289

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 94/263 (35%), Positives = 134/263 (50%), Gaps = 24/263 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + YNG  Y GWQ Q +G+++Q  +E A+   T + V    AGRTD+GVH L QV
Sbjct: 18  TRVALGVSYNGQRYNGWQSQPSGNTVQDHLEAALGRFTTQQVSTLCAGRTDAGVHGLMQV 77

Query: 62  AHFD--LVR---EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD  LVR    WV     +  NA+L     I++     V   FHAR SA+ R Y Y +
Sbjct: 78  VHFDTTLVRPDASWV-----RGTNAFLP--QDIAVQWARAVPSGFHARASAVARRYAYVL 130

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +      ++E GR   +  +L+ + MR AA  L+G HDFT+FR+  CQA SP++T+   D
Sbjct: 131 LQSPVRPSVEAGRVGWVFNALNEDAMRQAALRLLGEHDFTSFRASACQAKSPVKTLQRID 190

Query: 177 V--------NSFGNL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           +        ++ G            A +FLH  IR+ +GSL  VG G    + + + L A
Sbjct: 191 ITRTPCPRASAAGEFDACYWRFEFEANAFLHHMIRNIMGSLVAVGKGTKPPSWISEVLDA 250

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
             R    P   P+GLYF    Y+
Sbjct: 251 HSRDAAAPTFSPDGLYFQGPVYA 273


>gi|254480499|ref|ZP_05093746.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2148]
 gi|214039082|gb|EEB79742.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2148]
          Length = 277

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 88/241 (36%), Positives = 125/241 (51%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           IEYNG+ Y GWQ Q   N  ++Q  +E A+  V    + VH AGRTD+GVH   Q+ HFD
Sbjct: 16  IEYNGARYNGWQSQPHLNVLTVQQELESALSSVADHPLRVHCAGRTDTGVHGHCQIVHFD 75

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P       NA   ++  + +   ++V + FHARF A+ R Y Y I       A+
Sbjct: 76  APAARAPKAWVLGANA--SMAKDVRVHWATVVPESFHARFCAVARRYRYVIANTLVRPAV 133

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
             G+       LD   M  AAQ L+G  DF+ FR+  CQ++SP+R +    V   G+L+ 
Sbjct: 134 LVGQVSWYRYPLDAAIMDKAAQSLLGEQDFSAFRAAACQSNSPMRNVHSVAVRRIGDLVV 193

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + + A +FLH  +R+ VGSL  VG G+     + + L A+DR +    A P GLY   V 
Sbjct: 194 VDIQANAFLHHMVRNIVGSLLAVGSGRKPEAWIGQLLAARDRTQAADTAAPHGLYLADVL 253

Query: 246 Y 246
           Y
Sbjct: 254 Y 254


>gi|313606591|gb|EFR83384.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL F2-208]
          Length = 248

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 134/251 (53%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIITYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSDLDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G+HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGKHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ KAL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEY 246
           P+GLY   V+Y
Sbjct: 237 PQGLYLWRVDY 247


>gi|332982675|ref|YP_004464116.1| tRNA pseudouridine synthase A [Mahella australiensis 50-1 BON]
 gi|332700353|gb|AEE97294.1| tRNA pseudouridine synthase A [Mahella australiensis 50-1 BON]
          Length = 245

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 92/243 (37%), Positives = 131/243 (53%), Gaps = 6/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + ++Y+G+ Y GWQ QKN  +IQ  +E+AI  +TG+   V  AGRTD GVHAL QV +F 
Sbjct: 7   LTLQYDGTAYAGWQYQKNALTIQQVVEEAIESLTGQHSTVIAAGRTDRGVHALGQVTNFK 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-- 123
                       ALNA L   + I +++   V   FHARF A  +  LYR I   AP   
Sbjct: 67  TESNIPTDRWLYALNAVL--PEDIRVIDAQDVLPSFHARFDA--KGKLYRYIIWNAPYSS 122

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           AL +  +  + + LD + M+ AA + VG HDF++F++        +R I    + + G +
Sbjct: 123 ALLRNFSLHVARPLDADAMKRAALYFVGTHDFSSFQASGSTVRDTVRNIWDISIQTEGKM 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I I +    FL+  +R  VG+L  VG GK T+ D +  L+A+DRK  G  A P GLY   
Sbjct: 183 ISISISGDGFLYNMVRIMVGTLIDVGIGKITACDAKLILEARDRKRAGKTAGPHGLYLVE 242

Query: 244 VEY 246
           V Y
Sbjct: 243 VYY 245


>gi|170761533|ref|YP_001788787.1| tRNA pseudouridine synthase A [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169408522|gb|ACA56933.1| tRNA pseudouridine synthase A [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 246

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 78/241 (32%), Positives = 132/241 (54%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EK I  +T E V + G  RTDSGVHA   V +F 
Sbjct: 8   LEYDGTNYCGWQKQKNEKFITLQGTLEKVISNITKEKVEIIGVSRTDSGVHAKGYVCNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P  L K +N  L     I +L+   V  +FH+RF +  ++Y Y ++    P+A+
Sbjct: 68  TNTRIPPENLQKVINNNL--PQDIVVLSSEEVSNEFHSRFCSKGKTYEYTVLNSPQPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     L+ +NM+IA+++ +G HDF+ F++      + +RTI+ F+++  G+ I+
Sbjct: 126 GRNYIFQFKDKLNIDNMKIASRYFIGTHDFSAFKTKGSSVKTSVRTINEFEIDKKGDFIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG L  +G  K     +E  ++++DR++ G   P  GL    V 
Sbjct: 186 FTITGDGFLYNMVRIIVGILIEIGLNKREPEYVEYVIKSKDRRKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|78062974|ref|YP_372882.1| tRNA pseudouridine synthase A [Burkholderia sp. 383]
 gi|123728751|sp|Q393X8|TRUA_BURS3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|77970859|gb|ABB12238.1| Pseudouridylate synthase [Burkholderia sp. 383]
          Length = 270

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 91/250 (36%), Positives = 134/250 (53%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q  +E A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDRLEHALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFD--LVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD  L RE   WV     +  NA+L    T+++     + + FHARFSA  R+Y Y +
Sbjct: 61  VHFDTDLDREVFSWV-----RGTNAFLP--STVAVQWAKPMPETFHARFSAFERTYYYAL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   D
Sbjct: 114 YVHPVRSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQID 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ +  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    
Sbjct: 174 VRRVGHFVHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMA 233

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 234 DGLYLAHVGY 243


>gi|313622273|gb|EFR92777.1| tRNA pseudouridine synthase A [Listeria innocua FSL J1-023]
          Length = 248

 Score =  149 bits (376), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 131/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG+FG+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFFGYQVQPNTRTVQAEIEKALEKMHKGKSVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  I + Y Y I   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEAQADFHARFGTIGKEYRYVIKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD E M+ A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDIEKMKQASERLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ KAL A DR++     AP
Sbjct: 177 YEEDAETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLAHDRQKLISKTAP 236

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V+Y 
Sbjct: 237 PQGLYLWRVDYE 248


>gi|309809150|ref|ZP_07703023.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 2503V10-D]
 gi|308170595|gb|EFO72615.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 2503V10-D]
          Length = 260

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 136/249 (54%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD     +P   +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A+DR++    AP  G
Sbjct: 179 QNGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKDVEDVEKIILAKDRQQARNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>gi|116515069|ref|YP_802698.1| hypothetical protein BCc_129 [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256923|gb|ABJ90605.1| pseudouridylate synthase I [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 269

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +++   +EY+GS Y GWQ+QK+  +IQ  IE A+  +    + V  AGRTD GVHA+ Q+
Sbjct: 1   MKFVFGVEYDGSIYHGWQKQKSVLTIQECIEHALSKIANSKIEVICAGRTDKGVHAITQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF  +      +    LN+ L     I++L L  V   FHARFSA+ RSY Y I  R+ 
Sbjct: 61  VHFSSLIIRNEEVWFTGLNSLL--PKNITVLWLKKVSSNFHARFSALSRSYRYIIFNRKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             +  K   + +   LD   M+ ++Q L+G HDF++F+S  CQ+ S  + I    +    
Sbjct: 119 RSSFLKNYYFHVRNFLDIYKMKTSSQFLIGNHDFSSFKSSGCQSFSSRKNIFSLIIYRIN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A SFL+  +R+ VG L LVG  K     ++  LQ +D K+     P +GLYF
Sbjct: 179 DFIIIDITANSFLYHMVRNIVGCLILVGLSKKKPEWVQYILQKKDIKKTYSTVPAQGLYF 238

Query: 242 DSVEY 246
               Y
Sbjct: 239 LFASY 243


>gi|148245016|ref|YP_001219710.1| tRNA pseudouridine synthase A [Candidatus Vesicomyosocius okutanii
           HA]
 gi|146326843|dbj|BAF61986.1| tRNA pseudouridine synthase A [Candidatus Vesicomyosocius okutanii
           HA]
          Length = 247

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 133/246 (54%), Gaps = 13/246 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK N  ++Q  IE+A+  V  + V V  +GRTD+GVHA  Q
Sbjct: 1   MKLALGVEYLGTHFHGWQCQKSNIRTVQQVIEQALSSVANQPVRVFCSGRTDTGVHATCQ 60

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+       + W+           + +   ++   +  VD  FHARFS I R Y Y+
Sbjct: 61  VIHFETNIKRKNKAWL-------FGGNVHLPSDVNFTWVKPVDDNFHARFSVITRQYNYK 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I   +   ++    +   P+ LD   M  A Q+L G+H+F+ FR   CQA SPI+ I+  
Sbjct: 114 IHNTKIRSSIIATHSLWEPRKLDIVAMNKAGQYLTGKHNFSAFRGSLCQAKSPIKNIEFI 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +    + I + + A +FLH  +R+ VG+L  VG G+     + + L ++ RK+ GP AP
Sbjct: 174 KLTKHDDNILLDIKANAFLHHMVRNIVGTLLKVGKGEKPIEWVREVLNSKQRKQAGPTAP 233

Query: 236 PEGLYF 241
           P+GLYF
Sbjct: 234 PQGLYF 239


>gi|197302933|ref|ZP_03167984.1| hypothetical protein RUMLAC_01661 [Ruminococcus lactaris ATCC
           29176]
 gi|197298014|gb|EDY32563.1| hypothetical protein RUMLAC_01661 [Ruminococcus lactaris ATCC
           29176]
          Length = 297

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q N ++I+G +   +  +TG+ V V GA RTD+GVHA   
Sbjct: 26  MKRIRLTVAYDGTDYCGWQVQNNVATIEGELNTVLTQLTGQTVKVIGASRTDAGVHARGN 85

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P     A+NA L   + I +++   V   +H R     ++Y YR++ ++
Sbjct: 86  VAVFDTESSIPPERFLYAVNALL--PEDIVVVDSCEVAADWHPRHCNTEKTYEYRVLNQK 143

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  + +   + +   LD E MR AA +L G HDF +F ++H      +RTI   +V   
Sbjct: 144 LPDPMRRRDTYFVSFPLDLERMRQAAGYLEGEHDFKSFCNVHTHVEDTVRTIYRLEVIRE 203

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N+I  RV    FL+  +R   G+L  VG G     ++   L+A+DR+  G   PP+GL 
Sbjct: 204 ENVITFRVRGNGFLYNMVRILAGTLIGVGRGLIDPEEIPAMLEAKDRQAAGMTVPPQGLT 263

Query: 241 FDSVEY 246
              ++Y
Sbjct: 264 LMKIDY 269


>gi|168028382|ref|XP_001766707.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162682139|gb|EDQ68560.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 331

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 94/304 (30%), Positives = 151/304 (49%), Gaps = 60/304 (19%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G+QRQK   ++QG +E A     G+ V+   + RTD+GVHAL    
Sbjct: 11  RYLITVEYIGTRFLGFQRQKGKRTVQGCLESAFEKFIGQPVISAVSSRTDTGVHALANTC 70

Query: 63  HFDLVRE-----------WVPVILCKALNAYL---KISDTISILNLSIVDKQFHARFSAI 108
           H D+ R+             P ++  A+N +L   K +  ++++ +  V   FHAR+ A 
Sbjct: 71  HVDVERKSKRKPGEVMPPHEPRVVQTAINHFLHAQKDAGDMAVVGVQCVSPDFHARYRAQ 130

Query: 109 RRSYLYRIITRQAPLAL-EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R+Y YR++T    +++ +K +AW + + L+  +M  A + LVG HDF++FR+  CQA+S
Sbjct: 131 ERTYHYRVLTGNRQMSVFQKDQAWHVSEELNLTSMMEACKVLVGHHDFSSFRATGCQANS 190

Query: 168 PIRTIDHFDV----------------------------------------NSFGNLIEIR 187
           PIRT+D   V                                        +  G   ++R
Sbjct: 191 PIRTLDELHVCEMPAWPCFPSPEERQQSSQNAETKDLESTTSELKDPILTSKLGTSEKLR 250

Query: 188 VV-----ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
                  ARSFL+ Q+R  VG+LK VG G  T  D+++ L A+   +   +AP  GLY  
Sbjct: 251 CFVITARARSFLYHQVRLMVGTLKAVGCGDLTVQDVQRILDARTITQAPAMAPACGLYLA 310

Query: 243 SVEY 246
           +V+Y
Sbjct: 311 NVKY 314


>gi|254854197|ref|ZP_05243545.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL R2-503]
 gi|300763651|ref|ZP_07073649.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL N1-017]
 gi|258607589|gb|EEW20197.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL R2-503]
 gi|300515928|gb|EFK42977.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL N1-017]
          Length = 248

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 134/251 (53%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL A       IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQAMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ +AL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISEALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEY 246
           P+GLY   V+Y
Sbjct: 237 PQGLYLWRVDY 247


>gi|91789465|ref|YP_550417.1| tRNA pseudouridine synthase A [Polaromonas sp. JS666]
 gi|123059533|sp|Q126M3|TRUA_POLSJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91698690|gb|ABE45519.1| tRNA pseudouridine synthase A [Polaromonas sp. JS666]
          Length = 264

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 89/244 (36%), Positives = 126/244 (51%), Gaps = 6/244 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+GS Y GWQ Q +G+++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRIALGISYSGSAYEGWQSQLSGNTVQDKLESALARFAAQPVRTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD V         +  NA+L  SD I++     V   FH R SAI R Y Y ++    
Sbjct: 61  VHFDTVLHRDMGSWVRGTNAFLP-SD-IAVQWAREVPDTFHCRGSAIARRYAYVVLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--- 178
             ++E GR   + + LD   MR A  HLVG HDF++FR+  CQA SP++TI+  +++   
Sbjct: 119 RPSVEAGRVGWVYRPLDGAAMRQAITHLVGEHDFSSFRAAQCQAKSPVKTINRIEISERA 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +          A +FLH  IR+ +G L  +G G      L   + A+ R    P   P 
Sbjct: 179 GTGSKYWHFEFEANAFLHHMIRNIMGCLVAIGQGSHEPGWLLDVMAARSRDAAAPTFSPN 238

Query: 238 GLYF 241
           GLYF
Sbjct: 239 GLYF 242


>gi|221307961|ref|ZP_03589808.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221312282|ref|ZP_03594087.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221317216|ref|ZP_03598510.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221321479|ref|ZP_03602773.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767037|ref|NP_388029.2| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|321313820|ref|YP_004206107.1| tRNA pseudouridine synthase A [Bacillus subtilis BSn5]
 gi|239938721|sp|P70973|TRUA_BACSU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225184664|emb|CAB11924.2| pseudouridylate synthase I [Bacillus subtilis subsp. subtilis str.
           168]
 gi|291482520|dbj|BAI83595.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. natto
           BEST195]
 gi|320020094|gb|ADV95080.1| tRNA pseudouridine synthase A [Bacillus subtilis BSn5]
          Length = 247

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  + + + V  +GRTDSGVHA  
Sbjct: 1   MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAERWPYALNALL--PDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ ++MR AA+HL+G HDFT+F +   +    +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFSYRLNVQDMREAAKHLIGTHDFTSFCAAKTEVQDKVRTIYELDWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK +  +++  L+A+DR+  G  AP  GL
Sbjct: 179 TADGLQMRITGSGFLYNMVRIIAGTLLDAGIGKISPDEVKSMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLWNVYYD 246


>gi|312109293|ref|YP_003987609.1| tRNA pseudouridine synthase A [Geobacillus sp. Y4.1MC1]
 gi|311214394|gb|ADP72998.1| tRNA pseudouridine synthase A [Geobacillus sp. Y4.1MC1]
          Length = 248

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 88/241 (36%), Positives = 126/241 (52%), Gaps = 3/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G+ +FG+Q Q    ++QG +E+A+  +  G+ + V  +GRTD+GVHA  QV HFD 
Sbjct: 9   LSYDGTHFFGYQIQPGKRTVQGELEQALEQIHKGKAIRVTASGRTDAGVHAYGQVIHFDT 68

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                P    KALNA L   D I I +       FHARFSA  + Y Y++   Q      
Sbjct: 69  FLSLSPEQWKKALNALL--PDDIVIKDAQEAAPSFHARFSATAKEYRYKVRIAQERDVFL 126

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +   +  P  LD E M  A + + G HDFT+F S        +RTI   D+    +L+E 
Sbjct: 127 RHYCYHYPYPLDMEAMGRALRLIEGTHDFTSFCSAKTDVDDRVRTIYKADMTVRDDLLEF 186

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           R +   FL+  +R  VG++  VG GK +   +  AL A+DR+  G  APP+GLY   V Y
Sbjct: 187 RFIGNGFLYNMVRIIVGTILEVGQGKRSVDSISSALAAKDRRFAGKTAPPQGLYLWKVYY 246

Query: 247 S 247
            
Sbjct: 247 D 247


>gi|153938429|ref|YP_001392800.1| tRNA pseudouridine synthase A [Clostridium botulinum F str.
           Langeland]
 gi|152934325|gb|ABS39823.1| tRNA pseudouridine synthase A [Clostridium botulinum F str.
           Langeland]
 gi|295320780|gb|ADG01158.1| tRNA pseudouridine synthase A [Clostridium botulinum F str. 230613]
          Length = 246

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 133/241 (55%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA   + +F 
Sbjct: 8   LEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAKGYICNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++    P+A+
Sbjct: 68  TNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLNSSQPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N  G+ I+
Sbjct: 126 GRNYIFQFKNKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEINKKGDFIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  GL    V 
Sbjct: 186 FIITGDGFLYNMVRIMVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|317048970|ref|YP_004116618.1| tRNA pseudouridine synthase A [Pantoea sp. At-9b]
 gi|316950587|gb|ADU70062.1| tRNA pseudouridine synthase A [Pantoea sp. At-9b]
          Length = 268

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ+   S+Q  +EKA+  V    V V  AGRTD+GVH   QV HF+  
Sbjct: 14  IEYDGSRYYGWQRQQEVRSVQEKLEKALSKVANHDVSVFCAGRTDAGVHGTGQVVHFETT 73

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V + FHARFSA  R Y Y I   R  P  L 
Sbjct: 74  SQRADGAWTLGVNANL--PPDIAVRWVKAVPETFHARFSATARRYRYVIYNQRLRPAILG 131

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 132 SGVTHFY-HPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVMHLNVTRQGPYVIV 190

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  +G G    + +   L A+DR      A  EGLY  +V+Y
Sbjct: 191 DIKANAFVHHMVRNIVGSLMEIGCGNQPESWMATLLAAKDRTLAAATARAEGLYLVAVDY 250


>gi|308187626|ref|YP_003931757.1| pseudouridylate synthase I [Pantoea vagans C9-1]
 gi|308058136|gb|ADO10308.1| pseudouridylate synthase I [Pantoea vagans C9-1]
          Length = 267

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 90/240 (37%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +E+A+  V    V +  AGRTD+GVH   QV HF+  
Sbjct: 13  IEYDGSRYYGWQRQNEVRSVQEKVERALSKVADHPVSIFCAGRTDAGVHGTGQVVHFETT 72

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V  +FHARFSA  R Y Y I   R  P  L 
Sbjct: 73  SQRPDGAWTLGVNANLPAD--IAVRWVKAVPDEFHARFSATARRYRYLIYNQRLRPAVLA 130

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 131 QGVTHFY-HPLDAEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVIHLNVTRQGPYVIV 189

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  +G G    + +   L A+DR      A  EGLY  +V+Y
Sbjct: 190 DIKANAFVHHMVRNIVGSLMEIGCGNKPESWMATLLAAKDRTLAAATARAEGLYLVAVDY 249


>gi|154684666|ref|YP_001419827.1| tRNA pseudouridine synthase A [Bacillus amyloliquefaciens FZB42]
 gi|166228678|sp|A7Z0S0|TRUA_BACA2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|154350517|gb|ABS72596.1| TruA [Bacillus amyloliquefaciens FZB42]
          Length = 247

 Score =  149 bits (375), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 88/248 (35%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  T   V V+ +GRTDS VHA  
Sbjct: 1   MRVKCTIAYDGHLFNGYQVQPGKRTVQSELEKALAVIHKTDGRVPVYSSGRTDSDVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPGEKWPFALNALL--PDDIAVKTAEIADDGFHARFSAVQKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ + MR A++HLVG HDFT+F +        +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFAYPLNVQKMREASRHLVGTHDFTSFCAADTAVQDKVRTIYELDWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK++  D++  L+A+DR+  G  AP  GL
Sbjct: 179 TVDGLQMRITGNGFLYNMVRIIAGTLLDTGAGKFSPDDVKAMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  SV Y 
Sbjct: 239 YLWSVCYD 246


>gi|259500923|ref|ZP_05743825.1| tRNA pseudouridine synthase A [Lactobacillus iners DSM 13335]
 gi|302190624|ref|ZP_07266878.1| tRNA pseudouridine synthase A [Lactobacillus iners AB-1]
 gi|309803645|ref|ZP_07697735.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 11V1-d]
 gi|309804945|ref|ZP_07699003.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 09V1-c]
 gi|309806696|ref|ZP_07700691.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 03V1-b]
 gi|309808529|ref|ZP_07702428.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 01V1-a]
 gi|312871160|ref|ZP_07731258.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 3008A-a]
 gi|312872668|ref|ZP_07732733.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2062A-h1]
 gi|315653995|ref|ZP_07906911.1| tRNA pseudouridine synthase A [Lactobacillus iners ATCC 55195]
 gi|259167617|gb|EEW52112.1| tRNA pseudouridine synthase A [Lactobacillus iners DSM 13335]
 gi|308164243|gb|EFO66500.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 11V1-d]
 gi|308165705|gb|EFO67930.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 09V1-c]
 gi|308166876|gb|EFO69060.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 03V1-b]
 gi|308168357|gb|EFO70476.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 01V1-a]
 gi|311091710|gb|EFQ50089.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2062A-h1]
 gi|311093174|gb|EFQ51520.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 3008A-a]
 gi|315488691|gb|EFU78337.1| tRNA pseudouridine synthase A [Lactobacillus iners ATCC 55195]
          Length = 260

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 136/249 (54%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD     +P   +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A+DR++    AP  G
Sbjct: 179 QNGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKDVEDVEKIILAKDRQKARNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>gi|160941032|ref|ZP_02088370.1| hypothetical protein CLOBOL_05925 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435981|gb|EDP13748.1| hypothetical protein CLOBOL_05925 [Clostridium bolteae ATCC
           BAA-613]
          Length = 247

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q    +I+  + +A+  +  E + V GA RTDSGVHA   
Sbjct: 1   MKRIRLVVAYDGTQYHGWQIQPGAVTIESVLNEALTQLMREPIQVIGASRTDSGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD   +  P  +C ALN   ++ + I +     V   +H R     ++Y YRI+ R+
Sbjct: 61  VAVFDTESQMPPDKICMALNQ--RLPEDIRVQVSEEVPSDWHPRKCTCIKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
             + +E+  +      LD + M+ AA  L G HDF +F S+  Q +  +RT+   DV  +
Sbjct: 119 INMPMERLYSHFCYYKLDVDRMQAAANMLAGEHDFKSFCSVRTQVTDTVRTVYRIDVTRN 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IRV    FL+  +R   G+L  VG G   + D+   L+A+DR+  GP AP  GL
Sbjct: 179 ADDIITIRVTGNGFLYNMVRIIAGTLMAVGTGHIQAEDMPSILEAKDRRAAGPTAPARGL 238

Query: 240 YFDSVEYS 247
               ++Y 
Sbjct: 239 TLIEMKYE 246


>gi|295093665|emb|CBK82756.1| pseudouridylate synthase I [Coprococcus sp. ART55/1]
          Length = 247

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q NG +++  + K +  +  E + V GA RTDSGVHAL  
Sbjct: 3   MKRVKLIVAYDGTNYCGWQVQINGITVEEVLNKTLSELCHEDIKVIGASRTDSGVHALGN 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN   ++ + I I     V   FH R+    ++Y Y+I+ R+
Sbjct: 63  VAVFDTESGIPGEKFSFALNQ--RLPEDIRIQESCQVADDFHPRYCDTIKTYEYKILNRR 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  +  +   LD + M+ AA  LVG HDF +F S   Q  + +RTI    ++  
Sbjct: 121 FDMPTERLYSTFVYYPLDIDKMKRAAAVLVGEHDFKSFCSSRSQVENTVRTITDITIDKA 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IR+    FL+  +R  VG+L  +G G W    +E  L+A+DR + GP A  +GL 
Sbjct: 181 GDMIHIRISGNGFLYNMVRIIVGTLMKIGLGIWPEDCMESILEAKDRTKAGPKAEAKGLT 240

Query: 241 FDSVEY 246
              ++Y
Sbjct: 241 LVEIKY 246


>gi|304398239|ref|ZP_07380113.1| tRNA pseudouridine synthase A [Pantoea sp. aB]
 gi|304354105|gb|EFM18478.1| tRNA pseudouridine synthase A [Pantoea sp. aB]
          Length = 267

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 90/240 (37%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +E+A+  V    V +  AGRTD+GVH   QV HF+  
Sbjct: 13  IEYDGSRYYGWQRQNEVRSVQEKVERALSKVADHPVSIFCAGRTDAGVHGTGQVVHFETT 72

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V  +FHARFSA  R Y Y I   R  P  L 
Sbjct: 73  SQRPDGAWTLGVNANL--PPDIAVRWVKAVPDEFHARFSATARRYRYLIYNQRLRPAVLA 130

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 131 QGVTHFY-HPLDAEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVIHLNVTRQGPYVIV 189

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  +G G    + +   L A+DR      A  EGLY  +V+Y
Sbjct: 190 DIKANAFVHHMVRNIVGSLMEIGCGNKPESWMATLLAAKDRTLAAATARAEGLYLVAVDY 249


>gi|254496537|ref|ZP_05109407.1| tRNA pseudouridine synthase A [Legionella drancourtii LLAP12]
 gi|254354236|gb|EET12901.1| tRNA pseudouridine synthase A [Legionella drancourtii LLAP12]
          Length = 262

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    ++Q ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVLEYDGSHYHGWQAQTGLHTVQQALEHALSKVADCPISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  +E          N++L  S  + +     + + F+AR+SA  R Y Y I     
Sbjct: 61  VHFDTDKERSIRAWIHGANSFL--SKDVCVKWGKELSETFNARYSATARRYRYVIYNGAI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL +       + LD   M  AAQ L+G +DFT+FRS+ CQ+++P+R I    V    
Sbjct: 119 RPALLRSNVTWQYRQLDHRLMHQAAQLLLGENDFTSFRSVECQSNTPMRNIHKLQVTRTN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A +FLH  +R+  G L  VG GK   + +++ L+A+DR+     AP  GLY 
Sbjct: 179 DLVIIDITANAFLHHMVRNIAGVLIAVGSGKHPVSWVDEVLKARDRRLGAETAPAYGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VQVTY 243


>gi|163816009|ref|ZP_02207379.1| hypothetical protein COPEUT_02189 [Coprococcus eutactus ATCC 27759]
 gi|158448819|gb|EDP25814.1| hypothetical protein COPEUT_02189 [Coprococcus eutactus ATCC 27759]
          Length = 254

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +++  + K +  +  E + V GA RTDSGVHAL  
Sbjct: 10  MKRVKLVVAYDGTNYCGWQVQINGITVEEVLNKTLSELCHENIKVIGASRTDSGVHALGN 69

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN   ++ + I I     V   FH R+    ++Y Y+I+ R+
Sbjct: 70  VAVFDTESGIPGEKFSFALNQ--RLPEDIRIQESCQVADDFHPRYCDTIKTYEYKILNRR 127

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  +  +   LD + M+ AA  LVG HDF +F S   Q  + +RTI    ++  
Sbjct: 128 FDMPTERLYSTFVYYPLDIDKMKRAAAVLVGEHDFNSFCSTRSQVENTVRTITDITIDKV 187

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IR+    FL+  +R  VG+L  +G G W    +E  L A+DR + GP A  +GL 
Sbjct: 188 GDMIHIRISGNGFLYNMVRIIVGTLMKIGLGIWPEDCMESILAAKDRTKAGPKAEAKGLT 247

Query: 241 FDSVEY 246
              ++Y
Sbjct: 248 LVEIKY 253


>gi|161521167|ref|YP_001584594.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
 gi|189352656|ref|YP_001948283.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
 gi|42559801|sp|Q83WJ5|TRUA_BURM1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|28971662|dbj|BAC65262.1| tRNA pseudouridine synthase [Burkholderia multivorans]
 gi|160345217|gb|ABX18302.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
 gi|189336678|dbj|BAG45747.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
          Length = 270

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G+++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGNTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFLP--PTVAVQWAKSMPDAFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLDGRAGWIHTPLDDDAMRAAAAHLLGEHDFSAFRSSECQSKTPVKHLYEIDIRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  +   L  +DR    P    +GLY 
Sbjct: 179 HFLHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGRDRNRAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|255025629|ref|ZP_05297615.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J2-003]
          Length = 248

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 133/251 (52%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ KAL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEY 246
           P+GLY   V+Y
Sbjct: 237 PQGLYLWRVDY 247


>gi|239623391|ref|ZP_04666422.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522357|gb|EEQ62223.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 247

 Score =  148 bits (374), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 87/248 (35%), Positives = 132/248 (53%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q    +I+  + +A+  + GE V V GA RTDSGVHA   
Sbjct: 1   MKRVRLVVAYDGTHYHGWQIQPGKVTIESRLNEALTSLLGEPVQVIGASRTDSGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C ALN   ++ + I + +   VD  +H R     ++Y YRI+ R+
Sbjct: 61  VAVFDTSHRMPADRICMALNQ--RLPEDIRVQSSEEVDPDWHPRKCRCVKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
             + +++  +     +LD E M+ AA  LVG HDF +F S+  Q +  +RTI   +V   
Sbjct: 119 IEMPMQRFYSHFCYFNLDLEKMQKAAGLLVGEHDFKSFCSVRTQVTDTVRTIYSIEVKRD 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IRV    FL+  +R   G+L  VG G+    D+   L+A+DR+  GP AP  GL
Sbjct: 179 EEDMIGIRVTGNGFLYNMVRIIAGTLMAVGMGQIAPEDMGAILEARDRRAAGPTAPARGL 238

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 239 TLIQMEYD 246


>gi|169335662|ref|ZP_02862855.1| hypothetical protein ANASTE_02082 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258400|gb|EDS72366.1| hypothetical protein ANASTE_02082 [Anaerofustis stercorihominis DSM
           17244]
          Length = 244

 Score =  148 bits (374), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 127/242 (52%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + IEY+G  Y GWQ Q NG S++  ++ AI  +  E V ++G+GRTDSGVHAL Q A F
Sbjct: 5   LITIEYDGKNYVGWQMQNNGISVEEKVKTAIEKLVKEEVKLYGSGRTDSGVHALGQAASF 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     L   +N++L   + I ++     ++ FHAR+SA  + Y+Y I  R     
Sbjct: 65  YTNSNISADKLPYGINSFL--PEDIRVIKAEEKEEDFHARYSAKGKEYVYLIYNRSIMNP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           + KGRA  +   LD + M+ A++ L+G HDF  F        S +R I   D+    +LI
Sbjct: 123 IYKGRASHVFYKLDLDKMKRASKSLIGIHDFAGFMGSGSDVKSTVREIYDIDITKDNDLI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I++    FL+  +R  V SL  +G G++    +E+ L+ + R      AP  GLY + V
Sbjct: 183 KIKISGSGFLYNMVRIIVASLIDIGRGRFDENRIEEILETKQRSMANVTAPAVGLYLNKV 242

Query: 245 EY 246
            Y
Sbjct: 243 FY 244


>gi|307705317|ref|ZP_07642179.1| tRNA pseudouridine synthase A [Streptococcus mitis SK597]
 gi|307621104|gb|EFO00179.1| tRNA pseudouridine synthase A [Streptococcus mitis SK597]
          Length = 249

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FD 176
             P   + +  A   P  LD E M++A + L G HDFT F +        IRTI      
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTNVEDKIRTITEASLR 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A  
Sbjct: 178 VDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIDLILEKKDRQLAGPTAAS 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|170756303|ref|YP_001783087.1| tRNA pseudouridine synthase A [Clostridium botulinum B1 str. Okra]
 gi|169121515|gb|ACA45351.1| tRNA pseudouridine synthase A [Clostridium botulinum B1 str. Okra]
          Length = 246

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 133/241 (55%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA   + +F 
Sbjct: 8   LEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAKGYICNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++    P+A+
Sbjct: 68  TNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLNSSQPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N  G+ I+
Sbjct: 126 GRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEINKKGDFIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  GL    V 
Sbjct: 186 FIITGDGFLYNMVRIMVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|255284006|ref|ZP_05348561.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
 gi|255265459|gb|EET58664.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
          Length = 245

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q N  +I+  +   +  + GE + V GA RTD+GVHAL  
Sbjct: 1   MKRVKLIVAYDGTNYSGWQIQPNAVTIESMLNLHLSELLGEPIRVIGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  A+N   ++   I I +   V   FH RF    ++Y YRI+ R+
Sbjct: 61  VAVFDTSARMPAEKISYAMNT--RLPQDIRIQDSCEVAADFHPRFCKTIKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +      LD ENMR A  +LVG HDF +  +   +  + +RTI   D+   
Sbjct: 119 FPDPTRRLYSLFYYYPLDVENMRRALAYLVGEHDFKSLCTHKEEVENTVRTIYEADIQKD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IR+    FL+  +R  VG+L  VG G +    +++ L A++R+  G  APP+GL 
Sbjct: 179 GDMISIRISGNGFLYNMVRIIVGTLLRVGSGYYPPEYMQELLAAKNRQAAGETAPPQGLT 238

Query: 241 FDSVEY 246
              + Y
Sbjct: 239 LLEIRY 244


>gi|241759308|ref|ZP_04757414.1| tRNA pseudouridine synthase A [Neisseria flavescens SK114]
 gi|241320444|gb|EER56741.1| tRNA pseudouridine synthase A [Neisseria flavescens SK114]
          Length = 270

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  
Sbjct: 1   MQRWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALSSIAGEQINTIVAGRTDTGVHATA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           + +NA+L   D +++L    V   FHARF A  R Y Y + + 
Sbjct: 61  QVVHFDTSVSRPEQAWVRGVNAHLP--DGVAVLVAQKVAPHFHARFDAYGRHYRYLLESS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GR       LD   MR AA  L G HDF++FR+  CQA SPI+T+    ++ 
Sbjct: 119 PVRSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPIKTLYRTSISG 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + + +   +FLH  +R+ +G+L  VG G+ +  + E    A+ R +  P    +GL
Sbjct: 179 TSRYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFESVFHAKSRLKAPPTFMSDGL 238

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 239 YLTGVDY 245


>gi|283795894|ref|ZP_06345047.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
 gi|291076529|gb|EFE13893.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
          Length = 275

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 86/262 (32%), Positives = 141/262 (53%), Gaps = 23/262 (8%)

Query: 6   MIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           ++++Y+GS Y GWQ+Q N  ++IQG +E  +  + GE V +HG+GRTD+GVHAL QVA+F
Sbjct: 7   IVLQYDGSRYDGWQKQGNTKNTIQGKLEAVLEKLAGEPVEIHGSGRTDAGVHALGQVANF 66

Query: 65  DLVREWVPVILCKA--------------------LNAYLKISDTISILNLSIVDKQFHAR 104
            L    +  ++ K                     LN YL   + I++++   V ++FH+R
Sbjct: 67  RLEERCLEELVDKTPEKKENGGKASSVSAAVMDYLNRYL--PEDIAVISAMEVPERFHSR 124

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
            +A+ ++YLY+I T       E+   + + + LD   M+ AA+ L+G HDF  F S    
Sbjct: 125 LNAVEKTYLYQIETAGRKNVFERKYIYGLGEELDLLAMKEAAKLLLGSHDFRAFSSAKRM 184

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
             S +R +   +++  G+ + +      FL+  +R   G+L  +G  + T   + KAL++
Sbjct: 185 KKSTVRELRKIEIHRDGSRVLLEFTGNGFLYNMVRILTGTLIEIGLHRRTVDSVRKALES 244

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
           QDR+  G  AP EGL   SV Y
Sbjct: 245 QDRENAGFTAPAEGLLLKSVRY 266


>gi|217966203|ref|YP_002351881.1| tRNA pseudouridine synthase A [Listeria monocytogenes HCC23]
 gi|254789639|sp|B8DB42|TRUA_LISMH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217335473|gb|ACK41267.1| tRNA pseudouridine synthase A [Listeria monocytogenes HCC23]
 gi|307572187|emb|CAR85366.1| tRNA pseudouridine synthase A [Listeria monocytogenes L99]
          Length = 248

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 133/251 (52%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRDFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ KAL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEY 246
           P+GLY   V+Y
Sbjct: 237 PQGLYLWRVDY 247


>gi|220915529|ref|YP_002490833.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219953383|gb|ACL63767.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 245

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 123/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +      V  AGRTD+GVHA  QV  F 
Sbjct: 6   LVLEYDGTAYVGWQVQPNGPSIQAEVERALATLHKAPRRVTAAGRTDAGVHARGQVVSFP 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             R          +NA L     +++   S+    F AR SA  + Y Y I        L
Sbjct: 66  EERPLPVKAYVMGMNALL--PPDVAVRAASLAPDGFDARRSARGKRYRYVIENLPTRAPL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNSFGNLI 184
            + +AW     L+  N+R AA HLVGRHDF  F++  C     +R +   D V   G  I
Sbjct: 124 TRLQAWQHFHPLELANVREAAAHLVGRHDFAAFQASDCACEHAVREVRRLDVVGEGGGRI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E+ + A +F+   +R+ VG+L  VG G+     +   L   DR E GP APP+GL+ + V
Sbjct: 184 EVVIEATAFVKHMVRNIVGTLVEVGRGRRAPGSMLDLLARGDRTEAGPTAPPQGLFLEEV 243

Query: 245 EY 246
            Y
Sbjct: 244 FY 245


>gi|148381387|ref|YP_001255928.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           3502]
 gi|153931537|ref|YP_001385762.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           19397]
 gi|153934471|ref|YP_001389169.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. Hall]
 gi|148290871|emb|CAL85007.1| tRNA pseudouridine synthase [Clostridium botulinum A str. ATCC
           3502]
 gi|152927581|gb|ABS33081.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           19397]
 gi|152930385|gb|ABS35884.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. Hall]
          Length = 246

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 133/241 (55%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA   + +F 
Sbjct: 8   LEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHARGYICNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++    P+A+
Sbjct: 68  TNTKIPPENLQKVINNIL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLNSSKPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N  G+ I+
Sbjct: 126 GRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEINKKGDFIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  GL    V 
Sbjct: 186 FIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|322807772|emb|CBZ05347.1| tRNA pseudouridine synthase A [Clostridium botulinum H04402 065]
          Length = 246

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 133/241 (55%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA   + +F 
Sbjct: 8   LEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAKGYICNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++    P+A+
Sbjct: 68  TNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLNSSQPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N  G+ I+
Sbjct: 126 GRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEINKKGDFIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  GL    V 
Sbjct: 186 FIITGDGFLYNMVRIIVGTLIEIGLNKRKPEYIKYVIKSKDRTKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|325107879|ref|YP_004268947.1| tRNA pseudouridine synthase A [Planctomyces brasiliensis DSM 5305]
 gi|324968147|gb|ADY58925.1| tRNA pseudouridine synthase A [Planctomyces brasiliensis DSM 5305]
          Length = 278

 Score =  148 bits (373), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 88/260 (33%), Positives = 133/260 (51%), Gaps = 21/260 (8%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y+GSGY+GWQ Q +  +IQ  +E+AI  +TG    V GAGRTD+GVHA+ QVA F 
Sbjct: 8   LTLSYDGSGYYGWQVQPDRPTIQEHLERAIGNITGTPSRVAGAGRTDTGVHAIGQVACFR 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       AL +  ++ D I I         FHA +++  + Y Y ++  + P   
Sbjct: 68  TESNIPAERFRPALQS--QLPDDIVIWKSEEAADDFHAGYASRWKQYRYLVLNEEIPRPQ 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN------- 178
            +  A  I   LD + M  AA  LVG+HDF +F S     ++ +RT+ H  VN       
Sbjct: 126 MRRYATRIGTRLDLDAMNEAASALVGKHDFRSFESQFPNKATSVRTVLHCRVNEAETCPL 185

Query: 179 ------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
                       + G  + + + A  FL+  +R+ +G+L  +G G W ++  ++ L+A D
Sbjct: 186 WQPGLGGQRFGQAVGRCVYLDIAADGFLYNMVRAIMGTLLKIGIGSWPASAGKEVLEAMD 245

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R+  GP APPEGLY   VEY
Sbjct: 246 RRVAGPTAPPEGLYLMHVEY 265


>gi|225376773|ref|ZP_03753994.1| hypothetical protein ROSEINA2194_02415 [Roseburia inulinivorans DSM
           16841]
 gi|225211399|gb|EEG93753.1| hypothetical protein ROSEINA2194_02415 [Roseburia inulinivorans DSM
           16841]
          Length = 247

 Score =  148 bits (373), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 129/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q NG +I+  + + +  + GE + V GA RTDSGVH++  
Sbjct: 1   MKRVKLIVAYDGTNYCGWQVQPNGITIEQVLNENLSKLLGEEITVTGASRTDSGVHSMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN   ++ + I + +   V   +H R+   R++Y YRI+ R 
Sbjct: 61  VAIFDTETRMPADKISFALNQ--RLPEDIVVQDSCEVPSDWHPRYQVSRKTYEYRILNRT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +   +     LD + M+ AA +LVG HDF +F ++  Q  +  RTI   +V   
Sbjct: 119 FRMPNRRLDTYFYHHKLDVDKMKQAASYLVGEHDFKSFCAVGAQVKTTTRTIYSCEVEKD 178

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           GN +I IRV    FL+  +R   G+L  VG G+    ++ + L  +DR   GP AP  GL
Sbjct: 179 GNDIITIRVTGNGFLYNMVRIIAGTLIRVGGGEMAPDEIPQILGKKDRTAAGPTAPAHGL 238

Query: 240 YFDSVEY 246
               +EY
Sbjct: 239 TMMGIEY 245


>gi|331002224|ref|ZP_08325743.1| tRNA pseudouridine synthase A [Lachnospiraceae oral taxon 107 str.
           F0167]
 gi|330411318|gb|EGG90734.1| tRNA pseudouridine synthase A [Lachnospiraceae oral taxon 107 str.
           F0167]
          Length = 245

 Score =  148 bits (373), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ+Q NG +I+  +  AI  +TGE + V GA RTDSGVHA   
Sbjct: 1   MRRIRLIVSYDGTNYCGWQKQPNGITIEEVLNNAITKLTGEDIEVIGASRTDSGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD            A+N   ++ + I I     V+  +H R +   ++Y YRI+ R+
Sbjct: 61  IAVFDTNARIAADKFAFAINQ--RLPEDIRIQYSDEVESGWHPRKNDCIKTYTYRILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  A     +LD E MR A+ + +G HDFT+F S   QASSPIRTI   ++   
Sbjct: 119 IDIPTERLYAHFCYFNLDVEKMREASGYFIGTHDFTSFCSQKSQASSPIRTIFSLEILQD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ I +    FL+  IR   G+L  VG G +  + + + ++A++RK  G   P +GL 
Sbjct: 179 EDMVTIVIRGDGFLYNMIRIIAGTLIKVGMGVYPPSHITEIMKAKNRKLAGQTMPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LVEIEY 244


>gi|294669057|ref|ZP_06734143.1| tRNA pseudouridine synthase A [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291309049|gb|EFE50292.1| tRNA pseudouridine synthase A [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 326

 Score =  148 bits (373), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 86/245 (35%), Positives = 131/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS +FGWQ+Q +G  S+Q ++E A+  + GE V V  AGRTD+GVHA  QV
Sbjct: 62  RWALTLSYDGSRFFGWQKQADGVVSVQAALESALSQIAGETVNVVAAGRTDTGVHATAQV 121

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       + +N+ L     +++     V   FHARF A  R Y Y + +   
Sbjct: 122 VHFDTAAERGEQSWIRGVNSLLP--QGVAVWQAKRVASHFHARFDAFGRRYRYVLQSSPV 179

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L   R       LD   M+ AA  LVG HDF++FR+  CQA SP++T+    ++   
Sbjct: 180 RSPLLAARVGWTHTPLDFAAMQAAAALLVGEHDFSSFRASQCQAKSPVKTLYSVVLHGTP 239

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ VG+L  VG+G+ +     + L  + R +  P   P+GLY 
Sbjct: 240 QLMALDLHGNAFLHHMVRNIVGALVYVGNGRLSVQGFAELLAEKSRLKAPPTFMPDGLYL 299

Query: 242 DSVEY 246
             V+Y
Sbjct: 300 TGVDY 304


>gi|291522074|emb|CBK80367.1| pseudouridylate synthase I [Coprococcus catus GD/7]
          Length = 247

 Score =  148 bits (373), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 87/243 (35%), Positives = 130/243 (53%), Gaps = 4/243 (1%)

Query: 6   MIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           ++IEY+GS Y GWQR  + +G +IQG +E  +  +TGE V + GAGRTD+GVHA  QVA+
Sbjct: 7   LLIEYDGSRYDGWQRLGKGHGVTIQGKLEDVLSKMTGEQVELIGAGRTDAGVHAYEQVAN 66

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F          +   LN YL     I++  +  V ++FH+R++A  + YLYRI     P 
Sbjct: 67  FHTNSNMKCWEMKYYLNRYL--PGDIAVNRVDDVPERFHSRYNAKAKKYLYRIAIGDVPC 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
             ++   W     LD   M+ AA  LVG HDF  F S      S +R I   D+ +    
Sbjct: 125 VFDRKYTWYCFDKLDVTAMKKAAALLVGEHDFKAFCSNKRTNKSTVREIYDIDIYADTRE 184

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           ++I V    FL+  +R  VG+L  VG G+    ++   L++++R + G  A  +GL+   
Sbjct: 185 LQITVYGNGFLYNMVRIIVGTLIEVGKGERRPEEMTAILESRERTKAGATAAAQGLFLQE 244

Query: 244 VEY 246
           VEY
Sbjct: 245 VEY 247


>gi|311745793|ref|ZP_07719578.1| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
 gi|126575993|gb|EAZ80271.1| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
          Length = 252

 Score =  148 bits (373), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 96/255 (37%), Positives = 131/255 (51%), Gaps = 26/255 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y G+ Y GWQ Q N  S+Q  IE A+       + V G+GRTD+GVHA  QV 
Sbjct: 6   RYFLELSYKGTKYHGWQIQNNAFSVQECIESALSTYFRSPITVMGSGRTDTGVHAKMQVC 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFDL  +       KA+N  L I   ISI+++  V    HARF A+ RSY+YRII ++ P
Sbjct: 66  HFDLADDIDYGKFLKAINGILPID--ISIMSIRQVTPNAHARFDAVSRSYVYRIIFQKNP 123

Query: 123 LALEKGRAW---LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
                G AW    IP   D E M +AA+ L+   DF  F  +H +       + HF  D+
Sbjct: 124 FL--DGLAWHSYFIP---DLEKMNLAAETLLKHDDFECFSKVHTE-------VKHFRCDI 171

Query: 178 NSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
            S       G L+   + A  FL   +R+ VG+L  VG GK    D+EK + ++DR   G
Sbjct: 172 KSCSWEQKDGELL-FHITANRFLRGMVRAIVGTLMEVGLGKKAPEDMEKIILSKDRSNAG 230

Query: 232 PLAPPEGLYFDSVEY 246
             AP  GL+   + Y
Sbjct: 231 KSAPARGLFLSRIIY 245


>gi|225388793|ref|ZP_03758517.1| hypothetical protein CLOSTASPAR_02531 [Clostridium asparagiforme
           DSM 15981]
 gi|225045068|gb|EEG55314.1| hypothetical protein CLOSTASPAR_02531 [Clostridium asparagiforme
           DSM 15981]
          Length = 250

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 131/249 (52%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y MI++Y+G+ Y GWQRQ N   +IQG +E  +  +  E + VHG+GRTD GVHA  Q
Sbjct: 1   MNYKMILQYDGTRYDGWQRQGNTDRTIQGKLEAVLGRLAEETLEVHGSGRTDGGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F L +   P  +   LN YL   + I +L L+   ++FH+R +A R++Y Y+I    
Sbjct: 61  VANFHLKQAREPEEIRAYLNRYL--PEDICVLELTAAPERFHSRLNACRKTYRYQIWMDG 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++   + + K LD   M  AA  L+G HDF +F        S +RTI    +   
Sbjct: 119 KTDVFQRDYFYGLGKQLDIGQMERAAGTLLGTHDFKSFCGNKKMKKSTVRTITAIRLIRL 178

Query: 181 --GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + + V    FL   +R   G+L  VG GK  +  LE  L+ ++R   G  APPEG
Sbjct: 179 CDGKALAVDVTGNGFLQQMVRILAGTLIEVGLGKREADSLEAVLELKERSAAGFTAPPEG 238

Query: 239 LYFDSVEYS 247
           L   +V+Y 
Sbjct: 239 LCLMNVQYE 247


>gi|323706484|ref|ZP_08118045.1| tRNA pseudouridine synthase A [Thermoanaerobacterium xylanolyticum
           LX-11]
 gi|323534204|gb|EGB23994.1| tRNA pseudouridine synthase A [Thermoanaerobacterium xylanolyticum
           LX-11]
          Length = 239

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 131/242 (54%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY+G+ Y GWQ QKN  ++Q  I KAI  +T E V + G+ RTD+GVHAL QVA+F 
Sbjct: 1   MVIEYDGTNYHGWQIQKNAVTVQEVITKAIKKITSEDVNLIGSSRTDAGVHALNQVANF- 59

Query: 66  LVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +    +P+  +  ALN+ L     I I N    D  FH+R+SA  + Y Y I  R+    
Sbjct: 60  ISNCNIPLSKMPNALNSVL--PKDIVIKNAYEADMDFHSRYSAKGKRYKYIIYNRKFNSP 117

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           + +  +W I   LD + M  +  +L G HDF+ F+S        IRT+    +      +
Sbjct: 118 VYRNYSWHISDELDLDKMIESLTYLKGTHDFSAFKSSGSSVKDSIRTVRDISLRKNDFNV 177

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E  + A  FL+  +R  VG++  VG GK     +++ L+++DR   G  APP+GL+   +
Sbjct: 178 EFEIEADGFLYNMVRIIVGTIVDVGIGKINPIHVKEILESKDRCMAGKTAPPQGLFLTKI 237

Query: 245 EY 246
            Y
Sbjct: 238 YY 239


>gi|291524335|emb|CBK89922.1| pseudouridylate synthase I [Eubacterium rectale DSM 17629]
 gi|291527615|emb|CBK93201.1| pseudouridylate synthase I [Eubacterium rectale M104/1]
          Length = 244

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  MI+ Y+G+ Y GWQ Q NG +I+  + + +  +  E + V GA RTD+GVH+L  V
Sbjct: 1   MRVKMIVAYDGTNYCGWQIQPNGITIEQVLNEHLSRLLKEDIKVTGASRTDAGVHSLGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD         +  ALN   K+ + I +++   V   FH RFS  R++Y YRI+  + 
Sbjct: 61  CMFDTNTRMPAEKISYALNQ--KLPEDIVVVDSCEVSDDFHPRFSKSRKTYEYRILNARF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   +     LD E M  AA++L+G HDF +F S + QA + +RTI    V+  G
Sbjct: 119 RNPTRRLDTYFYHYPLDTEKMSEAAKYLIGEHDFASFCSANSQAQTTVRTIYDCTVSKAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IRV    FL+  +R   G+L  +G     +  ++  + A DR   GP AP  GL  
Sbjct: 179 DIITIRVTGNGFLYNMVRIIAGTLVKIGGSDMPADAMKDIIAATDRAAAGPTAPAHGLTM 238

Query: 242 DSVEY 246
             ++Y
Sbjct: 239 IGLKY 243


>gi|255571004|ref|XP_002526453.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223534233|gb|EEF35948.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 372

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 103/315 (32%), Positives = 149/315 (47%), Gaps = 71/315 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G Q+Q NG ++ G +E+A     G+ V V  + RTD+GVHAL  V 
Sbjct: 55  RYLIAVEYIGTKFAGSQKQLNGRTVVGVLEEAFCKFIGQQVSVSLSSRTDAGVHALSNVC 114

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+ ++  I + ++  V   FHARF A  R
Sbjct: 115 HVDIERISKRKPGEVLPPHEPAVVRRAVNHFLQKNEGDIMVTDVRCVPSDFHARFKAQER 174

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR ++   PL+  EK RAW + + LD   M+ A + LVG HDF++FR+  CQA SPI
Sbjct: 175 TYFYRFLSGPEPLSTFEKDRAWHVLEDLDIVAMQEACKVLVGHHDFSSFRASGCQAKSPI 234

Query: 170 RTI------------------------------------------DHFDVN----SFGNL 183
           RT+                                           H + N    SFG  
Sbjct: 235 RTLAEISVSEVASTLYFPSITEREQNCENGENSCCKKFKTDLPMGSHSNTNVAESSFGET 294

Query: 184 ---IEIRVVARSFLHT---------QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                IR   R F+ T         Q+R  VG LK VG G  T++D+E+ L A+      
Sbjct: 295 DLGFGIRRRHRCFVVTARARSFLYHQVRLLVGVLKSVGIGDLTTSDVERILSAKSVTAAS 354

Query: 232 PLAPPEGLYFDSVEY 246
           P+AP  GLY   V+Y
Sbjct: 355 PMAPARGLYLGHVKY 369


>gi|312874027|ref|ZP_07734062.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2052A-d]
 gi|312874727|ref|ZP_07734746.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2053A-b]
 gi|325912360|ref|ZP_08174756.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 143-D]
 gi|329920629|ref|ZP_08277316.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 1401G]
 gi|311089472|gb|EFQ47897.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2053A-b]
 gi|311090367|gb|EFQ48776.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2052A-d]
 gi|325475831|gb|EGC79001.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 143-D]
 gi|328935887|gb|EGG32347.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 1401G]
          Length = 260

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 88/249 (35%), Positives = 136/249 (54%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD     +P   +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A++R++    AP  G
Sbjct: 179 QHGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKEVEDVEKIILAKNRQQVRNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>gi|297618350|ref|YP_003703509.1| tRNA pseudouridine synthase A [Syntrophothermus lipocalidus DSM
           12680]
 gi|297146187|gb|ADI02944.1| tRNA pseudouridine synthase A [Syntrophothermus lipocalidus DSM
           12680]
          Length = 244

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   ++EY G+ Y G+QRQ  G +I+G +E AI  +TGE V V  AGRTD+GVHAL Q
Sbjct: 1   MNRIKALVEYEGTRYSGFQRQPRGLTIEGELEAAICKLTGERVKVLAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD      P     ALN+ L  SD I +L      + FH R+ A  ++Y Y I  ++
Sbjct: 61  VIAFDTESPIPPERFAPALNSVLP-SD-IRVLKSEKAKEGFHPRYQARAKAYRYLIYRQE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A+  P+ LD   M  AA+++ G HDF  F +      + +RT+    +N  
Sbjct: 119 EGRTFYRNLAYYYPQPLDLPAMAKAARYMEGTHDFMAFCASGSGVRNYVRTVFEVSINEK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              ++I V    FL+  +R  VG+L  VG  +    ++E+ L ++DR+  GP  P  GLY
Sbjct: 179 PPFLQIDVCGDGFLYNMVRIMVGTLLEVGRKRLAPEEVEQILLSRDRQRAGPTVPACGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LKRVFY 244


>gi|221196945|ref|ZP_03569992.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2M]
 gi|221203615|ref|ZP_03576634.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2]
 gi|221177549|gb|EEE09977.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2]
 gi|221183499|gb|EEE15899.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2M]
          Length = 270

 Score =  148 bits (373), Expect = 8e-34,   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   MRIALGIQYDGAAFCGWQAQPHGNTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFLP--PTVAVQWAKPMPDAFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLDGRAGWIHTPLDDDAMRAAAAHLLGEHDFSAFRSSECQSKTPVKHVYEIDIRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  +   L   DR    P    +GLY 
Sbjct: 179 HFLHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGCDRNRAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|116749101|ref|YP_845788.1| tRNA pseudouridine synthase A [Syntrophobacter fumaroxidans MPOB]
 gi|116698165|gb|ABK17353.1| tRNA pseudouridine synthase A [Syntrophobacter fumaroxidans MPOB]
          Length = 261

 Score =  147 bits (372), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 134/246 (54%), Gaps = 5/246 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + +I+EY+GS Y GWQRQ    +IQ  +E  + ++    V V  +GRTD+GVHA  QV +
Sbjct: 12  FKLILEYDGSHYHGWQRQLGVLTIQEVLESRLEVMLQSPVGVRASGRTDAGVHACGQVVN 71

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F +     P  + + +N+ L     I +L+  +  + FHARFSA  ++Y Y I+ R    
Sbjct: 72  FHVHTRLRPEEILRGINSLL--PPDIVVLHAEVAAESFHARFSATGKTYEYHILNRPIRS 129

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           AL++  AW +P+ L+ + MR     L+GRHDF  F +   +  S  RTI   D++   N 
Sbjct: 130 ALQRRYAWHVPQPLEPQRMRECLGSLLGRHDFAAFMASGSKVKSTERTIRRADLDCLEN- 188

Query: 184 IEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            E+R+V  A  FL   +R+ VG++  VG G     +    L ++DRK  G  AP  GL+ 
Sbjct: 189 GEMRLVFEANGFLRHMVRNLVGTIVEVGRGVRAPEEFLDILSSRDRKRAGMTAPAHGLFL 248

Query: 242 DSVEYS 247
            +V Y+
Sbjct: 249 TAVHYT 254


>gi|3915176|sp|Q45557|TRUA_BACSV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|289265|gb|AAA73188.1| unknown [Bacillus sp. KSM-64]
          Length = 244

 Score =  147 bits (372), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 133/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y ++I+Y+G  Y GWQR  NG ++IQG IE  +  + G  + + G+GRTD+GVHAL 
Sbjct: 1   MNNYKLMIQYDGGRYKGWQRLGNGENTIQGKIETVLSEMVGRKIEIIGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+  L   +    + + LN YL     IS+  +++V  +FH+R++A  ++YLY+I   
Sbjct: 61  QVANVKLSENFTVKEVKEYLNRYL--PHDISVTEVTLVPDRFHSRYNAKDKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  +  I K L  +NM  A+Q  VG HDFT F +   +  +  RTI    +  
Sbjct: 119 DYTHPFMRKYSLHIEKKLHIDNMVKASQLFVGEHDFTAFSNAKSKKKTNTRTIHSITIQD 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I+IRV    FL+  +R  VG+L  VG G+     +   L+++DR + G  A   GL
Sbjct: 179 NQGFIDIRVCGDGFLYNMVRKMVGTLIEVGLGEKEPEQVLTILESKDRSQAG-FADATGL 237

Query: 240 YFDSVEY 246
           Y + + +
Sbjct: 238 YLEGISF 244


>gi|330502915|ref|YP_004379784.1| tRNA pseudouridine synthase A [Pseudomonas mendocina NK-01]
 gi|328917201|gb|AEB58032.1| tRNA pseudouridine synthase A [Pseudomonas mendocina NK-01]
          Length = 287

 Score =  147 bits (372), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 97/254 (38%), Positives = 131/254 (51%), Gaps = 20/254 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           R  + +EY G+ Y G+QRQ    +SIQG +E A+  V G   V +H AGRTD+ VH+  Q
Sbjct: 19  RVALGLEYKGARYRGFQRQGGKVASIQGCLEDALSKVAGGAPVTIHCAGRTDASVHSSGQ 78

Query: 61  VAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD   E     WV       + A + +   IS+    ++   FHARFSA+ R Y Y 
Sbjct: 79  VVHFDTTVERSLHAWV-------MGANMNLPSDISVTWAKVMPAHFHARFSAMARRYRYV 131

Query: 116 IIT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           I     R A +A E    W   + LD   MR AA  LVG HDF+ FR+  CQA SPI+T+
Sbjct: 132 IYNDPIRPAHMAEEV--TW-NHRPLDVARMREAALALVGTHDFSAFRATRCQAKSPIKTV 188

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            H  +   G  I + + A +FLH  +R+  G L  +G G+       + L+  DR   G 
Sbjct: 189 HHLQLIEHGRFIVLDIRANAFLHHMVRNIAGVLMTIGAGERPPEWAREVLERGDRHSGGV 248

Query: 233 LAPPEGLYFDSVEY 246
            A P GLY   V+Y
Sbjct: 249 TAHPYGLYLVQVDY 262


>gi|327536150|gb|AEA94984.1| tRNA-pseudouridine synthase I [Enterococcus faecalis OG1RF]
          Length = 246

 Score =  147 bits (372), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 84/242 (34%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +  R  P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNRPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|261364797|ref|ZP_05977680.1| tRNA pseudouridine synthase A [Neisseria mucosa ATCC 25996]
 gi|288566820|gb|EFC88380.1| tRNA pseudouridine synthase A [Neisseria mucosa ATCC 25996]
          Length = 270

 Score =  147 bits (372), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 136/250 (54%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ +I+ Y+GS ++GWQ+Q  G  ++Q ++E A+  +  E +    AGRTD+GVHA  QV
Sbjct: 13  RWALILSYDGSRFYGWQKQAGGLPTVQTTLEYALSQIASENIRTIVAGRTDTGVHATAQV 72

Query: 62  AHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       + WV     + +NA+L   + +S+L    V   FHARF A  R Y Y +
Sbjct: 73  IHFDTTVVRPEQAWV-----RGVNAHLP--EGVSVLFAQQVASHFHARFDAYGRRYRYLL 125

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +      + +GR       LD + M+ AA  L G HDF++FR+  CQA SPI+T+    
Sbjct: 126 ESSPVRSPILQGRVGWTHLKLDPDKMQQAALLLEGEHDFSSFRAAECQAKSPIKTLYSAK 185

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++     +++ +   +FLH  +R+ +G+L  VG G+ + +  +  +  + R +  P   P
Sbjct: 186 ISGTPQFLKLDLHGNAFLHHMVRNIMGALVYVGSGRLSVSGFQTLIGERSRLKAPPTFMP 245

Query: 237 EGLYFDSVEY 246
           +GLY   V+Y
Sbjct: 246 DGLYLTGVDY 255


>gi|16804636|ref|NP_466121.1| tRNA pseudouridine synthase A [Listeria monocytogenes EGD-e]
 gi|224499270|ref|ZP_03667619.1| tRNA pseudouridine synthase A [Listeria monocytogenes Finland 1988]
 gi|224503609|ref|ZP_03671916.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL R2-561]
 gi|254829047|ref|ZP_05233734.1| truA [Listeria monocytogenes FSL N3-165]
 gi|254830971|ref|ZP_05235626.1| tRNA pseudouridine synthase A [Listeria monocytogenes 10403S]
 gi|254899951|ref|ZP_05259875.1| tRNA pseudouridine synthase A [Listeria monocytogenes J0161]
 gi|254912843|ref|ZP_05262855.1| tRNA pseudouridine synthase A [Listeria monocytogenes J2818]
 gi|254937223|ref|ZP_05268920.1| truA [Listeria monocytogenes F6900]
 gi|255029029|ref|ZP_05300980.1| tRNA pseudouridine synthase A [Listeria monocytogenes LO28]
 gi|284800516|ref|YP_003412381.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5578]
 gi|284993702|ref|YP_003415470.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5923]
 gi|24212550|sp|Q8Y457|TRUA_LISMO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|16412086|emb|CAD00676.1| truA [Listeria monocytogenes EGD-e]
 gi|258601456|gb|EEW14781.1| truA [Listeria monocytogenes FSL N3-165]
 gi|258609828|gb|EEW22436.1| truA [Listeria monocytogenes F6900]
 gi|284056078|gb|ADB67019.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5578]
 gi|284059169|gb|ADB70108.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5923]
 gi|293590841|gb|EFF99175.1| tRNA pseudouridine synthase A [Listeria monocytogenes J2818]
          Length = 248

 Score =  147 bits (372), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 133/251 (52%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ +AL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISEALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEY 246
           P+GLY   V+Y
Sbjct: 237 PQGLYLWRVDY 247


>gi|260588018|ref|ZP_05853931.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|331082412|ref|ZP_08331538.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
 gi|260541545|gb|EEX22114.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|330400898|gb|EGG80499.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 244

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 132/246 (53%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y + I+Y+GS Y GWQRQK+  ++IQG IE  +  + G  V + GAGRTD+GVHA  Q
Sbjct: 1   MNYRLDIQYDGSRYGGWQRQKDTDNTIQGKIEDVLTKMLGTEVQIQGAGRTDAGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F    E     +C+ LN YL   + I I  +S  +++FH+R +A  + Y YRI++  
Sbjct: 61  VANFHADCEKSCEEICQYLNEYL--PEDIEISKVSEAEERFHSRLNAKEKVYQYRIVSGI 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E+     + ++LD   M+ AA++L G HDF +F S      S +RTI   ++   
Sbjct: 119 HKNVFERKYQCPLHETLDVNAMQEAAKYLEGTHDFKSFCSNKKMKKSSVRTIYSIEIVDL 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I      FL+  +R   G+L  VG G+    +++  L+  DRKE G  AP  GL 
Sbjct: 179 TQEIVITYTGNGFLYNMVRILTGTLIEVGRGRRKPEEMKGILEGCDRKEAGFTAPARGLT 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LLEVRY 244


>gi|225075428|ref|ZP_03718627.1| hypothetical protein NEIFLAOT_00433 [Neisseria flavescens
           NRL30031/H210]
 gi|224953246|gb|EEG34455.1| hypothetical protein NEIFLAOT_00433 [Neisseria flavescens
           NRL30031/H210]
          Length = 281

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  
Sbjct: 12  MQRWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALSSIAGEQINTIVAGRTDTGVHATA 71

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           + +NA+L   D +++L    V   FHARF A  R Y Y + + 
Sbjct: 72  QVVHFDTSVSRPEQAWVRGVNAHLP--DGVAVLVAQKVAPHFHARFDAYGRHYRYLLESS 129

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GR       LD   MR AA  L G HDF++FR+  CQA SP++T+    ++ 
Sbjct: 130 PVRSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPVKTLYSTKISG 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + + +   +FLH  +R+ +G+L  VG G+ +  + E    A+ R +  P    +GL
Sbjct: 190 TSRYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFESVFHAKSRLKAPPTFMSDGL 249

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 250 YLTGVDY 256


>gi|257870548|ref|ZP_05650201.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804712|gb|EEV33534.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 247

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ V +HG+GRTD+GVHAL 
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTRMNNGQAVQIHGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +  P+   +      +  + I++  + IVD+ FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDF--DERPLEKMR-FGLDTQTPEDIAVKQVEIVDEHFHARYLVREKTYQFRVDIG 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  LD   ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 118 KPRSPFRRYYASYYPYPLDLMKIQQALPDLLGTHDFTSFCATGSSVEDKVRTIHQASMEV 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+  +  +   +  +DR   GP A PE
Sbjct: 178 NEAGDELLFTFRGDGFLYKMIRIMVGTLLKIGNGRLPADSIPAIIAQKDRNAAGPTAHPE 237

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 238 GLYLVRVAYE 247


>gi|257466765|ref|ZP_05631076.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917914|ref|ZP_07914154.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313691789|gb|EFS28624.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 251

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 92/247 (37%), Positives = 129/247 (52%), Gaps = 13/247 (5%)

Query: 8   IEYNGSGYFGWQR---QKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHALRQV 61
           IEY G+ Y GWQR   ++   +IQG IE+ +   F +  E V V  +GRTD+GVHA  Q+
Sbjct: 10  IEYEGTRYLGWQRLGEKQREKTIQGKIEQVLARLFALNPEEVSVIASGRTDAGVHAKEQI 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+  L     P  + +  N YL   + I I +   V++ FH+RF A  + Y Y I + Q 
Sbjct: 70  ANVHLPSGKSPQEIEEYCNQYL--PEDIRIFHAHFVEELFHSRFHAKTKEYHYEI-SLQK 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--S 179
           P    +   W  P  LD E M+ ++Q+ +G HDF  F S+     S IR ID  ++    
Sbjct: 127 PSVFHRNVTWYCPIQLDIEKMKESSQYFLGEHDFLAFSSLKKTKKSTIRRIDRIEIQETE 186

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG L   R V   FL   IR  VG+L  VG+GK T  D+    Q++ R++ G LAP +GL
Sbjct: 187 FGLL--FRFVGNGFLQNMIRILVGTLIEVGEGKKTKEDIISIFQSKARQKAGFLAPAKGL 244

Query: 240 YFDSVEY 246
               V Y
Sbjct: 245 TLYKVYY 251


>gi|121534665|ref|ZP_01666486.1| tRNA pseudouridine synthase A [Thermosinus carboxydivorans Nor1]
 gi|121306685|gb|EAX47606.1| tRNA pseudouridine synthase A [Thermosinus carboxydivorans Nor1]
          Length = 250

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 123/245 (50%), Gaps = 3/245 (1%)

Query: 3   RYC-MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           RY  + + Y+G+ Y G+QRQ N  ++Q  +E+ +  + G  + V GA RTD+GVHA  QV
Sbjct: 8   RYLKLTVAYDGTAYHGFQRQANAITVQQVLEERLATIFGHPLKVTGAARTDAGVHAYGQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F          + +A  + L     I ++    V   FHARFSA  + YLYRI     
Sbjct: 68  VGFATSGTIPAANIVRAAKSVLP--PDIVVVKAEEVSADFHARFSARSKIYLYRIYNAAV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD   M  A Q +VG HDF+ FR+      SP+RTI        G
Sbjct: 126 ADPFRRNYAWHVTQPLDEAAMDTAVQTVVGTHDFSAFRAAGGPPVSPVRTIYEAGCTREG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +++E R     FL+  +R+ VG+L  VG G+ T     + L  +DR   G  APP+GLY 
Sbjct: 186 DMLEFRFWGNGFLYHMVRNLVGTLVDVGLGRLTRDGFTRILAGRDRTRAGITAPPQGLYL 245

Query: 242 DSVEY 246
             + Y
Sbjct: 246 KEIFY 250


>gi|86156809|ref|YP_463594.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773320|gb|ABC80157.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 264

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 124/242 (51%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +      V  AGRTD+GVHA  QVA F 
Sbjct: 25  LVLEYDGTAYVGWQVQPNGPSIQAEVERALATLHKAPRRVTAAGRTDAGVHARGQVASFR 84

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             R          +NA L     +++   S+    F AR SA  + Y Y I        L
Sbjct: 85  EDRPLPVKAYVMGMNAVL--PPDVAVRAASLEPDGFDARRSARGKRYRYVIENLPTRAPL 142

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSFGNLI 184
            + +AW     L+  N+R AA HLVGRHDF  F++  C     +R +   +V    G  I
Sbjct: 143 TRLQAWQHFHPLELANVREAAAHLVGRHDFAAFQAADCACEHAVREVRRLEVLGEAGGRI 202

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E+ + A +F+   +R+ VG+L  VG G+     +   L   DR E GP APP+GL+ + V
Sbjct: 203 EVVIEATAFVKHMVRNIVGTLVEVGRGRRAPGSMLALLARGDRTEAGPTAPPQGLFLEEV 262

Query: 245 EY 246
            Y
Sbjct: 263 FY 264


>gi|311029085|ref|ZP_07707175.1| Pseudouridylate synthase I [Bacillus sp. m3-13]
          Length = 248

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 87/249 (34%), Positives = 135/249 (54%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R   I+ Y+G+G+ G+Q QK   ++Q  +++A+  +  G  V V  +GRTD+GVHA+ 
Sbjct: 1   MNRLKCILTYDGAGFEGYQIQKEKRTVQLEVQRALSRIHKGTEVKVSASGRTDAGVHAVG 60

Query: 60  QVAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD     +PV   + ALNA+L     I +  +  V   FHARF  +++ Y Y++  
Sbjct: 61  QVLHFDSPLS-IPVAAWQNALNAHL--PKDIWVKKVESVSGDFHARFDVVKKEYRYKVSL 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +     ++ + +  P  LD E ++ A  HL+G HDFT+F S   +    +RTI   +V 
Sbjct: 118 AKDFNVFDRDQVYHYPYPLDLEAVKEACGHLIGEHDFTSFCSAKTEVEDKVRTIYSLEVV 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +E R++   FL+  +R  VG+L  +G GK    D+   L+A+DR   G  AP  G
Sbjct: 178 RNGEELEFRIIGNGFLYNMVRIIVGTLLEIGQGKKLPRDIFSILEARDRGAAGKTAPAHG 237

Query: 239 LYFDSVEYS 247
           LY  +V Y 
Sbjct: 238 LYLWNVVYD 246


>gi|256822702|ref|YP_003146665.1| tRNA pseudouridine synthase A [Kangiella koreensis DSM 16069]
 gi|256796241|gb|ACV26897.1| tRNA pseudouridine synthase A [Kangiella koreensis DSM 16069]
          Length = 264

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 122/247 (49%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + IEY+G  Y GWQRQ + SS+Q ++EK +  +  E + V  AGRTD+GVHA  Q
Sbjct: 1   MTKVALCIEYDGHRYHGWQRQSHASSVQQTLEKVLSTIADEPIEVSCAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII-TR 119
           + HF+L  E    +    + A  ++ D I++     V   FHARFSA  R Y Y I  T 
Sbjct: 61  IIHFELSNE--RPLKAWTMGANTQLPDDIAVRWAHSVSDDFHARFSAKARRYRYIIANTP 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P     G  W     LD + M  A  +  G  DF  F++  CQ+ +  R I H  V  
Sbjct: 119 TRPAISRSGLTWCR-APLDIDVMNQACAYFPGEQDFAAFQAASCQSKTSFRNIHHLFVER 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I + A +FLH  +R+  GSL  +G         ++ L  +DR +    A P GL
Sbjct: 178 LGEYVVIDIKANAFLHHMVRNIAGSLIEIGRYNQKPEWAKQLLDGKDRTQAASTASPNGL 237

Query: 240 YFDSVEY 246
           Y   VEY
Sbjct: 238 YLVDVEY 244


>gi|257865435|ref|ZP_05645088.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257871770|ref|ZP_05651423.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257875038|ref|ZP_05654691.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|325569125|ref|ZP_08145372.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
 gi|257799369|gb|EEV28421.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257805934|gb|EEV34756.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257809204|gb|EEV38024.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|325157583|gb|EGC69741.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
          Length = 245

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 123/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  +   +IQ  +E  I L+TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYLGWQRLGDSEKTIQEKVEGVIKLLTGEEIEIVGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +     + +  N YL     I +  +  V ++FHAR+ A  + Y Y +     P  
Sbjct: 66  KTTHQMSLPEMQQFFNRYL--PQDIVVNKIEEVPERFHARYHAKGKQYSYYVWNNAIPSV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  ++  P+ LD E M+ AA+ L+G HDF  F ++     S +RTID   +   G+L+
Sbjct: 124 FARNTSFHCPQPLDLEKMQQAAEKLIGTHDFIGFSALKKSKKSTVRTIDEITITPEGDLL 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                   FLH  +R   G+L  +GDG      +++ L  + R+  G   P  GL+ D V
Sbjct: 184 RFTFKGNGFLHKMVRILTGTLIAIGDGTLPPEVIDQVLADKVRQAAGETVPSHGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|312880338|ref|ZP_07740138.1| tRNA pseudouridine synthase A [Aminomonas paucivorans DSM 12260]
 gi|310783629|gb|EFQ24027.1| tRNA pseudouridine synthase A [Aminomonas paucivorans DSM 12260]
          Length = 260

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 92/248 (37%), Positives = 125/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY   + Y G+ + G+Q Q N  S+QG +E A+  ++G  V  HGAGRTD+GVHA  Q
Sbjct: 1   MPRYAAEVAYVGASFAGFQAQPNRPSVQGVLEAALEALSGSPVRCHGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFDL R W P  L  A+ A+L  S  + IL ++ V   FHARF A+ R Y + +  + 
Sbjct: 61  VVHFDLPRPWDPFRLRGAMAAHLPPS--VEILQVAQVPDSFHARFDALWREYRFFLWNQA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
           A +   +   W +   LD   ++     L GRHDF  F RS+     S  RT+ H     
Sbjct: 119 ACVPHLRPFVWWVKSPLDWTLVQHLLPSLRGRHDFGAFCRSVDRPEDS-WRTLLHVSCRR 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I  R     FL   +R  VG+L+ V  G          L+   R E G  APP+GL
Sbjct: 178 RGPFIRFRFRGDGFLTNMVRILVGTLEGVARGGMEPEAFLNLLEGGCRSEAGRTAPPQGL 237

Query: 240 YFDSVEYS 247
           +F  V Y+
Sbjct: 238 FFWRVGYA 245


>gi|310829551|ref|YP_003961908.1| hypothetical protein ELI_4001 [Eubacterium limosum KIST612]
 gi|308741285|gb|ADO38945.1| hypothetical protein ELI_4001 [Eubacterium limosum KIST612]
          Length = 244

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 80/241 (33%), Positives = 120/241 (49%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           MII Y G+ Y GWQRQ N  +++ ++  AI  VTGE V ++G+GRTD+GVHAL Q AHF 
Sbjct: 6   MIIAYKGTRYAGWQRQPNAPTVEEALTGAIKAVTGETVTLYGSGRTDAGVHALGQSAHFH 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P     ALN   ++   I +L+     + FH+R+SA  + Y Y++         
Sbjct: 66  TESRVPPERFAAALNT--RLPGDIRVLSSCEAPEGFHSRYSAKGKVYTYQLYLNPVLSPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
               +W +   +D   M+ A+   +G HDF  F +        +RTI        G L+ 
Sbjct: 124 YAEYSWHVNYPVDVSRMKAASAAFLGEHDFCGFMAAGSSVRGTVRTIRAITFEQEGALLR 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I      FL+  +R   G+L  +G G+  +  L   + + DRK+ G  APP+GL+   V 
Sbjct: 184 ITYTGNGFLYNMVRIMTGTLAEIGMGRIKAEALPGIIASCDRKQAGMTAPPQGLFLREVL 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|15896350|ref|NP_349699.1| tRNA pseudouridine synthase A [Clostridium acetobutylicum ATCC 824]
 gi|30913407|sp|Q97EL1|TRUA_CLOAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|15026164|gb|AAK81039.1|AE007806_12 Pseudouridylate synthase, TRUA [Clostridium acetobutylicum ATCC
           824]
 gi|325510506|gb|ADZ22142.1| tRNA pseudouridine synthase A [Clostridium acetobutylicum EA 2018]
          Length = 244

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 83/241 (34%), Positives = 129/241 (53%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + +EY+G+ Y GWQ+QKN  ++Q  +EK I  +TGE + V G  RTDSGVHA     +F 
Sbjct: 6   LTLEYDGTNYCGWQKQKNVVTVQEEVEKIIGEITGEKIDVIGCSRTDSGVHAKAYTCNFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P      LN+ L   D I  LN   V   FH+RF    ++Y Y I+ R    A+
Sbjct: 66  TNTVIPPEKFYLVLNSVL--PDDIVALNSEEVPMDFHSRFDNKGKTYSYTILNRLQRAAI 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           ++   +     L+C+ MR A ++++G HDFT+F+S   +  S IRTI    +    N + 
Sbjct: 124 DRNYVYQYGHKLNCDLMREATKYILGTHDFTSFKSTGSKVKSNIRTIYEARIVEDENKVI 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             V    FL+  +R  VG+L  VG+ K T  +++  ++++DR + G + P +GL  + V 
Sbjct: 184 FYVTGDGFLYNMVRIIVGTLLEVGEEKITPLNVKTIVESKDRTKAGRVVPAKGLCLEKVM 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|326803064|ref|YP_004320882.1| tRNA pseudouridine synthase A [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650503|gb|AEA00686.1| tRNA pseudouridine synthase A [Aerococcus urinae ACS-120-V-Col10a]
          Length = 264

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 92/249 (36%), Positives = 132/249 (53%), Gaps = 9/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY   I Y+G+ Y G+Q Q NG SIQ ++EKA+ L+T G+ + V+G+GRTDSGVHAL QV
Sbjct: 4   RYKATIAYDGTPYVGFQVQPNGPSIQAALEKALKLMTKGQEIPVYGSGRTDSGVHALGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E     L +ALN+ L   D I +  +  V+K FHAR+ A R++YLY++    A
Sbjct: 64  VHFDYPSEIETEGLLRALNSIL--DDAICVKTVEPVEKHFHARYHAQRKAYLYKV--SLA 119

Query: 122 PLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           P      R +++  P   D   ++ A   L+G H+F +F S     +   R I   +  +
Sbjct: 120 PFVSPFERHYVLHHPYRTDVSRIQAALPALIGAHNFKSFCSTKTDKTVFDREIYRAECQA 179

Query: 180 F--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  +        FL+  +R  VG+   +GDG     +L   L+ QDR   GP A   
Sbjct: 180 SWDGQTLTFYFEGNGFLYNMVRIIVGTCLQIGDGLRPVENLSDLLRIQDRNAAGPTAKAH 239

Query: 238 GLYFDSVEY 246
           GLY   V+Y
Sbjct: 240 GLYLHHVDY 248


>gi|168181898|ref|ZP_02616562.1| tRNA pseudouridine synthase A [Clostridium botulinum Bf]
 gi|237796908|ref|YP_002864460.1| tRNA pseudouridine synthase A [Clostridium botulinum Ba4 str. 657]
 gi|182674803|gb|EDT86764.1| tRNA pseudouridine synthase A [Clostridium botulinum Bf]
 gi|229262719|gb|ACQ53752.1| tRNA pseudouridine synthase A [Clostridium botulinum Ba4 str. 657]
          Length = 246

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 132/241 (54%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V G  RTDSGVHA   V +F 
Sbjct: 8   LEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGVSRTDSGVHAKGYVCNFF 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++    P+A+
Sbjct: 68  TNTKIPPENLQKVINNNLPAD--IVVLSSEEASNEFHSRFCSKGKTYEYTVLNSSQPIAI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N  G+ I+
Sbjct: 126 GRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEINKKGDFIK 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  GL    V 
Sbjct: 186 FIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSGLCLKEVF 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|119471543|ref|ZP_01613957.1| tRNA pseudouridine synthase A [Alteromonadales bacterium TW-7]
 gi|119445486|gb|EAW26772.1| tRNA pseudouridine synthase A [Alteromonadales bacterium TW-7]
          Length = 264

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ Y GWQRQ + +S+Q  +EKA+  +    V +  AGRTD+GVH   QV
Sbjct: 1   MRVALGVEYNGARYSGWQRQSHVNSVQQEVEKALSSICNHPVEIVCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+       V     +N  L     I+I     V + FHARFSA  R Y Y I     
Sbjct: 61  VHFETNASREMVAFTMGMNTLL--PKDIAIRFAQPVVEDFHARFSATARRYRYVIYNYPY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M+ A QHL+G HDFT+FR++HCQA++  RTI H  V   G
Sbjct: 119 RGAVMNEGVTHFHHKLDEKVMQEACQHLIGEHDFTSFRALHCQANTAKRTIHHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +FLH  +R+  G L  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 DYVVIDIKANAFLHHMVRNITGCLMDIGLHKHQPVWLKELLDLKERAKASATAKAAGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|320107224|ref|YP_004182814.1| Pseudouridine synthase I, TruA, alpha/beta domain-containing
           protein [Terriglobus saanensis SP1PR4]
 gi|319925745|gb|ADV82820.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Terriglobus saanensis SP1PR4]
          Length = 287

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 93/257 (36%), Positives = 134/257 (52%), Gaps = 20/257 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ + GWQ Q    +IQGS+  AI  VT E V+  G+GRTD+GVHAL QV    L 
Sbjct: 21  LAYDGTDFAGWQVQPGLPTIQGSLASAIRSVTSEEVLPQGSGRTDAGVHALGQVVSLKLA 80

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII-------TRQ 120
               P  L +ALN  L  S  I +L   IV  +FHAR   + ++Y Y +          +
Sbjct: 81  VPIPPDNLKRALNRILPTS--IRVLEAGIVAPEFHARRGVLSKTYRYTLFLCRPTKDVEE 138

Query: 121 APLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--------IHCQASSP--I 169
              + E+ R  W  P  LD   M  AA+  VG HDFT+F +        +  ++++P  I
Sbjct: 139 IVCSPERARWVWQYPAPLDVAAMMQAAERFVGTHDFTSFAANDPERKTRLEAESNAPDNI 198

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           RT+        G+ +  +V    FLH  +R+ VG+   VG G+  +T++EK L A++R  
Sbjct: 199 RTLYSSAWTLCGDELSYQVRGSGFLHHMVRNLVGTCVDVGAGRILATEMEKILVAKNRGA 258

Query: 230 CGPLAPPEGLYFDSVEY 246
            GP APP+GL    VEY
Sbjct: 259 AGPTAPPQGLSLLEVEY 275


>gi|77360999|ref|YP_340574.1| tRNA pseudouridine synthase A [Pseudoalteromonas haloplanktis
           TAC125]
 gi|123587603|sp|Q3IF40|TRUA_PSEHT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76875910|emb|CAI87131.1| tRNA pseudouridylate synthase I [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 264

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ Y GWQRQ + +S+Q  +E A+  +    V +  AGRTD+GVH   QV
Sbjct: 1   MRVALGVEYNGARYSGWQRQSHVNSVQQEVETALSRICNHPVAIVCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V     +N  L     I+I     V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTDAPRDMVAFTLGMNTLL--PKDIAIRFAQPVADDFHARFSATARRYRYVIYNNPL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+          +LD   M+ A Q+L+G++DFT+FR+IHCQA++ IRTI H  V   G
Sbjct: 119 RGAVLNEGVTHFHHTLDETKMQEACQYLIGKYDFTSFRAIHCQANTAIRTIQHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +FLH  +R+  G L  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 SYVIIDIKANAFLHHMVRNITGCLMDIGLHKQQPVWLKELLDLKERAKASATAKAAGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|121605935|ref|YP_983264.1| tRNA pseudouridine synthase A [Polaromonas naphthalenivorans CJ2]
 gi|166228746|sp|A1VRR5|TRUA_POLNA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120594904|gb|ABM38343.1| tRNA pseudouridine synthase A [Polaromonas naphthalenivorans CJ2]
          Length = 264

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 93/249 (37%), Positives = 135/249 (54%), Gaps = 16/249 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+GS Y GWQ Q +G ++Q  +E A+     + + V  AGRTD+GVHAL QV
Sbjct: 1   MRIALGISYSGSAYEGWQSQLSGKTVQDKLELALSRFAVQPIRVMCAGRTDAGVHALMQV 60

Query: 62  AHFD--LVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD  L RE   WV     +  NA+L  SD I++     V  +FH+R SAI R Y Y +
Sbjct: 61  VHFDTPLQRETSSWV-----RGTNAFLP-SD-IAVQWAQPVPDEFHSRASAIARRYAYVV 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +      ++E GR   + + LD + MR AA HL+G HDF++FR+  CQA SP++T+   +
Sbjct: 114 LESPVRPSVEAGRVGWVYRPLDGDAMRQAALHLMGEHDFSSFRAAQCQAKSPVKTMSRIE 173

Query: 177 VNSFGN----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           ++               A +FLH  IR+ +G L  +G G      L + + A+ R    P
Sbjct: 174 ISQRAGPGSRYWRFEFEANAFLHHMIRNIMGCLLAIGQGNHPPEWLAEVVAARRRDAAAP 233

Query: 233 LAPPEGLYF 241
              P+GLYF
Sbjct: 234 TFSPDGLYF 242


>gi|323703112|ref|ZP_08114766.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
 gi|323531889|gb|EGB21774.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
          Length = 245

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + I+Y+GS Y GWQR  +   +IQG IE  +  +TGE + + G+GRTD+GVHAL QVA+F
Sbjct: 6   LTIQYDGSRYRGWQRLGDTDVTIQGKIEAVLSRMTGEEIEIFGSGRTDTGVHALAQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   L  YL   + I +  +  V  +FHAR++   + YLY+I   +    
Sbjct: 66  KTNSNMSTGEIMDYLYHYL--PEDIVVTRVEEVSDRFHARYNVKSKKYLYKIWNHKYHDP 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +     +P+ L  + M+ AA  L+G HDF +FR+   +  S ++TI   D+     LI
Sbjct: 124 FRRKFVHHVPEPLQIKAMQKAAAFLIGEHDFASFRASKSKKKSSVKTIYAIDIVKKDPLI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I V    FLH  +R  VG+L  VG G      +++ L  +DR   GP AP +GLY   V
Sbjct: 184 KITVHGNGFLHNMVRIIVGTLVEVGLGHMRPEQVKEILSKKDRSAAGPTAPAKGLYLLEV 243

Query: 245 EY 246
           EY
Sbjct: 244 EY 245


>gi|46908770|ref|YP_015159.1| tRNA pseudouridine synthase A [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47093538|ref|ZP_00231299.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 4b
           H7858]
 gi|226225144|ref|YP_002759251.1| pseudouridylate synthase I [Listeria monocytogenes Clip81459]
 gi|254825041|ref|ZP_05230042.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-194]
 gi|254992719|ref|ZP_05274909.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J2-064]
 gi|255520577|ref|ZP_05387814.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-175]
 gi|51316671|sp|Q71WI0|TRUA_LISMF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|259550404|sp|C1KZ13|TRUA_LISMC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46882043|gb|AAT05336.1| tRNA pseudouridine synthase A [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47018098|gb|EAL08870.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 4b
           H7858]
 gi|225877606|emb|CAS06320.1| Putative pseudouridylate synthase I [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|293594283|gb|EFG02044.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-194]
 gi|328468084|gb|EGF39090.1| tRNA pseudouridine synthase A [Listeria monocytogenes 1816]
          Length = 248

 Score =  147 bits (370), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 133/251 (52%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ +AL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISEALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEY 246
           P+GLY   V+Y
Sbjct: 237 PQGLYLWRVDY 247


>gi|254517504|ref|ZP_05129560.1| tRNA-pseudouridine synthase I [Clostridium sp. 7_2_43FAA]
 gi|226911253|gb|EEH96454.1| tRNA-pseudouridine synthase I [Clostridium sp. 7_2_43FAA]
          Length = 244

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 82/241 (34%), Positives = 138/241 (57%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + +EY+G+ Y GWQ+QK G++IQ ++E+AI L+T E   V G+ RTD+GVHA   VA+F 
Sbjct: 6   LTLEYDGTNYLGWQKQKIGATIQETLEEAIRLLTNEESEVIGSSRTDAGVHARGFVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                      +A+N   ++ + I IL    V++ FH+R+SA  ++Y Y I+ R    A+
Sbjct: 66  TNSTIPSEKFREAIN--YRLPNDIVILKSEEVEEDFHSRYSAKGKTYSYSILNRDVNSAI 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            K   + + + LD E+M+ A ++ +G  DF  F+S      + +RTI    ++   ++I+
Sbjct: 124 GKDYVYHVKRKLDVEDMKEACKYFIGTKDFMAFKSSGSSVKTTVRTISDLYIDIKDDIIK 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V    FL+  +R  VG+L +VG  K  S +++  ++++DRK+ G   P  GL  + V 
Sbjct: 184 IYVTGDGFLYNMVRIIVGTLIMVGSNKIDSREVKNIIESKDRKKAGICVPAAGLVLEKVY 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|146296772|ref|YP_001180543.1| tRNA pseudouridine synthase A [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|166228689|sp|A4XKB7|TRUA_CALS8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145410348|gb|ABP67352.1| tRNA pseudouridine synthase A [Caldicellulosiruptor saccharolyticus
           DSM 8903]
          Length = 244

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 85/241 (35%), Positives = 133/241 (55%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ YFGWQ+Q N  ++QG IE AI  +TGE V + G+GRTD GVHAL Q A+F 
Sbjct: 6   LTIEYDGTNYFGWQKQPNKKTVQGVIEDAIKKITGEDVNLVGSGRTDRGVHALGQKANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +        ALN+ L   + ISI + + V   F AR+SA +++Y Y I   +   A+
Sbjct: 66  TESKIPTEKFPLALNSVL--PNDISIKDAAEVSLDFSARYSAKQKTYKYLIYNHKFRPAI 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
                +  P  LD  +M+ + ++ +G +DF++F S   + +S +R I    +    + I 
Sbjct: 124 LCNYVYHFPYELDLVSMQKSCEYFIGEYDFSSFCSSGSETNSKVRRIFDCYLTFENDCIA 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I + A  FL+   R   G++  VG G++  TD+   ++++DR + G   PP GLY   V 
Sbjct: 184 IYITANGFLYNMARIIAGTILDVGVGRFKPTDIPLIIESKDRTKAGKTLPPWGLYLVDVV 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|253701944|ref|YP_003023133.1| tRNA pseudouridine synthase A [Geobacter sp. M21]
 gi|259550393|sp|C6E4S9|TRUA_GEOSM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|251776794|gb|ACT19375.1| tRNA pseudouridine synthase A [Geobacter sp. M21]
          Length = 247

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 124/242 (51%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ Y GWQ Q NG ++Q ++E+A+  + G    +HG+GRTD+GVHA   VA F 
Sbjct: 6   LIIEYDGTAYCGWQVQPNGRTVQEALEEALASMLGGKTALHGSGRTDAGVHARGMVACFQ 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             +        + LN  L     I++     V  +FH RF A+ + Y Y ++       L
Sbjct: 66  TDKGMPLRAFREGLNCLLPAD--IAVREACEVPLEFHPRFDALAKHYRYTMLLDDLRSPL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  AW +   LD + MR A    VG HDF  FR+ +C A + +R I   D+   G  + 
Sbjct: 124 SRLTAWRLKGKLDVDAMRSACAAFVGEHDFAAFRASNCAAKTTVRRIYSMDLVQEGPFLH 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE-CGPLAPPEGLYFDSV 244
           + V    FL   +R   G+L  VG GK +  D+ + L+  DR++  G   PP+GL    V
Sbjct: 184 LDVKGSGFLKNMVRIITGTLIEVGQGKKSVEDVARLLKGSDRQQNSGMTVPPQGLCLMQV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|257417873|ref|ZP_05594867.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
 gi|257159701|gb|EEU89661.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
          Length = 246

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE++ + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGELIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|257888836|ref|ZP_05668489.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257824892|gb|EEV51822.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
          Length = 246

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +     P A
Sbjct: 66  KTNTEIELSEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNNVIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +   G ++
Sbjct: 124 FERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIERKGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL+ D V
Sbjct: 184 HFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKARQHAGETVPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|269139760|ref|YP_003296461.1| tRNA pseudouridine synthase A [Edwardsiella tarda EIB202]
 gi|267985421|gb|ACY85250.1| tRNA pseudouridine synthase A [Edwardsiella tarda EIB202]
 gi|304559626|gb|ADM42290.1| tRNA pseudouridine synthase A [Edwardsiella tarda FL6-60]
          Length = 275

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 92/242 (38%), Positives = 127/242 (52%), Gaps = 8/242 (3%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y GWQRQ+   S+Q  +E A+  V  E V V  AGRTD+GVHA  QV HF   
Sbjct: 21  IEYDGSRYAGWQRQREVDSVQARLEAALSRVASEPVTVFCAGRTDAGVHATGQVVHFTTH 80

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA+L     +++  +  V   FHARFSA  R Y Y I   R  P  L+
Sbjct: 81  ALRQEGAWTMGVNAHLP--KDVAVRWVKSVSPDFHARFSATARRYRYVIYNHRYRPAVLQ 138

Query: 127 KG--RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            G    +L    LD E M  A Q L+G +DF+ FR+  CQ+ +P R + H  VN +G  +
Sbjct: 139 SGVTHCYL---PLDAERMARAGQALLGENDFSAFRAAQCQSRTPWRNVSHLRVNRYGPYV 195

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            + + A +F+H  +R+ VGSL  VG G    + + + L  +DR      A   GLY  +V
Sbjct: 196 VVDIKANAFVHHMVRNIVGSLLEVGCGNQPESWIAELLAGRDRTLAAATAKAAGLYLVAV 255

Query: 245 EY 246
           +Y
Sbjct: 256 DY 257


>gi|281412654|ref|YP_003346733.1| tRNA pseudouridine synthase A [Thermotoga naphthophila RKU-10]
 gi|281373757|gb|ADA67319.1| tRNA pseudouridine synthase A [Thermotoga naphthophila RKU-10]
          Length = 245

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 130/246 (52%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+   + +     K A+NA L   D + +  +  V   FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIKNAMNANL--PDDVYVKEVFEVPVNFHPRFDVTKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR AA++L G HDFT+F++       P+RTI    +  
Sbjct: 119 RQKNVFLRKYVWWFPYELDLDAMRKAAKYLEGTHDFTSFKT-GSDERDPVRTIYRIRILR 177

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|332532285|ref|ZP_08408166.1| tRNA pseudouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038383|gb|EGI74828.1| tRNA pseudouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 264

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 125/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG  Y GWQRQ + +S+Q  +EKA+  +    V V  AGRTD+GVH   Q+
Sbjct: 1   MRVALGVEYNGVRYSGWQRQSHVNSVQQEVEKALSRICNHPVEVVCAGRTDAGVHGTGQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+       V     +N  L     I       VD  FHARFSA  R Y Y I     
Sbjct: 61  IHFETEASRDMVAFTMGMNTLLPKDIAIRFAQPVAVD--FHARFSATARRYRYIIYNSPF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M+ A Q+L+G HDFT+FR+IHCQA++P RTI H  V   G
Sbjct: 119 RGAVLSEGVTHFHHPLDEVKMQEACQYLIGTHDFTSFRAIHCQANTPTRTIHHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +FLH  +R+  GSL  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 CYVIIDIKANAFLHHMVRNITGSLMDIGIHKQQPIWLKELLDCKERAKASATAKAAGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|312870517|ref|ZP_07730636.1| tRNA pseudouridine synthase A [Lactobacillus oris PB013-T2-3]
 gi|311093979|gb|EFQ52304.1| tRNA pseudouridine synthase A [Lactobacillus oris PB013-T2-3]
          Length = 256

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 88/253 (34%), Positives = 137/253 (54%), Gaps = 11/253 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           M RY +   Y+G+ + G+Q Q +  +++  ++ A+  +       + V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGANFSGFQIQPHKRTVEQVLKNAVNKIAKYPDPPISVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     + KALN+ L +   I +     VD+ FHAR+SA R++Y YR+ 
Sbjct: 61  LNQVAHFDLPYQLSDESMRKALNSLLPLD--ILVKKAERVDESFHARYSAHRKTYRYRVD 118

Query: 118 TRQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 P        + +P  +D + MR+AA+  +G HDFT+F +   QA S +RT++  
Sbjct: 119 QGDFVDPFKRNYTAHYKVP--VDIDKMRLAAKDFIGEHDFTSFVASGSQAKSNVRTVEKI 176

Query: 176 --DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             D +   N +        FL+ QIR  V  L  VG G+   +D+++ L A+DR +    
Sbjct: 177 TVDRDPAQNEVVFEFTGNGFLYNQIRIMVAFLLEVGSGQRPVSDVKRVLAAKDRTQARMT 236

Query: 234 APPEGLYFDSVEY 246
           AP  GLY  SV+Y
Sbjct: 237 APASGLYLVSVDY 249


>gi|69244266|ref|ZP_00602734.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257878927|ref|ZP_05658580.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257881556|ref|ZP_05661209.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257890781|ref|ZP_05670434.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|258615438|ref|ZP_05713208.1| tRNA pseudouridine synthase A [Enterococcus faecium DO]
 gi|261206813|ref|ZP_05921504.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289567364|ref|ZP_06447735.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|293563155|ref|ZP_06677615.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|293568529|ref|ZP_06679849.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
 gi|294614075|ref|ZP_06694002.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|294620867|ref|ZP_06700069.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|314939024|ref|ZP_07846289.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|314943424|ref|ZP_07850191.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|314948177|ref|ZP_07851572.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
 gi|314952740|ref|ZP_07855717.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|314991371|ref|ZP_07856849.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|314995418|ref|ZP_07860520.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|68196452|gb|EAN10879.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257813155|gb|EEV41913.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257817214|gb|EEV44542.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257827141|gb|EEV53767.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|260078943|gb|EEW66643.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289160842|gb|EFD08771.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|291588865|gb|EFF20693.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
 gi|291593065|gb|EFF24647.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|291599569|gb|EFF30584.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|291604885|gb|EFF34359.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|313590351|gb|EFR69196.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|313594045|gb|EFR72890.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|313595146|gb|EFR73991.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|313597796|gb|EFR76641.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|313641733|gb|EFS06313.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|313645389|gb|EFS09969.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
          Length = 246

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     +   +N YL     I I  +  + ++FH+R++A+ + Y Y +     P A
Sbjct: 66  KTNTEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHSRYNAVGKKYSYYVWNNVIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  P+ LD + +  A + LVG HDF  F ++     S +RTID   +   G ++
Sbjct: 124 FERNHSFYFPQELDMDKLNAACEKLVGTHDFIGFSALKKSKKSTVRTIDELSIERKGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL+ D V
Sbjct: 184 HFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|94677014|ref|YP_588808.1| tRNA pseudouridine synthase A [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94220164|gb|ABF14323.1| tRNA pseudouridine synthase A [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 267

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           I+  + I YNGS Y+GWQRQK   S+Q S+E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 7   IKIALGIAYNGSLYYGWQRQKELPSVQASLERALSIVANEKISVFCAGRTDTGVHATGQV 66

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+ V           +NA L  S  I++     V   FHARFSA  RSY Y I     
Sbjct: 67  VHFETVALRTNKAWTLGVNANLPAS--IAVRWAMTVTLNFHARFSATARSYRYIIYNHPL 124

Query: 122 PLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             A+     ++   + LD   M  A Q L+G  DFT+FR+  C + +P R +    V   
Sbjct: 125 RPAMLGSSGYMHFYQPLDPLKMDRAGQCLLGERDFTSFRAQQCTSRTPWRNLHQLIVKRH 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + + A +FL+  +R+ VG L  +G GK     +   L  +DR   G  A  +GLY
Sbjct: 185 GSYIIVDITANAFLYRMVRNIVGCLIEIGSGKKPENWIADLLARRDRSLAGITARAKGLY 244

Query: 241 FDSVEY 246
             +V Y
Sbjct: 245 LVNVYY 250


>gi|317471507|ref|ZP_07930858.1| tRNA pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316901002|gb|EFV22965.1| tRNA pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 249

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 128/244 (52%), Gaps = 9/244 (3%)

Query: 8   IEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           IEY+G+ Y GWQ+     N S+IQG +E  +  +TGE + + G+GRTD+GVHA  Q+A+F
Sbjct: 10  IEYDGTRYQGWQKLGKNANASTIQGKLESVLSKMTGESIQIIGSGRTDAGVHACGQIANF 69

Query: 65  DLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                +     C+ +  YL   +   I I+    V ++FH+R +A +++Y YRI      
Sbjct: 70  HTDCSFS----CREIKEYLTKYLPSDIGIVTADEVSERFHSRLNAKQKTYQYRIAIPGTV 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   W  P++L+ E M  AA   +G HDF  F S+     S +RTI    +    +
Sbjct: 126 NVFERKYLWKYPETLNIEKMNKAAAFCLGTHDFLGFSSVKKTKKSTVRTIYSIVIEEEHS 185

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I +      FL+  +R   G+L  +G G      +    Q++DRK+ G  APP+GL+  
Sbjct: 186 EIRLSFTGDGFLYNMVRILTGTLAEIGAGSRDPESIFHVFQSKDRKDAGITAPPQGLFLM 245

Query: 243 SVEY 246
           +VEY
Sbjct: 246 NVEY 249


>gi|257900124|ref|ZP_05679777.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838036|gb|EEV63110.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
          Length = 247

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +     P A
Sbjct: 66  KTNSEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNNVIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +   G ++
Sbjct: 124 FERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIERKGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL+ D V
Sbjct: 184 HFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|197117301|ref|YP_002137728.1| tRNA pseudouridine synthase A [Geobacter bemidjiensis Bem]
 gi|238690881|sp|B5EFM8|TRUA_GEOBB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|197086661|gb|ACH37932.1| tRNA pseudouridines 38,39,40 synthase [Geobacter bemidjiensis Bem]
          Length = 250

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 85/242 (35%), Positives = 123/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ Y GWQ Q NG ++Q  +++A+  + GE   +HG+GRTD+GVHA   VA F 
Sbjct: 6   LIIEYDGTAYCGWQVQPNGRTVQEVLQEALAAMLGEKTPLHGSGRTDAGVHARGMVACFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             +        + LN  L     I++     V  +FH RF A  + Y Y I+       L
Sbjct: 66  TDKAMPLRAFREGLNCLL--PGDIAVREACEVPLEFHPRFDAHAKHYRYTILLDDLRSPL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   W +   LD + MR A    VG HDF  FR+ +C A + +R I   D+   G L+ 
Sbjct: 124 SRLTVWRLKGKLDIQAMRAACAAFVGEHDFAAFRASNCAAKTTVRRIYSMDLVQEGCLLH 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE-CGPLAPPEGLYFDSV 244
           + V    FL   +R   G+L  VG GK +  D+ + LQ  DR++  G   PP+GL    V
Sbjct: 184 LDVKGSGFLKNMVRIITGTLIEVGQGKKSVEDVARLLQGGDRQQNSGMTVPPQGLCLMQV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|229548121|ref|ZP_04436846.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|257091270|ref|ZP_05585631.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257417169|ref|ZP_05594163.1| tRNA pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|300861430|ref|ZP_07107514.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|312905329|ref|ZP_07764444.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
 gi|229306807|gb|EEN72803.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|257000082|gb|EEU86602.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257158997|gb|EEU88957.1| tRNA pseudouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|295114364|emb|CBL33001.1| pseudouridylate synthase I [Enterococcus sp. 7L76]
 gi|300848891|gb|EFK76644.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|310631353|gb|EFQ14636.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
 gi|315145838|gb|EFT89854.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2141]
 gi|315162508|gb|EFU06525.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0645]
 gi|315578608|gb|EFU90799.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0630]
          Length = 246

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYLGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|293556963|ref|ZP_06675523.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
 gi|294618124|ref|ZP_06697719.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
 gi|291595614|gb|EFF26912.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
 gi|291600783|gb|EFF31075.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
          Length = 247

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     +   +N YL     I I  +  + ++FH+R++A+ + Y Y +     P A
Sbjct: 66  KTNTEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHSRYNAVGKKYSYYVWNNVIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  P+ LD + +  A + LVG HDF  F ++     S +RTID   +   G ++
Sbjct: 124 FERNHSFYFPQELDMDKLNAACEKLVGTHDFIGFSALKKSKKSTVRTIDELSIERKGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL+ D V
Sbjct: 184 HFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|291530837|emb|CBK96422.1| pseudouridylate synthase I [Eubacterium siraeum 70/3]
          Length = 250

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 128/251 (50%), Gaps = 18/251 (7%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + YNG+ Y G+QRQ N +SIQ ++E+ +  +  E + ++G  RTD+GVHA   V +  
Sbjct: 6   VTMAYNGTAYHGYQRQNNANSIQQTVEEVLSKLLCEDITINGCSRTDTGVHARAFVFN-- 63

Query: 66  LVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            V+   P+      K  NA L     I+ L+   +   FHARF +  + Y+YRI T    
Sbjct: 64  -VKTNCPIPCEGFIKGGNALL--PQDIAFLSCEDMPDSFHARFDSKGKEYIYRIYTGDVR 120

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS------SPIRTIDHFD 176
                  A   P   D E MR AA+ +VG HDF +F    C+A       + +RT+   D
Sbjct: 121 DVFSADTALHYPYKPDIEKMRKAARLIVGEHDFASF----CKAEAKEHLLTTVRTVYSID 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ +EI+V    FLH  +R  VG+L  + +GK T  D+  AL   DR+  G   PP
Sbjct: 177 VEQTGDFVEIKVCGNGFLHNMVRIIVGTLIYISEGKRTEQDIINALTKPDREFAGKTVPP 236

Query: 237 EGLYFDSVEYS 247
            GLY + V Y 
Sbjct: 237 CGLYLNKVFYE 247


>gi|78221826|ref|YP_383573.1| tRNA pseudouridine synthase A [Geobacter metallireducens GS-15]
 gi|78193081|gb|ABB30848.1| tRNA pseudouridine synthase [Geobacter metallireducens GS-15]
          Length = 256

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 86/243 (35%), Positives = 126/243 (51%), Gaps = 6/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+ Y GWQ Q NG S+Q  +E+A+  +  E V VH +GRTD+GVHA   VA F 
Sbjct: 18  LVLEYDGTNYAGWQIQPNGISVQQVVEEALARLLKEPVRVHSSGRTDAGVHARGMVAAFT 77

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--ITRQAPL 123
             +          LNA L     I+++        F+ RF A  + Y Y I    R++PL
Sbjct: 78  TAKGLPMRAFSDGLNALLP--PDIAVMEALEAPDGFNPRFDAAGKHYRYTIHRGERRSPL 135

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
              +   W   ++LD   M   A H+VG HDF +FR+  C A + +R ID  D+   G+L
Sbjct: 136 C--RHYVWHARETLDLAAMEKGASHMVGEHDFASFRTAGCAARTTVRRIDAVDLALEGDL 193

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + I V    FL   +R  VG+L  VG G+ ++ D+    +    +  GP APP+GL    
Sbjct: 194 LHIDVKGSGFLRNMVRIMVGTLVEVGRGRRSADDVALLFRYPGERFAGPTAPPQGLCLME 253

Query: 244 VEY 246
           V Y
Sbjct: 254 VYY 256


>gi|87308089|ref|ZP_01090231.1| Pseudouridylate synthase (tRNA [Blastopirellula marina DSM 3645]
 gi|87289171|gb|EAQ81063.1| Pseudouridylate synthase (tRNA [Blastopirellula marina DSM 3645]
          Length = 260

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 133/247 (53%), Gaps = 10/247 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I+ Y+G+ Y GWQ Q +  +IQG++E+ +  +TGE + V G+GRTDSGVHA+ QV  F 
Sbjct: 11  LIVSYDGTNYAGWQIQNDQRTIQGALERTLLKITGEKIRVTGSGRTDSGVHAIGQVVSFR 70

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  +  P ++ +ALNA L     +     +I   +F+A   AI++ Y Y +   +     
Sbjct: 71  MQSQLSPDVMRRALNAELPPDIVVQSARNAI--PEFNAIDCAIKKRYRYLLQEGRIDDVF 128

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG---- 181
            +  AW + K L+   M+ AAQHL+G HDF +F S+  +  + +R +  FDV        
Sbjct: 129 SRQYAWFVKKELNFAAMQAAAQHLIGEHDFASFESVGSERMTTVRHV--FDVQVLRSERH 186

Query: 182 --NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + I V A  FL+  +R  VG+L  VG G+     + + L A+ R   G  AP  GL
Sbjct: 187 EFDKVAIEVEANGFLYNMVRIIVGTLVDVGKGRRPPEWVAEVLAAKKRTAGGMTAPAHGL 246

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 247 YLLRVDY 253


>gi|218289976|ref|ZP_03494153.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           LAA1]
 gi|218239961|gb|EED07148.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           LAA1]
          Length = 262

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 127/245 (51%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +++ Y+GSG+ G+ RQ+   ++QG +E  +  + G  +VV G+GRTD GVHA  QV 
Sbjct: 6   RIRLVLGYDGSGFHGFARQEGLRTVQGVLEDELRRMLGVDIVVEGSGRTDRGVHARAQVV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFDL   + P         + ++   +       VD  FHARFS +R++Y Y +     P
Sbjct: 66  HFDL--PYGPPADRMVHVLHRRLPADLLPRQADEVDDGFHARFSVVRKTYRYTLDLAPLP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                  +W +P+ LD   M+ AA+HL+G HDFT+F +        +R ID  +    G+
Sbjct: 124 SLYWYRFSWHLPEYLDLAAMQEAARHLLGEHDFTSFCAAEAPQRDKVRRIDRVEFRQDGS 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + I      FL   +R  VG+L  VG GK     +   L+A+DR+  G  APP GL   
Sbjct: 184 RLHIEFEGNGFLQYMVRILVGTLVKVGRGKERPDRIPLILEARDRRLAGETAPPHGLCLW 243

Query: 243 SVEYS 247
           +VEY 
Sbjct: 244 NVEYP 248


>gi|295398321|ref|ZP_06808363.1| tRNA pseudouridine synthase A [Aerococcus viridans ATCC 11563]
 gi|294973460|gb|EFG49245.1| tRNA pseudouridine synthase A [Aerococcus viridans ATCC 11563]
          Length = 285

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+ + ++Y+G+ + G+Q Q NG ++Q ++EKA+ L++ G  + V G+GRTDSGVHAL 
Sbjct: 1   MPRFKVTLQYDGTPFVGFQVQPNGHTVQEALEKALKLMSKGHDIQVVGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     + +A+N+ L   D I I  +  V+  FHARF    + Y+Y++ T 
Sbjct: 61  QVIHFDYPAEIGEEAVLRAMNSIL--DDAIRITKVERVEDDFHARFHTNGKKYIYKVDTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P   D   M+ A + ++G HDF +F S     ++ +R I   +V +
Sbjct: 119 KFPSPFTRQYMYHHPYRTDVTRMQTALKDIIGVHDFKSFCSTKTDKTNFVREIYRAEVTA 178

Query: 180 FGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +   +  V     FL+  +R  VG+   +GDG     ++++ + A+DR E GP A   
Sbjct: 179 DPDAETLTFVFEGSGFLYNMVRILVGTTLQIGDGLRPVDEMKRLITAEDRNEAGPTAAAH 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLAEVYY 247


>gi|304405587|ref|ZP_07387246.1| tRNA pseudouridine synthase A [Paenibacillus curdlanolyticus YK9]
 gi|304345626|gb|EFM11461.1| tRNA pseudouridine synthase A [Paenibacillus curdlanolyticus YK9]
          Length = 248

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/242 (36%), Positives = 125/242 (51%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            M + Y+G+ Y G+Q Q +G++IQ  +E AI  +TGE + + G+GRTD+GVHA  QV +F
Sbjct: 6   VMTVSYDGTTYSGFQSQPSGNTIQDIVETAIHSLTGEQLRIIGSGRTDAGVHARGQVFNF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                        A+N   ++ D I IL      + FHAR SA R++Y Y I  R+ P  
Sbjct: 66  HTESRIPQERWALAMNT--RLPDDIVILEAWEAPEAFHARHSAKRKTYRYTIDRRKFPDV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  A+  P  L    MR A  HL+G HDFT+F SI       +RTI    +   G L+
Sbjct: 124 FSRMYAFHHPTPLQVGAMREALTHLIGEHDFTSFTSIQSTQPHHVRTIFEAWLEEDGPLL 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            + V    FL+  +R   G++  VG+GK    D+   L A DR   GP A   GL   +V
Sbjct: 184 YLFVTGNGFLYNMVRIIAGTMMWVGEGKLAPADIPAMLAAVDRTCAGPTAMAHGLMLWNV 243

Query: 245 EY 246
           EY
Sbjct: 244 EY 245


>gi|315127206|ref|YP_004069209.1| tRNA pseudouridine synthase A [Pseudoalteromonas sp. SM9913]
 gi|315015720|gb|ADT69058.1| tRNA pseudouridine synthase A [Pseudoalteromonas sp. SM9913]
          Length = 264

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 127/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ Y GWQRQ + +S+Q  +EKA+  +    V +  AGRTD+GVH   QV
Sbjct: 1   MRVALGVEYNGARYSGWQRQSHVNSVQQEVEKALSRICNHPVEIVCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V     +N  L     I+I     V + FHARFSA  R Y Y I     
Sbjct: 61  VHFDTHAEREMVAFTLGMNTLL--PKDIAIRFAQPVAEDFHARFSATARRYRYVIYNYAF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M+ A Q+L+G HDFT+FR++HCQA++  RTI H  V   G
Sbjct: 119 RGAVLNEGVTHFHHPLDEVKMQQACQYLLGEHDFTSFRALHCQANTATRTIHHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +FLH  +R+  G L  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 AYVIIDIKANAFLHHMVRNITGCLMDIGLHKHEPIWLKELLDVKERAKASATAKAAGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|227550954|ref|ZP_03981003.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257893717|ref|ZP_05673370.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257896582|ref|ZP_05676235.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|293379717|ref|ZP_06625853.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
 gi|227179913|gb|EEI60885.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257830096|gb|EEV56703.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257833147|gb|EEV59568.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|292641715|gb|EFF59889.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
          Length = 247

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +     P A
Sbjct: 66  KTNTEIELSEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNNVIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +   G ++
Sbjct: 124 FERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIERKGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL+ D V
Sbjct: 184 HFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|225026395|ref|ZP_03715587.1| hypothetical protein EUBHAL_00644 [Eubacterium hallii DSM 3353]
 gi|224956284|gb|EEG37493.1| hypothetical protein EUBHAL_00644 [Eubacterium hallii DSM 3353]
          Length = 256

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 83/254 (32%), Positives = 134/254 (52%), Gaps = 10/254 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +++ Y+G+ Y GWQ Q NG +++  + K +     E + + GA RTDSGVH+   
Sbjct: 4   MKRFKLVVAYDGTNYCGWQIQPNGITVEEVLNKTLSRFLKEEIHIIGASRTDSGVHSFGN 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  LC ALN   ++ + I I++   V   FH R+   R++Y Y I   +
Sbjct: 64  VAVFDSETTIPPEKLCFALNP--QLPEDIRIVSSEQVPGDFHPRYCDTRKTYEYHIQNGK 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL  E+  + L+   L+ + M+ A+Q+LVG HDF +F +   QA + +RT+   +V + 
Sbjct: 122 IPLPTERLYSHLVIFPLNIQAMQEASQYLVGTHDFKSFCAAKTQAQTTVRTVTGIEVEAH 181

Query: 181 --------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                      + IRV    FL+  +R   G+L  VG G +    +++ L+A DR + G 
Sbjct: 182 PLSEGEYPSKKVIIRVTGEGFLYNMVRIISGTLIKVGLGVYPPEHVKQILEACDRSQAGE 241

Query: 233 LAPPEGLYFDSVEY 246
             P +GL+   +EY
Sbjct: 242 TVPAKGLFLKKIEY 255


>gi|238925343|ref|YP_002938860.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
 gi|238877019|gb|ACR76726.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
          Length = 252

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 82/245 (33%), Positives = 127/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  MI+ Y+G+ Y GWQ Q NG +I+  + + +  +  E + V GA RTD+GVH+L  V
Sbjct: 9   MRVKMIVAYDGTNYCGWQIQPNGITIEQVLNEHLSRLLKEDIKVTGASRTDAGVHSLGNV 68

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD         +  ALN   K+ + I +++   V   FH RFS  R++Y YRI+  + 
Sbjct: 69  CMFDTNTRMPAEKISYALNQ--KLPEDIVVVDSCEVSDDFHPRFSKSRKTYEYRILNARF 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   +     LD E M  AA++L+G HDF +F S + QA + +RTI    V+  G
Sbjct: 127 RNPTRRLDTYFYHYPLDTEKMSEAAKYLIGEHDFASFCSANSQAQTTVRTIYDCTVSKAG 186

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IRV    FL+  +R   G+L  +G     +  ++  +   DR   GP AP  GL  
Sbjct: 187 DIITIRVTGNGFLYNMVRIIAGTLVKIGGSDMPADAMKDIIATTDRAAAGPTAPAHGLTM 246

Query: 242 DSVEY 246
             ++Y
Sbjct: 247 IGLKY 251


>gi|257886188|ref|ZP_05665841.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257822044|gb|EEV49174.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
          Length = 247

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     +   +N YL     I I  +  + ++FH+R++A+ + Y Y +     P A
Sbjct: 66  KTNTEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHSRYNAVGKKYSYYVWNNVIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  P+ LD + +  A + LVG HDF  F ++     S +RTID   +   G ++
Sbjct: 124 FERNHSFYFPQELDMDKLDAACEKLVGTHDFIGFSALKKSKKSTVRTIDELSIERKGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL+ D V
Sbjct: 184 HFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|323485798|ref|ZP_08091133.1| tRNA pseudouridine synthase A [Clostridium symbiosum WAL-14163]
 gi|323693150|ref|ZP_08107368.1| pseudouridylate synthase [Clostridium symbiosum WAL-14673]
 gi|323400786|gb|EGA93149.1| tRNA pseudouridine synthase A [Clostridium symbiosum WAL-14163]
 gi|323502633|gb|EGB18477.1| pseudouridylate synthase [Clostridium symbiosum WAL-14673]
          Length = 265

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 137/252 (54%), Gaps = 12/252 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           ++++Y+G+ Y GWQ+Q N   ++QG +E  +  + G  V VHG+GRTD+GVHAL QVA+F
Sbjct: 8   ILLQYDGTRYDGWQKQGNTQQTVQGKLEAVLSCLAGGPVEVHGSGRTDAGVHALGQVANF 67

Query: 65  DLV--------REWVPVILCKA-LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            L          E   +I  K  LN YL   + I +L       +FH+R +A+ ++Y+YR
Sbjct: 68  HLPLSVFCGSQTEAADMIRIKNYLNEYL--PEDIRVLVAEEARPRFHSRLNALSKTYIYR 125

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I T       E+   + + K  D E M+ AA  LVG HDF  F S+     S +RTI+  
Sbjct: 126 IETADKNDVFERKYRYGLGKEPDLEIMKRAASILVGTHDFRAFSSLKKTKKSTVRTINRI 185

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D+   G  +EI +    FL+  +R  VG+L   G  + +   +++AL++ DR   G  AP
Sbjct: 186 DIRRDGTQLEILLEGNGFLYNMVRIIVGTLVEAGLLERSVQSVKEALESLDRSLAGRTAP 245

Query: 236 PEGLYFDSVEYS 247
            +GL+  +V Y 
Sbjct: 246 AKGLFLAAVAYE 257


>gi|229496121|ref|ZP_04389842.1| tRNA pseudouridine synthase A [Porphyromonas endodontalis ATCC
           35406]
 gi|229316952|gb|EEN82864.1| tRNA pseudouridine synthase A [Porphyromonas endodontalis ATCC
           35406]
          Length = 264

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 132/252 (52%), Gaps = 12/252 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + I ++GS Y GWQRQ NG ++Q  IE+A+ L+    + + GAGRTD+GV+A   
Sbjct: 1   MPRYFLDIAFDGSSYCGWQRQPNGLAVQQVIEEALSLLFRTPISIVGAGRTDAGVNAYSL 60

Query: 61  VAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            AH D+    +  P    K+LN  L     I+I ++  V    HARF AI R YLY I  
Sbjct: 61  PAHVDIPETAKGTPYRWRKSLNGILP--HNINIRSIRPVQPSAHARFDAISRRYLYFIAE 118

Query: 119 RQAPLALEKGRAWLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH-- 174
            + P      R W++P     D E M  AAQ+L+G HDFT+F  +H    + I TI    
Sbjct: 119 ERDPF----NRQWVLPVRPFPDIEKMNQAAQYLLGTHDFTSFSRLHTDTHTNICTIQEAF 174

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +  +S+ +  +  + A  FL   +R+ VG+L  VG       D+ + ++AQDR   G   
Sbjct: 175 WSPSSYPSTWQFSITANRFLRNMVRAIVGTLLEVGASTLAPEDIIEIIRAQDRNRAGASV 234

Query: 235 PPEGLYFDSVEY 246
             E L+   VEY
Sbjct: 235 RGEALFLAHVEY 246


>gi|227550751|ref|ZP_03980800.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257887991|ref|ZP_05667644.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257893205|ref|ZP_05672858.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257896390|ref|ZP_05676043.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|293379476|ref|ZP_06625620.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
 gi|293570714|ref|ZP_06681764.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
 gi|227180069|gb|EEI61041.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257824045|gb|EEV50977.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257829584|gb|EEV56191.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257832955|gb|EEV59376.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|291609186|gb|EFF38458.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
 gi|292641999|gb|EFF60165.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
          Length = 248

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV ++FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEEFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|313631806|gb|EFR98984.1| tRNA pseudouridine synthase A [Listeria seeligeri FSL N1-067]
          Length = 248

 Score =  145 bits (367), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 134/252 (53%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL        +  I+  ++ D  FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDISAEKFQKALQVMTPFDISFLIVEEALAD--FHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT---IDHFD 176
           +      +  A   P  L+ E M++A++ LVG HDFT+F S   +  S +RT   ID ++
Sbjct: 119 KVFDPFSRNFALHYPYELNLEKMKLASERLVGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
            +   + + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR++     AP
Sbjct: 179 EDD--DTLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V+Y 
Sbjct: 237 PQGLYLWRVDYE 248


>gi|219853559|ref|YP_002470681.1| hypothetical protein CKR_0216 [Clostridium kluyveri NBRC 12016]
 gi|219567283|dbj|BAH05267.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 247

 Score =  145 bits (367), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 80/241 (33%), Positives = 130/241 (53%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++IEY+G+ Y GWQRQ N  +IQ  +E+AI   TGE   V G+ RTD+GVHA   V +F 
Sbjct: 9   LVIEYDGTNYSGWQRQYNAITIQQRLEEAIEKATGEFSPVIGSSRTDAGVHARGFVCNFF 68

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +     +   LN  L   + I++L+   VD  FH+R+    + Y Y I+T   P  +
Sbjct: 69  TASKIPTSNIKMVLNTLL--PEDIAVLDSKEVDSSFHSRYFTTGKEYSYTIVTGDRPPVI 126

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +   + LD E ++ + ++ +G HDF+ F+     A S IRTI    V    N+I+
Sbjct: 127 GRQYVYYFRRKLDIEKIKNSCEYFIGTHDFSAFKKKGSTARSSIRTIKELTVLKEKNIIK 186

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +V   FL+  +R  +G+L  VG G+++   ++  L+++DR + G   P +GL  + V 
Sbjct: 187 FNIVGDGFLYNMVRIIIGTLLEVGLGRFSIEYVKYILESKDRAKAGKPVPAKGLCLEKVF 246

Query: 246 Y 246
           Y
Sbjct: 247 Y 247


>gi|222056725|ref|YP_002539087.1| tRNA pseudouridine synthase A [Geobacter sp. FRC-32]
 gi|254789637|sp|B9M6W5|TRUA_GEOSF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221566014|gb|ACM21986.1| tRNA pseudouridine synthase A [Geobacter sp. FRC-32]
          Length = 244

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 87/241 (36%), Positives = 123/241 (51%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ Y GWQ Q NG +IQ  IE+++  + G+ V +  +GRTD+GVHAL  VA F 
Sbjct: 6   LIIEYDGTAYCGWQLQPNGITIQQVIEESLEKMLGQSVRLQSSGRTDAGVHALGMVAVFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             ++         LN  L     I+I + S V   F+ R  AI + Y Y I   +    L
Sbjct: 66  TQKDLPVRAFSDGLNCLLP--PDIAIRDASEVPLSFNPRADAISKHYRYTIYNSKRRSPL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  +W +   L+ E M++ A H VG HDF  FR+ +C A + IR + H  V   G+ + 
Sbjct: 124 TRLNSWHLRGILNMELMQLGASHFVGEHDFAAFRASNCVAKTTIRRMFHVSVAKVGDSVI 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V    FL   +R   G+L  VG GK   + +   L   DR   G  APP+GL    V 
Sbjct: 184 IDVHGSGFLKNMVRVIAGTLVAVGQGKLDPSAIPGLLAGGDRSASGITAPPQGLCLMEVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|16801808|ref|NP_472076.1| tRNA pseudouridine synthase A [Listeria innocua Clip11262]
 gi|24212565|sp|Q927P1|TRUA_LISIN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|16415283|emb|CAC97973.1| truA [Listeria innocua Clip11262]
 gi|313616961|gb|EFR89587.1| tRNA pseudouridine synthase A [Listeria innocua FSL S4-378]
          Length = 248

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 90/252 (35%), Positives = 130/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG+FG+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFFGYQVQPNTRTVQAEIEKALEKMHKGKSVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y I   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEAPADFHARFGTVGKEYRYVIKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M+ A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDIAKMKQASERLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ KAL A DR++     AP
Sbjct: 177 YEEDAETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLAHDRQKLISKTAP 236

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V+Y 
Sbjct: 237 PQGLYLWRVDYE 248


>gi|194366624|ref|YP_002029234.1| tRNA pseudouridine synthase A [Stenotrophomonas maltophilia R551-3]
 gi|238693473|sp|B4SQV6|TRUA_STRM5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|194349428|gb|ACF52551.1| tRNA pseudouridine synthase A [Stenotrophomonas maltophilia R551-3]
          Length = 256

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 95/246 (38%), Positives = 134/246 (54%), Gaps = 13/246 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EY+GS + GWQ   + G S+Q S+E+A+  V    + V  AGRTD+GVH   Q
Sbjct: 1   MRYALGVEYDGSDFRGWQNLGEGGPSVQASLEQALSSVADTPLQVVCAGRTDAGVHGQCQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD       R W+       L    ++  +I++     V   FHARFSA  R Y YR
Sbjct: 61  VVHFDTDVVRDPRAWM-------LGTTTRLPRSIAVRWCVPVADDFHARFSARARRYRYR 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++ R+   ALE+       ++LD   M IA Q L+G +DF  FRS+ CQA    R +   
Sbjct: 114 LLNREVRPALERQTLSWERRALDETRMHIAGQALLGENDFNAFRSVQCQALHARRELQSL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V+  G +IE+ V   +FLH  +R+ VGSL LVG G+     + + L  +DR   GP AP
Sbjct: 174 QVSRHGEVIEVSVQGNAFLHHMVRNIVGSLILVGSGEKPVEWIAELLAGRDRTVAGPTAP 233

Query: 236 PEGLYF 241
           P+GL F
Sbjct: 234 PQGLVF 239


>gi|319763817|ref|YP_004127754.1| tRNA pseudouridine synthase a [Alicycliphilus denitrificans BC]
 gi|330823919|ref|YP_004387222.1| tRNA pseudouridine synthase A [Alicycliphilus denitrificans K601]
 gi|317118378|gb|ADV00867.1| tRNA pseudouridine synthase A [Alicycliphilus denitrificans BC]
 gi|329309291|gb|AEB83706.1| tRNA pseudouridine synthase A [Alicycliphilus denitrificans K601]
          Length = 272

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 82/258 (31%), Positives = 125/258 (48%), Gaps = 14/258 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGQAYSGWQSQPSGNTVQDHLEAALGRFATQKVATICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FHAR  A+ R Y Y ++    
Sbjct: 61  VHFDTGLQRAPFSWVRGTNTFLP--PDIAVQWAQPVPDAFHARACAVARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +   LD + M+ A QHL+G HDF++FR+  CQA SP++T+    +   G
Sbjct: 119 RPSVEAGRVGWVFHELDGQAMQDAVQHLLGEHDFSSFRASACQAKSPVKTLHRIAITRRG 178

Query: 182 N------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                                 +FLH  IR+ +G +  +G G +    + + L A+ R  
Sbjct: 179 PANGPSLHGCAPCYWRFEFEGNAFLHHMIRNIMGCIVAIGQGLYPPQWMRQVLDARSRDA 238

Query: 230 CGPLAPPEGLYFDSVEYS 247
             P   P+GLYF    Y+
Sbjct: 239 AAPTFSPDGLYFLGPVYA 256


>gi|313201346|ref|YP_004040004.1| tRNA pseudouridine synthase a [Methylovorus sp. MP688]
 gi|312440662|gb|ADQ84768.1| tRNA pseudouridine synthase A [Methylovorus sp. MP688]
          Length = 225

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 80/209 (38%), Positives = 114/209 (54%), Gaps = 12/209 (5%)

Query: 43  VVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLK-----ISDTISILNLSIV 97
           V V  AGRTD+GVHAL QV HF+   E       + LNA+++     +  ++ +L    V
Sbjct: 6   VRVIAAGRTDTGVHALAQVVHFETTTE-------RPLNAWVRGVNAGLPSSVRVLWAQQV 58

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
           D +FHARFSA +R Y Y +  +    A+  G+     + LD + M  AA HL+G HDF+ 
Sbjct: 59  DDEFHARFSARQRYYQYILFDQAVAPAILAGKVGWFHQPLDVDAMAEAAAHLIGEHDFSA 118

Query: 158 FRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           FR+  CQA SP+RT+   +V   G  I       +FLH Q+R+ VG+L  VG G      
Sbjct: 119 FRAAECQAKSPVRTLQQAEVRRAGQAILFEFSGNAFLHHQVRNMVGALVYVGKGSQPPAF 178

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +++ LQ+ DR+   P   P+GLY   V Y
Sbjct: 179 IQQLLQSHDRRLAPPTFSPDGLYLSGVGY 207


>gi|227543592|ref|ZP_03973641.1| tRNA pseudouridine synthase A [Lactobacillus reuteri CF48-3A]
 gi|300909379|ref|ZP_07126840.1| tRNA-pseudouridine synthase I [Lactobacillus reuteri SD2112]
 gi|227186432|gb|EEI66503.1| tRNA pseudouridine synthase A [Lactobacillus reuteri CF48-3A]
 gi|300893244|gb|EFK86603.1| tRNA-pseudouridine synthase I [Lactobacillus reuteri SD2112]
          Length = 256

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 86/251 (34%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           M RY +   Y+G+ + G+Q Q N  +++ +++ A+  +       + V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGTNFSGFQIQPNKRTVEQTLKNAVNKIAKHPNPAIPVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD+        + KALN+ L +   I I    +VD  FHAR+SA R++Y YR+ 
Sbjct: 61  LNQVAHFDIPYHLSNESMRKALNSILPLD--ILIKKAELVDNDFHARYSAHRKTYRYRVD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         L+ E MR AA  LVG HDFT+F +   QA S +RTI+   +
Sbjct: 119 QGEFVNPFKRNYTSHFKYPLNLEKMRKAANDLVGTHDFTSFVASGSQAKSNVRTIESITI 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +   N +        FL+ Q+R  V  L  +G  +    D+ + L+A+DR      AP
Sbjct: 179 KRDELRNEVVFDFTGNGFLYNQVRIMVAFLLEIGSNQRPVDDVSRVLEAKDRTLARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  +V+Y
Sbjct: 239 ASGLYLVNVDY 249


>gi|167746683|ref|ZP_02418810.1| hypothetical protein ANACAC_01394 [Anaerostipes caccae DSM 14662]
 gi|167653643|gb|EDR97772.1| hypothetical protein ANACAC_01394 [Anaerostipes caccae DSM 14662]
          Length = 249

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 127/244 (52%), Gaps = 9/244 (3%)

Query: 8   IEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           IEY+G+ Y GWQ+     N S+IQG +E  +  +TGE + + G+GRTD+GVHA  Q+A+F
Sbjct: 10  IEYDGTRYQGWQKLGKNANASTIQGKLESVLSKMTGESIQIIGSGRTDAGVHACGQIANF 69

Query: 65  DLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                +     C+ +  YL   +   I I+    V ++FH+R +A +++Y YRI      
Sbjct: 70  HTDCSFS----CREIKEYLTKYLPSDIGIVTADEVSERFHSRLNAKQKTYQYRIAIPGTV 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   W  P++L+ E M  AA   +G HDF  F S+     S +RTI    +    +
Sbjct: 126 NVFERKYLWKYPETLNIEKMNKAAAFCLGTHDFLGFSSVKKTKKSTVRTIYSIVIEEEHS 185

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I +      FL+  +R   G+L  +G G      +    Q++DRK+ G  APP GL+  
Sbjct: 186 EIRLSFTGDGFLYNMVRILTGTLAEIGAGTRDPESIFHVFQSKDRKDAGITAPPHGLFLM 245

Query: 243 SVEY 246
           +VEY
Sbjct: 246 NVEY 249


>gi|153952894|ref|YP_001393659.1| tRNA pseudouridine synthase A [Clostridium kluyveri DSM 555]
 gi|189029994|sp|A5N4T0|TRUA_CLOK5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146345775|gb|EDK32311.1| TruA [Clostridium kluyveri DSM 555]
          Length = 244

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 80/241 (33%), Positives = 130/241 (53%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++IEY+G+ Y GWQRQ N  +IQ  +E+AI   TGE   V G+ RTD+GVHA   V +F 
Sbjct: 6   LVIEYDGTNYSGWQRQYNAITIQQRLEEAIEKATGEFSPVIGSSRTDAGVHARGFVCNFF 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +     +   LN  L   + I++L+   VD  FH+R+    + Y Y I+T   P  +
Sbjct: 66  TASKIPTSNIKMVLNTLL--PEDIAVLDSKEVDSSFHSRYFTTGKEYSYTIVTGDRPPVI 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +   + LD E ++ + ++ +G HDF+ F+     A S IRTI    V    N+I+
Sbjct: 124 GRQYVYYFRRKLDIEKIKNSCEYFIGTHDFSAFKKKGSTARSSIRTIKELTVLKEKNIIK 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +V   FL+  +R  +G+L  VG G+++   ++  L+++DR + G   P +GL  + V 
Sbjct: 184 FNIVGDGFLYNMVRIIIGTLLEVGLGRFSIEYVKYILESKDRAKAGKPVPAKGLCLEKVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|238920608|ref|YP_002934123.1| tRNA pseudouridine synthase A, [Edwardsiella ictaluri 93-146]
 gi|238870177|gb|ACR69888.1| tRNA pseudouridine synthase A, putative [Edwardsiella ictaluri
           93-146]
          Length = 275

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 91/241 (37%), Positives = 128/241 (53%), Gaps = 6/241 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y GWQRQ+   S+Q  +E A+  V  E V V  AGRTD+GVHA  QV HF   
Sbjct: 21  IEYDGSRYAGWQRQREVDSVQARLEAALSRVASEPVTVFCAGRTDAGVHATGQVVHFTTH 80

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA+L     +++  +  V   FHARFSA  R Y Y I   R  P  L+
Sbjct: 81  ALRQEGAWTMGVNAHLP--KDVAVRWVKDVSPDFHARFSATARRYRYVIYNHRYRPAVLQ 138

Query: 127 KGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            G   + +P  LD E M  A Q L+G +DF+ FR+  CQ+ +P R + H  V+ +G+ + 
Sbjct: 139 SGVTHFYLP--LDAERMARAGQALLGENDFSAFRAAQCQSRTPWRNVSHLRVDRYGSYVV 196

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + + A +F+H  +R+ VGSL  VG G    + +   L  +DR      A   GLY  +V+
Sbjct: 197 VDIKANAFVHHMVRNIVGSLLEVGCGNQPESWIAGLLAGRDRTLAAATAKAAGLYLVAVD 256

Query: 246 Y 246
           Y
Sbjct: 257 Y 257


>gi|148270348|ref|YP_001244808.1| tRNA pseudouridine synthase ACD [Thermotoga petrophila RKU-1]
 gi|166229847|sp|A5IM09|TRUA_THEP1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|147735892|gb|ABQ47232.1| tRNA pseudouridine synthase A [Thermotoga petrophila RKU-1]
          Length = 245

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 130/246 (52%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + + +  AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYIQAAGRTDTGVHANGQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+   + +    +  A+NA L   D + +  +  V   FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIRNAMNANL--PDDVYVKEVFEVPVNFHPRFDVTKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR A ++L G HDFT+F++       P+RTI    +  
Sbjct: 119 RQKNVFLRKYVWWFPYELDLDAMRKAVKYLEGTHDFTSFKT-GSDERDPVRTIYRIRILR 177

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|148544665|ref|YP_001272035.1| tRNA pseudouridine synthase A [Lactobacillus reuteri DSM 20016]
 gi|184154018|ref|YP_001842359.1| tRNA pseudouridine synthase A [Lactobacillus reuteri JCM 1112]
 gi|194466922|ref|ZP_03072909.1| tRNA pseudouridine synthase A [Lactobacillus reuteri 100-23]
 gi|227363788|ref|ZP_03847895.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM2-3]
 gi|325682999|ref|ZP_08162515.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM4-1A]
 gi|166991164|sp|A5VLH4|TRUA_LACRD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|229557996|sp|B2G8U7|TRUA_LACRJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148531699|gb|ABQ83698.1| tRNA pseudouridine synthase A [Lactobacillus reuteri DSM 20016]
 gi|183225362|dbj|BAG25879.1| tRNA pseudouridine synthase A [Lactobacillus reuteri JCM 1112]
 gi|194453958|gb|EDX42855.1| tRNA pseudouridine synthase A [Lactobacillus reuteri 100-23]
 gi|227071145|gb|EEI09461.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM2-3]
 gi|324977349|gb|EGC14300.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM4-1A]
          Length = 256

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 135/252 (53%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M RY +   Y+G+ + G+Q Q N  +++ +++ A+  +    T  I V+ G+GRTD+GVH
Sbjct: 1   MYRYKITFAYDGTNFSGFQIQPNKRTVEQTLKNAVNKIAKHPTPAIPVI-GSGRTDAGVH 59

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QVAHFD+        + KALN+ L +   I I    +VD  FHAR+SA R++Y YR+
Sbjct: 60  ALNQVAHFDIPYHLSNESMRKALNSILPLD--ILIKKAELVDNDFHARYSAHRKTYRYRV 117

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +     ++         L+ E MR AA  LVG HDFT+F +   QA S +RTI++  
Sbjct: 118 DQGEFVNPFKRNYTSHFKYPLNLEKMRKAADDLVGTHDFTSFVASGSQAKSNVRTIENIT 177

Query: 177 V--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +  +   N +        FL+ Q+R  V  L  +G  +    D+ + L+A+DR      A
Sbjct: 178 IKRDEVRNEVVFDFTGNGFLYNQVRIMVAFLLEIGSNQRPVDDVSRVLKAKDRTLARMTA 237

Query: 235 PPEGLYFDSVEY 246
           P  GLY  +V+Y
Sbjct: 238 PASGLYLVNVDY 249


>gi|222111761|ref|YP_002554025.1| tRNA pseudouridine synthase a [Acidovorax ebreus TPSY]
 gi|254789633|sp|B9MDL6|TRUA_ACIET RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221731205|gb|ACM34025.1| tRNA pseudouridine synthase A [Acidovorax ebreus TPSY]
          Length = 274

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 85/259 (32%), Positives = 128/259 (49%), Gaps = 16/259 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRMALGVSYNGQAYNGWQSQPSGNTVQDRLEAALGRFATQEVHTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FH+R  A+ R Y Y ++    
Sbjct: 61  VHFDTQLQRAPFSWVRGTNTFLPTD--IAVQWAQPVPDAFHSRACAVARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--- 178
             +++ GR   +  +LD + M  A QHL+G HDFT+FR+  CQA SP++T+   D+    
Sbjct: 119 RPSVDAGRVGWVFHALDEQAMHRAVQHLLGEHDFTSFRASACQAKSPVKTLHRIDITRRA 178

Query: 179 -----SFGNLIEIRVVAR------SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                S G    I    R      +FLH  IR+ +G +  +G G +    +   L+A+ R
Sbjct: 179 PPAGESTGTHGCIPCYWRFEFEGNAFLHHMIRNIMGCIVAIGQGLYPPEWMRTVLEARSR 238

Query: 228 KECGPLAPPEGLYFDSVEY 246
               P   P+GLYF    Y
Sbjct: 239 DAAAPTFSPDGLYFQGPVY 257


>gi|256956829|ref|ZP_05561000.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|257078499|ref|ZP_05572860.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294781084|ref|ZP_06746435.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|300861778|ref|ZP_07107858.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|307269121|ref|ZP_07550482.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|307286980|ref|ZP_07567055.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|312901088|ref|ZP_07760376.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|256947325|gb|EEU63957.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256986529|gb|EEU73831.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294451887|gb|EFG20338.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|295112531|emb|CBL31168.1| pseudouridylate synthase I [Enterococcus sp. 7L76]
 gi|300848303|gb|EFK76060.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|306501926|gb|EFM71215.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|306514601|gb|EFM83155.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|311291760|gb|EFQ70316.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|315031173|gb|EFT43105.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0017]
 gi|315035981|gb|EFT47913.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0027]
 gi|315145370|gb|EFT89386.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2141]
 gi|315165868|gb|EFU09885.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1302]
          Length = 249

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        IRTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKIRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|118581782|ref|YP_903032.1| tRNA pseudouridine synthase A [Pelobacter propionicus DSM 2379]
 gi|166228745|sp|A1AUF4|TRUA_PELPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|118504492|gb|ABL00975.1| tRNA pseudouridine synthase A [Pelobacter propionicus DSM 2379]
          Length = 244

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 88/243 (36%), Positives = 126/243 (51%), Gaps = 6/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ Y GWQ Q NG ++Q  +E+A+  + GE V +  +GRTD+GVHA   VA F 
Sbjct: 6   LTIEYDGTNYAGWQVQPNGLAVQQVLEEALLRLLGERVRLRSSGRTDAGVHARAMVASFT 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-- 123
             R           N +L   D I+IL+ +    +F     A  RS  YR     AP+  
Sbjct: 66  TSRSLPLQAFVGGANRFLP--DDIAILSAAEAAPEFRPIQDA--RSKWYRYTIYNAPVRS 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
            L +  +W + + LD + M++AA H  GRHDF  FR+ +C A + +R ID   + S G L
Sbjct: 122 PLRRLFSWHVREPLDTDAMQLAAHHFPGRHDFAAFRASNCAAKTTLRRIDSVTIASEGEL 181

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I I V+   FL   +R   G+L  VG G++    +   L+  DRK+ G  AP  GL    
Sbjct: 182 IVIDVIGEGFLKNMVRVMAGTLVDVGRGRFEPERVAWLLENPDRKKAGVTAPACGLCLMD 241

Query: 244 VEY 246
           V Y
Sbjct: 242 VSY 244


>gi|58582878|ref|YP_201894.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84624740|ref|YP_452112.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188577717|ref|YP_001914646.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|62901158|sp|Q5GXR2|TRUA_XANOR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123766543|sp|Q2P0T9|TRUA_XANOM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238689565|sp|B2SVP0|TRUA_XANOP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|58427472|gb|AAW76509.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84368680|dbj|BAE69838.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188522169|gb|ACD60114.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 257

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++         FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDAHREPRGWM-------LGTTARLPPSIAVRWCVPAAADFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M +AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRPLDADAMHVAAQALLGENDFSAFRSVQCQALHARRNLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP A
Sbjct: 174 IHVQRIGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|69247200|ref|ZP_00604262.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257878755|ref|ZP_05658408.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257881397|ref|ZP_05661050.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257890614|ref|ZP_05670267.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|258615179|ref|ZP_05712949.1| tRNA pseudouridine synthase A [Enterococcus faecium DO]
 gi|293562977|ref|ZP_06677444.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|314937639|ref|ZP_07844965.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|314942862|ref|ZP_07849675.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|314948002|ref|ZP_07851406.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
 gi|314950919|ref|ZP_07853988.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|314991433|ref|ZP_07856910.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|314995046|ref|ZP_07860166.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|68194965|gb|EAN09433.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257812983|gb|EEV41741.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257817055|gb|EEV44383.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257826974|gb|EEV53600.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|291605103|gb|EFF34570.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|313590772|gb|EFR69617.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|313593913|gb|EFR72758.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|313596928|gb|EFR75773.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|313598334|gb|EFR77179.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|313643016|gb|EFS07596.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|313645600|gb|EFS10180.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
          Length = 248

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        IRTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKIRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|166712630|ref|ZP_02243837.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 257

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++         FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSIAVRWCVPTAADFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M +AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRPLDADAMHVAAQALLGENDFSAFRSVQCQALHARRNLQT 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP A
Sbjct: 174 IHVQRIGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIAMLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|315149110|gb|EFT93126.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0012]
          Length = 246

 Score =  145 bits (366), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERSGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|257088682|ref|ZP_05583043.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|256997494|gb|EEU84014.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|315160761|gb|EFU04778.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0645]
 gi|315579360|gb|EFU91551.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0630]
          Length = 249

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLVRMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|329577713|gb|EGG59139.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1467]
          Length = 249

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGAHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        IRTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKIRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|295401888|ref|ZP_06811851.1| tRNA pseudouridine synthase A [Geobacillus thermoglucosidasius
           C56-YS93]
 gi|294976018|gb|EFG51633.1| tRNA pseudouridine synthase A [Geobacillus thermoglucosidasius
           C56-YS93]
          Length = 248

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 87/241 (36%), Positives = 125/241 (51%), Gaps = 3/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G+ +FG+Q Q    ++QG +E+A+  +  G+ + V  +GRTD+GVHA  QV HFD 
Sbjct: 9   LSYDGTHFFGYQIQPGKRTVQGELEQALEQIHKGKAIRVTASGRTDAGVHAYGQVIHFDT 68

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                P    KALNA L   D I I +       FHARFSA  + Y Y++   Q      
Sbjct: 69  FLSLSPEQWKKALNALL--PDDIVIKDAQEAAPSFHARFSATAKEYRYKVRIAQERDVFL 126

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +   +  P  LD E M  A + + G HDFT+F S        +RTI   D+    +L+E 
Sbjct: 127 RHYCYHYPYPLDMEAMGRALRLIEGTHDFTSFCSAKTDVDDRVRTIYKADMTVRDDLLEF 186

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             +   FL+  +R  VG++  VG GK +   +  AL A+DR+  G  APP+GLY   V Y
Sbjct: 187 CFIGNGFLYNMVRIIVGTILEVGQGKRSVDSISSALAAKDRRFAGKTAPPQGLYLWKVYY 246

Query: 247 S 247
            
Sbjct: 247 D 247


>gi|167750462|ref|ZP_02422589.1| hypothetical protein EUBSIR_01438 [Eubacterium siraeum DSM 15702]
 gi|167656613|gb|EDS00743.1| hypothetical protein EUBSIR_01438 [Eubacterium siraeum DSM 15702]
          Length = 250

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 87/251 (34%), Positives = 128/251 (50%), Gaps = 18/251 (7%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + YNG+ Y G+QRQ N +SIQ ++E+ +  +  E + ++G  RTD+GVHA   V +  
Sbjct: 6   VTMAYNGTAYHGYQRQNNANSIQQTVEEVLSKLLCEDITINGCSRTDTGVHARAFVFN-- 63

Query: 66  LVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            V+   P+      K  NA L     I+ L+   +   FHARF +  + Y+Y+I T    
Sbjct: 64  -VKTNCPIPCEGFIKGGNALL--PQDIAFLSCEDMPDSFHARFDSKGKEYIYKIYTGDVR 120

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS------SPIRTIDHFD 176
                  A   P   D E MR AA+ +VG HDF +F    C+A       + +RT+   D
Sbjct: 121 DVFSADTALHYPYKPDIEKMRKAARLIVGEHDFASF----CKAEAKEHLLTTVRTVYSID 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ +EI+V    FLH  +R  VG+L  + +GK T  D+  AL   DR+  G   PP
Sbjct: 177 VEQTGDFVEIKVCGNGFLHNMVRIIVGTLIYISEGKRTEQDIINALTKPDREFAGKTVPP 236

Query: 237 EGLYFDSVEYS 247
            GLY + V Y 
Sbjct: 237 CGLYLNKVFYE 247


>gi|312904650|ref|ZP_07763805.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
 gi|310632002|gb|EFQ15285.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
          Length = 249

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLVRMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLVGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|293388406|ref|ZP_06632914.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
 gi|291082181|gb|EFE19144.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
          Length = 280

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 40  LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 99

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 100 KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 157

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 158 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 217

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 218 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 277

Query: 245 EY 246
            Y
Sbjct: 278 YY 279


>gi|89900579|ref|YP_523050.1| tRNA pseudouridine synthase A [Rhodoferax ferrireducens T118]
 gi|123278889|sp|Q21XI4|TRUA_RHOFD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|89345316|gb|ABD69519.1| tRNA pseudouridine synthase A [Rhodoferax ferrireducens T118]
          Length = 260

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +  ++Q  +E A+  +    V    AGRTD+GVH L QV
Sbjct: 1   MRLALGVSYNGQAYQGWQSQLSRQTVQDQLEMALSKLASHRVSTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  NA L     I++     V  +FH R SA+ R Y Y ++    
Sbjct: 61  IHFDTPLDRAPNSWVRGTNALLP--RDIAVEWARPVPPEFHCRASALSRRYAYILLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             +++ G+     K L+   M+ AA HL+G HDF++FR+  CQA SP++ +   D++  G
Sbjct: 119 RPSIDAGQVGWTFKPLEQVAMQQAASHLLGEHDFSSFRASACQALSPVKMLQRLDISRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FLH  IR+ +G L  VG GK     L++ L A++R    P     GLYF
Sbjct: 179 ACWRFEFEANAFLHHMIRNIMGCLITVGQGKKPPEWLKEVLLARNRNVAAPTFSAHGLYF 238

Query: 242 DSVEYS 247
               Y+
Sbjct: 239 LGPRYA 244


>gi|140053519|gb|ABE79574.2| tRNA pseudouridine synthase [Medicago truncatula]
          Length = 361

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 100/315 (31%), Positives = 148/315 (46%), Gaps = 71/315 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ +FG+Q+Q    ++ G +E A     G+ V V  + RTD+GVHAL  V 
Sbjct: 43  RYLVAVEYIGTRFFGFQKQLTDRTVAGVLEDAFCKFVGQPVSVVCSSRTDAGVHALSNVC 102

Query: 63  HFDLVR-----------EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L K +  ++++++  V   FHAR+ A  R
Sbjct: 103 HVDIERISKRKPGEVLQPHEPAVVRRAVNHFLQKENGDLAVIDVRCVPSDFHARYKAQER 162

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS-- 167
           +Y YR+++    L+  EK RAW IP+ L+   M+ A + LVG HDF++FR+  CQA S  
Sbjct: 163 TYFYRLLSGPETLSTFEKDRAWHIPEELNLPAMQEACKVLVGHHDFSSFRASGCQAKSPI 222

Query: 168 -------------------------PIRTIDH---FDVNS-------------------- 179
                                    PI   D    F  NS                    
Sbjct: 223 RSLDELSVVEVTRSPYFPSVMDRENPINVTDDLHCFHSNSETVIPLGSSARIDEVSASKE 282

Query: 180 ---FGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
              FG       + +   AR+FL+ Q+R  VG LK VG G  T TD+E+ L A+      
Sbjct: 283 DVGFGKRRYHRCLVVTARARAFLYHQVRLLVGVLKDVGTGNITVTDVERILNAKTVTATS 342

Query: 232 PLAPPEGLYFDSVEY 246
           P+AP  GLY   V+Y
Sbjct: 343 PMAPACGLYLGEVKY 357


>gi|293567901|ref|ZP_06679242.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
 gi|291589486|gb|EFF21293.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
          Length = 248

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + +V + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEVVSEDFHARYLVTEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPAIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|225849320|ref|YP_002729484.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225643913|gb|ACN98963.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium azorense
           Az-Fu1]
          Length = 244

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 127/245 (51%), Gaps = 9/245 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + I Y G+ Y GWQRQKN   IQ  IE  +  +  E + + G+GRTD+GVHAL QVA+
Sbjct: 7   YKLTISYIGTRYSGWQRQKNAVGIQQIIEDLLEKLFKEKITLIGSGRTDAGVHALNQVAN 66

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P  +   LNA  K+   IS+  +  VD  F+ARFSA  ++YLYRI T+  P 
Sbjct: 67  FKTYSYKDPSTIYSYLNA--KLPRDISVKKVEEVDLNFNARFSAKGKTYLYRIYTKPDPF 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF--G 181
               GR W   K LD   M    + L    D T   S+  + +   + +D  ++  +  G
Sbjct: 125 LY--GRGWFFDKDLDIVKMLQGIEILKKYKDLT---SLAKEGNYIRKEVDLREIKLYYDG 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I+I + A  FL   +R  VG L  +G G  +  + E  ++A+D  +   LAPPEGLY 
Sbjct: 180 KIIDIEITASHFLRNLVRRIVGHLVAIGRGSLSLQEFEDIIKAKDSSKGKFLAPPEGLYL 239

Query: 242 DSVEY 246
             V Y
Sbjct: 240 KEVYY 244


>gi|197120829|ref|YP_002132780.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
 gi|196170678|gb|ACG71651.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
          Length = 245

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 86/242 (35%), Positives = 123/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +      V  AGRTD+GVHA  QV  F 
Sbjct: 6   LVLEYDGTAYVGWQVQPNGPSIQAEVERALATLHKAPRRVTAAGRTDAGVHARGQVVSFP 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             R          +NA L     +++   S+    F AR SA  + Y Y I        L
Sbjct: 66  EDRPLPVKAYVMGMNALL--PPDVAVRAASLEPDGFDARRSARGKRYRYVIENLPTRAPL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSFGNLI 184
            + +AW     L+  ++R AA HLVGRHDF  F++  C     +R +   DV    G  I
Sbjct: 124 TRLQAWQHFHPLELASVREAAAHLVGRHDFAAFQASDCACEHAVREVRRLDVLGEAGGRI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E+ + A +F+   +R+ VG+L  VG G+     +   L   DR E GP APP+GL+ + V
Sbjct: 184 EVVIEATAFVKHMVRNIVGTLVEVGRGRRAPGSMLDLLARGDRTEAGPTAPPQGLFLEEV 243

Query: 245 EY 246
            Y
Sbjct: 244 FY 245


>gi|227554442|ref|ZP_03984489.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|229547551|ref|ZP_04436276.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|255970776|ref|ZP_05421362.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|256761150|ref|ZP_05501730.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
 gi|256960384|ref|ZP_05564555.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|257080567|ref|ZP_05574928.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|293384357|ref|ZP_06630242.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|307274425|ref|ZP_07555609.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|307287287|ref|ZP_07567351.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|307289762|ref|ZP_07569700.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|312902050|ref|ZP_07761311.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|312908558|ref|ZP_07767502.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|312908972|ref|ZP_07767834.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
 gi|312951751|ref|ZP_07770643.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|227176427|gb|EEI57399.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|229307324|gb|EEN73311.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|255961794|gb|EET94270.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|256682401|gb|EEU22096.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
 gi|256950880|gb|EEU67512.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256988597|gb|EEU75899.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|291078349|gb|EFE15713.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|306499218|gb|EFM68695.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|306501620|gb|EFM70914.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|306508935|gb|EFM78021.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|310625525|gb|EFQ08808.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|310630239|gb|EFQ13522.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|311290672|gb|EFQ69228.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
 gi|311290832|gb|EFQ69388.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|315030617|gb|EFT42549.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4000]
 gi|315148974|gb|EFT92990.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4244]
 gi|315153400|gb|EFT97416.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0031]
 gi|315160015|gb|EFU04032.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0312]
 gi|315166006|gb|EFU10023.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1302]
 gi|315575028|gb|EFU87219.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309B]
 gi|315581086|gb|EFU93277.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309A]
 gi|323478960|gb|ADX78399.1| tRNA pseudouridine synthase A [Enterococcus faecalis 62]
          Length = 246

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|126697674|ref|YP_001086571.1| tRNA pseudouridine synthase 1 [Clostridium difficile 630]
 gi|254973765|ref|ZP_05270237.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-66c26]
 gi|255091155|ref|ZP_05320633.1| tRNA pseudouridine synthase 1 [Clostridium difficile CIP 107932]
 gi|255099266|ref|ZP_05328243.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-63q42]
 gi|255305049|ref|ZP_05349221.1| tRNA pseudouridine synthase 1 [Clostridium difficile ATCC 43255]
 gi|255312809|ref|ZP_05354392.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-76w55]
 gi|255515568|ref|ZP_05383244.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-97b34]
 gi|255648663|ref|ZP_05395565.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-37x79]
 gi|260681880|ref|YP_003213165.1| tRNA pseudouridine synthase 1 [Clostridium difficile CD196]
 gi|260685478|ref|YP_003216611.1| tRNA pseudouridine synthase 1 [Clostridium difficile R20291]
 gi|306518785|ref|ZP_07405132.1| tRNA pseudouridine synthase ACD [Clostridium difficile QCD-32g58]
 gi|115249111|emb|CAJ66922.1| transfer RNA pseudouridine synthase A 1 [Clostridium difficile]
 gi|260208043|emb|CBA60248.1| tRNA pseudouridine synthase 1 [Clostridium difficile CD196]
 gi|260211494|emb|CBE01638.1| tRNA pseudouridine synthase 1 [Clostridium difficile R20291]
          Length = 243

 Score =  145 bits (366), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 84/243 (34%), Positives = 132/243 (54%), Gaps = 11/243 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I+YNG  Y GWQ+Q +   IQG+IE+AI+ +T E   + G+GRTDSGVHA+ Q+A+F + 
Sbjct: 8   IQYNGKNYCGWQKQPDSLGIQGTIERAIYDITKEETSLIGSGRTDSGVHAIGQIANFKIN 67

Query: 68  R----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
                E +P+    ALNA  K+   IS++    V+  FH+R+SA  ++Y Y +   +   
Sbjct: 68  SGISIESIPM----ALNA--KLPKDISVIEACEVNDDFHSRYSAKGKTYKYLVYNSKFRN 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
            +    ++ +   LD + M   A+ L+G HDF  F S        +RTI   D++   +L
Sbjct: 122 PILSEISYQVKYELDFDKMCSEAKSLLGTHDFKGFMSSGSSVKDTVRTIYDIDISKKDDL 181

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I   +    FL+  +R  VG+L  +G G+     L+  +Q++ R  CG  AP +GL+   
Sbjct: 182 ITFEISGNGFLYNMVRIIVGTLVDMGRGRINEPFLD-IIQSKTRSRCGHTAPAQGLFLKK 240

Query: 244 VEY 246
           V Y
Sbjct: 241 VHY 243


>gi|319792244|ref|YP_004153884.1| tRNA pseudouridine synthase a [Variovorax paradoxus EPS]
 gi|315594707|gb|ADU35773.1| tRNA pseudouridine synthase A [Variovorax paradoxus EPS]
          Length = 273

 Score =  145 bits (366), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 90/249 (36%), Positives = 131/249 (52%), Gaps = 13/249 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---AGRTDSGVHAL 58
           +R  + I YNG  Y GWQ Q++G ++Q  +E A+     +     G   AGRTD+GVHAL
Sbjct: 1   MRLALGIRYNGQAYEGWQSQRSGRTVQDKLEAALAKFAADPSGRIGTLCAGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   E  P    +  N +L   D I++     V  +FH R SA+ R YLY  + 
Sbjct: 61  MQVVHFDTEIEREPFSWMRGTNRFLP--DDIAVQWAQPVPDEFHCRASALARRYLY--VL 116

Query: 119 RQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            Q+P+  +L+ GR       LD + MR AA  L+G HDF++FR+  CQA SP++ +   +
Sbjct: 117 SQSPVRPSLDSGRVGWSMHPLDGDAMRKAAAVLIGTHDFSSFRASACQAKSPVKNLRRIE 176

Query: 177 VNSFGNLIEIR----VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           +   G+    R      A +FLH  IR+ +G L  +G G      + + L+A+ RK   P
Sbjct: 177 ITRVGDGERCRWHFEFEADAFLHHMIRNLMGCLVRIGRGDERPEWIAEVLEARSRKVAAP 236

Query: 233 LAPPEGLYF 241
               +GLYF
Sbjct: 237 TFSADGLYF 245


>gi|227517362|ref|ZP_03947411.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
 gi|227075232|gb|EEI13195.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
          Length = 277

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 37  LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 96

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 97  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 154

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 155 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERDGEML 214

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 215 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 274

Query: 245 EY 246
            Y
Sbjct: 275 YY 276


>gi|315173151|gb|EFU17168.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1346]
          Length = 877

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 637 LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 696

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 697 KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 754

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 755 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGKML 814

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 815 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 874

Query: 245 EY 246
            Y
Sbjct: 875 YY 876


>gi|325567346|ref|ZP_08144013.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
 gi|325158779|gb|EGC70925.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
          Length = 248

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ + +HG+GRTD+GVHA  
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTKMNNGQPIQIHGSGRTDAGVHAQG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  ++     +   L+   +  + +++ ++ IVD  FHAR+  + ++Y +R+   
Sbjct: 61  QVIHFDFPQKRPLEKMRFGLDT--QTPEDVAVKSVEIVDDTFHARYLVVEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  LD E ++ A    +G HDFT+F +         RTI      V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLEKIQRALPDFLGTHDFTSFCATGSSVDDKTRTIHEASMAV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NDAGDELIFTFRGDGFLYKMIRIMVGTLLKIGNGRIAPDSIPAIIAQKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLVHVAYE 248


>gi|256962868|ref|ZP_05567039.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|307274272|ref|ZP_07555473.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
 gi|256953364|gb|EEU69996.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|306509045|gb|EFM78114.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
          Length = 246

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMERACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|260893342|ref|YP_003239439.1| tRNA pseudouridine synthase A [Ammonifex degensii KC4]
 gi|260865483|gb|ACX52589.1| tRNA pseudouridine synthase A [Ammonifex degensii KC4]
          Length = 259

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 125/242 (51%), Gaps = 2/242 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y+G+ + G+QRQ    ++QG +E+A+  +T E   V GAGRTD+GVHA  QV  F 
Sbjct: 8   LKVAYDGTAFSGFQRQPGLRTVQGVLEEALARLTKETCQVKGAGRTDAGVHAEGQVVSFR 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    L  ALN  L     +++L  + V +QFH R+ A+ + Y Y    R     L
Sbjct: 68  TASSIPTPRLVPALNGLL--PPDVAVLAAAEVPEQFHPRYDAVSKVYRYTFFRRAVRCPL 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A  +P+ LD E MR AA +L GRHDF  F++      S +RT+    +   G  + 
Sbjct: 126 TRFYALHVPEPLDVERMREAAAYLGGRHDFRAFQNTGRPVKSSVRTVFSCRLEEAGPFLY 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             + A  FL+  +R   G+L  +G GK   + +  AL+  +R+  GP APP GL    V+
Sbjct: 186 FWIEADGFLYQMVRVIAGTLLEIGRGKLEPSVILAALEKGERQLLGPTAPPHGLCLVQVK 245

Query: 246 YS 247
           Y 
Sbjct: 246 YP 247


>gi|253682551|ref|ZP_04863348.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
 gi|253562263|gb|EES91715.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
          Length = 246

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 81/242 (33%), Positives = 131/242 (54%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+GS Y GWQ+QK+  ++Q  +E+AI  +T     + G  RTD+GVHA   VA+F 
Sbjct: 7   LIIEYDGSNYSGWQKQKHSITVQQKVEEAISEITKTDTEIIGCSRTDAGVHARNFVANFI 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P     A+N+  K+   I I   S V   FHARF +  + Y+Y I+ R+ P  +
Sbjct: 67  TESSVPPSKFKYAINS--KLPKDIVIKKSSEVPLDFHARFHSKGKKYVYTILNREEPPTI 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
           ++   +   K LD   M++A+++ +G H+F +F +       S +RTI + DV    ++I
Sbjct: 125 DRNVMYHFNKDLDVNAMKMASKYFIGSHEFDSFYKKSGSSVKSTLRTIYYCDVTKCEDVI 184

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +  V+   FL+  +R   G+L   G G+    D++  + A+DR++ G   PP+GL    V
Sbjct: 185 KFTVIGEGFLYNMVRIMAGTLIEAGIGRIRPEDIKAIILAKDREKAGRSLPPQGLCLQEV 244

Query: 245 EY 246
            Y
Sbjct: 245 LY 246


>gi|229546930|ref|ZP_04435655.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|229550518|ref|ZP_04439243.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|255971742|ref|ZP_05422328.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|255974742|ref|ZP_05425328.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|256618347|ref|ZP_05475193.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|257081530|ref|ZP_05575891.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257417608|ref|ZP_05594602.1| tRNA pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257421532|ref|ZP_05598522.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|307276430|ref|ZP_07557553.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|307278640|ref|ZP_07559710.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|312952641|ref|ZP_07771505.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|229304375|gb|EEN70371.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|229307858|gb|EEN73845.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|255962760|gb|EET95236.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|255967614|gb|EET98236.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|256597874|gb|EEU17050.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256989560|gb|EEU76862.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257159436|gb|EEU89396.1| tRNA pseudouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|257163356|gb|EEU93316.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|306504700|gb|EFM73900.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|306506910|gb|EFM76057.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|310629429|gb|EFQ12712.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|315026801|gb|EFT38733.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2137]
 gi|315147137|gb|EFT91153.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4244]
 gi|315153575|gb|EFT97591.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0031]
 gi|315156245|gb|EFU00262.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0043]
 gi|315158610|gb|EFU02627.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0312]
 gi|315168134|gb|EFU12151.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1341]
 gi|315171426|gb|EFU15443.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1342]
 gi|323479455|gb|ADX78894.1| tRNA pseudouridine synthase A [Enterococcus faecalis 62]
 gi|327534038|gb|AEA92872.1| tRNA-pseudouridine synthase I [Enterococcus faecalis OG1RF]
          Length = 249

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|254931132|ref|ZP_05264491.1| tRNA pseudouridine synthase A [Listeria monocytogenes HPB2262]
 gi|293582680|gb|EFF94712.1| tRNA pseudouridine synthase A [Listeria monocytogenes HPB2262]
 gi|328469771|gb|EGF40688.1| tRNA pseudouridine synthase A [Listeria monocytogenes 220]
 gi|332313028|gb|EGJ26123.1| tRNA pseudouridine synthase A 1 [Listeria monocytogenes str. Scott
           A]
          Length = 248

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 87/252 (34%), Positives = 132/252 (52%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRIKASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G  + +  D+ +AL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQDRISPDDISEALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V+Y 
Sbjct: 237 PQGLYLWRVDYE 248


>gi|260558318|ref|ZP_05830514.1| tRNA pseudouridine synthase [Enterococcus faecium C68]
 gi|261207023|ref|ZP_05921712.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289565342|ref|ZP_06445792.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|294615363|ref|ZP_06695236.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|294618289|ref|ZP_06697870.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
 gi|260075492|gb|EEW63798.1| tRNA pseudouridine synthase [Enterococcus faecium C68]
 gi|260078651|gb|EEW66353.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289162832|gb|EFD10682.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|291591737|gb|EFF23373.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|291595383|gb|EFF26695.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
          Length = 248

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|333029910|ref|ZP_08457971.1| tRNA pseudouridine synthase A [Bacteroides coprosuis DSM 18011]
 gi|332740507|gb|EGJ70989.1| tRNA pseudouridine synthase A [Bacteroides coprosuis DSM 18011]
          Length = 260

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 131/245 (53%), Gaps = 5/245 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+GS Y GWQ Q NGSS+Q  +  A+ +   + + V GAGRTD+GVHA + +A
Sbjct: 13  RYFIYLSYDGSNYHGWQIQPNGSSVQECLMDALKMFLRKEIEVVGAGRTDAGVHAKQMIA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD  R+     +C  LN  L     I+I  +  V+K+ HARF A  R+Y Y I TR+ P
Sbjct: 73  HFDFERKLDVDKVCDKLNRIL--PHDIAIHKVIEVNKEAHARFDATARTYQYYITTRKDP 130

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG- 181
               +  A+ + +SLD   M  AAQ L    DFT+F  +H    + + TI   +      
Sbjct: 131 --FRRNYAYRLYQSLDILKMNEAAQILFEFEDFTSFSKLHSDTRTNLCTIMQAEWTEVDE 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +   + A  FL   +R+ VG+L  VG GK +  +  K ++ QDR   G   P + L+ 
Sbjct: 189 HTLVFTIQANRFLRNMVRAIVGTLIEVGRGKISLEEFRKIIEEQDRGLAGASVPGQALFL 248

Query: 242 DSVEY 246
            +VEY
Sbjct: 249 IAVEY 253


>gi|256960635|ref|ZP_05564806.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|293382724|ref|ZP_06628649.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|293388093|ref|ZP_06632621.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
 gi|312908619|ref|ZP_07767561.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|312909233|ref|ZP_07768090.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
 gi|256951131|gb|EEU67763.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|291079884|gb|EFE17248.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|291082544|gb|EFE19507.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
 gi|310625406|gb|EFQ08689.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|311290475|gb|EFQ69031.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
          Length = 249

 Score =  145 bits (365), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NKTGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|315154834|gb|EFT98850.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0043]
          Length = 277

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 37  LTIEYDGKRYSGWQRLGNSEKTIQGKIESILKQMTGEPIEIIGSGRTDAGTHARGQVANF 96

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 97  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 154

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 155 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 214

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 215 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 274

Query: 245 EY 246
            Y
Sbjct: 275 YY 276


>gi|257885664|ref|ZP_05665317.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|293553909|ref|ZP_06674515.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
 gi|257821520|gb|EEV48650.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|291601961|gb|EFF32207.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
          Length = 248

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPAIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|294666793|ref|ZP_06732027.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292603454|gb|EFF46871.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 257

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 135/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++         FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRPLDADAMHGAAQALLGENDFSAFRSVQCQALHARRHLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V  FG ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP A
Sbjct: 174 IHVQRFGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|227555887|ref|ZP_03985934.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|256964165|ref|ZP_05568336.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257418666|ref|ZP_05595660.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
 gi|307274205|ref|ZP_07555413.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
 gi|227175054|gb|EEI56026.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|256954661|gb|EEU71293.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257160494|gb|EEU90454.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
 gi|306509167|gb|EFM78229.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
 gi|315573548|gb|EFU85739.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309B]
 gi|315582104|gb|EFU94295.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309A]
          Length = 249

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|257876163|ref|ZP_05655816.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257810329|gb|EEV39149.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 248

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ + +HG+GRTD+GVHA  
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTKMNNGQPIQIHGSGRTDAGVHAQG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  ++     +   L+   +  + +++  + IVD  FHAR+  + ++Y +R+   
Sbjct: 61  QVIHFDFPQKRPLEKMRFGLDT--QTPEDVAVKAVEIVDDTFHARYLVVEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  LD E ++ A    +G HDFT+F +         RTI      V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLEKIQRALPDFLGTHDFTSFCATGSSVDDKTRTIHEASMAV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NDAGDELIFTFRGDGFLYKMIRIMVGTLLKIGNGRLAPDSIPAIIAQKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLVHVAYE 248


>gi|257084178|ref|ZP_05578539.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256992208|gb|EEU79510.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 249

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|256958303|ref|ZP_05562474.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|257078388|ref|ZP_05572749.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257420509|ref|ZP_05597499.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|294780153|ref|ZP_06745525.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|307268416|ref|ZP_07549794.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|256948799|gb|EEU65431.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256986418|gb|EEU73720.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257162333|gb|EEU92293.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|294452696|gb|EFG21126.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|306515223|gb|EFM83760.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|315036592|gb|EFT48524.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0027]
 gi|329575477|gb|EGG57017.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1467]
          Length = 246

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILKQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|322418344|ref|YP_004197567.1| tRNA pseudouridine synthase A [Geobacter sp. M18]
 gi|320124731|gb|ADW12291.1| tRNA pseudouridine synthase A [Geobacter sp. M18]
          Length = 250

 Score =  144 bits (364), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 84/241 (34%), Positives = 121/241 (50%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ Y GWQ Q NG ++Q  +E A+  + GE   +H +GRTD+GVHA   VA F 
Sbjct: 6   LIIEYDGTAYSGWQVQPNGVTVQAVMEDALSRMLGERTPLHASGRTDAGVHARGMVACFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             +        + LN  L  SD I++   + V   FH RF A  + Y Y ++       L
Sbjct: 66  TGKTMPLRAFREGLNTLLP-SD-IAVREAAEVPLGFHPRFDAQAKHYRYTMLLDDLRSPL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  AW I   LD E MR A    VG HDF  FR  +C A + +R I   ++     L+ 
Sbjct: 124 SRHTAWRIKGKLDLEAMRAACTVFVGEHDFAAFRGANCAAKTTVRRIYSMELVQEDRLLH 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + +    FL   +R   G+L  VG G+  + D+ + L+  DR+  G   PP+GL    V 
Sbjct: 184 LDIKGSGFLKNMVRIITGTLVDVGQGRLGAADVARLLKGGDRQNAGMTVPPQGLCLMRVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|220930998|ref|YP_002507906.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
 gi|220931093|ref|YP_002508001.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
 gi|219992308|gb|ACL68911.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
 gi|219992403|gb|ACL69006.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
          Length = 246

 Score =  144 bits (364), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 88/243 (36%), Positives = 130/243 (53%), Gaps = 5/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + +EY+G+ Y GWQ Q N   +IQG + K +F +    V + GA RTD+GVHA  QVA+F
Sbjct: 7   ITVEYDGTNYSGWQIQNNTPETIQGVLSKCLFDINKSPVKLIGASRTDAGVHARGQVANF 66

Query: 65  DLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            L +  +PV  +  ALN+  K+   I   +   V + FHARF A  + Y+YRI+  + P 
Sbjct: 67  RL-KVGIPVERIPLALNS--KLPPDIVCKDAEEVTEDFHARFDARGKRYIYRILNSEYPS 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
              +   + IP +L+ + MR A   L+G HDF +F++      + +RTI   D+      
Sbjct: 124 PFLRNYTYFIPHNLNIDKMREAGSLLIGEHDFASFQASGGSNKTTVRTITKLDIYRDQYQ 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I+I V    FL+  +R   G+L  VG GK T   + + L+ +DR   G  APP GL    
Sbjct: 184 IKIEVCGNGFLYKMVRIIAGTLIEVGLGKRTVKSVGQLLEIKDRDRAGFTAPPRGLTLIE 243

Query: 244 VEY 246
           V Y
Sbjct: 244 VFY 246


>gi|329894995|ref|ZP_08270775.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC3088]
 gi|328922563|gb|EGG29899.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC3088]
          Length = 274

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 91/248 (36%), Positives = 132/248 (53%), Gaps = 15/248 (6%)

Query: 6   MIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + +EYNGS + GWQRQ     ++Q ++E A+  +    V V  AGRTDSGVHA  QV  F
Sbjct: 16  LAVEYNGSLFHGWQRQGGTDQTVQATLEAALSQIANHDVRVACAGRTDSGVHATSQVVSF 75

Query: 65  DLVREWVPVILCKALNAYLKISD-----TISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                  PV   ++L A++  S+     T+ +     V  +FHARFSAI+R+Y Y    +
Sbjct: 76  K-----APV--SRSLKAWVVGSNAVLPPTVRVHWACAVPDEFHARFSAIQRTYRYVWCVQ 128

Query: 120 QA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +  P +L K   W    +L  + M  AAQ L+G  DF+ FR+  CQ+++P R +    V 
Sbjct: 129 EVRPTSLLKQVTWSR-NALCSQTMNEAAQSLLGEQDFSAFRAASCQSNTPFREVQAVSVV 187

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + + + A +FLH  +R+  GSL LVG G      + + LQ +DR      A P+G
Sbjct: 188 GRGPFVVMEIRANAFLHHMVRNIAGSLSLVGRGLKPVDWIAQLLQGKDRTVAADTASPDG 247

Query: 239 LYFDSVEY 246
           LY  SV Y
Sbjct: 248 LYLTSVAY 255


>gi|242277723|ref|YP_002989852.1| tRNA pseudouridine synthase A [Desulfovibrio salexigens DSM 2638]
 gi|259550311|sp|C6BW69|TRUA_DESAD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|242120617|gb|ACS78313.1| tRNA pseudouridine synthase A [Desulfovibrio salexigens DSM 2638]
          Length = 271

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 133/250 (53%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +II Y+G+ + GWQ Q    ++QG +EKAI  +TG  V VHG+GRTDSGVHAL Q
Sbjct: 1   MQRIKLIIAYDGTNFCGWQLQPKLRTVQGDLEKAITRITGTTVRVHGSGRTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI-ITR 119
           VAHFD+   +  V   +ALN+ L   D ++IL+  +V  +FH+R+SAIR++Y Y + +  
Sbjct: 61  VAHFDVDSCFASVKWQRALNSLL--PDDVTILDAQLVSPEFHSRYSAIRKTYTYTLWLEN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
              L   +   W     LD   +    Q+ +G HDF++F++   +  S +RTI  F    
Sbjct: 119 SFFLPWRRHYVWKC-GPLDFCALDQGMQYFLGEHDFSSFQNTGTEIKSTVRTIHEFKRYP 177

Query: 180 FGNLIE--IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                E  + V    FL   +R+ VG L  +G GK     +   LQ +DR      AP +
Sbjct: 178 GQTEQEMILEVCGSGFLKQMVRNMVGCLVRIGRGKAEPETVRSLLQMKDRTAAPATAPAQ 237

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 238 GLCMAGVYYG 247


>gi|291549528|emb|CBL25790.1| pseudouridylate synthase I [Ruminococcus torques L2-14]
          Length = 256

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q    +I+G + +AI  +T E ++V GA RTD+GVHA   
Sbjct: 1   MRRIRLRVAYDGTAYCGWQVQPEVPTIEGELNQAISRLTKEEIIVIGASRTDAGVHAKGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN  L   + I ++    V+  +H R     ++Y Y+I+  +
Sbjct: 61  VAVFDTESTIPADRFAYALNPLL--PEDIVVVASDEVEADWHPRHCDTEKTYEYKILNSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  + +   + +   L+ E MR AA++L G HDF +F ++H Q    +RTI   +V   
Sbjct: 119 FPDPMRRRDTYHVSFDLNLEKMREAAEYLKGEHDFKSFCNVHTQVEDTVRTIYDLEVEKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI IRV    FL+  +R   G+L  VG G      +   L+A+DR+  G   PP+GL 
Sbjct: 179 EELITIRVRGNGFLYNMVRILAGTLIGVGRGAIAPEQIPAILEAKDRQAAGMTVPPQGLT 238

Query: 241 FDSVEY 246
              ++Y
Sbjct: 239 LVKIDY 244


>gi|145588955|ref|YP_001155552.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|226708658|sp|A4SWX4|TRUA_POLSQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145047361|gb|ABP33988.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
          Length = 275

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 91/259 (35%), Positives = 143/259 (55%), Gaps = 21/259 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---IVVVHG--AGRTDSGVH 56
           +R  + ++Y+GS Y GWQ Q +  +IQ  +EKA+    GE      VH   AGRTD+GVH
Sbjct: 1   MRIALGLQYDGSPYAGWQTQLHQPTIQDELEKALTAFIGEEAKAFPVHTITAGRTDTGVH 60

Query: 57  ALRQVAHFD--LVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           AL QV HFD  + RE   WV     + +N +L  S  ++      V ++F ARFSA  R+
Sbjct: 61  ALGQVVHFDTNVGREDFSWV-----RGVNTFLPKSIVVNWAKE--VPEEFSARFSAYERT 113

Query: 112 YLYRIITR--QAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           Y+Y +     ++P+   +    ++P    LD E M+ +A+ L+G HDF++FRS  CQ+ +
Sbjct: 114 YIYALHAGPCRSPIVNARAGYLMLPPDQFLDVEAMKKSAECLIGEHDFSSFRSSECQSKT 173

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           P++TI   D+ S    +  R+   +FLH  IR+ VG    +G G+  S  + + L A++R
Sbjct: 174 PVKTIYAIDIISQEPWVYFRIRGNAFLHHMIRNIVGCFLQIGQGRQQSGWMAEVLTAKNR 233

Query: 228 KECGPLAPPEGLYFDSVEY 246
           +   P    +GLY   ++Y
Sbjct: 234 QIAAPTFMADGLYLAKIKY 252


>gi|238855099|ref|ZP_04645427.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 269-3]
 gi|260664884|ref|ZP_05865735.1| tRNA pseudouridine synthase A [Lactobacillus jensenii SJ-7A-US]
 gi|282931908|ref|ZP_06337380.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
 gi|238832343|gb|EEQ24652.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 269-3]
 gi|260561367|gb|EEX27340.1| tRNA pseudouridine synthase A [Lactobacillus jensenii SJ-7A-US]
 gi|281303960|gb|EFA96090.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
          Length = 262

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 135/253 (53%), Gaps = 10/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R+ M + Y+G  + G+Q+Q N  ++QG+IE+A+  +  G+ +VVHG+GRTD+GVHAL 
Sbjct: 1   MPRFKMTMAYDGHLFHGFQKQPNQRTVQGTIEEALKKMSKGKRIVVHGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD   + +P   +  ALN+ +     I     SIVD+ FH ++S   +   YR I 
Sbjct: 61  QVIHFDFPNDNIPANKMVLALNSMMPTD--IVFKEASIVDESFHVQYST--KGKWYRYIV 116

Query: 119 RQAPLALEKGRAWL--IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            Q        R +    P  LD   M+ AA  L+G HDFT+F +   Q    +RTI +  
Sbjct: 117 NQDRFVDPFKRFYTGHYPYKLDVSKMQEAASDLLGEHDFTSFAASGGQIIDKVRTIFYVK 176

Query: 177 V--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +      N I    +   FL+  +R  VG+L  +G+G+    DLE+ + A+DR+E    A
Sbjct: 177 IWQKPEENEIVFDFIGNGFLYNMVRIMVGALLEIGNGRRPIHDLERVILAKDRQEVRNTA 236

Query: 235 PPEGLYFDSVEYS 247
           P  GLY   V Y 
Sbjct: 237 PASGLYLYHVFYE 249


>gi|15644322|ref|NP_229374.1| tRNA pseudouridine synthase ACD [Thermotoga maritima MSB8]
 gi|8134772|sp|Q9X1R0|TRUA_THEMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|4982143|gb|AAD36641.1|AE001802_10 pseudouridylate synthase I [Thermotoga maritima MSB8]
          Length = 245

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 129/246 (52%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDTGVHANGQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+   + +    +  A+NA L   D + +  +  V   FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIRNAMNANL--PDDVYVKEVFEVPVNFHPRFDVTKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR A ++L G HDFT+F++       P+RTI    +  
Sbjct: 119 RQKNVFLRKYVWWFPYELDLDAMRKAVKYLEGTHDFTSFKT-GSDERDPVRTIYRIRILR 177

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|315221272|ref|ZP_07863195.1| tRNA pseudouridine synthase A [Streptococcus anginosus F0211]
 gi|315189631|gb|EFU23323.1| tRNA pseudouridine synthase A [Streptococcus anginosus F0211]
          Length = 249

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 132/252 (52%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  + +G  VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHGFAGFQRQLHARSVQEEIEKTLTKINSGASVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  + I  +++  V++ FH+R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDGEKLRFALDT--QTPEDIDFISVEEVNEAFHSRYCKHSKTYEFIVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH----F 175
           +    + +  A   P  LD   +  A + L G HDFT F +      + IRTI      F
Sbjct: 119 RPKNPMMRYYATHYPYPLDLSLIEEAIEKLEGTHDFTGFTASGTSVENKIRTITEARLVF 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D     N +        FL+ QIR+ VG+L  +G+G+     +++ L  +DR   GP A 
Sbjct: 179 DEKR--NFLMFTFSGNGFLYKQIRNMVGTLLKIGNGRMPVEQIDRILTEKDRHLAGPTAA 236

Query: 236 PEGLYFDSVEYS 247
           P GLY   + Y 
Sbjct: 237 PNGLYLKEIRYE 248


>gi|315172660|gb|EFU16677.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1346]
          Length = 249

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NEKGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|298530329|ref|ZP_07017731.1| tRNA pseudouridine synthase A [Desulfonatronospira thiodismutans
           ASO3-1]
 gi|298509703|gb|EFI33607.1| tRNA pseudouridine synthase A [Desulfonatronospira thiodismutans
           ASO3-1]
          Length = 247

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 133/247 (53%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+GY GWQ QK+G +IQG +EKA+  +    + VHG+GRTD+GVHAL QV
Sbjct: 3   MRVRLTLAYDGTGYNGWQIQKDGLTIQGELEKALSRICSASIRVHGSGRTDAGVHALGQV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD   +++ V   +ALNA L     I +L+ +  D++FHARFSA  + Y Y + T+ A
Sbjct: 63  AHFDPPPKFLNVPWNRALNAVLPPG--IRVLDFARTDRKFHARFSARAKQYSYTLWTQGA 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               ++         LD E M+ A   L G HDF  F +   + +  IRT+ +  +    
Sbjct: 121 FFYPQRRNFVWNTGPLDLEAMQEATTCLTGSHDFNCFMNKGTEITDTIRTVRNILLAPGF 180

Query: 182 NLIE--IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              E  + + A  FL    R+ V +L  VG  K +  +L+  +Q +DR      AP  GL
Sbjct: 181 TPQETVVWIQADGFLKQMARNIVSALVQVGRKKLSQAELKSIIQGRDRALAPATAPARGL 240

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


>gi|219684777|ref|ZP_03539719.1| tRNA pseudouridine synthase A [Borrelia garinii PBr]
 gi|219671722|gb|EED28777.1| tRNA pseudouridine synthase A [Borrelia garinii PBr]
          Length = 246

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 123/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    +IQG IEKA+  +  + V +H +GRTD GVHA +Q+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTIQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQIITFDIN 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + + I IL L  V   FH RF+A +R Y YRI+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNGIKILKLKYVKNSFHPRFNAQKRKYSYRILNSNNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ D V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESVSTFETILKSKNRNFARTTAPANALFLDKVYY 245


>gi|291296648|ref|YP_003508046.1| tRNA pseudouridine synthase A [Meiothermus ruber DSM 1279]
 gi|290471607|gb|ADD29026.1| tRNA pseudouridine synthase A [Meiothermus ruber DSM 1279]
          Length = 263

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 95/249 (38%), Positives = 128/249 (51%), Gaps = 9/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY+GSG+ G Q Q  G  ++Q  +E A+  + G    +   GRTD+GVHAL   
Sbjct: 14  RILLTLEYDGSGFAGLQTQAQGERTVQQELEAALSQIPGARPKIWPCGRTDAGVHALAMP 73

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H+D +       +  ALN  L     I  L    V   FHAR S   R Y YRI+ R+ 
Sbjct: 74  VHYDTLDNIPTEKIPHALNTLL--PPDIRALAAQEVPADFHARKSCHWREYRYRILQRRM 131

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDV-- 177
           P AL++ R W IP SL+   MR A + LVG HDF  F     +A+  +R I   H +V  
Sbjct: 132 PPALDRHRVWWIPHSLNLIPMRHALECLVGTHDFKAFAVKEERAT--VREIYRAHLEVWP 189

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  I I  V   FL  Q+RS VG+L  +G GK  S+ ++  L +  RK+ GP AP +
Sbjct: 190 TEGGREIWIEFVGSGFLRGQVRSMVGTLVEIGLGKRDSSSIQSLLASGSRKDAGPTAPAQ 249

Query: 238 GLYFDSVEY 246
           GLYF    Y
Sbjct: 250 GLYFVRAGY 258


>gi|255654196|ref|ZP_05399605.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-23m63]
 gi|296449765|ref|ZP_06891534.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296877828|ref|ZP_06901851.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
 gi|296261363|gb|EFH08189.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296431170|gb|EFH16994.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
          Length = 243

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 134/245 (54%), Gaps = 11/245 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF- 64
           + I+YNG  Y GWQ+Q +   IQG+IE+AI+ +T E V + G+GRTDSGVHA+ Q+A+F 
Sbjct: 6   ITIQYNGKNYCGWQKQLDSLGIQGTIERAIYDITKEKVSLIGSGRTDSGVHAIGQIANFK 65

Query: 65  ---DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               +  E +P+    ALNA  K+   IS+++   V+  FH+R+SA  ++Y Y +   + 
Sbjct: 66  TNSSISIESIPM----ALNA--KLPKDISVIDACEVNDDFHSRYSAKGKTYKYLVYNSKF 119

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +    ++ +   LD + M   A+ L+G HDF  F S        +RTI   D+    
Sbjct: 120 RNPILSEISYQVKYELDFDKMCSEAKLLLGTHDFKGFMSSGSSVKDTVRTIYDIDIIRKD 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +LI   +    FL+  +R  VG+L  +G G+     L+  +Q++ R  CG  AP +GL+ 
Sbjct: 180 DLITFEISGNGFLYNMVRIIVGTLVDIGRGRINEPFLD-IIQSKTRSRCGHTAPAQGLFL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 KKVHY 243


>gi|319938474|ref|ZP_08012868.1| pseudouridylate synthase [Coprobacillus sp. 29_1]
 gi|319806390|gb|EFW03057.1| pseudouridylate synthase [Coprobacillus sp. 29_1]
          Length = 244

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 81/246 (32%), Positives = 136/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   ++ Y+GS + G+Q Q    ++QG I+KA+  +  E V++H +GRTD+ VHA+ QV
Sbjct: 1   MRVKCVVSYDGSRFHGFQVQDKERTVQGEIQKALKKINEEEVIIHASGRTDAKVHAVHQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  ++  P    +A+N ++   + I IL+ S  D +FH+R+SAI++ Y Y + T++ 
Sbjct: 61  FHFDTKKDLPPQQWKRAINHFM--PNDIYILDASYTDDEFHSRYSAIKKEYRYLLSTKEY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +    +   + LD E MR A+Q  +G H+F +F S + Q  + IRT+  FD+    
Sbjct: 119 N-PFDTNYVFQYGRQLDIELMREASQIFIGEHNFASFCS-YDQYGNTIRTLYTFDIVEED 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I  R++   F    +R  VG +  VG  + +   L + L++   K+C   A P+GLY 
Sbjct: 177 GIITFRLIGNGFRRYMVRHLVGGIIQVGAKRISKEILSEMLESCGTKKCLFKAKPQGLYL 236

Query: 242 DSVEYS 247
             V Y 
Sbjct: 237 QEVYYE 242


>gi|310823108|ref|YP_003955466.1| tRNA pseudouridine synthase a [Stigmatella aurantiaca DW4/3-1]
 gi|309396180|gb|ADO73639.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 265

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+GS Y GWQ Q+NG S+Q  + +A+  + G  V V  AGRTDSGVHA  Q
Sbjct: 1   MPRLKLTIEYDGSRYVGWQVQRNGRSVQAELGEALGRLLGGDVEVVAAGRTDSGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD  R+       + LN  L   + I+++    V   F  R  +  + Y YR+    
Sbjct: 61  VVCFDTERQLPLKAYHRGLNGLLP--EDIAVVRAEEVSAAFDPRRWSRGKRYRYRVSNLP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
           +   L +   W I   L  E M  AA  L+GRHD++ FR+  CQA+  +R +    V  +
Sbjct: 119 SRSPLRRHTHWEIYAPLQVEAMARAATSLLGRHDYSAFRASDCQAAHAVREVRRLSVEGT 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   V   +FL   +R+ VG+L  VG G+     + + L + DR   GP APP GL
Sbjct: 179 PGDAVAFVVEGTAFLKHMVRNLVGTLVEVGKGRRPEAWVAEVLASGDRTLAGPTAPPHGL 238

Query: 240 YFDSVEY 246
             + V Y
Sbjct: 239 VLEEVFY 245


>gi|167855019|ref|ZP_02477793.1| ribonuclease G [Haemophilus parasuis 29755]
 gi|167853867|gb|EDS25107.1| ribonuclease G [Haemophilus parasuis 29755]
          Length = 262

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 132/252 (52%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+G  Y GWQRQ+   S+Q  +E+A+ ++      V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYDGRRYCGWQRQQYVDSVQQRLEEALSVIANSSCEVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD          C   NA+L   D +    + + D  FHARFSA+ R Y Y I     
Sbjct: 61  VHFDTDVNRPMQSWCLGTNAHLP-EDIVVKWAIGVSD-DFHARFSALARRYRYVIYN--- 115

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                K R+ ++PK       SLD E M  A Q L+G +DF++FR+  CQ+ +P R + H
Sbjct: 116 ----NKLRSAILPKGISHYHYSLDHEKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V+   + I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A
Sbjct: 172 LIVSRHQDYIILDIQANAFVHHMVRNIVGSLIEVGRGDKPVEWIKWLLEKRDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
             EGLY   V Y
Sbjct: 232 KAEGLYLVEVIY 243


>gi|227520026|ref|ZP_03950075.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
 gi|227072574|gb|EEI10537.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
          Length = 249

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|256830021|ref|YP_003158749.1| tRNA pseudouridine synthase A [Desulfomicrobium baculatum DSM 4028]
 gi|256579197|gb|ACU90333.1| tRNA pseudouridine synthase A [Desulfomicrobium baculatum DSM 4028]
          Length = 246

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 92/249 (36%), Positives = 128/249 (51%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y G+ Y GWQ Q  G +IQG+IE  +  + GE+V VHG+GRTDSGVHAL Q
Sbjct: 1   MPRIRLTVAYVGTRYQGWQIQGRGETIQGAIEDKLARICGELVRVHGSGRTDSGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+      +   +ALNA L   D ISIL        FHARFS   + Y Y + T +
Sbjct: 61  VAHFDVPESKRHIPWRQALNAML--PDDISILEAREAQDDFHARFSVRSKRYAYTLWT-E 117

Query: 121 APLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               + +   ++ P + LD E M  AA+ L G HDF  F++   +    +RT++      
Sbjct: 118 PRFTMPQRAPFVWPVRGLDFEAMDQAAEVLAGTHDFAAFQNAGTEIKGTVRTLEPIVRAP 177

Query: 180 FGNLIE--IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +  E   R  A  FL   +R+ +G L  VG G     D+   L+  DR++    AP  
Sbjct: 178 GTHSAEWVFRFQADGFLKQMVRNLMGLLVEVGRGGLAPADVRPILEGCDRRKAPATAPAR 237

Query: 238 GLYFDSVEY 246
           GL  + V Y
Sbjct: 238 GLTLEEVMY 246


>gi|154249373|ref|YP_001410198.1| tRNA pseudouridine synthase ACD [Fervidobacterium nodosum Rt17-B1]
 gi|171769414|sp|A7HKV8|TRUA_FERNB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|154153309|gb|ABS60541.1| tRNA pseudouridine synthase A [Fervidobacterium nodosum Rt17-B1]
          Length = 246

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 4/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +   Y+G+ +FG+Q Q N  ++QG +EKA+  V    +  + AGRTD+GVHA  Q
Sbjct: 1   MRRVAIEFSYDGTDFFGYQIQNNVRTVQGELEKALEKVFKIHIDTYAAGRTDTGVHANGQ 60

Query: 61  VAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V  FD   +  +   +  A+NA L     I I  +      F+ R+ A RR Y Y I T 
Sbjct: 61  VVSFDCPNDRLMENDIKNAINANL--PGDIYIKKVWFTHPTFNPRYEAKRRIYHYYIDTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++     +   W  P  LD E MRIAA++L+G HDF +F     + +  IRTI++  +  
Sbjct: 119 KSKNLFTRRYVWWFPYELDIEKMRIAAKYLIGEHDFISFSKKGEENTKTIRTINNLRIIE 178

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N LI IRV   SFL   +RS V +L  VG G W    +++ L+++DR +   LAP  G
Sbjct: 179 IKNGLILIRVEGISFLRGMVRSIVANLVRVGTGIWEPEKVKEVLESKDRSKSAGLAPAHG 238

Query: 239 LYFDSV 244
           L+   V
Sbjct: 239 LFLYKV 244


>gi|28212149|ref|NP_783093.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
 gi|38258761|sp|Q890R5|TRUA2_CLOTE RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|28204593|gb|AAO37030.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
          Length = 248

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 84/242 (34%), Positives = 130/242 (53%), Gaps = 4/242 (1%)

Query: 8   IEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +EY+G+ Y GWQ+QK  N  +IQ SIEKAI   T E V + G+ RTD+GVHAL   A+F 
Sbjct: 9   VEYDGTNYSGWQKQKDKNIKTIQSSIEKAIEEATKEEVELIGSSRTDAGVHALAYTANFK 68

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN +L   + I IL    V  +FH+RF  I ++Y+Y+I+ R     +
Sbjct: 69  TCSTIPGEKFKHALNRFL--PEDIVILESEEVPMEFHSRFDCIGKTYVYKILNRPLFSPI 126

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           ++   + +   LD  +M  A++ L+G HDF  F+       + +RTI + ++    +++E
Sbjct: 127 QRNYIYHVKDELDINSMIEASKFLIGTHDFNAFKKSGGNLKTTVRTITNINILKSNDIVE 186

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V    FL+  +R   G+L  VG  +    D+   LQ++DR + G  AP  GLY   + 
Sbjct: 187 IHVSGDGFLYNMVRIISGTLIEVGLSRRKPEDISIILQSKDRCKAGMCAPARGLYLKELF 246

Query: 246 YS 247
           Y+
Sbjct: 247 YN 248


>gi|325660678|ref|ZP_08149308.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 4_1_37FAA]
 gi|325473039|gb|EGC76247.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 4_1_37FAA]
          Length = 249

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 89/244 (36%), Positives = 124/244 (50%), Gaps = 5/244 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y M I Y+G GY GWQR  N   +IQG+IE+ +  + G  V + G+GRTD+GVHA  QVA
Sbjct: 9   YKMTIAYDGGGYKGWQRLTNEPGTIQGTIERVLSEIEGSPVKISGSGRTDAGVHAKGQVA 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H  L     P +L + LN  L   + I I  +  V + FH+R+SA+ + Y YRI  R   
Sbjct: 69  HVFLKTNEDPELLRQELNRML--PEDIRICRVESVSQSFHSRYSAVSKVYEYRIDQRSRA 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +   +  P  LD + MR AA HL G HDF +F     + +  +RTI   D+     
Sbjct: 127 DVFTRKYCYHRPVHLDLDRMRQAADHLTGTHDFGSFTD--NKEADSVRTIFSIDMKEENE 184

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + +      FL+  +R   G+L  VG+G  T   + +A   +DR   G LAP  GL   
Sbjct: 185 KLVLAFCGDGFLYHMVRILAGTLLEVGEGIRTPESVLEAFHHRDRSLTGFLAPAHGLCLR 244

Query: 243 SVEY 246
            V Y
Sbjct: 245 EVNY 248


>gi|219870357|ref|YP_002474732.1| tRNA pseudouridine synthase A [Haemophilus parasuis SH0165]
 gi|254789638|sp|B8F382|TRUA_HAEPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219690561|gb|ACL31784.1| tRNA pseudouridine synthase A [Haemophilus parasuis SH0165]
          Length = 262

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 16/246 (6%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+G  Y GWQRQ+   S+Q  +E+A+ ++      V  AGRTD+GVHA  QV HFD  
Sbjct: 7   IEYDGCRYCGWQRQQYVDSVQQRLEEALSVIANSSCEVFCAGRTDAGVHATGQVVHFDTD 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                   C   NA+L   D +    + + D  FHARFSA+ R Y Y I          K
Sbjct: 67  VNRPMQSWCLGTNAHLP-EDIVVKWAIGVSD-DFHARFSALARRYRYVIYN-------NK 117

Query: 128 GRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            R+ ++PK       SLD E M  A Q L+G +DF++FR+  CQ+ +P R + H  V+  
Sbjct: 118 LRSAILPKGISHYHYSLDHEKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLIVSRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A  EGLY
Sbjct: 178 QDYIILDIQANAFVHHMVRNIVGSLIEVGRGDKPVEWIKWLLEKRDRTLAAPTAKAEGLY 237

Query: 241 FDSVEY 246
              V Y
Sbjct: 238 LVEVIY 243


>gi|293572050|ref|ZP_06683062.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
 gi|291607912|gb|EFF37222.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
          Length = 246

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 76/242 (31%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +     P A
Sbjct: 66  KTNSEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNNVIPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +   G ++
Sbjct: 124 FERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIERKGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               V   FL+  +R  +G+L  +G        +++  +++ R+  G   P +GL+ D V
Sbjct: 184 HFTFVGDGFLYKMVRIIMGTLLEIGTSAMPIETIDEIFESKVRQHAGETVPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|313672355|ref|YP_004050466.1| tRNA pseudouridine synthase a [Calditerrivibrio nitroreducens DSM
           19672]
 gi|312939111|gb|ADR18303.1| tRNA pseudouridine synthase A [Calditerrivibrio nitroreducens DSM
           19672]
          Length = 248

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 80/239 (33%), Positives = 130/239 (54%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           +EY+G+ + GWQ QK   ++Q  IE A+  +  + + + G+GRTD+GVHAL QV +F   
Sbjct: 12  VEYDGTEFHGWQFQKGLVTVQSEIEAALSKIYKKQIHIIGSGRTDAGVHALAQVFNFRAE 71

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           +      L   LN+ L  S  I I  +  VD  FHA+ SA  ++YLY+I+  + P A  +
Sbjct: 72  KYIESEPLNLGLNSLLPRS--IIIKKVEDVDVNFHAQKSAKSKTYLYKILNSELPSAFLR 129

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            R W +  S+D E         VG  DF+   ++     + +RTI+  +V    ++I I 
Sbjct: 130 NRVWWVRNSIDIEIFSEILSQFVGTFDFSAMCTMKSLKENSVRTINFINVYKTEHIINIE 189

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A  FLH  +R+ +G+   +   K   + + + ++++DRK+ GP APP+GLY   V Y
Sbjct: 190 INANGFLHNMVRNIIGTAFFIYRKKLHPSTVMEIIESRDRKKGGPTAPPQGLYLKEVFY 248


>gi|219685340|ref|ZP_03540159.1| tRNA pseudouridine synthase A [Borrelia garinii Far04]
 gi|219673113|gb|EED30133.1| tRNA pseudouridine synthase A [Borrelia garinii Far04]
          Length = 246

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 123/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y GS Y G+Q Q    +IQG IEKA+  +  + V +H +GRTD GVHA +Q+  FD+ 
Sbjct: 8   IAYEGSIYHGFQIQPTKPTIQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQIITFDIN 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALN+ L + ++I IL L  V   FH RF+A +R Y YRI+        E 
Sbjct: 68  INIQLNNLKKALNSIL-LKNSIKILKLKYVKNSFHPRFNAQKRKYSYRILNSNNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ D V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESVSTFETILKSKNRNLARTTAPANALFLDKVYY 245


>gi|154502979|ref|ZP_02040039.1| hypothetical protein RUMGNA_00801 [Ruminococcus gnavus ATCC 29149]
 gi|153796518|gb|EDN78938.1| hypothetical protein RUMGNA_00801 [Ruminococcus gnavus ATCC 29149]
          Length = 244

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 126/247 (51%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+GS Y GWQRQ N   +IQG +E+A     G  V V G+GRTD GVHA  
Sbjct: 1   MRTYKLTIAYDGSRYQGWQRQSNTDKTIQGLLEQAASEAAGYPVEVQGSGRTDGGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +       + +N  L +   I ++ + +V   FHAR SA+ + Y Y I  R
Sbjct: 61  QTASVILRGKVQESEFLQNMNRLLPLD--IRVIEMELVKNGFHARLSAVGKCYEYWIDMR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  PK L+ E M+ AA  L+GR+DF  F +   +  S IRTI    V  
Sbjct: 119 EKPDVFMRKYTYHYPKELNIEAMQRAADDLIGRYDFAAF-TDKKEEKSTIRTIYAIIVEV 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I      F++  +R   G+L  VGDG+ T   ++ AL  +DR + G LAP  GL
Sbjct: 178 QGDKLRIEYRGSGFMYHMVRILTGTLLEVGDGRRTPESVKAALAGRDRADAGFLAPARGL 237

Query: 240 YFDSVEY 246
               V Y
Sbjct: 238 TLKEVYY 244


>gi|326559413|gb|EGE09838.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 46P47B1]
 gi|326564997|gb|EGE15197.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 103P14B1]
 gi|326566051|gb|EGE16211.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 12P80B1]
 gi|326572448|gb|EGE22440.1| tRNA pseudouridine synthase A [Moraxella catarrhalis BC8]
 gi|326572505|gb|EGE22494.1| tRNA pseudouridine synthase A [Moraxella catarrhalis CO72]
 gi|326574101|gb|EGE24049.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 101P30B1]
 gi|326576065|gb|EGE25984.1| tRNA pseudouridine synthase A [Moraxella catarrhalis O35E]
          Length = 268

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 83/239 (34%), Positives = 132/239 (55%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IE+ G+ Y GWQRQ+    +Q  IEKA+  +  E + +  AGRTD+GVHA   +AHF   
Sbjct: 10  IEFIGTRYRGWQRQEEVIGVQAVIEKALSTIANESIELIAAGRTDAGVHAGNMIAHFVTH 69

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
            E       +  N+ L   D I++  +  +   FHARFSAI R Y Y  + +    A+ +
Sbjct: 70  AERSAHSWLRGTNSLLP--DDIALRWVQPMPDDFHARFSAIARRYRYITLNQPYRPAILR 127

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +       LD + M IA+Q +VG HDF++FR+  CQ++ P+RT+ H ++   G+ + + 
Sbjct: 128 HQVTHEYTKLDIDAMIIASQFIVGTHDFSSFRAAACQSNQPVRTVTHANLFQHGSYLILD 187

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A  FLH  +R+ +G+L  VG G+ +     + + A++R    P A  +GLYF +  Y
Sbjct: 188 IQADGFLHHMVRNIMGALFAVGRGEISPETFYELMLAKNRTLAPPTASADGLYFINAYY 246


>gi|315151105|gb|EFT95121.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0012]
          Length = 249

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLAEVRYE 248


>gi|291557656|emb|CBL34773.1| pseudouridylate synthase I [Eubacterium siraeum V10Sc8a]
          Length = 243

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 88/248 (35%), Positives = 126/248 (50%), Gaps = 18/248 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + YNG+ Y G+QRQ N +SIQ ++E+ +  +  E + ++G  RTD+GVHA   V +   V
Sbjct: 1   MAYNGTAYHGYQRQNNANSIQQTVEEVLSKLLCEDITINGCSRTDTGVHARAFVFN---V 57

Query: 68  REWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +   P+      K  NA L     I+ L+   +   FHARF +  + Y+YRI T      
Sbjct: 58  KTTCPIPCEGFIKGGNALL--PQDIAFLSCEDMPDSFHARFDSKGKEYIYRIYTGDVRDV 115

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS------SPIRTIDHFDVN 178
                A   P   D E MR AA+ +VG HDF +F    C+A       S +RT+   DV 
Sbjct: 116 FSADTALHYPYKPDIEKMRKAARLIVGEHDFASF----CKAEAKEHLLSTVRTVYSIDVE 171

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +EI+V    FLH  +R  VG+L  + +GK T  D+  AL   DR+  G    P G
Sbjct: 172 QTGDFVEIKVCGNGFLHNMVRIIVGTLIYISEGKRTEQDIINALTKPDREFAGKTVSPCG 231

Query: 239 LYFDSVEY 246
           LY + V Y
Sbjct: 232 LYLNKVFY 239


>gi|239624119|ref|ZP_04667150.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522150|gb|EEQ62016.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 249

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 129/248 (52%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y + + Y+G+ Y GWQ+Q N   +IQG +E+ +  + GE V V G+GRTD+GVHA  Q
Sbjct: 1   MNYIIWLSYDGTRYDGWQKQGNTEKTIQGKLERVLEKLDGEPVEVRGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F L  +  P  + + LN YL   + I++  +    ++FH+R +A+R++Y Y+I    
Sbjct: 61  VADFQLKGKRAPEEVMEYLNRYL--PEDIAVWRIQTAPERFHSRLNAVRKTYRYQIELGP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   + + + LD  +M  A  +L G  DF +F        S +RT++       
Sbjct: 119 KKDVFRRSYYYGLGQELDVASMERAVAYLTGTRDFKSFCGNKKMKKSTVRTLESIRFERL 178

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +  + I      FL   +R   G+L  VG G+    D+   L+A DR+  G  APPEGL
Sbjct: 179 EDTRLHISFTGNGFLQQMVRILTGTLIEVGQGRRKPEDIRSILEALDRQAAGFTAPPEGL 238

Query: 240 YFDSVEYS 247
           + + VEY 
Sbjct: 239 FLEKVEYG 246


>gi|71065963|ref|YP_264690.1| tRNA pseudouridine synthase A [Psychrobacter arcticus 273-4]
 gi|71038948|gb|AAZ19256.1| probable tRNA pseudouridine synthase [Psychrobacter arcticus 273-4]
          Length = 276

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 84/244 (34%), Positives = 131/244 (53%), Gaps = 4/244 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + IE+ G+ Y GWQRQ+    +Q ++E AI  V  E V V  AGRTDS VHA   +AHF
Sbjct: 15  AIAIEFLGTHYHGWQRQREVLGVQQALETAISTVANEPVEVIAAGRTDSSVHASNMIAHF 74

Query: 65  DLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            +   + P     + +N+ L   D I++  +  +   FHARF+AI R Y Y  + +    
Sbjct: 75  -VTHAYRPTHNWLRGVNSLLP--DDIALRWVQPMPADFHARFAAIARRYRYITLNQTQRP 131

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+   +   I + LD + M++AA  +VG HDF+++R+  CQ++ P+R I H ++ + G  
Sbjct: 132 AILNHQVTHIYEPLDLKAMQLAAADIVGTHDFSSYRAAACQSNQPVRHISHANLFTHGPF 191

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I   + A  FLH  +R+ +G+L  +G  +    D    L  +DR    P A  +GLYF +
Sbjct: 192 IVFDIQADGFLHHMVRNLMGTLYAIGRHELEPADFLNILAKKDRTIAPPTASGDGLYFIN 251

Query: 244 VEYS 247
             Y 
Sbjct: 252 AYYP 255


>gi|51598275|ref|YP_072463.1| tRNA pseudouridine synthase A [Borrelia garinii PBi]
 gi|62901275|sp|Q663A0|TRUA_BORGA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|51572846|gb|AAU06871.1| pseudouridylate synthase I [Borrelia garinii PBi]
          Length = 246

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 124/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    +IQG IEKA+  +  + V +H +GRTD GVHA +Q+  FD+ 
Sbjct: 8   ITYDGSIYHGFQIQPTKPTIQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQIITFDIN 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  +   FH RF+A +R Y YRI+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLKYMKNSFHPRFNAQKRKYSYRILNSNNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIYLAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ D V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLDKVYY 245


>gi|258512640|ref|YP_003186074.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257479366|gb|ACV59685.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
          Length = 262

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 131/251 (52%), Gaps = 14/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +++ Y+GSG+ G+ RQ+   ++QG +E  +  + G  ++V G+GRTD GVHA  QV 
Sbjct: 6   RIRLVLGYDGSGFHGFARQEGLRTVQGVLEDELRRMLGVDILVEGSGRTDRGVHARAQVV 65

Query: 63  HFDLVREWVPV------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           HFDL   + P       +L + L A L   D         VD+ FHARFS +R++Y Y +
Sbjct: 66  HFDL--PYGPPADRMVHVLRRRLPADLLPRDA------GEVDEGFHARFSVVRKTYRYTL 117

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P       +W  P+ LD   M+ AA+HL+G HDFT+F +   +    +R ID  +
Sbjct: 118 DLAPLPSLYWYRFSWHHPEPLDLAAMQEAARHLLGEHDFTSFCAAEARQRDKVRRIDRVE 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G+ + I      FL   +R  VG+L  VG G+     +   L+A+DR+  G  APP
Sbjct: 178 FRQDGSRLHIEFEGNGFLQYMVRILVGTLVKVGRGQERPDRIPLILEARDRRLAGETAPP 237

Query: 237 EGLYFDSVEYS 247
            GL   +VEY 
Sbjct: 238 HGLCLWNVEYP 248


>gi|251799612|ref|YP_003014343.1| tRNA pseudouridine synthase A [Paenibacillus sp. JDR-2]
 gi|247547238|gb|ACT04257.1| tRNA pseudouridine synthase A [Paenibacillus sp. JDR-2]
          Length = 246

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 88/240 (36%), Positives = 127/240 (52%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ + G+Q Q  G +IQ  IE AI  +TGE +++ G+GRTD+GVHA  QV +F L 
Sbjct: 8   VSYDGTDFNGFQSQPYGRTIQQEIELAIKKLTGEDIIILGSGRTDAGVHANGQVFNF-LT 66

Query: 68  REWVPVIL-CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
              +P      ALN   ++   I IL    V + FH+R SA R++Y Y I   + P    
Sbjct: 67  ESTIPAERWAIALNT--RLPKDIVILEAHEVPEAFHSRRSAKRKTYRYTIDMGKFPDVFY 124

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +  A+  P  L+ E M+     LVG HDFT+F SIH      +RTI    +   G ++ +
Sbjct: 125 RRYAFHHPTPLNVEAMQKGLSFLVGEHDFTSFTSIHSTKPHHVRTIYEAYLEREGQMLHM 184

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +    FL+  IR  +G+L  VG GK    D+ + L+ + R   GP A P GL    VEY
Sbjct: 185 YMTGNGFLYNMIRIVMGTLLHVGHGKLKPEDMARILEGRKRSLAGPTAMPHGLMLMKVEY 244


>gi|313636153|gb|EFS02014.1| tRNA pseudouridine synthase A [Listeria seeligeri FSL S4-171]
          Length = 248

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 133/252 (52%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R+  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRFKAIISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDISAEKFQKALQVMTPFD--ISFLIVEEAPADFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  L+ E M++A++ LVG HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KVFDPFSRNFALHYPYELNLEKMKLASERLVGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  D+ KAL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V+Y 
Sbjct: 237 PQGLYLWRVDYE 248


>gi|114567807|ref|YP_754961.1| pseudouridylate synthase [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|122317314|sp|Q0AUL4|TRUA_SYNWW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|114338742|gb|ABI69590.1| Pseudouridylate synthase [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
          Length = 249

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++EY+GS Y G+Q QKN +++Q  +EKAI+ ++GE   +  AGRTD+GVHA  Q
Sbjct: 1   MSRIKLLLEYDGSNYHGFQLQKNANTVQAELEKAIYRLSGERATIVCAGRTDAGVHAWGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD            ALN+  ++ + I +L       +F+ RF A+++ Y Y I  ++
Sbjct: 61  VVAFDSCSTIPGDRWAYALNS--QLPEDIQVLESQETRAEFNPRFDALKKCYGYLIYRQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A    + L  E M+ AA+ L GR +F +F +    A +  R I H  ++  
Sbjct: 119 KKATFYRHYALCNTEPLKLEAMQEAAEILKGRQNFRSFCASGSSARTFEREIFHCRLSEK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + + + A  FL+  +R   G+L  VG GK+    L + + +QDR   GP APP+GLY
Sbjct: 179 GPCLLLHIAADGFLYNMVRIITGTLLEVGKGKYPPQHLREIIASQDRTRAGPTAPPQGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LLQVFY 244


>gi|58699741|ref|ZP_00374392.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533741|gb|EAL58089.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 156

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 71/156 (45%), Positives = 93/156 (59%)

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           +LN  +VD  FHARFSA +R Y YRI+ R AP ALE G  W +   LD   MR AA+HL+
Sbjct: 1   MLNAEVVDDAFHARFSAKKRYYEYRIVNRYAPAALETGYVWQVFSPLDVNIMREAAKHLL 60

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
           G+HD ++FRS  C A++PIRTID  D+   GN I I++ A SFLH Q+R   G+L   G 
Sbjct: 61  GKHDLSSFRSKDCHAANPIRTIDDIDIVQNGNHIHIKISAISFLHNQVRIIAGTLVEFGK 120

Query: 211 GKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +    ++   L    R   G  APP GLY   ++Y
Sbjct: 121 NRTNPQEMLHILSQCKRSAAGVTAPPFGLYLVKIDY 156


>gi|169830466|ref|YP_001716448.1| tRNA pseudouridine synthase A [Candidatus Desulforudis audaxviator
           MP104C]
 gi|238688213|sp|B1I1B5|TRUA_DESAP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169637310|gb|ACA58816.1| tRNA pseudouridine synthase A [Candidatus Desulforudis audaxviator
           MP104C]
          Length = 250

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 81/244 (33%), Positives = 131/244 (53%), Gaps = 5/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + Y+G+ Y G+Q+Q      +IQ ++E+ +  ++G  + V GA RTD+GVHA  QV +
Sbjct: 6   LTLAYDGTAYHGFQKQSGSGLPTIQETLERCLAELSGAALKVTGASRTDAGVHARGQVVN 65

Query: 64  FDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F   R  +P   +  ALN  L     I+ L+   V   FHAR+SA+ ++Y Y +      
Sbjct: 66  FVTGRWGIPTERIPAALNGVLP--GDIAALDAREVPADFHARYSAVAKTYSYTLYNHPVR 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              ++  +  +P++LD   MR+AA+HL+GRHDF+TF++      S +RT+   D+ +   
Sbjct: 124 SPFQRLYSLHVPRALDLRAMRLAARHLMGRHDFSTFQAAGRPVQSAVRTLTRADIEAQAP 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           L+ +   A  FL+  +R   G+L  VG  +     L   + + DR   GP  PP GL  +
Sbjct: 184 LVRLVFRADGFLYNMVRIMAGTLLEVGLERLDPEALPDIIASGDRARAGPTVPPHGLCLE 243

Query: 243 SVEY 246
            VEY
Sbjct: 244 EVEY 247


>gi|149926375|ref|ZP_01914636.1| tRNA pseudouridine synthase A [Limnobacter sp. MED105]
 gi|149824738|gb|EDM83952.1| tRNA pseudouridine synthase A [Limnobacter sp. MED105]
          Length = 254

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 129/246 (52%), Gaps = 3/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G  + GWQ Q +G ++Q  + KAI  +  E + +  AGRTD+GVHA +Q
Sbjct: 1   MNRVVLGLCYDGHEFEGWQTQPHGRTVQDYLTKAIEAIAQEPIALTCAGRTDTGVHARQQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       K +N  L  S  IS+     +D  FHARFSA+ R+Y Y   +  
Sbjct: 61  VVHFDTAAERPLTAWVKGVNNSLPSS--ISVQGAKQIDSGFHARFSAVSRTYRYYFYSAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++   W +   LD   MR AA  L+G HDF+ FR+  CQA+SP+RT+   ++   
Sbjct: 119 VRDPFKRFMTW-VHYPLDLAAMRRAAVCLLGTHDFSAFRASQCQAASPVRTLYALNLIEA 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +     +   +FLH  +R+ +GSL  VG  + +   L+  L +++R       P +GL 
Sbjct: 178 DDHCYFEIHGNAFLHHMVRNLMGSLMEVGQHRQSEAWLQDVLVSKNRSLAAKTYPAQGLS 237

Query: 241 FDSVEY 246
             ++EY
Sbjct: 238 LWNIEY 243


>gi|332970797|gb|EGK09777.1| tRNA pseudouridine synthase A [Desmospora sp. 8437]
          Length = 258

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 86/253 (33%), Positives = 130/253 (51%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + + Y+G+ + G+QRQ    ++QG++E+ +  VTGE + V GAGRTD+GVHAL Q
Sbjct: 1   MGKIKLTVAYDGTDFSGFQRQPGKRTVQGTLEETLTRVTGETISVTGAGRTDAGVHALGQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+         WV     + LNA L     + +     V ++FHAR+ A  + Y Y 
Sbjct: 61  VIHFETSVPIPTERWV-----RLLNASL--PRDLLVTQAKEVPREFHARYDACWKHYRYT 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           + T   P    +      P  L  + M+ AA+HL G HDFT+F +   Q     R++ H 
Sbjct: 114 LDTCPIPDLFRRRYQTHYPHPLSRDRMQRAARHLTGTHDFTSFSAARAQVKDRRRSLYHC 173

Query: 176 DVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +V      ++ I VV   FL+  +R   G+L  +G GK    ++   L+A+DR   G   
Sbjct: 174 EVKEVNPGVLSIEVVGDGFLYHMVRILTGTLVEIGAGKIPPDEIRGILKAKDRSAAGKTF 233

Query: 235 PPEGLYFDSVEYS 247
           PPEGL    V Y+
Sbjct: 234 PPEGLVMVEVGYT 246


>gi|229825283|ref|ZP_04451352.1| hypothetical protein GCWU000182_00637 [Abiotrophia defectiva ATCC
           49176]
 gi|229790655|gb|EEP26769.1| hypothetical protein GCWU000182_00637 [Abiotrophia defectiva ATCC
           49176]
          Length = 249

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +++ Y+G+ Y G+Q Q    +++G +  A+  + GE +V+ GA RTD+GVHA   
Sbjct: 1   MKRFKLVVAYDGTAYCGYQYQPELPTVEGFVNDALSELLGENIVIIGASRTDAGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         L  ALN   K++D I I+    V   FH R + I ++Y YRI T +
Sbjct: 61  VAVFDSDTRIPAEKLALALNT--KLADDIRIMESLEVAADFHPRKNVIDKTYEYRINTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
                ++  ++ +  +LD E MR AA+++ GRHDFT+F S        +RT+   DV  +
Sbjct: 119 ISFPTDRLYSYNVKHNLDIEAMREAAKYIEGRHDFTSFCSAKTDKEDKVRTVFQIDVEET 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + IRV    FL+  +R   G+L  VG+GK +  ++   ++ +DR   G   P +GL
Sbjct: 179 LRSELIIRVRGDGFLYNMVRIIAGTLVKVGEGKISPNEIPSIIERKDRGHLGTTLPAKGL 238

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 239 FLMGIRY 245


>gi|116873964|ref|YP_850745.1| tRNA pseudouridine synthase A [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|123466636|sp|A0ALT4|TRUA_LISW6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116742842|emb|CAK21966.1| tRNA pseudouridine synthase A [Listeria welshimeri serovar 6b str.
           SLCC5334]
          Length = 248

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 133/252 (52%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQIQPNARTVQAEIEKALKKMHKGKNVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSDLDITADKFQKALQVMTPFD--ISFLTVDEAPADFHARFGTVGKEYRYIVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KIFDPFSRNFALHYPYELDIAKMKLASECLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +S D+ +AL A+DR++     AP
Sbjct: 177 YEEDEETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISSEDITEALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V+Y 
Sbjct: 237 PQGLYLWRVDYE 248


>gi|93006392|ref|YP_580829.1| tRNA pseudouridine synthase A [Psychrobacter cryohalolentis K5]
 gi|92394070|gb|ABE75345.1| tRNA pseudouridine synthase A [Psychrobacter cryohalolentis K5]
          Length = 280

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/243 (34%), Positives = 131/243 (53%), Gaps = 4/243 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + IE+ G+ Y GWQRQ+    +Q ++E AI  V  E V V  AGRTDS VHA   +AHF
Sbjct: 19  AIAIEFLGTHYHGWQRQREVLGVQEALETAISTVANEPVEVIAAGRTDSSVHAGNMIAHF 78

Query: 65  DLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            +   + P     + +N+ L   D I++  +  +   FHARF+AI R Y Y  + +    
Sbjct: 79  -VTHAYRPSHNWLRGVNSLLP--DDIALRWVQPMPADFHARFAAIARRYRYITLNQTQRP 135

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+   +   I + LD + M++AA  +VG HDF+++R+  CQ++ P+R I H ++ + G  
Sbjct: 136 AILNHQVTHIHEPLDLKAMQLAAADIVGTHDFSSYRAAACQSNQPVRHISHANLFAHGQF 195

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I   + A  FLH  +R+ +G+L  +G  +    D    L  +DR    P A  +GLYF +
Sbjct: 196 IVFDIQADGFLHHMVRNLMGTLYAIGRHELEPADFLNILAKKDRTIAPPTASGDGLYFIN 255

Query: 244 VEY 246
             Y
Sbjct: 256 AYY 258


>gi|225164227|ref|ZP_03726501.1| tRNA-pseudouridine synthase I [Opitutaceae bacterium TAV2]
 gi|224801166|gb|EEG19488.1| tRNA-pseudouridine synthase I [Opitutaceae bacterium TAV2]
          Length = 354

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 86/250 (34%), Positives = 124/250 (49%), Gaps = 6/250 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+   + Y+G+ + GWQ Q +G++IQ  +E+ +  + GE V +HG+GRTD+GVHA  QV 
Sbjct: 100 RWKCTVAYDGTHFSGWQSQPDGNAIQDHLERRLARMLGESVRIHGSGRTDAGVHARAQVF 159

Query: 63  HFDLVREWVPVILCKALNA-----YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD      P  L  A  +        +   I + +  IV   FHARF A  + Y Y + 
Sbjct: 160 HFDAAWRHGPERLLAAFRSGGGEGGGGVPSGIQVTDARIVSAAFHARFDATGKRYTYDLH 219

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFD 176
                    +   W IP+ LD   MR AA  LVGRHDF  F ++  +   + +R +   D
Sbjct: 220 HGGFADPFTQDYCWSIPQKLDVVAMRAAAALLVGRHDFCAFSALSGEERETTVRHLTQLD 279

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +++ G  I I   A  FL+  +R  VG+L   G GK T  D+ + L    R      AP 
Sbjct: 280 ISARGARIRITARADGFLYRMVRRLVGALVHAGLGKLTPGDIAQILSEARRTPRIETAPA 339

Query: 237 EGLYFDSVEY 246
            GL+ D V Y
Sbjct: 340 HGLFLDRVFY 349


>gi|167755943|ref|ZP_02428070.1| hypothetical protein CLORAM_01463 [Clostridium ramosum DSM 1402]
 gi|167703935|gb|EDS18514.1| hypothetical protein CLORAM_01463 [Clostridium ramosum DSM 1402]
          Length = 245

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 134/247 (54%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R    + Y+GS + G+Q Q    ++QG I+KA+  +  E +++HG+GRTD+ VH  +Q
Sbjct: 1   MVRVKCSVSYDGSKFHGFQVQNKLRTVQGEIQKALKNICKEEIIIHGSGRTDAKVHGTKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  RE       +A+N +L   + I IL+   VD+ FH+R+SAI++ Y Y + T++
Sbjct: 61  VFHFDTTREMPEAQWKRAINHFL--PNDIYILDSYFVDENFHSRYSAIKKEYHYLLSTKE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E    +   + LD E MR AA+  +G HDF +F S + Q  + IR +    + + 
Sbjct: 119 YS-PFETNYIFQYGRPLDLELMREAAKIFIGEHDFASFCS-YDQYGNTIRELYELSITNE 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +I+  +V   F    +R  VG L  VG  + T   L++ L ++  ++C   A P+GLY
Sbjct: 177 KGIIKFILVGNGFRRYMVRHIVGGLIQVGAKRVTKERLQELLDSKGEQKCLFKAKPQGLY 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LHEVFYD 243


>gi|224534868|ref|ZP_03675437.1| tRNA pseudouridine synthase A [Borrelia spielmanii A14S]
 gi|224513808|gb|EEF84133.1| tRNA pseudouridine synthase A [Borrelia spielmanii A14S]
          Length = 246

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 88/239 (36%), Positives = 123/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    +IQG IEKA+  +  + + +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTIQGEIEKALMKINKKKIKIHSSGRTDKGVHAKRQIITFDMN 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L +   I IL L  V   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKSGIKILKLKHVKNSFHPRFSAQKRKYSYCILNSDNYYPWES 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A+ + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAYYVNKKLNISNLNQMAKILIGSHDFTTFSCIKDRSKSKFRHIHFAKFKKKGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS VG++  +     + +  EK LQ+++R      AP   L+ D V Y
Sbjct: 187 IIGSSFLWKMVRSIVGTMLDIEIKNESISTFEKILQSKNRNLARTTAPANALFLDKVYY 245


>gi|256855196|ref|ZP_05560557.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
 gi|307291679|ref|ZP_07571554.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|256709709|gb|EEU24756.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
 gi|306497298|gb|EFM66840.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|315028842|gb|EFT40774.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4000]
          Length = 249

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IE+ +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEETLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|227530236|ref|ZP_03960285.1| tRNA pseudouridine synthase A [Lactobacillus vaginalis ATCC 49540]
 gi|227349848|gb|EEJ40139.1| tRNA pseudouridine synthase A [Lactobacillus vaginalis ATCC 49540]
          Length = 256

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 134/252 (53%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M RY +   Y+GS + G+Q Q +  +++  ++ A+  +    T EI V+ G+GRTD+GVH
Sbjct: 1   MYRYKITFAYDGSNFSGFQIQPHKRTVEQVLKNAVNKIAKHPTPEIPVI-GSGRTDAGVH 59

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QVAHFD+        + KALN+ L +   I I    +VD  FHAR+SA  ++Y YR+
Sbjct: 60  ALNQVAHFDIPYHLSNESMRKALNSILPLD--ILIKKAELVDSDFHARYSAHNKTYRYRV 117

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +     ++         LD   MR AA++ +G HDFT+F +   QA S +RT+   D
Sbjct: 118 DQGEFVNPFKRNYTAHFKYPLDLTLMRKAAKNFIGEHDFTSFVASGSQAKSNVRTVYKID 177

Query: 177 V--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +  +   N +        FL+ QIR  V  L  +G  +    D+++ L A+DR +    A
Sbjct: 178 IKRDKLRNEVVFDFTGNGFLYNQIRIMVAFLLEIGSKQRPVDDVKRVLAAKDRTQARMTA 237

Query: 235 PPEGLYFDSVEY 246
           P  GLY  SV+Y
Sbjct: 238 PASGLYLVSVDY 249


>gi|1644206|dbj|BAA10987.1| unknown [Bacillus subtilis]
          Length = 247

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  + + + V  +GRTDSGVHA  
Sbjct: 1   MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAERWPYALNALL--PDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ ++MR AA+H +G HDFT+F +   +    +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFSYRLNVQDMREAAKHPIGTHDFTSFCAAKTEVQDKVRTIYELDWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK +  +++  L+A+DR+     AP  GL
Sbjct: 179 TADGLQMRITGSGFLYNMVRIIAGTLLDAGIGKISPDEVKSMLEAKDREAAERTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLWNVYYD 246


>gi|300857214|ref|YP_003782198.1| tRNA pseudouridine synthase A [Clostridium ljungdahlii DSM 13528]
 gi|300437329|gb|ADK17096.1| tRNA pseudouridine synthase A [Clostridium ljungdahlii DSM 13528]
          Length = 244

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ Y GWQRQ N  +IQ  +E+AI  +TG    V GA RTD+GVHA   
Sbjct: 1   MKNVMLTIEYDGTNYSGWQRQNNAMTIQQRLEEAIKKITGNFSEVIGASRTDAGVHARGF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +        ALN  L     I +LN   VD  FH+R+ ++ + Y+Y I+T  
Sbjct: 61  VCNFFTNSKMPSPNFKMALNGVL--PKDIVVLNAREVDNSFHSRYHSLGKKYVYTIVTGN 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               + +   +   + LD + M+ A ++ +G HDF+ F+     A S +RT+    +   
Sbjct: 119 NRPVIGRQYVYYFRRKLDIDKMKNACKYFIGTHDFSAFKKKGSSAKSSVRTVKELTIAQE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            NLI+  +V   FL+  +R  VG+L  VG G++T   ++  L ++DR + G   P  GL 
Sbjct: 179 DNLIKFSIVGDGFLYNMVRIIVGTLLEVGLGRFTPEYVKDILDSKDRSKAGKPVPALGLC 238

Query: 241 FDSVEY 246
            + + Y
Sbjct: 239 LEKIFY 244


>gi|256762037|ref|ZP_05502617.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
 gi|256683288|gb|EEU22983.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
          Length = 249

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++    + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERASEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|309389901|gb|ADO77781.1| tRNA pseudouridine synthase A [Halanaerobium praevalens DSM 2228]
          Length = 248

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 129/245 (52%), Gaps = 4/245 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y +I+EY+GS Y GWQRQKN   +IQ  IE+A+  +    V + GAGRTD+GVHA  Q A
Sbjct: 5   YKIIVEYDGSNYSGWQRQKNTEQTIQQKIEEALTKINKSQVKIDGAGRTDAGVHAAGQSA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F L  E  P  +  ALN  L   D I       V++ FHAR+ A  + Y YRI+     
Sbjct: 65  NFFLDVEIPPTKIPIALNTEL--PDDIICKKAIKVNQNFHARYDARGKKYRYRILNSNFN 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +   + + K LD + M+ AA+   G HDF +F +      S +RTI   D+ +  +
Sbjct: 123 SVFVRNFVYNVYKKLDLKMMQKAAKIFEGSHDFASFCAAGSSVESTVRTIRSIDIYAVDD 182

Query: 183 L-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + +V   FL+  +R   G+    G GK T ++LE  LQ+ +RK  G  AP +GL  
Sbjct: 183 SEIWLDIVGNGFLYNMVRILAGTFIETGMGKKTLSELEVILQSCNRKNAGFTAPAQGLTL 242

Query: 242 DSVEY 246
             V Y
Sbjct: 243 MEVFY 247


>gi|323703515|ref|ZP_08115161.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
 gi|323531506|gb|EGB21399.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
          Length = 249

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 86/244 (35%), Positives = 132/244 (54%), Gaps = 5/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + Y+G+ Y G+Q Q+    +++Q  +E A+  V  E V V GAGRTD+GVHA  QV +
Sbjct: 8   LTVAYDGTNYHGFQEQRGTGLATVQEVLEAALSKVANETVQVIGAGRTDAGVHARGQVVN 67

Query: 64  FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      VP   +  A+N+ L   D I+++    V   FHARFSA  ++Y Y I   +  
Sbjct: 68  FRSTNWPVPTEKIHLAVNSLL--PDDIAVIKAEEVPLDFHARFSATAKTYRYSIYNHRVM 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L +  A+  P+ LD E MR AAQ+L+G HDF +F++        +RTI   ++ S   
Sbjct: 126 SPLHRLYAYHEPRPLDIEAMRQAAQYLLGTHDFKSFQAQGTPVKDTVRTIYRAELVSEPP 185

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI + +    FL+  +R   G+L  VG GK +  +++  ++A++R   G   PP GL   
Sbjct: 186 LIHLYLRGNGFLYNMVRIITGTLLDVGKGKKSPPEMKSIIEARNRTRAGTTVPPHGLCLM 245

Query: 243 SVEY 246
            VEY
Sbjct: 246 EVEY 249


>gi|294624568|ref|ZP_06703244.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292601141|gb|EFF45202.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 257

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 95/248 (38%), Positives = 136/248 (54%), Gaps = 16/248 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++         FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRY 113

Query: 115 RIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R++ RQ  P    +  +W   + LD + M  AAQ L+G +DF+ FRS+ CQA    R + 
Sbjct: 114 RLLNRQIRPTLYRQTLSWER-RPLDADAMHGAAQALLGENDFSAFRSVQCQALHARRHLQ 172

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V  FG ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP 
Sbjct: 173 AIHVQRFGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPT 232

Query: 234 APPEGLYF 241
           APP+GL F
Sbjct: 233 APPQGLVF 240


>gi|295099211|emb|CBK88300.1| pseudouridylate synthase I [Eubacterium cylindroides T2-87]
          Length = 243

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 88/244 (36%), Positives = 128/244 (52%), Gaps = 4/244 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +I+ Y+GS Y GWQ+Q+N   IQ  IEKA+  +  + + +  +GRTD+ VHAL QV H
Sbjct: 3   YKVILAYDGSNYAGWQKQENALGIQEVIEKALTTIHKKEIFITASGRTDAKVHALGQVFH 62

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F+  ++  P     ALNA L   + I IL +S+    FHARFSA  + Y Y I T +   
Sbjct: 63  FEADKKIGPDRYKMALNALL--PEDIRILKVSMEADDFHARFSAKSKRYDY-ICTYEKEN 119

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNSFGN 182
                   ++  +L+ E MR A+++LVG HDFT+F S       P I+TI   D+     
Sbjct: 120 PFVYKYKEILNHTLNIEAMRKASEYLVGTHDFTSFSSSKIDPRKPRIKTITRIDIFEENQ 179

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I        FL  Q+R    +L +VG  K  + ++++ L  +D+  C   A P GLY  
Sbjct: 180 DIRFIYEGTGFLRYQVRMMTETLIMVGSNKIDTEEVKRILDKKDKSACRYNASPNGLYLV 239

Query: 243 SVEY 246
            V Y
Sbjct: 240 HVNY 243


>gi|332685695|ref|YP_004455469.1| tRNA pseudouridine synthase A [Melissococcus plutonius ATCC 35311]
 gi|332369704|dbj|BAK20660.1| tRNA pseudouridine synthase A [Melissococcus plutonius ATCC 35311]
          Length = 257

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 130/248 (52%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q Q NG ++Q  +EK ++ L   + + + G+GRTD+GVHAL 
Sbjct: 1   MPRYKAIIAYDGTNFNGFQSQINGRTVQDELEKTLYKLNNNQSITIFGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD ++      L  AL+   +    IS+  +  V   FHAR+  I ++Y ++I T 
Sbjct: 61  QVIHFDYLKARDVEKLRFALDT--QSPADISVKKIEEVSNNFHARYHVIEKTYQFKIDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P S+D   +  A   L+G HDFT+F +  C   S IRTI    V+ 
Sbjct: 119 KTRDPFRRFYASYFPHSIDLAKIEKALPDLLGEHDFTSFCAAGCSVDSKIRTIYEASVSQ 178

Query: 180 FG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + I        FL+  +R  VG+L  +G GK   T + + +  ++R+  GP A PEG
Sbjct: 179 TSEDEIIFTFRGNGFLYKMVRIIVGTLLKIGQGKIKETAIPEIIAGKNRRLAGPTAHPEG 238

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 239 LYLVQVIY 246


>gi|325920196|ref|ZP_08182154.1| pseudouridylate synthase I [Xanthomonas gardneri ATCC 19865]
 gi|325549321|gb|EGD20217.1| pseudouridylate synthase I [Xanthomonas gardneri ATCC 19865]
          Length = 257

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 132/247 (53%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G ++Q  ++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPTVQARLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++         FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARRDPRSWM-------LGTTARLPPSIAVRWCVPAAADFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       +SLD + M  AAQ L+G +DF  FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRSLDADAMHTAAQALLGENDFNAFRSVQCQAPHARRNLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+     +   L  +DR   GP A
Sbjct: 174 ISVQRIGEVVEMQVQANAFLHHMVRNIVGSLILVGTGEQPVDWIATLLAGRDRSVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|296113461|ref|YP_003627399.1| tRNA pseudouridine synthase A [Moraxella catarrhalis RH4]
 gi|295921155|gb|ADG61506.1| tRNA pseudouridine synthase A [Moraxella catarrhalis RH4]
 gi|326559732|gb|EGE10142.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 7169]
 gi|326568129|gb|EGE18213.1| tRNA pseudouridine synthase A [Moraxella catarrhalis BC7]
 gi|326568548|gb|EGE18620.1| tRNA pseudouridine synthase A [Moraxella catarrhalis BC1]
          Length = 268

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 83/239 (34%), Positives = 131/239 (54%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IE+ G+ Y GWQRQ+    +Q  IEKA+  +  E + +  AGRTD+GVHA   +AHF   
Sbjct: 10  IEFIGTRYRGWQRQEEVIGVQAVIEKALSTIANESIELIAAGRTDAGVHAGNMIAHFVTH 69

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
            E       +  N+ L   D I++  +  +   FHARFSAI R Y Y  + +    A+  
Sbjct: 70  AERSAHSWLRGTNSLLP--DDIALRWVQPMPDDFHARFSAIARRYRYITLNQPYRPAILH 127

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +       LD + M IA+Q +VG HDF++FR+  CQ++ P+RT+ H ++   G+ + + 
Sbjct: 128 HQVTHEYTKLDIDAMIIASQFIVGTHDFSSFRAAACQSNQPVRTVTHANLFQHGSYLILD 187

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A  FLH  +R+ +G+L  VG G+ +     + + A++R    P A  +GLYF +  Y
Sbjct: 188 IQADGFLHHMVRNIMGALFAVGRGEISPETFYELMLAKNRTLAPPTASADGLYFINAYY 246


>gi|303238754|ref|ZP_07325286.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
 gi|302593633|gb|EFL63349.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
          Length = 245

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 81/242 (33%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           ++I+Y+GS Y GWQR  +   +IQG +E+ +  ++ E + + G+GRTD+GVHA +QVA+F
Sbjct: 6   LVIQYDGSKYRGWQRLGDSDKTIQGKLEQVLSQMSNEKIELIGSGRTDAGVHAFKQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +     +   L  YL   + I +++   VD  FH+R     + YLYRI   +    
Sbjct: 66  HTKSDLAEDAMLDYLYKYL--PEDIVVIDAEEVDNMFHSRHHVKGKKYLYRIWNAKRHNP 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +     I + LD   MR AA+H  G HDF++F S+  +  S  R I   ++     ++
Sbjct: 124 FMRKHCTHIAEPLDIRLMRNAAEHFTGMHDFSSFTSLKTKNKSKEREIFSVEIEKENEIM 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I      FL+   R   G+L  VG G+  + ++ K L  +DRK  GP AP  GL    V
Sbjct: 184 DIVFYGNGFLYNMARIMAGTLIEVGAGRINADNIPKILAKKDRKLAGPTAPTNGLILYDV 243

Query: 245 EY 246
           EY
Sbjct: 244 EY 245


>gi|229823506|ref|ZP_04449575.1| hypothetical protein GCWU000282_00804 [Catonella morbi ATCC 51271]
 gi|229786950|gb|EEP23064.1| hypothetical protein GCWU000282_00804 [Catonella morbi ATCC 51271]
          Length = 257

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 89/253 (35%), Positives = 130/253 (51%), Gaps = 8/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
           M RY + + Y+GS + G+Q Q NG SIQ +++ A+  +     G  +    +GRTDSGVH
Sbjct: 1   MPRYAIQLAYDGSRFVGYQVQPNGPSIQANLDAALIKMAKCPEGVTIPTVASGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV HFD         + +ALNA L     I ++ ++ V   FHAR+ AI + Y YR+
Sbjct: 61  ALGQVVHFDYPAPMPQQAMQRALNALL--DPAIKVVAVARVADDFHARYHAIGKEYRYRV 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                    ++  +   P   D + +  A + +VG HDFT+F S        +RT+    
Sbjct: 119 DIGAYANPFKRLYSLHHPYRYDLDRINQALEAVVGTHDFTSFCSTKTDKEDKVRTVHLAR 178

Query: 177 VNSFGNLIEIRVVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           V    +  E+    R   FL+  IR  VG+   +GDG     +LE+ +Q Q+RKE GP A
Sbjct: 179 VWEDRDQQELVFQFRGTGFLYNMIRILVGTSLQIGDGLRPVNELERLIQVQNRKEAGPTA 238

Query: 235 PPEGLYFDSVEYS 247
           PP+GLY   V Y 
Sbjct: 239 PPQGLYLHQVFYE 251


>gi|148263121|ref|YP_001229827.1| tRNA pseudouridine synthase A [Geobacter uraniireducens Rf4]
 gi|189030134|sp|A5GB00|TRUA_GEOUR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146396621|gb|ABQ25254.1| tRNA pseudouridine synthase A [Geobacter uraniireducens Rf4]
          Length = 244

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 91/248 (36%), Positives = 126/248 (50%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +IIEY+G+ Y GWQ Q NG +IQ  IE ++  + GE V +H +GRTD+GVHAL  
Sbjct: 1   MRQIKLIIEYDGTNYSGWQVQPNGITIQQLIEASLATMLGEPVKLHSSGRTDAGVHALGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--IT 118
           VA F   +          LNA L   + I+I +       F+ R  A  + Y Y I    
Sbjct: 61  VAAFKTGKLLPLRAFSDGLNALLP--NDIAIRDAVEAPLSFNPRADAKSKHYRYTIYNAV 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R++PLA  +  +W +  +LD E M+ AA H VG HDF  FR+ +C A + +R +    V 
Sbjct: 119 RRSPLA--RLSSWHLRGALDIERMQAAASHFVGEHDFAAFRASNCAAKTTVRRLFSVSVA 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + I V    FL   +R   G+L  VG GK     +   L + DR   G  APP+G
Sbjct: 177 KDGESVIIDVHGSGFLKNMVRIIAGTLAEVGQGKKNPDAVPGLLVSGDRAASGITAPPQG 236

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 237 LCLVEVFY 244


>gi|322386788|ref|ZP_08060412.1| tRNA pseudouridine synthase A [Streptococcus cristatus ATCC 51100]
 gi|321269070|gb|EFX52006.1| tRNA pseudouridine synthase A [Streptococcus cristatus ATCC 51100]
          Length = 249

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 130/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  +I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ +V+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKALISYDGHDFAGFQRQPHARSVQEEIEKTLTRINKGQPIVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++++  V + FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLPSARDEEKLRFALDT--QTPEDIDVISVEEVTEDFHARYKPHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH----F 175
           +    + +  A   P  L+   M  A + L G HDFT F +      + +RTI      F
Sbjct: 119 RPKNPMMRHYATHYPYPLEIPLMEQAIKALEGTHDFTGFTASGTSVENKVRTITKASLTF 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D     N +        FL+ QIR+ VG+L  +G+ +     +E+ L+ +DR+  GP A 
Sbjct: 179 DAQR--NFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVNQIERILEEKDRQLAGPTAA 236

Query: 236 PEGLYFDSVEYS 247
           P GLY   + Y 
Sbjct: 237 PNGLYLKEIIYE 248


>gi|325689043|gb|EGD31051.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK115]
          Length = 249

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAEHNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|297620615|ref|YP_003708752.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
 gi|297375916|gb|ADI37746.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
          Length = 254

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 84/249 (33%), Positives = 137/249 (55%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +Y +II Y+G+ Y GWQ Q N  SIQ  +E+ + ++T     + GAGRTD+GVHA+ Q
Sbjct: 1   MKKYKLIIAYDGTQYSGWQMQPNALSIQEVLEEKLKVLTKTRTSLTGAGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF +   + P +L  +LN    +   I I+++  V   FHAR+SA  + Y Y +    
Sbjct: 61  VAHFKVEAPFNPSLLRLSLNG--LLPKDIRIMDVEEVPLDFHARYSATNKIYYYHLNLGP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS---PIRTIDHFDV 177
                EK  +W I  SL+ E ++    +L+G H+F+ F +   Q ++   PIRT+    V
Sbjct: 119 VQDPFEKQYSWNITNSLNMELLKKGISYLIGTHNFSAFANEANQGAAKKNPIRTLKRISV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + +     SFL+  +R+  G+L  V  GK +  +++K L+++DR+  G  AP +
Sbjct: 179 VPERIGMRLEFEGESFLYKMVRNMTGTLIDVAKGKLSPEEIKKILESKDRRNAGRAAPAK 238

Query: 238 GLYFDSVEY 246
           GL+   ++Y
Sbjct: 239 GLFLVRIDY 247


>gi|227494575|ref|ZP_03924891.1| tRNA-pseudouridine synthase I [Actinomyces coleocanis DSM 15436]
 gi|226832309|gb|EEH64692.1| tRNA-pseudouridine synthase I [Actinomyces coleocanis DSM 15436]
          Length = 302

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 90/266 (33%), Positives = 145/266 (54%), Gaps = 24/266 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ +   Y G+ + GW +Q    ++QG++E+A+ LV  E V +  AGRTD+GVHA  Q 
Sbjct: 1   MRFRLECAYRGTFFRGWAKQPGLRTVQGTLEEALALVLREPVELTVAGRTDAGVHASAQT 60

Query: 62  AHFDL-------VREWVPVI-----LCKALNAYLKISDT-------ISILNLSIVDKQFH 102
           AHFD+       V +   V+     L + LN  ++ +D+       + + ++  V   F 
Sbjct: 61  AHFDVCADRLMQVTKQAEVVHACEALTRRLNRLIRRADSNASGLPDVVVYSIEPVADVFD 120

Query: 103 ARFSAIRRSYLYRI--ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           ARF+A+RR Y+YR+  +  + PL  E    W + + L    MR AA+ LVG HDF +F  
Sbjct: 121 ARFAALRRHYVYRVADVAGRNPLYAES--VWWVEEPLQIHLMREAARALVGEHDFLSFCK 178

Query: 161 IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
              + +S IRT++  D+      +E+R+ A +F H+ +RS VG+L  VG G+   T +  
Sbjct: 179 PR-EGASTIRTLEAVDLVETDTGLEVRLSADAFCHSMVRSIVGALVEVGRGRKPVTWIAD 237

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEY 246
            +    R++  PLAPP GL   +V+Y
Sbjct: 238 LVAFPSREQAAPLAPPHGLTLRAVDY 263


>gi|168187780|ref|ZP_02622415.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
 gi|169294335|gb|EDS76468.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
          Length = 246

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 136/242 (56%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++IEY+GS Y GWQ+QK+  ++Q  IE+AIF +T + + + G  RTD+GVHA   VA+F 
Sbjct: 7   LVIEYDGSNYSGWQKQKHSMTVQQRIEEAIFDITKQNIEIIGCSRTDAGVHARNFVANFI 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +     P     A+N+  K+   I I     V   FHARF +  + Y+Y I+ R+ P  +
Sbjct: 67  IDSNIPPEKFKYAINS--KLPKDIVIKKSCEVPIDFHARFQSKGKKYVYTILNREEPPTI 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
           ++G  +   K LD + M+ A+++ +G H+F +F +       S +RTI + DV    ++I
Sbjct: 125 DRGVVYHFNKKLDVDLMKSASKYFIGSHEFDSFYKKAGSSVKSTLRTIYYCDVTKVDDII 184

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I V+   FL+  +R   G+L  VG  +    D++  + A+DR+  G   PP+GL  + V
Sbjct: 185 KIIVIGEGFLYNMVRIMAGTLVEVGITRIKPEDIKTIILAKDRERAGRSLPPQGLCLEEV 244

Query: 245 EY 246
            Y
Sbjct: 245 LY 246


>gi|319639209|ref|ZP_07993960.1| tRNA pseudouridine synthase A [Neisseria mucosa C102]
 gi|317399393|gb|EFV80063.1| tRNA pseudouridine synthase A [Neisseria mucosa C102]
          Length = 281

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 82/245 (33%), Positives = 128/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  QV
Sbjct: 14  RWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALTSIAGERINTIVAGRTDTGVHATAQV 73

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   D +++L    V   F+ARF A  R Y Y + +   
Sbjct: 74  VHFDTSVSRPEQAWVRGVNAHLP--DGVAVLLAQKVAPHFNARFDAYGRHYRYLLESSPV 131

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L  GR       LD   MR AA  L G HDF++FR+  CQA SPI+T+    ++   
Sbjct: 132 RSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPIKTLYSTKISGTS 191

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + +   +FLH  +R+ +G+L  VG G+ +  + E    A+ R    P    +GLY 
Sbjct: 192 RYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFESVFHAKSRLMAPPTFMSDGLYL 251

Query: 242 DSVEY 246
             V+Y
Sbjct: 252 TGVDY 256


>gi|332653968|ref|ZP_08419712.1| tRNA pseudouridine synthase A [Ruminococcaceae bacterium D16]
 gi|332517054|gb|EGJ46659.1| tRNA pseudouridine synthase A [Ruminococcaceae bacterium D16]
          Length = 250

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 123/239 (51%), Gaps = 6/239 (2%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           YNG+ Y GWQ QKN  S+  ++EKA+  V    V   GAGRTD+GVHA   +A+F     
Sbjct: 11  YNGTAYHGWQVQKNAISVAETLEKALSTVVCHPVKCTGAGRTDAGVHAEVYIANFRTTS- 69

Query: 70  WVPVILCK--ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
               I C    L    ++   I ++  + V  +F+A  S  R+ Y YRI   +       
Sbjct: 70  ---TIPCDRIPLAVNTRLPRDIVVVKATEVPMEFNAIGSCHRKEYTYRIYNSRLGNPFYV 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            RAW  PK LD + M+ AA   VG HDF   RS+  +  + +RT+ +FDV     LIE +
Sbjct: 127 DRAWFYPKYLDEKIMQQAADQFVGTHDFRAVRSVGTETRTTVRTVYYFDVTRHDQLIECK 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           V A  FL+  +R+  G++    +GK +  D+   L++ +R   GP  PP GLY   + Y
Sbjct: 187 VCANGFLYNMVRAMTGTIVYAAEGKLSPQDIPAILESGNRTLAGPTVPPGGLYMTKLWY 245


>gi|289435864|ref|YP_003465736.1| tRNA pseudouridine synthase A [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|289172108|emb|CBH28654.1| tRNA pseudouridine synthase A [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
          Length = 248

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 88/250 (35%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q +  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPDTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDISAEKFQKALQVMTPFD--ISFLIVEEAPADFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-N 178
           +      +  A   P  L+ E M++A++ LVG HDFT+F S   +  S +RT+   D   
Sbjct: 119 KVFDPFSRNFALHYPYELNLEKMKLASERLVGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAPPE 237
              + + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR++     APP+
Sbjct: 179 EEDDTLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|257866559|ref|ZP_05646212.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257872925|ref|ZP_05652578.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257800517|gb|EEV29545.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807089|gb|EEV35911.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 248

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ + + G+GRTD+GVHA  
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTKMNNGQPIQIQGSGRTDAGVHAQG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  ++     +   L+   +  + +++ ++ IVD  FHAR+  + ++Y +R+   
Sbjct: 61  QVIHFDFPQKRPLEKMRFGLDT--QTPEDVAVKSVEIVDDTFHARYLVVEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  LD E ++ A    +G HDFT+F +         RTI      V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLEKIQRALPDFLGTHDFTSFCATGSSVDDKTRTIHEASMAV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NDAGDELIFTFRGDGFLYKMIRIMVGTLLKIGNGRLAPDSIPAIIAQKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLVHVAYE 248


>gi|325697516|gb|EGD39402.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK160]
          Length = 249

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYNFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSNDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A  HL G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAHLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|167759245|ref|ZP_02431372.1| hypothetical protein CLOSCI_01592 [Clostridium scindens ATCC 35704]
 gi|167663119|gb|EDS07249.1| hypothetical protein CLOSCI_01592 [Clostridium scindens ATCC 35704]
          Length = 248

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 129/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I Y+G+ Y GWQ Q NG +++  + K +  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLTIAYDGTDYCGWQIQPNGITVEEILNKKLKKLTGEDIHVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF-SAIRRSYLYRIITR 119
           VA FD         +  ALN   ++ D I I++   V   +H R+   I ++Y Y I   
Sbjct: 61  VAVFDTESSIPAERMAYALNQ--RLPDDIVIVSSKEVPLDWHPRYQDEILKTYEYHIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L++  +  +   ++ E MR  A +L+G HDF +F ++       +RT+    +  
Sbjct: 119 PVQNPLKRRYSAFVSFPMNVEKMREGAAYLLGEHDFVSFCNVRTSVEDTVRTVKELMIEQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I IR+    FL+  +R   G+L  VG G +  T +++ L+A++R + G  APPEGL
Sbjct: 179 EGPDITIRITGNGFLYNMVRIIAGTLIRVGRGFYEPTKVKEILEARERTQAGVTAPPEGL 238

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 239 TLVCIEYD 246


>gi|121595540|ref|YP_987436.1| tRNA pseudouridine synthase A [Acidovorax sp. JS42]
 gi|166228674|sp|A1WAT5|TRUA_ACISJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120607620|gb|ABM43360.1| tRNA pseudouridine synthase A [Acidovorax sp. JS42]
          Length = 274

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 82/259 (31%), Positives = 125/259 (48%), Gaps = 16/259 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q + +++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGQAYNGWQSQPSANTVQDRLEAALGRFATQEVHTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FH+R  A+ R Y Y ++    
Sbjct: 61  VHFDTELQRAPFSWVRGTNTFLPAD--IAVQWAQPVPDAFHSRACAVARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--- 178
             +++ GR   +  +LD + M  A QHL+G HDFT+FR+  CQA SP++T+   D+    
Sbjct: 119 RPSVDAGRVGWVFHALDEQAMHKAVQHLLGEHDFTSFRASACQAKSPVKTLHRIDITRRA 178

Query: 179 -----SFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                S G                +FLH  IR+ +G +  +G G +    +   L+A+ R
Sbjct: 179 PPAGESTGTHGCVPCYWRFEFEGNAFLHHMIRNIMGCIVAIGQGLYPPEWMRTVLEARSR 238

Query: 228 KECGPLAPPEGLYFDSVEY 246
               P   P+GLYF    Y
Sbjct: 239 DAAAPTFSPDGLYFQGPVY 257


>gi|315640131|ref|ZP_07895253.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
 gi|315484108|gb|EFU74582.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
          Length = 248

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 130/248 (52%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY  II Y+G+ + G+QRQ  G ++Q  +E+ +  +  + +VVHG+GRTD+ VHAL Q
Sbjct: 3   MVRYKAIIAYDGTLFHGFQRQPQGRTVQEELERTLSKMASQPIVVHGSGRTDAHVHALGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  +E     +  A++   +  + I++  + IVD+ FHAR+    + Y + +   +
Sbjct: 63  VIHFDYPKERPLEKMRFAMDT--QTPEDIAVKQVEIVDELFHARYLVQEKVYEFHVQIGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A   P  LD   +  A   L+G HDF+ F +        +RTI    +   
Sbjct: 121 PRSPFRRHYASYYPYPLDLAKIERALPDLLGTHDFSAFCASGSSVEDKVRTIYEATMVHD 180

Query: 181 GNLIEIRVVAR--SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             L E+    R   FL+  IR  VG+L  +G+G+   T L K + ++DR   GP A PEG
Sbjct: 181 EALSELVFTFRGDGFLYKMIRILVGTLLKIGNGRLEETSLPKIIASKDRNCAGPTAHPEG 240

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 241 LYLKEVKY 248


>gi|332521721|ref|ZP_08398172.1| tRNA pseudouridine synthase A [Lacinutrix algicola 5H-3-7-4]
 gi|332042551|gb|EGI78752.1| tRNA pseudouridine synthase A [Lacinutrix algicola 5H-3-7-4]
          Length = 247

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 84/245 (34%), Positives = 125/245 (51%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQ Q N  S+Q  +EK +  +  E +   GAGRTD+GVHA++  
Sbjct: 1   MRYFIELSYNGKAYHGWQVQPNAISVQEVLEKGLSTLLKEKISTMGAGRTDAGVHAIQLF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD    +   +L   LN++L   + ISI N+  V    HARF A+ R YLYRI  ++ 
Sbjct: 61  AHFDTEVIFEEHMLQYKLNSFL--PEAISIQNIFKVKADAHARFDAVSRQYLYRIALQKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E  +A+L+   LD + ++ A + L    DF  F   +    +    I        G
Sbjct: 119 PFNTE--QAFLLKAKLDIDRIKEATKILFNYKDFQCFSKSNTDVKTYNCNIMKAQWEVVG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N ++  + A  FL   +R+ VG+L  VG GK    D+   +++++R E G   P   LY 
Sbjct: 177 NELQFTIKADRFLRNMVRAIVGTLINVGVGKLEVNDMHNIIKSKNRSEAGFSVPAHALYL 236

Query: 242 DSVEY 246
             V Y
Sbjct: 237 TEVAY 241


>gi|256854698|ref|ZP_05560062.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
 gi|256710258|gb|EEU25302.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
          Length = 246

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 82/242 (33%), Positives = 125/242 (51%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  ++ + ++FHAR++A  + Y Y +     P A
Sbjct: 66  KTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNSPIPNA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +   G ++
Sbjct: 124 FERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIERNGEML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +   V   FLH  +R  VG+L  +G G      +++    + R+     AP +GL+ D V
Sbjct: 184 QFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGASETAPAQGLFLDEV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|323350454|ref|ZP_08086117.1| tRNA pseudouridine synthase A [Streptococcus sanguinis VMC66]
 gi|322123391|gb|EFX95069.1| tRNA pseudouridine synthase A [Streptococcus sanguinis VMC66]
          Length = 249

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +    +   FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFLGNGFLYKQIRNMVGTLLKIGNKRMPVEQVQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|21243447|ref|NP_643029.1| tRNA pseudouridine synthase A [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|30913394|sp|Q8PJ25|TRUA_XANAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21109001|gb|AAM37565.1| tRNA pseudouridine synthase A [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 257

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 134/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++         FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRPLDADAMHGAAQALLGENDFSAFRSVQCQALHARRHLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP A
Sbjct: 174 IHVQRIGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|327404294|ref|YP_004345132.1| tRNA pseudouridine synthase A [Fluviicola taffensis DSM 16823]
 gi|327319802|gb|AEA44294.1| tRNA pseudouridine synthase A [Fluviicola taffensis DSM 16823]
          Length = 256

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 90/249 (36%), Positives = 128/249 (51%), Gaps = 11/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQ 60
            RY + + Y G+ Y GWQ Q N SSIQ  IE+ +  + G + + V G GRTD+GVHA   
Sbjct: 3   FRYALELAYRGTNYHGWQIQPNASSIQEEIERRLTQLNGNLPISVVGCGRTDTGVHATYY 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  +E     L   LN  L   + IS+ +  +V ++FHARFS   R+Y Y I  ++
Sbjct: 63  VLHFDSQKELDTEQLVFKLNKML--PEDISLFSAQLVSEEFHARFSPTTRTYHYFIHQKK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L+  R   I   +D E M  AA+ L+G  DFT+F  +H    + I T+     N  
Sbjct: 121 NPFLLDSHR---IVSEIDFEAMNRAARLLLGTQDFTSFSKLHTDVKTNICTVSEAKWNQV 177

Query: 181 GN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                  EI+  A  FL   +R+ VG+L  VG G     D+ K +  +DR E     P +
Sbjct: 178 SESEWYFEIK--ADRFLRNMVRAVVGTLLEVGYGNLGENDITKIVALKDRGEAKLSVPAK 235

Query: 238 GLYFDSVEY 246
           GL+  ++EY
Sbjct: 236 GLFLVNIEY 244


>gi|237733260|ref|ZP_04563741.1| tRNA pseudouridine synthase A [Mollicutes bacterium D7]
 gi|229383641|gb|EEO33732.1| tRNA pseudouridine synthase A [Coprobacillus sp. D7]
          Length = 245

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 133/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R    + Y+GS + G+Q Q    ++QG I+KA+  +  E +++HG+GRTD+ VH  +Q
Sbjct: 1   MVRVKCSVSYDGSKFHGFQVQNKLRTVQGEIQKALKNICKEEIIIHGSGRTDAKVHGTKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  RE       +A+N +L   + I IL+   VD+ FH+R+SAI++ Y Y + T +
Sbjct: 61  VFHFDTTREMPEAQWKRAINHFL--PNDIYILDSYFVDENFHSRYSAIKKEYHYLLSTNE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E    +   + LD E MR AA+  +G HDF +F S + Q  + IR +    + + 
Sbjct: 119 YS-PFETNYIFQYGRPLDLELMREAAKIFIGEHDFASFCS-YDQYGNTIRELYELSITNE 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +I+  +V   F    +R  VG L  VG  + T   L++ L ++  ++C   A P+GLY
Sbjct: 177 KGIIKFILVGNGFRRYMVRHIVGGLIQVGAKRVTKERLQELLDSKGEQKCLFKAKPQGLY 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LHEVFYD 243


>gi|39997968|ref|NP_953919.1| tRNA pseudouridine synthase A [Geobacter sulfurreducens PCA]
 gi|42559718|sp|P60350|TRUA_GEOSL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|39984913|gb|AAR36269.1| tRNA pseudouridine synthase A [Geobacter sulfurreducens PCA]
 gi|298506909|gb|ADI85632.1| tRNA pseudouridines 38,39,40 synthase [Geobacter sulfurreducens
           KN400]
          Length = 244

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/243 (34%), Positives = 127/243 (52%), Gaps = 6/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I+EY+G+ Y GWQ Q NG SIQ  +E A+  +  E V +  +GRTD+GVHA   VA FD
Sbjct: 6   LILEYDGTNYAGWQLQPNGLSIQEVVEGALARLLKEPVRLRASGRTDAGVHARGMVAAFD 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--ITRQAPL 123
             R          LNA L     I++ +       F+ RF+A  + Y Y I    R++PL
Sbjct: 66  TDRSIPLRAFSDGLNALL--PPDIAVRSADEALPGFNPRFAATGKHYRYTIHRGERRSPL 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
              + ++W +  +L+   MR AA+HL G  DF +FR+  C A + IR +D  +++  G +
Sbjct: 124 V--RLQSWHVRGALNLAAMREAARHLTGERDFASFRTAGCAARTTIRRVDAVEISDDGEM 181

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + V    FL   +R  VG+L  VG GK T   + + +        GP APP+GL    
Sbjct: 182 LTVDVHGSGFLRNMVRIMVGTLVEVGRGKLTPEHVAQMVVCPGVVPAGPTAPPQGLCLQK 241

Query: 244 VEY 246
           V +
Sbjct: 242 VRF 244


>gi|23097605|ref|NP_691071.1| tRNA pseudouridine synthase A [Oceanobacillus iheyensis HTE831]
 gi|38258776|sp|Q8CXP1|TRUA_OCEIH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|22775828|dbj|BAC12106.1| tRNA pseudouridine synthase A [Oceanobacillus iheyensis HTE831]
          Length = 253

 Score =  142 bits (359), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 130/249 (52%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+GS + G+Q Q +  ++QG +EKA++ +  G+ + +  +GRTD+GVHA+ 
Sbjct: 1   MERLKCTVSYDGSDFAGFQVQPDHRTVQGVLEKALYNMHKGKSIRIQASGRTDTGVHAVG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E       +ALN  L   D + I  +    ++FHAR+S   + Y Y ++  
Sbjct: 61  QVIHFDSPLEIPERNWKQALNTLL--PDDVRIQKVEKKTEEFHARYSVKEKEYHYFVLNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVN 178
           + P   ++G  +  P+ LD E M+ A Q+L G HDFT+F S       S +RT+ H   +
Sbjct: 119 EDPNVFQRGYVYHEPRKLDLERMQEACQYLEGTHDFTSFSSAKSSVKGSKVRTLYHVSCH 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  IE       FL+  +R  +  L  VG GK    D+   L +++R++ G    P+G
Sbjct: 179 QTGTNIEFIFRGSGFLYNMVRIMMSVLIDVGKGKRNPEDIIDLLASKNRQQIGKTMAPQG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLWRVSYE 247


>gi|225028683|ref|ZP_03717875.1| hypothetical protein EUBHAL_02962 [Eubacterium hallii DSM 3353]
 gi|224953993|gb|EEG35202.1| hypothetical protein EUBHAL_02962 [Eubacterium hallii DSM 3353]
          Length = 253

 Score =  142 bits (359), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 128/251 (50%), Gaps = 10/251 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y M I Y+GS Y+GW+ Q +  +IQG +E  +  + GE + V GAGRTD+GVHA   VA+
Sbjct: 5   YKMTICYDGSRYYGWEHQPDRDTIQGKLENVLTRMCGEFIDVLGAGRTDAGVHARGMVAN 64

Query: 64  --FDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
             FD        RE  P  +   +N YL   D I++  +    ++FHAR+ A+ + Y Y 
Sbjct: 65  AVFDATDKERGGRERTPDEIRDYMNRYL--PDDIAVKEVREASERFHARYKAVGKLYRYT 122

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                     ++    ++ K  D E M+ AA +L G+HD+ +F        S +R +D  
Sbjct: 123 CYDGPVKPVFQRKYVAVLEKRPDVEKMQQAAAYLEGKHDYKSFCGNPRMKKSTVRVVDKI 182

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           ++   G+ I        FL   +R  VG+L  VG GK     + + L+A++R+  GP AP
Sbjct: 183 EITRKGSFIYFDFHGTGFLQNMVRILVGTLLEVGKGKIKPEQIPEILEAKNRQMAGPTAP 242

Query: 236 PEGLYFDSVEY 246
            +GL    V+Y
Sbjct: 243 AQGLCLIKVDY 253


>gi|257899365|ref|ZP_05679018.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
 gi|257837277|gb|EEV62351.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
          Length = 248

 Score =  142 bits (358), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQRMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV ++FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRKVEIVSEEFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDV 177
           +      +  A   P  LD   ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLGKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPAIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|225569151|ref|ZP_03778176.1| hypothetical protein CLOHYLEM_05231 [Clostridium hylemonae DSM
           15053]
 gi|225161950|gb|EEG74569.1| hypothetical protein CLOHYLEM_05231 [Clostridium hylemonae DSM
           15053]
          Length = 246

 Score =  142 bits (358), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+GS Y GWQRQ    ++IQ  +E +I  + G  V V G+GRTD+GVHA  
Sbjct: 3   MRTYKLTVSYDGSRYQGWQRQATTDNTIQFVLEWSIGKLVGYRVHVDGSGRTDAGVHARG 62

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + + P     +LN YL   + I I+   +V   FHAR SA  + Y Y I  R
Sbjct: 63  QVASVKLSKLYDPQEFKDSLNRYL--PEDIRIVKAELVKNGFHARKSAKGKKYEYYIDCR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD E MR A ++LVG  +FT+F +   +   P+R I +  + S
Sbjct: 121 EKPDVFSRRYCYHYPEKLDIEAMRNAVEYLVGVKNFTSF-TDDKECRDPVRRITNIKIVS 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I      FL+  +R   G+L  +G GK  S  L   + A+DR   G LAP  GL
Sbjct: 180 TGDKVRITYYGTGFLYHMVRILTGTLLEIGTGKRDSAMLPVVIAAEDRSLAGFLAPARGL 239

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


>gi|58336660|ref|YP_193245.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus NCFM]
 gi|227903218|ref|ZP_04021023.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus ATCC 4796]
 gi|62901152|sp|Q5FM60|TRUA_LACAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|58253977|gb|AAV42214.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus NCFM]
 gi|227869023|gb|EEJ76444.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus ATCC 4796]
          Length = 262

 Score =  142 bits (358), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 86/251 (34%), Positives = 136/251 (54%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           + RY M + Y+G  + G+Q Q +  ++QG++E A+  +T G+ ++V G+GRTD+GVHA+ 
Sbjct: 2   LTRYKMTMAYDGHLFHGFQLQPDQRTVQGTVEDALKKMTKGKRIIVQGSGRTDAGVHAIG 61

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD   + +P   +  ALN+ +     I   +  IVD+ FHAR+S   + Y YR+  
Sbjct: 62  QVIHFDYPGKEIPANRMILALNSMMPTD--IVFTDCQIVDEDFHARYSIKGKWYRYRLSL 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
                  ++      P  LD E MRIAAQ L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 120 DYFVNPFKRFYTGHFPYQLDLEKMRIAAQDLLGKHDFTSFAASGGQIKDKVRTIYYINIT 179

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N I    +   FL+  +R  V +L  +G+ +    DL + + A+DR+E    A  
Sbjct: 180 KDEKENEIVFDFIGSGFLYNMVRIMVAALLEIGNERRPLHDLRRVIAAKDRQEVRQTAQG 239

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 SGLYLYHVFYD 250


>gi|327468298|gb|EGF13783.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK330]
          Length = 249

 Score =  142 bits (358), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQLHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V  +FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDEFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELRLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|160894723|ref|ZP_02075498.1| hypothetical protein CLOL250_02274 [Clostridium sp. L2-50]
 gi|156863657|gb|EDO57088.1| hypothetical protein CLOL250_02274 [Clostridium sp. L2-50]
          Length = 245

 Score =  142 bits (357), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 126/247 (51%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +I+  + + I  +  E + V GA RTD+GVHA   
Sbjct: 1   MKRVKLVVAYDGTNYHGWQVQDNGITIEEVLNRTISELVQEDIKVIGASRTDAGVHACGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN   ++ D I I     VD  FH R++   ++Y Y I+ R+
Sbjct: 61  VAVFDTESRIPGDKFSFALNQ--RLPDDIRIQESCEVDADFHPRYADTVKTYEYNILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  ++  A      +D E M  AA +LVG HDF +F S   Q  + +RTI   +V   
Sbjct: 119 FEMPSKRLYAAFCYYPMDIERMNQAAAYLVGEHDFKSFCSAGAQVQTTVRTIYAVNVTKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ IR+    FL+  +R   G+L  VG G      +++ L+A+DR + GP A  +GL 
Sbjct: 179 DDMVHIRITGNGFLYNMVRIIAGTLMQVGTGLMEPERVKEILEARDRSKAGPTAVAKGLT 238

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 239 LVEIRYE 245


>gi|315283801|ref|ZP_07871873.1| tRNA pseudouridine synthase A [Listeria marthii FSL S4-120]
 gi|313612551|gb|EFR86621.1| tRNA pseudouridine synthase A [Listeria marthii FSL S4-120]
          Length = 248

 Score =  142 bits (357), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 86/252 (34%), Positives = 133/252 (52%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLRVEEVADDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  L+   M++A++ L+G HDFT+F S   +  S +RT+  + ++ 
Sbjct: 119 KVFDPFSRNFALHYPYELNLAKMKLASERLIGEHDFTSFCSARTERDSKVRTL--YSIDF 176

Query: 180 FGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +    E  V+A     FL+  +R   G+L   G G+ +  ++ +AL A+DR++     AP
Sbjct: 177 YEEDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPEEITEALLARDRQKLISKTAP 236

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V+Y 
Sbjct: 237 PQGLYLWRVDYE 248


>gi|220928242|ref|YP_002505151.1| tRNA pseudouridine synthase A [Clostridium cellulolyticum H10]
 gi|254789632|sp|B8I814|TRUA_CLOCE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219998570|gb|ACL75171.1| tRNA pseudouridine synthase A [Clostridium cellulolyticum H10]
          Length = 245

 Score =  142 bits (357), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 89/243 (36%), Positives = 125/243 (51%), Gaps = 5/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ Y GWQ QKN  ++Q  I+KA+  + GE V V G  RTD GVHA  QVAHF 
Sbjct: 6   LTIEYDGTNYHGWQIQKNAKTVQEVIQKALSKLLGEDVGVTGCSRTDVGVHAYGQVAHF- 64

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           L    +P      A+N  L   D I I N   V ++FHAR+SA  + Y Y I       A
Sbjct: 65  LTDSKIPGDKFSYAINNLL--PDDIVIKNSEEVPEEFHARYSAKGKKYRYLIYNSPHASA 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFGNL 183
           + + R+  +   L+   M+ AA +  G HDF  F++   Q  S +R I   +V     N+
Sbjct: 123 IMRNRSCHVRPELNVAEMQKAAGYFKGEHDFLAFQATGGQVRSTVREIYGMEVYVKEDNM 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I I V    FL+  +R   G+L  VG GK   +++   +   DR + G  AP +GLY   
Sbjct: 183 ISIEVSGNGFLYNMVRIIAGTLIYVGMGKLHESEIPGIIAGLDRTKAGKTAPAQGLYLVQ 242

Query: 244 VEY 246
           + Y
Sbjct: 243 IYY 245


>gi|95928687|ref|ZP_01311433.1| tRNA pseudouridine synthase A [Desulfuromonas acetoxidans DSM 684]
 gi|95135032|gb|EAT16685.1| tRNA pseudouridine synthase A [Desulfuromonas acetoxidans DSM 684]
          Length = 251

 Score =  142 bits (357), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 127/247 (51%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R C+ +EY+G+ Y GWQ Q N  ++Q  IE A+  V G  V V+ +GRTD+GVHA+  
Sbjct: 1   MPRLCLTVEYDGTSYGGWQVQPNAQTVQEQIESALAQVIGASVRVYSSGRTDAGVHAIDM 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            AHFD V   +P+   +  +N +L     I +  +  V   FHARF A  + Y YR+   
Sbjct: 61  KAHFD-VETLLPLSAYREGVNRFLP--QDIVVRQVCRVADDFHARFDAQGKWYRYRLYRG 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    L +  +W +   LD E M  AA  LVG HDF  F++  C A++  RT+    +  
Sbjct: 118 RIRSPLHRLTSWHVAGGLDVEAMTQAADALVGTHDFAAFQASGCAAATTQRTLFEVLLID 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I V    FL   +R  VGSL  VG  K T+  L + L +  R   G  AP +GL
Sbjct: 178 EGDELIIDVRGSGFLKNMVRIIVGSLVEVGRAKLTAGQLAEILASGQRCRAGLTAPAQGL 237

Query: 240 YFDSVEY 246
               V Y
Sbjct: 238 CLMQVWY 244


>gi|146302394|ref|YP_001196985.1| tRNA pseudouridine synthase A [Flavobacterium johnsoniae UW101]
 gi|146156812|gb|ABQ07666.1| tRNA pseudouridine synthase A [Flavobacterium johnsoniae UW101]
          Length = 284

 Score =  142 bits (357), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 84/245 (34%), Positives = 125/245 (51%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG+ Y GWQ Q N SS+Q ++ KA+ ++    + V GAGRTD+GVHA    
Sbjct: 41  MRYFIHFAYNGTHYHGWQFQPNASSVQETLNKALSVLLNSTINVMGAGRTDTGVHAEEMY 100

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFDL +     +L   LN+YL     I++ NL  V    H RF A +R+Y Y I T + 
Sbjct: 101 GHFDLEKSIDIPVLVHKLNSYL--PKDIAVYNLIPVHDDAHCRFDATKRTYEYHINTVKN 158

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E   +W + + LD E M  AA+ L+   DF  F  ++   ++   TI         
Sbjct: 159 PFLEE--LSWYVTQKLDVELMNEAAKILLKHTDFQCFSKVNTDVNTFDCTIFEAYWKQEN 216

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG+L  +G  K T  D E  + +++R++ G   P  GLY 
Sbjct: 217 NKLVFTISANRFLRNMVRAIVGTLINIGLHKITLADFENIIASKNREKAGFSVPAHGLYL 276

Query: 242 DSVEY 246
             + Y
Sbjct: 277 TKIYY 281


>gi|42518460|ref|NP_964390.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii NCC 533]
 gi|51316717|sp|Q74L59|TRUA_LACJO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|41582745|gb|AAS08356.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii NCC 533]
          Length = 263

 Score =  142 bits (357), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 88/249 (35%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV
Sbjct: 4   RYKLTMAYDGHLFHGFQIQPNQRTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALNA + I DT+      IVD+ FH ++S   + Y Y +   +
Sbjct: 64  IHFDYPGKEIPAKNMMLALNALMPI-DTV-FFESEIVDEDFHVQYSTKGKWYRYVVDQHR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++   
Sbjct: 122 FTDPFNRFYTGHYPYPLDISLMKQAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITPD 181

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +  +I    +   FL+  +R  VG+L  +G+ K    D+ + L+A+DR+E    AP  G
Sbjct: 182 PDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLKAKDRQEVRTTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLQQVFYE 250


>gi|239618279|ref|YP_002941601.1| tRNA pseudouridine synthase A [Kosmotoga olearia TBF 19.5.1]
 gi|259550401|sp|C5CGS8|TRUA_KOSOT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239507110|gb|ACR80597.1| tRNA pseudouridine synthase A [Kosmotoga olearia TBF 19.5.1]
          Length = 250

 Score =  142 bits (357), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  ++ Y+GS +FG+Q Q N  ++QG  E+A+  +    +   GAGRTD+GVHA  Q
Sbjct: 1   MKRFAAVVVYDGSNFFGYQIQPNKRTVQGVFEEALERIHKAKIPTDGAGRTDTGVHAYGQ 60

Query: 61  VAHF--DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V  F  +L R   P  +  ALNA L   D I +  +  V   F  RF+A +R Y Y I+ 
Sbjct: 61  VIAFTSNLDR-LTPKHMKDALNANL--PDDIYVRRIHEVPSNFSPRFAAKKRIYHYYILN 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P    +   W  P  +D   MR A+++L+G HDFT+FR+ H   S+ IRTI    + 
Sbjct: 118 TKEPDLFRRKYFWWFPYEVDLNRMRQASRYLIGEHDFTSFRTGHDDRST-IRTITGIRIL 176

Query: 179 SF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N+I IRV   SFL   +R+ VG L  VG G       ++ L+A+DR +    AP  
Sbjct: 177 RLQKNIILIRVEGISFLRRMVRNIVGLLMRVGTGGIEPKKTKEILEARDRSKLPSSAPAH 236

Query: 238 GLYFDSV 244
           GL    V
Sbjct: 237 GLVLHKV 243


>gi|315925222|ref|ZP_07921436.1| tRNA pseudouridine synthase A [Pseudoramibacter alactolyticus ATCC
           23263]
 gi|315621456|gb|EFV01423.1| tRNA pseudouridine synthase A [Pseudoramibacter alactolyticus ATCC
           23263]
          Length = 249

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 118/247 (47%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    ++I Y G+ Y GWQRQ+N  SI  +I  AI  VTGE V ++GAGRTD+GVHA  Q
Sbjct: 1   MRNIALVIAYKGTRYAGWQRQQNAVSIDETIGDAIAAVTGERVTLYGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F             ALNA+L     I I     V   FH+R+ A  ++Y YR+    
Sbjct: 61  RANFKTRVRMPADRFAPALNAHL--PRDIRIQKSFEVPADFHSRYGAKEKTYCYRVWAAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L     W +   L+ + MR  A  LVG HDF TF +    A + +R ID   +   
Sbjct: 119 VADPLTDDFCWHVRFPLNVDAMRRGAAVLVGTHDFKTFMASGSGAKTTVRRIDAIGIEQK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I        FL+  +R   G+L  +G G+     +   L A+ R   G  AP  GL 
Sbjct: 179 GRMITFTFCGTGFLYNMVRIIAGTLVEMGSGRRDPESMAAILAAKGRTAAGATAPARGLT 238

Query: 241 FDSVEYS 247
            ++V Y 
Sbjct: 239 LEAVAYG 245


>gi|332529464|ref|ZP_08405423.1| tRNA pseudouridine synthase A [Hylemonella gracilis ATCC 19624]
 gi|332041110|gb|EGI77477.1| tRNA pseudouridine synthase A [Hylemonella gracilis ATCC 19624]
          Length = 270

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 81/255 (31%), Positives = 127/255 (49%), Gaps = 12/255 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ Y GWQ Q +G ++Q  +E A+     E +  + AGRTD+GVH L QV
Sbjct: 1   MRVALGLSYDGAAYDGWQSQPSGRTVQDRLEHALGRFANERITTNCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V  +FH+R SA  R Y Y ++    
Sbjct: 61  VHFDTQAQRTPYAWVRGTNTHLP--PDIAVQWAHPVPVEFHSRASATSRRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E  R   + + LD + M+ A  HL+G  DFT+FR+  CQA SPI+ +   +++  G
Sbjct: 119 RPSVEARRVGWVFQPLDLDAMQAALPHLLGERDFTSFRAAACQALSPIKNLMRVEISRRG 178

Query: 182 N----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                             A +FLH  IR+ +G L ++G GK     + + + A+ R    
Sbjct: 179 TRAGAEAPETCYWRFEFEASAFLHHMIRNIMGCLIVIGQGKKPPEWMAEVVAARSRDAAA 238

Query: 232 PLAPPEGLYFDSVEY 246
           P   P+GLYF    Y
Sbjct: 239 PTFMPDGLYFLGPRY 253


>gi|324989944|gb|EGC21886.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK353]
          Length = 249

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPDERDEEKLRFALDT--QTPEDIDFISVERVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELRLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITDAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTADPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|257454808|ref|ZP_05620059.1| tRNA pseudouridine synthase A [Enhydrobacter aerosaccus SK60]
 gi|257447741|gb|EEV22733.1| tRNA pseudouridine synthase A [Enhydrobacter aerosaccus SK60]
          Length = 268

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 83/243 (34%), Positives = 130/243 (53%), Gaps = 2/243 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + IE+ G+ Y GWQRQ+   SIQ  +E A+  +  E + V  AGRTD+GVHA   +AH
Sbjct: 6   YAISIEFIGTRYRGWQRQQEVDSIQQHVEAALSKIANEPIEVIAAGRTDAGVHASNMIAH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P    +A N+ L   D I++  + ++  +FHARFSAI R Y Y  +      
Sbjct: 66  FQTSATRQPYNWLRAANSLLP--DDIAVRWIQVMPAEFHARFSAIARRYRYITLNHPFRP 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+   +       L+ + M+ AA +L G HDFT+FR+  CQ++ P+R +    +   G L
Sbjct: 124 AILNQQITHEYAPLNVQLMQQAATYLEGTHDFTSFRAASCQSNQPVRHVHFAKLIQHGEL 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A  FLH  +R+ +G+L  +G G+     +E  L +++R      A  +GLYF +
Sbjct: 184 LVLDIQADGFLHHMVRNIMGTLFEIGRGEKPVAWIEALLLSKNRSLAAATASADGLYFIN 243

Query: 244 VEY 246
             Y
Sbjct: 244 ALY 246


>gi|322435303|ref|YP_004217515.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX9]
 gi|321163030|gb|ADW68735.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX9]
          Length = 258

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 87/262 (33%), Positives = 131/262 (50%), Gaps = 20/262 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + M + Y+G+ Y GWQ Q    ++QG +  A+ L+TGE V+  G+GRTD+GVHAL Q
Sbjct: 1   MRYWKMTLAYDGTAYHGWQVQPGLPTVQGRLAAALKLLTGETVLPQGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F L        L +ALN  L     I +L++  V+ +FHAR  A+R++Y YR+  R 
Sbjct: 61  VVSFGLEAPIPGENLLRALNRALP--GAIRVLSVEAVEAEFHARRGAVRKTYEYRLFPRV 118

Query: 121 --------APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--------IHCQ 164
                   +P+       W  P  +D      AA+ ++G HDF++F +        +   
Sbjct: 119 GVRPERICSPML--AAYVWDCPWEIDLGRAEAAARVILGEHDFSSFAASDPDRTERLSGV 176

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
             S +RT+     +    L+  RVV   FLH  +R+ VG       G+   +++   L A
Sbjct: 177 ERSNVRTVYESGWSELDGLMVYRVVGNGFLHHMVRNLVGCFVDAACGRTEVSEVAGILAA 236

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
           +DR  CG  AP  GL+   VEY
Sbjct: 237 KDRTACGATAPASGLFLVGVEY 258


>gi|327462829|gb|EGF09151.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1057]
          Length = 249

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVERVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRH 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLFKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|324992392|gb|EGC24313.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK405]
 gi|324996086|gb|EGC27997.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK678]
 gi|327460621|gb|EGF06956.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1]
 gi|327472350|gb|EGF17781.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK408]
 gi|327488890|gb|EGF20688.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1058]
          Length = 249

 Score =  141 bits (356), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMLVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|319939850|ref|ZP_08014205.1| tRNA pseudouridine synthase A [Streptococcus anginosus 1_2_62CV]
 gi|319810861|gb|EFW07180.1| tRNA pseudouridine synthase A [Streptococcus anginosus 1_2_62CV]
          Length = 249

 Score =  141 bits (356), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ V+VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHDFAGFQRQPHARSVQEEIEKTLTKINRGKPVIVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  + I  +++  V++ FH+R+    + Y + +   
Sbjct: 61  QVIHFDLPQKRDEEKLRFALDT--QTPEDIDFISVEEVNEDFHSRYWKHSKIYEFIVDVG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD   ++ A   L G HDFT F +      + +RTI     D 
Sbjct: 119 RPKNPMMRHYATHFPYPLDISLIKNAIAKLEGTHDFTGFTASGTSVENKVRTITEARLDF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N +        FL+ QIR+ VG+L  +G+G+     +++ L  ++R   GP A P 
Sbjct: 179 DEKRNFLIFTFSGNGFLYKQIRNMVGTLLKIGNGRMPVEQIDRILTEKNRHLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|221068666|ref|ZP_03544771.1| tRNA pseudouridine synthase A [Comamonas testosteroni KF-1]
 gi|220713689|gb|EED69057.1| tRNA pseudouridine synthase A [Comamonas testosteroni KF-1]
          Length = 276

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 82/255 (32%), Positives = 126/255 (49%), Gaps = 16/255 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTDSGVH L QV
Sbjct: 1   MRIALGVSYNGQAYRGWQSQPDGNTVQDKLEAALGRFAAQEVSTICAGRTDSGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ--FHARFSAIRRSYLYRIITR 119
            HFD   +  P    +  N +L   D        + D    FH+R  A  R Y Y ++  
Sbjct: 61  VHFDTGLQRTPNSWVRGTNTFLP-KDIAVQWAAEVADGPDGFHSRACATARRYAYVLLQS 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               ++++GR   + ++LD + MR AA  L+G HDF++FR+  CQA SP++T+   D++ 
Sbjct: 120 PVRPSVDQGRVGWVFQTLDAQRMRAAADLLLGEHDFSSFRAAGCQAKSPVKTLRRIDIHY 179

Query: 180 FG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
                                    +FLH  IR+ +G L  VG G      +++ L+A+ 
Sbjct: 180 RPAGQAPMRDTQMQCGYWRFEFEGSAFLHHMIRNIMGCLIYVGQGSKPVEWMQQVLEARS 239

Query: 227 RKECGPLAPPEGLYF 241
           R+   P   P+GLYF
Sbjct: 240 REVAAPTFSPDGLYF 254


>gi|221217465|ref|ZP_03588936.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 72a]
 gi|223889178|ref|ZP_03623767.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 64b]
 gi|225549711|ref|ZP_03770676.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 118a]
 gi|226321158|ref|ZP_03796699.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 29805]
 gi|221192743|gb|EEE18959.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 72a]
 gi|223885427|gb|EEF56528.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 64b]
 gi|225369671|gb|EEG99119.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 118a]
 gi|226233450|gb|EEH32190.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 29805]
          Length = 246

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 123/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQIITFDIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSDNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ + V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLERVYY 245


>gi|329666723|gb|AEB92671.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii DPC 6026]
          Length = 263

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV
Sbjct: 4   RYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALNA + I DT+      IVD+ FH ++S   + Y Y +   +
Sbjct: 64  IHFDYPGKEIPAKNMMLALNALMPI-DTV-FFESEIVDEDFHVQYSTKGKWYRYIVDQHR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                 +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++  +
Sbjct: 122 FTDPFNRFYTGHYPYPLDISLMQQAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITPD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           S    I    +   FL+  +R  VG+L  +G+ K    D+ + L+A+DR+E    AP  G
Sbjct: 182 SDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLKAKDRQEVRTTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLQQVFYE 250


>gi|238923689|ref|YP_002937205.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
 gi|238875364|gb|ACR75071.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
          Length = 276

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 84/244 (34%), Positives = 131/244 (53%), Gaps = 3/244 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y +I+ Y+G+ Y GWQ QK+   +IQG ++  +  + G+ V V G+GRTD+GVHA+ QVA
Sbjct: 30  YKIIVAYDGTRYKGWQVQKSTDDTIQGKLQHVLSTLAGKPVEVIGSGRTDAGVHAVGQVA 89

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F + + +    +   LN +L     I++ ++S V  +FHAR++A+ ++Y+Y I T    
Sbjct: 90  SFHMPKHFSKDEIFIWLNEHLPAD--IAVTDISNVPDRFHARYNAVSKTYVYTIHTGIVS 147

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +   +   K LD + M+ AA +L+G HDF  F        S +RTI   D+   G 
Sbjct: 148 DVFRRKYVYDYDKPLDTDRMKKAAAYLLGEHDFKAFCGNRHMKKSTVRTIFSIDIEKTGA 207

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I I      FL   IR   G+L  VGDG+     + + L ++DR + G  AP  GL  +
Sbjct: 208 DIVISYTGDGFLQNMIRIITGTLIEVGDGRKNPDAVMEILASKDRAQAGYTAPACGLRLE 267

Query: 243 SVEY 246
            V+Y
Sbjct: 268 RVDY 271


>gi|325695572|gb|EGD37472.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK150]
          Length = 249

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|190575294|ref|YP_001973139.1| tRNA pseudouridine synthase A [Stenotrophomonas maltophilia K279a]
 gi|229558000|sp|B2FNZ6|TRUA_STRMK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|190013216|emb|CAQ46850.1| putative tRNA pseudouridine synthase A [Stenotrophomonas
           maltophilia K279a]
          Length = 256

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 134/246 (54%), Gaps = 13/246 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EY+GS + GWQ   + G S+Q S+E+A+  V    + V  AGRTD+GVH   Q
Sbjct: 1   MRYALGVEYDGSDFRGWQNLGEGGPSVQASLEQALSSVADTPLQVVCAGRTDAGVHGQCQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD       R W+       L    ++  +I++     V   FHARFSA  R Y YR
Sbjct: 61  VVHFDTDVVRDPRAWM-------LGTTTRLPRSIAVRWCVPVADDFHARFSARARRYRYR 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++ R+   AL++       ++LD   M  A Q L+G +DF+ FRS+ CQA    R +   
Sbjct: 114 LLNREVRPALDRQTLSWERRALDETLMHAAGQALIGENDFSAFRSVQCQALHARRELQSL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V+  G +IE+ V   +FLH  +R+ VGSL LVG G+     + + L  +DR   GP AP
Sbjct: 174 QVSRQGEVIEVAVQGNAFLHHMVRNIVGSLILVGSGEKPVEWIAELLAGRDRTVAGPTAP 233

Query: 236 PEGLYF 241
           P+GL F
Sbjct: 234 PQGLVF 239


>gi|311111209|ref|ZP_07712606.1| tRNA pseudouridine synthase A [Lactobacillus gasseri MV-22]
 gi|311066363|gb|EFQ46703.1| tRNA pseudouridine synthase A [Lactobacillus gasseri MV-22]
          Length = 263

 Score =  141 bits (356), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV
Sbjct: 4   RYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALNA + I DT+   +  IVD  FH ++S   + Y Y +   +
Sbjct: 64  IHFDYPGKEIPAKNMMLALNALMPI-DTV-FFDSEIVDSDFHVQYSTKGKWYRYIVDQHR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++ S 
Sbjct: 122 FTDPFNRFYTGHYPYPLDIALMKKAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITSD 181

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +  +I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    AP  G
Sbjct: 182 PDNKKIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLQHVFYE 250


>gi|189423417|ref|YP_001950594.1| tRNA pseudouridine synthase A [Geobacter lovleyi SZ]
 gi|189419676|gb|ACD94074.1| tRNA pseudouridine synthase A [Geobacter lovleyi SZ]
          Length = 262

 Score =  141 bits (355), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 86/242 (35%), Positives = 123/242 (50%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +II+Y+G+ Y GWQ Q NG SIQ ++E A+  + G+ V V  +GRTD+GVHA+   A F 
Sbjct: 22  LIIQYDGTNYCGWQEQTNGPSIQETVELALAKILGQRVRVQSSGRTDAGVHAVAMPAVFR 81

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                +P+      +N +L   D I+I +   V   F A   A  ++Y Y I        
Sbjct: 82  -TESTIPLKAFVDGVNCHLP--DDIAIQSAVEVPTGFRAIGGARSKTYRYTIYNAPVRSP 138

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L +  +W + + LD + M+ AA + VG HDF  FR  +C A +  R ID   +N  G LI
Sbjct: 139 LNRRTSWHVREQLDLQAMQQAAAYFVGEHDFAAFRGANCSAVTSRRRIDAVQINQSGPLI 198

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I V    FL   +R   G+L  VG G++    +   L   DR+  G  APP+GL    V
Sbjct: 199 TIDVTGGGFLKYMVRIMAGTLVDVGRGRFAPEHVAGLLAEPDRQRGGVTAPPQGLSLLQV 258

Query: 245 EY 246
            Y
Sbjct: 259 IY 260


>gi|116628993|ref|YP_814165.1| tRNA pseudouridine synthase A [Lactobacillus gasseri ATCC 33323]
 gi|238853452|ref|ZP_04643830.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 202-4]
 gi|116094575|gb|ABJ59727.1| Pseudouridylate synthase [Lactobacillus gasseri ATCC 33323]
 gi|238833892|gb|EEQ26151.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 202-4]
          Length = 264

 Score =  141 bits (355), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV
Sbjct: 5   RYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 64

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALNA + I DT+   +  IVD  FH ++S   + Y Y +   +
Sbjct: 65  IHFDYPGKEIPAKNMMLALNALMPI-DTV-FFDSEIVDSDFHVQYSTKGKWYRYIVDQHR 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++ S 
Sbjct: 123 FTDPFNRFYTGHYPYPLDIALMKKAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITSD 182

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +  +I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    AP  G
Sbjct: 183 PDNKKIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTAPASG 242

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 243 LYLQHVFYE 251


>gi|225549204|ref|ZP_03770177.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 94a]
 gi|225370062|gb|EEG99502.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 94a]
 gi|312148421|gb|ADQ31080.1| tRNA pseudouridine synthase A [Borrelia burgdorferi JD1]
          Length = 246

 Score =  141 bits (355), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 83/239 (34%), Positives = 123/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQIITFDIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  +   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLRYIKNSFHPRFSAQKRKYSYCILNSDNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ + V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLERVYY 245


>gi|218249502|ref|YP_002374546.1| tRNA pseudouridine synthase A [Borrelia burgdorferi ZS7]
 gi|224532546|ref|ZP_03673169.1| tRNA pseudouridine synthase A [Borrelia burgdorferi WI91-23]
 gi|226322073|ref|ZP_03797598.1| tRNA pseudouridine synthase A [Borrelia burgdorferi Bol26]
 gi|226708642|sp|B7J0V1|TRUA_BORBZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1665842|emb|CAA70351.1| pseudouridylate synthase I [Borrelia burgdorferi]
 gi|2911585|emb|CAA11967.1| pseudouridylate synthase I [Borrelia burgdorferi]
 gi|218164690|gb|ACK74751.1| tRNA pseudouridine synthase A [Borrelia burgdorferi ZS7]
 gi|224512489|gb|EEF82867.1| tRNA pseudouridine synthase A [Borrelia burgdorferi WI91-23]
 gi|226232663|gb|EEH31417.1| tRNA pseudouridine synthase A [Borrelia burgdorferi Bol26]
          Length = 246

 Score =  141 bits (355), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 123/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQIITFDIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSDNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ + V Y
Sbjct: 187 IIGSSFLWKMVRSIMGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLERVYY 245


>gi|332886051|gb|EGK06295.1| tRNA pseudouridine synthase A [Dysgonomonas mossii DSM 22836]
          Length = 250

 Score =  141 bits (355), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 88/248 (35%), Positives = 124/248 (50%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  Y GWQ Q NG S+Q +IEKA+  +    + + GAGRTD+GVHA   
Sbjct: 1   MRRYFIYLAYNGENYCGWQIQPNGVSVQEAIEKALTTLLRTPIAIVGAGRTDAGVHARMM 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            AHFD     + + +L K LN+ L     ISI N+  V    HARF A  R Y Y I T 
Sbjct: 61  AAHFDYEAANLDLPLLAKKLNSIL--PKDISIYNIVEVKPDAHARFDATSRLYRYYITTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P        + +  +LD + M   A  L    DFT+F  +H    +   TI       
Sbjct: 119 KDPFLYH--LKYKVHGNLDIDKMNACADILFEYEDFTSFSKLHTDVKTNNCTILAAQWEK 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN     + A  FL   +RS VG+L   G GK  S ++ + ++A++R E G   P   L
Sbjct: 177 KGNDYIFTIKANRFLRNMVRSIVGTLLEAGKGKIDSGEMRRIIEAKNRGEAGISVPGHAL 236

Query: 240 YFDSVEYS 247
           + + +EY+
Sbjct: 237 FLEEIEYN 244


>gi|21231977|ref|NP_637894.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66767896|ref|YP_242658.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|188991012|ref|YP_001903022.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. B100]
 gi|30913393|sp|Q8P7R5|TRUA_XANCP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|81306127|sp|Q4UWD5|TRUA_XANC8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|229470759|sp|B0RR81|TRUA_XANCB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21113710|gb|AAM41818.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66573228|gb|AAY48638.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|167732772|emb|CAP50966.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris]
          Length = 257

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 133/247 (53%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q +++ A+  V    + V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQATLQAALSSVADAPIQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  ++++       + FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSVAVRWCVPAAEDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M  AAQ L+G +DF  FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRPLDAQAMHTAAQALLGENDFGAFRSVQCQALHARRNLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+     +   L  +DR   GP A
Sbjct: 174 ITVQRLGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPIDWIATLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|218186563|gb|EEC68990.1| hypothetical protein OsI_37759 [Oryza sativa Indica Group]
          Length = 391

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 98/316 (31%), Positives = 153/316 (48%), Gaps = 72/316 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V 
Sbjct: 72  RYLVAVEYVGTRFSGSQQQLNQRTVVGVLEEAFHKFIGQPVSIFCSSRTDTGVHALSNVC 131

Query: 63  HFDLVR-------EWVPV----ILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R       E +P     ++ +A+N +L+ ++  I + ++  V   FHAR+ A+ R
Sbjct: 132 HVDVERISKRKPGEMLPPHEPGVVKRAVNHFLQKNEGDIMVTDVRCVAPDFHARYKALER 191

Query: 111 SYLYRIITRQAPLAL-EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR+++   PL++ EK  AW IP+ L+ + M+ A   LVG HDF++FR+  CQA+SP+
Sbjct: 192 TYHYRLLSGSEPLSVFEKTSAWHIPEDLNVQAMKKACSILVGHHDFSSFRATGCQANSPM 251

Query: 170 RTIDHFDVNSF-------------------GNLIEIRVVA-------------------- 190
           RT+D   V                      G+L+  R                       
Sbjct: 252 RTLDELSVTEVFPSMFFPSSMERSEMESLDGHLVYSRTSVVESSGKGSDASSTSEQSRFE 311

Query: 191 -----------RSFLHT-QIRSF--------VGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                      R F+ T + RSF        VG LK VG G  T+ D+E+ L  +     
Sbjct: 312 NGEEFGKRLRHRCFVVTARARSFLYHQVRLMVGLLKSVGTGDLTTEDVERILNLKAVTAA 371

Query: 231 GPLAPPEGLYFDSVEY 246
            P+AP  GLY  +V+Y
Sbjct: 372 PPMAPACGLYLANVKY 387


>gi|289422511|ref|ZP_06424354.1| tRNA pseudouridine synthase A [Peptostreptococcus anaerobius 653-L]
 gi|289157083|gb|EFD05705.1| tRNA pseudouridine synthase A [Peptostreptococcus anaerobius 653-L]
          Length = 243

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 85/240 (35%), Positives = 128/240 (53%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y G+ Y GWQRQK+   IQG +E A   V    + V G+GRTD+GVHAL QVA+F  V
Sbjct: 8   VAYQGTNYCGWQRQKDSLGIQGELEYAGQKVFASKIDVTGSGRTDAGVHALGQVANFK-V 66

Query: 68  REWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
              +P+  + + LN   K+   I++L    VD+ FH+RFSA  ++Y Y+I   +      
Sbjct: 67  ETTIPIDKIPEVLNN--KLPKDIAVLEAVEVDEDFHSRFSAHNKTYRYQIYPSRIRSPFY 124

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           K   + +   LD + M+   + LVG HDF  F S      + +R I    V   G+LI +
Sbjct: 125 KDTCYQVKSPLDLDRMKKEVKGLVGVHDFVGFMSSGSSVKTTVREIYDAKVFEEGDLIVL 184

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +    FL+  +R   G+L  +G G    + ++  L+++DR   G  APP+GL+   VEY
Sbjct: 185 ELTGNGFLYNMVRIIAGTLVDMGRGHIGDSMVD-ILESKDRGRAGHTAPPQGLFLKEVEY 243


>gi|145352156|ref|XP_001420422.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580656|gb|ABO98715.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 308

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 95/283 (33%), Positives = 142/283 (50%), Gaps = 43/283 (15%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVH--GAGRTDSGVHALR 59
           RY   +EY+G+ + G+QRQ    +++QG++++A+   TG    +   G+ RTD GVHALR
Sbjct: 13  RYLAFLEYDGARFRGFQRQCGVAATVQGALDEALTAFTGARGAIECVGSSRTDVGVHALR 72

Query: 60  QVAHFDL-----------------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFH 102
             AHFD                  VR  V   L K L A +++++ + +  +   + +FH
Sbjct: 73  NSAHFDFARTTKDGTTVEPHDGASVRRGVNYHLRK-LGAAVRVTECVRVDEM---NPKFH 128

Query: 103 ARFSAIRRSYLYRIITRQAPLA---LEKGRAWLIPKS----LDCENMRIAAQHLVGRHDF 155
           AR  A+ R Y Y I+  +        +  RAW +  +    L+ + MR AA  L G HDF
Sbjct: 129 ARHDAVARRYRYDILVGERDDGGSLFDAERAWYVRATCDGRLNVDAMRDAAAALTGTHDF 188

Query: 156 TTFRSIHCQASSPIRTIDHFDVNS------------FGNLIEIRVVARSFLHTQIRSFVG 203
           ++FR+  CQASSP+RT+   DV                  I I V A SFL+ Q+R   G
Sbjct: 189 SSFRANGCQASSPVRTLTSIDVKEELTEWPAAEARGTKQKISIAVAAPSFLYHQVRLLAG 248

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +LK VG    T  D+++ L+A+D      +AP  GLY   V Y
Sbjct: 249 ALKAVGANDLTVKDVQELLEAKDVARAPQMAPAHGLYLADVAY 291


>gi|115487730|ref|NP_001066352.1| Os12g0194800 [Oryza sativa Japonica Group]
 gi|108862288|gb|ABA96079.2| tRNA pseudouridine synthase family protein, putative, expressed
           [Oryza sativa Japonica Group]
 gi|113648859|dbj|BAF29371.1| Os12g0194800 [Oryza sativa Japonica Group]
 gi|215678805|dbj|BAG95242.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|222616774|gb|EEE52906.1| hypothetical protein OsJ_35509 [Oryza sativa Japonica Group]
          Length = 391

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 98/316 (31%), Positives = 153/316 (48%), Gaps = 72/316 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V 
Sbjct: 72  RYLVAVEYVGTRFSGSQQQLNQRTVVGVLEEAFHKFIGQPVSIFCSSRTDTGVHALSNVC 131

Query: 63  HFDLVR-------EWVPV----ILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R       E +P     ++ +A+N +L+ ++  I + ++  V   FHAR+ A+ R
Sbjct: 132 HVDVERISKRKPGEMLPPHEPGVVKRAVNHFLQKNEGDIMVTDVRCVAPDFHARYKALER 191

Query: 111 SYLYRIITRQAPLAL-EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR+++   PL++ EK  AW IP+ L+ + M+ A   LVG HDF++FR+  CQA+SP+
Sbjct: 192 TYHYRLLSGSEPLSVFEKTSAWHIPEDLNVQAMKKACSILVGHHDFSSFRATGCQANSPM 251

Query: 170 RTIDHFDVNSF-------------------GNLIEIRVVA-------------------- 190
           RT+D   V                      G+L+  R                       
Sbjct: 252 RTLDELSVTEVFPSMFFPSSMERSEMESLDGHLVYSRTSVVESSGKGSDASSTSEQSRFE 311

Query: 191 -----------RSFLHT-QIRSF--------VGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                      R F+ T + RSF        VG LK VG G  T+ D+E+ L  +     
Sbjct: 312 NGEEFGKRLRHRCFVVTARARSFLYHQVRLMVGLLKSVGTGDLTTEDVERILNLKAVTAA 371

Query: 231 GPLAPPEGLYFDSVEY 246
            P+AP  GLY  +V+Y
Sbjct: 372 PPMAPACGLYLANVKY 387


>gi|77919497|ref|YP_357312.1| tRNA pseudouridine synthase A [Pelobacter carbinolicus DSM 2380]
 gi|123756611|sp|Q3A3B5|TRUA_PELCD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|77545580|gb|ABA89142.1| tRNA pseudouridine synthase A [Pelobacter carbinolicus DSM 2380]
          Length = 252

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 86/244 (35%), Positives = 129/244 (52%), Gaps = 6/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ Y GWQRQ NG S+Q  +E+A+  V G    +  +GRTD+GVHA   VAHF 
Sbjct: 6   LIIEYDGTPYVGWQRQPNGLSVQQVVEEALAKVCGGPHSLVSSGRTDAGVHARGMVAHFV 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR--QAPL 123
             +        + +N +L     I++ + +++   FHAR+SA+ + Y Y I     ++PL
Sbjct: 66  TPQPLPMAAYREGVNRFLPAQ--IAVRDAALMPDDFHARYSAVGKWYRYSIYRSPVRSPL 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A     +W +   LD + MR AA+ LVGRHDF  FR+  C A + +R +   D+      
Sbjct: 124 ACRF--SWHVRTVLDLQAMRQAARLLVGRHDFAAFRASGCAARTTVREVFSVDIVDAEEW 181

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + V    FL   +R  VG+L  VG G     ++   L    RK+ G  AP +GL    
Sbjct: 182 VYVDVRGSGFLRNMVRIMVGTLVEVGRGARPPEEVGAMLAGGCRKQSGITAPAQGLCLME 241

Query: 244 VEYS 247
           V Y+
Sbjct: 242 VAYA 245


>gi|264677138|ref|YP_003277044.1| tRNA pseudouridine synthase A [Comamonas testosteroni CNB-2]
 gi|299530680|ref|ZP_07044095.1| tRNA pseudouridine synthase A [Comamonas testosteroni S44]
 gi|262207650|gb|ACY31748.1| tRNA pseudouridine synthase A [Comamonas testosteroni CNB-2]
 gi|298721196|gb|EFI62138.1| tRNA pseudouridine synthase A [Comamonas testosteroni S44]
          Length = 276

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 83/255 (32%), Positives = 127/255 (49%), Gaps = 16/255 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTDSGVH L QV
Sbjct: 1   MRIALGVSYNGQAYRGWQSQPDGNTVQDKLEAALGRFAAQEVSTICAGRTDSGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD--KQFHARFSAIRRSYLYRIITR 119
            HFD   +  P    +  N +L   D        + D    FH+R  A  R Y Y ++  
Sbjct: 61  VHFDTELQRAPNSWVRGTNTFLP-KDIAVQWAAEVADGPNGFHSRACATARRYAYVLLQS 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
               +++ GR   + ++LD + MR AA  L+G HDF++FR+  CQA SP++T+   D++ 
Sbjct: 120 PVRPSVDHGRVGWVFQALDAQRMRAAADLLLGEHDFSSFRAAGCQAKSPVKTLRRIDIHY 179

Query: 179 --------SFGNL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
                     G +            +FLH  IR+ +G L  VG G      +++ L+A+ 
Sbjct: 180 RPAGQAPMRDGQMECGYWRFEFEGSAFLHHMIRNIMGCLIYVGQGSKPVEWMQQVLEARS 239

Query: 227 RKECGPLAPPEGLYF 241
           R+   P   P+GLYF
Sbjct: 240 REVAAPTFSPDGLYF 254


>gi|262282044|ref|ZP_06059813.1| tRNA pseudouridine synthase A [Streptococcus sp. 2_1_36FAA]
 gi|262262498|gb|EEY81195.1| tRNA pseudouridine synthase A [Streptococcus sp. 2_1_36FAA]
          Length = 249

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FHAR++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVERVSDDFHARYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRYYATHYPYPLELSLLEEAITQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPIEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|332365537|gb|EGJ43297.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1059]
          Length = 249

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVERVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMLVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|260662783|ref|ZP_05863677.1| tRNA pseudouridine synthase A [Lactobacillus fermentum 28-3-CHN]
 gi|260552864|gb|EEX25863.1| tRNA pseudouridine synthase A [Lactobacillus fermentum 28-3-CHN]
          Length = 258

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/252 (33%), Positives = 133/252 (52%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY +   Y+GS + G+Q Q    ++Q ++E+A+  +  +    ++V G+GRTD+GVHA
Sbjct: 1   MHRYKITFAYDGSNFAGFQVQPGERTVQQALERAVNKIAKKPQPPLMVFGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     L +ALN+ L +   + +   + V   FHARF A  + Y YR++
Sbjct: 61  LGQVAHFDLPYQIPGPSLVRALNSSLPLD--VLVKEATEVAPDFHARFDAHHKRYRYRVV 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D E M+ AAQ  VG HDFT+F +   QA+S +R ID   V
Sbjct: 119 GGEFTNPFKRNYTGHYKYPVDVERMQTAAQDFVGEHDFTSFVASGSQATSNVRRIDEVTV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +   + +    V   FL+ Q+R  V  L  +G+G+    D+ + ++A++R      AP
Sbjct: 179 VRDEENDEVVFDFVGNGFLYNQVRIMVAFLLEIGNGRRPVDDVMRVMKAKNRDLARGTAP 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ASGLYLVEVTYD 250


>gi|261380083|ref|ZP_05984656.1| tRNA pseudouridine synthase A [Neisseria subflava NJ9703]
 gi|284797300|gb|EFC52647.1| tRNA pseudouridine synthase A [Neisseria subflava NJ9703]
          Length = 281

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 129/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  QV
Sbjct: 14  RWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALTSIAGEQINTIVAGRTDTGVHATAQV 73

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   D +++L    V   F+ARF A  R Y Y + +   
Sbjct: 74  VHFDTSVSRPEQAWVRGVNAHLP--DGVAVLLAQKVAPHFNARFDAYGRHYRYLLESSPV 131

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L  GR       LD   MR AA  L G HDF++FR+  CQA SPI+T+    ++   
Sbjct: 132 CSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPIKTLYRASISGTP 191

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + +   +FLH  +R+ +G+L  VG G+ +  + +    A+ R +  P    +GLY 
Sbjct: 192 RYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFQSIFYARSRLKAPPTFMSDGLYL 251

Query: 242 DSVEY 246
             V+Y
Sbjct: 252 TGVDY 256


>gi|167767771|ref|ZP_02439824.1| hypothetical protein CLOSS21_02306 [Clostridium sp. SS2/1]
 gi|167710510|gb|EDS21089.1| hypothetical protein CLOSS21_02306 [Clostridium sp. SS2/1]
 gi|291558888|emb|CBL37688.1| pseudouridylate synthase I [butyrate-producing bacterium SSC/2]
          Length = 252

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+GY GWQ Q N  +++G + K I  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRVKLIVAYDGTGYCGWQVQPNEITVEGVLNKHISELTGEDIKVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         + KALNA  ++ + I I +   V   +H RF   R++Y Y     +
Sbjct: 61  VAVFDTESRIPGEKMAKALNA--RLPEDIIIQDSKEVPLDYHPRFQDTRKTYEYTFYNAR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E M+ AA + +G H F +  S   Q +S +R I   DV   
Sbjct: 119 YDNPVTSRHHHFVYVPLDVEKMKEAASYFLGEHCFISMCSSKAQVTSYVREIYECDVTQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I++RV    FL+  +R   G+L  VG GK     +++ L +++R   GP  P +GL 
Sbjct: 179 GRYIKMRVTGSGFLYNMVRLMAGTLLEVGRGKQEPQWVKEILASKERVTPGPKLPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LIQIEY 244


>gi|160900673|ref|YP_001566255.1| tRNA pseudouridine synthase A [Delftia acidovorans SPH-1]
 gi|238687164|sp|A9BNH5|TRUA_DELAS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160366257|gb|ABX37870.1| tRNA pseudouridine synthase A [Delftia acidovorans SPH-1]
          Length = 282

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 81/262 (30%), Positives = 129/262 (49%), Gaps = 24/262 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G++IQ  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVAYNGQRYSGWQSQLSGNTIQDHLEAALGRFAAQEVHTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FH+R  A  R Y Y ++    
Sbjct: 61  VHFDTPLDRAPFSWVRGTNTFLP--PDIAVQWAQPVPDAFHSRACATARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-- 179
             ++E GR   +  +LD + M+ AA+HL+G HDF++FR+  CQA SP++T+    +    
Sbjct: 119 RPSVEAGRVGWVFHALDGDAMQAAARHLLGEHDFSSFRASGCQAKSPVKTLHRLSITRRM 178

Query: 180 FGNLIEIRVVA--------------------RSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            G+  ++   +                     +FLH  +R+ +G L  +G G +    ++
Sbjct: 179 AGDGAQMAAASSMRPGDAAMECCYWRFEFEGSAFLHHMVRNIMGCLIAIGQGTYAPQWMQ 238

Query: 220 KALQAQDRKECGPLAPPEGLYF 241
           + L A+ R    P   P+GLYF
Sbjct: 239 QVLDARSRDAAAPTFSPDGLYF 260


>gi|291528184|emb|CBK93770.1| pseudouridylate synthase I [Eubacterium rectale M104/1]
          Length = 254

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/244 (34%), Positives = 130/244 (53%), Gaps = 3/244 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y +I+ Y+G+ Y GWQ QK+   +IQG ++  +  + G+ V V G+GRTD+GVHA+ QVA
Sbjct: 8   YKIIVAYDGTRYKGWQVQKSTDDTIQGKLQHVLSTLAGKPVEVIGSGRTDAGVHAVGQVA 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F + + +    +   LN +L     I++ ++S V  +FHAR++A+ ++Y+Y I T    
Sbjct: 68  SFHMPKHFSKDEIFIWLNEHLPAD--IAVTDISNVPDRFHARYNAVSKTYVYTIHTGIVS 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +   +   K LD + M+ AA +L+G HDF  F        S +RTI   D+   G 
Sbjct: 126 DVFRRKYVYDYDKPLDTDRMKKAAAYLLGEHDFKAFCGNKHMKKSTVRTIFSIDIEKTGA 185

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I I      FL   IR   G+L  VGDG+     +   L ++DR + G  AP  GL  +
Sbjct: 186 DIVISYTGDGFLQNMIRIITGTLIEVGDGRKNPDAVMGILASKDRAQAGYTAPACGLSLE 245

Query: 243 SVEY 246
            V+Y
Sbjct: 246 RVDY 249


>gi|312149333|gb|ADQ29404.1| tRNA pseudouridine synthase A [Borrelia burgdorferi N40]
          Length = 246

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 122/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQIITFDIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSDNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L   N+   A+ L+G HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLSISNLNQMAKTLIGNHDFTTFSCIKDKSKSKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ + V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLERVYY 245


>gi|297620993|ref|YP_003709130.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
 gi|297376294|gb|ADI38124.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
          Length = 254

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 80/239 (33%), Positives = 126/239 (52%), Gaps = 5/239 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + I Y+G+ + GWQ  K G SI+G ++KA+ ++  E + ++GA RTD+GVHAL Q+A+
Sbjct: 7   FLLTIAYDGTPFLGWQETKEGPSIEGELKKALRIILKEEIKLNGASRTDAGVHALGQLAN 66

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F   ++     L K++NA L     I +  +  V+  FHA  +   + Y YR+       
Sbjct: 67  FHTTKKPHLFTLLKSINALL--PGEIKVTAIEEVEASFHATLNNTGKQYRYRLSFGPVQF 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDVNSFG 181
              + R W IP  LD E MR+AA+ L G HDF  F ++    +  S IRT+    +    
Sbjct: 125 PHVRHREWHIPGKLDIEAMRLAAKSLEGTHDFKAFCNVKKNDTYDSTIRTLSKLSLAELE 184

Query: 182 N-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           N  +E+ +    FL+   R+ VG+L  +G  +     L+K +   DR + GP AP  GL
Sbjct: 185 NDTLEVIMEGNHFLYKMARNIVGTLVYIGKKRIQLNTLKKLVLNGDRTQLGPTAPAHGL 243


>gi|302390990|ref|YP_003826810.1| tRNA pseudouridine synthase A [Acetohalobium arabaticum DSM 5501]
 gi|302203067|gb|ADL11745.1| tRNA pseudouridine synthase A [Acetohalobium arabaticum DSM 5501]
          Length = 244

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 134/247 (54%), Gaps = 5/247 (2%)

Query: 2   IRYC-MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY   II Y+G+ Y+G+Q Q +  +IQ  +E+++ ++T E   V  AGRTD GVHA  Q
Sbjct: 1   MRYLKAIIAYDGTNYYGFQHQPDVPTIQDELEESLRILTKEKNKVIVAGRTDRGVHAQNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V +F   +   P+ L     A+   + + I I  +  V+  FHAR+ A  + Y YRI+ +
Sbjct: 61  VINF---KTESPIPLENIRFAWNNCLPNDILIKEVEDVNADFHARYDAEGKIYEYRILNQ 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P   ++   + I + LD   M  AA+ L+G +DF++F++      + +RTI   +V  
Sbjct: 118 PLPSVFKRNYTYHIKEELDSAAMAEAAECLIGTYDFSSFQASGSNVQTTVRTIQQAEVTQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              L+  R+    FL+  +R  VG+L  VG G+W    + + ++A+DR   GP AP +GL
Sbjct: 178 QDRLVIFRIEGDGFLYNMVRIIVGTLIKVGTGEWEVPRMSRIIEAEDRLAAGPTAPAQGL 237

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 238 RLIKVKY 244


>gi|194017442|ref|ZP_03056053.1| tRNA pseudouridine synthase A [Bacillus pumilus ATCC 7061]
 gi|194010714|gb|EDW20285.1| tRNA pseudouridine synthase A [Bacillus pumilus ATCC 7061]
          Length = 247

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 82/241 (34%), Positives = 126/241 (52%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + Y+G+ + G+Q Q    ++Q  IE A+  +    E++ +  +GRTDSGVHA  QV HFD
Sbjct: 7   VSYDGTHFKGYQVQPGQRTVQTEIESALARMHKQDELIPIVASGRTDSGVHAKGQVIHFD 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN+ L   D I +L    VD+ FHARFS + + Y Y++ T       
Sbjct: 67  TPLSIPMERWPFALNSLL--PDDIRVLKAEEVDESFHARFSVVSKEYRYKVSTETHQNVF 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A   P  LD + MR AA HL+G HDFT+F + + +    +R I   +  +  + +E
Sbjct: 125 TRQYACHFPYRLDADKMREAAGHLIGTHDFTSFCAANTEVQDKVREIYTLEWKNVSDGLE 184

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           +RV    FL+  +R   G+L  +G GK+   +++  L A++R+  G  AP  GLY   V 
Sbjct: 185 MRVRGNGFLYNMVRIIAGTLLEIGSGKFHPEEIKAMLAARNREAAGKTAPSHGLYLWEVF 244

Query: 246 Y 246
           Y
Sbjct: 245 Y 245


>gi|295692190|ref|YP_003600800.1| tRNA pseudouridine synthase a [Lactobacillus crispatus ST1]
 gi|295030296|emb|CBL49775.1| tRNA pseudouridine synthase A [Lactobacillus crispatus ST1]
          Length = 262

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/249 (33%), Positives = 137/249 (55%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ QV
Sbjct: 4   RYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGQRVIVQGSGRTDAGVHAVGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  A+N+ +     I   +  IVD+ FHAR+S   + Y YR+    
Sbjct: 64  IHFDYPGKTIPANRMILAMNSMMPTD--IIFDDCQIVDENFHARYSIKGKWYRYRVSLDH 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  LD E M++AAQ L+G+HDFT+F +   Q  + +RTI + ++  +
Sbjct: 122 FVNPFKRFYTGHFPYPLDIEKMQVAAQDLLGKHDFTSFAASGGQIENKVRTIYYVNITKD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   G
Sbjct: 182 EKENEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPIHDLQRVIAAKDRQEVRQTAHASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYD 250


>gi|15594358|ref|NP_212146.1| tRNA pseudouridine synthase A [Borrelia burgdorferi B31]
 gi|3915171|sp|P70830|TRUA_BORBU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2687883|gb|AAC66394.1| pseudouridylate synthase I (hisT) [Borrelia burgdorferi B31]
          Length = 246

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 83/239 (34%), Positives = 123/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA +Q+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQIITFDIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSDNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ + V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLERVYY 245


>gi|302388052|ref|YP_003823874.1| tRNA pseudouridine synthase A [Clostridium saccharolyticum WM1]
 gi|302198680|gb|ADL06251.1| tRNA pseudouridine synthase A [Clostridium saccharolyticum WM1]
          Length = 341

 Score =  140 bits (353), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 119/227 (52%), Gaps = 2/227 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  MI+ Y+G+ Y GWQ Q NG +I+  + K +  +  E + V GA RTDSGVH+   
Sbjct: 1   MKRVKMIVAYDGTNYCGWQIQNNGITIEEVLNKELTSLLKEPITVIGASRTDSGVHSEGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C ALN   ++ D I IL    V   +H R     ++Y Y+I+ R+
Sbjct: 61  VAVFDTENRMPADKICFALNQ--RLPDDIRILQSQEVRPDYHPRKQNCVKTYEYKIMNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +  ++     LD E MR    +LVG HDF +F +   QA   +RTI   D+   
Sbjct: 119 IEVPTLRLYSYFCYFPLDVERMREGGAYLVGEHDFKSFCTARGQAEETVRTIYSLDIEKS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           G+LI IR+    FL+  +R   G+L  VG G +  + +E+ L A+DR
Sbjct: 179 GDLITIRIKGSGFLYNMVRIIAGTLMKVGMGVYPPSHVEEILDARDR 225


>gi|268318882|ref|YP_003292538.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii FI9785]
 gi|262397257|emb|CAX66271.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii FI9785]
          Length = 263

 Score =  140 bits (353), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 88/249 (35%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV
Sbjct: 4   RYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALNA + I DT+      IVD+ FH ++S   + Y Y +   +
Sbjct: 64  IHFDYPGKEIPAKNMMLALNALMPI-DTV-FFESEIVDEDFHVQYSTKGKWYRYVVDQHR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++   
Sbjct: 122 FTDPFNRFYTGHYPYPLDISLMQQAARDLIGEHDFTSFAASGGQIVDKVRTIYYVNITPD 181

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +  +I    +   FL+  +R  VG+L  +G+ K    D+ + L+A+DR+E    AP  G
Sbjct: 182 PDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNQKRPVDDIPRVLKAKDRQEVRTTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLQHVFYE 250


>gi|118602946|ref|YP_904161.1| tRNA pseudouridine synthase A [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
 gi|118567885|gb|ABL02690.1| tRNA pseudouridine synthase A [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
          Length = 247

 Score =  140 bits (353), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + + Y G+ + GWQ QK N  ++Q  +E+A+  V    V V  +GRTD+GVHA  Q
Sbjct: 1   MKIALGVAYLGTNFHGWQCQKPNIRTVQQVVEQALSSVANHPVRVFCSGRTDAGVHATCQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+   +    +     NA L  SD ++   +  V+  FHARFSAI R Y Y+I   +
Sbjct: 61  VIHFETNIKRENKVWLFGGNANLP-SD-VNFTWVKHVNDNFHARFSAIARQYNYKIHNTK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              ++    +    K LD   M  A+++L+G+H+F+ FR   CQA S I+TI+   +N  
Sbjct: 119 VRCSIITAHSLWESKKLDIMAMNKASKYLIGKHNFSAFRGSLCQAKSSIKTIEFIKLNKC 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I + + A +FLH  +R+ VG+L  VG G+ +   +++ L  + RK+  P AP  GLY
Sbjct: 179 DDNILLDIKADAFLHHMVRNIVGTLLKVGKGEKSIEWVKEILDNKQRKQAAPAAPSHGLY 238

Query: 241 FDSVEYS 247
           F    YS
Sbjct: 239 FIKAFYS 245


>gi|242083078|ref|XP_002441964.1| hypothetical protein SORBIDRAFT_08g005650 [Sorghum bicolor]
 gi|241942657|gb|EES15802.1| hypothetical protein SORBIDRAFT_08g005650 [Sorghum bicolor]
          Length = 387

 Score =  140 bits (353), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 98/317 (30%), Positives = 149/317 (47%), Gaps = 73/317 (23%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V 
Sbjct: 67  RYLVAVEYIGTRFSGSQQQPNQRTVVGVLEEAFHRFIGQPVSIFCSSRTDAGVHALSNVC 126

Query: 63  HFDLVR-----------EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L K    I + ++  V   FHAR+ A+ R
Sbjct: 127 HVDVERISKRKPGEVLTPHEPGVVKRAVNHFLLKNEGDIMVTDVRCVAPDFHARYKALER 186

Query: 111 SYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR+++  ++    E   AW I + LD + M+ A   LVG HDF++FR+  CQA+SP+
Sbjct: 187 TYHYRLLSGPESTSVFETNSAWHISEDLDIQAMKKACSILVGHHDFSSFRAAGCQANSPM 246

Query: 170 RTIDHFDV-------------------NSFGNLIEIR----------------------- 187
           RT+D   V                   +S G+L+  R                       
Sbjct: 247 RTLDELSVTEVFPFMFFPSSVERSQLESSNGSLVYSRTPDIESSGKGSDLCCTSSVKSEL 306

Query: 188 ----------------VVAR--SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                           V AR  SFL+ Q+R  VG LK VG G  T+ D+E+ L A+    
Sbjct: 307 ENGEDFGKRSRHRCFVVTARARSFLYHQVRLMVGLLKSVGTGDLTTADVERILDAKTVTA 366

Query: 230 CGPLAPPEGLYFDSVEY 246
              +AP  GLY  +V+Y
Sbjct: 367 APRMAPAYGLYLANVKY 383


>gi|317497062|ref|ZP_07955389.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895607|gb|EFV17762.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 252

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+GY GWQ Q N  +++G + K I  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRVKLIVAYDGTGYCGWQVQPNEITVEGVLNKHISELTGEDIKVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         + KALNA  ++ + I I +   V   +H RF   R++Y Y     +
Sbjct: 61  VAVFDTESRIPGEKMAKALNA--RLPEDIIIQDSKEVPLDYHPRFQDTRKTYEYTFYNAR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E M+ AA + +G H F +  S   Q +S +R I   DV   
Sbjct: 119 YDNPVTSRHHHFVYVPLDVEKMKEAASYFLGEHCFISMCSSKAQVTSYVREIYECDVTQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +RV    FL+  +R   G+L  VG GK     +++ L +++R   GP  P +GL 
Sbjct: 179 GRYITMRVTGSGFLYNMVRLMAGTLLEVGRGKQEPQWVKEILASKERVTPGPKLPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LIQIEY 244


>gi|302669997|ref|YP_003829957.1| tRNA pseudouridine synthase A TruA1 [Butyrivibrio proteoclasticus
           B316]
 gi|302394470|gb|ADL33375.1| tRNA pseudouridine synthase A TruA1 [Butyrivibrio proteoclasticus
           B316]
          Length = 262

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 123/245 (50%), Gaps = 5/245 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + + Y+G+ Y GW  Q +  ++I+G + +AI  +TGE V V GA RTD+GVHA   V
Sbjct: 6   RIMLTVSYDGTAYNGWAEQTSTPNTIEGELNRAIERLTGEPVHVIGASRTDAGVHAYGNV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FD            ALN   ++   I I+N   V   FH R     ++Y YRI   Q 
Sbjct: 66  AVFDTASSIPGDRFVFALNH--ELPQDIRIVNSREVATSFHPRHCDTEKTYEYRIFNSQI 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               ++         LD   M  AA +LVG HDFT+F ++  QA S +RTI    V   G
Sbjct: 124 MDPTKRFYTCHFSMPLDIGRMNAAAHYLVGEHDFTSFCNVESQALSHVRTIKDIRVTRNG 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I V    FL+  +R   G+L  +G GK T  +++  L  + R   GP AP EGL+ 
Sbjct: 184 DEVVISVTGNGFLYNMVRIIAGTLMQIGRGKGTPAEVKDILDKKYRGAAGPTAPAEGLFL 243

Query: 242 DSVEY 246
             VEY
Sbjct: 244 --VEY 246


>gi|331085595|ref|ZP_08334679.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330407482|gb|EGG86984.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 239

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 123/242 (50%), Gaps = 5/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M I Y+G GY GWQR  N   +IQG+IE+ +  + G  V + G+GRTD+GVHA  QVAH 
Sbjct: 1   MTIAYDGGGYKGWQRLTNEPGTIQGTIERVLSKIEGSPVKISGSGRTDAGVHAKGQVAHA 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            L     P +L + LN  L   + I I  +  V + FH+R+SA+ + Y YRI  R     
Sbjct: 61  FLKTNEDPELLRQELNRML--PEDIRICLVESVSQSFHSRYSAVSKVYEYRIDQRSRADV 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +  P  LD + MR AA HL G HDF +F     + +  +RTI   D+      +
Sbjct: 119 FTRKYCYHRPVHLDLDRMRQAADHLTGTHDFGSFTD--NKEADSVRTIFSIDMKEENEKL 176

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R   G+L  VG+G  T   + +A   +DR   G LAP  GL    V
Sbjct: 177 VLAFRGDGFLYHMVRILAGTLLEVGEGIRTPESVLEAFHHRDRSLTGFLAPAHGLCLREV 236

Query: 245 EY 246
            Y
Sbjct: 237 NY 238


>gi|296877377|ref|ZP_06901416.1| tRNA-pseudouridine synthase I [Streptococcus parasanguinis ATCC
           15912]
 gi|296431616|gb|EFH17424.1| tRNA-pseudouridine synthase I [Streptococcus parasanguinis ATCC
           15912]
          Length = 251

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  S+Q  IEK +  L  G  V VHGAGRTDSGVHAL 
Sbjct: 4   MTRYKATISYDGTLFAGFQRQPHARSVQEEIEKTLTRLNQGTPVTVHGAGRTDSGVHALG 63

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I  + +  V   FH+R+    ++Y + +   
Sbjct: 64  QVIHFDLPQERDEEKLRFALDT--QTPEDIDFIRVEQVAADFHSRYKKHSKTYEFIVDYG 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD E M+ A Q L G HDFT F +        +RTI    +  
Sbjct: 122 RPKNPMMRHYATHYPYPLDVEKMQAAIQKLEGTHDFTGFTASGTSVEDKVRTITEARLVE 181

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  + +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR   GP A P 
Sbjct: 182 DAEHHRLVFTFSGNGFLYKQIRNMVGTLLKIGNDRMPIEQIDLILEQKDRNLAGPTAAPN 241

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 242 GLYLKEIRYE 251


>gi|157150719|ref|YP_001449723.1| tRNA pseudouridine synthase A [Streptococcus gordonii str. Challis
           substr. CH1]
 gi|189030148|sp|A8AVB3|TRUA_STRGC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157075513|gb|ABV10196.1| tRNA pseudouridine synthase A [Streptococcus gordonii str. Challis
           substr. CH1]
          Length = 249

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDGEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLLEEAITQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|206889178|ref|YP_002249342.1| tRNA pseudouridine synthase A [Thermodesulfovibrio yellowstonii DSM
           11347]
 gi|238057737|sp|B5YGE4|TRUA_THEYD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|206741116|gb|ACI20173.1| tRNA pseudouridine synthase A [Thermodesulfovibrio yellowstonii DSM
           11347]
          Length = 254

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 87/257 (33%), Positives = 127/257 (49%), Gaps = 14/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+   M I+Y+G+ YFGWQRQ+ G +IQ +IE+ +  +    + + GAGRTD+GVHAL Q
Sbjct: 1   MVNIKMTIQYDGTNYFGWQRQRKGRTIQATIEECLRKIFQREIKIRGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F    +    IL K LN+ L   + I I+ L  V+  FH + S  R+SY+Y +   +
Sbjct: 61  VATFKAELKMSLDILKKVLNSLL--PNDIKIIKLENVEDSFHPQHSVKRKSYIYYLCFDE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF----- 175
                 +   W  P  LD   M  A     G  DFT F S      + IRT+  F     
Sbjct: 119 ECSCFIQRYVWHYPWKLDLSLMEEALSLFTGTKDFTAF-SGSTDVKNKIRTVHDFTMQLL 177

Query: 176 ------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                 D+   GN I+ R+ A  FL   +R+ VG +  +G GK     +++A ++  R  
Sbjct: 178 TKLCFMDMCLNGNFIKFRIEADGFLRYMVRNLVGCIIEIGKGKLRIESIQEAFESGKRPS 237

Query: 230 CGPLAPPEGLYFDSVEY 246
               AP  GL+ + V Y
Sbjct: 238 TMQTAPSNGLFLEKVIY 254


>gi|331268447|ref|YP_004394939.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
 gi|329124997|gb|AEB74942.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
          Length = 246

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 130/242 (53%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+GS Y GWQ+QK+  ++Q  IE+AI  +T     + G  RTD+GVHA   VA+F 
Sbjct: 7   LIIEYDGSNYSGWQKQKHSITVQQKIEEAISQITKTDTEIIGCSRTDAGVHARNFVANFI 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P     A+N+  K+   I I   S V   FHARF +  + Y+Y I+ R+ P  +
Sbjct: 67  TNSSVPPSKFKYAINS--KLPKDIVIKKSSEVSLDFHARFHSKGKKYVYTILNREEPPTI 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
           ++   +   K L+ + M+ A+++ +G H+F +F +       S +RTI + DV    ++I
Sbjct: 125 DRNVMYHFNKDLNVDAMKEASKYFIGSHEFDSFYKKSGSSVKSTLRTIYYCDVTKCEDVI 184

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +  V+   FL+  +R   G+L   G G+    +++  + A+DR+  G   PP+GL    V
Sbjct: 185 KFTVIGEGFLYNMVRIMAGTLIEAGIGRIKPEEIKFIILAKDRERAGRSLPPQGLCLQEV 244

Query: 245 EY 246
            Y
Sbjct: 245 LY 246


>gi|322381099|ref|ZP_08055102.1| tRNA pseudouridine synthase A-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154675|gb|EFX46946.1| tRNA pseudouridine synthase A-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 252

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 134/247 (54%), Gaps = 11/247 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y G+Q Q +G+++Q  +E+AI ++TGE V +  +GRTD+GVHA  QV +F L 
Sbjct: 8   LSYDGTSYSGFQTQPDGNTVQDQLEEAIHMLTGEKVKITSSGRTDAGVHARGQVVNF-LT 66

Query: 68  REWVPVIL-CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
              +PV   C ALN+  ++   I +     V   FH+R SA R++Y Y I T + P    
Sbjct: 67  SSRIPVDRWCLALNS--RLPRDIVVYEAEEVSLTFHSRKSAKRKTYCYEIRTSRFPDVFH 124

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN---- 182
           +      P  L+ E M+ A    +G HDFT+F +      + +RTI    +    +    
Sbjct: 125 RAFEVHYPTPLNIEAMKEALSCFIGTHDFTSFCTTRTTMENRVRTIYEARLEYLPDQDDP 184

Query: 183 ---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              LI+I +    FL+  +R  VG++  VG+GK  S+++   L A+DR++ GP A  +GL
Sbjct: 185 ARGLIQIYLTGSGFLYNMVRIIVGTILQVGEGKEKSSEIPVILAAKDRRKAGPTAMAKGL 244

Query: 240 YFDSVEY 246
               VEY
Sbjct: 245 TLWKVEY 251


>gi|152973988|ref|YP_001373505.1| tRNA pseudouridine synthase A [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152022740|gb|ABS20510.1| tRNA pseudouridine synthase A [Bacillus cytotoxicus NVH 391-98]
          Length = 247

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 126/251 (50%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 1   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I+ +    ++FHAR+  +++ Y YR+
Sbjct: 61  QVIHFDTPLSLEEWQ---WGNALNTLL--PDDIVIVQVEKKTEEFHARYGVVKKEYRYRV 115

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  +D + +R A  + +G HDFT+F S        +RTI   D
Sbjct: 116 LLSKTADVFRRNYVYQYPYPIDIQLIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEID 175

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+ +  R V   FL+  +R  VG+L  VG GK     + + L  QDR+  G + P 
Sbjct: 176 LFEQGDELVFRFVGNGFLYNMVRIIVGTLLSVGQGKVDPDSIPEILAKQDRRFAGKMVPG 235

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 236 HGLYLWQVNYN 246


>gi|282920794|ref|ZP_06328512.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C427]
 gi|282315209|gb|EFB45593.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C427]
          Length = 264

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 123/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRIHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G++  +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRYEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|167759303|ref|ZP_02431430.1| hypothetical protein CLOSCI_01650 [Clostridium scindens ATCC 35704]
 gi|167663177|gb|EDS07307.1| hypothetical protein CLOSCI_01650 [Clostridium scindens ATCC 35704]
          Length = 244

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+GS Y GWQRQ    ++IQ  +E +I  + G  V V G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGSRYQGWQRQATTDNTIQFVLEWSIGKLVGYRVHVDGSGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + +    L  +LN YL   + I I+ + +V   FHAR SA  + Y Y I  R
Sbjct: 61  QVASVKLSKLYDTKELKDSLNRYL--PEDIRIVKVELVKNGFHARKSAKGKKYEYYIDCR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD E MR A Q+L+G  +FT+F +   +   PIR I +  + S
Sbjct: 119 EKPDVFSRRYCYHYPEKLDIEAMRDAVQYLIGPKNFTSF-TDDKECKDPIRRIINIKIVS 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I      FL+  +R   G+L  +G GK  ++ L   + A+DR   G LAP  GL
Sbjct: 178 TGEKVRITYYGTGFLYHMVRILTGTLLEIGTGKRDASMLPVVIAAEDRCLAGFLAPARGL 237

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 238 FLRKVYY 244


>gi|15605190|ref|NP_219976.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D/UW-3/CX]
 gi|8134751|sp|O84469|TRUA_CHLTR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3328897|gb|AAC68063.1| Pseudouridylate Synthase I [Chlamydia trachomatis D/UW-3/CX]
 gi|296436918|gb|ADH19088.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/11222]
 gi|297748594|gb|ADI51140.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-EC]
 gi|297749474|gb|ADI52152.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-LC]
          Length = 267

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 127/242 (52%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  Q+AHF   
Sbjct: 9   IAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQGQIAHFHCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I +  + D+ FH+RFSAI + Y Y +     PL 
Sbjct: 69  DHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDEDFHSRFSAIAKEYRYTLSLLPKPLP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D++   +L+
Sbjct: 127 HHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLDLSEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP GL    V
Sbjct: 187 TVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|226322882|ref|ZP_03798400.1| hypothetical protein COPCOM_00654 [Coprococcus comes ATCC 27758]
 gi|225208668|gb|EEG91022.1| hypothetical protein COPCOM_00654 [Coprococcus comes ATCC 27758]
          Length = 256

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 120/247 (48%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + KAI  +TGE + V GA RTDSGVHA   
Sbjct: 9   MRRIRLTVAYDGTNYCGWQIQPNGITIEEVLNKAICKLTGEEIQVIGASRTDSGVHARGN 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD            ALN   ++   I ++    VD  +H R+    ++Y Y II  +
Sbjct: 69  IAVFDTESRIPAERFSYALNQ--RLPKDIVVVKSDEVDLNWHPRYQDTLKTYEYHIINTK 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+   + +   LD   MR  A +L G HDF  F  I   A + +RTI    +   
Sbjct: 127 VPIPTERLYNYFVSFDLDVGQMRRGAAYLEGEHDFAPFCCIRTNAKTTVRTITDLQILQS 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I IR+    FL+  +R   G L  VG G +    +++ L+  +R      APP+GL 
Sbjct: 187 GEHITIRITGNGFLYNMVRIIAGVLVRVGRGFYEPEKVKELLEGGERTREAVTAPPQGLC 246

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 247 LMEIRYQ 253


>gi|282852680|ref|ZP_06262022.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 224-1]
 gi|282556422|gb|EFB62042.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 224-1]
          Length = 258

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 134/246 (54%), Gaps = 6/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV
Sbjct: 5   RYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 64

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALNA + I DT+   +  IVD  FH ++S   + Y Y +   +
Sbjct: 65  IHFDYPGKEIPAKNMMLALNALMPI-DTV-FFDSEIVDSDFHVQYSTKGKWYRYIVDQHR 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++ S 
Sbjct: 123 FTDPFNRFYTGHYPYPLDIALMKKAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITSD 182

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +  +I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    AP  G
Sbjct: 183 PDNKKIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTAPASG 242

Query: 239 LYFDSV 244
           LY   V
Sbjct: 243 LYLQHV 248


>gi|121611771|ref|YP_999578.1| tRNA pseudouridine synthase A [Verminephrobacter eiseniae EF01-2]
 gi|166229848|sp|A1WSF3|TRUA_VEREI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|121556411|gb|ABM60560.1| tRNA pseudouridine synthase A [Verminephrobacter eiseniae EF01-2]
          Length = 272

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/258 (33%), Positives = 128/258 (49%), Gaps = 14/258 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I YNG  Y GWQ Q +  ++Q ++E A+       V    AGRTD+GVH L QV
Sbjct: 1   MRMALGISYNGQAYCGWQSQPSVRTVQDALEAALGRFATHPVSTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  N +L     I++     V   FHAR SA+ R Y Y ++    
Sbjct: 61  VHFDTPLDRPAASWVRGTNGFLPAD--IAVQWAQAVPDSFHARASALARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +   LD + M+ AA +LVG HDF+ FR+  CQA SP++T+    ++  G
Sbjct: 119 RPSVESGRVGWVCHRLDHDAMQQAADYLVGEHDFSAFRASTCQAPSPVKTLRRIGISCRG 178

Query: 182 N------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                              VA +FLH  IR+ +G L  +G GK +   +++ L+A+ R  
Sbjct: 179 QSPPHPALGWSPCYWRFEFVANAFLHHMIRNIMGCLVAIGQGKQSPQWMQQLLRARSRAA 238

Query: 230 CGPLAPPEGLYFDSVEYS 247
             P   P+GLYF    Y+
Sbjct: 239 AAPTFAPDGLYFLGPVYA 256


>gi|299144417|ref|ZP_07037497.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298518902|gb|EFI42641.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 243

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/241 (34%), Positives = 123/241 (51%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I+ Y+GS Y G+Q Q   S+++G ++ AI       + ++ AGRTDSGVHA+ Q  +F 
Sbjct: 5   LIVSYDGSSYHGFQIQPQASTVEGVLKNAIEDTVKHEIKLYTAGRTDSGVHAMGQCVNFY 64

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    L K +N +L   D IS++  S VD  FHAR+SA  + Y Y I   +    L
Sbjct: 65  SETTINIGNLPKVINFHL--PDDISVVGASYVDDDFHARYSAKGKYYRYMIYRGKYRNPL 122

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            + RA   P  L+ + M+    +L+G +D+ TF   H      IR ID  +V   G+ I 
Sbjct: 123 YRNRAMHFPYELNLKKMQSTLNYLIGENDYKTFMGRHAIVKDTIRRIDKIEVVEDGDFIY 182

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I    +SFL   +R  VG+   +  G++    ++ AL  + RK  GP AP  GLY   + 
Sbjct: 183 IDFYGKSFLKNMVRIIVGTAVEIARGRFEEEYMKYALNKKHRKAAGPTAPSYGLYLMKIY 242

Query: 246 Y 246
           Y
Sbjct: 243 Y 243


>gi|291551097|emb|CBL27359.1| pseudouridylate synthase I [Ruminococcus torques L2-14]
          Length = 244

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 134/247 (54%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ N  +++QG++E+ I  V G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGTAYQGWQRQANTENTLQGTLERTISSVAGYPVEIDGSGRTDAGVHANG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L          + +N+  ++ + I IL+  +V   FHAR SA+ + Y+Y++   
Sbjct: 61  QTATVVLSGRVEDGFFTEKINS--RLPEDIRILDAELVRNGFHARKSAVGKKYIYQLDLA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD + MR AAQ L+G ++F  +     + S+  RTI    +  
Sbjct: 119 EKPDVFTRRYTYHFPQRLDLDAMRKAAQLLIGTYEFAGYTDKKDEKSTK-RTIYAIMICG 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I+     FL+  +R   G+L  VG G  +   +++ L+++DR + G LAP  GL
Sbjct: 178 QGSKVSIQYEGTGFLYHMVRILTGTLLEVGTGARSIESVKEPLKSKDRSQAGFLAPARGL 237

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 238 FLDEVYY 244


>gi|294101662|ref|YP_003553520.1| tRNA pseudouridine synthase A [Aminobacterium colombiense DSM
           12261]
 gi|293616642|gb|ADE56796.1| tRNA pseudouridine synthase A [Aminobacterium colombiense DSM
           12261]
          Length = 271

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 90/248 (36%), Positives = 127/248 (51%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY  ++ Y+G+ + GWQRQ   +S+Q S+E+A+  +    + +  AGRTD GVH+  QV
Sbjct: 1   MRYAAVVSYDGTAFCGWQRQLGVASVQQSLEEALSKLCATSIPIVAAGRTDGGVHSRGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F L   W P  L  A+N YL   +T+ I+ +  V++ F ARF A+ R Y Y I    A
Sbjct: 61  ISFSLPSFWEPRRLVLAINFYL--PETVRIMGVFPVEESFSARFCALWREYRYYIWHGPA 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  RAW      D   ++ A ++L G H+F  F  I       +RTI        G
Sbjct: 119 FPPYLAQRAWWNRWQWDKTAVKKACEYLEGTHNFKAFCPIKECPEDTVRTILRIKYLRSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGL 239
           +L  I V   SFL   +RS VGSL LVG GK     +++ L  + +DR   G  AP  GL
Sbjct: 179 HLSVITVRGNSFLMNMVRSIVGSLDLVGKGKNDPEWIKELLDDEKKDRTYAGMTAPAHGL 238

Query: 240 YFDSVEYS 247
           YF  V Y+
Sbjct: 239 YFWKVCYN 246


>gi|254467822|ref|ZP_05081228.1| tRNA pseudouridine synthase A [beta proteobacterium KB13]
 gi|207086632|gb|EDZ63915.1| tRNA pseudouridine synthase A [beta proteobacterium KB13]
          Length = 258

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/245 (33%), Positives = 126/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   I+EY G+ Y G+Q Q N ++IQ  I+KA+  +    V +  +GRTD+GVHAL QV
Sbjct: 1   MRIAAIVEYLGTNYAGFQIQPNLNTIQLCIQKALSKIANHDVKIEASGRTDAGVHALGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  N++L     ISI  +S VDK FHARF+ + R Y Y +     
Sbjct: 61  FHFDTESQRPLNSWKRGANSFL--PQDISIKWVSEVDKNFHARFNVMEREYQYLLHCNDT 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P A+   +A      ++ + +    +  +G+HDFT+FRS  CQ+  PIR +         
Sbjct: 119 PSAIWHQKAGHYGYEINFKLLDKVLKEFIGKHDFTSFRSSECQSKKPIRIMHDVSYQKKE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I  +  A  FLH QIR+ +  +  V  GK     ++   + +DR +      P GLY 
Sbjct: 179 NFILFKFTADGFLHHQIRNMMSVILDVVSGKKPLDYVQYLFEVKDRTKASNTFSPNGLYL 238

Query: 242 DSVEY 246
            +++Y
Sbjct: 239 ANIKY 243


>gi|89898653|ref|YP_515763.1| tRNA pseudouridine synthase A [Chlamydophila felis Fe/C-56]
 gi|123735904|sp|Q253C0|TRUA_CHLFF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|89332025|dbj|BAE81618.1| tRNA pseudouridine synthase A [Chlamydophila felis Fe/C-56]
          Length = 268

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 87/249 (34%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y G+ Y GWQRQ N  SIQ  IE A+  V G+ +VV  +GRTDSGVHA  Q
Sbjct: 1   MKRVVLLLAYQGTAYAGWQRQPNDLSIQEVIESALARVLGKPIVVSSSGRTDSGVHAYGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF      +   P  + K LNA L     I I ++ + D  FHARFSAI + Y Y + 
Sbjct: 61  VAHFSQPDHPLFSQPQSIKKMLNAIL--PKDIVIRDVVLSDVNFHARFSAIAKEYRYSLT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++  A+    S+  + M+  A++L+G HDF +F +     +S  RT+   D+
Sbjct: 119 RSPKPLPWQRYFAYYPRHSIKIDLMQKGAKYLLGTHDFASFANHGRDYTSTERTLFKLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                ++ I      FL+  +R+ VGSL  +   K+    +++ L  + R++  P AP  
Sbjct: 179 IDNEEIVTIICKGNGFLYKMVRNIVGSLLDISKEKYPPEYIQEILAQKSRRKGPPAAPSH 238

Query: 238 GLYFDSVEY 246
            L    V Y
Sbjct: 239 ALSLHHVCY 247


>gi|239908843|ref|YP_002955585.1| tRNA pseudouridine synthase A [Desulfovibrio magneticus RS-1]
 gi|259550383|sp|C4XPZ9|TRUA_DESMR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239798710|dbj|BAH77699.1| tRNA pseudouridine synthase A [Desulfovibrio magneticus RS-1]
          Length = 274

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 89/256 (34%), Positives = 129/256 (50%), Gaps = 13/256 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+G+ + GWQ Q    G ++QG +E+A+  + G+ V VHGAGRTDSGVHAL
Sbjct: 1   MARLRLTLAYDGTDFAGWQIQAAGGGRTVQGCLEEALATLCGQPVRVHGAGRTDSGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   KAL A L     +++    +V   FH+RF A  + Y Y + T
Sbjct: 61  AQVAHADVPEHRAGLPWGKALTALLP--KDVAVTEARLVAPDFHSRFDATGKEYRYTLWT 118

Query: 119 RQAP-LALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           R    L   +   W + +  +LD   M   A   VG HDF  F++      S +R +  +
Sbjct: 119 RPGHVLPWRRPYVWDVGRYGTLDVAAMEACAGLFVGEHDFAAFQNAGTDVHSTVRRV--W 176

Query: 176 DVNSFGNLIEIRVVAR----SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           DV+          V R     FL   +R+ +G+L  VG GK T+ D+   L A DR+   
Sbjct: 177 DVSRLAGTGPDETVWRFHGEGFLKQMVRNLMGALVAVGRGKATAEDVATLLAAGDRRRAP 236

Query: 232 PLAPPEGLYFDSVEYS 247
             AP +GL   +VEY 
Sbjct: 237 GTAPAQGLCLHAVEYG 252


>gi|147676690|ref|YP_001210905.1| tRNA pseudouridine synthase A [Pelotomaculum thermopropionicum SI]
 gi|146272787|dbj|BAF58536.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
          Length = 273

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 134/246 (54%), Gaps = 7/246 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + I Y+G+ Y+G+Q Q+     ++Q  IE+ +  + GE + V GAGRTD+GVHA  QV +
Sbjct: 31  VTIAYDGTNYYGFQEQRGTKFRTVQEVIEERLSRLAGEQIRVIGAGRTDAGVHARGQVIN 90

Query: 64  FDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           F+    W   P  +  ALN+ L     I+ L    V   FHARFSA+ ++Y Y I   + 
Sbjct: 91  FN-PGNWPIPPERVAYALNSLL--PRDIAALESVEVPPSFHARFSAVAKTYRYTIYNARV 147

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  ++ +P+ LD E M+  A  L+GRHDF+ FR++     S +RT+    V+  G
Sbjct: 148 HSPFLRLYSYHVPRRLDVEAMQAGAALLIGRHDFSAFRALGTPVKSTVRTMLEACVSREG 207

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A  FL+   R   G+L  VG GK    ++   L+++D    GP AP  GL  
Sbjct: 208 DLVYIDLKADGFLYHMARMIAGTLIRVGLGKIPPGEVAAILKSRDSLRGGPTAPARGLCL 267

Query: 242 DSVEYS 247
           + +EY+
Sbjct: 268 EKIEYT 273


>gi|15837974|ref|NP_298662.1| tRNA pseudouridine synthase A [Xylella fastidiosa 9a5c]
 gi|30913418|sp|Q9PDK6|TRUA_XYLFA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|9106376|gb|AAF84182.1|AE003968_13 tRNA pseudouridine synthase A [Xylella fastidiosa 9a5c]
          Length = 257

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 132/247 (53%), Gaps = 13/247 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY + +EY+GS + GWQ+  + G S+Q ++++A+  V    V V  AGRTD+GVH   
Sbjct: 1   MMRYALGVEYDGSEFLGWQQLGEMGPSVQATLQQALASVADASVRVVCAGRTDAGVHGQC 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  ++++       + FHARFSA  R Y Y
Sbjct: 61  QVVHFDSAVTRPPRAWI-------LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +  
Sbjct: 114 RLLNRQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V  +  +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A
Sbjct: 174 ISVRRYAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTA 233

Query: 235 PPEGLYF 241
              GL F
Sbjct: 234 SARGLVF 240


>gi|307297407|ref|ZP_07577213.1| tRNA pseudouridine synthase A [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916667|gb|EFN47049.1| tRNA pseudouridine synthase A [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 252

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  I+ Y+G+ +FG+Q Q    ++QG  E+A+  +    +   GAGRTD+GVH   Q
Sbjct: 3   MKRFAAIVSYDGTDFFGFQNQPGLRTVQGKFEEALHRIHKFCISSQGAGRTDTGVHGFGQ 62

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V  FD   + +     + ALNA L  SD + +  +  VD+ F  RF+A +R Y Y I T 
Sbjct: 63  VIAFDSNLDRLEATTMRDALNANLP-SD-MYVRKVHEVDENFSPRFAAKKRIYHYYIQTS 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P    +   W  P SLD ++MR AA +L+G HDF  FR+      +P+RTI    +  
Sbjct: 121 SEPDIFRRRFVWWFPYSLDIKSMRRAAVNLLGEHDFAAFRT-GKDDRNPVRTITAIRIIR 179

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +   +I IRV   SFL   +R+ VG+L  VG G  +   + + L + DR      APP+G
Sbjct: 180 YKPYIILIRVEGISFLKRMVRNIVGTLVKVGTGSVSEESVSEFLSSHDRSTLPGTAPPQG 239

Query: 239 LYFDSV 244
           L F  V
Sbjct: 240 LVFYKV 245


>gi|332359236|gb|EGJ37057.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK49]
          Length = 249

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++    +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERKFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|325261709|ref|ZP_08128447.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
 gi|324033163|gb|EGB94440.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
          Length = 248

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 127/248 (51%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+GS Y GWQRQK+   ++QG +E+A+  VTG    + G+GRTD GVHA  
Sbjct: 1   MRTYKLTVVYDGSRYQGWQRQKSTEKTVQGILERAVTEVTGRQTEIDGSGRTDGGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +      C +LN  L   + I +  + +V   FHAR++A  + Y Y I TR
Sbjct: 61  QTASMVLPGKVEETGFCASLNNAL--PEDIRVKEMKLVKNGFHARYNAKGKRYEYFIDTR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P  L+   M  AA++L+G HDF  F     + S+ IRTI    +  
Sbjct: 119 EKPDVFTRKYCYHYPYELNIPAMEEAAEYLIGTHDFAGFTDKKDEMST-IRTIYDIIIEK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I +      FL+  +R   G+L  +G G+    +   AL+A DR+  G LAP  GL
Sbjct: 178 QDSKIRMEFYGTGFLYHMVRILTGTLLEIGTGEKRPHEAAAALEAGDREYAGFLAPARGL 237

Query: 240 YFDSVEYS 247
           +   V Y+
Sbjct: 238 FLKEVYYN 245


>gi|290579596|ref|YP_003483988.1| putative tRNA pseudouridine synthase A [Streptococcus mutans
           NN2025]
 gi|254996495|dbj|BAH87096.1| putative tRNA pseudouridine synthase A [Streptococcus mutans
           NN2025]
          Length = 249

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 86/251 (34%), Positives = 130/251 (51%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           MIRY  II Y+G+ + G+QRQ    ++Q  IEK +  L +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MIRYKAIISYDGTNFSGFQRQPQMRTVQEEIEKTLLRLNSGQAVKVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L   L+   +  D I ++ +  V   FHAR+   R++Y + +   
Sbjct: 61  QVIHFDLPQQRDLEKLRFGLDT--QTPDDIDVIQVEQVADDFHARYQKHRKTYEFLVDLG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    L +  A   P  +D   ++ A + L G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPLMRHYATHFPYKVDFSVVKAAIKKLRGTHDFTGFTASGTSVENKVRTISRATVEK 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G LI        FL+ Q+R+ VG+L  +G+G+     +++ L++ DR   GP A  
Sbjct: 179 DEKTGFLI-FTFTGSGFLYKQVRNMVGTLLKIGNGRMPIDQIDRILESGDRSLAGPTAAS 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIIYD 248


>gi|66811154|ref|XP_639285.1| hypothetical protein DDB_G0283061 [Dictyostelium discoideum AX4]
 gi|60467961|gb|EAL65974.1| hypothetical protein DDB_G0283061 [Dictyostelium discoideum AX4]
          Length = 343

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 98/303 (32%), Positives = 145/303 (47%), Gaps = 63/303 (20%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           RY +I EY G  + G+QR K       +Q  +E ++  + G  + + G+ RTD GV A+ 
Sbjct: 4   RYKIIYEYIGKSFTGFQRLKYPVVKLPVQQVLEDSLEKIHGYKIPIVGSSRTDHGVSAVG 63

Query: 60  QVAHFDL----------VREWVPVILCKALN-----AYLKISDTISILNLSIVDKQFHAR 104
           QV+HFD+          +    P  L  A+N      YLK   +I I+   IVD +FH R
Sbjct: 64  QVSHFDVKTRTSKSGIEMPLLSPEELTMAINYNVGKEYLK---SIRIIKTEIVDDKFHCR 120

Query: 105 FSAIRRSYLYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F+A  R+YLYR++     +Q PL L   R +L+   L+ + MR A++  +G HDF++FRS
Sbjct: 121 FNATSRTYLYRVMANCGRKQIPLEL-LDRVYLVGPILNLDEMRKASEMFIGTHDFSSFRS 179

Query: 161 IHCQASSPIRTIDHFDV------------NSFGNL------------------------- 183
             C ++ PIR+I H  +             SF N+                         
Sbjct: 180 AKCSSTRPIRSISHIKIYDLPLPDIFQYNPSFQNISRSNTNYPIGDGEKNLDKKNTGLQY 239

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             I + AR+FLH Q+R  V SL  VG+G+ +   LE+    +DR    P A PE L   +
Sbjct: 240 FGIEIKARAFLHNQVRIMVASLIKVGEGEISIQQLEEIKDKKDRGAAPPTASPEPLTLLT 299

Query: 244 VEY 246
           V Y
Sbjct: 300 VSY 302


>gi|312868117|ref|ZP_07728321.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis F0405]
 gi|322390938|ref|ZP_08064444.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis ATCC
           903]
 gi|311096521|gb|EFQ54761.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis F0405]
 gi|321142313|gb|EFX37785.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis ATCC
           903]
          Length = 248

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 89/256 (34%), Positives = 129/256 (50%), Gaps = 17/256 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  S+Q  IEK +  L  G  V VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGTLFAGFQRQPHARSVQEEIEKTLTRLNQGTPVTVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L  AL+   +  + I  + +  V+  FH+R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDEEKLRFALDT--QTPEDIDFIRVEQVEDDFHSRYKKHSKTYEFIVDYG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD E M+ A Q L G HDFT F +        +RTI      +
Sbjct: 119 RPKNPMMRHYATHYPYPLDVEKMQAAIQKLEGTHDFTGFTASGTSVEDKVRTI------T 172

Query: 180 FGNLIEI----RVV----ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
              L+E     R+V       FL+ QIR+ VG+L  +G+ +     ++  L+ +DR   G
Sbjct: 173 EARLVEDAEHHRLVFTFSGNGFLYKQIRNMVGTLLKIGNDRMPIEQIDLILEKKDRNLAG 232

Query: 232 PLAPPEGLYFDSVEYS 247
           P A P GLY   + Y 
Sbjct: 233 PTAAPNGLYLKEIRYE 248


>gi|293380407|ref|ZP_06626478.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 214-1]
 gi|290923090|gb|EFE00022.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 214-1]
          Length = 262

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/249 (34%), Positives = 134/249 (53%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ QV
Sbjct: 4   RYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  A+N+ +     I   N  IV+  FHAR+S   + Y YR+    
Sbjct: 64  IHFDYPGKTIPANRMILAMNSMMPTD--IIFNNCQIVNDDFHARYSIKGKWYRYRVSLDH 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  LD E M+IAAQ L+G+HDFT+F +   Q    +RTI +  +  +
Sbjct: 122 FVNPFKRFYTGHFPYPLDIEKMQIAAQDLLGKHDFTSFAASGGQIEDKVRTIYYVKITED 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   G
Sbjct: 182 KKDNEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLQRVIAAKDRQEVRQTAHASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYD 250


>gi|256847793|ref|ZP_05553238.1| tRNA pseudouridine synthase A [Lactobacillus coleohominis
           101-4-CHN]
 gi|256715482|gb|EEU30458.1| tRNA pseudouridine synthase A [Lactobacillus coleohominis
           101-4-CHN]
          Length = 253

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHA 57
           MIRY +   Y+G+ + G+Q Q +  +I+ +++  +  +       + + G+GRTD+GVHA
Sbjct: 1   MIRYKITFAYDGTNFSGFQIQPHKRTIEQTLKTIVNRMAKNPDPAISIIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD         + +ALN+ L +   I +    IV  +FHAR++A R+ Y YR+ 
Sbjct: 61  LNQVAHFDFPYHIPEQSMVRALNSQLPLD--IIVKKAEIVSNEFHARYNAHRKRYRYRVT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D  +M  AAQ LVG HDFT+F +   QA S IRTI    V
Sbjct: 119 QGEFVDPFKRNYTAHFKYPVDIAHMNRAAQDLVGTHDFTSFVASGSQAKSNIRTIYEAKV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +    V   FL+ Q+R  V  L  +G G+    D+++ L A+DR+E    AP
Sbjct: 179 YYEDHDHEVIFEFVGNGFLYNQVRIMVALLLEIGSGQRPVDDVQRVLAARDRQEARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  +V+Y
Sbjct: 239 ASGLYLVNVDY 249


>gi|332366230|gb|EGJ43985.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK355]
          Length = 249

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L+ +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILEEKDRYLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|225871229|ref|YP_002747176.1| tRNA pseudouridine synthase A [Streptococcus equi subsp. equi 4047]
 gi|254764866|sp|C0M8L4|TRUA_STRE4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225700633|emb|CAW95185.1| tRNA pseudouridine synthase A [Streptococcus equi subsp. equi 4047]
          Length = 249

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+QRQ    ++Q  IEK +  +TG + + +HGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGTLFSGFQRQSQARTVQEEIEKTLQKLTGGQGIQIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++  P  L  AL+   +  D I +++L I    FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLEQKRDPEKLRFALDT--QTPDDIDVISLEIAADDFHARYHKHFKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDIAKMQAAIKDLVGTHDFTGFTAAGTSVKNKVRTITAATLTQ 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +   L++++R+  GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRLPIEQIRLVLESKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|24378608|ref|NP_720563.1| tRNA pseudouridine synthase A [Streptococcus mutans UA159]
 gi|38258780|sp|Q8DWH1|TRUA_STRMU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|24376463|gb|AAN57869.1|AE014860_6 putative tRNA pseudouridine synthase A [Streptococcus mutans UA159]
          Length = 249

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           MIRY  II Y+G+ + G+QRQ    ++Q  IEK +  L +G+ V +HGAGRTD+GVHA  
Sbjct: 1   MIRYKAIISYDGTNFSGFQRQPQVRTVQEEIEKTLLRLNSGQAVKIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L   L+   +  D I ++ +  V   FHAR+   R++Y + +   
Sbjct: 61  QVIHFDLPQQRDLEKLRFGLDT--QTPDDIDVIQVEQVADDFHARYQKHRKTYEFLVDLG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    L +  A   P  +D   ++ A + L G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPLMRHYATHFPYKVDFSVVKAAIKKLRGTHDFTGFTASGTSVENKVRTISRATVEK 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +  G LI        FL+ Q+R+ VG+L  +G+G+     +++ L++ DR   GP A  
Sbjct: 179 DDKTGFLI-FTFTGSGFLYKQVRNMVGTLLKIGNGRMPIDQIDRILESGDRSLAGPTAAS 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIIYD 248


>gi|300776045|ref|ZP_07085904.1| tRNA-pseudouridine synthase I [Chryseobacterium gleum ATCC 35910]
 gi|300505178|gb|EFK36317.1| tRNA-pseudouridine synthase I [Chryseobacterium gleum ATCC 35910]
          Length = 250

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 125/247 (50%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG  YFG+Q Q +  S+Q  +EKA+  +  E +   GAGRTD+GVHA +  
Sbjct: 8   LRYFIEFSYNGKNYFGYQIQPDAISVQEELEKALSTILREEIKTTGAGRTDTGVHAKKIF 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +E +   L + LN++L     ISI  +  V   FHARF A  R+Y Y I   + 
Sbjct: 68  AHFDTEKE-LDDQLPRRLNSFL--PPDISIKRIFPVKDDFHARFDATYRTYEYYISLEKN 124

Query: 122 PLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P   E   AW    +SLD + M  A + L    DFT+F  +     + I  I   +    
Sbjct: 125 PFTQES--AWQHWKRSLDVDAMNEACKILFEYEDFTSFAKLKTDNKTNICKIYKAEWEQN 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  ++  V A  FL   +R+ VG++  +G GK    DL K ++ ++R   G  AP  GLY
Sbjct: 183 GAELKFTVSANRFLRNMVRAIVGTMVEIGTGKLKPEDLRKVIEDKNRNAAGTSAPGHGLY 242

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 243 LVDVGYE 249


>gi|188584870|ref|YP_001916415.1| tRNA pseudouridine synthase A [Natranaerobius thermophilus
           JW/NM-WN-LF]
 gi|229557997|sp|B2A4Q5|TRUA_NATTJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|179349557|gb|ACB83827.1| tRNA pseudouridine synthase A [Natranaerobius thermophilus
           JW/NM-WN-LF]
          Length = 253

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 137/252 (54%), Gaps = 16/252 (6%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVAHF 64
           + I Y+GS Y G+Q Q+N  ++Q  +EKA+  V     +  + A RTDSGVHA  QVA+F
Sbjct: 6   LTIAYDGSNYHGYQLQENAVTVQEKLEKALNTVYYPYKITPYSASRTDSGVHAKGQVANF 65

Query: 65  DLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
               + +P+  +  ALN    + + I+I+N  +V   F AR  AI++ Y Y +    AP 
Sbjct: 66  -FAPKQIPIHKIPLALNT--NLPNDIAIINAEVVGSNFRARRDAIKKEYRYYVY--HAPY 120

Query: 124 ALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS--PIRTIDHFDVN 178
                R + +    ++LD   ++ AA   +G+HDF+ FR+I     S  P++ I  FD++
Sbjct: 121 MDPFWRNYALHYREQNLDYTKLQQAANDFIGKHDFSPFRAIQGSNPSIDPVKEIYEFDID 180

Query: 179 ----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                 GNLI  +V+  +FL+  +R  VG+L  +G+GK     ++KALQ  DR   GP A
Sbjct: 181 VNAGEDGNLIIFKVIGNAFLYKMVRILVGTLLQIGNGKLEINAVKKALQTGDRLFVGPTA 240

Query: 235 PPEGLYFDSVEY 246
            P+GL    + Y
Sbjct: 241 SPQGLVLQQIWY 252


>gi|56478134|ref|YP_159723.1| tRNA pseudouridine synthase A [Aromatoleum aromaticum EbN1]
 gi|62901200|sp|Q5P1J2|TRUA_AZOSE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56314177|emb|CAI08822.1| pseudouridylate synthase A [Aromatoleum aromaticum EbN1]
          Length = 264

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 130/251 (51%), Gaps = 12/251 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY GS + G+Q Q +G ++Q  +E AI  +    V +H AGRTD+GVHA  QV
Sbjct: 1   MRIVLGVEYAGSAFEGFQSQAHGRTVQDHLEAAIGHIAAHPVRLHCAGRTDAGVHATAQV 60

Query: 62  AHFDL--VRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD   VR    WV     + +N+  ++S  + +   +     FHARF A+ R Y Y +
Sbjct: 61  VHFDTESVRPNSGWV-----RGVNS--RLSSPVVVRWATEAGDGFHARFCAVSRRYRYIL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                  AL  GR       LD   M  AA+ L G HDF+ FR+  CQA SP++ +    
Sbjct: 114 HNSPVRPALLAGRVGWFHPPLDEIAMAEAARCLEGWHDFSAFRAAGCQAKSPVKLMHEVR 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ +     A +FLH  +R+ VG+L  VG G+ ++  L + L A+DR         
Sbjct: 174 VQRAGDYVVFDFWANAFLHHMVRNLVGALVYVGKGRHSAAWLAEVLAARDRSLAALTFSA 233

Query: 237 EGLYFDSVEYS 247
           +GLY   VEY+
Sbjct: 234 DGLYLCGVEYA 244


>gi|227515518|ref|ZP_03945567.1| tRNA-pseudouridine synthase I [Lactobacillus fermentum ATCC 14931]
 gi|227086131|gb|EEI21443.1| tRNA-pseudouridine synthase I [Lactobacillus fermentum ATCC 14931]
          Length = 258

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/252 (33%), Positives = 132/252 (52%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY +   Y+GS + G+Q Q    ++Q  +E+A+  +  +    ++V G+GRTD+GVHA
Sbjct: 1   MHRYKITFAYDGSNFAGFQVQPGERTVQQVLERAVNKIAKKPQPPLMVFGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     L +ALN+ L +   + +   + V   FHARF A  + Y YR++
Sbjct: 61  LGQVAHFDLPYQIPGPSLVRALNSSLPLD--VLVKEATEVAPDFHARFDAHHKRYRYRVV 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D E M+ AAQ  VG HDFT+F +   QA+S +R ID   V
Sbjct: 119 GGEFTNPFKRNYTGHYKYPVDVERMQTAAQDFVGEHDFTSFVASGSQATSNVRRIDEVTV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +   + +    V   FL+ Q+R  V  L  +G+G+    D+ + ++A++R      AP
Sbjct: 179 VRDEENDEVVFDFVGNGFLYNQVRIMVAFLLEIGNGRRPVDDVMRVMKAKNRDLARGTAP 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ASGLYLVEVTYD 250


>gi|323141117|ref|ZP_08076020.1| tRNA pseudouridine synthase A [Phascolarctobacterium sp. YIT 12067]
 gi|322414383|gb|EFY05199.1| tRNA pseudouridine synthase A [Phascolarctobacterium sp. YIT 12067]
          Length = 250

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/241 (34%), Positives = 129/241 (53%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++ Y+GS Y G+Q+QKN  ++Q  +E+A+ ++ GE VV  G+GRTD+GVHAL Q   F 
Sbjct: 6   LVVAYDGSAYHGFQKQKNVQTVQNVLEEALTMLCGEKVVTAGSGRTDTGVHALAQTVTFT 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    L +A  + L   + I +++   + + FHARFSA  ++Y Y+++  +     
Sbjct: 66  TNGRIPCANLVRAAASLL--PEDIVVVSAEEMPEGFHARFSARWKTYHYKLLVNEHVNPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
               AW + + L+ + M  AA+ L+G HDF+ FRS     +SPI+TI        G  I 
Sbjct: 124 MVRYAWQLRQQLEVKAMNEAAELLLGTHDFSAFRSSGSVDTSPIKTIFAAKWQQQGEEIL 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            R+    FL+  +R+ V S+  VG GK T  D    L AQ  +     AP +GLY   V 
Sbjct: 184 FRISGDGFLYHMVRNIVWSMVQVGMGKRTVQDFAAELTAQRCEFLNEPAPAQGLYLAEVG 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|285017777|ref|YP_003375488.1| tRNA pseudouridine synthase a (tRNA-uridine isomeraseI (tRNA
           pseudouridylate synthaseI protein [Xanthomonas
           albilineans GPE PC73]
 gi|283472995|emb|CBA15500.1| probable trna pseudouridine synthase a (trna-uridine isomeraseI
           (trna pseudouridylate synthaseI protein [Xanthomonas
           albilineans]
          Length = 257

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 92/247 (37%), Positives = 134/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q +++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSAFQGWQQLGESGGPSVQATLQGALSSVADVPVSVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L A  ++  ++ +     V   FHARFSA  R Y Y
Sbjct: 61  QVVHFDCAALRPPRGWM-------LGATARLPPSVCVRWCVPVADDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + L  E M IAAQ L+G  DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQVRPALYRQTLSWERRPLQVEAMHIAAQALLGEQDFSAFRSVQCQALHARRELQS 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G L+E ++ A +FLH  +R+ VGSL +VG G+   + + + L  ++R+  GP A
Sbjct: 174 IVVTRNGELVEFQLQANAFLHHMVRNIVGSLVMVGTGEKPVSWIGELLSGRNRRIAGPTA 233

Query: 235 PPEGLYF 241
            P+GL F
Sbjct: 234 SPQGLVF 240


>gi|323463783|gb|ADX75936.1| tRNA pseudouridine synthase A [Staphylococcus pseudintermedius
           ED99]
          Length = 267

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 83/244 (34%), Positives = 121/244 (49%), Gaps = 2/244 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I YNG+ + G+Q Q  G +IQG  EK +  +  + V +H + RTD GVHA  Q
Sbjct: 1   MQRVLVKISYNGAQFLGFQIQNQGRTIQGYFEKILKRMHQQHVRIHPSSRTDRGVHAKAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             HFD      P     A+N+ L   D I + ++S +D+ FH R+  + + Y Y I   +
Sbjct: 61  YFHFDTHLNITPERWQHAMNSAL--PDDIYVHDVSFIDRDFHCRYDCVGKRYRYSIYQAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                        PK+LD E M+ AAQ+ VG H+FTTF S   +  S  RTI    +   
Sbjct: 119 HRNPFWSQLKTFEPKALDIEAMQRAAQYFVGTHNFTTFCSQKTEVESKERTIYESRIEQT 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I+  +    FL+  +R  +  L  VG GK ++ D+   L  QDR      AP EGLY
Sbjct: 179 ADGIDFVITGSGFLYNMVRVIMAYLLEVGKGKRSADDVSNLLAQQDRNLVPHTAPAEGLY 238

Query: 241 FDSV 244
            + +
Sbjct: 239 LEKI 242


>gi|37523138|ref|NP_926515.1| tRNA-pseudouridine synthase A [Gloeobacter violaceus PCC 7421]
 gi|42559743|sp|Q7MBB9|TRUA_GLOVI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|35214141|dbj|BAC91510.1| tRNA-pseudouridine synthase A [Gloeobacter violaceus PCC 7421]
          Length = 304

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 120/245 (48%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + ++Y G  +FGWQ Q    ++Q  +E+A   +    V  H AGRTD+GVHA  QV 
Sbjct: 16  RLALRVQYLGGHFFGWQWQPGQRTVQQCLEEATERIARHPVRYHAAGRTDTGVHASGQVV 75

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD  ++  P    + LN+ L   D I++   + V   +HARF+A+ R Y Y I     P
Sbjct: 76  HFDTHKKLAPETWVRGLNSLLP--DDIAVRAAAYVSDHWHARFTALWREYRYCIHNSTVP 133

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + ++W  P   LD E +  A   L G HDF  FR         +  +   +    G
Sbjct: 134 DLFVRAQSWYYPYCPLDSEAVAAALATLPGHHDFRAFRRAGSSRPHSLVHVYTAECTREG 193

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I IRV A SFL+  +R  +G+L  VG G+W+        QA +R++    APP+GL  
Sbjct: 194 EQIAIRVRANSFLYGMMRLLIGALAEVGSGRWSVERFAGLWQAGNREQVKYAAPPQGLCL 253

Query: 242 DSVEY 246
             V Y
Sbjct: 254 VGVGY 258


>gi|157690932|ref|YP_001485394.1| tRNA pseudouridine synthase A [Bacillus pumilus SAFR-032]
 gi|166991159|sp|A8F9B7|TRUA_BACP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157679690|gb|ABV60834.1| tRNA-pseudouridine synthase I [Bacillus pumilus SAFR-032]
          Length = 247

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 129/246 (52%), Gaps = 14/246 (5%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + Y+G+ + G+Q Q    ++Q  IE A+  +    E+V +  +GRTDSGVHA  QV HFD
Sbjct: 7   VSYDGTHFKGYQVQPGQRTVQTEIESALAKMHKQDELVPIVASGRTDSGVHAKGQVIHFD 66

Query: 66  L-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                 +  W P     ALN+ L   D I +L    VD+ FHARFS + + Y Y++ T  
Sbjct: 67  TPLSIPMERW-PF----ALNSLL--PDDIRVLKAEEVDESFHARFSVVSKEYRYKVSTET 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A   P  LD + MR AA +L+G HDFT+F + + +    +R I   +  + 
Sbjct: 120 HQNVFTRQYACHFPYRLDADKMREAAGYLIGTHDFTSFCAANTEVQDKVREIYTLEWKNV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + +E+RV    FL+  +R   G+L  VG GK+   +++  L A++R+  G  AP  GLY
Sbjct: 180 SDGLEMRVRGNGFLYNMVRIIAGTLLEVGSGKFHPDEIKAMLAARNREAAGKTAPSHGLY 239

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


>gi|195941752|ref|ZP_03087134.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 80a]
 gi|216264809|ref|ZP_03436801.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 156a]
 gi|224533912|ref|ZP_03674497.1| tRNA pseudouridine synthase A [Borrelia burgdorferi CA-11.2a]
 gi|215981282|gb|EEC22089.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 156a]
 gi|224512915|gb|EEF83281.1| tRNA pseudouridine synthase A [Borrelia burgdorferi CA-11.2a]
          Length = 246

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 83/239 (34%), Positives = 122/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQIITFDIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSDNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L   N+   A+ L+G+HDFTTF  I  ++    R I        G  I   
Sbjct: 127 YQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKFKFRHIYFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ + V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLERVYY 245


>gi|284992843|ref|YP_003411397.1| tRNA pseudouridine synthase A [Geodermatophilus obscurus DSM 43160]
 gi|284066088|gb|ADB77026.1| tRNA pseudouridine synthase A [Geodermatophilus obscurus DSM 43160]
          Length = 282

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 87/255 (34%), Positives = 132/255 (51%), Gaps = 15/255 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+   GW RQ    ++QG +E+A+  V  + V +  AGRTD+GVHA  Q
Sbjct: 18  LVRLRLGIAYDGTALHGWARQPAQRTVQGDLEEALSRVLRQPVSLTVAGRTDAGVHATGQ 77

Query: 61  VAHFDLVR----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           VAH D+ R    E  P  L + L   L     I++  +    + F ARF A+RR Y+YR+
Sbjct: 78  VAHGDVPRAVWAEQRPR-LVRRLRGVLPPD--IAVHTVEEAPRDFDARFGALRRHYVYRL 134

Query: 117 I-TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIRTI 172
                 P  L +      P+ LD + M +AA+ L+G HDF  F    C   + ++ IRT+
Sbjct: 135 TDADSGPPPLRRADTVGWPRRLDADAMAVAAELLLGLHDFAAF----CRRREGATTIRTL 190

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
               V   G+L+ +R  A +F H+ +RS VG+L  VG+G+         L + +R    P
Sbjct: 191 LTLAVTREGDLVTVRASADAFCHSMVRSLVGALTAVGEGRRPPEWPAALLTSTERSSEVP 250

Query: 233 LAPPEGLYFDSVEYS 247
           + PP GL    V+Y 
Sbjct: 251 VVPPGGLTLVGVDYP 265


>gi|184155960|ref|YP_001844300.1| tRNA pseudouridine synthase A [Lactobacillus fermentum IFO 3956]
 gi|238692990|sp|B2GDT8|TRUA_LACF3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|183227304|dbj|BAG27820.1| pseudouridylate synthase A [Lactobacillus fermentum IFO 3956]
          Length = 258

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/252 (33%), Positives = 132/252 (52%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY +   Y+GS + G+Q Q    ++Q  +E+A+  +  +    ++V G+GRTD+GVHA
Sbjct: 1   MHRYKITFAYDGSNFAGFQIQPGERTVQQVLERAVNKIAKKPQPPLMVFGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     L +ALN+ L +   + +   + V   FHARF A  + Y YR++
Sbjct: 61  LGQVAHFDLPYQIPGPSLVRALNSSLPLD--VLVKEATEVAPDFHARFDAHHKRYRYRVV 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D E M+ AAQ  VG HDFT+F +   QA+S +R ID   V
Sbjct: 119 GGEFTNPFKRNYTGHYKYPVDVERMQTAAQDFVGEHDFTSFVASGSQATSNVRRIDEVTV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +   + +    V   FL+ Q+R  V  L  +G+G+    D+ + ++A++R      AP
Sbjct: 179 VRDEENDEVVFDFVGNGFLYNQVRIMVAFLLEIGNGRRPVDDVMRVMKAKNRDLARGTAP 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ASGLYLVEVTYD 250


>gi|308070945|ref|YP_003872550.1| tRNA pseudouridine synthase A [Paenibacillus polymyxa E681]
 gi|305860224|gb|ADM72012.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I)
           [Paenibacillus polymyxa E681]
          Length = 261

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 94/260 (36%), Positives = 135/260 (51%), Gaps = 20/260 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M   CM + Y+G+ Y G+Q Q NG++IQ  +E AI+ +TGE + + G+GRTD+GVHA  Q
Sbjct: 1   MRNLCMKVNYDGTHYDGFQTQPNGNTIQDCLEHAIYSLTGERLKITGSGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVIL---CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           V +F       P+ L   C ALNA+L     I + +   V   FHAR  A R++Y Y I 
Sbjct: 61  VFNF---HTESPIPLQRWCLALNAWLPRD--IIVTDAREVPLSFHARRMAKRKTYRYSIN 115

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI----- 172
             + P    +      P SLD   M     HLVG  D+T+F S   Q ++ +RTI     
Sbjct: 116 ANRFPDIFHRRTQVHHPTSLDVRAMEEGLAHLVGTFDYTSFASRRSQKTNHVRTIYEAYM 175

Query: 173 --DHF----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
             DH     D +  G +I   +    FL   +R  +G+L  VG+GK +S D+   L+A++
Sbjct: 176 TVDHSFSRPDSDDQG-IIHTYITGSGFLQHMVRIIMGTLLEVGEGKKSSDDIPSILEAKN 234

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R + GP A    L   +VEY
Sbjct: 235 RSKAGPTAVGHALTLWNVEY 254


>gi|138893815|ref|YP_001124268.1| tRNA pseudouridine synthase A [Geobacillus thermodenitrificans
           NG80-2]
 gi|196250992|ref|ZP_03149674.1| tRNA pseudouridine synthase A [Geobacillus sp. G11MC16]
 gi|166228701|sp|A4IJL9|TRUA_GEOTN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|134265328|gb|ABO65523.1| tRNA pseudouridine synthase A [Geobacillus thermodenitrificans
           NG80-2]
 gi|196209464|gb|EDY04241.1| tRNA pseudouridine synthase A [Geobacillus sp. G11MC16]
          Length = 253

 Score =  139 bits (350), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/242 (35%), Positives = 123/242 (50%), Gaps = 3/242 (1%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++ Y+G+ + G+Q Q    ++QG  E  +  +  G+ V +  +GRTD+GVHA  QV HFD
Sbjct: 8   VVAYDGTYFSGYQVQPGKRTVQGEFEGVLKRMHKGDDVRITASGRTDAGVHAYGQVIHFD 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P    KALNA  ++ D I++ ++   D  FHARFSA  + Y Y + T       
Sbjct: 68  TPLALSPEQWKKALNA--QLPDDIAVRSVDEADSTFHARFSAKAKEYRYNVWTAAERDVF 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +      P  L  + M  A   L G HDFT+F S        +RTI   ++   G +++
Sbjct: 126 RRHYCAWHPYPLRVDAMSEALGLLKGTHDFTSFCSAKTVIEDRVRTIYQAEMEVDGPMLQ 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            R V   FL+  +R  VG++  VG GK    D+E  L A+DR+  GP AP EGLY   V 
Sbjct: 186 FRFVGSGFLYNMVRIIVGTVLEVGQGKRPPDDIEALLAAKDRRLAGPTAPAEGLYLWRVY 245

Query: 246 YS 247
           Y 
Sbjct: 246 YD 247


>gi|315022484|gb|EFT35511.1| tRNA pseudouridine synthase A [Riemerella anatipestifer RA-YM]
 gi|325335444|gb|ADZ11718.1| Pseudouridylate synthase [Riemerella anatipestifer RA-GD]
          Length = 246

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 127/248 (51%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RYC+   YNG  YFG+Q Q    S+Q ++E+A+  +  E +   GAGRTD+GVHA + 
Sbjct: 1   MLRYCIEFSYNGEKYFGYQIQPKQISVQETLEQALSTILREEIKTTGAGRTDTGVHAKKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD        +L K LN++L     IS+  L  V   FHARF A  R+Y Y I   +
Sbjct: 61  FAHFDTDLILEEELLPKRLNSFL--PPDISVKRLFRVSSDFHARFDATYRTYEYYISLEK 118

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +  AW    + L+ E M  A + L    DFT+F  ++    + +  I       
Sbjct: 119 NPFT--QNSAWGYWRRPLNLEAMNEACKILFEYTDFTSFSKLNTDTKTNLCEIYKAFWVQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  ++  + A  FL   +R+ VG++  +G GK    DL K ++A++R   G  AP +GL
Sbjct: 177 EGAELKFTISANRFLRNMVRAIVGTMVDIGSGKIAPQDLRKVIEAKERNAAGTSAPAQGL 236

Query: 240 YFDSVEYS 247
           +   V Y+
Sbjct: 237 FLVDVGYN 244


>gi|226309840|ref|YP_002769734.1| tRNA pseudouridine synthase A [Brevibacillus brevis NBRC 100599]
 gi|254789606|sp|C0ZIL2|TRUA_BREBN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226092788|dbj|BAH41230.1| tRNA pseudouridine synthase A [Brevibacillus brevis NBRC 100599]
          Length = 244

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 127/247 (51%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   ++ Y+G+ + G+Q Q +  ++QG IE A+  VTGE + V G+GRTD+GVHA  Q
Sbjct: 1   MKRLRCVLAYDGTDFSGFQVQPDQVTVQGEIEAALNRVTGEDIQVFGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD     +P+   +  LN   ++ D+I I  +  VD  FHARF    + Y Y I   
Sbjct: 61  VIHFDTASN-IPMDKWRFVLNN--QLPDSIVIRTVEEVDASFHARFDVQVKEYRYCIDNN 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                     A  +   LD + M+ AA +LVG HDFT+F S        +RT+    V  
Sbjct: 118 PVADVFRHRYADHVRFPLDVDAMQQAAHYLVGEHDFTSFCSAKTYVEDKVRTVYGLSVEK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + +      FL+  +R  VG+L  VG GK    +L + L A DR++ G  AP +GL
Sbjct: 178 IGDEVWVTCRGNGFLYNMVRIIVGTLVEVGQGKRNPAELREILAACDREKAGKTAPAKGL 237

Query: 240 YFDSVEY 246
               V Y
Sbjct: 238 TMWEVVY 244


>gi|270285538|ref|ZP_06194932.1| tRNA pseudouridine synthase A [Chlamydia muridarum Nigg]
 gi|270289549|ref|ZP_06195851.1| tRNA pseudouridine synthase A [Chlamydia muridarum Weiss]
 gi|301336935|ref|ZP_07225137.1| tRNA pseudouridine synthase A [Chlamydia muridarum MopnTet14]
 gi|13431951|sp|Q9PJT0|TRUA_CHLMU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 267

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 129/242 (53%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  +E  +  ++   + V  +GRTD+GVHA  QVAHF   
Sbjct: 9   IAYQGTAYSGWQYQPNALSIQEVLETLLQKISRTRISVIASGRTDAGVHAQGQVAHFCCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I ++   ++ FH+RFSAI + Y Y +     PL 
Sbjct: 69  DHPHFSDPGQIKKMLNALL--PHDIVIRDVIATNEDFHSRFSAITKEYHYTLSLLPKPLP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L  E+MR AA++LVG HDF +F ++  + SS +RT+   D+    +L+
Sbjct: 127 HHRLFCFSPRHKLCLESMREAAKYLVGTHDFASFANLGREYSSTVRTLYALDLLEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L + L+ +DRK+  P APP GL    V
Sbjct: 187 TVICKGNGFLYKMVRNIVGALLDIGKGKYPPEHLLEMLEKKDRKKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|125718790|ref|YP_001035923.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK36]
 gi|166229844|sp|A3CQB8|TRUA_STRSV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|125498707|gb|ABN45373.1| tRNA pseudouridine synthase A, putative [Streptococcus sanguinis
           SK36]
          Length = 249

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G  VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGRPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEDRDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPIEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|220906745|ref|YP_002482056.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7425]
 gi|219863356|gb|ACL43695.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7425]
          Length = 282

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 87/244 (35%), Positives = 121/244 (49%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ ++GWQRQ +  S+Q  +E+AI +V G  V VHGAGRTD+GVHA  QVA
Sbjct: 12  RIALVIQYLGTHFYGWQRQPHHRSVQEELEQAIAIVVGHPVTVHGAGRTDTGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD      P    + LN   ++   + I   + VD  +H+RFSA+ R Y Y + T   P
Sbjct: 72  HFDTDSVIPPHRWAEILNN--RLPQDVLIRASAGVDSSWHSRFSALWRRYRYTLYTDCRP 129

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               K   W   + LD E M+ A   L+GRH    F             +   +    G+
Sbjct: 130 NLFLKSFTWHYYRPLDTELMQTALNPLLGRHHLAAFHRSKSGRKHSWVEVQVAECVRRGS 189

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           L+EI V A  FL+  +R  VG L  VG G+ +     +  Q Q R +    AP  GL   
Sbjct: 190 LVEIEVQASGFLYGMMRLLVGMLVQVGTGERSLASFTQIWQKQQRDQVKYAAPARGLCLL 249

Query: 243 SVEY 246
            V Y
Sbjct: 250 RVGY 253


>gi|120434790|ref|YP_860476.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
 gi|117576940|emb|CAL65409.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
          Length = 259

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 85/249 (34%), Positives = 128/249 (51%), Gaps = 12/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G  Y GWQ Q N  S+Q  IEK +  V    + + GAGRTD+GVHA +  
Sbjct: 12  LRYFIELSYFGKAYHGWQIQPNSISVQEVIEKNLSKVLRSTIEIVGAGRTDAGVHAKQMF 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+ R     +L   LN+ L     I+I ++  V+K  HARF A  RSY Y +I  + 
Sbjct: 72  AHFDVDRVLDLELLKYKLNSML--PKDIAISDIFPVNKNVHARFDATSRSYEYHLIQEKD 129

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT----IDHFDV 177
           P   E   AW +   +  E M +AA  L G  +F  F     ++ + +RT    ID  + 
Sbjct: 130 PFNRES--AWFLKHEVKIEKMNMAAATLRGYTNFKCF----SKSKTDVRTYNCRIDEAEW 183

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              GNL+   + A  FL   +R+ VG+L  +G  K   + + + ++++DR + G   P  
Sbjct: 184 RMEGNLMVFHITADRFLRNMVRAVVGTLIEIGQNKHPVSYMHEVIKSEDRGKAGASVPAH 243

Query: 238 GLYFDSVEY 246
           GLY   ++Y
Sbjct: 244 GLYLTRIKY 252


>gi|56418673|ref|YP_145991.1| tRNA pseudouridine synthase A [Geobacillus kaustophilus HTA426]
 gi|62901182|sp|Q5L3Q7|TRUA_GEOKA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56378515|dbj|BAD74423.1| pseudouridylate synthaseI [Geobacillus kaustophilus HTA426]
          Length = 258

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 87/241 (36%), Positives = 123/241 (51%), Gaps = 3/241 (1%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           II Y+G+ + G+Q Q    ++QG  E+ +  +  G  V V  +GRTD+GVHA  QV HFD
Sbjct: 8   IIAYDGTHFSGYQIQPGKRTVQGEFEEVLRRMHKGTKVRVAASGRTDAGVHAYGQVIHFD 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                      KALNA  ++ D I +  +   D  FHARFSA  + Y Y++ T       
Sbjct: 68  TPLSLSSEQWKKALNA--QLPDDIVVRFVQEADADFHARFSAKAKEYRYKVWTAAERDVF 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +      P SL    M  A + L G HDFT+F S        +RT+   +V + G ++E
Sbjct: 126 RRHYCAWHPYSLHISAMNEALRLLHGTHDFTSFCSAKTSIEDRVRTMYRAEVKADGPMLE 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            R V   FL+  +R  VG++  +G GK +  D+   L A+DR+  GP AP EGLY   V 
Sbjct: 186 FRFVGSGFLYNMVRIIVGTVLEIGQGKRSPADISTLLAAKDRRLAGPTAPAEGLYLWRVY 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|313676221|ref|YP_004054217.1| tRNA pseudouridine synthase a [Marivirga tractuosa DSM 4126]
 gi|312942919|gb|ADR22109.1| tRNA pseudouridine synthase A [Marivirga tractuosa DSM 4126]
          Length = 247

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 82/249 (32%), Positives = 127/249 (51%), Gaps = 12/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY   I Y G+ Y GWQ+Q N   +Q  IE+    +  +   + G+GRTDSGVHA  QV
Sbjct: 1   MRYFFTIAYKGTQYHGWQKQPNAIGVQQKIEEVFSTILNQKSEIVGSGRTDSGVHATAQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E  P+ L    N  L     +++ +  +V ++ HARF A  R+Y Y I+T + 
Sbjct: 61  FHFDYSGELDPLQLVFKANKML--PKDVALKHAKLVKEEAHARFDAESRAYQYHIVTEKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA----SSPIRTIDHFDV 177
           P A++  +A+   + L  E M +AA+ L+   DF +F  +         S    I   +V
Sbjct: 119 PFAID--QAYFFTQELAIEKMNLAAEKLLNYQDFESFSKVKTDVFTFNCSIFEAIWKQEV 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +S    +   + A  FL   +R+ VG+L  VG  K +  + E+ ++A++RK  G   P  
Sbjct: 177 DS----LVFHIKANRFLRGMVRAIVGTLLDVGQHKISIENFEEIIKAKNRKSAGRAVPAH 232

Query: 238 GLYFDSVEY 246
           GLY   V+Y
Sbjct: 233 GLYLTEVQY 241


>gi|171058363|ref|YP_001790712.1| tRNA pseudouridine synthase A [Leptothrix cholodnii SP-6]
 gi|170775808|gb|ACB33947.1| tRNA pseudouridine synthase A [Leptothrix cholodnii SP-6]
          Length = 262

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 122/245 (49%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y GS Y GWQ Q NG+++Q  +E A+       + V  AGRTD+GVHAL QV
Sbjct: 1   MRLALGLSYRGSAYRGWQSQTNGATVQDVLEAALCRFAATPIRVSCAGRTDAGVHALNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D  R+  P    +  N YL     +++     V   FHAR +A  R Y Y ++    
Sbjct: 61  VHLDTDRDREPFSWVRGTNTYLPPD--VAVQWCRPVPDAFHARNAARARRYAYVLLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+E G+   I + LD   M  +A  L+G HDF+ FRS  CQA SP++ +    +   G
Sbjct: 119 RPAMEAGQVGWIFRPLDQARMEASAALLIGEHDFSAFRSADCQALSPVKQMRTIRIGRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FLH  IR+ +G L  VG G      L   L ++DR+   P   P+GLYF
Sbjct: 179 PYWRFDFEASAFLHHMIRNLMGCLIAVGTGARDPAWLAGVLASRDRRLAAPTFSPDGLYF 238

Query: 242 DSVEY 246
               Y
Sbjct: 239 LGPRY 243


>gi|119511153|ref|ZP_01630270.1| tRNA pseudouridine synthase A [Nodularia spumigena CCY9414]
 gi|119464141|gb|EAW45061.1| tRNA pseudouridine synthase A [Nodularia spumigena CCY9414]
          Length = 296

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 122/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   S+Q  IE AI  V G  + +HGAGRTDSGVHA  QVA
Sbjct: 13  RVALVIQYVGTHFHGWQRQKQHRSVQEEIETAIATVLGYHLTLHGAGRTDSGVHAAAQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+      P      LN+YL     I I   + VD ++HARFSA  R Y Y I T + P
Sbjct: 73  HFEATGLIPPHRWASILNSYLP--QDILIKASAAVDNRWHARFSAAYRRYRYTIYTEERP 130

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W      LD   ++ A + L+G+H    F     + S     +   + +  G
Sbjct: 131 NLFVRPFSWHYYYAPLDECLIQAALEPLMGKHHLAAFHRAGSKRSHSWVEVQAAECHRSG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A  FL+  +R  VG L  VG GK T     +  Q + R+E    APP+GL  
Sbjct: 191 PFLHIEIQANGFLYGMVRLLVGMLAQVGTGKLTLAGFTELWQEERREEVKYAAPPQGLCL 250

Query: 242 DSVEYS 247
             V Y 
Sbjct: 251 LRVGYP 256


>gi|323440101|gb|EGA97816.1| tRNA pseudouridine synthase A [Staphylococcus aureus O11]
 gi|323442775|gb|EGB00401.1| tRNA pseudouridine synthase A [Staphylococcus aureus O46]
          Length = 267

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 124/243 (51%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M+ AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMKRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEILKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHDVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|237802891|ref|YP_002888085.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
 gi|237804813|ref|YP_002888967.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|255311275|ref|ZP_05353845.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 6276]
 gi|255317577|ref|ZP_05358823.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 6276s]
 gi|231273113|emb|CAX10026.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231274125|emb|CAX10919.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
          Length = 267

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 126/242 (52%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  Q+AHF   
Sbjct: 9   IAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQGQIAHFHCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +     PL 
Sbjct: 69  DHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTLSLLPKPLP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D++   +L+
Sbjct: 127 HHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLDLSEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP GL    V
Sbjct: 187 TVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|282906560|ref|ZP_06314408.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282329459|gb|EFB58980.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Btn1260]
          Length = 264

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRIHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLHQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|227888821|ref|ZP_04006626.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii ATCC 33200]
 gi|227850658|gb|EEJ60744.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii ATCC 33200]
          Length = 263

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 87/249 (34%), Positives = 134/249 (53%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV
Sbjct: 4   RYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALNA + I DT+      IVD+ FH ++S   + Y Y +   +
Sbjct: 64  IHFDYPGKEIPAKNMMLALNALMPI-DTV-FFESEIVDEDFHVQYSTKGKWYRYVVDQHR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++   
Sbjct: 122 FTDPFNRFYTGHYPYPLDISLMQQAARDLIGEHDFTSFAASGGQIVDKVRTIYYVNITPD 181

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +  +I    +   FL+  +R  VG+L  +G+ K    D+ + L+ +DR+E    AP  G
Sbjct: 182 PDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNQKRPVDDIPRVLKTKDRQEVRTTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLQHVFYE 250


>gi|76789199|ref|YP_328285.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|123606852|sp|Q3KLN5|TRUA_CHLTA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76167729|gb|AAX50737.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
          Length = 267

 Score =  139 bits (349), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 126/242 (52%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  Q+AHF   
Sbjct: 9   IAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQGQIAHFHCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +     PL 
Sbjct: 69  DHPHFTDPRQIQKMLNALL--PHDIVIHDAVMTDGDFHSRFSAIAKEYRYTLSLLPKPLP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D++   +L+
Sbjct: 127 HHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLDLSEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP GL    V
Sbjct: 187 TVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|110803601|ref|YP_698382.1| tRNA pseudouridine synthase A [Clostridium perfringens SM101]
 gi|110684102|gb|ABG87472.1| tRNA pseudouridine synthase A [Clostridium perfringens SM101]
          Length = 248

 Score =  139 bits (349), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVHA   V
Sbjct: 6   ITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVHAKNYV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          + K +N YL   + I +  +    ++FHARF+   ++Y Y I   + 
Sbjct: 66  ANFKTNSLMTLEQIIKYINEYL--PEDIRVKEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  + +   
Sbjct: 124 KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFHENN 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP  GL  
Sbjct: 184 NILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPAHGLCL 243

Query: 242 DSVEY 246
             + Y
Sbjct: 244 LELNY 248


>gi|160947056|ref|ZP_02094223.1| hypothetical protein PEPMIC_00987 [Parvimonas micra ATCC 33270]
 gi|158446190|gb|EDP23185.1| hypothetical protein PEPMIC_00987 [Parvimonas micra ATCC 33270]
          Length = 247

 Score =  138 bits (348), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 124/243 (51%), Gaps = 2/243 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + I Y+GS +FG+Q+QKN  ++QG IE A+  +T E + +  AGRTD GVH+LR + +F
Sbjct: 5   MLTISYDGSLFFGFQKQKNVVTVQGEIEDALKKITEENINIISAGRTDRGVHSLRHIINF 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                   +    ALN +L I   + +L+   V + FH+RF A  ++Y Y +   +    
Sbjct: 65  HTESNVGVLNFKTALNHFLPIG--VRVLDSKEVSENFHSRFDAKMKTYKYILNLDEVMDP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           +        P  LD E M+ A ++ +GR  F  F        +PIR I+ F++    N +
Sbjct: 123 IYYNYKANFPYPLDIEKMKRAKEYFIGRKSFKAFMGPRTGNINPIREINSFEIYKENNDL 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
              +  +SF+  Q+R  VG+L  +G G     +LE+ L ++DR   G    P GLY   +
Sbjct: 183 IFLIKGQSFIRNQVRIMVGTLVDIGRGLIEEDELERILDSEDRTRAGVTLSPNGLYLMEI 242

Query: 245 EYS 247
            Y 
Sbjct: 243 LYD 245


>gi|226945473|ref|YP_002800546.1| tRNA pseudouridine synthase A [Azotobacter vinelandii DJ]
 gi|226720400|gb|ACO79571.1| tRNA pseudouridine synthase A [Azotobacter vinelandii DJ]
          Length = 288

 Score =  138 bits (348), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 95/249 (38%), Positives = 132/249 (53%), Gaps = 10/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALRQ 60
           R  + +EY G+ Y G+QRQ    +SIQ ++E A+  V G + + V  AGRTD+ VHA  Q
Sbjct: 20  RVALGLEYRGARYHGFQRQNPRVASIQAALESALSRVAGGVPLNVVCAGRTDALVHASGQ 79

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-- 118
           V HFD   E    +    + A + +   IS+     +   FHARFSA  R Y Y I    
Sbjct: 80  VVHFDTPIERS--MHAWTMGANMNLPADISVAWAREMPAHFHARFSATARRYRYVIYNDP 137

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R A +A E    W   + LD E MR AA+ LVG HDF+ FR+  CQA SPI+T+ H  +
Sbjct: 138 IRPAHMAEEV--TW-NHRPLDIERMRQAARPLVGCHDFSAFRASQCQARSPIKTVHHLQL 194

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G LI + + A +FLH  +R+  G L  +G G+       + L+ + R + G  A P 
Sbjct: 195 IRHGRLIVLDIRANAFLHHMVRNIAGVLMTIGAGERPVEWAREVLEGRQRHKGGVTAHPY 254

Query: 238 GLYFDSVEY 246
           GLY   V+Y
Sbjct: 255 GLYLVQVDY 263


>gi|319893169|ref|YP_004150044.1| tRNA pseudouridine synthase A [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162865|gb|ADV06408.1| tRNA pseudouridine synthase A [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 267

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 83/244 (34%), Positives = 121/244 (49%), Gaps = 2/244 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I YNG+ + G+Q Q  G +IQG  EK +  +  + V +H + RTD GVHA  Q
Sbjct: 1   MQRVLVKISYNGAQFLGFQIQNQGRTIQGYFEKILKRMHQQHVRIHPSSRTDRGVHAKAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             HFD      P     A+N+ L   D I + ++S +D+ FH R+  + + Y Y I   +
Sbjct: 61  YFHFDTHLNITPERWQHAMNSAL--PDDIYVHDVSFIDRDFHCRYDCVGKRYRYSIYQAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                        PK+LD E M+ AAQ+ VG H+FTTF S   +  S  RTI    V   
Sbjct: 119 HRNPFWSQLKTFEPKALDIEAMQRAAQYFVGTHNFTTFCSQKTEVESKERTIYESRVEQT 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I+  +    FL+  +R  +  L  VG G+ ++ D+   L  QDR      AP EGLY
Sbjct: 179 ADGIDFVITGSGFLYNMVRVIMAYLLEVGKGRRSADDVPNLLAQQDRNLVPHTAPAEGLY 238

Query: 241 FDSV 244
            + +
Sbjct: 239 LEKI 242


>gi|153853827|ref|ZP_01995183.1| hypothetical protein DORLON_01174 [Dorea longicatena DSM 13814]
 gi|149753577|gb|EDM63508.1| hypothetical protein DORLON_01174 [Dorea longicatena DSM 13814]
          Length = 244

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+GS Y GWQRQ    ++IQ  +E +I  + G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTISYDGSRYQGWQRQATTDNTIQYILEWSIGKLVGYRVHIDGSGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + +    L  +LN YL   + I I+ + +    FHAR SA  + Y Y I  R
Sbjct: 61  QVASVKLSKLYDTKELKDSLNRYL--PEDIRIVKVELAKNGFHARKSAKGKKYEYYIDCR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD E MR A ++L+G  +FT+F +   +   PIR I +  + S
Sbjct: 119 EKPDVFSRRYCYHYPEKLDIEAMRDATKYLIGPKNFTSF-TDDKECKDPIRKITNIKIVS 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I      FL+  +R   G+L  +G GK  ++ L   + A+DR   G LAP  GL
Sbjct: 178 SGEKVRITYYGTGFLYHMVRILTGTLLEIGAGKRDASMLPVVIAAEDRSLAGFLAPARGL 237

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 238 FLRKVYY 244


>gi|331092366|ref|ZP_08341192.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401390|gb|EGG80976.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 246

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 83/243 (34%), Positives = 129/243 (53%), Gaps = 4/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MII Y+G+ Y GWQRQ     +IQG IEK I  V G  V + G+GRTD GVHA  QVA+ 
Sbjct: 1   MIIAYDGTKYQGWQRQSGTPMTIQGIIEKTIGEVVGYPVEIDGSGRTDGGVHAGGQVANV 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            L  +    +  + LN   K+ + I I ++ +V  +FH+R  A+ ++Y Y +  R+    
Sbjct: 61  RLSGKVEEAVFQEKLNE--KLPEDIRICHVELVLNRFHSRLDAVAKTYEYVVDMREKADV 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +   K L+ E MR AA  L+G+HDF+ F     + S+ +R +    + ++   +
Sbjct: 119 FTRKYCYHYTKPLEPEKMRKAAALLIGKHDFSAFTDKKDEKSA-VRELYDIQIETYRQKL 177

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R     F++ Q+R FVG+L   G G+ +   + +AL+++ R   G LAP   L    V
Sbjct: 178 YFRFYGNGFMYHQVRIFVGTLLEAGAGERSVESVLEALKSKKRVNAGFLAPAHALTLKEV 237

Query: 245 EYS 247
           EY 
Sbjct: 238 EYK 240


>gi|319945640|ref|ZP_08019892.1| tRNA pseudouridine synthase A [Streptococcus australis ATCC 700641]
 gi|319748239|gb|EFW00481.1| tRNA pseudouridine synthase A [Streptococcus australis ATCC 700641]
          Length = 248

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  S+Q  IEK +  L  G  V +HGAGRTD+GVHAL 
Sbjct: 1   MTRYKATISYDGTLFAGFQRQPHARSVQEEIEKTLMRLNQGNPVTIHGAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L  AL+   +  + I  + +  V   FH+R+    ++Y + +   
Sbjct: 61  QVIHFDLPQPRDEEKLRFALDT--QTPEDIDFIRVEQVPDDFHSRYQKHSKTYEFIVDYG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   M+ A Q L G HDFT F +        +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDVAKMQAAIQKLEGTHDFTGFTASGTSVEDKVRTITEARLVE 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  + +        FL+ QIR+ VG+L  +G+G+     ++  L+ +DR   GP A P 
Sbjct: 179 DAEHHRLVFTFSGNGFLYKQIRNMVGTLLKIGNGRMPVDQIDLILEKKDRNLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|153853813|ref|ZP_01995169.1| hypothetical protein DORLON_01160 [Dorea longicatena DSM 13814]
 gi|149753563|gb|EDM63494.1| hypothetical protein DORLON_01160 [Dorea longicatena DSM 13814]
          Length = 246

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 124/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + K++  +TGE + + GA RTDSGVHAL  
Sbjct: 1   MKRIRIFVAYDGTNYCGWQVQPNGVTIEEKLNKSLARLTGEEIRIIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA-IRRSYLYRIITR 119
           VA FD      P     ALN   ++ + I ++    V   +H R+   I ++Y Y I   
Sbjct: 61  VAVFDTESSIPPERFAYALNQ--RLPEDIVVVRSDEVPADWHPRYQENISKTYEYHIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L+      +   +D E MR  A++LVG HDF +F +I       +RT+    +  
Sbjct: 119 AVPNPLKTRYCTFVSFPMDVEAMRAGAKYLVGEHDFVSFCNIRTNTQDTVRTVYDLIIEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I +R+    FL+  +R   G L  VG G +T   +++ L A+     G  APP GL
Sbjct: 179 KDDEIVLRITGNGFLYNMVRIIAGVLIRVGRGFYTPEKVKEILDAKVHTSEGATAPPNGL 238

Query: 240 YFDSVEYS 247
               ++Y+
Sbjct: 239 VLMKIDYN 246


>gi|182625331|ref|ZP_02953105.1| tRNA pseudouridine synthase A [Clostridium perfringens D str.
           JGS1721]
 gi|177909489|gb|EDT71936.1| tRNA pseudouridine synthase A [Clostridium perfringens D str.
           JGS1721]
          Length = 248

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVHA   V
Sbjct: 6   ITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVHAKNYV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          + + +N YL   + I I  +    ++FHARF+   ++Y Y I   + 
Sbjct: 66  ANFKTNSLMTLEQIIEYINEYL--PEDIRITEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  + +   
Sbjct: 124 KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFHENN 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP  GL  
Sbjct: 184 NILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPAHGLCL 243

Query: 242 DSVEY 246
             + Y
Sbjct: 244 LELNY 248


>gi|309777173|ref|ZP_07672136.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308915043|gb|EFP60820.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 253

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 124/251 (49%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +I+ Y+GS Y GWQRQ N  SIQ  +E AI  V G  V +  +GRTD+ VHAL Q
Sbjct: 1   MPRYKVILSYDGSAYGGWQRQTNTHSIQQEVEAAIEKVEGRFVSITASGRTDAHVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           V HFD V+   P    +ALN+ L     I I  + +VD  FHARF AI + Y Y I T  
Sbjct: 61  VFHFDSVKHLEPENWKRALNSLL--PHDIRIQEVCLVDDAFHARFHAISKRYDYLITTEV 118

Query: 120 QAPL---ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHF 175
           Q P     + K R       LD E MR  A   +G HDFT+F S       S I+TI   
Sbjct: 119 QNPFYYNYMGKDRT-----RLDVERMRECACIFLGTHDFTSFTSSKVDPRKSKIKTITRL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           DV    + + +      FL   +R    +L   G  + +   +++ L  +D+  C   A 
Sbjct: 174 DVVQEEHAVRMIFEGNGFLRYMVRMIAQTLIEAGKHRLSVAAVKEMLYGKDKHLCRYKAQ 233

Query: 236 PEGLYFDSVEY 246
            EGLY   V Y
Sbjct: 234 AEGLYLVEVRY 244


>gi|62184804|ref|YP_219589.1| tRNA pseudouridine synthase A [Chlamydophila abortus S26/3]
 gi|81313017|sp|Q5L6V3|TRUA_CHLAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62147871|emb|CAH63617.1| putative tRNA pseudouridine synthase a [Chlamydophila abortus
           S26/3]
          Length = 268

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 131/249 (52%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +++ Y G+ Y GWQRQ N  SIQ  IE ++  V G+ + V  +GRTD+ VHA  Q
Sbjct: 1   MTQVVILLAYQGTAYAGWQRQPNDLSIQEVIENSLAQVVGKRIPVTSSGRTDAEVHAFGQ 60

Query: 61  VAHF---DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF   D  +      + K LNA L     I I ++ + D +FH+RFSAI + Y Y + 
Sbjct: 61  VAHFSQPDHPQFSQASSIKKMLNALL--PKDIVIRDVVLGDDKFHSRFSAIAKEYRYVLT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  E+  A+     L  + M+  AQ+L+G HDF +F +     +S IRT+ + D+
Sbjct: 119 RSPKPLPWERYFAYYPRHHLKTDLMQEGAQYLLGTHDFASFANHGRDYTSTIRTLFNLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  + I      FL+  +R+ VGSL  +  GK+    +++ L  ++R++  P AP  
Sbjct: 179 VDHGETVTIICRGNGFLYKMVRNIVGSLLDISRGKYPPEYIQEILMQKNRRQGPPAAPSH 238

Query: 238 GLYFDSVEY 246
            L    V Y
Sbjct: 239 ALSLYHVCY 247


>gi|226322792|ref|ZP_03798310.1| hypothetical protein COPCOM_00564 [Coprococcus comes ATCC 27758]
 gi|225208773|gb|EEG91127.1| hypothetical protein COPCOM_00564 [Coprococcus comes ATCC 27758]
          Length = 259

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ Y GWQRQ+N   ++QG +E+ I  + G+  VV G+GRTDSGVHAL 
Sbjct: 1   MNTYRITVAYDGTAYRGWQRQENTELTVQGILERRISEIAGKKTVVSGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q     L +E       K LNA L   + I +L++S   + FHAR SA+ + Y Y+I  R
Sbjct: 61  QECSLYLEQEIDMDSFKKQLNALL--PEDIRVLDISREKRDFHARKSAVGKCYEYQIDLR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +   +  P  +D   M  AA++L+G HDF+ F  +  +    +RTI    +  
Sbjct: 119 DKMEVFHRKYRFHFPHPVDIAAMEQAAEYLMGTHDFSAFTDLK-EDKDTVRTIYAVGIVY 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + +  +   FL+  +R   G+L  VG GK  + ++ + L+A+DRK+ G  AP +GL
Sbjct: 178 EKDTLTLSWIGDGFLYHMVRILTGTLLDVGIGKIKAEEIPEILKAKDRKKSGFPAPAKGL 237

Query: 240 YFDSVEYS 247
           +   V Y+
Sbjct: 238 FLGRVFYT 245


>gi|312866252|ref|ZP_07726471.1| tRNA pseudouridine synthase A [Streptococcus downei F0415]
 gi|311098225|gb|EFQ56450.1| tRNA pseudouridine synthase A [Streptococcus downei F0415]
          Length = 248

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 130/249 (52%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+QRQ    S+Q  +EK +  L +G  V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKAIISYDGTLFAGFQRQSKERSVQEELEKTLERLNSGNPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++++  V + FHAR++   ++Y + + T 
Sbjct: 61  QVIHFDLPQTRDEEKLRFGLDT--QSPEDIDVVSVEQVPEVFHARYNPHSKTYEFLVDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  +D   M+ A   L+G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRAYATHFPYPVDLGAMQEAIADLLGTHDFTGFTASGTSVENKVRTISQAKVER 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+   + ++  L A+DR   GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTILAAKDRNLAGPTAAGN 238

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 239 GLYLKEITY 247


>gi|325686853|gb|EGD28878.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK72]
 gi|332359857|gb|EGJ37671.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1056]
          Length = 249

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I  +++  V + FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEDRDEEKLRFALDT--QTPEDIDFISVEQVSEDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|312144215|ref|YP_003995661.1| tRNA pseudouridine synthase A [Halanaerobium sp. 'sapolanicus']
 gi|311904866|gb|ADQ15307.1| tRNA pseudouridine synthase A [Halanaerobium sp. 'sapolanicus']
          Length = 248

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 124/245 (50%), Gaps = 4/245 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + +EY+GS Y GWQRQKN   +IQ  +E A+  +    V V G+GRTD+GVHA  Q A
Sbjct: 5   YKITLEYDGSNYSGWQRQKNTKETIQEKLENALSKINKNKVEVIGSGRTDAGVHAAGQTA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F L  +     +  A+N +L   D I       V K FHAR+ A  + Y YRI+     
Sbjct: 65  NFFLDIQIPTYKIPIAINTHL--PDDIICYKAEKVAKDFHARYDARGKKYRYRILNSNFN 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +   + + + LD + M+  A+  +G HDF  F S      S IR I  FD+NS  N
Sbjct: 123 SVFVRNYVYKVHQRLDLDIMQKGAKIFLGSHDFAAFCSAGSSVDSTIREIYSFDINSKTN 182

Query: 183 -LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I+I +    FL+  +R  VG+L  +  GK    DLE+ L    R+  G  AP +GL  
Sbjct: 183 GEIQIDISGSGFLYNMVRILVGTLIELAKGKRNLADLEEILAGTQRERAGFTAPAKGLTL 242

Query: 242 DSVEY 246
             V Y
Sbjct: 243 LEVFY 247


>gi|313207118|ref|YP_004046295.1| tRNA pseudouridine synthase a [Riemerella anatipestifer DSM 15868]
 gi|312446434|gb|ADQ82789.1| tRNA pseudouridine synthase A [Riemerella anatipestifer DSM 15868]
          Length = 246

 Score =  138 bits (348), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 126/248 (50%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RYC+   YNG  YFG+Q Q    S+Q ++E+A+  +  E +   GAGRTD+GVHA + 
Sbjct: 1   MSRYCIEFSYNGEKYFGYQIQPKQISVQETLEQALSTILREEIKTTGAGRTDTGVHAKKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD        +L K LN++L     IS+  L  V   FHARF A  R+Y Y I   +
Sbjct: 61  FAHFDTDLILEEELLPKRLNSFL--PPDISVKRLFRVSSDFHARFDATYRTYEYYISLEK 118

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +  AW    + L+ E M  A + L    DFT+F  ++    + +  I       
Sbjct: 119 NPFT--QNSAWGYWRRPLNLEAMNEACKILFEYTDFTSFSKLNTDTKTNLCEIYKAFWVQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  ++  + A  FL   +R+ VG++  +G GK    DL K ++A++R   G  AP +GL
Sbjct: 177 EGTELKFTISANRFLRNMVRAIVGTMVDIGSGKIAPQDLRKVIEAKERNAAGTSAPAQGL 236

Query: 240 YFDSVEYS 247
           +   V Y+
Sbjct: 237 FLVDVGYN 244


>gi|49484433|ref|YP_041657.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257423704|ref|ZP_05600133.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257426382|ref|ZP_05602784.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257429022|ref|ZP_05605409.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257431668|ref|ZP_05608031.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257434628|ref|ZP_05610679.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M876]
 gi|282902120|ref|ZP_06310013.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C160]
 gi|282909528|ref|ZP_06317341.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911780|ref|ZP_06319576.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282915068|ref|ZP_06322845.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M899]
 gi|282925699|ref|ZP_06333347.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C101]
 gi|283958992|ref|ZP_06376435.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|293497472|ref|ZP_06665326.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293511047|ref|ZP_06669744.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M809]
 gi|293549653|ref|ZP_06672325.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M1015]
 gi|295428801|ref|ZP_06821425.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297589714|ref|ZP_06948355.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|56749728|sp|Q6GEL6|TRUA_STAAR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|49242562|emb|CAG41283.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|257272722|gb|EEV04824.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257276013|gb|EEV07464.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257279503|gb|EEV10090.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257282547|gb|EEV12679.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257285224|gb|EEV15340.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M876]
 gi|282312528|gb|EFB42932.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C101]
 gi|282320789|gb|EFB51123.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M899]
 gi|282323476|gb|EFB53792.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326638|gb|EFB56938.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282596579|gb|EFC01538.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C160]
 gi|283789551|gb|EFC28376.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|290918700|gb|EFD95776.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291096403|gb|EFE26661.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466034|gb|EFF08563.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127150|gb|EFG56792.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297578225|gb|EFH96938.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|312437370|gb|ADQ76441.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|315193148|gb|EFU23548.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 264

 Score =  138 bits (348), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRIHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|299820989|ref|ZP_07052878.1| tRNA-pseudouridine synthase I [Listeria grayi DSM 20601]
 gi|299818010|gb|EFI85245.1| tRNA-pseudouridine synthase I [Listeria grayi DSM 20601]
          Length = 247

 Score =  138 bits (348), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 88/248 (35%), Positives = 127/248 (51%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+GSG+ G+Q Q +  ++Q  +E+A+  +  GE V V  +GRTD+GVHA  
Sbjct: 1   MPRYKVILAYDGSGFSGYQVQPHKRTVQSELEEALLKMHKGEFVRVTASGRTDTGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       +AL         I I ++  V   FHAR+  + + Y Y I   
Sbjct: 61  QVIHFDSPLQIPNEKFQRALQRMTPFD--IGIHSVEQVPDDFHARYGTVGKEYRYVIKNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  A   P  L  E M+ A+Q L+G HDFT+F S   +  S +RTI   +   
Sbjct: 119 TDYDPFSRNFALHYPYPLSIEKMQEASQILIGEHDFTSFCSARTEQDSKVRTIYSIEFLK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL-APPEG 238
               I I      FL+  +R   G+L  +G G+ T+  LEKALQA+DR +   + AP +G
Sbjct: 179 EKETITICYRGDGFLYNMVRILTGALLDIGQGRMTAETLEKALQAKDRTKLPSVTAPAQG 238

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 239 LYLWEVAY 246


>gi|328957471|ref|YP_004374857.1| tRNA pseudouridine synthase A [Carnobacterium sp. 17-4]
 gi|328673795|gb|AEB29841.1| tRNA pseudouridine synthase A [Carnobacterium sp. 17-4]
          Length = 246

 Score =  138 bits (347), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 120/243 (49%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M IEY+G  Y GWQR   +  +IQG IE  +  +TG    + G+GRTD+G HA  QVA+F
Sbjct: 6   MTIEYDGGRYLGWQRLSDSDKTIQGKIENILTAMTGTKTEIIGSGRTDAGAHAKGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  L  V ++FHAR++A  + Y Y +     P  
Sbjct: 66  KTTSTMEFPAMLDHLNRYL--PRDIVVKKLEEVPERFHARYNASGKKYSYYVWNNSIPSV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            ++  ++  P  LD + M  A   LVG HDF  F S+     S +RTID   ++  G+L+
Sbjct: 124 FDRNFSYDFPGELDIDKMNEACNKLVGTHDFIGFSSLKKSKKSTVRTIDEIKIHKEGDLL 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                   FL+  IR  +G+L  +G G    + ++   ++  R + G   P +GL+ D V
Sbjct: 184 HFTFKGEGFLYKMIRIIMGTLLEIGSGMADPSSIDAIFKSGIRSDAGMTVPSQGLFLDEV 243

Query: 245 EYS 247
            Y 
Sbjct: 244 YYD 246


>gi|291544350|emb|CBL17459.1| pseudouridylate synthase I [Ruminococcus sp. 18P13]
          Length = 273

 Score =  138 bits (347), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 82/242 (33%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           CM+  Y G+ Y G+QRQ N  ++Q ++E+A+  V      ++G  RTD+GVHA +    F
Sbjct: 6   CMM-AYRGTKYHGFQRQDNAHTVQEAVEQALGSVLNHPATIYGCSRTDTGVHARQYCFSF 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              R   P+ L + +N   ++ D IS+L+       FHAR++   + YLY I   ++P  
Sbjct: 65  QTERPIQPLNLVRGVNG--RLPDDISLLSAEDAALSFHARYACRGKEYLYLIHNSESPNP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  A    + +D   ++  A   +G HDF +F S   Q +S +RTI  F V   G+ I
Sbjct: 123 FLRDLACHHRRPIDPALLQACADRFIGTHDFKSFCSAQAQRTSTVRTIYDFSVEMSGDSI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            + V    FL+  IR  VG++  V DGK   +DL+  L A+DR+  G  A   GLY + V
Sbjct: 183 ILLVKGDGFLYNMIRILVGTMLQVNDGKLKLSDLDGILAARDRRCAGKTAMACGLYLNRV 242

Query: 245 EY 246
            Y
Sbjct: 243 FY 244


>gi|255507054|ref|ZP_05382693.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D(s)2923]
 gi|289525508|emb|CBJ14985.1| tRNA pseudouridine synthase A [Chlamydia trachomatis Sweden2]
 gi|296435064|gb|ADH17242.1| tRNA pseudouridine synthase A [Chlamydia trachomatis E/150]
 gi|296438784|gb|ADH20937.1| tRNA pseudouridine synthase A [Chlamydia trachomatis E/11023]
          Length = 267

 Score =  138 bits (347), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 126/242 (52%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  Q+AHF   
Sbjct: 9   IAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQGQIAHFHCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +     PL 
Sbjct: 69  DHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTLSLLPKPLP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D++   +L+
Sbjct: 127 HHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLDLSEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP GL    V
Sbjct: 187 TVICRGNGFLYKMVRNIVGALLDIGKGKYPPEYLLDMLATKDRRKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|328944888|gb|EGG39047.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1087]
          Length = 249

 Score =  138 bits (347), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYNFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSNDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++    +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERKFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|222152501|ref|YP_002561676.1| tRNA pseudouridine synthase A [Streptococcus uberis 0140J]
 gi|254764869|sp|B9DTJ0|TRUA_STRU0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|222113312|emb|CAR40884.1| tRNA pseudouridine synthase A [Streptococcus uberis 0140J]
          Length = 250

 Score =  138 bits (347), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GS + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHA  
Sbjct: 1   MTRYKAIISYDGSQFQGFQRQSHARSVQEEIEKTLTKLTNGKEIKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLDQDRDLEKLRFALDT--QSPEDIDFISVEKVSDDFHSRYTKHLKTYEFIVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD +N+++A + L+G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRHYATHFPYPLDLDNIQLAIKDLIGTHDFTGFTASGATIENKVRTIIDASVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +        FL+ Q+R+ VG+L  +G+ +     ++  L+ +DR+  GP     
Sbjct: 179 EEDKNFLIFTFTGNGFLYKQVRNMVGTLLKIGNNRMPVDQIKTILEKKDRQLAGPTPAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|227824316|ref|ZP_03989148.1| tRNA pseudouridine synthase A [Acidaminococcus sp. D21]
 gi|226904815|gb|EEH90733.1| tRNA pseudouridine synthase A [Acidaminococcus sp. D21]
          Length = 253

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 84/241 (34%), Positives = 122/241 (50%), Gaps = 3/241 (1%)

Query: 7   IIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++ Y+G+ Y G+QRQK+ G  +Q  +EKA+     E + +  AGRTD+GVHAL QV  F+
Sbjct: 8   VVAYDGTNYQGFQRQKDYGVGVQQVLEKALSTALHEDISIKAAGRTDAGVHALGQVISFE 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P    +AL   L     I+I    I    FHARF A+ ++Y Y ++    P   
Sbjct: 68  TSSPIPPENYRRALQHLL--PPDIAIREAFIKPDGFHARFDALDKTYRYTVLYAPLPDPC 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  AW +  SL    M  AA  LVG HDF++F++   + +SP+RT+             
Sbjct: 126 ARRYAWEVRSSLTLAAMNEAAALLVGTHDFSSFKNQGSEKTSPVRTLYEAYWTQEKERFT 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             +    FL+  +R+ VG L  VG G+WT  D    + A+DRK+ G  AP  GL    V 
Sbjct: 186 FTIRGDGFLYRMVRNIVGCLVKVGTGEWTVADFAAVMAAKDRKKAGVAAPACGLSLVHVS 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|254521233|ref|ZP_05133288.1| tRNA pseudouridine synthase A [Stenotrophomonas sp. SKA14]
 gi|219718824|gb|EED37349.1| tRNA pseudouridine synthase A [Stenotrophomonas sp. SKA14]
          Length = 256

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 132/246 (53%), Gaps = 13/246 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EY+GS + GWQ   + G S+Q S+E A+  V    + V  AGRTD+GVH   Q
Sbjct: 1   MRYALGVEYDGSDFRGWQNLGEGGPSVQASLELALSSVADAPLQVVCAGRTDAGVHGQCQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD       R W+       L    ++  +I++     V   FHARFSA  R Y YR
Sbjct: 61  VVHFDTDVVRDPRAWM-------LGTTTRLPRSIAVRWCVPVADDFHARFSARARRYRYR 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++ R+   AL +       ++LD   M  A Q L+G +DF+ FRS+ CQA    R +   
Sbjct: 114 LLNREVRPALGRQTLSWERRTLDEALMHAAGQALLGENDFSAFRSVQCQALHARRELQSL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V+  G +IE+ V   +FLH  +R+ VGSL LVG G+     + + L  +DR   GP AP
Sbjct: 174 QVSRQGEVIEVAVQGNAFLHHMVRNIVGSLILVGSGEKPVEWIAELLAGRDRTVAGPTAP 233

Query: 236 PEGLYF 241
           P+GL F
Sbjct: 234 PQGLVF 239


>gi|124008085|ref|ZP_01692784.1| tRNA pseudouridine synthase A [Microscilla marina ATCC 23134]
 gi|123986499|gb|EAY26305.1| tRNA pseudouridine synthase A [Microscilla marina ATCC 23134]
          Length = 248

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 130/249 (52%), Gaps = 8/249 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ QKN  S+Q  I+ A+ ++  +   + G+GRTD+GVHA++Q 
Sbjct: 1   MRYFLELAYSGTQYHGWQIQKNAHSVQAEIQNALSVLLRQPTDILGSGRTDAGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +     +  K +N  L   + ISI  +  V ++ H RF A +R Y+YRI   + 
Sbjct: 61  AHFDTEQTLDGEVFAKKMNGIL--PEDISIKRVINVHEEAHTRFDATQRHYMYRINQEKT 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF----DV 177
           P    +G ++      D + M  AAQ ++   DF  F  +H   +  +  I       + 
Sbjct: 119 PFL--RGVSYYNFHRFDIDLMNKAAQIMLKHEDFQCFSKVHTDVNHYLCNIQQAYWQKET 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   NL+   + A  FL   +R+  G++  VG GK T  + E+ +  +DRK+ G   P +
Sbjct: 177 SYNVNLLVFYIQANRFLRGMVRAITGTMLNVGSGKITLEEFEQIILNKDRKQAGWSVPAQ 236

Query: 238 GLYFDSVEY 246
           GL+   VEY
Sbjct: 237 GLFLAKVEY 245


>gi|297528514|ref|YP_003669789.1| tRNA pseudouridine synthase A [Geobacillus sp. C56-T3]
 gi|297251766|gb|ADI25212.1| tRNA pseudouridine synthase A [Geobacillus sp. C56-T3]
          Length = 258

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 87/241 (36%), Positives = 123/241 (51%), Gaps = 3/241 (1%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           II Y+G+ + G+Q Q    ++QG  E+ +  +  G  V V  +GRTD+GVHA  QV HFD
Sbjct: 8   IIAYDGTHFSGYQIQPGKRTVQGEFEEVLRRMHKGTKVRVAASGRTDAGVHAYGQVIHFD 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                      KALNA  ++ D I +  +   D  FHARFSA  + Y Y++ T       
Sbjct: 68  TSLSLSSEQWKKALNA--QLPDDIVVRFVQEADADFHARFSAKAKEYRYKVWTAAERDVF 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +      P SL    M  A + L G HDFT+F S        +RT+   +V + G ++E
Sbjct: 126 RRHYCAWHPYSLHISAMNEALRLLHGTHDFTSFCSAKTLIEDRVRTMYRAEVKADGPMLE 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            R V   FL+  +R  VG++  +G GK +  D+   L A+DR+  GP AP EGLY   V 
Sbjct: 186 FRFVGSGFLYNMVRIIVGTVLEIGQGKRSPADISMLLAAKDRRLAGPTAPAEGLYLWRVY 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|18309973|ref|NP_561907.1| tRNA pseudouridine synthase A [Clostridium perfringens str. 13]
 gi|24212547|sp|Q8XLQ0|TRUA1_CLOPE RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|18144651|dbj|BAB80697.1| tRNA-pseudouridine synthase I [Clostridium perfringens str. 13]
          Length = 248

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVHA   V
Sbjct: 6   ITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVHAKNYV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I   + 
Sbjct: 66  ANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  + +   
Sbjct: 124 KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFHENN 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP  GL  
Sbjct: 184 NILSIKINGNGFLLNMVRIMVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPAHGLCL 243

Query: 242 DSVEY 246
             + Y
Sbjct: 244 LELNY 248


>gi|168213913|ref|ZP_02639538.1| tRNA pseudouridine synthase A [Clostridium perfringens CPE str.
           F4969]
 gi|170714597|gb|EDT26779.1| tRNA pseudouridine synthase A [Clostridium perfringens CPE str.
           F4969]
          Length = 248

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVHA   V
Sbjct: 6   ITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVHAKNYV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I   + 
Sbjct: 66  ANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  + +   
Sbjct: 124 KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFHENN 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP  GL  
Sbjct: 184 NILSIKINGNGFLLNMVRIIVGTLVNVGLGKIEPKYINDILEAKERAKASEKAPAHGLCL 243

Query: 242 DSVEY 246
             + Y
Sbjct: 244 LELNY 248


>gi|183219967|ref|YP_001837963.1| tRNA pseudouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910091|ref|YP_001961646.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|238687801|sp|B0SJC4|TRUA_LEPBP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238687833|sp|B0SC03|TRUA_LEPBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167774767|gb|ABZ93068.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167778389|gb|ABZ96687.1| tRNA pseudouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 264

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 131/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA--IFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y +++EY+G+ + GWQ+QKN  ++Q SIE A  I L       +  AGRTD+GVHAL
Sbjct: 1   MPNYALLVEYDGTHFNGWQKQKNLPTVQSSIESALGIILRRNPASRLSVAGRTDTGVHAL 60

Query: 59  RQVAHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             V +F      +P    L  +LNA       +S+ N+  V   FHARFS   R Y+Y++
Sbjct: 61  GMVCNFK-TEHPIPNFHKLLVSLNALTPTG--VSVKNVVEVPSDFHARFSCTGREYIYKL 117

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS-PIRTIDHF 175
              +   +  +GRA+ +   +D E ++   Q LVG  DF +F      A    +R I   
Sbjct: 118 YYSKYESSFVEGRAFWVKGHIDWERVKKQLQVLVGEKDFRSFTKAKSMAGKRAVREILAI 177

Query: 176 DVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            + +      +IR+ A  F+H  +R  VG+L  +G G+W S  ++  L+ ++R + G   
Sbjct: 178 QLENLSPEWYQIRIRANGFMHNMVRITVGTLLDIGKGRWESRSIDSILEEKNRTQAGVTL 237

Query: 235 PPEGLYFDSVEY 246
           PP+GLYF    Y
Sbjct: 238 PPDGLYFVRAYY 249


>gi|258422666|ref|ZP_05685571.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9635]
 gi|257847077|gb|EEV71086.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9635]
          Length = 267

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 123/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNKAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|329730365|gb|EGG66755.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           21193]
          Length = 267

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 123/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|261417639|ref|YP_003251321.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC61]
 gi|319765297|ref|YP_004130798.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC52]
 gi|261374096|gb|ACX76839.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC61]
 gi|317110163|gb|ADU92655.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC52]
          Length = 258

 Score =  138 bits (347), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 86/241 (35%), Positives = 122/241 (50%), Gaps = 3/241 (1%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           II Y+G+ + G+Q Q    ++QG +E+ +  +  G+ V V  +GRTD+GVHA  QV HFD
Sbjct: 8   IIAYDGTHFSGYQIQPGKRTVQGELEEVLRRMHKGKGVRVAASGRTDAGVHAYGQVIHFD 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                      KALNA  ++ D I +  +   D  FHARFSA  + Y Y++ T       
Sbjct: 68  TSLSLSSEQWKKALNA--QLPDDIVVRFVQEADADFHARFSAKAKEYRYKVWTAAERDVF 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +      P  L  + M  A +   G HDFT+F S        +RTI    V   G ++E
Sbjct: 126 RRHYCAWHPYPLHMDAMNEALRLFCGTHDFTSFCSAKTTIEDRVRTIYRAKVKVDGPMLE 185

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            R V   FL+  +R  VG++  +G GK +  D+   L A+DR+  GP AP EGLY   V 
Sbjct: 186 FRFVGSGFLYNMVRIMVGTVLEIGQGKRSPADISTLLAAKDRRLAGPTAPAEGLYLWRVY 245

Query: 246 Y 246
           Y
Sbjct: 246 Y 246


>gi|291288851|ref|YP_003505667.1| tRNA pseudouridine synthase A [Denitrovibrio acetiphilus DSM 12809]
 gi|290886011|gb|ADD69711.1| tRNA pseudouridine synthase A [Denitrovibrio acetiphilus DSM 12809]
          Length = 245

 Score =  138 bits (347), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 80/241 (33%), Positives = 127/241 (52%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I+EY G+ + GWQ Q NG ++Q  + KA+  +    V V G+GRTDSGVHAL QVA+F 
Sbjct: 7   LIVEYVGTDFAGWQVQPNGRTVQEELHKALSKMYKTKVTVIGSGRTDSGVHALGQVANFR 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             R   P  +   LN+ L   + ISI ++  V + FHA+ +A+ ++YLYRI   +   A+
Sbjct: 67  TERYIPPENVHMGLNSML--PEDISISSVEDVPEDFHAQLNAVSKTYLYRIFPSRVRSAM 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
             GR W +   L+ + M    ++  G HDFT+F        + +R I++        +I 
Sbjct: 125 LAGRTWWVKDELNYKRMCELLKYFEGEHDFTSFCVQTSLRENNVRRINNIRCYREDKVIC 184

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I +    FLH  +R   G++       +    +++A++ +DR + GP A   GLY   V 
Sbjct: 185 IEINGNGFLHNMVRIIAGTVVEALRKGYGDEYIKEAIEGRDRSKAGPTAHAAGLYLKKVY 244

Query: 246 Y 246
           Y
Sbjct: 245 Y 245


>gi|94984145|ref|YP_603509.1| tRNA pseudouridine synthase A [Deinococcus geothermalis DSM 11300]
 gi|94554426|gb|ABF44340.1| tRNA pseudouridine synthase A [Deinococcus geothermalis DSM 11300]
          Length = 266

 Score =  137 bits (346), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 128/252 (50%), Gaps = 11/252 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +++ ++G+ + GWQ Q++  S+Q ++  A+  +T E      AGRTD+GVHA    A
Sbjct: 15  RLRLLLAWDGTDFAGWQAQRDVPSVQDTLYAALLRLTEEAARPVAAGRTDAGVHAEAMPA 74

Query: 63  HFDLVREW-VPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           H D+ + + +P   L +ALNA+L  S  +++L        FHARFS   R Y YR++   
Sbjct: 75  HVDVPQSFRIPAKKLARALNAHLPPS--VAVLEAEEAPTGFHARFSCTERRYTYRLLNTP 132

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
               L +GRA  +P +LD   M  AA  L+G HDF  F +   + +  +R +    V+  
Sbjct: 133 QRHPLWRGRALHVPGALDVPAMNAAAACLLGTHDFAAFATREDRQT--VRELRALAVHPG 190

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G + E+RV   SFL   +R  VG+L LVG GK    D+   L  ++R   G   P
Sbjct: 191 PVVPGGRIWEVRVAGESFLRQMVRGLVGTLLLVGQGKLGQEDVTAVLVGRERARAGANVP 250

Query: 236 PEGLYFDSVEYS 247
             GL F    Y 
Sbjct: 251 GYGLTFTGASYG 262


>gi|116495915|ref|YP_807649.1| tRNA pseudouridine synthase A [Lactobacillus casei ATCC 334]
 gi|122262685|sp|Q035B5|TRUA_LACC3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116106065|gb|ABJ71207.1| Pseudouridylate synthase [Lactobacillus casei ATCC 334]
          Length = 247

 Score =  137 bits (346), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 84/249 (33%), Positives = 126/249 (50%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +T G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMTKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + KA+N+ + +   I IL   IVD  FHAR+SA  + YLYR+   
Sbjct: 61  QVISFDYPGNIPAESMLKAMNSLMPLD--IEILKAEIVDADFHARYSAKGKRYLYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVQRIEVALKDLVGTHDFTSFAASGGVIVDKVRTIYEATVRE 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +S  N I        FL+  +R  V +   +G+G+    D ++    +DR++    AP  
Sbjct: 179 DSVTNEIIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFAVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|228989350|ref|ZP_04149341.1| tRNA pseudouridine synthase A [Bacillus pseudomycoides DSM 12442]
 gi|228995533|ref|ZP_04155201.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock3-17]
 gi|228764262|gb|EEM13141.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock3-17]
 gi|228770428|gb|EEM19001.1| tRNA pseudouridine synthase A [Bacillus pseudomycoides DSM 12442]
          Length = 252

 Score =  137 bits (346), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHARG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I +  +    + FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WMNALNTML--PDDIVVRQVEKKTEDFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+ E++R A  + +G HDFT+F S        +RTI   D
Sbjct: 121 LLSKNADVFRRNYVYQYPYPLEIESIRKAIPYFIGTHDFTSFCSTKTDKKDKVRTIYEID 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  +G GK     + + L+ QDR+  G + P 
Sbjct: 181 LMEQDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKMVPDSIPEILKKQDRRFAGKMVPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|294778889|ref|ZP_06744305.1| tRNA pseudouridine synthase A [Bacteroides vulgatus PC510]
 gi|294447198|gb|EFG15782.1| tRNA pseudouridine synthase A [Bacteroides vulgatus PC510]
          Length = 257

 Score =  137 bits (346), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 124/246 (50%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +
Sbjct: 1   MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+ 
Sbjct: 61  AHFDYDRELDCVQITEKLNRLLPPD--IAVYAVKRVKDDAHARFDATYRTYKYYVTTRKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
           P    +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     
Sbjct: 119 P--FNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVS 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+
Sbjct: 177 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALF 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LVDVGY 242


>gi|15925209|ref|NP_372743.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15927799|ref|NP_375332.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           N315]
 gi|148268659|ref|YP_001247602.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH9]
 gi|150394724|ref|YP_001317399.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH1]
 gi|156980534|ref|YP_001442793.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253316980|ref|ZP_04840193.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. CF-Marseille]
 gi|253734372|ref|ZP_04868537.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|255006999|ref|ZP_05145600.2| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu50-omega]
 gi|257794565|ref|ZP_05643544.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9781]
 gi|258408833|ref|ZP_05681117.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9763]
 gi|258422432|ref|ZP_05685344.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9719]
 gi|258439820|ref|ZP_05690566.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9299]
 gi|258442624|ref|ZP_05691184.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8115]
 gi|258446678|ref|ZP_05694833.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6300]
 gi|258450204|ref|ZP_05698296.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6224]
 gi|258455424|ref|ZP_05703384.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5937]
 gi|269203852|ref|YP_003283121.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ED98]
 gi|282893658|ref|ZP_06301890.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8117]
 gi|282926765|ref|ZP_06334392.1| tRNA pseudouridine synthase A [Staphylococcus aureus A10102]
 gi|295404895|ref|ZP_06814708.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8819]
 gi|296275990|ref|ZP_06858497.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MR1]
 gi|297243953|ref|ZP_06927843.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8796]
 gi|54039782|sp|P65849|TRUA_STAAN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54042087|sp|P65848|TRUA_STAAM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166229841|sp|A7X5B5|TRUA_STAA1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189029998|sp|A5IV03|TRUA_STAA9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030146|sp|A6U3U4|TRUA_STAA2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|13702019|dbj|BAB43311.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           N315]
 gi|14247992|dbj|BAB58381.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|147741728|gb|ABQ50026.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH9]
 gi|149947176|gb|ABR53112.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH1]
 gi|156722669|dbj|BAF79086.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253727689|gb|EES96418.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257788537|gb|EEV26877.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9781]
 gi|257840516|gb|EEV64976.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9763]
 gi|257841863|gb|EEV66300.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9719]
 gi|257847596|gb|EEV71598.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9299]
 gi|257851745|gb|EEV75679.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8115]
 gi|257854746|gb|EEV77694.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6300]
 gi|257856296|gb|EEV79205.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6224]
 gi|257862635|gb|EEV85403.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5937]
 gi|262076142|gb|ACY12115.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ED98]
 gi|282591216|gb|EFB96289.1| tRNA pseudouridine synthase A [Staphylococcus aureus A10102]
 gi|282763716|gb|EFC03844.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8117]
 gi|283471441|emb|CAQ50652.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ST398]
 gi|285817881|gb|ADC38368.1| tRNA pseudouridine synthase A [Staphylococcus aureus 04-02981]
 gi|294969840|gb|EFG45858.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8819]
 gi|297178731|gb|EFH37976.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8796]
 gi|312830568|emb|CBX35410.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ECT-R 2]
 gi|315129701|gb|EFT85692.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|329723462|gb|EGG59991.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           21172]
          Length = 267

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 123/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|256849152|ref|ZP_05554585.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-1A-US]
 gi|262047168|ref|ZP_06020126.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-3A-US]
 gi|256713928|gb|EEU28916.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-1A-US]
 gi|260572413|gb|EEX28975.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-3A-US]
          Length = 262

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 84/249 (33%), Positives = 134/249 (53%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ QV
Sbjct: 4   RYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  A+N+ +     I   N  IV+  FHAR+S   + Y YR+    
Sbjct: 64  IHFDYPGKTIPANRMILAMNSMMPTD--IIFNNCQIVNDDFHARYSIKGKWYRYRVSLDH 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  LD E M+IAAQ L+G+HDFT+F +   +    +RTI +  +  +
Sbjct: 122 FVNPFKRFYTGHFPYPLDIEKMQIAAQDLLGKHDFTSFAASGGRIEDKVRTIYYVKITED 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   G
Sbjct: 182 KKDNEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLQRVIAAKDRQEVRQTAHASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYD 250


>gi|150005081|ref|YP_001299825.1| tRNA pseudouridine synthase A [Bacteroides vulgatus ATCC 8482]
 gi|149933505|gb|ABR40203.1| tRNA pseudouridine synthase A [Bacteroides vulgatus ATCC 8482]
          Length = 267

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 125/246 (50%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +
Sbjct: 11  MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMI 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+ 
Sbjct: 71  AHFDYDRELDCVQITEKLNRLLPPD--IAVYAVKRVKDDAHARFDATYRTYKYYVTTRKD 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     
Sbjct: 129 P--FNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVS 186

Query: 182 NLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               + ++ A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+
Sbjct: 187 GTEWVFIIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALF 246

Query: 241 FDSVEY 246
              V Y
Sbjct: 247 LVDVGY 252


>gi|168208061|ref|ZP_02634066.1| tRNA pseudouridine synthase A [Clostridium perfringens E str.
           JGS1987]
 gi|168215906|ref|ZP_02641531.1| tRNA pseudouridine synthase A [Clostridium perfringens NCTC 8239]
 gi|169341141|ref|ZP_02863234.1| tRNA pseudouridine synthase A [Clostridium perfringens C str.
           JGS1495]
 gi|169299748|gb|EDS81800.1| tRNA pseudouridine synthase A [Clostridium perfringens C str.
           JGS1495]
 gi|170660642|gb|EDT13325.1| tRNA pseudouridine synthase A [Clostridium perfringens E str.
           JGS1987]
 gi|182381869|gb|EDT79348.1| tRNA pseudouridine synthase A [Clostridium perfringens NCTC 8239]
          Length = 248

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVHA   V
Sbjct: 6   ITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVHAKNYV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I   + 
Sbjct: 66  ANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  + +   
Sbjct: 124 KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFHENN 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP  GL  
Sbjct: 184 NILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPAHGLCL 243

Query: 242 DSVEY 246
             + Y
Sbjct: 244 LELNY 248


>gi|222150476|ref|YP_002559629.1| tRNA pseudouridine synthase A [Macrococcus caseolyticus JCSC5402]
 gi|222119598|dbj|BAH16933.1| tRNA pseudouridine synthase A [Macrococcus caseolyticus JCSC5402]
          Length = 273

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++YNG  + G+Q Q  G ++Q  +E+ +  +  + V +H + RTD GVHA  Q
Sbjct: 1   MERILLQLQYNGVNFQGFQIQNEGRTVQYELERILKRMHKQFVRIHPSSRTDKGVHARMQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             HFD            A N+ L   D I I  ++ + + FH+R+  I ++Y Y++   +
Sbjct: 61  YVHFDTPLSIPESKWQHAFNSAL--PDDIYITQVTKISEHFHSRYDCIGKAYRYKVYVAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  G+   I   LD + M  AAQH +G HDFT+F S   +  +  RT+  F+V   
Sbjct: 119 HRNVMHSGQITHIKTKLDVKRMNDAAQHFLGTHDFTSFCSAKTEIENKERTLYRFEVTET 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               +  V+   FL+  +R  V  L  VG G+     +   +QAQDR + G  AP EGLY
Sbjct: 179 AEGYDFYVIGSGFLYNMVRIMVQYLIDVGTGQKDGDSIPAIIQAQDRTKAGKTAPAEGLY 238

Query: 241 FDSV 244
            + +
Sbjct: 239 LEKI 242


>gi|329116632|ref|ZP_08245349.1| tRNA pseudouridine synthase A [Streptococcus parauberis NCFD 2020]
 gi|326907037|gb|EGE53951.1| tRNA pseudouridine synthase A [Streptococcus parauberis NCFD 2020]
          Length = 249

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GSG+ G+QRQ +  S+Q  IEK +  L  G+++ +HGAGRTD+GVHA  
Sbjct: 1   MTRYKATISYDGSGFSGFQRQPHARSVQEEIEKTLLKLYKGQVIKIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     +  AL+   +  D I  + +  V   +H R+   +++Y + +   
Sbjct: 61  QVIHFDLPLERDIEKIRFALDT--QTPDDIDFIKVEKVADDYHCRYLKHKKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD   M  A + LVG HDFT F +      + +RTI       
Sbjct: 119 RPKNPMMRNYATHYPYPLDISLMDEAIKDLVGTHDFTGFTASGTSIENKVRTISEAKLTY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           ++  N +        FL+ Q+R+ VG+L  +G+ +   + +++ L+ ++R+  GP A   
Sbjct: 179 DAKRNFLIFSFTGNGFLYKQVRNMVGTLLKIGNQRMPVSQVQRILEEKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|254883215|ref|ZP_05255925.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_3_47FAA]
 gi|254836008|gb|EET16317.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_3_47FAA]
          Length = 263

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 124/246 (50%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +
Sbjct: 7   MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMI 66

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+ 
Sbjct: 67  AHFDYDRELDCVQITEKLNRLLPPD--IAVYAVKRVKDDAHARFDATYRTYKYYVTTRKD 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
           P    +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     
Sbjct: 125 P--FNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVS 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+
Sbjct: 183 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALF 242

Query: 241 FDSVEY 246
              V Y
Sbjct: 243 LVDVGY 248


>gi|168211805|ref|ZP_02637430.1| tRNA pseudouridine synthase A [Clostridium perfringens B str. ATCC
           3626]
 gi|170710235|gb|EDT22417.1| tRNA pseudouridine synthase A [Clostridium perfringens B str. ATCC
           3626]
          Length = 248

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVHA   V
Sbjct: 6   ITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVHAKNYV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I   + 
Sbjct: 66  ANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  + +   
Sbjct: 124 KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFHENN 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP  GL  
Sbjct: 184 NILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPSHGLCL 243

Query: 242 DSVEY 246
             + Y
Sbjct: 244 LELNY 248


>gi|28198519|ref|NP_778833.1| tRNA pseudouridine synthase A [Xylella fastidiosa Temecula1]
 gi|28056603|gb|AAO28482.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
          Length = 258

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 131/247 (53%), Gaps = 13/247 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY + +EY+GS + GWQ+  + G S+Q ++++A+  V    V V  AGRTD+GVH   
Sbjct: 2   MMRYALGVEYDGSEFLGWQQLGEMGPSVQATLQQALASVADSSVRVVCAGRTDAGVHGQC 61

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  ++++       + FHARFSA  R Y Y
Sbjct: 62  QVVHFDSAVTRPPRAWI-------LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRY 114

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +  
Sbjct: 115 RLLNRQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQA 174

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V     +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A
Sbjct: 175 ISVRRDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTA 234

Query: 235 PPEGLYF 241
              GL F
Sbjct: 235 SARGLVF 241


>gi|296435991|gb|ADH18165.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/9768]
 gi|296437852|gb|ADH20013.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/11074]
 gi|297140352|gb|ADH97110.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/9301]
          Length = 267

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 126/242 (52%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  Q+AHF   
Sbjct: 9   IAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQGQIAHFHCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +     P+ 
Sbjct: 69  DHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTLSLLPKPVP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D++   +L+
Sbjct: 127 HHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLDLSEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP GL    V
Sbjct: 187 TVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|81429336|ref|YP_396337.1| tRNA pseudouridine synthase A [Lactobacillus sakei subsp. sakei
           23K]
 gi|123742201|sp|Q38UV3|TRUA_LACSS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78610979|emb|CAI56031.1| tRNA pseudouridylate synthase A (Pseudouridylate synthase I)
           [Lactobacillus sakei subsp. sakei 23K]
          Length = 249

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 128/247 (51%), Gaps = 5/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G+ + G+Q Q    ++QG++EKA+  +  G  + V+G+GRTDSGVHA+ QV
Sbjct: 4   RYRVTVAYDGTDFAGFQVQPKQRTVQGTLEKALTKMSKGAYIQVYGSGRTDSGVHAMGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E     + +ALN+ L +   + +++  + D  FHARFS + + Y+YR+     
Sbjct: 64  VHFDYPSELPAKSMLRALNSLLPLD--MEVVDSQLADDDFHARFSTVGKRYMYRVDLGHY 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--NS 179
               ++      P  +D E ++ A   ++G HD+T+F +        +RTI    V  N 
Sbjct: 122 TNPFKRRYTGHYPYPIDVERIKAALSDVMGTHDYTSFAAAGGVIKDKVRTIYEATVVYNE 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N +        FL+  +R  V +L  +G+G+    D  +  + +DR++    AP  GL
Sbjct: 182 AENELIFEFHGNGFLYNMVRILVATLLEIGNGRRDVHDFLRLYEVKDRQQARSTAPASGL 241

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 242 YLKEVYY 248


>gi|225867856|ref|YP_002743804.1| tRNA pseudouridine synthase A [Streptococcus equi subsp.
           zooepidemicus]
 gi|259550446|sp|C0MFQ1|TRUA_STRS7 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225701132|emb|CAW98001.1| tRNA pseudouridine synthase A [Streptococcus equi subsp.
           zooepidemicus]
          Length = 249

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+QRQ    ++Q  IEK +  +TG + + +HGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGTLFSGFQRQSQARTVQEEIEKTLQKLTGGQGIQIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++  P  L  AL+   +  D I +++L      FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLEQKRDPEKLRFALDT--QTPDDIDVISLEAAADDFHARYHKHFKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDIAKMQAAIKDLVGTHDFTGFTAAGTSVKNKVRTITAATLTQ 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +   L++++R+  GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRLPIEQIRLVLESKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|123966948|ref|YP_001012029.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9515]
 gi|166228749|sp|A2BYR1|TRUA_PROM5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123201314|gb|ABM72922.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9515]
          Length = 268

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 126/242 (52%), Gaps = 3/242 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS + GWQRQKN  S+Q  IE A+F V+ +++    AGRTDSGVHA  Q
Sbjct: 1   MKRVALLVQYDGSYFSGWQRQKNAISVQEMIEDALFKVSNQMIKTFAAGRTDSGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN+  ++  TI IL    V K +HA +SA+ R Y Y I   +
Sbjct: 61  VVHFDIDFVIPSDRYANVLNS--RLPSTIRILESVEVKKNWHACYSAVYRHYRYVINNSK 118

Query: 121 AP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P L L K       KSLD   M  A   ++G HDF  F+      S+ + TI   ++  
Sbjct: 119 IPNLFLNKWSWHRYQKSLDEFLMSKALNGMIGEHDFYAFQKSGSTRSTSVTTIKSIEIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI I + A  FL+  +RS VG L LVG+ K +    +     + +++    AP  GL
Sbjct: 179 TEDLILIDIKATGFLYGMVRSIVGQLVLVGEKKISPEIFKDRWVGKKKQDVHESAPANGL 238

Query: 240 YF 241
            F
Sbjct: 239 CF 240


>gi|182681198|ref|YP_001829358.1| tRNA pseudouridine synthase A [Xylella fastidiosa M23]
 gi|32130280|sp|Q87DS1|TRUA_XYLFT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238691112|sp|B2I9J0|TRUA_XYLF2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|182631308|gb|ACB92084.1| tRNA pseudouridine synthase A [Xylella fastidiosa M23]
          Length = 257

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 131/247 (53%), Gaps = 13/247 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY + +EY+GS + GWQ+  + G S+Q ++++A+  V    V V  AGRTD+GVH   
Sbjct: 1   MMRYALGVEYDGSEFLGWQQLGEMGPSVQATLQQALASVADSSVRVVCAGRTDAGVHGQC 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  ++++       + FHARFSA  R Y Y
Sbjct: 61  QVVHFDSAVTRPPRAWI-------LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +  
Sbjct: 114 RLLNRQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V     +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A
Sbjct: 174 ISVRRDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTA 233

Query: 235 PPEGLYF 241
              GL F
Sbjct: 234 SARGLVF 240


>gi|308809101|ref|XP_003081860.1| COG0101: Pseudouridylate synthase (ISS) [Ostreococcus tauri]
 gi|116060327|emb|CAL55663.1| COG0101: Pseudouridylate synthase (ISS) [Ostreococcus tauri]
          Length = 338

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 96/301 (31%), Positives = 142/301 (47%), Gaps = 55/301 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG----SSIQGSIEKAIFLVTGE--IVVVHGAGRTDSG 54
           + RY   +EY+G+ + G+QRQ  G    +++Q ++++A+   TG    V   G+ RTD G
Sbjct: 11  LPRYLAFLEYDGAKFRGFQRQNLGERATTTVQDALDEALETFTGNRGAVASVGSSRTDVG 70

Query: 55  VHALRQVAHFDLVR--------EWVPVILCKALNAYLKISD----TISILNLSIVDKQFH 102
           VHA R  AHFD  R         +    + + LN +LK  +        + +  ++  FH
Sbjct: 71  VHATRNSAHFDCGRVGKDGSMDAYDSESVRRGLNYHLKSRERAMRVTECVRVDTLNPTFH 130

Query: 103 ARFSAIRRSYLYRIIT---RQAPLALEKGRAWLI----------------------PKSL 137
           AR  A+ R Y Y I+           ++  AW +                         L
Sbjct: 131 ARHDAVSRRYRYEILVGDRDDGGSVFDRDGAWYLRAVVASDRGAKQTSSRRYTTCEATGL 190

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL------------IE 185
           D + MR AA  L+G+HDF++FR+  CQA SPIRTI   DV S                + 
Sbjct: 191 DVDAMRRAASVLIGKHDFSSFRASGCQAKSPIRTITSLDVVSRTTEWPSPEARGTRQEVS 250

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           +RV A SFL+ Q+R  VG+LK VG G  T  D+ + L+A+D  +   +AP  GLY   V 
Sbjct: 251 VRVEAPSFLYHQVRLLVGALKSVGAGDLTVDDVRELLEAKDVSQAPQMAPAHGLYLMDVG 310

Query: 246 Y 246
           Y
Sbjct: 311 Y 311


>gi|229107828|ref|ZP_04237464.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-15]
 gi|228675677|gb|EEL30885.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-15]
          Length = 252

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 86/251 (34%), Positives = 126/251 (50%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + I  R V   FL+  +R  VG+L  VG GK  S  + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDSDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|323126548|gb|ADX23845.1| tRNA pseudouridine synthase A [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 249

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 82/251 (32%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  ++Q  IEK +  L +G+ V +HGAGRTD+GVHA  
Sbjct: 1   MTRYKATISYDGTLFSGFQRQSHARTVQEEIEKTLQKLASGQPVPIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  D I +++L+IV   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDLEKLRFALDT--QTPDDIDVVDLAIVADDFHCRYQKHSKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDINKMQEAIKDLVGTHDFTGFTAAGTSVENKVRTITEATLVQ 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +  G L+        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP    
Sbjct: 179 DDKTGFLV-FTFSGNGFLYKQVRNMVGTLLKIGNGRMPVEQIKVILDSKNRQLAGPTPAG 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|86606117|ref|YP_474880.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-3-3Ab]
 gi|86554659|gb|ABC99617.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-3-3Ab]
          Length = 287

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 121/247 (48%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I+Y GSG+ GWQRQ    ++QG +E+AI L  G  V ++GAGRTD+GVHA  QVA
Sbjct: 5   RIALKIQYLGSGFRGWQRQAGHRTVQGVLEEAIALRAGHPVALYGAGRTDTGVHASGQVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD      P    + LN  L   + + +L  + V   +HARFSA  R Y Y I+ R+ P
Sbjct: 65  HFDTTSGIPPTEWARVLNDCLP--EDVVVLASAQVPDFWHARFSARWRRYRYLILNRELP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  +W +   L  E M  A   L+G H    FR            +        G+
Sbjct: 123 DVFWRLFSWQVRWPLQVEPMAEALNSLLGEHSLEAFRRRGSDRPHSRVQVQEVLCQRLGD 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLY 240
           LI I V A  FL+  +R  VGSL++VG G+ +        Q  D  R      APP+GL 
Sbjct: 183 LISIEVQASGFLYRMMRLLVGSLEVVGRGEISPQQFVHLWQHNDWSRMRTRYSAPPQGLC 242

Query: 241 FDSVEYS 247
              V Y+
Sbjct: 243 LVDVGYA 249


>gi|166154677|ref|YP_001654795.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|166155552|ref|YP_001653807.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335947|ref|ZP_07224191.1| tRNA pseudouridine synthase A [Chlamydia trachomatis L2tet1]
 gi|238687386|sp|B0B836|TRUA_CHLT2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238687485|sp|B0BCA1|TRUA_CHLTB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|165930665|emb|CAP04162.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|165931540|emb|CAP07116.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 267

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 126/242 (52%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  ++  +  + G  + V  +GRTD+GVHA  Q+AHF   
Sbjct: 9   IAYQGTSYSGWQYQPNALSIQEVLKTILKKIAGFRISVISSGRTDAGVHAQGQIAHFHCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +     PL 
Sbjct: 69  DHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTLSLLPKPLP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D++   +L+
Sbjct: 127 HHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLDLSEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP GL    V
Sbjct: 187 TVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|110800554|ref|YP_695694.1| tRNA pseudouridine synthase A [Clostridium perfringens ATCC 13124]
 gi|110675201|gb|ABG84188.1| tRNA pseudouridine synthase A [Clostridium perfringens ATCC 13124]
          Length = 248

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVHA   V
Sbjct: 6   ITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVHAKNYV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I   + 
Sbjct: 66  ANFKTNSLMTLEQIIEYINEYL--PEDIRVKEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  + +   
Sbjct: 124 KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFHENN 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP  GL  
Sbjct: 184 NILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPAHGLCL 243

Query: 242 DSVEY 246
             + Y
Sbjct: 244 LELNY 248


>gi|82751809|ref|YP_417550.1| tRNA pseudouridine synthase A [Staphylococcus aureus RF122]
 gi|123727496|sp|Q2YYM7|TRUA_STAAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|82657340|emb|CAI81781.1| tRNA pseudouridine synthase A [Staphylococcus aureus RF122]
          Length = 267

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 123/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L +   I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTLPVD--IYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               ++G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQRGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|317154696|ref|YP_004122744.1| tRNA pseudouridine synthase A [Desulfovibrio aespoeensis Aspo-2]
 gi|316944947|gb|ADU63998.1| tRNA pseudouridine synthase A [Desulfovibrio aespoeensis Aspo-2]
          Length = 258

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 127/251 (50%), Gaps = 10/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + + Y+G+ + GWQ Q    ++QG IE A+  + G  V +HGAGRTD+GVHAL Q
Sbjct: 1   MPRFLLTLAYDGTDFSGWQLQARDRTVQGVIETALTEIMGSPVRLHGAGRTDAGVHALGQ 60

Query: 61  VAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
            AHFD   +R  +P     ALNA  ++ + + +L    V   FHAR+ A  ++Y Y +  
Sbjct: 61  TAHFDCQDIRASIPWQC--ALNA--RLPEDVRVLACRRVADDFHARYQAQAKTYEYTLWH 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           TR+  L   +  AW     LD   M  AA+ L G HDF +F++      S IRT+     
Sbjct: 117 TREFCLPQRRRFAWNC-GPLDFTAMEAAARLLTGEHDFASFQNTGTPVRSTIRTVTAISR 175

Query: 178 NSFGNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +      E   R  A  FL   +R+ VG L   G G+    +  + L A DR      AP
Sbjct: 176 HPGPTPHESVWRFTANGFLKQMVRNLVGCLAACGRGRLAPDEAGRILLAADRALAPATAP 235

Query: 236 PEGLYFDSVEY 246
           P+GL   SV Y
Sbjct: 236 PQGLTLISVAY 246


>gi|323342828|ref|ZP_08083060.1| tRNA pseudouridine synthase A [Erysipelothrix rhusiopathiae ATCC
           19414]
 gi|322463940|gb|EFY09134.1| tRNA pseudouridine synthase A [Erysipelothrix rhusiopathiae ATCC
           19414]
          Length = 245

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R+   ++Y+GS + GWQ+Q  G  +Q  IE  +  +  E + + G+GRTD+GVHAL Q
Sbjct: 1   MMRFKATVQYDGSMFKGWQKQPFGRCVQTEIESVLTRINKEPIHISGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD V +     L +ALN  L   + I I ++  V+  FHARF  + ++Y YR+    
Sbjct: 61  VFHFDNVVDMDEKQLFRALNTLL--PNDIVITDIHPVEPNFHARFDVVSKTYEYRLNMGA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS 179
             L  E+   +   K+LD + +R A +  VG HDFT+F +    +  + +RTI +FD+  
Sbjct: 119 YNL-FERNYVYQYNKALDLQAIRDAMESFVGTHDFTSFNATGLDEIENQVRTITNFDLIV 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +   ++   FL   +R  V +    G GK  + ++ + L+A D+          GL
Sbjct: 178 SDDHLNFVIIGDGFLRYMVRMIVATCVACGSGKCDAHEIAQMLKAADKNSISYNIDACGL 237

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 238 YLKKVNY 244


>gi|163791438|ref|ZP_02185847.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
 gi|159873302|gb|EDP67397.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
          Length = 246

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 121/243 (49%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M +EY+G+ Y GWQR  +   +IQG IE  I  +TG    + G+GRTD+G HA  QVA+F
Sbjct: 6   MTVEYDGARYLGWQRLTDSDKTIQGKIENTITAMTGTKTEIVGSGRTDAGAHAKGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I +  L  V ++FHAR++A  + Y Y +     P  
Sbjct: 66  KTESTMELQAMLDHLNRYL--PRDIVVKKLEEVPERFHARYNASGKKYSYYVWNNSVPSV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+  ++     LD + M  A   LVG+HDF  F S+     S +RTI+   ++  G+L+
Sbjct: 124 FERNFSYEYAGDLDIDKMNKACDKLVGKHDFIGFSSLKKSKKSTVRTINEIKIHKEGDLL 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               +   FL+  IR  +G++  +G G      ++   ++  R E G   P +GL+ D V
Sbjct: 184 HFTFIGEGFLYKMIRIIMGTILEIGAGTTELESIDAIFKSGIRSEAGMTVPSQGLFLDEV 243

Query: 245 EYS 247
            Y 
Sbjct: 244 YYD 246


>gi|313906313|ref|ZP_07839656.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
 gi|313468869|gb|EFR64228.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
          Length = 271

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 86/256 (33%), Positives = 130/256 (50%), Gaps = 14/256 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +II Y+G+ Y G+Q Q NG ++Q  + +A+  +TGE +   GA RTD+GVHA   
Sbjct: 4   MKRIMLIIAYDGTNYCGFQVQPNGVTVQELVNRAVSELTGEEIRTIGASRTDAGVHARGN 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD            ALN   ++ D I +     V   FH R++   ++Y YRI+ R+
Sbjct: 64  VVVFDTKARMPGDKYSYALNP--RLPDDIKVQLSREVSPDFHPRYTDTVKTYEYRILNRR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFD 176
            P    +        SLD + M+ AA++L G HDF +F++     ++P    +RTI    
Sbjct: 122 MPDPTRRLNTLFNYFSLDADRMQAAARYLEGTHDFRSFQA--SGETNPDKETVRTIYSAS 179

Query: 177 VN----SFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           V     + GN  LI  R+    FL+  +R   G+L  +G GK    D++K + A+ R   
Sbjct: 180 VTRGNAADGNEDLITFRITGNGFLYNMVRILAGTLIEIGRGKLEPEDMKKIMDARSRDAA 239

Query: 231 GPLAPPEGLYFDSVEY 246
           GP APP+GL    + Y
Sbjct: 240 GPTAPPQGLTLVEIRY 255


>gi|71899860|ref|ZP_00682009.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
 gi|71730377|gb|EAO32459.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
          Length = 257

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 131/247 (53%), Gaps = 13/247 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY + +EY+GS + GWQ+  + G S+Q ++++A+  V    V V  AGRTD+GVH   
Sbjct: 1   MMRYALGVEYDGSEFLGWQQLGEMGPSVQATLQQALASVADASVRVVCAGRTDAGVHGQC 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  ++++       + FHARFSA  R Y Y
Sbjct: 61  QVVHFDSAVTRPPRAWI-------LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +  
Sbjct: 114 RLLNRQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V     +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A
Sbjct: 174 ISVRRDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTA 233

Query: 235 PPEGLYF 241
              GL F
Sbjct: 234 SARGLVF 240


>gi|71274838|ref|ZP_00651126.1| tRNA pseudouridine synthase [Xylella fastidiosa Dixon]
 gi|71902311|ref|ZP_00684298.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
 gi|170729917|ref|YP_001775350.1| tRNA pseudouridine synthase A [Xylella fastidiosa M12]
 gi|238687976|sp|B0U6K4|TRUA_XYLFM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|71164570|gb|EAO14284.1| tRNA pseudouridine synthase [Xylella fastidiosa Dixon]
 gi|71727947|gb|EAO30171.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
 gi|167964710|gb|ACA11720.1| Pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 257

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 131/247 (53%), Gaps = 13/247 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY + +EY+GS + GWQ+  + G S+Q ++++A+  V    V V  AGRTD+GVH   
Sbjct: 1   MMRYALGVEYDGSEFLGWQQLGEMGPSVQATLQQALASVADASVRVVCAGRTDAGVHGQC 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  ++++       + FHARFSA  R Y Y
Sbjct: 61  QVVHFDSAVTRPPRAWI-------LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +  
Sbjct: 114 RLLNRQVRPALQHQFLSWERYPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V     +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A
Sbjct: 174 ISVRRDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTA 233

Query: 235 PPEGLYF 241
              GL F
Sbjct: 234 SARGLVF 240


>gi|218960843|ref|YP_001740618.1| putative pseudouridylate synthase I [Candidatus Cloacamonas
           acidaminovorans]
 gi|167729500|emb|CAO80411.1| putative pseudouridylate synthase I [Candidatus Cloacamonas
           acidaminovorans]
          Length = 274

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/248 (33%), Positives = 126/248 (50%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + I Y+G+GY GWQ+QKNG +IQ  +EK + +  G+   +  AGRTD+GVH+L Q
Sbjct: 3   MARYLIKICYDGTGYCGWQKQKNGLAIQEVMEKMLEIFAGKKTSLIAAGRTDAGVHSLGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD         L  A N YL   D+I +L +  V    +AR+ A  RSY YR+   +
Sbjct: 63  YAHFDYSGSMQEKQLFLAFNRYL--PDSIKVLEIMKVSPCLNARYQAYERSYRYRLAKEK 120

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +  +   P   L+ E M+ A Q+L+G+HDF+TF   + +  + I  + H  ++ 
Sbjct: 121 TP--FNRNYSGFFPHLHLNLEKMQSAVQYLLGKHDFSTFGKSNPEVPNRICELKHISISE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEG 238
                     A  FLH  +R  VG+L  +         + + L+ +  R+     AP  G
Sbjct: 179 TERYFVFDFTADRFLHNMVRRIVGTLANISHLHLPPETVLEILENRCPRQNLVITAPASG 238

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 239 LYLMDVKY 246


>gi|256844460|ref|ZP_05549946.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 125-2-CHN]
 gi|256613538|gb|EEU18741.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 125-2-CHN]
          Length = 262

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V  +GRTD+GVHA+ QV
Sbjct: 4   RYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGQRVIVQVSGRTDAGVHAVGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  A+N+ +     I   +  IVD+ FHAR+S   + Y YR+    
Sbjct: 64  IHFDYPGKTIPANRMILAMNSMMPTD--IIFDDCQIVDENFHARYSIKGKWYRYRVSLDH 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  LD E M++AAQ L+G+HDFT+F +   Q    +RTI + ++  +
Sbjct: 122 FVNPFKRFYTGHFPYPLDIEKMQVAAQDLLGKHDFTSFAASGGQIEDKVRTIYYINITKD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   G
Sbjct: 182 EKENEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPIHDLQRVIAAKDRQEVRQTAHASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYD 250


>gi|229003158|ref|ZP_04161004.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock1-4]
 gi|228758121|gb|EEM07320.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock1-4]
          Length = 252

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHARG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I +  +    + FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WMNALNTML--PDDIVVRQVEKKIEDFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+ E++R A  + +G HDFT+F S        +RTI   D
Sbjct: 121 LLSKNADVFRRNYVYQYPYPLEIESIRKAIPYFIGTHDFTSFCSTKTDKKDKVRTIYEID 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  +G GK     + + L+ QDR+  G + P 
Sbjct: 181 LMEQDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKMVPDSIPEILKKQDRRFAGKMVPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|225850198|ref|YP_002730432.1| tRNA pseudouridine synthase A [Persephonella marina EX-H1]
 gi|225645344|gb|ACO03530.1| tRNA pseudouridine synthase A [Persephonella marina EX-H1]
          Length = 244

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 131/245 (53%), Gaps = 9/245 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y ++I Y G  Y GWQ+Q    ++QG +E+ + ++  E +V+ G+GRTD+GVHAL QVA+
Sbjct: 7   YKLVIMYIGKNYHGWQKQPKHRTVQGVLEEKLKVLFKEDIVLIGSGRTDAGVHALGQVAN 66

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F  +    P  + + LNA L     IS+ ++  V   FHARFSA  ++Y+YRI T+  P 
Sbjct: 67  FKTISYRKPEEIYRYLNATL--PRDISVKSVEEVPLSFHARFSAKGKTYIYRIYTKPDPF 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFDVNSFG 181
               G  W I K LD + M  A + +    D  +   +  + +    IR +    +   G
Sbjct: 125 L--HGFGWYISKKLDLKGMLEALEIVKKSKDLRSLSKKGEYLREDVEIREL---SMTYDG 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +IEI++ A  FL   +R  VG +  +G G  +  + E  ++A+D  +   +APPEGL+ 
Sbjct: 180 KIIEIQITASHFLRYMVRKIVGHVVQIGLGSLSIQEFENIIEAKDPTKGLFIAPPEGLFL 239

Query: 242 DSVEY 246
             V Y
Sbjct: 240 KEVYY 244


>gi|325915522|ref|ZP_08177833.1| pseudouridylate synthase I [Xanthomonas vesicatoria ATCC 35937]
 gi|325538238|gb|EGD09923.1| pseudouridylate synthase I [Xanthomonas vesicatoria ATCC 35937]
          Length = 257

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 135/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    + V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASVQAALSSVADAPIQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++     V   FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDALRQPRGWM-------LGTTARLPPSIAVRWCVPVADDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD E M  AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRPLDAEAMHAAAQALLGENDFSAFRSVQCQALHARRNLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E+RV A +FLH  +R+ VGSL L+G G+  +  +   L  +DR   GP A
Sbjct: 174 ITVQRIGEVVEVRVQANAFLHHMVRNIVGSLILIGTGEQPTDWIATLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|255348836|ref|ZP_05380843.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 70]
 gi|255503376|ref|ZP_05381766.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 70s]
          Length = 267

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 126/242 (52%), Gaps = 5/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--- 64
           I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  Q+AHF   
Sbjct: 9   IAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQGQIAHFHCP 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +     P+ 
Sbjct: 69  DHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTLSLLPKPVP 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D++   +L+
Sbjct: 127 HHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLDLSEQEHLV 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP GL    V
Sbjct: 187 TVICRGNGFLYKMVRNIVGALLDIGKGKYPPEYLLDMLATKDRRKGPPSAPPYGLSLHHV 246

Query: 245 EY 246
            Y
Sbjct: 247 CY 248


>gi|253729885|ref|ZP_04864050.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253726332|gb|EES95061.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 267

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L+ ++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLELKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|126658015|ref|ZP_01729167.1| tRNA pseudouridine synthase A [Cyanothece sp. CCY0110]
 gi|126620653|gb|EAZ91370.1| tRNA pseudouridine synthase A [Cyanothece sp. CCY0110]
          Length = 285

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 120/245 (48%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y GS + GWQRQ N  ++Q  IE +I  V G    +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYQGSRFHGWQRQPNQRTVQEVIESSIAEVLGYHTPIHGAGRTDAGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD +    P    + LN   ++ D I I   + V   +HARFSA+ R Y Y   T + P
Sbjct: 72  HFDYISPIPPQRWVEILNQ--RLPDDILIRGCAEVSLTWHARFSALWRRYRYSFYTDKCP 129

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W    + LD E M+ A   L+GRH    FR            +        G
Sbjct: 130 NLFVRPFSWHYYYEPLDAELMQKALTPLLGRHHLAAFRRAGSHRHHSWVEVQETRCYRQG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK + T+  +  Q Q R++    AP +GL  
Sbjct: 190 QFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLTNFTEIWQNQRREQVKYSAPAKGLCL 249

Query: 242 DSVEY 246
             V Y
Sbjct: 250 LRVGY 254


>gi|323490654|ref|ZP_08095859.1| tRNA pseudouridine synthase A [Planococcus donghaensis MPA1U2]
 gi|323395746|gb|EGA88587.1| tRNA pseudouridine synthase A [Planococcus donghaensis MPA1U2]
          Length = 247

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 129/248 (52%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R    I Y+GSG+ G+Q Q +  ++Q  + K +  +  G+++ V  +GRTD+ VHA  
Sbjct: 1   MKRLKATIAYDGSGFAGYQVQPDSRTVQLELMKVLETIHKGKVIQVVASGRTDAKVHATG 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD     +P+I   KALN  L   + I + ++  VD  FHAR+    ++Y Y+   
Sbjct: 61  QVIHFD-TELSIPIIGWLKALNVLL--PEDIRVHSIEEVDTSFHARYHTTGKTYRYKWDR 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            Q      +     + + LD E M+ A+Q +VG HDF++F + +      +RT+   D  
Sbjct: 118 SQIISPFTRSLMVHVKQPLDVEAMKKASQAIVGTHDFSSFCAANTAVVDKVRTVRRLDFE 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             GN + + +    FL+  +R   G+L  VG G+  + +LE  + A DR   G  AP  G
Sbjct: 178 EHGNELHMVIEGTGFLYNMVRIIAGTLAEVGMGRRKAEELEDIVSATDRDAAGITAPAHG 237

Query: 239 LYFDSVEY 246
           LY ++V Y
Sbjct: 238 LYLENVMY 245


>gi|257868757|ref|ZP_05648410.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257802921|gb|EEV31743.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 246

 Score =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 76/242 (31%), Positives = 125/242 (51%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G  Y GWQR  +   +IQ  IE  +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6   LTIEYDGKRYLGWQRLGDSDRTIQEKIESILTQMTNEKIEIIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  P  + + LN YL     I I  ++   ++FHAR++A  + Y Y +     P  
Sbjct: 66  KTASDLSPEKMLQFLNRYL--PQDIVIKEVAEASERFHARYNATGKQYSYYVWNSPIPTV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+ R++  P+ LD + M+ A +  +G HDF  F ++     S  RTI+   +   G+++
Sbjct: 124 FERHRSFHCPQELDWDKMQAACEKFIGTHDFIGFSALKKTKKSTTRTIEELSLTREGDML 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R     FL+  +R   G++  +G G    + +++    Q RK  G   P +GL+ D+V
Sbjct: 184 RFRFKGDGFLYKMVRIITGTILEIGAGTMDISAIDEIFTNQVRKAAGETVPSQGLFLDAV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|297205058|ref|ZP_06922454.1| tRNA-pseudouridine synthase I [Lactobacillus jensenii JV-V16]
 gi|297149636|gb|EFH29933.1| tRNA-pseudouridine synthase I [Lactobacillus jensenii JV-V16]
          Length = 262

 Score =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 135/251 (53%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R+ M + Y+G  + G+Q+Q N  ++QG+IE+A+  +  G+ +VVHG+GRTD+GVHAL 
Sbjct: 1   MPRFKMTMAYDGHLFHGFQKQPNQRTVQGTIEEALKKMAKGQRIVVHGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD   + +P   +  ALN+ +     I   +  IV++ FH ++S   + Y Y +  
Sbjct: 61  QVIHFDFPNDNIPANRMVLALNSMMPTD--IIFKDAEIVNEDFHVQYSTHGKWYRYIVNQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
            +     ++      P  L+   M+ AA  L+G HDFT+F +   Q    +RTI +  + 
Sbjct: 119 DRFVDPFKRFYTGHYPYKLNVSKMQEAALDLLGEHDFTSFAASGGQIIDKVRTIYYVKIW 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             S  N I    +   FL+  +R  VG+L  +G+ +    DL++ + A+DR+E    AP 
Sbjct: 179 QKSEENEIIFDFIGNGFLYNMVRIMVGALLEIGNERRPVHDLKRVILAKDRQEVRNTAPA 238

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 239 SGLYLYHVFYE 249


>gi|291562296|emb|CBL41112.1| pseudouridylate synthase I [butyrate-producing bacterium SS3/4]
          Length = 344

 Score =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 129/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + KA+  +  E V V GA RTDSGVHA   
Sbjct: 1   MRRIKLTVAYDGTAYKGWQLQPNGVTIEEMLNKALSDLLKEPVCVIGASRTDSGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD          C A+N  L   + I ++    V   +H R     ++Y Y+I+  +
Sbjct: 61  VAVFDTESRIPGDKFCYAVNRGL--PEDIRVVESEEVPLDWHPRKQNCVKTYEYQILNCK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +  A      L+ E M  AA++L+G HDF +F + + QA   +RTI   +V   
Sbjct: 119 IEIPTRRLYAHFCYYPLNVEKMNEAAKYLIGEHDFISFCAANHQAEETVRTIYGAEVKKN 178

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +++ IR+    FL+  +R   G+L  VG G+W    +++ L+A++RKE G  AP +GL
Sbjct: 179 DEDIVTIRLCGSGFLYNMVRIIAGTLLKVGTGEWEPEHVKEVLEARNRKEAGQTAPAKGL 238

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 239 TLVGIEYE 246


>gi|329942480|ref|ZP_08291290.1| tRNA pseudouridine synthase A [Chlamydophila psittaci Cal10]
 gi|332287117|ref|YP_004422018.1| tRNA pseudouridine synthase A [Chlamydophila psittaci 6BC]
 gi|313847713|emb|CBY16703.1| putative tRNA pseudouridine synthase a [Chlamydophila psittaci RD1]
 gi|325507334|gb|ADZ18972.1| tRNA pseudouridine synthase A [Chlamydophila psittaci 6BC]
 gi|328815390|gb|EGF85378.1| tRNA pseudouridine synthase A [Chlamydophila psittaci Cal10]
 gi|328914357|gb|AEB55190.1| tRNA pseudouridine synthase A [Chlamydophila psittaci 6BC]
          Length = 268

 Score =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 85/249 (34%), Positives = 131/249 (52%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +++ Y G+ Y GWQRQ N  S+Q  IE ++  V G+ + V  +GRTD+GVHA  Q
Sbjct: 1   MTQVVLLLAYQGTAYAGWQRQPNDLSVQEVIENSLTKVVGKRIHVTSSGRTDAGVHAFGQ 60

Query: 61  VAHF---DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF   D  R      + K LNA L     I I ++ + D  FH+RFSAI + Y Y + 
Sbjct: 61  VAHFPQPDHPRFSQASGIKKMLNALL--PKDIVIRDVVLGDDTFHSRFSAIAKEYRYLLT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  E+  ++     L  + M+  A++L+G HDF +F +     +S IRT+ + D+
Sbjct: 119 RSPKPLPWERYFSYYPRHHLRTDLMQEGAKYLIGTHDFASFANHGRDYTSTIRTLFNLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  + I      FL+  +R+ VGSL  +  GK+    +++ L  ++R++  P AP  
Sbjct: 179 VDNGETVTIICKGNGFLYKMVRNIVGSLLDISRGKYPPEYIQEILIQKNRRKGPPAAPSY 238

Query: 238 GLYFDSVEY 246
            L    V Y
Sbjct: 239 ALSLYHVCY 247


>gi|73662003|ref|YP_300784.1| tRNA pseudouridine synthase A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|123761549|sp|Q49ZD7|TRUA_STAS1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|72494518|dbj|BAE17839.1| tRNA pseudouridine synthase A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 267

 Score =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 121/243 (49%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q++G +IQ   EK +  +    V +H + RTD GVHA+ Q 
Sbjct: 1   MRVLVNISYQGSQFLGFQIQQHGRTIQQQFEKILKRMHKHEVRIHPSSRTDRGVHAIEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + ++S V+  FH R+  + +SY Y+I     
Sbjct: 61  FHFDTELNIPEQQWQYAMNRAL--PDDIYVNDVSFVNDDFHCRYDCVGKSYRYKIYQSAH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                 G    +P+ LD E M +AAQH +G HDFT F S   +  S IRT+    +    
Sbjct: 119 KDPFLCGLKTYVPEQLDIEKMNMAAQHFIGTHDFTGFCSQKTEVESKIRTLYESRIEKTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  +  L  VG GK    ++ + L+A+DR +    AP EGLY 
Sbjct: 179 SGFDYIVTGSGFLYNMVRVLIAFLIEVGKGKREPQEVPQLLEARDRNQVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|57650803|ref|YP_187018.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           COL]
 gi|87160970|ref|YP_494808.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|88196131|ref|YP_500948.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|151222333|ref|YP_001333155.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|161510423|ref|YP_001576082.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|221140179|ref|ZP_03564672.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. JKD6009]
 gi|258450785|ref|ZP_05698844.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5948]
 gi|262048488|ref|ZP_06021372.1| tRNA pseudouridine synthase A [Staphylococcus aureus D30]
 gi|262052013|ref|ZP_06024224.1| tRNA pseudouridine synthase A [Staphylococcus aureus 930918-3]
 gi|282922088|ref|ZP_06329784.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9765]
 gi|284025245|ref|ZP_06379643.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           132]
 gi|294848752|ref|ZP_06789497.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9754]
 gi|304379403|ref|ZP_07362138.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|62901165|sp|Q5HDY9|TRUA_STAAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123098008|sp|Q2FW37|TRUA_STAA8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123763262|sp|Q2FES0|TRUA_STAA3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|172049003|sp|A6QJ61|TRUA_STAAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030147|sp|A8Z326|TRUA_STAAT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57284989|gb|AAW37083.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           COL]
 gi|87126944|gb|ABD21458.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87203689|gb|ABD31499.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|150375133|dbj|BAF68393.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160369232|gb|ABX30203.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|257861568|gb|EEV84370.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5948]
 gi|259160068|gb|EEW45101.1| tRNA pseudouridine synthase A [Staphylococcus aureus 930918-3]
 gi|259163346|gb|EEW47904.1| tRNA pseudouridine synthase A [Staphylococcus aureus D30]
 gi|269941808|emb|CBI50218.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|282593556|gb|EFB98549.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9765]
 gi|294824131|gb|EFG40555.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9754]
 gi|302752092|gb|ADL66269.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304341935|gb|EFM07839.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|315198251|gb|EFU28582.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320140243|gb|EFW32102.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320143513|gb|EFW35294.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MRSA177]
 gi|329314902|gb|AEB89315.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           T0131]
 gi|329732055|gb|EGG68410.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           21189]
          Length = 267

 Score =  136 bits (343), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD   M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLGKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|313890306|ref|ZP_07823938.1| tRNA pseudouridine synthase A [Streptococcus pseudoporcinus SPIN
           20026]
 gi|313121292|gb|EFR44399.1| tRNA pseudouridine synthase A [Streptococcus pseudoporcinus SPIN
           20026]
          Length = 249

 Score =  136 bits (343), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           MIRY  II Y+GS + G+QRQ N  +IQ  IEK +  L  G+ + + GAGRTD+GVHA  
Sbjct: 1   MIRYKAIISYDGSQFSGFQRQTNARTIQEEIEKTLMRLNKGKTITIQGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++++  V   FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLAERRDLEKLRFALDT--QTPEDIDVISVEEVSNDFHARYSKHLKTYEFIVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  LD   +++A + LVG HDFT F +      + +RT+   D N 
Sbjct: 119 RPKNPMMRQYATHYPYPLDFSLIKLAIKDLVGTHDFTGFTAAGTSVENKVRTLYQADCNF 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S    +        FL+ Q+R+ VG+L  +G+ +     +   L+ ++R+  GP     
Sbjct: 179 DSHRQFLIFTFTGNGFLYKQVRNMVGTLLKIGNQRMPVEQVRIILEQKNRQLAGPTIAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|76787537|ref|YP_328824.1| tRNA pseudouridine synthase A [Streptococcus agalactiae A909]
 gi|123602597|sp|Q3K3S9|TRUA_STRA1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76562594|gb|ABA45178.1| tRNA pseudouridine synthase A [Streptococcus agalactiae A909]
          Length = 258

 Score =  136 bits (343), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 130/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  L +G  V++HGAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI  FD   
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMKEAIKDLVGTHDFTGFTASGTSVENKVRTI--FDAKI 176

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A 
Sbjct: 177 QFEASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAA 236

Query: 236 PEGLYFDSVEYS 247
             GLY   + Y 
Sbjct: 237 GNGLYLKEIIYE 248


>gi|224024234|ref|ZP_03642600.1| hypothetical protein BACCOPRO_00957 [Bacteroides coprophilus DSM
           18228]
 gi|224017456|gb|EEF75468.1| hypothetical protein BACCOPRO_00957 [Bacteroides coprophilus DSM
           18228]
          Length = 249

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 124/248 (50%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + ++G+ Y GWQ Q NG+S+Q ++ KA+       + V GAGRTD+GVHA   
Sbjct: 1   MFRYFIYLSFDGTNYHGWQIQPNGASVQETLMKALSTFLRREIEVVGAGRTDAGVHARLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD   E    ++   LN  L     I++  +  V  + HARF A  R+Y Y I TR+
Sbjct: 61  VAHFDFDTELDGEVVTDKLNRLLPPD--IAVYGVRRVKPEAHARFDATSRTYKYYIHTRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVN 178
            P    +G +W I + LD E M  AAQ L    DFT+F  +H    +    I    ++  
Sbjct: 119 DP--FRRGYSWRIFQPLDFERMNEAAQTLFDYTDFTSFSKLHTDVKTNNCRIMLARWEQT 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A  FL   +R+ VG+L  VG GK T     + ++ ++R   G   P   
Sbjct: 177 GDGEWV-FTIRADRFLRNMVRAVVGTLVEVGRGKLTVDGFRRVIEEKNRCSAGTSVPGHA 235

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 236 LYLTDVSY 243


>gi|225570923|ref|ZP_03779946.1| hypothetical protein CLOHYLEM_07027 [Clostridium hylemonae DSM
           15053]
 gi|225160385|gb|EEG73004.1| hypothetical protein CLOHYLEM_07027 [Clostridium hylemonae DSM
           15053]
          Length = 282

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 79/246 (32%), Positives = 126/246 (51%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I Y+G+ Y GWQ Q NG +I+  +   +  +TGE + V GA RTDSGVHAL  VA
Sbjct: 38  RIRLVIAYDGTDYCGWQIQPNGITIEEVLNGVLTKLTGEDIHVIGASRTDSGVHALGNVA 97

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF-SAIRRSYLYRIITRQA 121
            FD      P  +  ALN   ++   I I+    V   +H R+   + ++Y Y I     
Sbjct: 98  VFDTASSIPPERMAYALNQ--RLPKDIVIVRSDEVPAGWHPRYRDVVIKTYEYHIYNAPV 155

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L++  +  I   L+ E MR  A++L+G HDF +F ++       +RT+    ++S G
Sbjct: 156 QNPLKRRTSTHISFPLNVEKMREGAKYLIGEHDFASFCNVRTSVKDTVRTVTELRIDSDG 215

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I +R+    FL+  +R   G+L  VG G +    +++ L+A++R   G   PP GL  
Sbjct: 216 PEIIMRITGNGFLYNMVRIIAGTLIRVGRGFYEPEKVKEILEAKERTGAGVTVPPNGLVL 275

Query: 242 DSVEYS 247
             ++Y 
Sbjct: 276 VEIDYG 281


>gi|160903290|ref|YP_001568871.1| tRNA pseudouridine synthase A [Petrotoga mobilis SJ95]
 gi|189030138|sp|A9BGW7|TRUA_PETMO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160360934|gb|ABX32548.1| tRNA pseudouridine synthase A [Petrotoga mobilis SJ95]
          Length = 245

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/238 (35%), Positives = 131/238 (55%), Gaps = 5/238 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+GS ++G+Q Q    ++Q   EKA+ ++  + +  +  GRTD+GVHA+ QV  F + 
Sbjct: 8   VMYDGSNFYGYQSQPTFRTVQDEFEKALKVIFKKEIPSYACGRTDTGVHAVGQVISFKVE 67

Query: 68  REWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            E +     K ALNA L   + + +  +  V + F+ R  A +R Y Y I   + P    
Sbjct: 68  NENMTEKNIKDALNAIL--PEDVYVKEVKEVKEGFNPRAEAKKRIYHYFIYISEDPNIFL 125

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-GNLIE 185
           + R W IP +L+ E MR AA++  G HDFT+F++ + +  +PIRTI    +     +LI 
Sbjct: 126 RDRVWWIPFALNLEKMRQAAKYFEGEHDFTSFKTGNDE-RNPIRTIYRVRIIELRKDLIL 184

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           IRV  +SFL   +R+ VGSL  VG   W    +++ L+A+ R      AP +GLYF S
Sbjct: 185 IRVEGKSFLKRMVRNIVGSLVKVGTDVWEVEKIQEILEAKKRALAPASAPAQGLYFYS 242


>gi|229067907|ref|ZP_04201224.1| tRNA pseudouridine synthase A [Bacillus cereus F65185]
 gi|228715266|gb|EEL67125.1| tRNA pseudouridine synthase A [Bacillus cereus F65185]
          Length = 252

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 126/251 (50%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW  +    ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTSLSLEEWQWI---NALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQNDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|260887817|ref|ZP_05899080.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
 gi|330838710|ref|YP_004413290.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
 gi|260862493|gb|EEX76993.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
 gi|329746474|gb|AEB99830.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
          Length = 258

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 127/245 (51%), Gaps = 6/245 (2%)

Query: 5   CMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           C+ + Y+G+ Y G+QRQ     ++Q  +E+ + LV G+ + +  AGRTD+GVHA+ QV +
Sbjct: 17  CLTVAYDGTAYHGFQRQSPPIRAVQNVLEEKLALVFGDAIELAAAGRTDAGVHAMGQVVN 76

Query: 64  FDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +P   + +A+N+ L     I +       + F AR SA  +SY+YRI     P
Sbjct: 77  F-FTDGRIPTERIVRAMNSVL--PPDIVVKAAREEGRDFSARHSAKSKSYIYRIQEGDTP 133

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-G 181
               +  AW +   LD   M  AA  L+G HDF+ FR+       P+RT+   +     G
Sbjct: 134 NPFSERYAWYVGTPLDLAAMNEAAALLLGTHDFSAFRAAGGAPMLPVRTMYSAEGRRIEG 193

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             IE R  A  FL+   R+ VG+L  VG G+ T  D    L +++RK     AP  GL+ 
Sbjct: 194 ERIEFRFHANGFLYHMARNIVGTLVDVGKGRRTRADFAAILASRERKRASATAPACGLFL 253

Query: 242 DSVEY 246
           +SVEY
Sbjct: 254 ESVEY 258


>gi|320451375|ref|YP_004203471.1| tRNA pseudouridine synthase A [Thermus scotoductus SA-01]
 gi|320151544|gb|ADW22922.1| tRNA pseudouridine synthase A [Thermus scotoductus SA-01]
          Length = 254

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 126/252 (50%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ+ G  ++QG +E+ +    G +     AGRTD+GVHAL 
Sbjct: 1   MRRILILTEYDGTHFAGLQRQRTGLRTVQGELER-VLPGIGALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              HFDL        + +ALN  L   + + ++    V   FHAR  A+ R+YLYRI+ R
Sbjct: 60  MPFHFDLGSRIPTEKIPQALNRLL--PEDLKVVAAREVAPDFHARKDALWRAYLYRILLR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L + RA  +   LD   +R A   L GRH+F  F     +A    R +    +  
Sbjct: 118 SHPSPLLRHRALWLRHPLDLAAIREALSFLPGRHNFLGFAKEEVRAGE--RELYEARMEE 175

Query: 180 F----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G  +      +SFL  Q+R  VG+L  VG GK +   +   LQ QDR + GP AP
Sbjct: 176 VEGEAGRELRFYFRGQSFLRGQVRGMVGTLLEVGLGKRSPESIRLILQTQDRGQAGPSAP 235

Query: 236 PEGLYFDSVEYS 247
           P+GLYF    Y 
Sbjct: 236 PQGLYFLEAAYP 247


>gi|225175641|ref|ZP_03729635.1| tRNA pseudouridine synthase A [Dethiobacter alkaliphilus AHT 1]
 gi|225168970|gb|EEG77770.1| tRNA pseudouridine synthase A [Dethiobacter alkaliphilus AHT 1]
          Length = 246

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y+G+GY G+Q QKN  ++Q  +E+AI  V G+ V +  +GRTD+GVHA  Q
Sbjct: 1   MPNIKLTLGYDGTGYHGFQLQKNAVTVQQKLEEAIEKVMGQKVRITASGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F       P  +  ALNA L     I I    IV   FHARF A+ ++Y Y I    
Sbjct: 61  VINFFAQTGIPPQRIPHALNAVL--PRDIVIYAAEIVSDSFHARFDAVGKTYTYTIDNGA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +  A+ +   LD   M+ AA  L G+HDFT+F +      + +R +   DV   
Sbjct: 119 HPQVLSRHHAYHVRFPLDANLMKQAAATLQGKHDFTSFMASGSSVKTTVRNLYRLDVEIN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I   A  FL+  +R   G+L  VG GK    +L   + A++R   G   P  GL 
Sbjct: 179 WPYITITAAADGFLYNMVRIIAGTLIEVGRGK-RDHNLGPVIDAKNRHRAGWTVPAHGLV 237

Query: 241 FDSVEYS 247
              VEY+
Sbjct: 238 LREVEYN 244


>gi|256852067|ref|ZP_05557454.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 27-2-CHN]
 gi|260661364|ref|ZP_05862277.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 115-3-CHN]
 gi|256615479|gb|EEU20669.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 27-2-CHN]
 gi|260547819|gb|EEX23796.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 115-3-CHN]
          Length = 262

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 135/251 (53%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R+ M + Y+G  + G+Q+Q N  ++QG+IE+A+  +  G+ +VVHG+GRTD+GVHAL 
Sbjct: 1   MPRFKMTMAYDGHLFHGFQKQPNQRTVQGTIEEALKKMAKGQRIVVHGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD   + +P   +  ALN+ +     I   +  IV++ FH ++S   + Y Y +  
Sbjct: 61  QVIHFDFPNDNIPANRMVLALNSMMPTD--IIFKDAEIVNEDFHVQYSTHGKWYRYIVNQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
            +     ++      P  L+   M+ AA  L+G HDFT+F +   Q    +RTI +  + 
Sbjct: 119 DRFVDPFKRFYTGHYPYKLNVSKMQEAALDLLGEHDFTSFAASGGQIIDKVRTIYYVKIW 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             S  N I    +   FL+  +R  VG+L  +G+ +    DL++ + A+DR+E    AP 
Sbjct: 179 QKSEENEIIFDFIGNGFLYNMVRIMVGALLEIGNERRPVHDLKRVILAKDRQEVINTAPA 238

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 239 SGLYLYHVFYE 249


>gi|196041154|ref|ZP_03108450.1| tRNA pseudouridine synthase A [Bacillus cereus NVH0597-99]
 gi|196028089|gb|EDX66700.1| tRNA pseudouridine synthase A [Bacillus cereus NVH0597-99]
          Length = 252

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 125/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P SL+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LVSKTADVFRRNYVYQYPYSLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|218230830|ref|YP_002364991.1| tRNA pseudouridine synthase A [Bacillus cereus B4264]
 gi|228950690|ref|ZP_04112824.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|229077443|ref|ZP_04210092.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-2]
 gi|229148551|ref|ZP_04276807.1| tRNA pseudouridine synthase A [Bacillus cereus m1550]
 gi|229176742|ref|ZP_04304146.1| tRNA pseudouridine synthase A [Bacillus cereus 172560W]
 gi|218158787|gb|ACK58779.1| tRNA pseudouridine synthase A [Bacillus cereus B4264]
 gi|228606785|gb|EEK64202.1| tRNA pseudouridine synthase A [Bacillus cereus 172560W]
 gi|228634967|gb|EEK91540.1| tRNA pseudouridine synthase A [Bacillus cereus m1550]
 gi|228705869|gb|EEL58206.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-2]
 gi|228809041|gb|EEM55526.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 252

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 126/251 (50%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW  +    ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQWI---NALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQNDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|191639397|ref|YP_001988563.1| tRNA pseudouridine synthase A [Lactobacillus casei BL23]
 gi|239630320|ref|ZP_04673351.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|301067471|ref|YP_003789494.1| pseudouridylate synthase [Lactobacillus casei str. Zhang]
 gi|238693010|sp|B3WAI6|TRUA_LACCB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|190713699|emb|CAQ67705.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Lactobacillus casei BL23]
 gi|239527932|gb|EEQ66933.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|300439878|gb|ADK19644.1| Pseudouridylate synthase [Lactobacillus casei str. Zhang]
 gi|327383485|gb|AEA54961.1| tRNA pseudouridine synthase A 1 [Lactobacillus casei LC2W]
 gi|327386676|gb|AEA58150.1| tRNA pseudouridine synthase A 1 [Lactobacillus casei BD-II]
          Length = 247

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 125/249 (50%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +T G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMTKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + KA+N+ + +   I IL   IVD  FHAR+SA  + YLYR+   
Sbjct: 61  QVISFDYPGNIPAESMLKAMNSLMPLD--IEILKAEIVDADFHARYSAKGKRYLYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVQRIEVALKDLVGTHDFTSFAASGGVIVDKVRTIYEATVRE 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N I        FL+  +R  V +   +G+G+    D ++    +DR++    AP  
Sbjct: 179 DPVTNEIIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFAVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|227533991|ref|ZP_03964040.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I)
           [Lactobacillus paracasei subsp. paracasei ATCC 25302]
 gi|227188368|gb|EEI68435.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I)
           [Lactobacillus paracasei subsp. paracasei ATCC 25302]
          Length = 254

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 125/249 (50%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +T G+ V V G+GRTDSGVHAL 
Sbjct: 8   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMTKGQPVHVDGSGRTDSGVHALG 67

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + KA+N+ + +   I IL   IVD  FHAR+SA  + YLYR+   
Sbjct: 68  QVISFDYPGNIPAESMLKAMNSLMPLD--IEILKAEIVDADFHARYSAKGKRYLYRVARG 125

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 126 YYTNPFNRLYTGHYPYKLDVQRIEVALKDLVGTHDFTSFAASGGVIVDKVRTIYEATVRE 185

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N I        FL+  +R  V +   +G+G+    D ++    +DR++    AP  
Sbjct: 186 DPVTNEIIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFAVKDRQQARGTAPAS 245

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 246 GLYLKEVYY 254


>gi|224369316|ref|YP_002603480.1| TruA1 [Desulfobacterium autotrophicum HRM2]
 gi|223692033|gb|ACN15316.1| TruA1 [Desulfobacterium autotrophicum HRM2]
          Length = 246

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 124/245 (50%), Gaps = 5/245 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + +EY+G+ Y GWQ Q N  ++Q  IEKA+  +  + + + G+GRTD+GVHAL QVA+
Sbjct: 5   FKLTLEYDGTPYSGWQVQNNCPTVQEEIEKALSRMLNQPIRISGSGRTDAGVHALGQVAN 64

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F          L ++LN+ LK    I +     VD+ FH+R+SA  + Y Y  + R+ P 
Sbjct: 65  FQAATTIGAAQLKRSLNSLLK--GPIVVHECRKVDQSFHSRYSARAKEYHYHFLNREDPC 122

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVNSFG 181
            + +   W I   L    M      + G HDF  F       S+ +RT+    F+  +  
Sbjct: 123 GVGRNYVWHIRTPLSIPAMEECCPIITGTHDFKAFEGSGSPRSTTVRTLFSTGFERTA-E 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +    ++    FL   +R+ VG+L L G GK T  + +  L+ +DR   G  AP +GL+ 
Sbjct: 182 DRFTFKIKGDGFLRFMVRNIVGTLVLAGAGKITPENFKTILEGKDRGRAGATAPAKGLFL 241

Query: 242 DSVEY 246
             V Y
Sbjct: 242 VEVFY 246


>gi|195978825|ref|YP_002124069.1| tRNA pseudouridine synthase A [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|238689837|sp|B4U545|TRUA_STREM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|195975530|gb|ACG63056.1| tRNA pseudouridine synthase A TruA [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 249

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+QRQ    ++Q  IEK +  +TG + + +HGAG TD+GVHA  
Sbjct: 1   MTRYKAIISYDGTLFSGFQRQSQARTVQEEIEKTLQKLTGGQGIQIHGAGITDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++  P  L  AL+   +  D I +++L I    FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLEQKRDPEKLRFALDT--QTPDDIDVISLEIAADDFHARYHKHFKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDIAKMQAAIKDLVGTHDFTGFTAAGTSVKNKVRTITAATLTQ 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +   L++++R+  GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRLPIEQIRLVLESKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|229170993|ref|ZP_04298594.1| tRNA pseudouridine synthase A [Bacillus cereus MM3]
 gi|228612533|gb|EEK69754.1| tRNA pseudouridine synthase A [Bacillus cereus MM3]
          Length = 252

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 125/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIKQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEISSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+ +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQGDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|197303593|ref|ZP_03168631.1| hypothetical protein RUMLAC_02321 [Ruminococcus lactaris ATCC
           29176]
 gi|197297327|gb|EDY31889.1| hypothetical protein RUMLAC_02321 [Ruminococcus lactaris ATCC
           29176]
          Length = 264

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 88/248 (35%), Positives = 124/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y ++I Y+G+ Y GWQRQ N   +IQG +E  I    G  V V+G+GRTD+GVHA  
Sbjct: 13  MRTYRLVIAYDGTAYQGWQRQANTEMTIQGILESCISKAAGYAVEVNGSGRTDAGVHARG 72

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +       + +N  L     I I    +    FHAR SA+ + Y+Y+I T 
Sbjct: 73  QTASVVLHGKAEDGFFTEKVNKLL--PPDIRIREAGLEKNGFHARKSAVGKRYVYQIDTD 130

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++   +  PK LD   M+ AA+ L G H+F  +     + S+  RTI    V  
Sbjct: 131 EKPDVFDRRYTYHFPKKLDIAAMQQAAELLTGTHEFAAYTDKKDETSTK-RTIYAIMVGG 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I I+     FL+  +R   G+L  VG G      +  AL+A+DR + G LAP  GL
Sbjct: 190 QGGRINIQYEGTGFLYHMVRILTGTLLEVGMGTRRIESVTIALEAKDRTKVGFLAPARGL 249

Query: 240 YFDSVEYS 247
           + D V Y 
Sbjct: 250 FLDEVYYK 257


>gi|25010174|ref|NP_734569.1| tRNA pseudouridine synthase A [Streptococcus agalactiae NEM316]
 gi|77414646|ref|ZP_00790784.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 515]
 gi|42559816|sp|Q8E7Q5|TRUA_STRA3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|23094525|emb|CAD45744.1| Unknown [Streptococcus agalactiae NEM316]
 gi|77159310|gb|EAO70483.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 515]
 gi|319744038|gb|EFV96416.1| tRNA pseudouridine synthase A [Streptococcus agalactiae ATCC 13813]
          Length = 258

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 130/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  L +G  V++HGAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI  FD   
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTI--FDAKI 176

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A 
Sbjct: 177 QFEASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAA 236

Query: 236 PEGLYFDSVEYS 247
             GLY   + Y 
Sbjct: 237 GNGLYLKEIIYE 248


>gi|294497016|ref|YP_003560716.1| tRNA pseudouridine synthase A [Bacillus megaterium QM B1551]
 gi|295702381|ref|YP_003595456.1| tRNA pseudouridine synthase A [Bacillus megaterium DSM 319]
 gi|294346953|gb|ADE67282.1| tRNA pseudouridine synthase A [Bacillus megaterium QM B1551]
 gi|294800040|gb|ADF37106.1| tRNA pseudouridine synthase A [Bacillus megaterium DSM 319]
          Length = 246

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 123/247 (49%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   I+ Y+G+ + G+Q Q N  ++Q  IE  +  +  + V ++ +GRTD+ VHA  Q
Sbjct: 1   MKRLKCIVAYDGTHFSGYQVQPNKRTVQLEIEAVLEKMHNKKVPIYASGRTDTNVHAQGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           KALN+ L   D I + N+  VD  FHAR+    + Y Y I+  +
Sbjct: 61  VIHFDTNLNIPCDKWKKALNSML--PDDIVMKNVCEVDAHFHARYDVTSKEYRYHILRGE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A+  P  LD   M+ A  +L+G HDFT+F S   +    IRTI   D+   
Sbjct: 119 DRNPFTRSYAYHYPYPLDYSKMKKAITYLLGTHDFTSFCSARTEVEDKIRTIYKIDMYEE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + +  R V   FL+  +R  VG+L  VG G+     ++  L+++ R   G  AP +GLY
Sbjct: 179 NSQLVFRFVGSGFLYNMVRILVGTLLEVGQGRIEPDAIKDILESKSRPRAGKTAPSQGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LWRVFYD 245


>gi|224477189|ref|YP_002634795.1| tRNA pseudouridine synthase A [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|254764865|sp|B9DM46|TRUA_STACT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|222421796|emb|CAL28610.1| putative tRNA pseudouridine synthase A [Staphylococcus carnosus
           subsp. carnosus TM300]
          Length = 267

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 119/243 (48%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q++G ++Q   EK +  +    V +H + RTD GVHA+ Q 
Sbjct: 1   MRILVKISYQGSNFLGFQIQQHGRTVQQQFEKILKRMHKRHVRIHPSSRTDRGVHAIEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   D I +  +SIVD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIAPDKWQYAMNSAL--PDDIYVNEVSIVDDDFHCRYDCVGKRYRYKVYQGKH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                 G       SLD E M  AAQ  +G HDFT F S   +  S  RT+   ++    
Sbjct: 119 RDVFMSGLKTFYADSLDLEKMNEAAQQFIGTHDFTGFCSQKTEVESKERTLYQSEIIKTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N  +  V    FL+  +R  V  L  VG GK    ++   L+A+DRK+    AP EGLY 
Sbjct: 179 NGFDYIVTGSGFLYNMVRVLVAFLIEVGKGKRQPEEVPILLEAKDRKQVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|51340814|sp|Q814C2|TRUA1_BACCR RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
          Length = 247

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 125/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 61  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRV 115

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 116 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 175

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 176 LIEQDDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 235

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 236 HGLYLWEVNYN 246


>gi|229159315|ref|ZP_04287339.1| tRNA pseudouridine synthase A [Bacillus cereus R309803]
 gi|228624207|gb|EEK81009.1| tRNA pseudouridine synthase A [Bacillus cereus R309803]
          Length = 252

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 125/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+ +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQGDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|218134082|ref|ZP_03462886.1| hypothetical protein BACPEC_01972 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991457|gb|EEC57463.1| hypothetical protein BACPEC_01972 [Bacteroides pectinophilus ATCC
           43243]
          Length = 272

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 125/249 (50%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M  Y M +EY+G  Y GWQR     N +++   I + +  +TG  V +    RT++GVHA
Sbjct: 27  MYNYRMTLEYDGGRYAGWQRMGRDDNSNTVSAKITEVLKKMTGSDVEIFCGSRTETGVHA 86

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QVA+F L RE+    +   LN YL     I++L L    ++FH++ +A  R+Y+YR+ 
Sbjct: 87  YGQVANFKLDREYRAREIQNYLNRYL--PQDIAVLELEETQERFHSQLNAKSRTYVYRVD 144

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T+      E+   +      D + M  AAQ+ +G HD+  F ++  +  S +R ++  D+
Sbjct: 145 TKNIANVFERRYMYHTFHKPDVDAMNKAAQYFLGEHDYKVFSTVK-KNKSTVRNVESVDI 203

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ +EI + A  FLH   R  +G L  +G G+    D+ K L      E    A   
Sbjct: 204 YDDGDTLEITIKADDFLHNMARLMIGILLDIGSGERRPEDVRKLLDGVKGVEISKPAESY 263

Query: 238 GLYFDSVEY 246
           GLY   VEY
Sbjct: 264 GLYLLEVEY 272


>gi|30018411|ref|NP_830042.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|206972233|ref|ZP_03233180.1| tRNA pseudouridine synthase A [Bacillus cereus AH1134]
 gi|228956583|ref|ZP_04118379.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229041047|ref|ZP_04189810.1| tRNA pseudouridine synthase A [Bacillus cereus AH676]
 gi|229125659|ref|ZP_04254691.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-Cer4]
 gi|229142948|ref|ZP_04271389.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST24]
 gi|229188427|ref|ZP_04315475.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10876]
 gi|296500975|ref|YP_003662675.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
 gi|29893951|gb|AAP07243.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|206732807|gb|EDZ49982.1| tRNA pseudouridine synthase A [Bacillus cereus AH1134]
 gi|228595101|gb|EEK52872.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10876]
 gi|228640569|gb|EEK96958.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST24]
 gi|228657851|gb|EEL13657.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-Cer4]
 gi|228727344|gb|EEL78538.1| tRNA pseudouridine synthase A [Bacillus cereus AH676]
 gi|228803148|gb|EEM49970.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|296322027|gb|ADH04955.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
          Length = 252

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 125/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|322411078|gb|EFY01986.1| tRNA pseudouridine synthase A [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 249

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 82/251 (32%), Positives = 132/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  ++Q  IEK +  +TG + V +HGAGRTD+GVHA  
Sbjct: 1   MTRYKATISYDGTLFSGFQRQSHERTVQEEIEKTLQKLTGGQPVPIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  D I +++L+IV   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDLEKLRFALDT--QTPDDIDVVDLAIVADDFHCRYQKHSKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDMNKMQEAIKTLVGTHDFTGFTAAGTSVKNKVRTITEATLVQ 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +  G L+        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP    
Sbjct: 179 DDKTGFLV-FTFSGNGFLYKQVRNMVGTLLKIGNGRMPVEQIKVILDSKNRQLAGPTPAG 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIHYE 248


>gi|169350826|ref|ZP_02867764.1| hypothetical protein CLOSPI_01600 [Clostridium spiroforme DSM 1552]
 gi|169292412|gb|EDS74545.1| hypothetical protein CLOSPI_01600 [Clostridium spiroforme DSM 1552]
          Length = 243

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 131/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R   I+ Y+GS ++G+Q Q    ++QG I+KA+  +  E V +H +GRTD+ VH  +Q
Sbjct: 1   MVRVKCIVSYDGSKFYGFQIQNKLRTVQGEIQKALKKICEEEVTIHASGRTDAKVHGNKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD +R+       +A+N +L   + I IL+   V + FH+R+SA ++ Y Y + T++
Sbjct: 61  VFHFDTLRQMPEKQWKRAINHFL--PNDIYILDSLFVSEDFHSRYSATKKEYRYLLSTKE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E    +   + LD E M+ AA   +G HDF +F S + Q  + IR +    +   
Sbjct: 119 YS-PFETNYIYQYGRPLDLELMKDAANIFIGEHDFASFCS-YDQYGNTIRELYKILIEDN 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +I   +V   F    +R  VG L  VG  + T   L++ L ++ +++C   A P+GLY
Sbjct: 177 NGIITFTIVGNGFRRYMVRHIVGGLIQVGAKRITKKRLQEFLDSKGKEKCLFKAKPQGLY 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LYEVFYD 243


>gi|332827815|gb|EGK00550.1| tRNA pseudouridine synthase A [Dysgonomonas gadei ATCC BAA-286]
          Length = 254

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 89/248 (35%), Positives = 123/248 (49%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  Y GWQ Q NG S+Q +IEKA+  +    V + GAGRTD+GVHA   
Sbjct: 1   MKRYFIYLSYNGEKYCGWQIQPNGVSVQETIEKALSTLLRMPVSIVGAGRTDAGVHARMM 60

Query: 61  VAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            AHFD  +E    ++L   LN+ L     I+I  +  V    HARF A  R Y Y I T 
Sbjct: 61  TAHFDSEQEITDLLLLANKLNSLL--PKDIAIQKIIEVKPDAHARFDAESRLYRYYITTD 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P        + I  + D E M   A+ L    DFT+F  +H    +   TI       
Sbjct: 119 KDPFL--HHLKYKIYGNPDIEIMNACAKVLFDYEDFTSFSKLHTDVKTNNCTIMLARWEQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN     + A  FL   +RS VG+L   G GK T+ D  + ++A+DR + G   P   L
Sbjct: 177 AGNDYIFTIKANRFLRNMVRSIVGTLLEAGRGKITTDDFRRIIEAKDRCKAGTSVPGHAL 236

Query: 240 YFDSVEYS 247
           + + +EY+
Sbjct: 237 FLEEIEYN 244


>gi|328875656|gb|EGG24020.1| hypothetical protein DFA_06158 [Dictyostelium fasciculatum]
          Length = 403

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 90/260 (34%), Positives = 134/260 (51%), Gaps = 35/260 (13%)

Query: 21  QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV------------R 68
           ++NG SIQ +IE  +  +  + + + G+ RTDSGV++L QVAH DL              
Sbjct: 80  RENGRSIQYAIEHGLSHIMRQRIQIVGSSRTDSGVNSLCQVAHCDLPNQRYDKKGTIEQE 139

Query: 69  EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRRSYLYRIIT----RQAPL 123
           +  P I+  ALN  LK  +  I I+++  VD +FH+R++A  R+YLY+I+T     + PL
Sbjct: 140 QLTPSIIKIALNQQLKRHNHDIRIVSVEKVDNEFHSRYNATSRTYLYKIMTGVRPTEVPL 199

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF-------- 175
            L K + W I ++LD + M+  A  L G HDF + RS  CQA SPIR+I H         
Sbjct: 200 EL-KNKVWPIWETLDIDQMKETASFLQGLHDFDSLRSAKCQAKSPIRSISHIKIIDLPLP 258

Query: 176 DVNSFGN---------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           D+  + N          I + +  RSFLH Q+R     L  +G G  T  +L++ ++ +D
Sbjct: 259 DIWRYNNDDSTPPKIQYIGLEIKGRSFLHNQVRIMSSCLAEIGRGHMTLDNLKEIMKGRD 318

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R      AP   L    V Y
Sbjct: 319 RTLAPATAPAYPLTLVKVSY 338


>gi|317502836|ref|ZP_07960938.1| tRNA pseudouridine synthase A [Prevotella salivae DSM 15606]
 gi|315666051|gb|EFV05616.1| tRNA pseudouridine synthase A [Prevotella salivae DSM 15606]
          Length = 243

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 88/251 (35%), Positives = 128/251 (50%), Gaps = 13/251 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG S+Q +++ A+  +  + V + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYFCYDGTAYHGWQIQPNGMSVQETLQNALSTILRQRVEIVGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAH DL  E    I C+ L   L   +   IS+ N+  VD   HARFSA  R+Y Y I T
Sbjct: 61  VAHLDLAEE----IECEQLTYKLNRLLPRDISVFNIQPVDSNMHARFSAKWRTYRYFIHT 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH---F 175
           R+ P    +  ++  P  LD E M   A+ L    DF  F       ++ + TI      
Sbjct: 117 RKDPFL--RKYSYESPYLLDFELMEQGAELLKQHQDFAAFCKSGADNTTTLCTIKESKWV 174

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             + +    EI   A  FL   +R+ VG+L L+G  + T  DLE+ L+  +R + G   P
Sbjct: 175 KTSPYSWYFEI--TANRFLRNMVRATVGTLILLGRHRITIKDLERILEEGNRSQAGESMP 232

Query: 236 PEGLYFDSVEY 246
              L+ +++EY
Sbjct: 233 GHALFLENIEY 243


>gi|170017912|ref|YP_001728831.1| tRNA pseudouridine synthase A [Leuconostoc citreum KM20]
 gi|238688937|sp|B1MVY3|TRUA_LEUCK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169804769|gb|ACA83387.1| tRNA pseudouridine synthase A [Leuconostoc citreum KM20]
          Length = 260

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 89/256 (34%), Positives = 133/256 (51%), Gaps = 12/256 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIFLVTGEIVV---VHGAGRTD 52
           M RY  I+ Y+GS +FG+Q Q K+G     ++QG + KA+  +  + V    V GA RTD
Sbjct: 1   MTRYKAIVAYDGSNFFGFQVQTKSGVEVQRTVQGELNKAVNQMAKQPVTPIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL  +  PV + K LN  L     I I  ++ V   FHARFS   + Y
Sbjct: 61  TGVHAFGQVVHFDLPFDINPVGVSKGLNTLL--PRDILIKAVTKVSDDFHARFSTHAKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            YR+ T       ++         LD   ++ A   L+G HDF +F +   Q +S +RTI
Sbjct: 119 FYRVSTTAFTDPFKRHYTGHFHWHLDTSRIQEALPDLIGEHDFASFAASGNQTASTVRTI 178

Query: 173 DHFDVNSFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
               +    +  E+  V    +FL+ QIR  VG L  +G+G+    D+++ +  +DR++ 
Sbjct: 179 TSAQLIEKPDEQELVFVFEGNAFLYNQIRIMVGVLLEIGNGRREIHDIQRLIAVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEY 246
              AP  GLY D ++Y
Sbjct: 239 RFTAPASGLYLDEIDY 254


>gi|150392315|ref|YP_001322364.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
 gi|149952177|gb|ABR50705.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
          Length = 246

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 123/243 (50%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MI+EY+G+ Y GWQRQ     +IQG +E  I  + G+   + G+GRTD+G HA  QVA+F
Sbjct: 6   MIVEYDGTKYRGWQRQTATDMTIQGKLEHVISEMVGKKTEIVGSGRTDAGAHAYGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + + +N YL     I +  L     +FH+R++   + Y+YRI        
Sbjct: 66  HTKSTLSIKEMYQYINQYL--PQDIVVKELKEAGPRFHSRYNVKGKKYVYRIWNESTASV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  ++ +P++L+ E M+ AA  LVG +DF  F S+     + +RTI+   +      +
Sbjct: 124 FHRKHSYHVPQALNLELMQEAAAKLVGTYDFLPFSSVKKSEKTTVRTIESITIEKKDAFV 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           EI +V   FL+  +R   G+L  +G  K   T +++      R+  G   P +GL+   V
Sbjct: 184 EITIVGDGFLYNMVRIITGTLIEIGSKKKKPTYIDEIFSVGKRQNAGETVPSQGLFLIEV 243

Query: 245 EYS 247
            Y+
Sbjct: 244 YYN 246


>gi|75906940|ref|YP_321236.1| tRNA pseudouridine synthase A [Anabaena variabilis ATCC 29413]
 gi|75700665|gb|ABA20341.1| tRNA pseudouridine synthase [Anabaena variabilis ATCC 29413]
          Length = 282

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 119/245 (48%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++++Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 12  RVALVVQYLGTNFHGWQRQKQHRTVQEEIETAIAKILGHHVTLHGAGRTDSGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD      P      LN+YL     I I   + V  ++HARFSA  R Y Y I T   P
Sbjct: 72  HFDATGLIPPHKWASVLNSYL--PKDILIKASAAVGDRWHARFSAAYRRYRYTIYTEDRP 129

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W      LD   M+ A + L+G+H    F     + S     +   + +  G
Sbjct: 130 NLFVTPFSWHYYYAPLDESLMQAALKPLMGKHHLAAFHRAGSKRSHSWVEVQAVECHRSG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+  +R  VG L  VG G+ T  +  +  + Q R+E    AP +GL  
Sbjct: 190 PFIHIEIQADGFLYGMVRLLVGMLVQVGSGQRTLANFTELWKEQRREEVKHAAPSQGLCL 249

Query: 242 DSVEY 246
             V Y
Sbjct: 250 LRVGY 254


>gi|294340919|emb|CAZ89314.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) (PSU-I) [Thiomonas sp. 3As]
          Length = 257

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 86/241 (35%), Positives = 130/241 (53%), Gaps = 1/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M + Y G+ Y GWQ Q  G  +Q  +E+A+    G       AGRTD+GVHAL QV H D
Sbjct: 1   MGLSYGGTSYCGWQSQPGGCGVQDFLERALAQFLGFPTRTVCAGRTDAGVHALGQVVHLD 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +  P    + +NA+L   D       + + + F AR SA +R Y Y +       AL
Sbjct: 61  TPLQREPSSWVRGVNAFLP-RDMAVQWARTDLPQTFDARRSAYQRRYRYVLRNHPVRPAL 119

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           +  +     + LD + +R+AAQ L+G HDF+ FRS  CQA SP++T+   ++   G+ + 
Sbjct: 120 DFAKVGWTHRPLDLDLLRLAAQCLLGEHDFSAFRSSECQALSPVKTLHAIEIARHGHTLV 179

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + + A +FLH  +R+ VGSL  VG+G    + L + L ++DR+   P   P+GLYF   +
Sbjct: 180 LDLRANAFLHHMVRNIVGSLLAVGNGSKPVSWLAEVLASRDRRLAAPTFMPDGLYFLGPD 239

Query: 246 Y 246
           Y
Sbjct: 240 Y 240


>gi|288904465|ref|YP_003429686.1| tRNA pseudouridylate synthase I [Streptococcus gallolyticus UCN34]
 gi|306830500|ref|ZP_07463669.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|306832735|ref|ZP_07465871.1| tRNA pseudouridine synthase A [Streptococcus bovis ATCC 700338]
 gi|325977479|ref|YP_004287195.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|288731190|emb|CBI12738.1| tRNA pseudouridylate synthase I [Streptococcus gallolyticus UCN34]
 gi|304425084|gb|EFM28214.1| tRNA pseudouridine synthase A [Streptococcus bovis ATCC 700338]
 gi|304427346|gb|EFM30449.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325177407|emb|CBZ47451.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 249

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G  + G+QRQ +  S+Q  +EK +  L +G  V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKATISYDGRLFAGFQRQPSERSVQEELEKTLQKLNSGNPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++ +  V  +FHAR++   ++Y + +   
Sbjct: 61  QVVHFDLPQARDVEKLRFGLDT--QSPEDIDVVKVEQVSDEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD  +M+ A + LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLDLTSMQEAIKDLVGTHDFTGFTASGTSVENKVRTITRATVAI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L++++R   GP A   
Sbjct: 179 DDKTGFFVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTVLESKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 239 GLYLKEINY 247


>gi|330718940|ref|ZP_08313540.1| tRNA pseudouridine synthase A [Leuconostoc fallax KCTC 3537]
          Length = 250

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 86/252 (34%), Positives = 130/252 (51%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           M RY  I+ Y+GSG+FG+Q Q +  ++QG + K +  +       + V GA RTD+GVHA
Sbjct: 1   MPRYKAIVSYDGSGFFGFQVQNDVRTVQGELNKVVNQMAKNPATPIRVIGASRTDTGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV +FDL        + K LN  L     I I  + IV+  FHARF++  + Y YR+ 
Sbjct: 61  LGQVINFDLPFNIPAASVRKGLNTLL--PRDIMIREVEIVNDDFHARFNSHHKRYFYRLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T+      ++  A      LD + +  A   L+G HDF +F +   Q  + IR I   D+
Sbjct: 119 TQDFVDPFKRKYAGHFHWPLDIQRIEKALPDLLGEHDFASFAASGNQTQTTIRRITRADI 178

Query: 178 NSFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +  +  EI  +    +FL+ QIR  VG L  +G GK    D+++ ++ +DR +    A 
Sbjct: 179 INKPDEQEIVFIFEGNAFLYNQIRIMVGVLLEIGTGKRPVHDIQRLIEVKDRSQARFTAA 238

Query: 236 PEGLYFDSVEYS 247
             GLY D + YS
Sbjct: 239 AAGLYLDEISYS 250


>gi|154494877|ref|ZP_02033882.1| hypothetical protein PARMER_03921 [Parabacteroides merdae ATCC
           43184]
 gi|154085427|gb|EDN84472.1| hypothetical protein PARMER_03921 [Parabacteroides merdae ATCC
           43184]
          Length = 297

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 121/245 (49%), Gaps = 5/245 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG  + GWQ Q NG ++Q SIE+A+  +  + V + GAGRTD+GVHA   VA
Sbjct: 46  RYFIYLGYNGKKFCGWQIQPNGITVQQSIEEALATLLRQPVPIVGAGRTDAGVHARLMVA 105

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD       +  L + LN  L     I++  +  V    HARF AI R+Y Y + TR+ 
Sbjct: 106 HFDWQEPIADLAFLAEKLNRLL--PKDIAVYRIVPVRPDAHARFDAISRTYKYYVTTRKD 163

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E    + IP  LD E M  A   L    DFT+F  +H    +    I        G
Sbjct: 164 PFNYE--LVYKIPGKLDFEAMNKACSVLFDYIDFTSFSKLHTDVKTNNCRIYKAGWEREG 221

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++    + A  FL   +R+ VG+L  VG GK T     + ++A+DR   G  AP   LY 
Sbjct: 222 DVWVFTIQADRFLRNMVRAIVGTLLEVGRGKLTVDGFRQVIEAKDRGRAGTSAPGHALYL 281

Query: 242 DSVEY 246
             V Y
Sbjct: 282 VDVTY 286


>gi|307244438|ref|ZP_07526548.1| tRNA pseudouridine synthase A [Peptostreptococcus stomatis DSM
           17678]
 gi|306492195|gb|EFM64238.1| tRNA pseudouridine synthase A [Peptostreptococcus stomatis DSM
           17678]
          Length = 253

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 84/243 (34%), Positives = 130/243 (53%), Gaps = 6/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQVAHF 64
           +++ Y G+ Y GWQ+Q +   IQG +E A       + + + G+GRTD+GVHAL QVA+F
Sbjct: 8   LVVAYEGTRYCGWQKQPDSPGIQGELEYACTQAFNKKNINITGSGRTDAGVHALGQVANF 67

Query: 65  DLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
             V   +PV  + + LN   ++   I++L    V  +FHAR SA +++Y Y+I   +   
Sbjct: 68  -TVDTTIPVDKIPEVLNN--RLPKDIAVLRAQEVKSEFHARHSAHKKTYRYQIYPSRIRS 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
              K  A+ +   LD + M+    HL+G+HDF  F S      S +RTI   D+   G+L
Sbjct: 125 PFLKDFAYQVKYDLDLDRMKEEIIHLLGQHDFKGFMSSGSDIKSTVRTIYRADIYKRGDL 184

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I I V    FL+  +R   G++  +G GK T + L   + +  R   G  APP+GL+   
Sbjct: 185 IVIEVEGNGFLYNMVRIIAGTMVDIGRGKITES-LRDIIGSGVRARAGHTAPPQGLFLVG 243

Query: 244 VEY 246
           V+Y
Sbjct: 244 VDY 246


>gi|302333855|gb|ADL24048.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JKD6159]
          Length = 267

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ   G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFKGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  +  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLLAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|307579643|gb|ADN63612.1| tRNA pseudouridine synthase A [Xylella fastidiosa subsp. fastidiosa
           GB514]
          Length = 256

 Score =  135 bits (340), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 13/246 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EY+GS + GWQ+  + G S+Q ++++A+  V    V V  AGRTD+GVH   Q
Sbjct: 1   MRYALGVEYDGSEFLGWQQLGEMGPSVQATLQQALASVADSSVRVVCAGRTDAGVHGQCQ 60

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD       R W+       L    ++  ++++       + FHARFSA  R Y YR
Sbjct: 61  VVHFDSAVTRPPRAWI-------LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRYR 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++ RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +   
Sbjct: 114 LLNRQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQAI 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V     +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A 
Sbjct: 174 SVRRDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTAS 233

Query: 236 PEGLYF 241
             GL F
Sbjct: 234 ARGLVF 239


>gi|104773573|ref|YP_618553.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103422654|emb|CAI97262.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
          Length = 263

 Score =  135 bits (340), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH++ QV
Sbjct: 5   RYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKQMTKGQEVRVFGSGRTDAGVHSVGQV 64

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD     +P   + KALN+ L +   +   +  IVDK FH+RFS   + Y YR+    
Sbjct: 65  IHFDYPGREIPAANMIKALNSQLPMD--MVFTDCEIVDKDFHSRFSVKGKWYRYRVSLDG 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +V  +
Sbjct: 123 FVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVNVALD 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A   G
Sbjct: 183 EENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTAQACG 242

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 243 LYLYHVFYE 251


>gi|312898257|ref|ZP_07757648.1| tRNA pseudouridine synthase A [Megasphaera micronuciformis F0359]
 gi|310620754|gb|EFQ04323.1| tRNA pseudouridine synthase A [Megasphaera micronuciformis F0359]
          Length = 266

 Score =  135 bits (339), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 82/241 (34%), Positives = 131/241 (54%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ ++G+QRQ +  S+Q  +E A+  + G  + ++GA RTDSGVHA  QV +F   
Sbjct: 11  LAYDGTEFYGFQRQSSLPSVQQHVEAALSGIYGRNIRIYGAARTDSGVHARGQVVNF-YG 69

Query: 68  REWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            + +PV  L  AL   L     I +L+ ++  + F  R     + Y Y ++    P    
Sbjct: 70  DDTIPVERLPYALKGSL--PPAIVVLSATLERENFSVRHDNKGKHYRYTLVNDGVPDPFM 127

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
              AW I K L+CE+M+ AA +L G HDF+ F   +    +P++T+    V S  N I I
Sbjct: 128 LRYAWYIRKPLNCESMKEAASYLKGTHDFSAFEGANTTPMNPVKTMYGIFVVSKKNRIII 187

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            VV   FL+  +R+  G+L  VG G+ +S  +++ L+  DR++ G  AP +GL  + V Y
Sbjct: 188 DVVGSGFLYHMVRNMAGALVDVGMGRKSSQRIKEILKGGDRRKLGATAPAQGLCLEEVYY 247

Query: 247 S 247
           S
Sbjct: 248 S 248


>gi|163756865|ref|ZP_02163974.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
 gi|161323254|gb|EDP94594.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
          Length = 250

 Score =  135 bits (339), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 124/245 (50%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQ Q N  S+Q  IEKA+ ++    + + GAGRTD+GVHA +  
Sbjct: 1   MRYFIELSYNGEKYHGWQNQPNAISVQEVIEKALSILLRSNIAIVGAGRTDAGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD    +    L   LN++L     ++I  +  V +  HARF A  R+Y Y I++ + 
Sbjct: 61  AHFDTDVVFNRAELTFKLNSFL--PKDVAIQQIHTVKEDAHARFDATGRTYEYWIVSEKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   +   A  + K LD + M  AA+ L    DF  F   H    + I  ++       G
Sbjct: 119 PFYTQS--AHTVYKKLDVDLMNKAAKKLFNYQDFKCFSKTHTDVKTYICQLEKAVWEQKG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+   + A  FL   +R+ VG+L  VG GK +    ++ + ++DR + G   P + LY 
Sbjct: 177 ELLVFTIRADRFLRNMVRAIVGTLLEVGLGKLSIEGFKEIIASRDRNKAGTSVPGKALYL 236

Query: 242 DSVEY 246
            +V Y
Sbjct: 237 TAVTY 241


>gi|56961964|ref|YP_173686.1| pseudouridylate synthase I [Bacillus clausii KSM-K16]
 gi|62901228|sp|Q5WLN0|TRUA_BACSK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56908198|dbj|BAD62725.1| pseudouridylate synthase I [Bacillus clausii KSM-K16]
          Length = 261

 Score =  135 bits (339), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 125/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G+ + G+Q Q    ++Q  +E+A+  +  G  V V  +GRTD+GVHA  
Sbjct: 1   MSRMACKLSYDGTAFAGYQVQPGKRTVQSEVERALQEIHKGARVPVVASGRTDAGVHACG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P     ALN +L   D I + N ++V+  FHAR+ A  + Y Y I   
Sbjct: 61  QVLHFDTELTIAPERWVSALNTHL--PDDIVVTNAAMVEPDFHARYGAQAKEYRYYIQCG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  A  I ++LD   M+ AA+HL+G HDF+ F + +   +  +RTI H  V  
Sbjct: 119 PFENVFRRHFAVHIKQALDVPAMQTAAKHLLGTHDFSAFCAANTTVTDKVRTITHVAVQP 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + I +    FL+  +R  VG+L  +G GK  +++++  L  + R   G  AP  GL
Sbjct: 179 SEEGLLISIRGTGFLYNMVRIIVGTLLEIGTGKRVASEMKVILAGKSRNLAGKTAPAHGL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 CLYEVDY 245


>gi|228919092|ref|ZP_04082471.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228840617|gb|EEM85879.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 252

 Score =  135 bits (339), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 125/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + I  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDEIIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|116513570|ref|YP_812476.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|122275660|sp|Q04BY4|TRUA_LACDB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116092885|gb|ABJ58038.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|325125205|gb|ADY84535.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 262

 Score =  135 bits (339), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH++ QV
Sbjct: 4   RYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKQMTKGQEVRVFGSGRTDAGVHSVGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD     +P   + KALN+ L +   +   +  IVDK FH+RFS   + Y YR+    
Sbjct: 64  IHFDYPGREIPAANMIKALNSQLPMD--MVFTDCEIVDKDFHSRFSVKGKWYRYRVSLDG 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +V  +
Sbjct: 122 FVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVNVALD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A   G
Sbjct: 182 EENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTAQACG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYE 250


>gi|293374636|ref|ZP_06620951.1| tRNA pseudouridine synthase A [Turicibacter sanguinis PC909]
 gi|325845439|ref|ZP_08168732.1| tRNA pseudouridine synthase A [Turicibacter sp. HGF1]
 gi|292646726|gb|EFF64721.1| tRNA pseudouridine synthase A [Turicibacter sanguinis PC909]
 gi|325488545|gb|EGC90961.1| tRNA pseudouridine synthase A [Turicibacter sp. HGF1]
          Length = 258

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 134/248 (54%), Gaps = 8/248 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R    + Y+G+ + G+QRQ    ++QG IE A+  ++ + V +H +GRTD+GVHA  Q
Sbjct: 1   MKRIKCTVAYDGTLFNGYQRQPGQRTVQGEIEAALEKISKQPVTIHSSGRTDTGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI-ITR 119
           V HFD V         +ALN+ L   + I I++   V  +FH+R+    + Y YR+ +  
Sbjct: 61  VFHFDSVVNMDGSRYVRALNSIL--PEDIYIIDSQEVHPEFHSRYHGKVKEYRYRLSLNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VN 178
             P  +++   +    SLD E MR A  +L+G H+FT+F   +      +RTI   D ++
Sbjct: 119 YNP--MKRNYVYYHRFSLDVEKMREAMTYLLGTHNFTSFCG-NLDDIDKVRTIYQADLID 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G L  I  V   FL   IR  VG+L  +G+GK    D++  ++A++RK  G  A P+G
Sbjct: 176 EDGELTFI-FVGNGFLRYMIRIMVGTLIQIGEGKKKPEDIKTIIEAKNRKLAGHTAKPQG 234

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 235 LYLQRVDY 242


>gi|295103893|emb|CBL01437.1| pseudouridylate synthase I [Faecalibacterium prausnitzii SL3/3]
          Length = 254

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + + + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL   
Sbjct: 1   MNFLLTLAYDGTNYCGFQVQPNGRSVAATFQDALEAVLGSRPDIKGCSRTDAGVHALGFR 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F       P  L  ALN +L     I +L +  V + FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPPQKLPLALNQHLPPD--IRVLAVQTVPEDFHARYAAHTKTYLYRIHNHPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDVN 178
               +      +P+ LD   M+ AAQ  VG HDF    +    A      +RTI    V 
Sbjct: 119 DSPFDAAYYTRVPRRLDESAMQAAAQQFVGTHDFLALCAAGSSAAAHGDTVRTITDCHVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ ++I V A  +L+  +R   G+L  VG G+  + D+   L ++DR   GP  P +G
Sbjct: 179 RRGDEVDIEVTADGYLYNMVRILAGTLCEVGAGRLRAADIPAILASRDRSRAGPTLPAKG 238

Query: 239 LYFDSVEYS 247
           L+   VEY 
Sbjct: 239 LFLKRVEYP 247


>gi|300812341|ref|ZP_07092776.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496646|gb|EFK31733.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 262

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH++ QV
Sbjct: 4   RYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKRMTKGQEVRVFGSGRTDAGVHSVGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD     +P   + KALN+ L +   +   +  IVDK FH+RFS   + Y YR+    
Sbjct: 64  IHFDYPGREIPAANMIKALNSQLPMD--MVFTDCEIVDKDFHSRFSVKGKWYRYRVSLDG 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +V  +
Sbjct: 122 FVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVNVALD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A   G
Sbjct: 182 EENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTAQSCG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYE 250


>gi|227894551|ref|ZP_04012356.1| tRNA pseudouridine synthase A [Lactobacillus ultunensis DSM 16047]
 gi|227863710|gb|EEJ71131.1| tRNA pseudouridine synthase A [Lactobacillus ultunensis DSM 16047]
          Length = 262

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 81/251 (32%), Positives = 136/251 (54%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           + RY M + Y+G  + G+Q Q +  ++QG++E A+  +T G+ V+V G+GRTD+GVHA+ 
Sbjct: 2   LTRYKMTMAYDGHLFHGFQLQPDQRTVQGTVEDALKKMTKGKRVIVQGSGRTDAGVHAIG 61

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD   + +P   +  A+N+ + +   I      IVD+ FHAR+S   + Y YR+  
Sbjct: 62  QVIHFDYPGKTIPANRMILAMNSMMPMD--IIFNKCQIVDEDFHARYSIKGKWYRYRVSL 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
                  ++      P  L+   M+ AA+ L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 120 DHFVNPFKRFYTGHFPYQLNISKMQEAARDLLGKHDFTSFAASGGQIEDKVRTIYYVNIE 179

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N +    +   FL+  +R  V +L  +G+G+    DL++ + A+DR+E    A  
Sbjct: 180 KDEKENEVIFDFIGSGFLYNMVRIMVAALLEIGNGRRPIHDLKRVISAKDRQEVRQTAQA 239

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 SGLYLYHVFYE 250


>gi|313123140|ref|YP_004033399.1| tRNA pseudouridine synthase a [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312279703|gb|ADQ60422.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|325684750|gb|EGD26904.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           lactis DSM 20072]
          Length = 262

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH++ QV
Sbjct: 4   RYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKRMTKGQEVRVFGSGRTDAGVHSVGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD     +P   + KALN+ L +   +   +  IVDK FH+RFS   + Y YR+    
Sbjct: 64  IHFDYPGREIPAANMIKALNSQLPMD--MVFTDCEIVDKDFHSRFSVKGKWYRYRVSLDG 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +V  +
Sbjct: 122 FVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVNVALD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A   G
Sbjct: 182 EENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTAQACG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYE 250


>gi|256841433|ref|ZP_05546940.1| tRNA pseudouridine synthase A [Parabacteroides sp. D13]
 gi|256737276|gb|EEU50603.1| tRNA pseudouridine synthase A [Parabacteroides sp. D13]
          Length = 265

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 125/250 (50%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++  + V + GAGRTD+GVHA   +A
Sbjct: 16  RYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRKPVPIVGAGRTDAGVHARLMIA 75

Query: 63  HFDLVREWVP-----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD    W       V L + LN  L     I++  +  V  + HARF A  R+Y Y + 
Sbjct: 76  HFD----WEEPIGDLVFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYVT 129

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T++ P   E    + +P  LD E M  A + L    DFT+F  +H    +    I H D 
Sbjct: 130 TKKDPFNHE--LVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHADW 187

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P  
Sbjct: 188 TQEGDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGH 247

Query: 238 GLYFDSVEYS 247
            L+   V Y 
Sbjct: 248 ALFLVDVTYP 257


>gi|218262724|ref|ZP_03477082.1| hypothetical protein PRABACTJOHN_02761 [Parabacteroides johnsonii
           DSM 18315]
 gi|218223213|gb|EEC95863.1| hypothetical protein PRABACTJOHN_02761 [Parabacteroides johnsonii
           DSM 18315]
          Length = 292

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 90/246 (36%), Positives = 123/246 (50%), Gaps = 7/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG  + GWQ Q NG ++Q SIE+A+  +  + V + GAGRTD+GVHA   VA
Sbjct: 46  RYFIYLGYNGKKFCGWQIQPNGITVQQSIEEALATLLRQPVPIVGAGRTDAGVHARLMVA 105

Query: 63  HFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           HFD  +E +   V L + LN  L     I++  +  V    HARF A  R+Y Y I TR+
Sbjct: 106 HFDW-KEPIDDLVFLVEKLNRLL--PKDIAVYRIVPVRTDAHARFDATSRTYKYYITTRK 162

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E    + IP  LD E M  A   L    DFT+F  +H    +    I        
Sbjct: 163 DPFNYE--LVYKIPGKLDFEAMNKACPVLFDYIDFTSFSKLHTDVKTNNCRIYKAGWEKD 220

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++    + A  FL   +R+ VG+L  VG GK T     + ++A+DR   G  AP   LY
Sbjct: 221 GDVWFFTIQADRFLRNMVRAIVGTLLEVGRGKLTVDGFRQVIEAKDRGRAGTSAPGHALY 280

Query: 241 FDSVEY 246
              V Y
Sbjct: 281 LVDVTY 286


>gi|119952818|ref|YP_945027.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
 gi|254789604|sp|A1QYG5|TRUA_BORT9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119861589|gb|AAX17357.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
          Length = 245

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 81/240 (33%), Positives = 120/240 (50%), Gaps = 2/240 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y+G+Q Q    +IQG IEK +  ++   + +H AGRTD GVHA  Q+  F + 
Sbjct: 8   ITYDGSLYYGFQIQPKKPTIQGEIEKVLEKISKTKIKIHSAGRTDKGVHARGQIISFYIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L  A+N+ LK  D I I+ L  V+ +F  RF A RR Y Y I+  +     E 
Sbjct: 68  INIKLKNLKTAINSLLK--DDIRIIKLKYVEDKFQPRFDAKRRKYSYYILNNENHYPWEG 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            RA+ + K L+   +   A+ L+G HDFTTF  I  Q +S ++ I +         I   
Sbjct: 126 YRAYYVKKKLNINRLNEMAEMLIGIHDFTTFSCIRDQTNSKLKEIYYARFKKKNKFIIFE 185

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++  SFL   +RS VG +  +          +K L +++RK     AP + L+ D V Y 
Sbjct: 186 IIGSSFLWKMVRSIVGVMIDIEIKNEPVDTFKKILNSKNRKLTRKTAPAKALFLDKVFYE 245


>gi|323340405|ref|ZP_08080662.1| tRNA pseudouridine synthase A [Lactobacillus ruminis ATCC 25644]
 gi|323092181|gb|EFZ34796.1| tRNA pseudouridine synthase A [Lactobacillus ruminis ATCC 25644]
          Length = 250

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 126/249 (50%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQ 60
           RY + + Y+G+ + G+Q Q N  ++Q  +E A+  ++   + + ++G+GRTD+GVHAL Q
Sbjct: 4   RYKITLAYDGTNFAGFQVQPNQRTVQSVLEAAVNKMSKNSDYITIYGSGRTDAGVHALGQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +     + K LN+ L ++    ++   IV   FHARF+   + Y+YR+   +
Sbjct: 64  VVHFDFPHDIPAEGMLKGLNSMLPLA--CEVVGCEIVPNDFHARFTTHGKRYMYRVSRGR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++         LD E ++ A   LVG HDF++F +   Q  + +RTI    V   
Sbjct: 122 FTNPFKRFYTGHYKYPLDIEKIKEAMPDLVGTHDFSSFVASGSQTKNHVRTIYEATVRED 181

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               EI        FL+ Q+R  V +L  +G+GK    D  +  + +DR EC   AP  G
Sbjct: 182 KENDEIIFEFCGNGFLYNQVRIMVATLLEIGNGKRPVHDFLRLYEVKDRNECRETAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLKEVYYD 250


>gi|171777516|ref|ZP_02919238.1| hypothetical protein STRINF_00067 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171283226|gb|EDT48650.1| hypothetical protein STRINF_00067 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 249

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 130/249 (52%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G  + G+QRQ +  S+Q  +EK +  L +G+ V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKATISYDGRLFAGFQRQPSERSVQEELEKTLQRLNSGQPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++ + +V   FH+R++   ++Y + + + 
Sbjct: 61  QVVHFDLPQARDVEKLRFGLDT--QSPEDIDVVKVELVSDDFHSRYNKHSKTYEFLVDSG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI     D+
Sbjct: 119 RPKNPMMRHYATHYPYPLDLALMQEAIKDLVGTHDFTGFTASGTSVENKVRTITRATVDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L +++R   GP A   
Sbjct: 179 DEKTGFFVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTVLASKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 239 GLYLKEIIY 247


>gi|313903119|ref|ZP_07836513.1| tRNA pseudouridine synthase A [Thermaerobacter subterraneus DSM
           13965]
 gi|313466621|gb|EFR62141.1| tRNA pseudouridine synthase A [Thermaerobacter subterraneus DSM
           13965]
          Length = 345

 Score =  135 bits (339), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 82/242 (33%), Positives = 124/242 (51%), Gaps = 6/242 (2%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           ++ Y+G+ + GWQRQ    ++Q  +E+A+  + G  V V  AGRTD+GVHA  QV H+  
Sbjct: 88  VLAYDGTDFAGWQRQAGRRTVQQVVEEALSRLLGHPVRVTAAGRTDAGVHARAQVIHWQT 147

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA-- 124
            R +    L  AL   L +         +     FHAR++A R++Y+Y +   +AP+A  
Sbjct: 148 ARPFPAERLVPALRGLLPLDVAAVAAGEAP--AGFHARYAARRKTYVYHLW--RAPVADP 203

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L +   W +P +LD   M  AA+ L GRHDF  F++      +  RT+    +   G L+
Sbjct: 204 LHRRWQWHLPLALDVAAMAEAARRLEGRHDFAAFKAAGSPVRNTRRTLYRCRLEEHGPLL 263

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL    R  VG+L  +G G+W +  ++  L    R+  GP AP  GL    V
Sbjct: 264 RIVLEADGFLMHMARGIVGTLVEIGRGRWPAGHVDMLLATGRRQLAGPTAPAHGLVLWRV 323

Query: 245 EY 246
           EY
Sbjct: 324 EY 325


>gi|29349645|ref|NP_813148.1| tRNA pseudouridine synthase A [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253569984|ref|ZP_04847393.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_6]
 gi|42559809|sp|Q89ZY4|TRUA_BACTN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|29341555|gb|AAO79342.1| tRNA pseudouridine synthase A [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251840365|gb|EES68447.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_6]
          Length = 269

 Score =  135 bits (339), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 92/251 (36%), Positives = 123/251 (49%), Gaps = 11/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NGSS+Q  + KA+       V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGSSVQECLMKALSTFLRRDVEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDHEDVLDTVTVADKLNRLLPPD--ISVYRVRQVKPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   + +  SLD E M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRYRVYGSLDYERMNEAARTLFEYIDFTSFSKLHTDVKTNICHISHAEWTKM 176

Query: 181 GN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  +  IR  A  FL   +R+ VG+L  VG GK T     K ++ QDR + G  AP
Sbjct: 177 EGEDTTWVFTIR--ADRFLRNMVRAIVGTLLEVGRGKLTVEGFRKVIEQQDRCKAGTSAP 234

Query: 236 PEGLYFDSVEY 246
              L+  +VEY
Sbjct: 235 GNALFLVNVEY 245


>gi|161833682|ref|YP_001597878.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri GWSS]
 gi|152206172|gb|ABS30482.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri GWSS]
          Length = 250

 Score =  134 bits (338), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 130/247 (52%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + I Y+G+ ++GWQ QK   S+Q +IE  +  +  + + + GAGRTD+GVHA++  
Sbjct: 1   MRFFLEISYHGASFYGWQIQKKNISVQETIENCLSFLLKKSIKIIGAGRTDTGVHAIQMF 60

Query: 62  AHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHF+   + + +        N++L ++  I I+N+  V K+ HARF+AI R Y YRI   
Sbjct: 61  AHFEFYEKKILLYRNFLFKFNSFLPLN--IKIINIFTVKKKIHARFTAISRVYEYRISLG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P +L+    WL  K +    +   A+ L    D+++F    C   + I  I +   + 
Sbjct: 119 KNPFSLDISWQWLSKKKIKLNPLNKGAKILKKYKDYSSFCKKKCNYKTYICNIFNAKWHI 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N++   + A  +L   +RS VG+L  +G GK T  D    L A+DR      AP +GL
Sbjct: 179 KNNILYFNIEANRYLRNMVRSIVGTLIELGIGKITIKDFINILYAKDRNIIS--APAKGL 236

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 237 FLTKINY 243


>gi|33862089|ref|NP_893650.1| tRNA pseudouridine synthase A [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|42559755|sp|Q7TU31|TRUA_PROMP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33634307|emb|CAE19992.1| tRNA pseudouridine synthase A [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
          Length = 268

 Score =  134 bits (338), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 87/243 (35%), Positives = 128/243 (52%), Gaps = 5/243 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++I+Y+GS + GWQRQKN  S+Q +IE  +F ++ +I+    +GRTD+GVHA  Q
Sbjct: 1   MKRVALVIQYDGSYFSGWQRQKNAISVQETIENCLFKISNQIIKTFASGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD +   +P+      LN+  ++  TI IL    V   +HA +SA+ R Y Y I   
Sbjct: 61  VIHFD-IDFLIPIDRYADVLNS--RLPHTIRILESVEVKSSWHACYSAVYRHYRYVINNN 117

Query: 120 QAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           + P L L K       K LD  +M IA   ++G HDF  F+      S+ + TI    + 
Sbjct: 118 KIPNLFLNKWSWHRYQKYLDEVSMSIALDGMIGEHDFFAFQKSGSNRSTSVTTIKDIKLE 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +LI I + A  FL+  +RS VG L LVG+ K T    +     + + +    AP +G
Sbjct: 178 RTEDLILIDIKATGFLYGMVRSIVGQLVLVGEKKITPDIFKDRWVLKKKHDVRESAPAKG 237

Query: 239 LYF 241
           L F
Sbjct: 238 LCF 240


>gi|320548017|ref|ZP_08042298.1| tRNA pseudouridine synthase A [Streptococcus equinus ATCC 9812]
 gi|320447363|gb|EFW88125.1| tRNA pseudouridine synthase A [Streptococcus equinus ATCC 9812]
          Length = 249

 Score =  134 bits (338), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G  + G+QRQ +  S+Q  +EK +  L +G  V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKATISYDGGLFAGFQRQPSERSVQEELEKTLQKLNSGTPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++ + +V   FH+R++   ++Y + +   
Sbjct: 61  QVVHFDLPQARDVEKLRFGLDT--QSPEDIDVVKVELVSDDFHSRYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI     D+
Sbjct: 119 RPKNPMMRHYATHYPYPLDLALMQEAIKDLVGTHDFTGFTASGTSVENKVRTITRATVDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L++++R   GP A   
Sbjct: 179 DEKTGFFVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTVLESKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 239 GLYLKEIIY 247


>gi|320333111|ref|YP_004169822.1| tRNA pseudouridine synthase A [Deinococcus maricopensis DSM 21211]
 gi|319754400|gb|ADV66157.1| tRNA pseudouridine synthase A [Deinococcus maricopensis DSM 21211]
          Length = 266

 Score =  134 bits (338), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 125/248 (50%), Gaps = 5/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + ++++G+ + GWQ Q N  S+Q  +  A   +  +      AGRTD+GVHA    
Sbjct: 13  VRYRLTVQWDGTHFAGWQSQPNARSVQDDLHAAFKALGMQAFRPVAAGRTDAGVHAEAMP 72

Query: 62  AHFDLVREW--VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            H D +     +P             +D +++L+ +     FHARFS   R+Y YR++  
Sbjct: 73  VHVDALSASARIPAARLARALNAHLPTD-VAVLDAAPAPAHFHARFSCTERAYSYRVLNA 131

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GRA L+   LD   M++AA  L+G HDF  F +   + +  +R +   +V  
Sbjct: 132 PQRQPLWAGRALLVHAPLDVAAMQVAATQLLGEHDFAAFATREERQT--VRRLHALEVRP 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L+E+ V   SFL   +R  VG+L +VG+G+  ++D+   L  + R   GP  PP GL
Sbjct: 190 VGPLLEVHVRGESFLRHMVRGIVGTLLMVGEGRLGASDVAGILVGRARSGAGPNVPPHGL 249

Query: 240 YFDSVEYS 247
           YF    Y+
Sbjct: 250 YFTDASYA 257


>gi|224531952|ref|ZP_03672584.1| tRNA pseudouridine synthase A [Borrelia valaisiana VS116]
 gi|224511417|gb|EEF81823.1| tRNA pseudouridine synthase A [Borrelia valaisiana VS116]
          Length = 246

 Score =  134 bits (338), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 82/239 (34%), Positives = 122/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + + +H +GRTD GVHA  Q+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPKKPTVQGEIEKALMKINKKKIKIHSSGRTDKGVHAKGQIITFDIN 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  V   FH RF+A +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLKYVKNSFHPRFNAKKRKYRYCILNSNNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIHFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ D V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISIFETILKSKNRNLARTTAPANALFLDKVYY 245


>gi|28211488|ref|NP_782432.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
 gi|42559805|sp|Q893H3|TRUA1_CLOTE RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|28203929|gb|AAO36369.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
          Length = 245

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 124/242 (51%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MI+EY+G+ Y GWQ+QK    +IQ  IE  +  +TGE + V G GRTD+GVHA   VA+F
Sbjct: 6   MILEYDGTRYKGWQKQKKDVLTIQDKIETVLSKMTGEDIQVIGCGRTDAGVHAENYVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               ++    +   L  +L   + I +  +    ++FHAR++   ++Y+YRI   +    
Sbjct: 66  HTNCDFTVDYMLDYLYEFL--PEDIVVKTMKDTSERFHARYNVKSKTYVYRINNNKFRSV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             K  A+   + L+   M+ AA+ L+G HDF +F  +   + S IR I + ++     +I
Sbjct: 124 FNKKYAYHDNEKLNISAMKDAAEFLIGTHDFKSFTRLKSNSKSTIRAIKYINITENQGII 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I V    FL   +R   G+L  VG       D+EK L  + R +   + P +GL    +
Sbjct: 184 SIEVNGNGFLLNMVRIVAGALLEVGKENIKPIDIEKMLNEKKRADASLILPAKGLCLKDI 243

Query: 245 EY 246
           +Y
Sbjct: 244 QY 245


>gi|298695476|gb|ADI98698.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ED133]
          Length = 267

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RNPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     A  EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAAAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|289663172|ref|ZP_06484753.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 257

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 135/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADGQVQVICAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++     V   FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSIAVRWCVPVADDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTVSWERRPLDADAMHAAAQALLGENDFSAFRSVQCQALHARRNLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP A
Sbjct: 174 IHVQRIGEVVEVQVQANAFLHHMVRNIVGSLILVGTGERPADWIATLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|77406326|ref|ZP_00783390.1| tRNA pseudouridine synthase A [Streptococcus agalactiae H36B]
 gi|77175064|gb|EAO77869.1| tRNA pseudouridine synthase A [Streptococcus agalactiae H36B]
          Length = 258

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 129/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  L +G  V++HGAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y   +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEILVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI  FD   
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMKEAIKDLVGTHDFTGFTASGTSVENKVRTI--FDAKI 176

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A 
Sbjct: 177 QFEASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAA 236

Query: 236 PEGLYFDSVEYS 247
             GLY   + Y 
Sbjct: 237 GNGLYLKEIIYE 248


>gi|22536285|ref|NP_687136.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 2603V/R]
 gi|76798489|ref|ZP_00780725.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 18RS21]
 gi|77412040|ref|ZP_00788367.1| tRNA pseudouridine synthase A [Streptococcus agalactiae CJB111]
 gi|42559812|sp|Q8CX20|TRUA_STRA5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|22533107|gb|AAM99008.1|AE014196_4 tRNA pseudouridine synthase A [Streptococcus agalactiae 2603V/R]
 gi|76586154|gb|EAO62676.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 18RS21]
 gi|77161897|gb|EAO72881.1| tRNA pseudouridine synthase A [Streptococcus agalactiae CJB111]
          Length = 258

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 129/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  L +G  V++HGAGRTD GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDVGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI  FD   
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTI--FDAKI 176

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A 
Sbjct: 177 QFEASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAA 236

Query: 236 PEGLYFDSVEYS 247
             GLY   + Y 
Sbjct: 237 GNGLYLKEIIYE 248


>gi|301309451|ref|ZP_07215393.1| tRNA pseudouridine synthase A [Bacteroides sp. 20_3]
 gi|300832540|gb|EFK63168.1| tRNA pseudouridine synthase A [Bacteroides sp. 20_3]
          Length = 252

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 87/252 (34%), Positives = 125/252 (49%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++  + V + GAGRTD+GVHA   
Sbjct: 1   MRRYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRKPVPIVGAGRTDAGVHARLM 60

Query: 61  VAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           +AHFD    W   I     L + LN  L     I++  +  V  + HARF A  R+Y Y 
Sbjct: 61  IAHFD----WEGPIEDLAFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYY 114

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I TR+ P   E    + +P  LD E M  A + L    DFT+F  +H    +    I H 
Sbjct: 115 ITTRKDPFNYE--LVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHA 172

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P
Sbjct: 173 GWTQEGDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVP 232

Query: 236 PEGLYFDSVEYS 247
              L+   V Y 
Sbjct: 233 GHALFLVDVTYP 244


>gi|300119545|ref|ZP_07057089.1| tRNA pseudouridine synthase A [Bacillus cereus SJ1]
 gi|298723017|gb|EFI63915.1| tRNA pseudouridine synthase A [Bacillus cereus SJ1]
          Length = 252

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|282917564|ref|ZP_06325316.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           D139]
 gi|283767311|ref|ZP_06340226.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           H19]
 gi|282318526|gb|EFB48884.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           D139]
 gi|283461190|gb|EFC08274.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           H19]
          Length = 267

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     A  EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAAAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|317472004|ref|ZP_07931336.1| tRNA pseudouridine synthase A [Anaerostipes sp. 3_2_56FAA]
 gi|316900408|gb|EFV22390.1| tRNA pseudouridine synthase A [Anaerostipes sp. 3_2_56FAA]
          Length = 252

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/246 (32%), Positives = 122/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q   ++I+G + + +  + GE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLEVAYDGTNYCGWQIQPKDTTIEGVLNEKLGSLLGEEITVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD   E     + +ALN   ++ D I I + S V   FH R+   R++Y Y I   +
Sbjct: 61  VAVFDTETEIPGERIARALNQ--RLPDDIVIQSSSEVKDDFHPRYQDTRKTYEYTIYNAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E MR AA+  +G HDF +F +      + +RTI   +V   
Sbjct: 119 FDNPVTARHHHFVYVPLDVERMRTAARCFLGEHDFLSFSTTGSPTKTTVRTIYECEVRQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +RV    FL+  +R   G+L  +G G+     + +      R + GP AP +GL 
Sbjct: 179 GRYITMRVTGNGFLYNMVRMMAGTLISIGRGRRDPEWVRELFLHPKRGKAGPNAPAKGLT 238

Query: 241 FDSVEY 246
             ++ Y
Sbjct: 239 LINIHY 244


>gi|49183176|ref|YP_026428.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Sterne]
 gi|49476722|ref|YP_034493.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52145077|ref|YP_081752.1| tRNA pseudouridine synthase A [Bacillus cereus E33L]
 gi|165873347|ref|ZP_02217948.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0488]
 gi|167642077|ref|ZP_02400301.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0193]
 gi|196046214|ref|ZP_03113441.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB108]
 gi|270000591|ref|YP_003329029.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Ames]
 gi|291612229|ref|YP_003541012.1| tRNA pseudouridine synthase A [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|62901423|sp|Q63H59|TRUA1_BACCZ RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|62901430|sp|Q6HPM7|TRUA1_BACHK RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|62901432|sp|Q6I4Q2|TRUA1_BACAN RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|49177103|gb|AAT52479.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Sterne]
 gi|49328278|gb|AAT58924.1| tRNA pseudouridine synthase A (pseudouridylate synthase) [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51978546|gb|AAU20096.1| tRNA-pseudouridylate synthase I [Bacillus cereus E33L]
 gi|164710915|gb|EDR16491.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0488]
 gi|167509964|gb|EDR85386.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0193]
 gi|196022959|gb|EDX61639.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB108]
 gi|224552852|gb|ACN55064.1| tRNA pseudouridine synthase A [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|269850235|gb|ACZ49980.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Ames]
          Length = 247

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 61  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 115

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 116 LVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 175

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 176 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 235

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 236 HGLYLWQVNYN 246


>gi|268608385|ref|ZP_06142112.1| tRNA pseudouridine synthase A [Ruminococcus flavefaciens FD-1]
          Length = 257

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 125/242 (51%), Gaps = 2/242 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I Y G+ Y G+Q Q N  ++QG++EK +  V  E V + G  RTD+GVHA     +  
Sbjct: 6   VTIAYRGTNYHGFQIQNNAVTVQGTLEKHLSKVLNEPVSITGCSRTDTGVHANMFCFNVK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                  +  C+ +N   ++ D ISIL+   V   FHARF    + Y+Y++   ++    
Sbjct: 66  TNSRISTLGFCRGVNG--ELPDDISILSCEEVPIDFHARFDCKGKEYIYKMHCSESKDPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
                +   +  D E  R AAQ+ VG HDF++F +     S+ +RTI  F + + G+ + 
Sbjct: 124 APDMKFHYRRPFDIEAARKAAQYFVGTHDFSSFCADCTNVSTTVRTIYSFKIENSGDTVI 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + V    FL+  IR   G+L  V + +++  D+ + L+A+DR + G  A   GLY + V 
Sbjct: 184 MLVKGNGFLYNMIRIMAGTLIDVSEKRFSPDDMPRILEAKDRLQAGRTAMAHGLYLNRVF 243

Query: 246 YS 247
           YS
Sbjct: 244 YS 245


>gi|170689686|ref|ZP_02880864.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0465]
 gi|177656196|ref|ZP_02937177.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0174]
 gi|190567334|ref|ZP_03020248.1| tRNA pseudouridine synthase A [Bacillus anthracis Tsiankovskii-I]
 gi|196036037|ref|ZP_03103438.1| tRNA pseudouridine synthase A [Bacillus cereus W]
 gi|218901347|ref|YP_002449181.1| tRNA pseudouridine synthase A [Bacillus cereus AH820]
 gi|225862194|ref|YP_002747572.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB102]
 gi|227812815|ref|YP_002812824.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CDC 684]
 gi|228912881|ref|ZP_04076528.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228925395|ref|ZP_04088491.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228943947|ref|ZP_04106332.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229089273|ref|ZP_04220554.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-42]
 gi|229119804|ref|ZP_04249065.1| tRNA pseudouridine synthase A [Bacillus cereus 95/8201]
 gi|229182536|ref|ZP_04309787.1| tRNA pseudouridine synthase A [Bacillus cereus BGSC 6E1]
 gi|229604554|ref|YP_002864793.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0248]
 gi|254686641|ref|ZP_05150500.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CNEVA-9066]
 gi|254726279|ref|ZP_05188061.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A1055]
 gi|254735284|ref|ZP_05192992.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Western
           North America USA6153]
 gi|254739476|ref|ZP_05197174.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Kruger B]
 gi|254755530|ref|ZP_05207564.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Vollum]
 gi|301051879|ref|YP_003790090.1| tRNA pseudouridine synthase A [Bacillus anthracis CI]
 gi|170666357|gb|EDT17142.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0465]
 gi|172079844|gb|EDT64958.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0174]
 gi|190561461|gb|EDV15432.1| tRNA pseudouridine synthase A [Bacillus anthracis Tsiankovskii-I]
 gi|195991406|gb|EDX55373.1| tRNA pseudouridine synthase A [Bacillus cereus W]
 gi|218535501|gb|ACK87899.1| tRNA pseudouridine synthase A [Bacillus cereus AH820]
 gi|225789774|gb|ACO29991.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB102]
 gi|227005095|gb|ACP14838.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CDC 684]
 gi|228600991|gb|EEK58560.1| tRNA pseudouridine synthase A [Bacillus cereus BGSC 6E1]
 gi|228663705|gb|EEL19284.1| tRNA pseudouridine synthase A [Bacillus cereus 95/8201]
 gi|228694112|gb|EEL47794.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-42]
 gi|228815780|gb|EEM62016.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228834317|gb|EEM79858.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228846817|gb|EEM91822.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229268962|gb|ACQ50599.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0248]
 gi|300374048|gb|ADK02952.1| tRNA pseudouridine synthase A [Bacillus cereus biovar anthracis
           str. CI]
          Length = 252

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|218282056|ref|ZP_03488361.1| hypothetical protein EUBIFOR_00932 [Eubacterium biforme DSM 3989]
 gi|218216974|gb|EEC90512.1| hypothetical protein EUBIFOR_00932 [Eubacterium biforme DSM 3989]
          Length = 247

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/242 (34%), Positives = 124/242 (51%), Gaps = 4/242 (1%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           ++ Y+G  Y GWQ+Q+N   IQ  IE+A++ +T E V V  +GRTD+GVHA  QV HF+ 
Sbjct: 6   LVSYDGFNYAGWQKQENALGIQQVIEEALYKITKENVDVVASGRTDAGVHAFGQVFHFET 65

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            +    +   +ALNA L     I IL    +   FHARFSA+ + Y Y   +        
Sbjct: 66  NKNIPAIQYERALNALL--PKDIRILKTEEMPDDFHARFSAVGKRYDY-YCSYDIKNPFN 122

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNSFGNLIE 185
                L+ K LD E M+ A++  +G HDFT+F S       P ++TI + ++   G  + 
Sbjct: 123 YKYRNLLTKKLDIEAMKNASKVFLGSHDFTSFASSKIDPRKPRVKTISNIEIIEEGMDVH 182

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
                  FL  Q+R   G+L  VG  K    D+++ L A+D+  C   A   GLY   V+
Sbjct: 183 FIFEGTGFLRYQVRMMTGTLIAVGQHKIGVDDVQRMLDAKDKSACRYNASSCGLYLVEVK 242

Query: 246 YS 247
           Y+
Sbjct: 243 YN 244


>gi|65317587|ref|ZP_00390546.1| COG0101: Pseudouridylate synthase [Bacillus anthracis str. A2012]
          Length = 257

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 11  MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 70

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 71  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 125

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 126 LVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 185

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 186 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 245

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 246 HGLYLWQVNYN 256


>gi|118475910|ref|YP_893061.1| tRNA pseudouridine synthase A [Bacillus thuringiensis str. Al
           Hakam]
 gi|118415135|gb|ABK83554.1| tRNA pseudouridine synthase A [Bacillus thuringiensis str. Al
           Hakam]
          Length = 264

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 18  MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 77

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 78  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 132

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 133 LVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 192

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 193 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 252

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 253 HGLYLWQVNYN 263


>gi|146320154|ref|YP_001199865.1| tRNA pseudouridine synthase A [Streptococcus suis 98HAH33]
 gi|253751190|ref|YP_003024331.1| tRNA pseudouridine synthase A [Streptococcus suis SC84]
 gi|253753091|ref|YP_003026231.1| tRNA pseudouridine synthase A [Streptococcus suis P1/7]
 gi|253754913|ref|YP_003028053.1| tRNA pseudouridine synthase A [Streptococcus suis BM407]
 gi|166229843|sp|A4VZC6|TRUA_STRS2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145690960|gb|ABP91465.1| Pseudouridylate synthase [Streptococcus suis 98HAH33]
 gi|251815479|emb|CAZ51057.1| tRNA pseudouridine synthase A [Streptococcus suis SC84]
 gi|251817377|emb|CAZ55113.1| tRNA pseudouridine synthase A [Streptococcus suis BM407]
 gi|251819336|emb|CAR44702.1| tRNA pseudouridine synthase A [Streptococcus suis P1/7]
 gi|319757459|gb|ADV69401.1| tRNA pseudouridine synthase A [Streptococcus suis JS14]
          Length = 249

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  L +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQPHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   + S+ I ++++  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTSEDIDVVSVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTITVASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   
Sbjct: 179 DQQRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRGLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|161506903|ref|YP_001576857.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DPC 4571]
 gi|260102386|ref|ZP_05752623.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DSM 20075]
 gi|172048171|sp|A8YTB0|TRUA_LACH4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160347892|gb|ABX26566.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DPC 4571]
 gi|260083830|gb|EEW67950.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DSM 20075]
          Length = 263

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 82/249 (32%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY M + Y+G  + G+Q Q +  ++QG++E A+  +T G+ ++V G+GRTD+GVHA+ QV
Sbjct: 4   RYKMTMAYDGHLFHGFQLQPDQRTVQGTVEDALKKMTKGKRIIVQGSGRTDAGVHAIGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALN+ +     I   N  IV++ FHAR+S   + Y YR+    
Sbjct: 64  IHFDYPGKTIPANRMILALNSMMPTD--IIFNNCEIVNENFHARYSIKGKWYRYRVSLDH 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++        +LD   M+ AA+ L+G+HDFT+F +   Q    +RTI + ++  +
Sbjct: 122 FVNPFKRFYTGHFSYALDVGKMQEAAKDLLGKHDFTSFAASGGQIEDKVRTIYYVNIAKD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N I    +   FL+  +R  V +L  +G+G+    DL++ + A+DR+E    A   G
Sbjct: 182 EKENEIVFDFIGSGFLYNMVRIMVAALLEIGNGRRPVHDLKRVIAAKDRQEVRQTAQASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYD 250


>gi|256820760|ref|YP_003142039.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea DSM 7271]
 gi|256582343|gb|ACU93478.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea DSM 7271]
          Length = 250

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 124/245 (50%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + + G  Y+GWQ Q    S+Q  ++KA+  +    + V GAGRTDSGVHAL+  
Sbjct: 1   MRYFIELSFFGKNYYGWQFQPKAISVQEVLQKALSTLLRTPIEVVGAGRTDSGVHALQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD V E +P  L   LNA+L     I++ ++  V    HARF A++R+Y Y I T++ 
Sbjct: 61  AHFD-VTEALPANLVHKLNAFL--PKDIAVHHIYEVQPNAHARFDALKRTYQYHISTQKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A +   A  +P  L+   M  AAQ L    DF  F   H    +    I     +   
Sbjct: 118 AFAYDYAMALTLP--LNVALMNEAAQILFDYTDFQCFSKTHTDVKTYNCKIYEAHWDKVE 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG+L  VG  K + TD E  + ++ R + G   P  GLY 
Sbjct: 176 NQLIFTITADRFLRNMVRAIVGTLIDVGLQKLSLTDFEDIILSKKRSKAGASVPACGLYL 235

Query: 242 DSVEY 246
             +EY
Sbjct: 236 THIEY 240


>gi|225552068|ref|ZP_03773008.1| tRNA pseudouridine synthase A [Borrelia sp. SV1]
 gi|225371066|gb|EEH00496.1| tRNA pseudouridine synthase A [Borrelia sp. SV1]
          Length = 246

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 124/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSIYHGFQIQPTKPTVQGEIEKALTKINKKKVKIHSSGRTDKGVHAKRQIITFDIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYFILNNDNYYPWEG 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A  + K L+  N+   A+ L+G+HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAHYVNKKLNINNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIHFAKFKKRGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ D V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLDRVYY 245


>gi|167748465|ref|ZP_02420592.1| hypothetical protein ANACAC_03209 [Anaerostipes caccae DSM 14662]
 gi|167652457|gb|EDR96586.1| hypothetical protein ANACAC_03209 [Anaerostipes caccae DSM 14662]
          Length = 252

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/246 (32%), Positives = 122/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q   ++I+G + + +  + GE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLEVAYDGTNYCGWQIQPKDTTIEGILNEKLGSLLGEEITVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD   E     + +ALN   ++ D I I + S V   FH R+   R++Y Y I   +
Sbjct: 61  VAVFDTETEIPGERIARALNQ--RLPDDIVIQSSSEVKDDFHPRYQDTRKTYEYTIYNAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E MR AA+  +G HDF +F +      + +RTI   +V   
Sbjct: 119 FDNPVTARHHHFVYVPLDAERMRTAARCFLGEHDFLSFSTTGSPTKTTVRTIYECEVRQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +RV    FL+  +R   G+L  +G G+     + +      R + GP AP +GL 
Sbjct: 179 GRYITMRVTGNGFLYNMVRMMAGTLISIGRGRKDPEWVRELFLHPKRGKAGPNAPAKGLT 238

Query: 241 FDSVEY 246
             ++ Y
Sbjct: 239 LINIHY 244


>gi|21283867|ref|NP_646955.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49487001|ref|YP_044222.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|297209968|ref|ZP_06926364.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|300910980|ref|ZP_07128430.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|30913392|sp|Q8NVB7|TRUA_STAAW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56749699|sp|Q6G7A2|TRUA_STAAS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21205309|dbj|BAB96003.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49245444|emb|CAG43921.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|296885641|gb|EFH24578.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|300887960|gb|EFK83155.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
          Length = 267

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 122/243 (50%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     A  EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLESKNRKNVPFTATAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|225619823|ref|YP_002721080.1| tRNA pseudouridine synthase A [Brachyspira hyodysenteriae WA1]
 gi|254789605|sp|C0QZT8|TRUA_BRAHW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225214642|gb|ACN83376.1| tRNA pseudouridine synthase A [Brachyspira hyodysenteriae WA1]
          Length = 249

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 81/238 (34%), Positives = 127/238 (53%), Gaps = 4/238 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I+Y+G+ ++GWQ Q N  ++QG I KA+  V GE + ++G GRTD+GVHAL QVA+F 
Sbjct: 6   ITIQYDGTDFYGWQIQPNLRTVQGEIYKAVQKVYGEKITIYGCGRTDAGVHALGQVANFR 65

Query: 66  LVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           + +  VP+     ALN+YL     + I+    +   F+AR SA  R YLY +        
Sbjct: 66  VPKMLVPINKVHIALNSYL--DRDLRIIKAEEMPDSFNARASATFREYLYIVHNSSTSFP 123

Query: 125 LEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
             +  AW   K+ +D + +   A++L+G H+FT+F S   +  S  R ++       G+ 
Sbjct: 124 FYERYAWFYRKNVIDEKLINEYARYLIGEHNFTSFCSTEDENDSKFRYLERVKAIRKGDT 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           I   +   +FLH  +R  VG+L      K     +E  L+++DR +    AP  GLYF
Sbjct: 184 IYFIIRGNAFLHNMVRIIVGTLVEGQKKKKPINFIEDILKSEDRAKAFVTAPAHGLYF 241


>gi|255036264|ref|YP_003086885.1| tRNA pseudouridine synthase A [Dyadobacter fermentans DSM 18053]
 gi|254949020|gb|ACT93720.1| tRNA pseudouridine synthase A [Dyadobacter fermentans DSM 18053]
          Length = 248

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 126/246 (51%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G+ Y GWQ+Q N   +Q  +E A+  V    V V G+ RTD+GVHA +Q 
Sbjct: 1   MRYFIEFSYRGTAYNGWQKQNNALGVQEVLEAALAKVLRAPVEVTGSSRTDAGVHAEQQF 60

Query: 62  AHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFDL      V ++   LNA   +   I++  L  V +  H+RF+A  R Y YRI  ++
Sbjct: 61  AHFDLPAAIPDVDLMVYKLNAL--VPKDIAVQRLIPVAEDVHSRFAATHRKYEYRITFQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   +   A  + ++LD   M  AA  L+  +DF +F  IH   ++   TI        
Sbjct: 119 NPFLTDL--ATQMRRNLDVPRMNEAAALLLAHNDFESFSKIHTNVNNFRCTITESRWVEV 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G ++   V A  FL   +R+ VG++  VG  K T  D E+ + +++RK  G  AP EGL+
Sbjct: 177 GEMLVFHVKANRFLRGMVRALVGTMLEVGRQKITVDDFEQIILSRNRKNAGAQAPAEGLF 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LVEVGY 242


>gi|146317967|ref|YP_001197679.1| tRNA pseudouridine synthase A [Streptococcus suis 05ZYH33]
 gi|166229845|sp|A4VT40|TRUA_STRSY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145688773|gb|ABP89279.1| Pseudouridylate synthase [Streptococcus suis 05ZYH33]
          Length = 249

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  L +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQPHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   + S+ I ++++  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTSEDIDVVSVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDNVRTITVASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   
Sbjct: 179 DQQRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRGLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|313114592|ref|ZP_07800100.1| tRNA pseudouridine synthase A [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310623056|gb|EFQ06503.1| tRNA pseudouridine synthase A [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 248

 Score =  134 bits (336), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + + + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL   
Sbjct: 1   MNFLLTLAYDGTNYCGFQVQPNGRSVAQTFQDALQAVLGSRPDIKGCSRTDAGVHALGFK 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F          L  ALN +L     I +L+  +V + FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPAAKLPLALNQHLPPD--IRVLDAQVVPEDFHARYAAHTKTYLYRIHNHPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDVN 178
               +      +P+ LD   M+ AAQ  VGRHDF    +    A      +RTI    V 
Sbjct: 119 DSPFDAAYYTRVPRHLDEARMQAAAQQFVGRHDFLALCAAGSSAAAHGDTVRTITDCHVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+I V A  +L+  +R   G+L   G G+    ++   L+++DR   GP  P +G
Sbjct: 179 REGDEIDIEVTADGYLYNMVRILAGTLCEAGAGRLDPAEIPAILESRDRSRAGPTLPAKG 238

Query: 239 LYFDSVEYS 247
           L+   VEY 
Sbjct: 239 LFLKCVEYD 247


>gi|315641606|ref|ZP_07896674.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
 gi|315482647|gb|EFU73175.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
          Length = 248

 Score =  134 bits (336), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 126/243 (51%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           +IIEY+G+ Y GWQR  +   +IQG +EK +  +TGE + + G+GRTD+G HA  QVA+F
Sbjct: 6   LIIEYDGTRYQGWQRLGDSDKTIQGKLEKIVSQLTGETIELIGSGRTDAGTHARGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +      YL     I + ++  V ++FHAR++A+ + Y Y +   + P A
Sbjct: 66  KTNCNKSLEEMHHFFLTYL--PKDIVVTSIDEVPERFHARYNAVSKQYSYYVRHAELPSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            ++   + + + LD E M  A   L G HDF  F ++     S +RTI+  ++     +I
Sbjct: 124 FDRNYHFYVAEPLDWEAMTEACLRLTGAHDFLGFSALKKSKKSTVRTIESIEMEKEEAMI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                   FL+  +R  +G++  VG G+ T   ++   QA+ R+  G   P +GL+ D V
Sbjct: 184 RFVFRGDGFLYKMVRIMMGTILAVGKGEMTVNQIDDIFQAKIRQAAGETVPAQGLFLDGV 243

Query: 245 EYS 247
            Y 
Sbjct: 244 FYE 246


>gi|315223896|ref|ZP_07865742.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea F0287]
 gi|314946125|gb|EFS98128.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea F0287]
          Length = 262

 Score =  134 bits (336), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 124/245 (50%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + + G  Y+GWQ Q    S+Q  ++KA+  +    + V GAGRTDSGVHA +  
Sbjct: 13  MRYFIELSFFGKNYYGWQSQPKAISVQEVLQKALSTLLRTPIEVVGAGRTDSGVHASQMY 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD V E +P  L   LNA+L     I+I ++  V    HARF A++R+Y Y I TR+ 
Sbjct: 73  AHFD-VTEALPANLVHKLNAFL--PKDIAIHHIYEVQPNAHARFDALKRTYQYHISTRKD 129

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A +   A+ +P  L+   M  AA+ L    DF  F   H    +    I     +   
Sbjct: 130 AFAYDYAMAFTLP--LNVALMNEAAEILFDYTDFQCFSKTHTDVKTYNCKIYEAHWDKVE 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG+L  VG  K + TD E  + ++ R + G   P  GLY 
Sbjct: 188 NQLIFTITADRFLRNMVRAIVGTLIDVGLQKLSLTDFEDIIISKKRSKAGASVPACGLYL 247

Query: 242 DSVEY 246
             +EY
Sbjct: 248 THIEY 252


>gi|327182857|gb|AEA31304.1| tRNA pseudouridine synthase A [Lactobacillus amylovorus GRL 1118]
          Length = 264

 Score =  134 bits (336), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 134/251 (53%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           + RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ 
Sbjct: 2   LTRYKMTMSYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVG 61

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD   + +P   +  ALN+ +     I   +  IVD+ FHAR+S   + Y YR+  
Sbjct: 62  QVIHFDYPGKTIPANRMILALNSMMPTD--IVFTDCQIVDENFHARYSIKGKWYRYRVSL 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
                  ++         LD + M+ AA+ L+G HDFT+F +   Q    +RTI + ++ 
Sbjct: 120 DHFVNPFKRFYTGHFQYHLDIKKMQEAAKDLLGTHDFTSFAASGGQIEDKVRTIYYVNIR 179

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            N   N I    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A  
Sbjct: 180 KNEEENEIIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLKRVILAKDRQEVRQTAQA 239

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 SGLYLYHVFYD 250


>gi|315037561|ref|YP_004031129.1| tRNA pseudouridine synthase A [Lactobacillus amylovorus GRL 1112]
 gi|325956034|ref|YP_004286644.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus 30SC]
 gi|312275694|gb|ADQ58334.1| tRNA pseudouridine synthase A [Lactobacillus amylovorus GRL 1112]
 gi|325332599|gb|ADZ06507.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus 30SC]
          Length = 264

 Score =  134 bits (336), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 134/251 (53%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           + RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ 
Sbjct: 2   LTRYKMTMSYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVG 61

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD   + +P   +  ALN+ +     I   +  IVD+ FHAR+S   + Y YR+  
Sbjct: 62  QVIHFDYPGKTIPANRMILALNSMMPTD--IVFTDCQIVDENFHARYSIKGKWYRYRVSL 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
                  ++         LD + M+ AA+ L+G HDFT+F +   Q    +RTI + ++ 
Sbjct: 120 DHFVNPFKRFYTGHFQYHLDIKKMQEAAKDLLGTHDFTSFAASGGQIEDKVRTIYYVNIR 179

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            N   N I    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A  
Sbjct: 180 KNEEENEIIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLKRVILAKDRQEVRQTAQA 239

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 SGLYLYHVFYD 250


>gi|229083462|ref|ZP_04215810.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-44]
 gi|228699895|gb|EEL52532.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-44]
          Length = 252

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 125/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGENVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLTLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  +L+G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYLIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK  +  + + L  Q+RK  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLDVGQGKLDADSIPEILAKQNRKFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|218440649|ref|YP_002378978.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7424]
 gi|218173377|gb|ACK72110.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7424]
          Length = 306

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 124/246 (50%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ N  ++Q  IE+AI +V G+ V +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYLGTHFHGWQRQPNRRTVQEEIERAIAVVIGQPVTLHGAGRTDTGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD +    P      LN+  ++ D I +   + V  ++HARFSA  R Y Y I T + P
Sbjct: 72  HFDQISPIPPGRWASILNS--RLPDDIIVRASNRVCDRWHARFSACWRRYRYTIYTDKQP 129

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               K  +W    + L+   M+ A   L+G+H    F   +   +     I        G
Sbjct: 130 NLFIKPFSWHYYHQPLEESLMQSALDPLLGKHHLAAFHRANSARTHSWVEIQAAHCYRIG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A  FL+  +R  VG L  VG+ + +  D  +  Q Q R+E    AP +GL  
Sbjct: 190 PFVHIEIQANGFLYGMVRLLVGMLIEVGNKQRSIEDFTRIWQNQRREEVKYAAPAKGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|227879273|ref|ZP_03997143.1| tRNA pseudouridine synthase A [Lactobacillus crispatus JV-V01]
 gi|227861167|gb|EEJ68816.1| tRNA pseudouridine synthase A [Lactobacillus crispatus JV-V01]
          Length = 256

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 132/246 (53%), Gaps = 6/246 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVAHF 64
           M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ QV HF
Sbjct: 1   MTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQVIHF 60

Query: 65  DLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           D   + +P   +  A+N+ +     I   N  IV+  FHAR+S   + Y YR+       
Sbjct: 61  DYPGKTIPANRMILAMNSMMPTD--IIFNNCQIVNDDFHARYSIKGKWYRYRVSLDHFVN 118

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--NSFG 181
             ++      P  LD E M+IAAQ L+G+HDFT+F +   +    +RTI +  +  +   
Sbjct: 119 PFKRFYTGHFPYPLDIEKMQIAAQDLLGKHDFTSFAASGGRIEDKVRTIYYVKITEDKKD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   GLY 
Sbjct: 179 NEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLQRVIAAKDRQEVRQTAHASGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 YHVFYD 244


>gi|25027130|ref|NP_737184.1| tRNA pseudouridine synthase A [Corynebacterium efficiens YS-314]
 gi|23492410|dbj|BAC17384.1| putative tRNA pseudouridine synthase A [Corynebacterium efficiens
           YS-314]
          Length = 300

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 92/263 (34%), Positives = 138/263 (52%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + ++Y+G+ + GW RQ +    ++Q  +E  + +V    V +  AGRTD+GVHA  
Sbjct: 19  VRIRLDLDYDGTDFHGWARQGDSDLRTVQKVLEDNLGMVLRAPVELTVAGRTDAGVHAAG 78

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+ RE +        P  L + L+  L   + I +  ++   + F ARFSA+RR 
Sbjct: 79  QVAHFDIPRESLQQRSIDGDPTKLVRRLSRLLP--EDIRVHGVNYAPEGFDARFSALRRH 136

Query: 112 YLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YRI T  A   P  +    AW  PK +D + M+ AA  L+G HDF  F      AS+ 
Sbjct: 137 YVYRITTHPAGPLPTRVRDTAAW--PKPVDIQAMQTAADVLIGLHDFVAFCKAKPNAST- 193

Query: 169 IRTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R +  F   DV++     L E  VVA +F  + +RS VGS   VG+G+       + L 
Sbjct: 194 VRELQEFTWHDVSTPTEPQLYEAHVVADAFCWSMVRSLVGSCMAVGEGRRAGDFTAQLLT 253

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A +R    P+AP +GL    V+Y
Sbjct: 254 ATERSPDVPVAPAKGLSLVGVDY 276


>gi|228983397|ref|ZP_04143610.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228776387|gb|EEM24740.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 252

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|166030569|ref|ZP_02233398.1| hypothetical protein DORFOR_00232 [Dorea formicigenerans ATCC
           27755]
 gi|166029571|gb|EDR48328.1| hypothetical protein DORFOR_00232 [Dorea formicigenerans ATCC
           27755]
          Length = 244

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ    ++IQ  +E +I  + G  V V G+GRTD+GVHA  
Sbjct: 1   MRTYKLTISYDGTRYQGWQRQATTDNTIQHILEWSIGKLVGYRVRVDGSGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + +    L  ++N YL   + I I+ + ++   FHAR SA  + Y Y I  R
Sbjct: 61  QVASVQLSKLYDVKELKDSINRYL--PEDIRIMKVELMKNGFHARKSAKGKKYEYYIDCR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P  LD E MR AA +++G  +FT+F +   +   P+R + +  + S
Sbjct: 119 EKPDVFSRRYCYHYPHKLDIEAMREAADYMIGPKNFTSF-TDDSENKDPVRRVTNIKIVS 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I      F++  +R   G+L  VG G+  ++ +   + A+DR   G LAP  GL
Sbjct: 178 NGEKLRITYYGTGFMYHMVRIMTGTLLEVGTGEREASMIPVVIAAEDRSLAGFLAPARGL 237

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 238 FLRKVYY 244


>gi|238917621|ref|YP_002931138.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
 gi|238872981|gb|ACR72691.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
          Length = 249

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 123/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y MII Y+G+ Y+GW+ Q     +IQG +E  +  +TG  V V GAGRTD+GVHA  
Sbjct: 1   MKNYKMIITYDGTRYYGWEHQPTTDMTIQGKLESVLSAMTGTEVEVIGAGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+  +  +     +C  +N YL   + I +  + I   +FH+R++A  ++Y Y     
Sbjct: 61  MVANAHMETKMKEDDICDYMNRYL--PEDICVQEVRIASDRFHSRYNAQGKTYCYTCYVG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +    +I   LD E M+ AA  L G HD+ +F        S +R I   DV+ 
Sbjct: 119 DKKPVFNRKYVNIIEGKLDVEAMKKAADILTGEHDYASFCGNPKMKKSTVREIYSIDVSL 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + +      FL   +R   G+L  VG GK T   + + L+ ++R   G  AP +GL
Sbjct: 179 KGSFLNLTYHGSGFLQYMVRILSGTLLEVGQGKRTPESMYELLEERNRSLAGATAPAKGL 238

Query: 240 YFDSVEYS 247
               V+YS
Sbjct: 239 CLLKVDYS 246


>gi|237715548|ref|ZP_04546029.1| tRNA pseudouridine synthase A [Bacteroides sp. D1]
 gi|262408556|ref|ZP_06085102.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_22]
 gi|294643196|ref|ZP_06721024.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CC 2a]
 gi|294809320|ref|ZP_06768031.1| tRNA pseudouridine synthase A [Bacteroides xylanisolvens SD CC 1b]
 gi|229444257|gb|EEO50048.1| tRNA pseudouridine synthase A [Bacteroides sp. D1]
 gi|262353421|gb|EEZ02515.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_22]
 gi|292641462|gb|EFF59652.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CC 2a]
 gi|294443478|gb|EFG12234.1| tRNA pseudouridine synthase A [Bacteroides xylanisolvens SD CC 1b]
          Length = 249

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  +  V+   HARF A  R+Y Y + T +
Sbjct: 61  VAHFDFDELLDEVSVADKLNRLLPPD--ISVYRVCRVNPDAHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   LD   M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRVYNQLDYALMNEAARTLFEYTDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +   +  + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 DDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRVIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEY 246
           +  +VEY
Sbjct: 237 FLVNVEY 243


>gi|282898331|ref|ZP_06306322.1| tRNA pseudouridine synthase [Raphidiopsis brookii D9]
 gi|281196862|gb|EFA71767.1| tRNA pseudouridine synthase [Raphidiopsis brookii D9]
          Length = 292

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 121/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   ++Q  IE AI  V G  V +HGAGRTD+GVHA  QVA
Sbjct: 13  RVALVIQYLGTNFHGWQRQKAQRTVQEEIEIAIASVLGYHVTLHGAGRTDAGVHAAAQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             LN+YL     I I   + V + +HARFSA+ R Y Y I T+  P
Sbjct: 73  HFNATGHIPAHKWATVLNSYL--PPDILIRASAGVKESWHARFSAVYRRYRYTIYTQALP 130

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W      L+ E M+ A   LVG+H    F       S     I   +    G
Sbjct: 131 NLFVSPFSWHYYYAPLEEELMQAALTPLVGKHHLAAFHRAGSARSHSWVEIQAVECCRQG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A  FL+  +R  VG L  VG  + +  D     Q +DR++    APP+GL  
Sbjct: 191 SLVHIEIQANGFLYGMVRLLVGMLVQVGSKQKSLEDFTNIWQTEDREKVKYAAPPQGLCL 250

Query: 242 DSVEYS 247
             V Y+
Sbjct: 251 LRVGYN 256


>gi|228937445|ref|ZP_04100091.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970331|ref|ZP_04130990.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228976901|ref|ZP_04137313.1| tRNA pseudouridine synthase A [Bacillus thuringiensis Bt407]
 gi|228782871|gb|EEM31037.1| tRNA pseudouridine synthase A [Bacillus thuringiensis Bt407]
 gi|228789440|gb|EEM37360.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228822278|gb|EEM68260.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|326937937|gb|AEA13833.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 252

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+ + +R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEIKKIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|310644170|ref|YP_003948929.1| tRNA pseudouridine synthase a [Paenibacillus polymyxa SC2]
 gi|309249121|gb|ADO58688.1| tRNA pseudouridine synthase A [Paenibacillus polymyxa SC2]
          Length = 261

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 90/261 (34%), Positives = 133/261 (50%), Gaps = 22/261 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M   CM + Y+G+ Y G+Q Q +G++IQ  +E AI+ +TGE + + G+GRTD+GVHA  Q
Sbjct: 1   MRNLCMKVNYDGTHYDGFQTQPSGNTIQDCLENAIYSLTGERLKITGSGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V +F      +P+   C ALNA+L     I + +   V   FHAR  A R++Y Y I   
Sbjct: 61  VFNFH-TESPIPIHRWCLALNAWLPRD--IIVTDAREVPLSFHARRMAKRKTYRYSINAN 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI------- 172
           + P    +      P +LD   M     HLVG  D+T+F S   Q ++ +RTI       
Sbjct: 118 RFPDIFHRRTQAHHPTNLDVRAMEKGLAHLVGTFDYTSFASRRSQKTNHVRTIYEAYITV 177

Query: 173 DHFDVNSFG-------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           DH    SF         +I   +    FL   +R  +G+L  VG+GK +  D+   L+A+
Sbjct: 178 DH----SFSRPGSDDQGIIHTYITGSGFLQHMVRIIMGTLLEVGEGKKSPDDIPSILEAK 233

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
           +R + GP A    L   +VEY
Sbjct: 234 NRSKAGPTAVGHALTLWNVEY 254


>gi|77409358|ref|ZP_00786059.1| tRNA pseudouridine synthase A [Streptococcus agalactiae COH1]
 gi|77172030|gb|EAO75198.1| tRNA pseudouridine synthase A [Streptococcus agalactiae COH1]
          Length = 258

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 84/252 (33%), Positives = 130/252 (51%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  L +G  V+++GAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIYGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI  FD   
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTI--FDAKI 176

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A 
Sbjct: 177 QFEASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAA 236

Query: 236 PEGLYFDSVEYS 247
             GLY   + Y 
Sbjct: 237 GNGLYLKEIIYE 248


>gi|282899978|ref|ZP_06307939.1| tRNA pseudouridine synthase [Cylindrospermopsis raciborskii CS-505]
 gi|281195248|gb|EFA70184.1| tRNA pseudouridine synthase [Cylindrospermopsis raciborskii CS-505]
          Length = 292

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 119/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   ++Q  IE AI  V G  V +HGAGRTD+GVHA  QVA
Sbjct: 13  RVALVIQYLGTNFHGWQRQKAQRTVQEEIETAIASVLGYHVTLHGAGRTDAGVHAAAQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             LN+YL     I I   + V + +HARFSA  R Y Y I T   P
Sbjct: 73  HFNATGHIPAHKWATVLNSYL--PPDILIRASAGVKESWHARFSATYRRYRYTIYTEALP 130

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W      L+ + M+ A   LVG+H    F       S     I   +    G
Sbjct: 131 NLFVSPFSWHYYYAPLEEKLMQAALTPLVGKHHLAAFHRAGSARSHSWVEIQAVECGRQG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A  FL+  +R  VG L  VG  + +  D     Q +DR++    APP+GL  
Sbjct: 191 SLVHIEIQANGFLYGMVRLLVGMLVQVGSKQKSLEDFTNIWQTEDREKVKYAAPPQGLCL 250

Query: 242 DSVEYS 247
             V YS
Sbjct: 251 LRVGYS 256


>gi|149797294|ref|YP_001294664.1| tRNA-pseudouridine synthase A [Symbiobacterium thermophilum IAM
           14863]
          Length = 267

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 130/247 (52%), Gaps = 10/247 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE--IVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+ Y G+QRQ NG +IQ  +E+A+  VTGE  + +   AGRTD+GVHA  QV H
Sbjct: 6   LILAYDGTAYAGFQRQPNGITIQQRLEEALRAVTGEPDLRIGAAAGRTDAGVHARGQVVH 65

Query: 64  FDLVREWVPVILCK---ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              +R +  + + +   ALN +L   D I+++        FHAR+ A  + Y Y      
Sbjct: 66  ---LRTYATIPIDRWPAALNGHL--PDDIAVIGAEEAPPDFHARYWAREKRYRYTFCLSP 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             L + +  ++   + +D + MR AA  LVGRHDF  FR+    A + +RTI    +   
Sbjct: 121 YRLPMARLYSYHWHRPVDVDAMRRAAALLVGRHDFAAFRATGGSARTTVRTITRLTLTEE 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + V A  FL+  +R   G+L  VG G+ +   + +AL+   R++ G   PP GL 
Sbjct: 181 PPFLHLDVTADGFLYNMVRIIAGTLLEVGAGRRSLDRVAQALRHGRREDAGRTLPPHGLC 240

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 241 LEEVVYG 247


>gi|323465853|gb|ADX69540.1| tRNA pseudouridine synthase A [Lactobacillus helveticus H10]
          Length = 262

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 82/249 (32%), Positives = 134/249 (53%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           RY M + Y+G  + G+Q Q +  ++QG+IE A+  +  G+ ++V G+GRTD+GVHA+ QV
Sbjct: 4   RYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMSKGKRIIVQGSGRTDAGVHAIGQV 63

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD   + +P   +  ALN+ +     I   N  IV++ FHAR+S   + Y YR+    
Sbjct: 64  IHFDYPGKTIPANRMILALNSMMPTD--IIFNNCEIVNENFHARYSIKGKWYRYRVSLDH 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++        +LD   M+ AA+ L+G+HDFT+F +   Q    +RTI + ++  +
Sbjct: 122 FVNPFKRFYTGHFSYALDVGKMQEAAKDLLGKHDFTSFAASGGQIEDKVRTIYYVNIAKD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N I    +   FL+  +R  V +L  +G+G+    DL++ + A+DR+E    A   G
Sbjct: 182 EKENEIVFDFIGSGFLYNMVRIMVAALLEIGNGRRPVHDLKRVIAAKDRQEVRQTAQASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYD 250


>gi|300362359|ref|ZP_07058535.1| tRNA-pseudouridine synthase I [Lactobacillus gasseri JV-V03]
 gi|300353350|gb|EFJ69222.1| tRNA-pseudouridine synthase I [Lactobacillus gasseri JV-V03]
          Length = 255

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 85/244 (34%), Positives = 133/244 (54%), Gaps = 6/244 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G  + G+Q Q    ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV HFD 
Sbjct: 1   MAYDGHLFHGFQIQPKERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQVIHFDY 60

Query: 67  VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             + +P   +  ALNA + I DT+   +  IV+  FH ++S   + Y Y +   +     
Sbjct: 61  PGKEIPAKNMMLALNALMPI-DTV-FFDSEIVNSDFHVQYSTKGKWYRYIVDQHRFTDPF 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +      P  LD + M+ AA+ L+G+HDFT+F +   Q    +RTI + ++ S  +  +
Sbjct: 119 NRFYTGHYPYPLDIDLMQRAAKDLIGKHDFTSFAASGGQIVDKVRTIYYVNITSDPDNKK 178

Query: 186 I--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    AP  GLY   
Sbjct: 179 IIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTAPASGLYLQH 238

Query: 244 VEYS 247
           V Y 
Sbjct: 239 VFYE 242


>gi|269792760|ref|YP_003317664.1| tRNA pseudouridine synthase A [Thermanaerovibrio acidaminovorans
           DSM 6589]
 gi|269100395|gb|ACZ19382.1| tRNA pseudouridine synthase A [Thermanaerovibrio acidaminovorans
           DSM 6589]
          Length = 251

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 121/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY   + Y GS + G+QRQ N  ++QG++E+++  + GE V   GAGRTD+GVHA  Q
Sbjct: 1   MFRYAAQVSYVGSCFAGFQRQPNLVTVQGALEESLSALAGEGVTCTGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+   W    L  A+ A  ++   + ++ L+ V   FHARF A  R Y Y +   +
Sbjct: 61  VVHFDMPSRWDLERLRLAIRA--RLPRGLEVIRLAEVPGDFHARFDARWREYRYLVWNAR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   W + + LD   +R  A   +GR DF  F     +    +RT+    V  F
Sbjct: 119 WCYPHMEPYVWPVRRHLDLGVLRELAGMCLGRRDFGAFCRSADRPDDSVRTMMRCSVRRF 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+     A  FL   IR  VG++  V  G+ +       L+   R   G   PP+GL+
Sbjct: 179 GHLLVFTFRADGFLTNMIRILVGTMLEVEAGRMSRERFASLLEGGHRSRAGRTCPPQGLF 238

Query: 241 FDSVEY 246
           F  V Y
Sbjct: 239 FWRVGY 244


>gi|223984957|ref|ZP_03635058.1| hypothetical protein HOLDEFILI_02362 [Holdemania filiformis DSM
           12042]
 gi|223963077|gb|EEF67488.1| hypothetical protein HOLDEFILI_02362 [Holdemania filiformis DSM
           12042]
          Length = 268

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 86/250 (34%), Positives = 135/250 (54%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R+  ++ Y+G  Y GWQ Q  + G++IQ +I+ AI ++  + V + G+GRTD+ VHA 
Sbjct: 2   MQRFKAVVSYDGFDYAGWQIQPAERGATIQQTIQDAISVICQQPVSITGSGRTDAQVHAW 61

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD+          +A+N +L     I I ++  VD +FHARF AI + Y YRI  
Sbjct: 62  GQVFHFDVDFSLNAFQWKRAINGHL--PKDIHIRSVEAVDSRFHARFDAIGKRYEYRIQL 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFD 176
            +A +   +  A+  P +L+ + MR  A +L+G HDF++F   + +A  P   RTI   +
Sbjct: 120 GEANV-FTRRYAFQSPWTLNVQAMREGAAYLIGEHDFSSF-CANSRAEMPDQARTITRLE 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + + +      FL   +R   G+L  VG G+    D++  LQAQD++ C   A P
Sbjct: 178 LAEENDQLRLIYEGSGFLRYMVRMMTGTLIEVGRGRLAPQDVQWMLQAQDKQICHFNAKP 237

Query: 237 EGLYFDSVEY 246
           +GL    V Y
Sbjct: 238 QGLTLVEVYY 247


>gi|315656237|ref|ZP_07909128.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. holmesii
           ATCC 35242]
 gi|315493239|gb|EFU82839.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. holmesii
           ATCC 35242]
          Length = 297

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 89/272 (32%), Positives = 134/272 (49%), Gaps = 28/272 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++QG++E A+ ++  + V +  AGRTD+GVHA  QV
Sbjct: 1   MRIRLDIRYDGTPFHGWAAQPGLPTVQGALESALTVIYRQTVELTVAGRTDAGVHASGQV 60

Query: 62  AHFDLV----REWVPVILCKALNAYLKIS---------------------DTISILNLSI 96
           AHF +     R   P  L   L A L+                       D + +   ++
Sbjct: 61  AHFTVPEVGDRIVSPDTLAPRLGAVLRAVLSGNLASPLPDSPAAYPPNAIDALVVTAATV 120

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
           V + F ARFSA+ R Y+YRI+   A    L +   W  P  LD   M  +A  L+G HDF
Sbjct: 121 VPETFDARFSALARHYVYRIVDDLAARNPLSRNYCWWYPTQLDAAAMNTSAAVLLGEHDF 180

Query: 156 TTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             F     + ++ IRT+   + + +   ++EIRV A +F H+ +RS VG+L  VG  K  
Sbjct: 181 AAFCKPR-EGATTIRTLQQLETLRTAPGMMEIRVRADAFCHSMVRSLVGALTEVGRAKRD 239

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  L  AL A+ R    P+AP  GL    V+Y
Sbjct: 240 TAWLADALAAKARIPEIPVAPALGLTLTQVDY 271


>gi|78048428|ref|YP_364603.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325924659|ref|ZP_08186097.1| pseudouridylate synthase I [Xanthomonas perforans 91-118]
 gi|123743895|sp|Q3BRL0|TRUA_XANC5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78036858|emb|CAJ24551.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325544865|gb|EGD16210.1| pseudouridylate synthase I [Xanthomonas perforans 91-118]
          Length = 257

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 134/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++         FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTLSWERRPLDADAMHAAAQALLGENDFSAFRSVQCQALHARRHLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP A
Sbjct: 174 IHVQRIGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|296125792|ref|YP_003633044.1| tRNA pseudouridine synthase A [Brachyspira murdochii DSM 12563]
 gi|296017608|gb|ADG70845.1| tRNA pseudouridine synthase A [Brachyspira murdochii DSM 12563]
          Length = 247

 Score =  133 bits (335), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/238 (33%), Positives = 126/238 (52%), Gaps = 4/238 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I+Y+G+ ++GWQ Q N  ++QG I KA+  + GE + ++G GRTD+GVHAL QVA+F 
Sbjct: 6   ITIQYDGTDFYGWQIQPNLRTVQGEIYKAVQKIYGEKITIYGCGRTDAGVHALGQVANFR 65

Query: 66  LVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           + +  VP+     ALN+ L     + I+    +D  F+AR SA  R YLY +        
Sbjct: 66  VPKMLVPINKVHIALNSCL--DRDLRIIKAEEMDDNFNARASATFREYLYVVHNSSTSFP 123

Query: 125 LEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
             +  AW   K+ +D + +   A++L+G H+FT+F S   +  S  R ++       G+ 
Sbjct: 124 FYERYAWFYRKNIIDEKLINEYAKYLIGEHNFTSFCSTEDENDSKFRYLEKVKAVRKGDT 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           I   +   +FLH  +R  VG+L      K     +E  L+ ++R E    AP  GLYF
Sbjct: 184 IYFIIKGNAFLHNMVRIIVGTLVEGQKKKMPVNFIEDILKRENRTEAFVTAPAHGLYF 241


>gi|284036658|ref|YP_003386588.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
 gi|283815951|gb|ADB37789.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
          Length = 252

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 129/247 (52%), Gaps = 8/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ Y GWQRQ NG S+Q  +E A+  V  + + + G+GRTD+GVHA +Q 
Sbjct: 1   MRYFLHLAYKGTKYHGWQRQPNGLSVQEVLETALSTVLRQPIAIVGSGRTDAGVHAGQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD     +P  L ++LN+   I   I++     V    HARF+A  R Y Y+I  R+ 
Sbjct: 61  AHFD-TDVALPTQLLRSLNSM--IPPDIAVYECFPVRPDDHARFTAQSRYYQYQISRRKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDVNS 179
           P    +G  ++    L+ E M  AA  L+   DF +F  +     +    I+  ++    
Sbjct: 118 P--FREGLVYVFTLPLNVELMNEAASRLLHHIDFESFSKVKTDVKTFNCQIEWAYWAQQP 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+   + A  FLH  +R+ VG+L  VG  + + TD E+ +   DRK  G  AP EGL
Sbjct: 176 NGDLV-FHIKANRFLHGMVRAIVGTLLAVGQERLSVTDFEQIILDHDRKRAGRAAPAEGL 234

Query: 240 YFDSVEY 246
               V Y
Sbjct: 235 SLVEVGY 241


>gi|319642589|ref|ZP_07997236.1| pseudouridylate synthase [Bacteroides sp. 3_1_40A]
 gi|317385823|gb|EFV66755.1| pseudouridylate synthase [Bacteroides sp. 3_1_40A]
          Length = 251

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 84/240 (35%), Positives = 120/240 (50%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +AHFD  
Sbjct: 1   MAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMIAHFDYD 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+ P    +
Sbjct: 61  RELDCVQITEKLNRLLPPD--IAVYAVKRVKDDAHARFDATYRTYKYYVTTRKDP--FNR 116

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-GNLIEI 186
             AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     G     
Sbjct: 117 HYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVSGTEWVF 176

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+   V Y
Sbjct: 177 TIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALFLVDVGY 236


>gi|47570254|ref|ZP_00240905.1| tRNA pseudouridine synthase A [Bacillus cereus G9241]
 gi|47553078|gb|EAL11478.1| tRNA pseudouridine synthase A [Bacillus cereus G9241]
          Length = 247

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 61  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 115

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 116 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 175

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP 
Sbjct: 176 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPG 235

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 236 HGLYLWQVNYN 246


>gi|255637177|gb|ACU18919.1| unknown [Glycine max]
          Length = 370

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 73/189 (38%), Positives = 109/189 (57%), Gaps = 13/189 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + G Q+Q N  ++ G +E+A     G+ V V  + RT +GVHAL  V 
Sbjct: 51  RYLVAIEYIGTRFSGSQKQLNVRTVVGVLEEAFSKFVGQPVSVSCSSRTVAGVHALSNVC 110

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+  D+ + ++++  V   FHARF A  R
Sbjct: 111 HVDIQRISKRRPGEVLTPHEPAVVGRAVNHFLQKQDSDLMVIDVRCVPSDFHARFKAQER 170

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            Y YR+++   PL+  EK RAW +P+ L    M+ A + LVG HDF++FR+  CQA SPI
Sbjct: 171 IYFYRLLSGPEPLSTFEKDRAWHVPEELSLPAMQEACRVLVGFHDFSSFRAAGCQAKSPI 230

Query: 170 RTIDHFDVN 178
           RT+D   VN
Sbjct: 231 RTLDELSVN 239



 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 34/57 (59%)

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           AR+FL+ Q+R  VG LK VG G  T  D+E+ L A+      P+AP  GLY   V+Y
Sbjct: 309 ARAFLYHQVRLLVGVLKAVGTGNLTIPDVERILNARTVTAASPMAPACGLYLGEVKY 365


>gi|298482201|ref|ZP_07000389.1| tRNA pseudouridine synthase A [Bacteroides sp. D22]
 gi|298271758|gb|EFI13331.1| tRNA pseudouridine synthase A [Bacteroides sp. D22]
          Length = 249

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       + +   LN  L     ISI  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDFDEPLDEISVADKLNRLLPPD--ISIYRVCRVRPDAHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   LD   M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRVYNQLDYALMNEAARTLFEYTDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +   +  + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 DDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRVIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEY 246
           +  +VEY
Sbjct: 237 FLVNVEY 243


>gi|229194532|ref|ZP_04321335.1| tRNA pseudouridine synthase A [Bacillus cereus m1293]
 gi|228588998|gb|EEK47013.1| tRNA pseudouridine synthase A [Bacillus cereus m1293]
 gi|324324133|gb|ADY19393.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 252

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 123/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|229153920|ref|ZP_04282050.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 4342]
 gi|228629601|gb|EEK86298.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 4342]
          Length = 252

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGIHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|298383909|ref|ZP_06993470.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_14]
 gi|298263513|gb|EFI06376.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_14]
          Length = 269

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 93/252 (36%), Positives = 124/252 (49%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NGSS+Q  + KA+       V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGSSVQECLMKALSTFLRRDVEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDHEDVLDTVTVADKLNRLLPPD--ISVYRVRQVKPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P   + + R +    SLD E M  AA+ L    DFT+F  +H    + I  I H +   
Sbjct: 119 YPFNRQYRCRVY---GSLDYERMNEAARTLFEYIDFTSFSKLHTDVKTNICHISHAEWTK 175

Query: 180 FGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                   +  IR  A  FL   +R+ VG+L  VG GK T     K ++ QDR + G  A
Sbjct: 176 MEGEDTTWVFTIR--ADRFLRNMVRAIVGTLLEVGRGKLTVEGFRKVIEQQDRCKAGTSA 233

Query: 235 PPEGLYFDSVEY 246
           P   L+  +VEY
Sbjct: 234 PGNALFLVNVEY 245


>gi|186684484|ref|YP_001867680.1| tRNA pseudouridine synthase A [Nostoc punctiforme PCC 73102]
 gi|186466936|gb|ACC82737.1| tRNA pseudouridine synthase A [Nostoc punctiforme PCC 73102]
          Length = 282

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 120/245 (48%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 12  RVALVIQYLGTHFHGWQRQKQHRTVQEEIETAIATILGHHVTLHGAGRTDSGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+      P      LN+YL     I I   + VD ++HARFSA  R Y Y I T    
Sbjct: 72  HFEATGLIPPHKWATILNSYL--PPDILIRASASVDNRWHARFSAAYRRYRYTIYTEDRL 129

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W      LD   ++ A + L+G+H    F     + S     +   +    G
Sbjct: 130 NLFVRPFSWHYYYAPLDESLIQAALKPLLGKHHLAAFHRAGSKRSHSWVEVQAVECRRSG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+  +R  VG L  VG G+ T +   +  + Q R+E    APP+GL  
Sbjct: 190 PFIHIEIQADGFLYGMVRLLVGMLVEVGSGQRTLSSFTELWKEQRREEVKYAAPPQGLCL 249

Query: 242 DSVEY 246
             V Y
Sbjct: 250 LRVGY 254


>gi|259506738|ref|ZP_05749638.1| tRNA pseudouridine synthase A [Corynebacterium efficiens YS-314]
 gi|42559821|sp|Q8FS31|TRUA_COREF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|259165679|gb|EEW50233.1| tRNA pseudouridine synthase A [Corynebacterium efficiens YS-314]
          Length = 282

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 92/264 (34%), Positives = 138/264 (52%), Gaps = 23/264 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + ++Y+G+ + GW RQ +    ++Q  +E  + +V    V +  AGRTD+GVHA  
Sbjct: 1   MRIRLDLDYDGTDFHGWARQGDSDLRTVQKVLEDNLGMVLRAPVELTVAGRTDAGVHAAG 60

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+ RE +        P  L + L+  L   + I +  ++   + F ARFSA+RR 
Sbjct: 61  QVAHFDIPRESLQQRSIDGDPTKLVRRLSRLLP--EDIRVHGVNYAPEGFDARFSALRRH 118

Query: 112 YLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YRI T  A   P  +    AW  PK +D + M+ AA  L+G HDF  F      AS+ 
Sbjct: 119 YVYRITTHPAGPLPTRVRDTAAW--PKPVDIQAMQTAADVLIGLHDFVAFCKAKPNAST- 175

Query: 169 IRTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R +  F   DV++     L E  VVA +F  + +RS VGS   VG+G+       + L 
Sbjct: 176 VRELQEFTWHDVSTPTEPQLYEAHVVADAFCWSMVRSLVGSCMAVGEGRRAGDFTAQLLT 235

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           A +R    P+AP +GL    V+Y 
Sbjct: 236 ATERSPDVPVAPAKGLSLVGVDYP 259


>gi|86141215|ref|ZP_01059761.1| tRNA pseudouridine synthase A [Leeuwenhoekiella blandensis MED217]
 gi|85831774|gb|EAQ50229.1| tRNA pseudouridine synthase A [Leeuwenhoekiella blandensis MED217]
          Length = 263

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 82/248 (33%), Positives = 126/248 (50%), Gaps = 7/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y+G+ Y GWQRQ    ++Q  +E+A+  +    V V GAGRTD+GVHA +  
Sbjct: 10  LRYFIEIAYDGTSYHGWQRQPQSITVQEVLEEALSTLLRSEVPVVGAGRTDAGVHATQLF 69

Query: 62  AHFDLVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           AHF++   +    L      LN +L   + +++  L  V  + HARF A+RRSY Y+I  
Sbjct: 70  AHFEIEESYSFEALSHLKFRLNRFL--PEAVAVNALLPVSAEAHARFDAVRRSYEYKIHM 127

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P  +   +++   K L+ + M  AA  L+GR DF  F        + I  I     +
Sbjct: 128 VKNPFLV--NQSYYFEKPLNVDAMNEAAAFLLGRQDFKCFSRSKTDVKTYICEITEARWD 185

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  ++  + A  FL   +R+ VG+L  +G GK     L+  + ++ R E G  AP  G
Sbjct: 186 QDGAQLKFSISADRFLRNMVRAIVGTLLEIGQGKLKPAALKTIIASRTRSEAGASAPAHG 245

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 246 LYLTEVAY 253


>gi|325287217|ref|YP_004263007.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
 gi|324322671|gb|ADY30136.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
          Length = 251

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 122/245 (49%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G+ Y GWQ Q N  ++Q  +EKA   +  E + + GAGRTD+GVHA +  
Sbjct: 1   MRYFVAFSYFGAAYHGWQIQPNAITVQEELEKAFSTLLKEKISLMGAGRTDAGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+       V L + LN++L   D I+I N+  V +  HARF+A  R+Y Y I T++ 
Sbjct: 61  AHFNTTPISNTVDLMRRLNSFL--PDDIAIQNIYEVPEDAHARFNATERTYEYLITTQKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P ++       I + LD E M  AAQ L+G+ DF  F        +   T+         
Sbjct: 119 PFSIVTTH--YIKQKLDIEKMNKAAQLLLGKQDFECFSKSKTDVKTYYCTVKKAIWEQKE 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +     + A  FL   +R+ VG+L  VG GK T   +   + ++ R E G   P + LY 
Sbjct: 177 DKFVFTITADRFLRNMVRAIVGTLLDVGTGKITIDHIHTIIASKSRAEAGTSVPAKALYL 236

Query: 242 DSVEY 246
             V Y
Sbjct: 237 TQVLY 241


>gi|48374280|gb|AAT41969.1| putative t-RNA pseudouridine synthase I [Fremyella diplosiphon
           Fd33]
          Length = 268

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 86/242 (35%), Positives = 122/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+I+Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTD+GVHA  QVAHF+
Sbjct: 1   MVIQYLGTHFHGWQRQKQQRTVQEEIETAIAKILGYHVTLHGAGRTDAGVHAAAQVAHFE 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P      LN+YL   + I I   + V  ++HARFSA  R Y Y I T   P   
Sbjct: 61  ATGLIPPHKWAAVLNSYL--PNDILIRASAGVGNRWHARFSAAYRRYRYTIYTEDQPNLF 118

Query: 126 EKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            +  +W      LD   ++ A + L+G+H    F     + S     +   + +  G LI
Sbjct: 119 VRPFSWHYYYAPLDESLIKAALKPLLGKHHLAAFHRAGSKRSHSWVEVQAAECHRSGPLI 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG L  VG G+ T  +  +  +A+ R+E    AP +GL    V
Sbjct: 179 HIEIQADGFLYGMVRLLVGMLVQVGTGQRTLANFTELWKAERREEVKYAAPAQGLCLLRV 238

Query: 245 EY 246
            Y
Sbjct: 239 GY 240


>gi|229830208|ref|ZP_04456277.1| hypothetical protein GCWU000342_02317 [Shuttleworthia satelles DSM
           14600]
 gi|229791506|gb|EEP27620.1| hypothetical protein GCWU000342_02317 [Shuttleworthia satelles DSM
           14600]
          Length = 267

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 121/233 (51%), Gaps = 3/233 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ Y GWQ Q NG S+Q  +   +  + GE +   GA RTD+GVH++     F+  
Sbjct: 5   IAYDGTEYCGWQVQPNGISVQEVVNAGLSKLLGEEITCVGASRTDAGVHSMGNEILFETK 64

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  +  ALN YL   + I     S+    FH RFS   ++Y YRI+ R+ P+   +
Sbjct: 65  TRIPADKIAYALNQYLP--EDIVCQGSSLAADDFHPRFSESYKTYEYRILNRRFPMPTMR 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFGNLIEI 186
             +      LD + M+ AA  L+G HDF++F SIH Q+ + +RTI    V+ +  +LI I
Sbjct: 123 RDSLFYHYDLDEKRMQEAADCLLGEHDFSSFASIHTQSKTRVRTIYQALVSRNADDLITI 182

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           R+    FL+  +R   G+L  VG G  +    ++ L   +R+  GP AP  GL
Sbjct: 183 RLCGDGFLYNMVRIIAGTLIEVGAGITSPRAFQQILDGMNRELAGPTAPAHGL 235


>gi|222093912|ref|YP_002527962.1| tRNA pseudouridine synthase a [Bacillus cereus Q1]
 gi|221237960|gb|ACM10670.1| tRNA pseudouridine synthase A [Bacillus cereus Q1]
          Length = 247

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 123/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 61  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 115

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   +
Sbjct: 116 LLSKTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 175

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 176 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 235

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 236 HGLYLWQVNYN 246


>gi|86609047|ref|YP_477809.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86557589|gb|ABD02546.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-2-3B'a(2-13)]
          Length = 285

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 120/247 (48%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I+Y GS ++GWQRQ    ++QG +E+AI    G  V ++GAGRTD+GVHA  QVA
Sbjct: 5   RIALRIQYLGSRFYGWQRQAARRTVQGVLEEAIASRAGHPVTLYGAGRTDTGVHAAGQVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD       V   + LN  L   + + +L  + V   +HARFSA  R Y Y I+ R+ P
Sbjct: 65  HFDTTSGIPAVEWSRVLNDCLP--EDVVVLASAQVPDSWHARFSARWRRYRYLILNRERP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  +W +   L  E M  A   L+G H    FR            +        G+
Sbjct: 123 DVFWRLFSWQVRWPLQVEPMAEALNSLLGEHSLEAFRRRGSDRPHSRVQVQEVLCQRLGD 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL--APPEGLY 240
           LI I V A  FL+  +R  VGSL++VG G+ +        Q  D  +      APP+GL 
Sbjct: 183 LISIEVQASGFLYRMMRLLVGSLEVVGRGQLSPAQFVHLWQHNDWSQMRTRYSAPPQGLC 242

Query: 241 FDSVEYS 247
              V Y+
Sbjct: 243 LTDVGYA 249


>gi|298345431|ref|YP_003718118.1| tRNA-pseudouridine synthase I [Mobiluncus curtisii ATCC 43063]
 gi|304390987|ref|ZP_07372939.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. curtisii
           ATCC 35241]
 gi|298235492|gb|ADI66624.1| tRNA-pseudouridine synthase I [Mobiluncus curtisii ATCC 43063]
 gi|304325870|gb|EFL93116.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. curtisii
           ATCC 35241]
          Length = 297

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 89/272 (32%), Positives = 134/272 (49%), Gaps = 28/272 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++QG++E A+ ++  + V +  AGRTD+GVHA  QV
Sbjct: 1   MRIRLDIRYDGTPFHGWAAQPGLPTVQGALESALTVIYRQTVELTVAGRTDAGVHASGQV 60

Query: 62  AHFDLV----REWVPVILCKALNAYLKIS---------------------DTISILNLSI 96
           AHF +     R   P  L   L A L+                       D + +   ++
Sbjct: 61  AHFTVPEVGDRIVSPDTLAPRLGAVLRAVLSGNLASPLPDSPAAYPPNAIDALVVTAATV 120

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
           V + F ARFSA+ R Y+YRI+   A    L +   W  P  LD   M  +A  L+G HDF
Sbjct: 121 VPETFDARFSALARHYVYRIVDDLAARNPLSRNCCWWYPTQLDAAAMNTSAAVLLGEHDF 180

Query: 156 TTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             F     + ++ IRT+   + + +   ++EIRV A +F H+ +RS VG+L  VG  K  
Sbjct: 181 AAFCKPR-EGATTIRTLQQLETLRTAPGMMEIRVRADAFCHSMVRSLVGALTEVGRAKRD 239

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  L  AL A+ R    P+AP  GL    V+Y
Sbjct: 240 TAWLADALAAKARIPEIPVAPALGLTLTQVDY 271


>gi|206978041|ref|ZP_03238926.1| tRNA pseudouridine synthase A [Bacillus cereus H3081.97]
 gi|217957717|ref|YP_002336261.1| tRNA pseudouridine synthase A [Bacillus cereus AH187]
 gi|229136988|ref|ZP_04265615.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST26]
 gi|206743754|gb|EDZ55176.1| tRNA pseudouridine synthase A [Bacillus cereus H3081.97]
 gi|217063029|gb|ACJ77279.1| tRNA pseudouridine synthase A [Bacillus cereus AH187]
 gi|228646526|gb|EEL02733.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST26]
          Length = 252

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 123/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE++ V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELIRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|163847952|ref|YP_001635996.1| tRNA pseudouridine synthase ACD [Chloroflexus aurantiacus J-10-fl]
 gi|222525832|ref|YP_002570303.1| tRNA pseudouridine synthase ACD [Chloroflexus sp. Y-400-fl]
 gi|189030130|sp|A9WH95|TRUA_CHLAA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789612|sp|B9LJG1|TRUA_CHLSY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|163669241|gb|ABY35607.1| tRNA pseudouridine synthase A [Chloroflexus aurantiacus J-10-fl]
 gi|222449711|gb|ACM53977.1| tRNA pseudouridine synthase A [Chloroflexus sp. Y-400-fl]
          Length = 278

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 125/246 (50%), Gaps = 6/246 (2%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +++ Y+G+ + G Q Q +  ++QG++E A   +T E   +  AGRTD+GVHA  QVAH 
Sbjct: 5   ALLLAYDGTDFAGSQWQTDIRTVQGALESAWEALTQERRRIVLAGRTDAGVHATGQVAHV 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + + LNA+L +   ++I N+      FHARFSAI+R Y Y I    APL 
Sbjct: 65  QTTTRHNLQTIWRGLNAHLPVD--LAIQNVGEAVPDFHARFSAIQREYRYLIDCAAAPLP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG--- 181
             + +      +LD   M  A + L G HDF  F +      S +RT+    V  +    
Sbjct: 123 QLRHQVLHYAGTLDVAAMTAALKLLEGTHDFAAFTTATPAQRSTVRTMYWTRVGDYEWFE 182

Query: 182 -NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ I V A +FL   +R  VG+L LVG G+ T     + L ++DR+  GP AP  GL 
Sbjct: 183 RRLLAIEVAANAFLQHMVRMIVGTLLLVGRGRMTVDQFGEVLASRDRRLAGPTAPAHGLT 242

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


>gi|229094864|ref|ZP_04225869.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-29]
 gi|229100941|ref|ZP_04231745.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-28]
 gi|229113818|ref|ZP_04243253.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-3]
 gi|228669689|gb|EEL25096.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-3]
 gi|228682520|gb|EEL36593.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-28]
 gi|228688607|gb|EEL42480.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-29]
          Length = 252

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIFEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|223933386|ref|ZP_03625373.1| tRNA pseudouridine synthase A [Streptococcus suis 89/1591]
 gi|330832153|ref|YP_004400978.1| tRNA pseudouridine synthase A [Streptococcus suis ST3]
 gi|223897953|gb|EEF64327.1| tRNA pseudouridine synthase A [Streptococcus suis 89/1591]
 gi|329306376|gb|AEB80792.1| tRNA pseudouridine synthase A [Streptococcus suis ST3]
          Length = 249

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  L +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQTHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++ +  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTPEDIDVVQVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTIKAASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   
Sbjct: 179 DQRRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRGLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|293402539|ref|ZP_06646674.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291304053|gb|EFE45307.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 251

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 127/248 (51%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  ++ Y+GS Y GWQ+Q N +SIQ  IE+A+  +    V +  +GRTD+GVHA+ Q
Sbjct: 1   MARYKAVVSYDGSSYGGWQKQLNTTSIQEVIEQALAKMHKHDVAIVASGRTDAGVHAIAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       KALN+ L     I I ++  V + FHARF AI + Y Y +I+  
Sbjct: 61  VFHFDSEMKIQEKHWIKALNSLL--PKDIRIQSVKQVTEAFHARFDAIGKRYDY-LISND 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNS 179
                ++         LD   M+  A  L+G HDFT+F S       P ++TI   +V  
Sbjct: 118 ILNPFKENYMAKDAHKLDVAYMQECATVLIGTHDFTSFTSNKIDPRKPRVKTITRLEVLQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + +      FL   +R    +L   G  + T  D++K L+A+D+  C   A P+GL
Sbjct: 178 EKDHVHMIFEGNGFLRYMVRMLSQTLIEAGKHRITKADIKKMLEAKDKHACRYKAVPQGL 237

Query: 240 YFDSVEYS 247
           Y   V+Y+
Sbjct: 238 YLVRVDYA 245


>gi|237786326|ref|YP_002907031.1| tRNA pseudouridine synthase A [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237759238|gb|ACR18488.1| tRNA pseudouridine synthase A [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 298

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 92/262 (35%), Positives = 127/262 (48%), Gaps = 21/262 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW RQ +  S+QG IE+A   V  + V +  AGRTD+GVHA  Q
Sbjct: 22  LVRLRLDIAYDGTDFHGWARQNDVRSVQGDIEQAFQTVVRQPVQLVVAGRTDAGVHASGQ 81

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+ R  +        P  L       L+    + I   S     F ARFSA+RR Y
Sbjct: 82  VAHVDIPRGILNTRSIHNDPSTLVSRFARLLRPD--VRIRGCSFAPDGFDARFSALRRHY 139

Query: 113 LYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YR+ T +A   P        W  P +LD  +M  AA+ LVG HDF  F      A++ I
Sbjct: 140 VYRVTTNRAGALPTRARDTAVWDRPVNLD--SMNNAAEVLVGLHDFAAFCRARPHATT-I 196

Query: 170 RTIDHFDVNSFGNLI-----EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           R + HF  +     +     E RV A +F    +RS VG+   VG+GK     +E  L  
Sbjct: 197 RDLQHFSWHEVSTAVEPDVYEARVTADAFCWNMVRSIVGASLAVGEGKRPDGFMEDMLAH 256

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
             R    P+AP  GL    V+Y
Sbjct: 257 DSRHPMVPVAPANGLTLTGVDY 278


>gi|228931644|ref|ZP_04094550.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228828072|gb|EEM73800.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 252

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   + I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PNDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|294464718|gb|ADE77866.1| unknown [Picea sitchensis]
          Length = 382

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 72/188 (38%), Positives = 110/188 (58%), Gaps = 13/188 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + ++Y G+ + G Q+Q N  ++QG +E A     G+ V    + RTD+GVHAL  V 
Sbjct: 30  RYLVAVDYIGTNFAGMQKQPNFRTVQGVLEDAFNKFIGQPVSSASSSRTDAGVHALTNVC 89

Query: 63  HFDLVR-----------EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L K +  ISI+++  V   FHAR+ A  R
Sbjct: 90  HVDVERISKRKPGEVLPPHEPEVVKRAVNHFLQKDAGDISIIDVRFVPMTFHARYRAQER 149

Query: 111 SYLYRIITRQAPLAL-EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YRI++ + PL++ EK RAW +P+ L    M+ A + LVG HDF++FR+  CQA SPI
Sbjct: 150 TYYYRILSGKEPLSIFEKDRAWHVPEDLGLSCMQEACKVLVGHHDFSSFRASGCQAKSPI 209

Query: 170 RTIDHFDV 177
           + +D   V
Sbjct: 210 KILDELRV 217



 Score = 51.6 bits (122), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 37/57 (64%)

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           A+SFL+ Q+R  VG+LK VG GK +  D+E  L+A+      P+AP  GLY  +V+Y
Sbjct: 311 AQSFLYHQVRLLVGTLKCVGTGKLSVDDVESILKARTITVAPPMAPACGLYLAAVKY 367


>gi|258406231|ref|YP_003198973.1| tRNA pseudouridine synthase A [Desulfohalobium retbaense DSM 5692]
 gi|257798458|gb|ACV69395.1| tRNA pseudouridine synthase A [Desulfohalobium retbaense DSM 5692]
          Length = 254

 Score =  132 bits (333), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 87/256 (33%), Positives = 126/256 (49%), Gaps = 18/256 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y G+ + GWQ Q    ++QG +E A   +    + VHGAGRTDSGVHA+ Q
Sbjct: 1   MPRLKLVVAYTGTHFAGWQLQPRDRTVQGCLEDAFATLCQHPLRVHGAGRTDSGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-- 118
           V H D+  E   +   KALNA L     I++   + V   FHARFSA  + Y Y I T  
Sbjct: 61  VCHCDIPPEKNHIPWQKALNAIL--PKDIAVCEAAYVRDDFHARFSAQAKEYAYTIWTEP 118

Query: 119 -----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
                ++ PL    GR       +D   M +AA+ L G  DF  F++     S  +RT+ 
Sbjct: 119 RYVLPQRRPLVWSVGR-------VDEHKMAVAARMLTGTFDFAAFQNTGTPVSHTVRTVY 171

Query: 174 HF--DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           H   +  + GN       A  FL   +R+ +G L  VG  K +  +++  L+ Q R+   
Sbjct: 172 HLAPEPGAAGNESTWLFHADGFLKQMVRNIMGCLVAVGRNKISVDEVKILLEGQKREMAP 231

Query: 232 PLAPPEGLYFDSVEYS 247
             APP+GL    V+Y 
Sbjct: 232 ATAPPQGLCLRKVKYG 247


>gi|167770549|ref|ZP_02442602.1| hypothetical protein ANACOL_01895 [Anaerotruncus colihominis DSM
           17241]
 gi|167667144|gb|EDS11274.1| hypothetical protein ANACOL_01895 [Anaerotruncus colihominis DSM
           17241]
          Length = 246

 Score =  132 bits (333), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 121/247 (48%), Gaps = 14/247 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I Y G+ Y G+Q Q+N  ++  +++ A+  + GE + + G  RTD+GVHA      F 
Sbjct: 6   LTIRYRGTRYHGYQVQQNAVTVAQTVQDAVERIFGERLPIKGCSRTDAGVHA----NCFA 61

Query: 66  LVREWVPVILC----KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII--TR 119
           L      V+ C    +A+N +L  SD I++     V + FH R+    + YLYRI   T 
Sbjct: 62  LTLRTASVMACDAVVRAMNVHLP-SD-IAVTGCREVPEAFHPRYDCKGKRYLYRIYNGTV 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P + +    W  P  LD   M  AAQ  VG HDF  F S        +RT+    V  
Sbjct: 120 RDPFSADLALFWKYP--LDERRMDAAAQGFVGTHDFAAFCSSGSGVQDTVRTVTDASVTR 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   V    FL+  +R  VG+L     G +T  D+   L+ +DR   GP APP GL
Sbjct: 178 HGDFVIYSVTGNGFLYNMVRIMVGTLLEAARGVYTPADVLHMLEGRDRSAAGPTAPPHGL 237

Query: 240 YFDSVEY 246
           Y D+V Y
Sbjct: 238 YLDAVFY 244


>gi|189461835|ref|ZP_03010620.1| hypothetical protein BACCOP_02501 [Bacteroides coprocola DSM 17136]
 gi|189431429|gb|EDV00414.1| hypothetical protein BACCOP_02501 [Bacteroides coprocola DSM 17136]
          Length = 252

 Score =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 127/250 (50%), Gaps = 10/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA-IFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + + Y+G+ Y GWQ Q NG+S+Q ++ +A I  +  + + V GAGRTD+GVHA  
Sbjct: 1   MFRYFIYLAYDGANYHGWQIQPNGNSVQETLTRALITFLRDDAIEVTGAGRTDAGVHARL 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            VAHFD+ R    ++ C ++   L   +   IS+  +  V +  H RF A  R+Y Y I 
Sbjct: 61  MVAHFDIER----MLDCDSVTDKLNRLLPPDISVYQVRRVRQDAHTRFDATYRTYKYYIT 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           TR+ P    +  AW + +SLD + M  AA+ L    DFT+F  +H    +    I H   
Sbjct: 117 TRKDP--FNRNYAWRVFQSLDFDKMNEAAKVLFEYTDFTSFSKLHTDVKTNNCRIMHARW 174

Query: 178 NSFGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              G    +  + A  FL   +R+ VG+L  VG GK T     K ++ ++R   G   P 
Sbjct: 175 EQIGEDEWVFTIQADRFLRNMVRAVVGTLVEVGRGKLTVEGFRKVIEEKNRCSAGTSVPG 234

Query: 237 EGLYFDSVEY 246
             L+   + Y
Sbjct: 235 HALFLVDIGY 244


>gi|226357340|ref|YP_002787080.1| tRNA-pseudouridine synthase I [Deinococcus deserti VCD115]
 gi|226319330|gb|ACO47326.1| putative tRNA-pseudouridine synthase I (tRNA pseudouridylate
           synthase I) (tRNA-uridine isomerase) [Deinococcus
           deserti VCD115]
          Length = 266

 Score =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 118/247 (47%), Gaps = 6/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + ++G  Y GWQ Q N  S+Q ++  A   +         AGRTD+GVHA     
Sbjct: 19  RLRLTLAWDGGPYAGWQSQPNAPSVQDTLHAAFGRLGSGAFRPVAAGRTDAGVHAEAMPV 78

Query: 63  HFDLVREW-VPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           H D+   + VP   L +ALNA+L  S  +S+L        FHARFS   R Y+YR++   
Sbjct: 79  HVDVPGGFRVPAPKLARALNAWLPPS--VSVLEAFDAPAGFHARFSCTERRYVYRLLVSS 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  GRA  +P +LD   M  AA +L G HDF  F +   + +  +R +    V   
Sbjct: 137 QRHPLWHGRALHLPGALDAGAMNAAATYLTGTHDFAAFATQEDRQT--VRELRVLRVVPE 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G + E++V   SFL   +R  VG+L L G GK     +   L  + R + G   P  GLY
Sbjct: 195 GPVWEVQVTGESFLRHMVRGLVGTLLLCGQGKLEPLAVRDVLAHRQRSQAGANVPAYGLY 254

Query: 241 FDSVEYS 247
           F    Y 
Sbjct: 255 FTGASYP 261


>gi|42779223|ref|NP_976470.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10987]
 gi|51316699|sp|Q73F64|TRUA1_BACC1 RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|42735138|gb|AAS39078.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10987]
          Length = 247

 Score =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 123/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 61  QVIHFDTPLSLEEWQ---WNNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 115

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   +
Sbjct: 116 LLSKTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 175

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 176 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 235

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 236 HGLYLWQVNYN 246


>gi|327438309|dbj|BAK14674.1| pseudouridylate synthase [Solibacillus silvestris StLB046]
          Length = 249

 Score =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 83/253 (32%), Positives = 131/253 (51%), Gaps = 14/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+R    I Y+G+G+ G+Q Q    ++Q  IEK +  +  G  V +  +GRTD+ VHA  
Sbjct: 1   MVRLKTTISYDGTGFAGYQVQPGERTVQLEIEKVLTTMQKGTQVKITASGRTDARVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF--SAIRRSYLYRII 117
           QV HFD   E  P    KALN  +++   I +L++  V + FHAR+  S  R  Y++   
Sbjct: 61  QVIHFDTALEIPPEKFQKALN--VQLPRDIRVLHMEQVKEDFHARYDVSGKRYRYIWDCS 118

Query: 118 TRQAPL----ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           T Q+P      +E G         + E MR AA+ +VG HDF+ F + +      +RT++
Sbjct: 119 TVQSPFRRHYTVETGGV-----KPNVEAMREAAKAIVGTHDFSCFCAANTSVVDKVRTVE 173

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             ++   G  + + +    FL+  +R   G+L  VG G+  ++ LEK + + DR + G  
Sbjct: 174 TLELVWQGEELHMTISGNGFLYNMVRIIAGTLWEVGIGRREASSLEKTIASMDRAQAGKT 233

Query: 234 APPEGLYFDSVEY 246
           AP  GLY + V Y
Sbjct: 234 APAHGLYLEQVFY 246


>gi|46199569|ref|YP_005236.1| tRNA pseudouridine synthase A [Thermus thermophilus HB27]
 gi|55981600|ref|YP_144897.1| tRNA pseudouridine synthase A [Thermus thermophilus HB8]
 gi|51316686|sp|Q72I65|TRUA_THET2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901217|sp|Q5SHU9|TRUA_THET8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46197195|gb|AAS81609.1| tRNA pseudouridine synthase A [Thermus thermophilus HB27]
 gi|55773013|dbj|BAD71454.1| tRNA pseudouridine synthase A (pseudouridylate synthase I) [Thermus
           thermophilus HB8]
          Length = 253

 Score =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 127/251 (50%), Gaps = 8/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ  G  ++QG +E+A+  + G +     AGRTD+GVHAL 
Sbjct: 1   MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGI-GALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
              H D V   +PV  + +ALN  L   + + ++    V   FHAR  A+ R+Y YRI+ 
Sbjct: 60  MPFHVD-VESAIPVEKVPEALNRLL--PEDLKVVGAREVAPDFHARKDALWRAYRYRILV 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R  P  L + RA  + + LD E M  A   L+GRH+F  F     +            V 
Sbjct: 117 RPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVA 176

Query: 179 SFGNLIEIRVVAR--SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                +E+R+  R  SFL  Q+R  VG+L  VG GK     L+  L+  DR+  GP AP 
Sbjct: 177 EGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPA 236

Query: 237 EGLYFDSVEYS 247
            GLYF    Y 
Sbjct: 237 HGLYFVEAAYP 247


>gi|229074203|ref|ZP_04207249.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-18]
 gi|228708973|gb|EEL61100.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-18]
          Length = 252

 Score =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIFEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNIGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|291459136|ref|ZP_06598526.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
 gi|291418390|gb|EFE92109.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
          Length = 252

 Score =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 126/250 (50%), Gaps = 9/250 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAI---FLVTGEI---VVVHGAGRTDSGVH 56
           Y ++I Y+GS Y GW+RQ     +IQG IE  +    L  G++   V + GAGRTD+GVH
Sbjct: 5   YKLLISYDGSRYLGWERQPGIDRTIQGKIEAVLSRMLLAEGKLQQPVDLIGAGRTDAGVH 64

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A    A+  L  +     +   LN YL   D IS+  LSI  K+FHAR+ AI + Y Y  
Sbjct: 65  ARGMCANVFLDSKRSEGEIRAYLNRYL--PDDISVDALSICGKRFHARYHAIGKLYRYSC 122

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +     E+    ++P+  D E MR+AA+ L+G  D+ +F        S +R ID  +
Sbjct: 123 YFGEKKPVFERKYLLILPEMPDVERMRLAAEALIGEKDYRSFCGNPRMKKSTLRRIDRIE 182

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +      I        FL  QIR  VG+L  +G GK    D+E+ L A+DR + G  A  
Sbjct: 183 ILERKGCIRFYFHGNGFLQHQIRIMVGTLLEIGLGKREPGDMERILLAKDRSQAGYTAEA 242

Query: 237 EGLYFDSVEY 246
            GL    VEY
Sbjct: 243 GGLCLMRVEY 252


>gi|163816114|ref|ZP_02207482.1| hypothetical protein COPEUT_02298 [Coprococcus eutactus ATCC 27759]
 gi|158448534|gb|EDP25529.1| hypothetical protein COPEUT_02298 [Coprococcus eutactus ATCC 27759]
          Length = 271

 Score =  132 bits (331), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 81/273 (29%), Positives = 126/273 (46%), Gaps = 28/273 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGE------------------ 41
           M  Y     Y+G+ Y GW+ + N  +++G IE  +  +V G+                  
Sbjct: 1   MTNYRFTFSYDGTRYHGWESKTNADTVEGRIEAVLSKMVDGDNGKTADVCRENMSADIRD 60

Query: 42  -----IVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSI 96
                 V +HGAGRTD+GVHA   VA   L     P  +   LN YL     I  L++++
Sbjct: 61  TKTPAKVDIHGAGRTDAGVHARAMVASGRLNTNRTPDEIKDYLNRYLPAD--ICALDVTV 118

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHD 154
              +FHAR +A  + Y Y +         ++   W +P+   LD + M+ AA +LVG+HD
Sbjct: 119 AGDRFHARLNATGKIYEYTLYVGLEKPVFDRNYVWCVPQGSVLDVDAMKKAASYLVGKHD 178

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           F +F   +    S +RTI   ++   G+ + +R     FL   +R   G+L  +G G   
Sbjct: 179 FRSFCGNNKMKKSTVRTIYDVEIVKEGDYVRMRFHGNGFLQNMVRILTGTLVEIGYGHMD 238

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  + + +   DR+  GP APP GL    VEY 
Sbjct: 239 AEHMPEIIVGMDRQLAGPTAPPHGLCLLKVEYD 271


>gi|122919612|pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua
           From Thermus Thermophilus Hb8
 gi|122919613|pdb|1VS3|B Chain B, Crystal Structure Of The Trna Pseudouridine Synthase Trua
           From Thermus Thermophilus Hb8
          Length = 249

 Score =  132 bits (331), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 127/251 (50%), Gaps = 8/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ  G  ++QG +E+A+  + G +     AGRTD+GVHAL 
Sbjct: 1   MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGI-GALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
              H D V   +PV  + +ALN  L   + + ++    V   FHAR  A+ R+Y YRI+ 
Sbjct: 60  MPFHVD-VESAIPVEKVPEALNRLL--PEDLKVVGAREVAPDFHARKDALWRAYRYRILV 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R  P  L + RA  + + LD E M  A   L+GRH+F  F     +            V 
Sbjct: 117 RPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVA 176

Query: 179 SFGNLIEIRVVAR--SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                +E+R+  R  SFL  Q+R  VG+L  VG GK     L+  L+  DR+  GP AP 
Sbjct: 177 EGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPA 236

Query: 237 EGLYFDSVEYS 247
            GLYF    Y 
Sbjct: 237 HGLYFVEAAYP 247


>gi|228905939|ref|ZP_04069836.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 200]
 gi|228853754|gb|EEM98514.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 200]
          Length = 252

 Score =  132 bits (331), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPNSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|46445962|ref|YP_007327.1| putative tRNA pseudouridylate synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
 gi|51316632|sp|Q6MEE7|TRUA1_PARUW RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|46399603|emb|CAF23052.1| putative tRNA pseudouridylate synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 256

 Score =  132 bits (331), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 133/249 (53%), Gaps = 8/249 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + I Y+G+ Y GWQ Q N SSIQ  I++A+  L+  E VV+ G+GRTD+GVHA  QVA
Sbjct: 4   YKLTIAYDGTNYSGWQIQPNASSIQQKIQEALCILLKKEKVVLVGSGRTDAGVHAKGQVA 63

Query: 63  HFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HF   ++++ +  L  +LN  L     I I  +  V  +FH+++SAIR+ Y Y +   + 
Sbjct: 64  HFHF-QDYIDLSRLHVSLNGLL--PRDIRIKAVEPVSPRFHSQYSAIRKEYHYYLHLNKV 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIH--CQASSPIRTIDHFDVN 178
               ++  +W   + +D   ++ AA    G HDFT+F    H    A +P+RT+   D+ 
Sbjct: 121 MDPFQRLYSWHFQRKIDVNILKKAAILFTGTHDFTSFANEAHRGTAAKNPVRTLYRLDIK 180

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + +      FL+  +R+ VG+L  V   K    ++ +   A++R++    APPEG
Sbjct: 181 PNEGGLRLEFEGDGFLYKMVRNIVGTLMDVASHKRAIEEINQIFAAKNRRQASLAAPPEG 240

Query: 239 LYFDSVEYS 247
           L+   V Y 
Sbjct: 241 LFLIQVFYE 249


>gi|149370146|ref|ZP_01889997.1| tRNA pseudouridine synthase A [unidentified eubacterium SCB49]
 gi|149356637|gb|EDM45193.1| tRNA pseudouridine synthase A [unidentified eubacterium SCB49]
          Length = 259

 Score =  132 bits (331), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 83/246 (33%), Positives = 124/246 (50%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I YNG+ Y GWQ+Q +  ++Q  IE  +  V  + V   GAGRTD+GVHA +  
Sbjct: 7   LRYFLEIAYNGAKYCGWQKQPDAKTVQQEIEYFLSTVLRQDVTTMGAGRTDTGVHARQMF 66

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD+ +   +P  L KA N++L     IS+LN   V    HARF+AI R Y Y +   +
Sbjct: 67  LHFDVSKSISIPNFLYKA-NSFLP--PDISVLNYYEVLDDHHARFNAIAREYEYYVSVVK 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P +++   A+ +    D   M  AA  L+   DF +F  +  +  +    +   +    
Sbjct: 124 DPFSIDS--AYYLKNFPDINLMNEAASSLLTYSDFQSFSKVRTEVKTFNCNVTKAEWILN 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN++   + A  FL   +RS VG+L  VG GK T  D    + +++R   G   P  GLY
Sbjct: 182 GNMLIFTISADRFLRNMVRSIVGTLLEVGSGKITIEDFHNIIASKNRSNAGISVPAHGLY 241

Query: 241 FDSVEY 246
              V Y
Sbjct: 242 LTKVIY 247


>gi|150008550|ref|YP_001303293.1| tRNA pseudouridine synthase A [Parabacteroides distasonis ATCC
           8503]
 gi|255014350|ref|ZP_05286476.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_7]
 gi|166228743|sp|A6LDA7|TRUA_PARD8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|149936974|gb|ABR43671.1| tRNA pseudouridine synthase A [Parabacteroides distasonis ATCC
           8503]
          Length = 252

 Score =  132 bits (331), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 124/252 (49%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++    V + GAGRTD+GVHA   
Sbjct: 1   MRRYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRTPVPIVGAGRTDAGVHAHLM 60

Query: 61  VAHFDLVREWVP-----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           +AHFD    W       V L + LN  L     I++  +  V  + HARF A  R+Y Y 
Sbjct: 61  IAHFD----WEEPIGDLVFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYY 114

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           + T++ P   E    + +P  LD E M  A + L    DFT+F  +H    +    I H 
Sbjct: 115 VTTKKDPFNHE--LVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHA 172

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P
Sbjct: 173 GWTQEGDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVP 232

Query: 236 PEGLYFDSVEYS 247
              L+   V Y 
Sbjct: 233 GHALFLVDVTYP 244


>gi|218895277|ref|YP_002443688.1| tRNA pseudouridine synthase A [Bacillus cereus G9842]
 gi|218542262|gb|ACK94656.1| tRNA pseudouridine synthase A [Bacillus cereus G9842]
          Length = 252

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    I Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTIAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|293977793|ref|YP_003543223.1| pseudouridylate synthase I [Candidatus Sulcia muelleri DMIN]
 gi|292667724|gb|ADE35359.1| pseudouridylate synthase I [Candidatus Sulcia muelleri DMIN]
          Length = 250

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 131/247 (53%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + I Y+G+ ++GWQ QK   S+Q +IE  +  +  + + + GAGRTD+GVHA++  
Sbjct: 1   MRFFLEISYHGASFYGWQIQKKNISVQETIENCLSFLLKKSIKIIGAGRTDTGVHAIQMF 60

Query: 62  AHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHF+   + + +       LN++L ++  I I+N+  V K+ HARF+AI R Y YRI   
Sbjct: 61  AHFEFYEKKILLYRNFLFKLNSFLPLN--IKIINIFPVKKKIHARFTAISRVYEYRISLG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P +L     WL  + +  + +   A+ L    D+++F    C   + I  I +   + 
Sbjct: 119 KNPFSL--SWQWLSKQKIKLKPLNKGAKILKKYKDYSSFCKKKCNYKTYICNIFNAKWHI 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N++   + A  +L   +RS VG+L  +G GK T  D    L A+DR      AP +GL
Sbjct: 177 KNNILYFNIEANRYLRNMVRSIVGTLIELGIGKITIKDFINILYAKDRNLALISAPAKGL 236

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 237 FLTKINY 243


>gi|307719509|ref|YP_003875041.1| hypothetical protein STHERM_c18330 [Spirochaeta thermophila DSM
           6192]
 gi|306533234|gb|ADN02768.1| hypothetical protein STHERM_c18330 [Spirochaeta thermophila DSM
           6192]
          Length = 248

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 125/242 (51%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++ Y+G+ + GWQRQ NG S+QG +E A+  +    V VH AGRTDSGVHA+ Q  +F 
Sbjct: 8   VVLAYDGTDFVGWQRQPNGRSVQGVVEDALARMHKHPVHVHAAGRTDSGVHAVGQCINFI 67

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              + +PV     ALN++L     +  L    V   FHAR+SA+RR Y Y +    +P  
Sbjct: 68  TDIDSLPVEKFALALNSFLP--RDVKALQAEEVPPDFHARYSAVRREYRYYVFPSPSPYP 125

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  +  + +  D   +   A  +VG HDF++F S    + S +R I        G+ +
Sbjct: 126 HLRRYSLWVNRLPDVRLLNAYASCIVGEHDFSSFCSPSDPSPSKVRLIHTASWFPEGSQL 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+V  +FL   +R+ VG++  +   K     + K L+A+DR      AP  GL+   V
Sbjct: 186 VFRIVGNAFLWRMVRALVGTMLDLEKQKADPEMMRKILEARDRSAASDSAPAWGLFLHEV 245

Query: 245 EY 246
           +Y
Sbjct: 246 QY 247


>gi|257790805|ref|YP_003181411.1| tRNA pseudouridine synthase A [Eggerthella lenta DSM 2243]
 gi|257474702|gb|ACV55022.1| tRNA pseudouridine synthase A [Eggerthella lenta DSM 2243]
          Length = 255

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 129/255 (50%), Gaps = 21/255 (8%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + YNG+ + G+ RQ   +++QG +E A+ ++    V    AGRTD+GVHAL QV  FD
Sbjct: 8   LTLSYNGAPFSGFARQPGQTTVQGDLEDALRMLFRRDVETTCAGRTDAGVHALGQVVSFD 67

Query: 66  -----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                +    +P  L ++LNA     D I++  +      F ARF A  R Y Y +    
Sbjct: 68  VDDRDIAGRSLPS-LRRSLNAL--THDAITVREVEPKKLGFSARFDAQAREYHYHLCVDS 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 K  +W +P  LD   M   AQ+L+G HDF +F    C A+S      H +V   
Sbjct: 125 TCPIFMKDFSWFVPGGLDITAMEAGAQYLLGEHDFKSF----CMAASAEGKPTHRNVREI 180

Query: 181 G---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                     NL+ I+VV  +FLH+ +R+ VG+L +VG G+  +  + + L+A DR+  G
Sbjct: 181 SFHPETVMGENLMSIKVVGNAFLHSMVRTIVGTLVMVGKGQRDADWVGEVLEACDRRVAG 240

Query: 232 PLAPPEGLYFDSVEY 246
             AP +GL F  V Y
Sbjct: 241 ENAPAQGLVFWRVIY 255


>gi|116331308|ref|YP_801026.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116124997|gb|ABJ76268.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 265

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 134/249 (53%), Gaps = 15/249 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y +++EY+G  + G+Q QK+  SIQ ++EKAI ++  E + + GAGRTD+GVHA   V
Sbjct: 1   MNYALLVEYDGLCFNGFQTQKDLPSIQENLEKAIKILLKEEISITGAGRTDTGVHARGMV 60

Query: 62  AHFDLVREWVPVILCKALNAYL----KISDT-ISILNLSIVDKQFHARFSAIRRSYLYRI 116
            +F  ++        +  N +L     I+D+ +SIL ++ V + F +RFS   R Y Y I
Sbjct: 61  VNFKTIKT------VQNFNKFLLSMNAITDSGLSILGMTEVGENFDSRFSCNSREYEYLI 114

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHF 175
           +  + P  + K RA+     +D   ++   + L G HDF +  ++   +  S IRTI   
Sbjct: 115 LNTKYPRPIWKNRAFWYQHKIDVPRLKTELELLKGEHDFRSLAKTASMKDRSTIRTILDA 174

Query: 176 DV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            +   + +  L++I++ A  FLH  IR   G+L  + +GK    ++   L ++DR   G 
Sbjct: 175 KLERSSEWEGLLKIKIRANGFLHNMIRILTGTLLEIANGKLKVPNILDILSSKDRTIAGI 234

Query: 233 LAPPEGLYF 241
             PP GLYF
Sbjct: 235 TLPPYGLYF 243


>gi|317488484|ref|ZP_07947035.1| tRNA pseudouridine synthase A [Eggerthella sp. 1_3_56FAA]
 gi|316912416|gb|EFV33974.1| tRNA pseudouridine synthase A [Eggerthella sp. 1_3_56FAA]
          Length = 280

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 129/255 (50%), Gaps = 21/255 (8%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + YNG+ + G+ RQ   +++QG +E A+ ++    V    AGRTD+GVHAL QV  FD
Sbjct: 33  LTLSYNGAPFSGFARQPGQTTVQGDLEDALRMLFRRDVETTCAGRTDAGVHALGQVVSFD 92

Query: 66  -----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                +    +P  L ++LNA     D I++  +      F ARF A  R Y Y +    
Sbjct: 93  VDDRDIAGRSLPS-LRRSLNAL--THDAITVREVEPKKLGFSARFDAQAREYHYHLCVDS 149

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 K  +W +P  LD   M   AQ+L+G HDF +F    C A+S      H +V   
Sbjct: 150 TCPIFMKDFSWFVPGGLDITAMEAGAQYLLGEHDFKSF----CMAASAEGKPTHRNVREI 205

Query: 181 G---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                     NL+ I+VV  +FLH+ +R+ VG+L +VG G+  +  + + L+A DR+  G
Sbjct: 206 SFHPETVMGENLMSIKVVGNAFLHSMVRTIVGTLVMVGKGQRDADWVGEVLEACDRRVAG 265

Query: 232 PLAPPEGLYFDSVEY 246
             AP +GL F  V Y
Sbjct: 266 ENAPAQGLVFWRVIY 280


>gi|325832022|ref|ZP_08165119.1| tRNA pseudouridine synthase A [Eggerthella sp. HGA1]
 gi|325486343|gb|EGC88795.1| tRNA pseudouridine synthase A [Eggerthella sp. HGA1]
          Length = 284

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 129/255 (50%), Gaps = 21/255 (8%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + YNG+ + G+ RQ   +++QG +E A+ ++    V    AGRTD+GVHAL QV  FD
Sbjct: 37  LTLSYNGAPFSGFARQPGQTTVQGDLEDALRMLFRRDVETTCAGRTDAGVHALGQVVSFD 96

Query: 66  -----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                +    +P  L ++LNA     D I++  +      F ARF A  R Y Y +    
Sbjct: 97  VDDRDIAGRSLPS-LRRSLNAL--THDAITVREVEPKKLGFSARFDAQAREYHYHLCVDS 153

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 K  +W +P  LD   M   AQ+L+G HDF +F    C A+S      H +V   
Sbjct: 154 TCPIFMKDFSWFVPGGLDITAMEAGAQYLLGEHDFKSF----CMAASAEGKPTHRNVREI 209

Query: 181 G---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                     NL+ I+VV  +FLH+ +R+ VG+L +VG G+  +  + + L+A DR+  G
Sbjct: 210 SFHPETVMGENLMSIKVVGNAFLHSMVRTIVGTLVMVGKGQRDADWVGEVLEACDRRVAG 269

Query: 232 PLAPPEGLYFDSVEY 246
             AP +GL F  V Y
Sbjct: 270 ENAPAQGLVFWRVIY 284


>gi|229015543|ref|ZP_04172540.1| tRNA pseudouridine synthase A [Bacillus cereus AH1273]
 gi|229021754|ref|ZP_04178334.1| tRNA pseudouridine synthase A [Bacillus cereus AH1272]
 gi|228739541|gb|EEL89957.1| tRNA pseudouridine synthase A [Bacillus cereus AH1272]
 gi|228745766|gb|EEL95771.1| tRNA pseudouridine synthase A [Bacillus cereus AH1273]
          Length = 252

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLAEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|163938150|ref|YP_001643034.1| tRNA pseudouridine synthase A [Bacillus weihenstephanensis KBAB4]
 gi|163860347|gb|ABY41406.1| tRNA pseudouridine synthase A [Bacillus weihenstephanensis KBAB4]
          Length = 252

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 126/251 (50%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q +  ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGIHFCGYQIQPHHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN+ L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNSML--PDDIIIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|319952056|ref|YP_004163323.1| tRNA pseudouridine synthase a [Cellulophaga algicola DSM 14237]
 gi|319420716|gb|ADV47825.1| tRNA pseudouridine synthase A [Cellulophaga algicola DSM 14237]
          Length = 250

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 129/247 (52%), Gaps = 8/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G  Y GWQ+Q N  ++QG +E A+  +    +++ GAGRTD+GVHA    
Sbjct: 1   MRYFIRFSYFGKHYHGWQKQPNAVTVQGVLEDALSKLLANEIILMGAGRTDAGVHAKELY 60

Query: 62  AHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHFD   E +P        LNA+L     I+IL++  V +  HARF+A+ R+Y Y I+ +
Sbjct: 61  AHFDF--EEIPNKENFVFRLNAFL--PKDIAILDVFQVPEDAHARFNAVARTYEYWIVQQ 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P       A LI   LD   M  AAQ  +   DF  F   +   ++    + + +   
Sbjct: 117 KNPFL--TNHAHLIKYPLDINKMNEAAQVFLSHIDFECFSKSNTAVNTFNCDVKYAEWKV 174

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              ++   + A  FL   +R+ VG+L  VG GK   ++++  L+++DR + G  AP +GL
Sbjct: 175 TDGILVFTITADRFLRNMVRAIVGTLLEVGLGKIDISNVKAILKSKDRSKAGASAPAKGL 234

Query: 240 YFDSVEY 246
           Y  SV Y
Sbjct: 235 YLTSVLY 241


>gi|317126894|ref|YP_004093176.1| tRNA pseudouridine synthase A [Bacillus cellulosilyticus DSM 2522]
 gi|315471842|gb|ADU28445.1| tRNA pseudouridine synthase A [Bacillus cellulosilyticus DSM 2522]
          Length = 260

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R   I+ Y+G+ Y G+Q Q +  +IQ  +EKA+  +   +   V  +GRTD+GVH+L 
Sbjct: 1   MKRVKGIVTYDGTKYSGYQVQVDKKTIQAELEKALAKIHKADSWNVVSSGRTDTGVHSLG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           +A N  L   D I + +L  V   FHARF ++ + Y+Y++ T 
Sbjct: 61  QTIHFDTSLSIPEERWPQAFNRLL--PDDIQVRDLQYVHHDFHARFDSVGKKYVYKVNTA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++   +  P  L  E M  AA HL G HDFT+F S        +RTI   ++  
Sbjct: 119 REKDIFKRNFVYHHPYVLSYEKMLEAAMHLEGTHDFTSFSSPRTDVIDKVRTIYAIELEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+      +   FL+  +R   G+L  VG GK    ++ +  + +DR   GP  P  GL
Sbjct: 179 NGDEWTFTYIGNGFLYQMVRVLTGTLLHVGKGKIRPEEIPEIFEGKDRSLAGPSIPGTGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLTNVYYD 246


>gi|262383400|ref|ZP_06076536.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_33B]
 gi|262294298|gb|EEY82230.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_33B]
          Length = 265

 Score =  131 bits (330), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 86/250 (34%), Positives = 122/250 (48%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG  + GWQ Q NG ++Q SIE+A+  +  + V + GAGRTD+GVHA   +A
Sbjct: 16  RYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALATLMRKPVPIVGAGRTDAGVHARLMIA 75

Query: 63  HFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD    W   I     L + LN  L     I++  +  V  + HARF A  R+Y Y I 
Sbjct: 76  HFD----WEGPIEDLAFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYIT 129

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           TR+ P   E    +  P  LD E M  A + L    DFT+F  +H    +    I H   
Sbjct: 130 TRKDPFNYE--LVYKFPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHAGW 187

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P  
Sbjct: 188 TQEGDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGH 247

Query: 238 GLYFDSVEYS 247
            L+   V Y 
Sbjct: 248 ALFLVDVTYP 257


>gi|326790769|ref|YP_004308590.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
 gi|326541533|gb|ADZ83392.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
          Length = 246

 Score =  131 bits (330), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 122/248 (49%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y + I Y+GS Y G+Q+Q      +IQG +E  +     E + +  +GRTD+GVH+ 
Sbjct: 1   MTNYKLTIAYDGSKYNGFQKQSKHPEKTIQGRLENVLTQCFEEDIQIIASGRTDAGVHSK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV +F       P  +   L+ YL     I+IL LSI   +FHAR++ +R+ Y Y I  
Sbjct: 61  GQVCNFHAEHYLEPTTVLNYLSNYL--PQDIAILELSIASPRFHARYNVLRKCYTYTIDN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                      A+ +   LD   M+ AA +L+G HDF  F S+  +  S  R + + D+ 
Sbjct: 119 GLFANPFTLKYAYHLASPLDISRMQAAANYLLGTHDFKAFTSLKSKTKSTTRHLFNIDIT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G++I++      FL   +R   G+L  VG G+ +  ++   L  Q R E G  AP  G
Sbjct: 179 QEGSMIKLTYEGNGFLQHMVRILTGTLIEVGLGERSPEEMLVLLNNQIRSEAGFTAPAHG 238

Query: 239 LYFDSVEY 246
           L    V+Y
Sbjct: 239 LCMQRVDY 246


>gi|21911175|ref|NP_665443.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS315]
 gi|28895139|ref|NP_801489.1| tRNA pseudouridine synthase A [Streptococcus pyogenes SSI-1]
 gi|25453306|sp|Q8K5W2|TRUA_STRP3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21905386|gb|AAM80246.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes
           MGAS315]
 gi|28810384|dbj|BAC63322.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes
           SSI-1]
          Length = 249

 Score =  131 bits (330), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ++  ++Q  IEK ++ L  G  +++HGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQRHLRTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I ++N+  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQEQEVEKLRFALDT--QTPEDIDVVNIEKVADDFHCRYQKHLKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +      P +L+ + M+ A   LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRHYTTHYPYTLNIKLMQDAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSR 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   + +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DEKTDFLVFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPTISGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>gi|203283942|ref|YP_002221682.1| pseudouridylate synthase I [Borrelia duttonii Ly]
 gi|203287485|ref|YP_002222500.1| pseudouridylate synthase I [Borrelia recurrentis A1]
 gi|238690561|sp|B5RLM0|TRUA_BORDL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690579|sp|B5RQJ5|TRUA_BORRA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|201083385|gb|ACH92976.1| pseudouridylate synthase I [Borrelia duttonii Ly]
 gi|201084705|gb|ACH94279.1| pseudouridylate synthase I [Borrelia recurrentis A1]
          Length = 245

 Score =  131 bits (330), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 80/240 (33%), Positives = 120/240 (50%), Gaps = 2/240 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    +IQG IEKA+  +    V +  AGRTD GVHA RQ+  F + 
Sbjct: 8   IAYDGSLYHGFQIQPTKPTIQGEIEKALEKINKTKVKIQSAGRTDKGVHAKRQIISFYIK 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L  A+N+ LK  + I I+ L  V  +F  RF A +R Y Y I+  +     E+
Sbjct: 68  ININLKNLKTAINSLLK--NDIRIIKLKYVSNEFQPRFHAKKRKYTYYILNNENHYPWEE 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A+ + K L+   +   A+ L+G HDFTTF  I  Q +S ++ I           I   
Sbjct: 126 YQAYYVRKKLNINRLNTMAEMLIGLHDFTTFSCIRDQTNSKLKEIYLAKFKKKNKFIVFE 185

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++  SFL   +RS VG++  +     +     K L++++RK     AP + L+ D V Y 
Sbjct: 186 IIGSSFLWKMVRSIVGTMIDIEIKNESVDTFIKILKSKNRKYARTTAPAKALFLDRVFYE 245


>gi|293369414|ref|ZP_06615999.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CMC 3f]
 gi|292635581|gb|EFF54088.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CMC 3f]
          Length = 267

 Score =  131 bits (330), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     ISI  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLLPPD--ISIYRVCRVRPDTHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +   +  + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 DDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRVIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEY 246
           +  +VEY
Sbjct: 237 FLVNVEY 243


>gi|15675714|ref|NP_269888.1| tRNA pseudouridine synthase A [Streptococcus pyogenes M1 GAS]
 gi|19746822|ref|NP_607958.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS8232]
 gi|50914971|ref|YP_060943.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10394]
 gi|71904268|ref|YP_281071.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS6180]
 gi|71911430|ref|YP_282980.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS5005]
 gi|94989250|ref|YP_597351.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS9429]
 gi|94991194|ref|YP_599294.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10270]
 gi|94993138|ref|YP_601237.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS2096]
 gi|94995068|ref|YP_603166.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10750]
 gi|139473113|ref|YP_001127828.1| tRNA pseudouridine synthase A [Streptococcus pyogenes str.
           Manfredo]
 gi|209560051|ref|YP_002286523.1| tRNA pseudouridine synthase A [Streptococcus pyogenes NZ131]
 gi|54039783|sp|P65851|TRUA_STRP8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54042088|sp|P65850|TRUA_STRP1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901238|sp|Q5XA03|TRUA_STRP6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122986813|sp|Q1J4W4|TRUA_STRPF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122986985|sp|Q1JF09|TRUA_STRPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123257716|sp|Q1J9W8|TRUA_STRPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123258127|sp|Q1JK16|TRUA_STRPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123775214|sp|Q48RE4|TRUA_STRPM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166229842|sp|A2RCK6|TRUA_STRPG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238057736|sp|B5XIG6|TRUA_STRPZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|13622931|gb|AAK34609.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes M1
           GAS]
 gi|19749059|gb|AAL98457.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes
           MGAS8232]
 gi|50904045|gb|AAT87760.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10394]
 gi|71803363|gb|AAX72716.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS6180]
 gi|71854212|gb|AAZ52235.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS5005]
 gi|94542758|gb|ABF32807.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS9429]
 gi|94544702|gb|ABF34750.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10270]
 gi|94546646|gb|ABF36693.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS2096]
 gi|94548576|gb|ABF38622.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10750]
 gi|134271359|emb|CAM29579.1| tRNA pseudouridine synthase A [Streptococcus pyogenes str.
           Manfredo]
 gi|209541252|gb|ACI61828.1| tRNA pseudouridine synthase A [Streptococcus pyogenes NZ131]
          Length = 249

 Score =  131 bits (330), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ++  ++Q  IEK ++ L  G  +++HGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQRHLRTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I ++N+  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQEQEVEKLRFALDT--QTPEDIDVVNIEKVADDFHCRYQKHLKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +      P +L+ + M+ A   LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRHYTTHYPYTLNIKLMQEAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSR 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   + +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DEKTDFLVFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPTISGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>gi|237711190|ref|ZP_04541671.1| tRNA pseudouridine synthase A [Bacteroides sp. 9_1_42FAA]
 gi|237727555|ref|ZP_04558036.1| tRNA pseudouridine synthase A [Bacteroides sp. D4]
 gi|229434411|gb|EEO44488.1| tRNA pseudouridine synthase A [Bacteroides dorei 5_1_36/D4]
 gi|229455034|gb|EEO60755.1| tRNA pseudouridine synthase A [Bacteroides sp. 9_1_42FAA]
          Length = 267

 Score =  131 bits (330), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 124/246 (50%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A      + + V GAGRTD+GVHA   V
Sbjct: 11  MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRAFSTFLRQEIEVVGAGRTDAGVHARLMV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +E   V + + LN  L  SD I++ ++  V    HARF A  R+Y Y +  R+ 
Sbjct: 71  AHFDYDQELDCVQITEKLNRLLP-SD-IAVYDVKRVKDDAHARFDATYRTYKYYVTIRKD 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
           P    +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I + +     
Sbjct: 129 P--FNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMYAEWTRVS 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T     K ++ +DR   G   P   L+
Sbjct: 187 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTLDGFRKVIENKDRCSAGSSVPGHALF 246

Query: 241 FDSVEY 246
              V Y
Sbjct: 247 LVDVGY 252


>gi|17231681|ref|NP_488229.1| tRNA pseudouridine synthase A [Nostoc sp. PCC 7120]
 gi|42559852|sp|Q8YPK5|TRUA_ANASP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|17133324|dbj|BAB75888.1| tRNA-pseudouridine synthase I [Nostoc sp. PCC 7120]
          Length = 282

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 88/250 (35%), Positives = 121/250 (48%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++++Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 12  RVALVVQYLGTHFHGWQRQKQHRTVQEEIETAIAKILGHHVTLHGAGRTDSGVHAAAQVA 71

Query: 63  HFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD        +W  VI     N+YL     I I   + V  ++HARFSA  R Y Y I 
Sbjct: 72  HFDATGLIPAHKWASVI-----NSYL--PKDILIKASAAVGDRWHARFSAAYRRYRYTIY 124

Query: 118 TRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           T   P       +W      LD   M+ A + L+G+H    F     + S     +   +
Sbjct: 125 TEDRPNLFVTPFSWHYYYAPLDESLMQAALKPLMGKHHLAAFHRAGSKRSHSWVEVQAVE 184

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +  G  I I + A  FL+  +R  VG L  VG G+ T  +  +  + Q R+E    AP 
Sbjct: 185 CHRSGPFIHIEIQADGFLYGMVRLLVGMLVQVGSGQRTLANFTELWKEQRREEVKHAAPS 244

Query: 237 EGLYFDSVEY 246
           +GL    V Y
Sbjct: 245 QGLCLLRVGY 254


>gi|295425622|ref|ZP_06818309.1| tRNA pseudouridine synthase A [Lactobacillus amylolyticus DSM
           11664]
 gi|295064638|gb|EFG55559.1| tRNA pseudouridine synthase A [Lactobacillus amylolyticus DSM
           11664]
          Length = 262

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 130/249 (52%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY M++ Y+G  + G+Q Q N  ++QG++E+A+  +T G+ V+V G+GRTD+GVHA+ QV
Sbjct: 4   RYKMLMAYDGHLFHGFQVQPNQRTVQGTVEEALKKMTKGKRVIVEGSGRTDAGVHAMGQV 63

Query: 62  AHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             FD     +P   +  ALN+ + +   I      I    FH R+S   + Y YR+    
Sbjct: 64  IQFDYPGNRIPAEKMILALNSMMPMD--IIFKECEIASPDFHVRYSIKGKWYRYRMSLDH 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  +D   M+ AA+ L+G+HDFT+F +   Q  + +RT+ + +V  N
Sbjct: 122 FVNPFKRFYTGHYPYPIDVSKMKEAAKDLLGKHDFTSFAASGGQIKNKVRTMYYVNVEKN 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N +    +   FL+  +R  V +L  +G GK    D  + ++A+DR +    AP  G
Sbjct: 182 ESQNELVFDFICSGFLYNMVRILVATLLEIGSGKRPVHDFPRIIKAKDRLQVTQTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLYHVFYD 250


>gi|306826655|ref|ZP_07459958.1| tRNA pseudouridine synthase A [Streptococcus pyogenes ATCC 10782]
 gi|304431103|gb|EFM34109.1| tRNA pseudouridine synthase A [Streptococcus pyogenes ATCC 10782]
          Length = 249

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ++  ++Q  IEK ++ L  G  +++HGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQRHLRTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I ++N+  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQEQEVEKLRFALDT--QTPEDIDVVNIKKVADDFHCRYQKHLKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +      P +L+ + M+ A   LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRHYTTHYPYTLNIKLMQEAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSR 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   + +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DEKTDFLVFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPTISGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>gi|313897268|ref|ZP_07830812.1| tRNA pseudouridine synthase A [Clostridium sp. HGF2]
 gi|312957989|gb|EFR39613.1| tRNA pseudouridine synthase A [Clostridium sp. HGF2]
          Length = 252

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 86/252 (34%), Positives = 125/252 (49%), Gaps = 12/252 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQRQ N  SIQ  IE A+  + G  + +  +GRTD+ VHAL Q
Sbjct: 1   MPRYKVTLSYDGTAYGGWQRQTNTHSIQQEIEAAMEKIEGNFIRITASGRTDAHVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           V HFD  ++  P    +ALN+ L     I I ++ +V+  FHARF A+ + Y Y I T  
Sbjct: 61  VFHFDSAKDLAPENWRRALNSLL--PHDIRIQDVCLVEDDFHARFHAVSKRYDYLITTDV 118

Query: 120 QAPL---ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHF 175
             P     + K R     K LD + M   A+  +G HDFT+F S       S ++TI   
Sbjct: 119 NNPFYYHYMGKDR-----KVLDVKRMSECARVFLGTHDFTSFTSSKLDPRKSKVKTITRL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D+    + + +      FL   +R    +L   G  +    D+++ L  QD+  C   A 
Sbjct: 174 DIVQEEHAVRLVFEGNGFLRYMVRMIAQTLIEAGKHRLDVADVKQMLYGQDKHLCRYKAQ 233

Query: 236 PEGLYFDSVEYS 247
            EGLY   V Y+
Sbjct: 234 AEGLYLVHVTYA 245


>gi|212694471|ref|ZP_03302599.1| hypothetical protein BACDOR_03999 [Bacteroides dorei DSM 17855]
 gi|265750782|ref|ZP_06086845.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_33FAA]
 gi|212662972|gb|EEB23546.1| hypothetical protein BACDOR_03999 [Bacteroides dorei DSM 17855]
 gi|263237678|gb|EEZ23128.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_33FAA]
          Length = 257

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 124/246 (50%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A      + + V GAGRTD+GVHA   V
Sbjct: 1   MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRAFSTFLRQEIEVVGAGRTDAGVHARLMV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +E   V + + LN  L  SD I++ ++  V    HARF A  R+Y Y +  R+ 
Sbjct: 61  AHFDYDQELDCVQITEKLNRLLP-SD-IAVYDVKRVKDDAHARFDATYRTYKYYVTIRKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
           P    +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I + +     
Sbjct: 119 P--FNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMYAEWTRVS 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T     K ++ +DR   G   P   L+
Sbjct: 177 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTLDGFRKVIENKDRCSAGSSVPGHALF 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LVDVGY 242


>gi|83591242|ref|YP_431251.1| tRNA pseudouridine synthase A [Moorella thermoacetica ATCC 39073]
 gi|123766692|sp|Q2RFT1|TRUA_MOOTA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83574156|gb|ABC20708.1| tRNA pseudouridine synthase A [Moorella thermoacetica ATCC 39073]
          Length = 246

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 88/248 (35%), Positives = 125/248 (50%), Gaps = 14/248 (5%)

Query: 6   MIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + Y+GS Y GWQ Q   +G ++QG +  A+  +TGE +    AGRTD+GVHA  QV  
Sbjct: 6   ITLAYDGSNYAGWQVQPEAHGPTVQGEVAAALKRLTGEEITPVAAGRTDAGVHARGQVIS 65

Query: 64  FDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F   R  +PV     ALN+ L     I+ L    V   FHAR+ A R+ Y Y I   + P
Sbjct: 66  FS-TRARIPVERWPLALNSVLPAD--IAALEAVEVAPDFHARYCAKRKWYRYTIYNNRVP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR----TIDHFDVN 178
               +  +W + + LD   M  AA +L G HDF +F    C A SP+R     +    V+
Sbjct: 123 DVFCRRYSWHLRQPLDVIAMARAAAYLQGCHDFRSF----CAAGSPVRHFERQVQQASVS 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I   V+A  FL+  +R  VG+L  +G  +     +   L A+ R++ GP AP  G
Sbjct: 179 QNGPFIYFDVIADGFLYHMVRIMVGTLVEIGRRRLVPEAIPAILAARSREKAGPTAPARG 238

Query: 239 LYFDSVEY 246
           L  + VEY
Sbjct: 239 LCLERVEY 246


>gi|326522897|dbj|BAJ88494.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 328

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 90/254 (35%), Positives = 130/254 (51%), Gaps = 13/254 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG----EIVVVHGAGRTDSGVHAL 58
           ++ M+I Y+G+ + GWQ Q +  +IQ  +EKA+  +T     E+ +V GAGRTD+GVHA 
Sbjct: 48  KWRMVIAYDGTKFKGWQYQPSPPTIQCFLEKALMRITKLDRKELCLV-GAGRTDTGVHAR 106

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF     +  +     A+N  L     I +  +S    +FHAR S   + Y Y+I 
Sbjct: 107 GQVAHFTTPFAYHCLDSFHSAINGLL--PPDIRVREISAACGEFHARTSTKSKIYHYKIY 164

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHC-QASSPIRTIDHF 175
                       A+     L+   M+ AA H VG HDFT+F  ++H  +  SPI+ I  F
Sbjct: 165 NEAVMDPFHTNYAYHSAHKLNPHAMQEAANHFVGVHDFTSFANAVHNDRVRSPIKKISRF 224

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL-- 233
           DV     +I++ V    FL+ Q+R+ V  L  VG        + K + A+DRKE   +  
Sbjct: 225 DVTKMDAIIQLEVEGTGFLYRQVRNMVALLIQVGREGLPPEIVPKIIAAKDRKELAKVAL 284

Query: 234 -APPEGLYFDSVEY 246
            APP GLY  SV Y
Sbjct: 285 SAPPHGLYLMSVNY 298


>gi|229009651|ref|ZP_04166877.1| tRNA pseudouridine synthase A [Bacillus mycoides DSM 2048]
 gi|229131150|ref|ZP_04260062.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST196]
 gi|229165130|ref|ZP_04292925.1| tRNA pseudouridine synthase A [Bacillus cereus AH621]
 gi|228618393|gb|EEK75423.1| tRNA pseudouridine synthase A [Bacillus cereus AH621]
 gi|228652363|gb|EEL08288.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST196]
 gi|228751673|gb|EEM01473.1| tRNA pseudouridine synthase A [Bacillus mycoides DSM 2048]
          Length = 252

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGIHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIIIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|317495541|ref|ZP_07953909.1| tRNA pseudouridine synthase A [Gemella moribillum M424]
 gi|316914355|gb|EFV35833.1| tRNA pseudouridine synthase A [Gemella moribillum M424]
          Length = 265

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GSGY G+Q Q N +++Q  IEKA+  +  + + V+ +GRTDSGVHA  QV
Sbjct: 1   MRVVLLCRYDGSGYHGFQIQPNNNTVQEEIEKALKKINKKDIRVYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           KALNA L     I I  ++  ++ FH R+++ R++Y Y++   Q 
Sbjct: 61  LHFDTELNIPNEAWKKALNANLPAD--IRIFGVTTSNEDFHVRYNSTRKTYHYKLYIGQN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV---N 178
                         + + E  + A  + +G HDF++F S +      IR I +F++    
Sbjct: 119 VDPFLLNYVGQHKYNFNFEKAQKALNYFIGEHDFSSFCSKNSSVEDKIREIYYFNMYYDK 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +   +I   V    FL+  +R  +G+++ V  GK+ +  +++ L  ++RK  GP A   G
Sbjct: 179 TNPRVINFDVCGNGFLYNMVRIIIGTIQDVAAGKYGAEYVKEILDKKERKYAGPKADAAG 238

Query: 239 LYFDSVEYS 247
           LY   V Y+
Sbjct: 239 LYLKEVIYN 247


>gi|210617714|ref|ZP_03291708.1| hypothetical protein CLONEX_03932 [Clostridium nexile DSM 1787]
 gi|210149156|gb|EEA80165.1| hypothetical protein CLONEX_03932 [Clostridium nexile DSM 1787]
          Length = 249

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 128/247 (51%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y MII Y+GS Y GWQRQ     +IQ  +E+ +  + G  V + G+GRTD+GVHA  
Sbjct: 1   MRNYKMIIVYDGSRYKGWQRQNLTNLTIQTILERTVEQIVGYPVEIDGSGRTDAGVHANG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+   V   +       LN  L   + I +  + +V   FH+R+SA  + Y Y I TR
Sbjct: 61  QVANMK-VSGLLDESFVGELNCLL--PEDICVKEMELVPGSFHSRYSAKAKKYKYCIDTR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +   K L  ++M+ AA++L G HDF+ F + +    S +RTI    +  
Sbjct: 118 KKPCVFTRRYTYHFTKELHLDDMKKAAEYLKGTHDFSAF-TDNKDEKSKVRTIYEIKIVK 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +E       FL+  +R   G+L  VG  + +  D++ AL+ ++R+  G LAP  GL
Sbjct: 177 KWTRLEFEFYGTGFLYHMVRILTGTLLEVGCAEKSIEDIKMALEQKERELTGFLAPARGL 236

Query: 240 YFDSVEY 246
           + + V Y
Sbjct: 237 FLEKVYY 243


>gi|325288607|ref|YP_004264788.1| tRNA pseudouridine synthase A [Syntrophobotulus glycolicus DSM
           8271]
 gi|324964008|gb|ADY54787.1| tRNA pseudouridine synthase A [Syntrophobotulus glycolicus DSM
           8271]
          Length = 267

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 82/252 (32%), Positives = 129/252 (51%), Gaps = 12/252 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M   C+ + Y+G+ Y G+Q Q  ++G +IQG +EKA   +  E + +  AGRTD GVHA 
Sbjct: 1   MNNICLRLAYDGTQYHGFQSQPEEHGKTIQGELEKAWKRLAQEEIKIVTAGRTDKGVHAA 60

Query: 59  RQVAHFD----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            QV +F     + ++ +P+    A+N+ L   + I IL   +V  +F+AR SA  + Y Y
Sbjct: 61  GQVINFKSAARIPQDKIPI----AMNSVL--PEEIRILEAKLVGAEFNARTSAYWKRYDY 114

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +I  ++      +  +   P  LD   MR AA  + G+HDF TF +    A S +RT+ H
Sbjct: 115 KIENKRTADVFTRLYSLHEPVPLDLNKMRQAAARIEGKHDFKTFSAAGSNAKSFVRTVYH 174

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V S    I +  +   FL+  +R   G+L  VG GK    D+   L++++R   G   
Sbjct: 175 CKVQSSSGYITVTCIGNGFLYNMVRIITGTLLYVGKGKIVPEDMPGILKSRNRALAGKTV 234

Query: 235 PPEGLYFDSVEY 246
            P GL    ++Y
Sbjct: 235 SPAGLVLRYIDY 246


>gi|260438183|ref|ZP_05791999.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
 gi|292809373|gb|EFF68578.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
          Length = 250

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 124/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+GY GWQ+Q N  +++  + KA   +  + + + GA RTD+GVH+   V
Sbjct: 1   MRVMLRVAYDGTGYSGWQKQPNAITVEEVLCKACKNLFAQDIDIIGASRTDAGVHSYGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FD+        +  ALN+  ++ + I ++    V + FH R    R++Y Y+I   + 
Sbjct: 61  AVFDVDTRIPAEKISYALNS--RLPEDIRVVESRQVSENFHPRHVECRKTYEYKIWNDKF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L +  +     +LD   M  A ++ +G HDFT+F S+  Q  S IR I    V    
Sbjct: 119 ENPLVRYYSHFFYGNLDIGKMNEACRYFIGLHDFTSFCSVGSQVQSKIREIYSISVEKNN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI IRV    FL+  +R   G+L  VG G+    ++ K +  ++R+  GP AP  GL  
Sbjct: 179 RLITIRVTGNGFLYNMVRIIAGTLIKVGQGQLEPAEIPKIIDGKNRELAGPTAPARGLAL 238

Query: 242 DSVEYS 247
             + Y 
Sbjct: 239 VEINYE 244


>gi|228898895|ref|ZP_04063177.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 4222]
 gi|228963242|ref|ZP_04124411.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228796500|gb|EEM43939.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228860795|gb|EEN05173.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 4222]
          Length = 252

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWEVNYN 251


>gi|116328579|ref|YP_798299.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116121323|gb|ABJ79366.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 265

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 134/249 (53%), Gaps = 15/249 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y +++EY+G  + G+Q QK+  SIQ ++EKA+ ++  E + + GAGRTD+GVHA   V
Sbjct: 1   MNYALLVEYDGLCFNGFQTQKDLPSIQENLEKAVKILLKEEISITGAGRTDTGVHARGMV 60

Query: 62  AHFDLVREWVPVILCKALNAYL----KISDT-ISILNLSIVDKQFHARFSAIRRSYLYRI 116
            +F  ++        +  N +L     I+D+ +SIL ++ V + F +RFS   R Y Y I
Sbjct: 61  VNFKTIKT------VQNFNKFLLSMNAITDSGLSILGMTEVGENFDSRFSCNSREYEYLI 114

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHF 175
           +  + P  + K RA+     +D   ++   + L G HDF +  ++   +  S IRTI   
Sbjct: 115 LNTKYPRPIWKNRAFWYQHKIDVPRLKTELELLKGEHDFRSLAKTASMKDRSTIRTILDA 174

Query: 176 DV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            +   + +  L++I++ A  FLH  IR   G+L  + +GK    ++   L ++DR   G 
Sbjct: 175 KLERSSEWEGLLKIKIRANGFLHNMIRILTGTLLEIANGKLKVPNILDILSSKDRTIAGI 234

Query: 233 LAPPEGLYF 241
             PP GLYF
Sbjct: 235 TLPPYGLYF 243


>gi|300088167|ref|YP_003758689.1| tRNA pseudouridine synthase A [Dehalogenimonas lykanthroporepellens
           BL-DC-9]
 gi|299527900|gb|ADJ26368.1| tRNA pseudouridine synthase A [Dehalogenimonas lykanthroporepellens
           BL-DC-9]
          Length = 261

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 83/246 (33%), Positives = 124/246 (50%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+G+ Y G Q Q +G+++Q  +E A+  +TGE + +H A RTD+GV A  QVA
Sbjct: 8   KLVLTIEYDGAQYRGSQAQGHGATVQSELETAVARLTGEKIRIHLASRTDAGVSAAEQVA 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F          +  ALN +L     I++  +  V   F  R  A+ R Y YRI+  + P
Sbjct: 68  SFRTSLRLPGRTVADALNHFLPAD--IAVKKVFRVPDTFDVRRHAVSREYRYRILNTRIP 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFG 181
             L +  ++ +   LD   +  A   LVG HD   F S +  +  + IR I    + S G
Sbjct: 126 SPLRERHSYRVYGELDIAAIEQAVGKLVGEHDLAAFASKLGRRPGTTIRRILAAGLTSEG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +  R+VA+SFL   +R+ VG L  +G G+ T  + EK L A      GP AP +GL  
Sbjct: 186 EELVFRIVAKSFLPHMVRNIVGVLVKIGTGRLTVAEFEKLLSAAVPGSAGPAAPGKGLCL 245

Query: 242 DSVEYS 247
             V Y+
Sbjct: 246 IKVNYA 251


>gi|187917895|ref|YP_001883458.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
 gi|238689303|sp|B2S1K1|TRUA_BORHD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119860743|gb|AAX16538.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
          Length = 245

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 82/240 (34%), Positives = 121/240 (50%), Gaps = 2/240 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y+G+Q Q    +IQG IEKA+  ++   V VH AGRTD GVHA  Q+  F + 
Sbjct: 8   IAYDGSLYYGFQIQPTKPTIQGEIEKALEKISKTKVKVHSAGRTDKGVHARGQIISFYIR 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L  A+N+ L+    I I+ L  V  +F  RF+A RR Y Y I+  +     E 
Sbjct: 68  INIKLKNLKTAINSLLR--KDIRIIKLKYVADEFQPRFNAKRRKYSYYILNNENHYPWEG 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A+ + K L+   +   A+ L+G HDFTTF  I  Q +S ++ I          LI   
Sbjct: 126 YQAYYVKKKLNINRLNEMAKMLIGIHDFTTFSCIKDQTNSKLKKIYFARFKKKNKLIIFE 185

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++  SFL   +RS VG++  +          +K L +++RK     AP + L+ D V Y 
Sbjct: 186 IIGSSFLWKMVRSIVGTIIDIEIKNEPVYTFKKILNSKNRKFTRTTAPAKALFLDKVFYE 245


>gi|75764616|ref|ZP_00744060.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74487896|gb|EAO51668.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 264

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 18  MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 77

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 78  QVIHFDTPLSLEEWQ---WNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRV 132

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   +
Sbjct: 133 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIE 192

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 193 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPG 252

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 253 HGLYLWEVNYN 263


>gi|213418519|ref|ZP_03351585.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 239

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 83/222 (37%), Positives = 116/222 (52%), Gaps = 4/222 (1%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKI 85
           S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+             +NA L  
Sbjct: 3   SVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANL-- 60

Query: 86  SDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRI 144
              I++  +  V   FHARFSA  R Y Y I   R  P  L KG      + LD E M  
Sbjct: 61  PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLAKGVTHYY-EPLDAERMHR 119

Query: 145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
           AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + + + A +F+H  +R+ VGS
Sbjct: 120 AAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGS 179

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           L  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 180 LLEVGAHNQPESWIAELLAARDRTLAAATAKAEGLYLVAVDY 221


>gi|317123065|ref|YP_004103068.1| tRNA pseudouridine synthase A [Thermaerobacter marianensis DSM
           12885]
 gi|315593045|gb|ADU52341.1| tRNA pseudouridine synthase A [Thermaerobacter marianensis DSM
           12885]
          Length = 298

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 81/241 (33%), Positives = 116/241 (48%), Gaps = 2/241 (0%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           ++ Y+G+ + GWQRQ    ++Q  +E A+  + G  V V  AGRTD+GVHA  QV H+  
Sbjct: 49  VLAYDGTDFAGWQRQPRQRTVQQVVEDALERLLGHPVRVTAAGRTDAGVHARAQVIHWRT 108

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            R +    L  AL   L  +D +++         FHAR+SA R++Y Y +     P  L 
Sbjct: 109 PRPFPVDRLVPALRGLLP-ADVVAV-EAGEAPPGFHARYSARRKTYAYHVWRDPVPDPLH 166

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +   W +P  LD + M  AA+ L G HDF  F++         RT+    V   G L+  
Sbjct: 167 RRWQWHLPLDLDVDAMVEAARRLEGTHDFAPFKAAGSPVRRTRRTLYRCAVEERGPLLRF 226

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL    R  VG+L  +G G+W +  +E  L    R   GP AP  GL    V Y
Sbjct: 227 VLEADGFLMHMARGIVGTLVEIGRGRWQADRVEAILAEGRRDLAGPTAPAHGLVLWQVVY 286

Query: 247 S 247
            
Sbjct: 287 D 287


>gi|160914527|ref|ZP_02076742.1| hypothetical protein EUBDOL_00533 [Eubacterium dolichum DSM 3991]
 gi|158433685|gb|EDP11974.1| hypothetical protein EUBDOL_00533 [Eubacterium dolichum DSM 3991]
          Length = 252

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 121/251 (48%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ+Q N  SIQ  IE A+  +  E V +  +GRTD+ VHAL Q
Sbjct: 1   MDRYKVTVCYDGTNYAGWQKQDNARSIQEEIECALAKINEEAVEIVASGRTDAHVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  +        +A N+ L     I IL +  V   FHARF A+R+ Y Y I    
Sbjct: 61  VFHFDAKKALSDEQWVRACNSLL--PKDIRILKVEKVSDSFHARFDAVRKRYDYYITNDV 118

Query: 121 APLALE----KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHF 175
               LE    K R     KSLD   M+  A   +G HDFT+F S    +  S I+TI   
Sbjct: 119 LNPFLENYMGKDR-----KSLDVAYMQECANVFIGTHDFTSFTSSKIDERKSRIKTIYRL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +V    N + I     +FL   +R     L   G  + T   + + L+A+D+  C   A 
Sbjct: 174 EVQQEANAVHIIFEGNAFLRYMVRMLAQVLIEAGKHRLTKEAISQMLEAKDKHACRYKAS 233

Query: 236 PEGLYFDSVEY 246
             GLY   V+Y
Sbjct: 234 ANGLYLVRVDY 244


>gi|212637986|ref|YP_002314506.1| Pseudouridylate synthase I [Anoxybacillus flavithermus WK1]
 gi|226708641|sp|B7GJ99|TRUA_ANOFW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|212559466|gb|ACJ32521.1| Pseudouridylate synthase I [Anoxybacillus flavithermus WK1]
          Length = 246

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 82/248 (33%), Positives = 129/248 (52%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R    I Y+G+ + G+Q Q+   ++QG +E+A+ ++  G+ V V+ +GRTD+ VHA  
Sbjct: 1   MRRIKCTIAYDGTNFAGYQIQQQKRTVQGELERALSIIHKGQFVRVYASGRTDATVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           KALNA L   D + +   S V   FHARFS  ++ Y YR+   
Sbjct: 61  QVIHFDTPLTIPDERWPKALNALL--PDDVIVKEASEVPSSFHARFSVKKKEYRYRVWIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  + L +   +  P  +    M  A ++L+G HDFT+F S   +    +RTI   +V  
Sbjct: 119 EKNVFL-RHYVYHHPYDVSVPAMNEALRYLIGTHDFTSFCSAKTEVDDKVRTIYEAEVVQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +  R+V   FL+  +R  VG++  VG G+  + +++  L+ ++R   G  AP  GL
Sbjct: 178 EGEELIFRLVGNGFLYNMVRIIVGTVLEVGRGERCAEEIKTILEQKNRSVAGKTAPGHGL 237

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 238 YLWHVSYD 245


>gi|298376183|ref|ZP_06986139.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_19]
 gi|298267220|gb|EFI08877.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_19]
          Length = 265

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 123/250 (49%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++    V + GAGRTD+GVHA   +A
Sbjct: 16  RYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRTPVPIVGAGRTDAGVHAHLMIA 75

Query: 63  HFDLVREWVP-----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD    W       V L + LN  L     I++  +  V  + HARF A  R+Y Y + 
Sbjct: 76  HFD----WEEPIGDLVFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYVT 129

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T++ P   E    + +P  LD E M  A + L    DFT+F  +H    +    I H   
Sbjct: 130 TKKDPFNHE--LVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHAGW 187

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P  
Sbjct: 188 TQEGDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGH 247

Query: 238 GLYFDSVEYS 247
            L+   V Y 
Sbjct: 248 ALFLVDVTYP 257


>gi|262341374|ref|YP_003284229.1| tRNA pseudouridine synthase A [Blattabacterium sp. (Blattella
           germanica) str. Bge]
 gi|262272711|gb|ACY40619.1| tRNA pseudouridine synthase A [Blattabacterium sp. (Blattella
           germanica) str. Bge]
          Length = 247

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 134/246 (54%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  ++GWQ QK  S+++G++E  +  +  E + V GAGRTD GVHA +  
Sbjct: 1   MRFFIELAYNGKYFYGWQVQKKVSTVEGNLEYCLSKLLKESINVIGAGRTDKGVHAKQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +  +   L K LN +L    +I +LN+  V +  HARF+AI+R Y Y ++  + 
Sbjct: 61  AHFDY-KGKISNNLIKKLNVFL--PKSIKVLNIFPVKENIHARFNAIKRIYKYYLVRDKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSF 180
           P    +  +W     L+ + M IA++ L+G  DF++F +    +  + I  ++H   +  
Sbjct: 118 PFY--QDFSWHCFYPLNIQRMNIASKKLMGHKDFSSFCKKKTFETRNNICKVNHVCWSVN 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N+    + A  FL + +RS +G+L  VG  K +  +  + +++++   C  + P  GL+
Sbjct: 176 NNVFCFTIEANRFLRSMVRSIIGTLIDVGRNKISVNEFSEIIESKNSNFCKSIVPACGLF 235

Query: 241 FDSVEY 246
              + Y
Sbjct: 236 LTRILY 241


>gi|315186691|gb|EFU20450.1| tRNA pseudouridine synthase A [Spirochaeta thermophila DSM 6578]
          Length = 248

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 125/242 (51%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++ Y+G+ + GWQRQ NG S+QG +E A+  +    V VH AGRTDSGVHA+ Q  +F 
Sbjct: 8   VVLAYDGTDFVGWQRQPNGRSVQGVVEDALARMHKHPVHVHAAGRTDSGVHAVGQCINFI 67

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              + +PV     ALN++L     +  L    V   FHAR+SA+RR Y Y + +  +P  
Sbjct: 68  TDIDSLPVEKFALALNSFLP--RDVKALQAEEVPPDFHARYSAVRREYRYYVFSSPSPYP 125

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  +  + +  D   +   A  +VG HDF++F S    + S +R I        G  +
Sbjct: 126 HLRRYSLWVNRLPDVRLLNAYASCIVGEHDFSSFCSPSDPSPSKVRLIHTASWFPEGARL 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+V  +FL   +R+ VG++  +   K     + K L+A+DR      AP  GL+   V
Sbjct: 186 VFRIVGNAFLWRMVRALVGTMLDLEKQKADPEMMWKILEARDRSAASDSAPAWGLFLHEV 245

Query: 245 EY 246
           +Y
Sbjct: 246 QY 247


>gi|294055498|ref|YP_003549156.1| tRNA pseudouridine synthase A [Coraliomargarita akajimensis DSM
           45221]
 gi|293614831|gb|ADE54986.1| tRNA pseudouridine synthase A [Coraliomargarita akajimensis DSM
           45221]
          Length = 250

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 85/249 (34%), Positives = 136/249 (54%), Gaps = 8/249 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+  I  Y+G+ + GWQRQ+NG ++Q  +E A+  +    +  HG+GRTD+GVHA  Q 
Sbjct: 1   MRWKCICSYDGTDFEGWQRQRNGLAVQNVLEAALSQIFNLPLKTHGSGRTDAGVHARGQC 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI-ITRQ 120
            HFD         L +AL++ L  S  + I  + +VD++FHAR SAI + Y+YR  + R 
Sbjct: 61  FHFDGDWPHDTGKLIRALHSILPKS--LRIERIDLVDERFHARHSAIGKRYVYRYHLGRA 118

Query: 121 APLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDV 177
            P  LE+   W     +++   M+ AA  LVG HDF+ + + H + S  +P++ +   D+
Sbjct: 119 HP--LEQRYVWACRDTAINFGAMQEAALRLVGTHDFSAYGATHGKDSDPNPVKNVYRLDL 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  I +      +L+  +RSF G+L  VG  + +  D+E+ L+++ R      AP  
Sbjct: 177 VKHGRQIILTTEGSGYLYRMVRSFAGALYSVGRDRLSPDDIEEILRSKIRTHRIVTAPGV 236

Query: 238 GLYFDSVEY 246
           GL  D V Y
Sbjct: 237 GLCLDEVFY 245


>gi|257463955|ref|ZP_05628340.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
 gi|317061478|ref|ZP_07925963.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
 gi|313687154|gb|EFS23989.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
          Length = 242

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 83/238 (34%), Positives = 129/238 (54%), Gaps = 4/238 (1%)

Query: 9   EYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           +Y+GS + G+QRQ N  ++QG IEK++F +  E + +  +GRTD GVHA++QV++F    
Sbjct: 9   QYDGSSFMGFQRQPNQRTVQGEIEKSLFHILREKIDLTSSGRTDRGVHAIQQVSNFFTAV 68

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
                 L  AL+  L   + I +L +  VD +FHARFSA  RSY Y I  ++ P    + 
Sbjct: 69  NIPSDRLFYALSRNL--PEDILLLQVEEVDSEFHARFSAKTRSYRYCITWKKNPFE-HRY 125

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
           +A++  K    E ++I  Q  +GRH+F  FR      ++P+R I    V    N + I +
Sbjct: 126 KAYVKEKIESTEFLKI-LQVFIGRHNFQNFRLQDSSFANPMREIYSISVEEVENGMNIDI 184

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           VA +FL +QIR  +G+   V  GK     + + L+  + +    LA   GLY   +EY
Sbjct: 185 VANAFLKSQIRIMIGTALQVYFGKVEGDRITRMLEELETEFPKYLADSSGLYLYRIEY 242


>gi|224119986|ref|XP_002331109.1| predicted protein [Populus trichocarpa]
 gi|222872837|gb|EEF09968.1| predicted protein [Populus trichocarpa]
          Length = 326

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 98/317 (30%), Positives = 146/317 (46%), Gaps = 73/317 (23%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G Q+Q N  ++ G +++A     G+ V +  + RTD+GVHAL  V 
Sbjct: 7   RYLVAVEYIGTRFCGSQQQLNHRTVVGVLQEAFHKFIGQPVTICLSSRTDAGVHALSNVC 66

Query: 63  HFDLVR-----------EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ KA+N +L K    I + ++  V   FHARF A  R
Sbjct: 67  HVDVERISKRKPGEVLPPHEPAVVRKAVNHFLQKKEGDIMVTDVRSVSAHFHARFKAQER 126

Query: 111 SYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR++     L+  EK RAW + + LD  +M+ A + LVG HDF++FR+  CQA SP 
Sbjct: 127 TYFYRLLIGPELLSTFEKDRAWHVSEELDLVSMQEACKVLVGHHDFSSFRASGCQAKSPF 186

Query: 170 RTIDHFDV-------------------------NSFGNLIE------------------- 185
           RT++   V                         +SF N  +                   
Sbjct: 187 RTLEELSVLEVVSTPYFPSITEREQNSSNGEGPHSFHNKCKTGLPTGSISNGFMAGGSNS 246

Query: 186 -------IRVVARSFLHT-QIRSFV--------GSLKLVGDGKWTSTDLEKALQAQDRKE 229
                  IR   R ++ T + RSF+        G LK VG G  T +D+E+ L A+    
Sbjct: 247 GTDLGFGIRRRHRCYVITARSRSFLYHQVRLLVGVLKSVGTGDLTVSDVERILNARSITA 306

Query: 230 CGPLAPPEGLYFDSVEY 246
             P+AP  GLY   V+Y
Sbjct: 307 ASPMAPACGLYLGHVKY 323


>gi|326692205|ref|ZP_08229210.1| tRNA pseudouridine synthase A [Leuconostoc argentinum KCTC 3773]
          Length = 261

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 89/258 (34%), Positives = 132/258 (51%), Gaps = 14/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIF----LVTGEIVVVHGAGRT 51
           M RY  ++ Y+GS +FG+Q Q KNG     ++QG + +A+     L T  I VV GA RT
Sbjct: 1   MPRYKAVVAYDGSEFFGFQVQTKNGVERQRTVQGELNRAVNQMAKLPTPAIKVV-GASRT 59

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D+GVHA  QV HFDL  +  P  + K LN  L     I I  +  V   FHARF+   + 
Sbjct: 60  DTGVHAFGQVVHFDLPFDIQPEGVRKGLNTLLPRD--IMIKQVEKVADDFHARFNTHAKR 117

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y+YR+ T+      ++         LD   ++ A   L+G HDF +F +   Q ++ +RT
Sbjct: 118 YIYRVSTQDFTDPFKRRYTGHFHWRLDVARIQAALPDLLGEHDFASFAASGNQTATTVRT 177

Query: 172 IDHFDVNSFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           I   DV    +  E+       +FL+ QIR  VG L  +G+G+    D+ + +  +DR++
Sbjct: 178 ITRADVEVKPDEQELVFTFEGNAFLYNQIRIMVGVLLEIGNGRRDVHDIVRLIAVKDREQ 237

Query: 230 CGPLAPPEGLYFDSVEYS 247
               AP  GLY D + Y 
Sbjct: 238 ARFTAPASGLYLDEIYYD 255


>gi|299148560|ref|ZP_07041622.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_23]
 gi|298513321|gb|EFI37208.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_23]
          Length = 267

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     ISI  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLLPPD--ISIYRVCRVRPDTHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +   +  + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 EDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEY 246
           +  +VEY
Sbjct: 237 FLVNVEY 243


>gi|309789641|ref|ZP_07684222.1| tRNA pseudouridine synthase A [Oscillochloris trichoides DG6]
 gi|308228377|gb|EFO82024.1| tRNA pseudouridine synthase A [Oscillochloris trichoides DG6]
          Length = 262

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 88/250 (35%), Positives = 128/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y+G+ + G Q Q  G S+Q ++E+A   +T E   V+ AGRTD+GVHA+ Q
Sbjct: 1   MRNIALRLAYDGTDFIGSQYQNQGRSVQEALEQAWEGLTQERRRVNLAGRTDAGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+           + + +NA  K+   ++I  ++ VD  FHAR SA RRSY Y I    
Sbjct: 61  VANIRTETRHSRRTILRGMNA--KLPPDVAIQAVAEVDPDFHARHSANRRSYRYLIDNNA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A L   +   W + + LD   M  A   L G HDF  F ++  +  S +RT     ++S 
Sbjct: 119 AWLPNLRNYVWFVEQPLDQAAMAEALVRLEGTHDFAAFTALVPEQRSTVRTCYTARLSSV 178

Query: 181 G----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                +LI I + A +FL   +R  VG++ LVG GK T    +  L+ +DRK  GP A  
Sbjct: 179 TMFDRHLIAIDLAANAFLQHMVRVIVGTVVLVGRGKITPDGFQAILEGRDRKAAGPTAVA 238

Query: 237 EGLYFDSVEY 246
            GL   SV Y
Sbjct: 239 HGLTLVSVGY 248


>gi|237756326|ref|ZP_04584878.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237691512|gb|EEP60568.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 243

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 125/246 (50%), Gaps = 11/246 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + I Y G+ Y GWQRQKNG  IQ  IE  +  +  E + + GAGRTD+GVHALRQVA+
Sbjct: 6   YKLEISYIGTNYNGWQRQKNGIGIQQVIEDLLSELLKEKITLIGAGRTDAGVHALRQVAN 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F   +      +   LNA  K+   ISIL +  V   F+ARFSA  ++Y+Y+I T+  P 
Sbjct: 66  FKTNKHKNTKTIYTYLNA--KLPRDISILKVEEVPLSFNARFSAKGKTYIYKINTKPDPF 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT-IDHFDVNSF-- 180
             +   AW   K LD   M      +    D ++      +A   IR  ID  ++  +  
Sbjct: 124 LYK--LAWYYDKKLDLIKMVEGINIIKQYKDLSSL----AKAGDYIRKEIDLRELKLYFD 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I I + A  FL   +R  VG L  +G G  +  +L+  ++ +        APPEGLY
Sbjct: 178 GKIITIEITASHFLRNMVRRIVGHLVALGRGSLSLEELKDIIEKKSPSHGKYTAPPEGLY 237

Query: 241 FDSVEY 246
             +V Y
Sbjct: 238 LKAVYY 243


>gi|289669396|ref|ZP_06490471.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 257

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 134/247 (54%), Gaps = 14/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADGQVQVICAGRTDAGVHGEC 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R W+       L    ++  +I++     V   FHARFSA  R Y Y
Sbjct: 61  QVVHFDSDARREPRGWM-------LGTTARLPPSIAVRWCVPVADDFHARFSARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++ RQ   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +  
Sbjct: 114 RLLNRQIRPALYRQTVSWERRPLDADAMHAAAQALLGENDFSAFRSVQCQALHARRNLQA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   G  A
Sbjct: 174 IHVQRIGEVVEVQVQANAFLHHMVRNIVGSLILVGTGERPADWIATLLAGRDRTVAGQTA 233

Query: 235 PPEGLYF 241
           PP+GL F
Sbjct: 234 PPQGLVF 240


>gi|237736308|ref|ZP_04566789.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
 gi|229421656|gb|EEO36703.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
          Length = 243

 Score =  130 bits (327), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 128/244 (52%), Gaps = 17/244 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS ++G+QRQ N  ++QG IEK + +V  + + +  +GRTD GVHAL QV++F     
Sbjct: 10  YDGSMFYGFQRQPNKRTVQGEIEKLLNVVLKDEIDMVSSGRTDRGVHALIQVSNF-YTTS 68

Query: 70  WVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +P+     +L + L         I +L++  VD +F++RF A +R Y Y I   + P  
Sbjct: 69  TIPLDRLKYVLMRGLPL------DIELLDIEEVDIEFNSRFDAQKRGYTYIISWERDPF- 121

Query: 125 LEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-N 182
             K R    + K ++ E  +     LVG HDF  FR   C + + IR I   +V   G N
Sbjct: 122 --KNRYETYVNKEIEAERFQKILDILVGVHDFNNFRMSDCGSKTSIREIYSIEVKKIGSN 179

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + ++  SFL +QIR  +G+   +  G   S  +E+ L+  D+K    +A P GLY  
Sbjct: 180 RISVEILGSSFLKSQIRIIIGTALNIYFGNLPSNYMEEMLKNPDKKYLKKVAEPNGLYLS 239

Query: 243 SVEY 246
            V+Y
Sbjct: 240 KVDY 243


>gi|332522319|ref|ZP_08398571.1| tRNA pseudouridine synthase A [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332313583|gb|EGJ26568.1| tRNA pseudouridine synthase A [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 249

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 79/250 (31%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           MIRY  +I Y+GS + G+QRQ    +IQ  IEK +  L  G+ + + GAGRTD+GVHA  
Sbjct: 1   MIRYKAVISYDGSQFSGFQRQTKARTIQEEIEKTLMRLNKGKFIAIQGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++++  V   FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLAERRDLEKLRFALDT--QTPEDIDVISVEEVSNNFHARYSKHLKTYEFIVDVG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD   + +A + LVG HDFT F +      + +RT+   D   
Sbjct: 119 RPKNPMMRKYATHYPYPLDFSLIELAIKDLVGTHDFTGFTAAGTSVENKVRTLYQADCSF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +S    +        FL+ Q+R+ VG+L  +G+ +     +   L+ ++R+  GP     
Sbjct: 179 DSHRQCLIFTFTGNGFLYKQVRNMVGTLLKIGNQRMPVEQVRIILEQKNRQLAGPTIAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|15618490|ref|NP_224776.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae CWL029]
 gi|33241935|ref|NP_876876.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae TW-183]
 gi|4376873|gb|AAD18719.1| Pseudouridylate Synthase I [Chlamydophila pneumoniae CWL029]
 gi|33236445|gb|AAP98533.1| pseudouridylate synthase I [Chlamydophila pneumoniae TW-183]
          Length = 267

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 125/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  ++I Y G+ Y GWQ+Q N  SIQ  IE ++  +T     +  +GRTD+GVHA  Q
Sbjct: 1   MTKVALLIAYQGTAYSGWQQQPNDLSIQEVIESSLKKITKTRTPLIASGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF      +     +  KALNA L     I I ++++ D  FHAR+ AI + Y Y + 
Sbjct: 61  VAHFRAPDHPLFANANLTKKALNAILP--KDIVIRDVALFDDNFHARYLAIAKEYRYSLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++   +        E M+  A  L+G HDF +F +     +S +RTI   D+
Sbjct: 119 RLAKPLPWQRHFCYTPRHPFSTELMQEGANLLIGTHDFASFANHGRDYNSTVRTIYTLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ + I      FL+  +R+ VG+L  VG G +    L   L+ ++R+E    AP  
Sbjct: 179 VDKGDSLSIICRGNGFLYKMVRNLVGALLDVGKGAYPPEHLLDILEQKNRREGPSAAPAY 238

Query: 238 GLYFDSVEYS 247
           GL    V YS
Sbjct: 239 GLSLHHVCYS 248


>gi|313888069|ref|ZP_07821747.1| tRNA pseudouridine synthase A [Peptoniphilus harei ACS-146-V-Sch2b]
 gi|312846024|gb|EFR33407.1| tRNA pseudouridine synthase A [Peptoniphilus harei ACS-146-V-Sch2b]
          Length = 244

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 80/239 (33%), Positives = 120/239 (50%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+Q Q N  +++G +   I       V +  AGRTD GVHA  Q A+F   
Sbjct: 8   INYDGTNFHGFQLQPNERTVEGELNLGIEKTVKHPVKIFYAGRTDRGVHAEGQYANFYSD 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L K LN    + + +S+++   V   FHARF A  + Y Y +   +   AL +
Sbjct: 68  TTIDIGNLPKVLN--FNLPEDVSVVDAKYVPDAFHARFDAKLKKYRYVVHRSRYRHALLR 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            RA+  P  +D + MR A   L+G HDF +F          IR+I+  DV   G+ +   
Sbjct: 126 NRAYEYPYDVDPDRMREALASLIGEHDFNSFMGRGAIVKDSIRSIERIDVIEDGDFLYFD 185

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            VA+SFL   IR   G++  +G G+     +++AL+ + RK  GP AP  GLY   V+Y
Sbjct: 186 FVAKSFLKNMIRIVTGTVLEIGRGQREIEYMKEALEKKSRKAAGPTAPACGLYLLDVKY 244


>gi|257440210|ref|ZP_05615965.1| tRNA pseudouridine synthase A [Faecalibacterium prausnitzii A2-165]
 gi|257197244|gb|EEU95528.1| tRNA pseudouridine synthase A [Faecalibacterium prausnitzii A2-165]
          Length = 249

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 125/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + + Y+G+ Y G+Q Q NG S+  + +  +  V      + G  RTD+GVHAL  
Sbjct: 1   MQNYLLTLAYDGTNYCGFQVQPNGRSVAQTFQDGLEAVLHSRPDIKGCSRTDAGVHALGF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             +F       P  L  A+N +L     I +L   +V ++FHAR++A  ++YLYRI    
Sbjct: 61  ALNFHAETRIPPEKLPLAINQHLPPD--IRVLCARVVPEEFHARYAAHTKTYLYRIHNHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDV 177
                ++     +P+ LD + M+ AA+  VG+HDF    +    A      +RTI    V
Sbjct: 119 IDSPFDEKYYTRVPRRLDVDAMQRAAEQFVGKHDFLALCAAGSSAAAHGDTVRTITDCHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ ++I V A  +L+  +R   G+L  VG G+     +   L ++DR + GP  P +
Sbjct: 179 TRKGDEVDIEVTADGYLYNMVRILAGTLCEVGAGRMQPDAIPGILASRDRSQAGPTLPAK 238

Query: 238 GLYFDSVEYS 247
           GL+ + V+Y 
Sbjct: 239 GLFLEKVDYD 248


>gi|326335636|ref|ZP_08201823.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325692402|gb|EGD34354.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 247

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 128/245 (52%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  YFGWQ+Q +  S+Q  +E+AI L+  E + + GAGRTD+GVHA    
Sbjct: 1   MRFFIELSYNGKNYFGWQKQPHSLSVQEELERAISLLLHEEITLVGAGRTDTGVHARDYF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD     +P  L   LN++L    TI+I  +  +    HARF AI R+Y Y I   + 
Sbjct: 61  AHFDFSLP-LPENLVNKLNSFL--PKTIAIKGIFPMKDAAHARFDAISRTYQYFISREKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E+  ++ + + L    M  A + L+  +DF  F   +    + I  +         
Sbjct: 118 PFLYEQ--SYYVYQPLAISQMNRACEILLKHNDFQCFSKTNTDVRTYICHLTEAFWKEED 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+  R+ A  FL   +R+ VG++  VG GK + ++ E+ L +++R + G   P   L+ 
Sbjct: 176 SLLIFRITADRFLRNMVRAIVGTMIEVGIGKISLSNFEQILLSKNRSQAGYSVPGHALFL 235

Query: 242 DSVEY 246
           + V Y
Sbjct: 236 EKVVY 240


>gi|303234561|ref|ZP_07321198.1| tRNA pseudouridine synthase A [Finegoldia magna BVS033A4]
 gi|302494395|gb|EFL54164.1| tRNA pseudouridine synthase A [Finegoldia magna BVS033A4]
          Length = 244

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 131/247 (53%), Gaps = 14/247 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  QV +F 
Sbjct: 6   LTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVHQPVKINGAGRTDKGVHAKGQVCNFI 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR---QAP 122
           +  +         +N +   SD+I I+    VD  FHARFSA  ++Y Y +  +   +  
Sbjct: 66  VDTDISANQFLMGVNHF--TSDSIVIVKSEEVDLDFHARFSAKSKTYKYILCNKYYMEPW 123

Query: 123 LALEKG-RAWLIPKSL--DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               KG R + +   L   C +M      L+GRHDFT+F +   +  +P+RTID   +  
Sbjct: 124 FNDYKGHRKYYLDFDLLLKCRDM------LIGRHDFTSFVNDLEEDINPVRTIDEITIEK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I     A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GL
Sbjct: 178 IDDDIVFTFKAESFLRNMVRILVGSMVDVARGRKSIDWLKNALENKDRQSAGITIEPCGL 237

Query: 240 YFDSVEY 246
           Y  ++EY
Sbjct: 238 YLMNIEY 244


>gi|291542954|emb|CBL16064.1| pseudouridylate synthase I [Ruminococcus bromii L2-63]
          Length = 266

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 78/242 (32%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I Y+G  + GWQ Q+N  ++Q + + A+  + G    V G  RTDSGVHA        
Sbjct: 15  LTISYDGKEFHGWQIQQNAMTVQEAFQTALSKIIGNDFDVKGCSRTDSGVHANMYCISLK 74

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P  L  ALN +L +S  I++L+   V   FHAR+S   + Y+Y+I   +     
Sbjct: 75  TEHPIKPERLKAALNRWLPLS--IAVLDCKEVAPDFHARYSCTSKEYIYKIWNSEVRNPF 132

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTIDHFDVNSFGNLI 184
             G A      +D   +  AAQ  VGRHDFT+F ++  +    + R +  F V   G+L+
Sbjct: 133 LDGYALHYRYKIDENLLDKAAQAYVGRHDFTSFCTLDNREKGDMTRNVKAFSVTREGDLV 192

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            ++V A  FL+  +R  VG+L  +  GK    ++   ++ ++RK  GP A   GLY + V
Sbjct: 193 TMKVEADGFLYNMVRIMVGTLLRIQQGKIAPDEIPSIIEKKNRKYSGPTAQACGLYLNCV 252

Query: 245 EY 246
            Y
Sbjct: 253 NY 254


>gi|220903970|ref|YP_002479282.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219868269|gb|ACL48604.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 259

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 89/268 (33%), Positives = 130/268 (48%), Gaps = 33/268 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQ---RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R  ++I Y G+GY GWQ   + K   ++QG++E A+  + G+ V VHG+GRTDSGVHA 
Sbjct: 1   MRLKLLISYVGTGYSGWQIQEKPKPPPTVQGALEAALRTIAGKAVRVHGSGRTDSGVHAH 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +    +LNA L     I +L+ S     FHAR  A+R++Y Y+   
Sbjct: 61  GQVAHCDIPDTRAGLDWRHSLNAVL--PRDIRVLDASPAAPDFHARKDALRKTYAYQFW- 117

Query: 119 RQAPLALEKGRAWLIPK---------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                   + R +L P           LD + MR A   L+GRHDF   R+      S  
Sbjct: 118 --------QDRRFLPPHVRPYVWNCGMLDLDAMRDALPFLLGRHDFAGLRNAGTDVESTE 169

Query: 170 RTIDHFDVNSF---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           RTI    +++            ++ + + A  FL   +R+  G L   G GK     +  
Sbjct: 170 RTIMDARLDALAPCEYYPPHAPMLRLTITADGFLKQMVRNVAGLLAACGQGKIQPAQIPA 229

Query: 221 ALQAQDRKECGPL-APPEGLYFDSVEYS 247
            L A+DR+    + APPEGL   SV+Y 
Sbjct: 230 LLAARDRQAVPSVTAPPEGLALVSVKYP 257


>gi|116617361|ref|YP_817732.1| pseudouridylate synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
 gi|122272438|sp|Q03ZL3|TRUA_LEUMM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116096208|gb|ABJ61359.1| Pseudouridylate synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
          Length = 255

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 86/258 (33%), Positives = 132/258 (51%), Gaps = 14/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIFLV----TGEIVVVHGAGRT 51
           M RY  +I Y+G+ +FG+Q Q KNG     ++QG + K I  +    + +I VV GA RT
Sbjct: 1   MPRYKAVIAYDGAEFFGFQLQTKNGVESVRTVQGELNKVINKMAKNPSPQIKVV-GASRT 59

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D+GVHA  QV HFDL     P  + K +N  L     + + ++  V   FHARF+   + 
Sbjct: 60  DTGVHAFGQVVHFDLPFNIDPEGVRKGMNTLLPFD--VVVNHVEHVSDDFHARFNTHSKR 117

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y+YR+ T       ++         LD   ++ A   L+G HDF +F +   + ++ IR 
Sbjct: 118 YIYRVSTTDYKDPFKRKYTGHFHWKLDINRIKAALPDLLGEHDFASFAASGNETATTIRL 177

Query: 172 IDHFDVNSFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           I   DV+      EI       +FL+ QIR  VG L  +G GK    D+ + ++ +DR++
Sbjct: 178 ITRADVDEKPEEHEIVFTFEGNAFLYNQIRIMVGVLLEIGTGKRPVHDIVRLIEVKDREQ 237

Query: 230 CGPLAPPEGLYFDSVEYS 247
               AP  GLY D ++Y+
Sbjct: 238 ARYTAPASGLYLDEIDYN 255


>gi|302379698|ref|ZP_07268183.1| tRNA pseudouridine synthase A [Finegoldia magna ACS-171-V-Col3]
 gi|302312605|gb|EFK94601.1| tRNA pseudouridine synthase A [Finegoldia magna ACS-171-V-Col3]
          Length = 244

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 130/247 (52%), Gaps = 14/247 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  QV +F 
Sbjct: 6   LTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVHQPVKINGAGRTDKGVHAKGQVCNFI 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR---QAP 122
           +  +         +N +   SD+I I+    VD  FHARFSA  ++Y Y +  +   +  
Sbjct: 66  VDTDISANQFLMGVNHF--TSDSIVIVKSEEVDLDFHARFSAKSKTYKYILCNKYYMEPW 123

Query: 123 LALEKG-RAWLIPKSL--DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               KG R + +   L   C +M      L+G+HDFT+F +   +  +P+RTID   +  
Sbjct: 124 FNDYKGHRKYYLDFDLLLKCRDM------LIGKHDFTSFVNDLEEDINPVRTIDEITIEK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I     A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GL
Sbjct: 178 IDDDIVFSFKAESFLRNMVRILVGSMVDVARGRKSIDWLKNALENKDRQSAGITIEPSGL 237

Query: 240 YFDSVEY 246
           Y   +EY
Sbjct: 238 YLMDIEY 244


>gi|188994646|ref|YP_001928898.1| tRNA pseudouridine synthase A [Porphyromonas gingivalis ATCC 33277]
 gi|238691471|sp|B2RIV6|TRUA_PORG3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|188594326|dbj|BAG33301.1| putative tRNA pseudouridine synthase A [Porphyromonas gingivalis
           ATCC 33277]
          Length = 252

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 124/252 (49%), Gaps = 12/252 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + + YNG+ Y GWQ Q N  S+Q ++E+AI  +  + V V GAGRTD+GVHA   
Sbjct: 1   MARFFIYLAYNGTRYSGWQTQPNAPSVQQTVEEAISTIVRQPVGVVGAGRTDAGVHAHEM 60

Query: 61  VAHFDLVREWVP---VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAH DL  +  P     L + LN  L     I I  ++ V    HARF AI R+Y Y + 
Sbjct: 61  VAHADLPCD-TPAEAATLTERLNKLLPRD--IVIYRMAPVKADAHARFDAISRTYHYYLT 117

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP---IRTIDH 174
            ++ P    +G      + LD E M  AA  L    DFT+F  +H    +    I     
Sbjct: 118 EQKDPFM--EGLMLKTYRKLDFERMNEAAALLPRYIDFTSFSKLHTDVKTNNCRITEARW 175

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  +   + A  FL   +R+ VG+L  VG GK + TD    +++QDR   G  A
Sbjct: 176 MPLAQTGQWV-FSITADRFLRNMVRAIVGTLFHVGTGKLSITDFRDIIESQDRSRAGSSA 234

Query: 235 PPEGLYFDSVEY 246
           P   LY + V Y
Sbjct: 235 PAHALYLERVVY 246


>gi|160887061|ref|ZP_02068064.1| hypothetical protein BACOVA_05075 [Bacteroides ovatus ATCC 8483]
 gi|156107472|gb|EDO09217.1| hypothetical protein BACOVA_05075 [Bacteroides ovatus ATCC 8483]
          Length = 267

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLLPPD--ISVYRVCRVRPDTHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +   +  + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 EDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEY 246
           +  +VEY
Sbjct: 237 FLVNVEY 243


>gi|304384407|ref|ZP_07366813.1| tRNA pseudouridine synthase A [Prevotella marshii DSM 16973]
 gi|304334505|gb|EFM00792.1| tRNA pseudouridine synthase A [Prevotella marshii DSM 16973]
          Length = 260

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 85/259 (32%), Positives = 127/259 (49%), Gaps = 27/259 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+GY GWQ Q NG S+Q  +++A+ +V    + V GAGRTD+GVHA R 
Sbjct: 1   MHRYFIHFSYDGTGYHGWQIQPNGISVQEVLQQALSVVLRREMTVTGAGRTDTGVHARRM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD+        L   LN  L     +++ N+  V    HARFSA RR+Y Y I   +
Sbjct: 61  TAHFDIDDATDCTQLTYKLNRLLPRD--VAVENIEEVAPDLHARFSARRRTYHYYIHFAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P           P  LD   M  AA+ L+  +DF  F    C++ + ++T       +F
Sbjct: 119 NPFKERYSCELHFP--LDFNRMNEAARLLLQTNDFAAF----CKSHTDVKT-------TF 165

Query: 181 GNLIE------------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            N+ E             R+ A  FL   +R+ VG+L  VG G+ ++ D    ++ + R 
Sbjct: 166 CNVTEAVWIRQTADEWYFRISADRFLRNMVRAVVGTLIDVGRGRLSTDDFRAIIETKRRT 225

Query: 229 ECGPLAPPEGLYFDSVEYS 247
             G   P +GL+ + +EY 
Sbjct: 226 AAGESMPAKGLFLEEIEYE 244


>gi|317968841|ref|ZP_07970231.1| tRNA pseudouridine synthase A [Synechococcus sp. CB0205]
          Length = 289

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 122/247 (49%), Gaps = 6/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQ 60
           R  + ++Y+GS Y GWQRQ    S+Q ++E+A+  +   G   VV  AGRTDSGVHA  Q
Sbjct: 12  RIALCLQYDGSAYCGWQRQPRDPSVQEALERALVQLDPDGPATVV-AAGRTDSGVHAAGQ 70

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P     ALN  L  S  I + + + V   +HA FSA  R Y Y I   +
Sbjct: 71  VVHFDCAGPIPPHRWPAALNGRLPAS--IRVRSAASVPADWHACFSATYRRYRYTIYNAR 128

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD + MR A + ++G HDF  F       S    T+    V  
Sbjct: 129 IPNLFLAPWSWHRYQFRLDEDRMREALEGMLGEHDFAAFERAGSARSHSRTTLQEVSVQR 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+E+ + A  FL+  +R  +G L  VG+G+ +     +  + Q R+E    APP+GL
Sbjct: 189 RGDLLEVELQASGFLYGMVRLVMGQLVAVGEGRLSLEAFSRRWRNQAREEVKEAAPPQGL 248

Query: 240 YFDSVEY 246
               V Y
Sbjct: 249 CLLRVGY 255


>gi|56751899|ref|YP_172600.1| tRNA pseudouridine synthase A [Synechococcus elongatus PCC 6301]
 gi|60416392|sp|O24712|TRUA_SYNP6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56686858|dbj|BAD80080.1| tRNA pseudouridine synthase [Synechococcus elongatus PCC 6301]
          Length = 294

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 115/245 (46%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G G+ GWQRQ    S+QG +E AI  V G  V V  AGRTD+GVHA  QVA
Sbjct: 15  RIALVIQYLGQGFCGWQRQPRQRSVQGELESAIAAVVGHPVSVQSAGRTDTGVHAAAQVA 74

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             LN   +++  ++I   +IV   +HARFSA  R Y Y I T   P
Sbjct: 75  HFETTSPIPAHRWPSVLNG--RLTPDLNIRAAAIVPANWHARFSASYRRYRYTIYTDPCP 132

Query: 123 LALEKGRAWLIPKSLDCEN-MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                   W   ++  CEN M+ A Q LVG H    F+    +       +    V    
Sbjct: 133 NLFLNSYVWHYYQAPLCENQMQAALQTLVGYHHLAAFQRSGSKRQHAWVHVQDAWVRRRD 192

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +LIEI V A  FL+  IR  VG L  VG+G  +          Q R      APP+GL  
Sbjct: 193 SLIEIEVQASGFLYGMIRLLVGLLVQVGEGSRSLESFTDIWVNQRRDRVRHAAPPQGLCL 252

Query: 242 DSVEY 246
             + Y
Sbjct: 253 LRIGY 257


>gi|297587193|ref|ZP_06945838.1| tRNA-pseudouridine synthase I [Finegoldia magna ATCC 53516]
 gi|297575174|gb|EFH93893.1| tRNA-pseudouridine synthase I [Finegoldia magna ATCC 53516]
          Length = 244

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 130/247 (52%), Gaps = 14/247 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  QV +F 
Sbjct: 6   LTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVNQPVKINGAGRTDKGVHAKGQVCNFI 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR---QAP 122
           +  +         +N +   SD+I I+    VD  FHARFSA  ++Y Y +  +   +  
Sbjct: 66  VDTDISANQFLMGVNHF--TSDSIVIVKSEEVDLDFHARFSAKSKTYKYILCNKYYMEPW 123

Query: 123 LALEKG-RAWLIPKSL--DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               KG R + +   L   C +M      L+G+HDFT+F +   + ++PIRTID   +  
Sbjct: 124 FNDYKGHRKYYLDFDLLLKCRDM------LIGKHDFTSFVNDLEEDTNPIRTIDEITIEK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +       A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GL
Sbjct: 178 IDDDFVFTFKAESFLRNMVRILVGSMVDVARGRKSIEWLKNALENKDRQSAGITIEPCGL 237

Query: 240 YFDSVEY 246
           Y   +EY
Sbjct: 238 YLMDIEY 244


>gi|255556594|ref|XP_002519331.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223541646|gb|EEF43195.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 344

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 86/254 (33%), Positives = 134/254 (52%), Gaps = 11/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ ++I Y+G+ Y GWQ Q++  +IQ  +EKA+  VT    + +++ GA RTD+GVHA  
Sbjct: 72  KWRLVIAYDGTRYAGWQFQQSPPTIQCYLEKALIQVTKLDRKDLLLVGASRTDTGVHAFG 131

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +  +  +  ALN  L     I +  +S    +FHARFS I + Y Y+I  
Sbjct: 132 QVAHFVTPFNYPSLDTIHAALNGLL--PPDIRVREISPAVPEFHARFSTISKLYHYKIYN 189

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR--SIHCQASSPIRTIDHFD 176
                   +  A+     L+   MR AA++ +G HDF+ F   S   +  +P++TI  FD
Sbjct: 190 DTFMDPFLRHYAYHSTYKLNAAAMRQAAKYFIGSHDFSAFANASRDDRVPNPVKTIFRFD 249

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA-- 234
           V   G L+++ V    FL+ Q+R+ V  L  +G        + K L A+DR+E    A  
Sbjct: 250 VIEMGALLQLEVEGTGFLYRQVRNMVALLLQIGKEAVPPEIVPKILAARDRRELAKYALP 309

Query: 235 -PPEGLYFDSVEYS 247
            PP GL   S++Y+
Sbjct: 310 TPPHGLCLVSIKYN 323


>gi|229053988|ref|ZP_04195422.1| tRNA pseudouridine synthase A [Bacillus cereus AH603]
 gi|228721406|gb|EEL72927.1| tRNA pseudouridine synthase A [Bacillus cereus AH603]
          Length = 252

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 123/251 (49%), Gaps = 9/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGIHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   ++ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIIIRQVEKKTEEFHARYGVEKKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI    
Sbjct: 121 LLSKTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIG 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP 
Sbjct: 181 LIEQDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPG 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y+
Sbjct: 241 HGLYLWQVNYN 251


>gi|256370635|ref|YP_003108460.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri SMDSEM]
 gi|256009427|gb|ACU52787.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri SMDSEM]
          Length = 270

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 135/275 (49%), Gaps = 40/275 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R+ + I Y GS  FGWQ QK   SIQ +IE  + FL+  +I ++ GAGRTD+GVHA++ 
Sbjct: 1   MRFFIEISYKGSSLFGWQIQKKNLSIQETIETCLSFLLKKKIKII-GAGRTDTGVHAIQM 59

Query: 61  VAHFDLVREW---------------VPVILCK---------ALNAYLKISDTISILNLSI 96
            AHFDL  +                +   L K          LN++L ++  I I+N+  
Sbjct: 60  FAHFDLTFDLTFDLTFDLTFDLTFDLTFDLTKNHINNHFKSKLNSFLPLN--IKIINIFS 117

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           V K  HARF+AI R Y YRI   + P   +    WL    ++ + ++  A  L    DF+
Sbjct: 118 VKKNIHARFNAISRVYEYRISLSKDPFLFQTSWQWLSKNQIELKILKKGANILKKYKDFS 177

Query: 157 TF-----RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           +F     +   C+ S+    +         N++  R+ A  FL   +RS VG+L  +G  
Sbjct: 178 SFCKEKSKKNLCEISTAKWILKK-------NILYFRIEANRFLRNMVRSLVGTLIELGIK 230

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           K T  D  K ++A++R   G  AP +GL+   + Y
Sbjct: 231 KITIKDFIKIIEAKNRNLAGITAPAKGLFLIKINY 265


>gi|81301016|ref|YP_401224.1| tRNA pseudouridine synthase A [Synechococcus elongatus PCC 7942]
 gi|81169897|gb|ABB58237.1| tRNA pseudouridine synthase A [Synechococcus elongatus PCC 7942]
          Length = 294

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 115/245 (46%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G G+ GWQRQ    S+QG +E AI  V G  V V  AGRTD+GVHA  QVA
Sbjct: 15  RIALVIQYLGQGFCGWQRQPRQRSVQGELESAIAAVVGHPVSVQSAGRTDTGVHAAAQVA 74

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             LN   +++  ++I   +IV   +HARFSA  R Y Y I T   P
Sbjct: 75  HFETTSPIPAHRWPSVLNG--RLTPDLNIRAAAIVPANWHARFSASYRRYRYTIYTDPCP 132

Query: 123 LALEKGRAWLIPKSLDCEN-MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                   W   ++  CEN M+ A Q LVG H    F+    +       +    V    
Sbjct: 133 NLFLNSYVWHYYQAPLCENQMQAALQTLVGYHHLAAFQRSGSKRQHAWVHVQDAWVRRRD 192

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +LIEI V A  FL+  IR  VG L  VG+G  +          Q R      APP+GL  
Sbjct: 193 SLIEIEVQASGFLYGMIRLLVGLLVQVGEGSRSLESFTDIWVNQRRDRVRHAAPPQGLCL 252

Query: 242 DSVEY 246
             + Y
Sbjct: 253 LRIGY 257


>gi|251781741|ref|YP_002996043.1| tRNA pseudouridine synthase A [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390370|dbj|BAH80829.1| phosphomethylpyrimidine kinase [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 249

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 130/251 (51%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  ++Q  IEK +  L + + V +HGAGRTD+GVHA  
Sbjct: 1   MTRYRATISYDGTLFSGFQRQSHARTVQEEIEKTLQKLASVQPVPIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +    I +++L+IV   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDLEKLRFALDT--QTPADIDVVDLAIVADDFHCRYQKHSKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDINKMQEAIKDLVGTHDFTGFTAAGTSVENKVRTITEATLVQ 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +  G L+        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP    
Sbjct: 179 DDKTGFLV-FTFSGNGFLYKQVRNMVGTLLKIGNGRMPVEQIKVILDSKNRQLAGPTPAG 237

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 238 NGLYLKEIRYE 248


>gi|229542172|ref|ZP_04431232.1| tRNA pseudouridine synthase A [Bacillus coagulans 36D1]
 gi|229326592|gb|EEN92267.1| tRNA pseudouridine synthase A [Bacillus coagulans 36D1]
          Length = 245

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 119/247 (48%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+GS + G+Q Q    ++Q  IEKA+  L  G  V    +GRTD+GVHA+ 
Sbjct: 1   MKRVKCTVSYDGSRFAGYQVQPGQRTVQQEIEKALATLHKGRHVKTAASGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L     IS+   +  D  FHAR+S   + Y YRI   
Sbjct: 61  QVIHFDTDLSIPETSWPAALNSLL--PGDISVSKAAYADPAFHARYSVKEKEYRYRIYFS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 +   A  +  SLD E M  AA+ ++G HDFT+F S   +    IRT+       
Sbjct: 119 HVRSPFKHRYALRVWYSLDIEAMEAAAETVLGTHDFTSFCSAKTEVEDKIRTLKEIRFLQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + I      FL+  +R   G+L  +G GK    ++ + L+ ++R   G  APPEGL
Sbjct: 179 QDDELVICFKGNGFLYNMVRILTGTLLEIGSGKRDPGEMREILEKRNRIYAGKTAPPEGL 238

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 239 YLWKVSY 245


>gi|218245114|ref|YP_002370485.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8801]
 gi|226708647|sp|B7K222|TRUA_CYAP8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|218165592|gb|ACK64329.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8801]
          Length = 293

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 117/245 (47%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y GS + GWQ Q N  ++Q  IE AI  V GE V +HGAGRTD+GVHA  QVA
Sbjct: 11  RVALVIQYLGSRFHGWQWQPNQRTVQAEIENAIAEVLGETVTLHGAGRTDAGVHAAAQVA 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+V           LNA  ++ + I I   + V   +HARFSA  R Y Y   T Q P
Sbjct: 71  HFDMVSPIPASRWVDILNA--RLPEDILIRGSAQVPLTWHARFSAQWRRYRYTFYTEQRP 128

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               K  +W      LD   M+ A   L+GRH    F     +       +     +  G
Sbjct: 129 NLFVKPYSWHYYHFPLDESLMQQALNPLLGRHHLAAFHRAGSRRDHSWVEVQSTHCHRQG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK +  +  +  + Q R+     AP +GL  
Sbjct: 189 PFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLENFTEIWRKQQREAVKYAAPAKGLCL 248

Query: 242 DSVEY 246
             V Y
Sbjct: 249 LRVGY 253


>gi|257058139|ref|YP_003136027.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8802]
 gi|256588305|gb|ACU99191.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8802]
          Length = 293

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 117/245 (47%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y GS + GWQ Q N  ++Q  IE AI  V GE V +HGAGRTD+GVHA  QVA
Sbjct: 11  RVALVIQYLGSRFHGWQWQPNQRTVQAEIENAIAEVLGETVTLHGAGRTDAGVHAAAQVA 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+V           LNA  ++ + I I   + V   +HARFSA  R Y Y   T Q P
Sbjct: 71  HFDMVSPIPASRWVDILNA--RLPEDILIRGSAQVPLTWHARFSAQWRRYRYTFYTEQRP 128

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               K  +W      LD   M+ A   L+GRH    F     +       +     +  G
Sbjct: 129 NLFVKPYSWHYYHFPLDESLMQQALNPLLGRHHLAAFHRAGSRRDHSWVEVQSTHCHRQG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK +  +  +  + Q R+     AP +GL  
Sbjct: 189 PFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLENFTEIWRKQQREAVKYAAPAKGLCL 248

Query: 242 DSVEY 246
             V Y
Sbjct: 249 LRVGY 253


>gi|227431309|ref|ZP_03913362.1| pseudouridylate synthase [Leuconostoc mesenteroides subsp. cremoris
           ATCC 19254]
 gi|227352902|gb|EEJ43075.1| pseudouridylate synthase [Leuconostoc mesenteroides subsp. cremoris
           ATCC 19254]
          Length = 255

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/258 (33%), Positives = 132/258 (51%), Gaps = 14/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIFLV----TGEIVVVHGAGRT 51
           M RY  +I Y+G+ +FG+Q Q KNG     ++QG + K I  +    + +I VV GA RT
Sbjct: 1   MPRYKAVIAYDGAEFFGFQLQTKNGVESVRTVQGELNKVINKMAKNPSPQIKVV-GASRT 59

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D+GVHA  QV HFDL     P  + K +N  L     + + ++  V   FHARF+   + 
Sbjct: 60  DTGVHAFGQVIHFDLPFNIDPEGVRKGMNTLLPFD--VVVNHVEHVSDDFHARFNTHSKR 117

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y+YR+ T       ++         LD   ++ A   L+G HDF +F +   + ++ IR 
Sbjct: 118 YIYRVSTTDYKDPFKRKYTGHFHWKLDINRIKAALPDLLGEHDFASFAASGNETATTIRL 177

Query: 172 IDHFDVNSFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           I   DV+      EI       +FL+ QIR  VG L  +G GK    D+ + ++ +DR++
Sbjct: 178 ITRADVDEKPEEHEIVFTFEGNAFLYNQIRIMVGVLLEIGTGKRPVHDIVRLIEVKDREQ 237

Query: 230 CGPLAPPEGLYFDSVEYS 247
               AP  GLY D ++Y+
Sbjct: 238 ARYTAPASGLYLDEIDYN 255


>gi|295102064|emb|CBK99609.1| pseudouridylate synthase I [Faecalibacterium prausnitzii L2-6]
          Length = 251

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 123/248 (49%), Gaps = 5/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL  +
Sbjct: 1   MNYLLKLSYDGTNYCGFQVQPNGRSVAAAFQDALEAVLGCRPDIKGCSRTDAGVHALGFM 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F          L  ALN +L     I  L   +V   FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPAAKLPLALNQHLPPD--IRALEARVVPDDFHARYAAHTKTYLYRIHNSPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS---PIRTIDHFDVN 178
                      +P  LD + M+ AAQ+ VG+HDF    +    A++    +RTI   DV 
Sbjct: 119 DSPFAARYYTKVPGRLDADRMQQAAQYFVGKHDFLALCASGSSAAAHGDTVRTITACDVQ 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+I V A  +L+  +R   G+L   G G+     +   L +++RK  GP    +G
Sbjct: 179 RRGDDIDITVTADGYLYNMVRILAGTLCEAGAGRLAPEAVPGILASRERKNAGPTLAAKG 238

Query: 239 LYFDSVEY 246
           L+  SV+Y
Sbjct: 239 LFLKSVDY 246


>gi|330444180|ref|YP_004377166.1| tRNA pseudouridine synthase A [Chlamydophila pecorum E58]
 gi|328807290|gb|AEB41463.1| tRNA pseudouridine synthase A [Chlamydophila pecorum E58]
          Length = 267

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 125/249 (50%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +++ Y G+ Y GWQRQ    +IQ  +E     +    V +  +GRTDSGVHA  Q
Sbjct: 1   MKKIVLLLAYQGTAYAGWQRQPQHLTIQEVLETLFMPILHSRVPMVASGRTDSGVHAYGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           V HF L    +   P  L K LNA  ++   I + ++++ D  FHAR+ AI + Y Y + 
Sbjct: 61  VVHFSLPDHPLTSDPCKLKKLLNA--RLPKDIVVRDIALTDASFHARYCAIAKEYHYTLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++  ++  P  +  + M   AQ+L+G HDF +F ++  + +S IRT+    +
Sbjct: 119 KNIKPLPWQRNFSYSPPHRIRADLMHQGAQYLIGTHDFASFANLGREYTSTIRTLYKVAI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + + +      FL+  +R+ VG+L  +  G +    +   L+ ++R++  P AP  
Sbjct: 179 EETEHTLTLIFKGNGFLYKMVRNLVGALLDINKGAYPPEHILNMLKEKNRRKGPPSAPAH 238

Query: 238 GLYFDSVEY 246
            L    V Y
Sbjct: 239 ALSLHHVCY 247


>gi|198276843|ref|ZP_03209374.1| hypothetical protein BACPLE_03048 [Bacteroides plebeius DSM 17135]
 gi|198270368|gb|EDY94638.1| hypothetical protein BACPLE_03048 [Bacteroides plebeius DSM 17135]
          Length = 252

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/251 (34%), Positives = 127/251 (50%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY + + Y+G+ Y GWQ Q NGSS+Q ++ KA+   +  E + V GAGRTD+GVHA  
Sbjct: 1   MFRYFIYLAYDGTNYHGWQIQPNGSSVQETLMKALHTFLRDEAIEVVGAGRTDAGVHARL 60

Query: 60  QVAHFDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            VAHFD+  EW+     +   LN  L     IS+  +  V++  HARF A  R+Y Y + 
Sbjct: 61  MVAHFDV--EWMLDEDTVTDKLNRLLPPD--ISVYRVRRVNQDAHARFDATYRTYKYYVT 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHF 175
           T++ P    +   W + + LD   M  AAQ L    DFT+F  +H    +    I   H+
Sbjct: 117 TQKNP--FNRAYCWRLFQPLDFTKMNEAAQILFDYTDFTSFSKLHTDVKTNNCKIMHAHW 174

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D  S    +   + A  FL   +R+ VG+L  VG GK +     K ++ ++R   G   P
Sbjct: 175 DQVSETEWV-FTIQADRFLRNMVRAIVGTLVEVGRGKLSVEGFRKVIEEKNRCSAGTSVP 233

Query: 236 PEGLYFDSVEY 246
              L+   + Y
Sbjct: 234 GHALFLVDIGY 244


>gi|225387194|ref|ZP_03756958.1| hypothetical protein CLOSTASPAR_00946 [Clostridium asparagiforme
           DSM 15981]
 gi|225046673|gb|EEG56919.1| hypothetical protein CLOSTASPAR_00946 [Clostridium asparagiforme
           DSM 15981]
          Length = 259

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q N  +I+  + KA+  +  E + V GA RTD+GVHA   
Sbjct: 7   MRRIRLVVAYDGTNYHGWQYQPNAVTIEEVLNKALTELLREPIAVIGASRTDAGVHAQGN 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C A+N   ++ + I + +   V   +H R     ++Y Y+I+ R+
Sbjct: 67  VAVFDTKNRMAADKICLAVNQ--RLPEDIRVQSSEEVATDWHPRKRRCVKTYEYKILNRR 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
             +  ++   +     LD E MR AA+ ++G HDF +F S   Q +  +RT+    +   
Sbjct: 125 IEMPDKRLYTYHCYYDLDLEKMRQAAEFILGEHDFKSFCSAKTQVTDTVRTVYDLKLERD 184

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IR+    FL+  +R   G+L   G G      + + L A+DR++ GP AP +GL
Sbjct: 185 QEDVITIRITGSGFLYNMVRIIAGTLLWAGTGLIRPEAVGEILAAEDRRKAGPTAPAKGL 244

Query: 240 YFDSVEY 246
               + Y
Sbjct: 245 TLIRMHY 251


>gi|320528746|ref|ZP_08029898.1| tRNA pseudouridine synthase A [Solobacterium moorei F0204]
 gi|320130956|gb|EFW23534.1| tRNA pseudouridine synthase A [Solobacterium moorei F0204]
          Length = 361

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 125/248 (50%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY  ++ Y G  Y GWQ Q+ G SIQ  +E  I  +T E V V G+GRTD+GV+A  Q
Sbjct: 1   MMRYKCVVSYVGRNYSGWQSQRKGDSIQEILETVIERITQEKVNVIGSGRTDAGVNAKAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD  RE        A+NA+L   + I I+++   D  FHAR++   + Y YRI    
Sbjct: 61  VFMFDTKREMPARKWMGAINAFL--PNDIHIMSVEEEDDCFHARYNVRFKQYNYRI--NN 116

Query: 121 APL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVN 178
            P     K  A+  P  LD E M+    +LVG HDFT+  S   +     +RT+    + 
Sbjct: 117 GPYNVFTKDTAFQCPIHLDVEKMKEGIPYLVGTHDFTSLNSSSLEEYPDQVRTVRSITLT 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               +I +  V + FL   +R     L  +G  K+  + +++ L+A+ +      +P EG
Sbjct: 177 EEDGVITLAFVGKGFLRYMVRMMASVLIEIGKRKYEPSHIQEILEAKRKSFPHKNSPAEG 236

Query: 239 LYFDSVEY 246
           L  + V+Y
Sbjct: 237 LTLEYVDY 244


>gi|258509450|ref|YP_003172201.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus GG]
 gi|257149377|emb|CAR88350.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus GG]
 gi|259650729|dbj|BAI42891.1| tRNA pseudouridine synthase [Lactobacillus rhamnosus GG]
          Length = 247

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + +A+N+ + +   I IL   IV   FHAR+SA  + Y YR+   
Sbjct: 61  QVISFDYPGNIPAESMLRAMNSLMPLD--IEILKAEIVAADFHARYSAKGKRYRYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEE 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  
Sbjct: 179 DPAANELVFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|16329915|ref|NP_440643.1| tRNA pseudouridine synthase A [Synechocystis sp. PCC 6803]
 gi|3915173|sp|P73295|TRUA_SYNY3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1652401|dbj|BAA17323.1| pseudouridine synthase 1 [Synechocystis sp. PCC 6803]
          Length = 275

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 121/246 (49%), Gaps = 4/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++++Y G+ + GWQRQ N SSIQ  +E AI  V G+ V +HGAGRTD+GVHA  QVA
Sbjct: 11  RVALVMQYLGTHFHGWQRQPNFSSIQEEVELAIAKVVGQPVTLHGAGRTDAGVHAAAQVA 70

Query: 63  HF-DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HF D V +  P    K LN +L     I +   + VD  +HARFSA+ R Y Y I T Q 
Sbjct: 71  HFDDPVGQIPPHRWSKILNGHLP--QDIIVRGSAAVDSHWHARFSALWRRYRYSIYTDQW 128

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P       +W   +  L  + ++ A + L+G+H    F             +   +    
Sbjct: 129 PNLFADQFSWHYYRFPLQEKTIQAAMEPLLGKHHLAAFHRAGSARRHSWVEVQGVECYRR 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G ++ + + A  FL+  +R  VG L  VG G+ + TD       Q R      AP +GL 
Sbjct: 189 GPMVYLEIQANGFLYGMVRLLVGMLAEVGSGQRSLTDFNDIWVNQRRDLVKYAAPAKGLC 248

Query: 241 FDSVEY 246
              V Y
Sbjct: 249 LLRVGY 254


>gi|67923564|ref|ZP_00517037.1| tRNA pseudouridine synthase [Crocosphaera watsonii WH 8501]
 gi|67854590|gb|EAM49876.1| tRNA pseudouridine synthase [Crocosphaera watsonii WH 8501]
          Length = 285

 Score =  129 bits (325), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 115/246 (46%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y GS + GWQRQ N  ++Q  IE AI  V G    +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYQGSRFHGWQRQPNQRTVQEDIETAIAQVLGYHTPIHGAGRTDAGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD V    P      LN   ++ + I I     V   +HARFSA+ R Y Y   T + P
Sbjct: 72  HFDYVSPIPPQRWADILNH--RLPEDILIRGSQGVPATWHARFSALWRRYRYSFYTDKCP 129

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               K  +W    + L+ E M+ A   L+G+H    FR            +        G
Sbjct: 130 NLFVKPFSWHYYYEPLNVELMQKALNPLLGKHHLAAFRRAGSHRHHSWVEVQDTQCYRQG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK +  +     Q Q R+     AP +GL  
Sbjct: 190 PFIHLEIQANGFLYGMVRLLVGMLVEVGSGKRSLHNFTDIWQNQRRELVKYSAPAKGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|228473082|ref|ZP_04057839.1| tRNA pseudouridine synthase A [Capnocytophaga gingivalis ATCC
           33624]
 gi|228275664|gb|EEK14441.1| tRNA pseudouridine synthase A [Capnocytophaga gingivalis ATCC
           33624]
          Length = 240

 Score =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 126/245 (51%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQRQ +  S+Q  +E+A+ ++  + + + GAGRTD+GVHA    
Sbjct: 1   MRYFIQLSYNGKNYCGWQRQPHSPSVQEELEEAMSMLLKKEIALVGAGRTDTGVHARDYY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD     +P  L + LN++L     I+I  +  V    HARF A  R+Y Y I   + 
Sbjct: 61  AHFD-SDSSLPDRLVEKLNSFL--PKEIAIKQIFPVKNDAHARFDACSRTYQYFIALEKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E+  ++ I   LD   M  A + L+   DF  F  ++    +    +        G
Sbjct: 118 PFLYEQ--SYYIHFPLDLSLMNKAGEILLQHTDFQCFSKVNTDVKTYNCQLKEAYWRKEG 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           NL+  R+ A  FL   +R+ VG++  +G G+ +  DL++ L ++DR + G   P   L+ 
Sbjct: 176 NLLIFRITADRFLRNMVRAIVGTMIEIGRGRLSLEDLQQILLSKDRSKAGYSVPGHALFL 235

Query: 242 DSVEY 246
           + + Y
Sbjct: 236 EEIIY 240


>gi|225872353|ref|YP_002753808.1| tRNA pseudouridine synthase A [Acidobacterium capsulatum ATCC
           51196]
 gi|225793375|gb|ACO33465.1| tRNA pseudouridine synthase A [Acidobacterium capsulatum ATCC
           51196]
          Length = 254

 Score =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 88/254 (34%), Positives = 124/254 (48%), Gaps = 11/254 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + + + + Y+G+ Y GWQ Q    +IQG +  A+  +TGE V+  G+GRTD+GVHAL QV
Sbjct: 3   LNWKLTLAYDGTDYRGWQVQPELPTIQGELAAAVERITGERVLPQGSGRTDAGVHALGQV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A F L        L +ALN  L  +  I +L    + + FHAR SA  + Y YRI   + 
Sbjct: 63  ASFVLKAPIPAENLHRALNRTLPAA--IRVLGAESMPEDFHARHSARSKWYEYRIFRGEV 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---------RSIHCQASSPIRTI 172
                    + +   LD E MR AA   VG HDF +F         R       S +RTI
Sbjct: 121 CPPWTARYVYALHWPLDVEAMRRAAAAFVGEHDFRSFAASDPDVAARGSEDAEESHVRTI 180

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                    +L+  RV    FLH  +R+ VG++  VG  ++ + D+   L  +DR   G 
Sbjct: 181 FASGWAEEDDLLIYRVHGNGFLHHMVRNLVGTMIGVGRRQFDAEDMPGLLALRDRSAAGA 240

Query: 233 LAPPEGLYFDSVEY 246
            AP  GL+  SV Y
Sbjct: 241 TAPARGLFLYSVCY 254


>gi|166033550|ref|ZP_02236379.1| hypothetical protein DORFOR_03276 [Dorea formicigenerans ATCC
           27755]
 gi|166026735|gb|EDR45492.1| hypothetical protein DORFOR_03276 [Dorea formicigenerans ATCC
           27755]
          Length = 266

 Score =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/266 (32%), Positives = 132/266 (49%), Gaps = 22/266 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +I+  + + I  +TGE + + GA RTDSGVHAL  
Sbjct: 1   MRRIRIVVAYDGTNYCGWQIQPNGITIEEILNRQISKLTGEDIRIIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF-SAIRRSYLYRIITR 119
           VA FD            ALN   K+ + I I+    V   +H R+ + I ++Y Y I   
Sbjct: 61  VAVFDTESRIPGDRFAYALNQ--KMPEDIVIVRSDEVQIDWHPRYQNEISKTYEYHIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI------- 172
           +    L+   +  +   LD E MR  A++++G HDF +F ++   A   +RT+       
Sbjct: 119 KVRNPLKNRYSTFVSFDLDVEKMRQGAKYILGEHDFASFCNVRTNAKDTVRTVHEITIKE 178

Query: 173 ---DHFDVNSFG----NL-----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
              D F  +++G    NL     I IRV    FL+  +R   G+L  VG G +    +  
Sbjct: 179 IPMDKFQASNWGQENSNLENEKEIVIRVTGNGFLYNMVRIIAGTLIRVGRGFYEPEKIRD 238

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEY 246
            L+A++    G  APP GL   S++Y
Sbjct: 239 ILEAKEHTSEGITAPPNGLVLVSIDY 264


>gi|327314538|ref|YP_004329975.1| tRNA pseudouridine synthase A [Prevotella denticola F0289]
 gi|326944120|gb|AEA20005.1| tRNA pseudouridine synthase A [Prevotella denticola F0289]
          Length = 255

 Score =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 83/268 (30%), Positives = 128/268 (47%), Gaps = 37/268 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E+++ ++  E + V GAGRTD+GVH    
Sbjct: 3   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLERSLSILLKETITVTGAGRTDAGVHGRMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  + +    L   +N  L     +S+  +  V    HARFSA+ R+Y Y I T +
Sbjct: 63  VAHFDTAQPFDSEQLVYKMNRLLP--RDVSVSRIKAVSADLHARFSAVSRTYHYYIHTGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P +  +  +  I   LD + M  AA +L+G  DF  F    C+A + ++T       +F
Sbjct: 121 QPFS--RRYSCEIHYPLDFDKMNEAASYLIGEKDFKCF----CKAGADVKT-------TF 167

Query: 181 GNLIEIR----------------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            NL E R                      + A  FL   +R+ VG+L  VG G+ +  D 
Sbjct: 168 CNLTEARWIPSGDGLSLSSGGTIANWCFVITANRFLRNMVRAVVGTLVDVGRGRLSLADF 227

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + +    R + G   P   L+   ++Y
Sbjct: 228 RQIVDGGTRSDAGESMPGNALFLWDIKY 255


>gi|330790485|ref|XP_003283327.1| hypothetical protein DICPUDRAFT_25596 [Dictyostelium purpureum]
 gi|325086752|gb|EGC40137.1| hypothetical protein DICPUDRAFT_25596 [Dictyostelium purpureum]
          Length = 323

 Score =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 94/289 (32%), Positives = 134/289 (46%), Gaps = 47/289 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           RY +  EY G  + GWQR     N   +Q  +E ++  +  + + V G+ RTDSGV AL 
Sbjct: 4   RYKITYEYVGKYFTGWQRLTYDINPLPVQNVLENSLKHICNKEIKVFGSSRTDSGVSALG 63

Query: 60  QVAHFDL----VREWVPVILCKALNAYLKIS--------DTISILNLSIVDKQFHARFSA 107
             +HFD+     R+  P+ L       + I+        D + I+   IVD  FH+RF A
Sbjct: 64  NTSHFDIDQRTSRKGKPLPLLTTDELTMAINYNVGEQYLDRVRIIKTEIVDDNFHSRFHA 123

Query: 108 IRRSYLYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
             R+YLY+I+     +Q PL L   R   I   LD   M+ AA+ LVGRHDF++FRS  C
Sbjct: 124 TSRTYLYKILANCGKKQTPLEL-LDRVLEISFILDVNKMKEAAEILVGRHDFSSFRSKDC 182

Query: 164 QASSPIRTIDHF--------------------------DVNSFGNLIEIRVVARSFLHTQ 197
              +P+RTI++                           +VN     I I + A+SFLH Q
Sbjct: 183 -TKNPVRTIEYIKIIELPTPEIIRYHPDFINCSKEINNNVNHGLQYIGIEIKAQSFLHNQ 241

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +R    +L  VG G  T   L++ L+ +DR         E L    V Y
Sbjct: 242 VRIMSSALIEVGKGTITKDQLKEILEKKDRLAAPSTIASEPLTLIKVSY 290


>gi|257088005|ref|ZP_05582366.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
 gi|256996035|gb|EEU83337.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
          Length = 234

 Score =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 123/235 (52%), Gaps = 5/235 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGP 233


>gi|300870453|ref|YP_003785324.1| tRNA-pseudouridine synthase TrmA [Brachyspira pilosicoli 95/1000]
 gi|300688152|gb|ADK30823.1| tRNA-pseudouridine synthase, TrmA [Brachyspira pilosicoli 95/1000]
          Length = 247

 Score =  129 bits (324), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 130/244 (53%), Gaps = 6/244 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I+Y+G+ +FGWQ Q N  ++QG I KA+  +  +   ++G GRTD+GVHAL Q
Sbjct: 1   MTNIKITIQYDGTDFFGWQIQPNLRTVQGEIYKAVQKIYSKKSTIYGCGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA+F + +  VP+  + +ALN+ L     I I+   +VD  F+AR SA  R Y+Y +   
Sbjct: 61  VANFRVEKMLVPIERVTRALNSAL--PKDIRIIKSEVVDDSFNARASATFREYIYVVQNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENM-RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              +   +  +W   K++  E +    A++LVG H+FT+F S   +  S  R I+     
Sbjct: 119 DISVPFYERYSWFYRKNIINEKLINEYAKYLVGEHNFTSFCSTEDENDSKFRYIERVRAI 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD-LEKALQAQDRKECGPLAPPE 237
              + I   +   +FLH  +R  VG+L + G  K    + +E+ L+ +DR      AP  
Sbjct: 179 RKKDTIYFIIRGNAFLHNMVRIIVGTL-VEGQRKNMPVNFIEEILKKEDRTLAFVTAPAH 237

Query: 238 GLYF 241
           GLYF
Sbjct: 238 GLYF 241


>gi|169824810|ref|YP_001692421.1| tRNA pseudouridine synthase A [Finegoldia magna ATCC 29328]
 gi|238687759|sp|B0S2E1|TRUA_FINM2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167831615|dbj|BAG08531.1| tRNA pseudouridine synthase A [Finegoldia magna ATCC 29328]
          Length = 244

 Score =  129 bits (323), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 130/247 (52%), Gaps = 14/247 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  QV +F 
Sbjct: 6   LTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVHQPVKINGAGRTDKGVHAKGQVCNFI 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR---QAP 122
           +  +         +N +   SD+I I+    +D  FHARFSA  ++Y Y +  +   +  
Sbjct: 66  VDTDISANQFLMGVNHF--TSDSIVIVKSEEMDLDFHARFSAKSKTYKYILCNKYYMEPW 123

Query: 123 LALEKG-RAWLIPKSL--DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               KG R + +   L   C +M      L+G+HDFT+F +   +  +P+RTID   +  
Sbjct: 124 FNDYKGHRKYYLDFDLLLKCRDM------LIGKHDFTSFVNDLEEDINPVRTIDEITIEK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I     A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GL
Sbjct: 178 IDDDIVFTFKAESFLRNMVRILVGSMVDVARGRKSIDWLKNALENKDRQSAGITIEPSGL 237

Query: 240 YFDSVEY 246
           Y   +EY
Sbjct: 238 YLMDIEY 244


>gi|332881976|ref|ZP_08449617.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332680102|gb|EGJ53058.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 250

 Score =  129 bits (323), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 82/245 (33%), Positives = 119/245 (48%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG  Y GWQ Q    ++QG ++ A+  +  E + V GAGRTDSGVHAL+  
Sbjct: 1   MRYFIEFSYNGKNYHGWQLQPKAITVQGVLQNALTTILREEISVIGAGRTDSGVHALQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE +   L + LNA+L     I++ ++  V    HARF A++R+Y Y I   ++
Sbjct: 61  AHFDTERE-LSDDLVRKLNAFLPYD--IAVHSICAVKPDAHARFDALKRTYQYHISIEKS 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P          +P ++D   M  AAQ L    DF  F   H    +    I        G
Sbjct: 118 PFRYNYSMPLTLPLNIDV--MNEAAQILFDYTDFQCFSKTHTDVKTFNCKIYEAHWAVVG 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   + A  FL   +R+ VG+L  VG  K + T  E  + ++ R + G   P  GL+ 
Sbjct: 176 GELVFTITADRFLRNMVRAIVGTLINVGLQKLSLTGFEDIIISKSRSKAGASVPACGLFL 235

Query: 242 DSVEY 246
             V Y
Sbjct: 236 TQVTY 240


>gi|51245176|ref|YP_065060.1| tRNA pseudouridine synthase A [Desulfotalea psychrophila LSv54]
 gi|62901428|sp|Q6ANM1|TRUA1_DESPS RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|50876213|emb|CAG36053.1| related to tRNA pseudouridine synthase A [Desulfotalea psychrophila
           LSv54]
          Length = 251

 Score =  129 bits (323), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 84/259 (32%), Positives = 132/259 (50%), Gaps = 21/259 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M   C++I ++G+ Y GWQ+Q + ++IQG IE  +  ++ + + +HGAGRTD+GVHA   
Sbjct: 1   MRNICLLIAFDGTDYSGWQKQHHANTIQGEIEARLKRLSVKEISLHGAGRTDAGVHADGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHF            +ALN  L     I IL +  +   FHARF+A  + Y YR+ T  
Sbjct: 61  TAHFHTDTRLTCNDFQRALNRML--PGAIRILQVREMADDFHARFAATGKEYHYRLFT-- 116

Query: 121 APLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ------ASSPIRTI 172
             +   + R +++   K +D E M+   Q ++G HDF++F +   +          +RTI
Sbjct: 117 GGVIPPQKRLYMLHQEKPIDQEAMQKCLQIIIGTHDFSSFENTGSRDKTRTGGKGAVRTI 176

Query: 173 -----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                + F+ +S+        +   FL   +R+ VGS+  VG GK +    E+AL+ +DR
Sbjct: 177 LEARYEQFEEDSW----HFVFIGDGFLRNMVRNIVGSILEVGRGKESVEWFEQALKEKDR 232

Query: 228 KECGPLAPPEGLYFDSVEY 246
              GP AP  GL    V Y
Sbjct: 233 NAAGPTAPAHGLKLFQVFY 251


>gi|258513673|ref|YP_003189895.1| tRNA pseudouridine synthase A [Desulfotomaculum acetoxidans DSM
           771]
 gi|257777378|gb|ACV61272.1| tRNA pseudouridine synthase A [Desulfotomaculum acetoxidans DSM
           771]
          Length = 250

 Score =  129 bits (323), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 84/244 (34%), Positives = 125/244 (51%), Gaps = 5/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+ Y G+Q QK     +IQG +++ +  +  E + V  AGRTDSGVHA  QV +
Sbjct: 9   VILAYDGTNYHGFQIQKGKRLPTIQGVLQRELSHLAKETITVTTAGRTDSGVHARGQVFN 68

Query: 64  FDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +PV  +  ALN+ L     I  L+   VD  FHAR+SA+ ++Y Y I   Q  
Sbjct: 69  FFTGNWQIPVDRVIYALNSVL--PPDIRALSAEEVDLGFHARYSALAKTYCYYISRDQIV 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  ++     LD ++MR A  H+ G HDF +F +      S IRTI   D+     
Sbjct: 127 SPFTRLYSYQYNYPLDLDDMRQAVLHITGEHDFKSFMASGSLVKSTIRTIYQIDLIEKDK 186

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           ++        FL+  +R   G+L  VG GK   +++E  L+  DRK  G   P  GL+ +
Sbjct: 187 MLIFTFRGNGFLYHMVRIITGTLLQVGTGKIHYSEIETILKKCDRKSAGATVPALGLFLE 246

Query: 243 SVEY 246
            VEY
Sbjct: 247 RVEY 250


>gi|288817539|ref|YP_003431886.1| pseudouridylate synthase [Hydrogenobacter thermophilus TK-6]
 gi|288786938|dbj|BAI68685.1| pseudouridylate synthase [Hydrogenobacter thermophilus TK-6]
 gi|308751142|gb|ADO44625.1| tRNA pseudouridine synthase A [Hydrogenobacter thermophilus TK-6]
          Length = 241

 Score =  129 bits (323), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 131/244 (53%), Gaps = 5/244 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y +++ Y G+ + GWQ Q N  ++QG I++++  V  E + + G  RTD+GVHA   
Sbjct: 1   MPNYVLLLSYVGTNFHGWQVQPNLRTVQGVIKESLEKVFREDIKLVGCCRTDAGVHAKEY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F   +E  P  L KALN+ L   + + I  +  V + F+AR+S   + Y+YR++   
Sbjct: 61  VANFYAKKEMEPYKLLKALNSLL--PEDVGIKRV-WVQEGFNARYSVRGKVYVYRVLNSF 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  A  +  AW +P+ LD   M+ A + L GR DF+ F     +  + +  ++   ++  
Sbjct: 118 SRDAFIEPFAWRVPQKLDLSKMQKACELLAGRRDFSAFAKKEEEDKNTVIDLEEVRLSKV 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LIEI   ARSFL   +R  VG +  +G G+   + LE+ L   +RK C   A  +GL 
Sbjct: 178 EDLIEISFRARSFLRYMVRRMVGCMVQIGLGRINLSHLEEYL--SNRKTCPYTAKAKGLT 235

Query: 241 FDSV 244
            + V
Sbjct: 236 LEKV 239


>gi|255655803|ref|ZP_05401212.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-23m63]
 gi|296450959|ref|ZP_06892706.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296879075|ref|ZP_06903071.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
 gi|296260177|gb|EFH07025.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296429948|gb|EFH15799.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
          Length = 245

 Score =  129 bits (323), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 82/242 (33%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MI+ Y+GS Y G+Q+   N  +IQ  +E  +  +T E V + G+GRTD G HA  QV +F
Sbjct: 6   MIVAYDGSRYKGYQKLGDNNMTIQEKLENVLSKMTNETVEIIGSGRTDMGAHARGQVVNF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + K L  YL   + I +  +  VD++FH+R++   ++Y+YRI   +    
Sbjct: 66  RTNCMDSLDKIQKYLYEYL--PEDIVVKAVEEVDERFHSRYNVKSKTYMYRIDNNKYHNP 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  A  + K LD + MR A+++LVG HDFT+F S   +  S +R I   ++    N+I
Sbjct: 124 FIRKYATHVSKKLDLDRMRKASEYLVGEHDFTSFASSKSKKKSNVREIYSINIKEDDNII 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           EI V    FL+  +R  VG+L  VG  +    D++  L+++DR +    AP +GL    V
Sbjct: 184 EIYVEGNGFLYNMVRIIVGALIDVGLKRRAPQDIKYMLESRDRCQSSDTAPAKGLCLWKV 243

Query: 245 EY 246
            Y
Sbjct: 244 RY 245


>gi|254446439|ref|ZP_05059915.1| tRNA pseudouridine synthase A [Verrucomicrobiae bacterium DG1235]
 gi|198260747|gb|EDY85055.1| tRNA pseudouridine synthase A [Verrucomicrobiae bacterium DG1235]
          Length = 243

 Score =  129 bits (323), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 131/248 (52%), Gaps = 8/248 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+     Y+G+ Y GWQ+Q    S+Q  IE+ +  +  E V +HG+GRTD+GVHAL QV
Sbjct: 1   MRWKCSCSYDGTNYAGWQKQSGQISVQQVIEEVLEQLLKEKVAIHGSGRTDAGVHALEQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD         L KAL++  K+   I + + + V ++FHARFSA+ + Y YR+   +A
Sbjct: 61  FHFDYDWRHGGESLVKALHS--KLPKEIRVESATEVGEEFHARFSAVSKRYQYRLALGEA 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---RSIHCQASSPIRTIDHFDVN 178
               +    W + + LD   ++ A    VG HDF  F   R I  +++   R +    V+
Sbjct: 119 N-PFQWAYCWPVSRKLDLNLVKEAMDRFVGTHDFGAFAANRGIEYESTE--RKMLATGVS 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + +   A  F++  +RS VG++  VG G+   +++E+ L++  R      AP +G
Sbjct: 176 QDTEYVGLSFQADGFMYKMVRSLVGAVVNVGLGRMQVSEIERLLESAVRSPMVQAAPAKG 235

Query: 239 LYFDSVEY 246
           L+ + V Y
Sbjct: 236 LFLEKVFY 243


>gi|15836112|ref|NP_300636.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae J138]
 gi|16752458|ref|NP_444720.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae AR39]
 gi|12644497|sp|Q9Z7X4|TRUA_CHLPN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|7189101|gb|AAF38045.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae AR39]
 gi|8978952|dbj|BAA98787.1| pseudouridylate synthase I [Chlamydophila pneumoniae J138]
          Length = 267

 Score =  129 bits (323), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  ++I Y G+ Y GWQ+Q N  SIQ  IE ++  +T     +  +GRTD+GVHA  Q
Sbjct: 1   MTKVALLIAYQGTAYSGWQQQPNDLSIQEVIESSLKKITKTRTPLIASGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF      +     +  KALNA L     I I ++++ D  FHAR+  I + Y Y + 
Sbjct: 61  VAHFRAPDHPLFANANLTKKALNAILP--KDIVIRDVALFDDNFHARYLTIAKEYRYSLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++   +        E M+  A  L+G HDF +F +     +S +RTI   D+
Sbjct: 119 RLAKPLPWQRHFCYTPRHPFSTELMQEGANLLIGTHDFASFANHGRDYNSTVRTIYTLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ + I      FL+  +R+ VG+L  VG G +    L   L+ ++R+E    AP  
Sbjct: 179 VDKGDSLSIICRGNGFLYKMVRNLVGALLDVGKGAYPPEHLLDILEQKNRREGPSAAPAY 238

Query: 238 GLYFDSVEYS 247
           GL    V YS
Sbjct: 239 GLSLHHVCYS 248


>gi|325269743|ref|ZP_08136354.1| tRNA pseudouridine synthase A [Prevotella multiformis DSM 16608]
 gi|324987944|gb|EGC19916.1| tRNA pseudouridine synthase A [Prevotella multiformis DSM 16608]
          Length = 255

 Score =  128 bits (322), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 83/268 (30%), Positives = 126/268 (47%), Gaps = 37/268 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E+++ ++  E + V GAGRTD+GVH    
Sbjct: 3   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLERSLSILLKETITVTGAGRTDAGVHGRMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  + +    L   +N  L     +S+  +  V    HARFSA+ R+Y Y I T +
Sbjct: 63  VAHFDTAQPFDSGQLVYKMNRLLP--RDVSVSRIEAVSADLHARFSAVSRTYHYYIHTGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P +         P  LD + M  AA +L+G  DF  F    C+A + ++T       +F
Sbjct: 121 QPFSHRYSCEIHYP--LDFDKMNEAASYLIGEKDFKCF----CKAGADVKT-------TF 167

Query: 181 GNLIEIR----------------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            NL E R                      + A  FL   +R+ VG+L  VG G+ +  D 
Sbjct: 168 CNLTEARWIPFGDGLSLSSGSTIANWCFVITANRFLRNMVRAVVGTLVDVGRGRLSLADF 227

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + +    R + G   P   L+   ++Y
Sbjct: 228 RQIVDGGTRSDAGESMPGNALFLWDIKY 255


>gi|257453277|ref|ZP_05618576.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|317059811|ref|ZP_07924296.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|313685487|gb|EFS22322.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
          Length = 245

 Score =  128 bits (322), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 82/240 (34%), Positives = 127/240 (52%), Gaps = 6/240 (2%)

Query: 9   EYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           +Y+GS + G+QRQ    ++QG IEK +F +  E + +  +GRTD GVHA+ QV++F    
Sbjct: 9   QYDGSSFMGFQRQPEKRTVQGEIEKCLFRILKEKIDLTSSGRTDRGVHAMHQVSNFFTA- 67

Query: 69  EWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
             V + L K   A  + + + I +L L    K FHARFSA  RSY YRI   ++P   E+
Sbjct: 68  --VNIPLDKLFYALSRCLPEDILLLELEEARKDFHARFSAKTRSYCYRITWEKSP--FER 123

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
                + K +D ++     +  +G+H+F  FR      ++PIR I    V      ++I 
Sbjct: 124 RYKTYVKKKIDSQSFFKILEIFMGKHNFQNFRLQDDAFANPIREIYSIQVKEVDEGMDIY 183

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + A +FL +QIR  +G+   V   K  S  +EK L+  D++    LA P GLY   ++Y 
Sbjct: 184 IEANAFLKSQIRIMLGTAFQVYFQKVESNRIEKMLKEPDKEFPKYLADPNGLYLYHIKYD 243


>gi|260171626|ref|ZP_05758038.1| tRNA pseudouridine synthase A [Bacteroides sp. D2]
          Length = 267

 Score =  128 bits (322), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 120/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     ISI  +  V    H RF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLLPPD--ISIYRVCRVRPDAHVRFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA  L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAAHILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +   +  + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 EDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEY 246
           +  +VEY
Sbjct: 237 FLVNVEY 243


>gi|172038954|ref|YP_001805455.1| tRNA pseudouridine synthase A [Cyanothece sp. ATCC 51142]
 gi|171700408|gb|ACB53389.1| tRNA pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 286

 Score =  128 bits (322), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 116/246 (47%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G  + GWQRQ    ++Q  IE +I  V G  V +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYQGGRFHGWQRQPTQRTVQEDIETSIAQVLGYHVPIHGAGRTDAGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD V    P      LN   ++ D I +   + V   +HARFSA+ R Y Y   T + P
Sbjct: 72  HFDDVSPIPPQRWADILNQ--RLPDDILVRGSAEVPLTWHARFSALWRRYRYTFYTDKCP 129

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W    + L+ E M  A   L+GRH    FR    +       +        G
Sbjct: 130 NLFVSPFSWHYYYEPLEVELMTKALNPLLGRHHLAAFRRAGSKRHHSWVEVQETQCYRQG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK +  +  +  Q Q R++    AP +GL  
Sbjct: 190 PFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLANFTEIWQHQQREQVKYSAPAKGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|313157719|gb|EFR57130.1| tRNA pseudouridine synthase A [Alistipes sp. HGB5]
          Length = 257

 Score =  128 bits (322), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 126/247 (51%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG+ Y GWQRQ +  S+Q ++E+A+  +  E + V GAGRTD+GV+A   V
Sbjct: 4   MRYFLELRYNGAAYCGWQRQPDMPSVQQTLERALTTLLREKIEVTGAGRTDTGVNASYYV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD   E VP            +   I++ +++ V    HARF+A  R Y Y I  R+ 
Sbjct: 64  AHFD-CEEPVPDPAQVVYKLNFLLPGDIAVGSMTPVGADAHARFAAREREYRYYIEPRKN 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDVNS 179
           P   +    + +P  LD E M  AA  L+   DFT+F  ++    + I  I H  +  + 
Sbjct: 123 PFTRDATWQYYVP--LDMERMNEAAASLLEYDDFTSFAKLNSNNKTNICRIMHAAWTADE 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L    + A  FL   +RS VG+L  VG G++T     + + ++D       AP +GL
Sbjct: 181 RGVLC-FTIRADRFLRNMVRSLVGTLVDVGRGRYTPDGFREIVGSRDLSRSSGGAPAQGL 239

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


>gi|291515704|emb|CBK64914.1| pseudouridylate synthase I [Alistipes shahii WAL 8301]
          Length = 259

 Score =  128 bits (322), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 86/253 (33%), Positives = 128/253 (50%), Gaps = 18/253 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG+ Y GWQRQ +  S+Q ++E+A+  +  E V + GAGRTD+GV+A   V
Sbjct: 1   MRYFLELRYNGAAYCGWQRQPDQPSVQQTLERALATLLREPVALTGAGRTDTGVNAAYYV 60

Query: 62  AHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD  R    P      LN +L   D I++ +++ V +  HARF A  R Y Y I  R+
Sbjct: 61  AHFDCERPVADPAQTVYKLN-FLLPGD-IAVGSMTPVAEDAHARFHAREREYRYFIEPRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-------CQASSPIRTID 173
            P    +   + +P  LD   M  AA  L    DFT+F  ++       C+    + TID
Sbjct: 119 NPFTRHETWQYYVP--LDVGRMNEAAAMLTAYDDFTSFAKLNSNNKTNICRVKEAVWTID 176

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                S G +    + A  FL   +RS VG+L  VG G++T       ++++D       
Sbjct: 177 -----SRGTMC-FTIRADRFLRNMVRSLVGTLVDVGRGRYTPDGFRSIVESRDLSRSSAG 230

Query: 234 APPEGLYFDSVEY 246
           AP +GL+   V Y
Sbjct: 231 APAQGLFLSDVVY 243


>gi|255083272|ref|XP_002504622.1| predicted protein [Micromonas sp. RCC299]
 gi|226519890|gb|ACO65880.1| predicted protein [Micromonas sp. RCC299]
          Length = 253

 Score =  128 bits (322), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 91/259 (35%), Positives = 131/259 (50%), Gaps = 26/259 (10%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQ 60
           Y + + Y+G  Y G+Q Q  G ++QG +E+A+  +TG   E + +  +GRTD+GVHA  Q
Sbjct: 3   YALKLAYDGEAYLGFQYQPKGKTVQGEVERALTKLTGHDREFLGMQASGRTDTGVHARGQ 62

Query: 61  VAHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           + HF   +E V  +    K+LN  +     +  + +      FHARF A+R++Y Y +  
Sbjct: 63  ILHF-YTKEPVSDLERFHKSLNGIM--PKDVRCVEVMRPHPAFHARFHAVRKTYHYFLDP 119

Query: 119 RQA--PL----ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS---SPI 169
           R    P     AL  G  W  P     E +R AA   VG HDFT+F +     +   SP 
Sbjct: 120 RLVLDPFVRRHALHCG--WKPPS---VERLREAAAVFVGTHDFTSFSNKSRDKTLVRSPT 174

Query: 170 RTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG---DGKWTSTDLEKALQAQ 225
           RTI  FD V     LI + V    FL+  +R+ VG+L L     DGK+T+ DL   L+ +
Sbjct: 175 RTIYRFDVVEQPDGLIRLEVEGNGFLYRMVRNMVGALMLAATGEDGKFTAEDLRDMLEGK 234

Query: 226 DRKECGPLAPPEGLYFDSV 244
           DR      APP GL+   V
Sbjct: 235 DRGVAPMGAPPHGLFLHEV 253


>gi|257467128|ref|ZP_05631439.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315918259|ref|ZP_07914499.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313692134|gb|EFS28969.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 245

 Score =  128 bits (322), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 82/240 (34%), Positives = 127/240 (52%), Gaps = 6/240 (2%)

Query: 9   EYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           +Y+GS + G+QRQ    ++QG IEK +F +  E + +  +GRTD GVHA+ QV++F    
Sbjct: 9   QYDGSSFMGFQRQPEKRTVQGEIEKCLFRILKEKIDLTSSGRTDRGVHAMHQVSNFFTA- 67

Query: 69  EWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
             V + L K   A    + + I +L L    K FHARFSA  RSY YRI  +++P   E+
Sbjct: 68  --VNIPLDKLFYALSHCLPEDILLLELEEARKDFHARFSAKTRSYCYRITWKKSP--FER 123

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
                + K +D ++     +  +G+H+F  FR      ++PIR I    V      ++I 
Sbjct: 124 RYKTYVKKKIDSQSFFKILEIFMGKHNFQNFRLQDDAFANPIREIYSIQVKEVDEGMDIY 183

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + A +FL +QIR  +G+   V   K  S  +EK L+  D++    LA P GLY   ++Y 
Sbjct: 184 IEANAFLKSQIRIMLGTAFQVYFQKVESNRIEKMLKEPDKEFPKYLADPNGLYLYHIKYD 243


>gi|258540648|ref|YP_003175147.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus Lc 705]
 gi|257152324|emb|CAR91296.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus Lc 705]
          Length = 247

 Score =  128 bits (322), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + +A+N+ + +   I IL   IV   FHAR+SA  + Y YR+   
Sbjct: 61  QVISFDYPGNIPAESMLRAMNSLMPLD--IEILKAEIVAADFHARYSAKGKRYRYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEE 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  
Sbjct: 179 DPATNELIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|325856892|ref|ZP_08172390.1| tRNA pseudouridine synthase A [Prevotella denticola CRIS 18C-A]
 gi|325483265|gb|EGC86242.1| tRNA pseudouridine synthase A [Prevotella denticola CRIS 18C-A]
          Length = 255

 Score =  128 bits (322), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 83/268 (30%), Positives = 127/268 (47%), Gaps = 37/268 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E ++ ++  E + V GAGRTD+GVH    
Sbjct: 3   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLEHSLSILLKETITVTGAGRTDAGVHGRMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  + +    L   +N  L     +S+  +  V    HARFSA+ R+Y Y I T +
Sbjct: 63  VAHFDTAQPFDSEQLVYKMNRLLP--RDVSVSRIEAVSADLHARFSAVSRTYHYYIHTGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P +  +  +  I   LD + M  AA +L+G  DF  F    C+A + ++T       +F
Sbjct: 121 QPFS--RRYSCEIHYPLDFDKMNEAASYLIGEKDFKCF----CKAGADVKT-------TF 167

Query: 181 GNLIEIR----------------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            NL E R                      + A  FL   +R+ VG+L  VG G+ +  D 
Sbjct: 168 CNLTEARWIPFGDGLSLSSGGTIANWCFVITANRFLRNMVRAVVGTLVDVGRGRLSLADF 227

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + +    R + G   P   L+   ++Y
Sbjct: 228 RQIVDGGTRSDAGESMPGNALFLWDIKY 255


>gi|134298133|ref|YP_001111629.1| tRNA pseudouridine synthase A [Desulfotomaculum reducens MI-1]
 gi|172044244|sp|A4J151|TRUA_DESRM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|134050833|gb|ABO48804.1| tRNA pseudouridine synthase A [Desulfotomaculum reducens MI-1]
          Length = 247

 Score =  128 bits (322), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 79/244 (32%), Positives = 126/244 (51%), Gaps = 5/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + Y+G+ Y G+Q Q+    ++IQ ++EKA+  +    + V GAGRTD+GVHA  QV +
Sbjct: 6   LTLAYDGTNYHGFQEQRGTGLATIQEALEKALSTIAQTPIQVIGAGRTDAGVHAQGQVVN 65

Query: 64  FDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F   +  VP      ALN  L     I ++    V   FHARFSA+ ++Y Y I   +  
Sbjct: 66  FRSEKWPVPAEKAPLALNVLL--PGDIKVVKAEEVPMDFHARFSAVAKTYRYSIYHHRVM 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +   +  P+ LD   M+  A +L+G +DF +F++        IRTI   D+     
Sbjct: 124 SPFHRYYCYHEPRRLDVNAMQEGAAYLLGTYDFKSFQAQGTPVKDTIRTIYRADIIEDAP 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +I + +    FL+  +R   G+L  +G GK    D+ K +++++R   G  APP+GL   
Sbjct: 184 VINLYLRGNGFLYNMVRIITGTLLNIGFGKIKPEDMVKIIESKNRTLAGTTAPPQGLCLM 243

Query: 243 SVEY 246
            VEY
Sbjct: 244 EVEY 247


>gi|15843050|ref|NP_338087.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis CDC1551]
 gi|148824665|ref|YP_001289419.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis F11]
 gi|161352460|ref|NP_217972.2| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Rv]
 gi|161511525|ref|NP_857124.2| tRNA pseudouridine synthase A [Mycobacterium bovis AF2122/97]
 gi|253800500|ref|YP_003033501.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           1435]
 gi|254234047|ref|ZP_04927372.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis C]
 gi|254366056|ref|ZP_04982101.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289555726|ref|ZP_06444936.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           605]
 gi|289747288|ref|ZP_06506666.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           02_1987]
 gi|298526939|ref|ZP_07014348.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis
           94_M4241A]
 gi|308377357|ref|ZP_07441941.2| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu008]
 gi|308378330|ref|ZP_07482228.2| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu009]
 gi|308379519|ref|ZP_07668975.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu010]
 gi|54039781|sp|P65847|TRUA_MYCBO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54042086|sp|P65846|TRUA_MYCTU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|13883394|gb|AAK47901.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis CDC1551]
 gi|124599576|gb|EAY58680.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis C]
 gi|134151569|gb|EBA43614.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148723192|gb|ABR07817.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis F11]
 gi|253322003|gb|ACT26606.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           1435]
 gi|289440358|gb|EFD22851.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           605]
 gi|289687816|gb|EFD55304.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           02_1987]
 gi|298496733|gb|EFI32027.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis
           94_M4241A]
 gi|308348190|gb|EFP37041.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu008]
 gi|308352914|gb|EFP41765.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu009]
 gi|308356757|gb|EFP45608.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu010]
 gi|328460231|gb|AEB05654.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           4207]
          Length = 297

 Score =  128 bits (322), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 84/263 (31%), Positives = 134/263 (50%), Gaps = 22/263 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW  Q    ++ G ++ A+  +    V +  AGRTD+GVHA  Q
Sbjct: 21  VVRLRLDIAYDGTDFAGWAAQVGQRTVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQ 80

Query: 61  VAHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           VAH D+  + +P              + L + L  +L     + IL+++     F ARFS
Sbjct: 81  VAHVDVPADALPNAYPRAGHVGDPEFLPLLRRLGRFLPAD--VRILDITRAPAGFDARFS 138

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A+RR Y+YR+ T  AP  +E  +A  I   P+ LD + M  A++ L+G HDF  F   H 
Sbjct: 139 ALRRHYVYRLST--APYGVEPQQARYITAWPRELDLDAMTAASRDLMGLHDFAAF-CRHR 195

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           + ++ IR +   D +  G L+   V A +F  + +RS VG+L  VG+ +  +T   + L 
Sbjct: 196 EGATTIRDLQRLDWSRAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRELLT 255

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A  R     +AP  GL    V+Y
Sbjct: 256 ATGRSSDFAVAPAHGLTLIQVDY 278


>gi|308371354|ref|ZP_07424662.2| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu003]
 gi|308372553|ref|ZP_07667408.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu004]
 gi|308373747|ref|ZP_07667643.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu005]
 gi|308374881|ref|ZP_07667891.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu006]
 gi|308380705|ref|ZP_07669261.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu011]
 gi|308406162|ref|ZP_07669527.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu012]
 gi|308329092|gb|EFP17943.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu003]
 gi|308332900|gb|EFP21751.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu004]
 gi|308336560|gb|EFP25411.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu005]
 gi|308340435|gb|EFP29286.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu006]
 gi|308360702|gb|EFP49553.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu011]
 gi|308364317|gb|EFP53168.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu012]
 gi|323717939|gb|EGB27128.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           CDC1551A]
          Length = 303

 Score =  128 bits (321), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 84/263 (31%), Positives = 134/263 (50%), Gaps = 22/263 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW  Q    ++ G ++ A+  +    V +  AGRTD+GVHA  Q
Sbjct: 27  VVRLRLDIAYDGTDFAGWAAQVGQRTVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQ 86

Query: 61  VAHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           VAH D+  + +P              + L + L  +L     + IL+++     F ARFS
Sbjct: 87  VAHVDVPADALPNAYPRAGHVGDPEFLPLLRRLGRFLPAD--VRILDITRAPAGFDARFS 144

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A+RR Y+YR+ T  AP  +E  +A  I   P+ LD + M  A++ L+G HDF  F   H 
Sbjct: 145 ALRRHYVYRLST--APYGVEPQQARYITAWPRELDLDAMTAASRDLMGLHDFAAF-CRHR 201

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           + ++ IR +   D +  G L+   V A +F  + +RS VG+L  VG+ +  +T   + L 
Sbjct: 202 EGATTIRDLQRLDWSRAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRELLT 261

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A  R     +AP  GL    V+Y
Sbjct: 262 ATGRSSDFAVAPAHGLTLIQVDY 284


>gi|304440310|ref|ZP_07400199.1| tRNA pseudouridine synthase A [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304371062|gb|EFM24679.1| tRNA pseudouridine synthase A [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 247

 Score =  128 bits (321), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 119/239 (49%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ ++G+Q+Q  G +I+  + KA+       V +  +GRTDSGVHA  Q A+F   
Sbjct: 7   ITYDGTNFYGFQKQDRGRTIEKVLTKAVENTVKHPVKLFYSGRTDSGVHAFGQYANFYTE 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L K +N +L     IS++    VD  FH+R+SA  + Y Y I   +   AL +
Sbjct: 67  STIDIGNLPKVINYHLPTD--ISVVEAKYVDDNFHSRYSAKGKFYRYIIYNNKYRNALFE 124

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            RAW  P  +D E +  +  +LVG HDF +F   +      IR I   +VN  G++I I 
Sbjct: 125 NRAWQYPHKIDMEILEKSLSYLVGEHDFKSFMGRYATVKDTIRIIHKIEVNKVGDVINID 184

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
              +SFL   +R  VG+   +     +    ++AL  ++R   G  AP  GLY   V +
Sbjct: 185 FYGKSFLKNMVRIIVGTSVQISSKNKSPEITKEALVRKERISAGMTAPACGLYLMDVYF 243


>gi|126699393|ref|YP_001088290.1| tRNA pseudouridine synthase A [Clostridium difficile 630]
 gi|254975421|ref|ZP_05271893.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-66c26]
 gi|255092808|ref|ZP_05322286.1| tRNA pseudouridine synthase A [Clostridium difficile CIP 107932]
 gi|255100921|ref|ZP_05329898.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-63q42]
 gi|255306811|ref|ZP_05350982.1| tRNA pseudouridine synthase A [Clostridium difficile ATCC 43255]
 gi|255314550|ref|ZP_05356133.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-76w55]
 gi|255517225|ref|ZP_05384901.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-97b34]
 gi|255650331|ref|ZP_05397233.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-37x79]
 gi|260683444|ref|YP_003214729.1| tRNA pseudouridine synthase A [Clostridium difficile CD196]
 gi|260687040|ref|YP_003218173.1| tRNA pseudouridine synthase A [Clostridium difficile R20291]
 gi|306520297|ref|ZP_07406644.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-32g58]
 gi|115250830|emb|CAJ68654.1| Pseudouridylate synthase (tRNA pseudouridine synthase A)
           [Clostridium difficile]
 gi|260209607|emb|CBA63265.1| tRNA pseudouridine synthase 2 [Clostridium difficile CD196]
 gi|260213056|emb|CBE04418.1| tRNA pseudouridine synthase 2 [Clostridium difficile R20291]
          Length = 245

 Score =  128 bits (321), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 79/235 (33%), Positives = 127/235 (54%), Gaps = 3/235 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MI+ Y+GS Y G+Q+   N  +IQ  +E  +  +T E V + G+GRTD G HA  QV +F
Sbjct: 6   MIVAYDGSRYKGYQKLGDNNMTIQEKLENVLSKMTNETVEIIGSGRTDMGAHARGQVVNF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + K L  YL   + I +  +  VD++FH+R++   ++Y+Y+I   +    
Sbjct: 66  RTNCMDSLDKIQKYLYEYL--PEDIVVKTVEEVDERFHSRYNVKSKTYMYKIDNNKYHNP 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  A  + K LD + MR A+++LVG HDFT+F S   +  S +R I   ++    N+I
Sbjct: 124 FIRKYATHVSKKLDLDRMRKASEYLVGEHDFTSFASSKSKKKSNVREIYSINIKEDDNVI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           EI V    FL+  +R  VG+L  VG  +    D++  L+++DR +    AP +GL
Sbjct: 184 EIYVEGNGFLYNMVRIIVGALIDVGLKRRAPQDIKYMLESKDRCQSSDTAPAKGL 238


>gi|260072704|gb|ACX30601.1| pseudouridylate synthase [uncultured SUP05 cluster bacterium]
          Length = 218

 Score =  128 bits (321), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 77/220 (35%), Positives = 119/220 (54%), Gaps = 13/220 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK+G  ++Q  +E+A+  V    V V  +GRTD+GVHAL Q
Sbjct: 1   MKLALGVEYLGTNFHGWQLQKSGIRTVQQVVEQALSSVADHPVRVFCSGRTDAGVHALEQ 60

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+       + WV       L   + +   ++      V+  FHARF A  R Y Y+
Sbjct: 61  VIHFETTAKREDKAWV-------LGGNVNLPFDVNFKWAKQVNDDFHARFDAHARQYHYK 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I       A++        ++LD + M  AA+ L+G HDF++FR   CQA SPI+T++  
Sbjct: 114 IHNTPVRSAVKHAYTLWESRTLDIKLMNQAAECLIGEHDFSSFRGSLCQAKSPIKTVEFI 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
            +   GN I + + A +FLH  +R+ VG+L  VG G+  S
Sbjct: 174 RLTQSGNGILLDIKANAFLHHMVRNIVGTLIKVGKGEQDS 213


>gi|325279339|ref|YP_004251881.1| tRNA pseudouridine synthase A [Odoribacter splanchnicus DSM 20712]
 gi|324311148|gb|ADY31701.1| tRNA pseudouridine synthase A [Odoribacter splanchnicus DSM 20712]
          Length = 245

 Score =  128 bits (321), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 123/248 (49%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY + + YNGS Y GWQ Q   SS+Q  I +A+  +  + + V GAGRTD+GVHA   
Sbjct: 1   MVRYFIELAYNGSRYHGWQIQPGASSVQEEINRALSTLLRQDIYVVGAGRTDTGVHASFF 60

Query: 61  VAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAHFD+  E   P  +   LN  L     I+I  +  V    HARFSAI R+Y Y I   
Sbjct: 61  VAHFDIECELPEPQQVVYKLNGLL--DKDIAIYKIYRVPMDKHARFSAISRTYKYYIDKT 118

Query: 120 QAPLALEKG-RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           + P       +A+ +P   D + M  A + L    DFT+F  +H    +    I      
Sbjct: 119 KDPFTYPFAWKAYPLP---DIQTMNEACRVLFDYTDFTSFSKLHTDVKTNNCIIYEAQWE 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                +   V A  FL   +R+ VG+L  VG GK T  D+ K +++++R   G   P + 
Sbjct: 176 ETDKQLIFTVKANRFLRNMVRAIVGTLIDVGRGKLTPEDVRKIIESKNRCNAGTSVPAQA 235

Query: 239 LYFDSVEY 246
           L+   +EY
Sbjct: 236 LFLCHIEY 243


>gi|111114834|ref|YP_709452.1| tRNA pseudouridine synthase A [Borrelia afzelii PKo]
 gi|216264050|ref|ZP_03436044.1| tRNA pseudouridine synthase A [Borrelia afzelii ACA-1]
 gi|122956439|sp|Q0SPF2|TRUA_BORAP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|110890108|gb|ABH01276.1| pseudouridylate synthase I [Borrelia afzelii PKo]
 gi|215980094|gb|EEC20916.1| tRNA pseudouridine synthase A [Borrelia afzelii ACA-1]
          Length = 246

 Score =  128 bits (321), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 122/239 (51%), Gaps = 1/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS Y G+Q Q    +IQG IEKA+  +  + + +H +GRTD GVHA RQ+  FD+ 
Sbjct: 8   IAYDGSMYHGFQIQPTKPTIQGEIEKALMKINKKKIKIHSSGRTDKGVHAKRQIITFDIN 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L KALNA L +   I IL L  V   FH RF+A +R Y Y I+        E 
Sbjct: 68  INIQLNNLKKALNAIL-LKPGIKILKLKHVKNSFHPRFNAQKRKYSYCILNSDNYYPWES 126

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +A+ + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        G  I   
Sbjct: 127 YQAYYVNKKLNINNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIHSAKFKKKGKYIIFE 186

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+ D V Y
Sbjct: 187 IIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALFLDKVYY 245


>gi|154507834|ref|ZP_02043476.1| hypothetical protein ACTODO_00316 [Actinomyces odontolyticus ATCC
           17982]
 gi|153797468|gb|EDN79888.1| hypothetical protein ACTODO_00316 [Actinomyces odontolyticus ATCC
           17982]
          Length = 302

 Score =  128 bits (321), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 91/277 (32%), Positives = 135/277 (48%), Gaps = 37/277 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW  Q    ++QG +E A+ + + E VV   AGRTD+GVHA  QV 
Sbjct: 5   RLRLDLGYDGTDFRGWAAQPGLRTVQGEVEAALAMASREDVVTTVAGRTDAGVHARHQVC 64

Query: 63  HFDLVR---------------EWVPVILCKALNAYL----------------KISDTISI 91
           H D+                 + V   + + LN  L                + +  + I
Sbjct: 65  HADISEAAWARLSPRGGESNEQAVASAIVRRLNKILSGRYGERARGRDLAAARGTCDVRI 124

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
            + ++VD  F ARFSA+ RSY YR+  R  PL     R W + + LD   M  A   L+G
Sbjct: 125 YSAAVVDPSFDARFSALGRSYAYRVSDRPEPLG-RWDRLW-VEEPLDEAAMNEAGAALLG 182

Query: 152 RHDFTTFRSIHCQASSPIRTIDHF--DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
            HDF  F     + ++ IRT+     + ++ G L+  RV A +F H+ +RS VG+L LVG
Sbjct: 183 EHDFLGFCRPR-EGATTIRTLRTLLAERDAEGTLV-FRVEADAFCHSMVRSLVGALLLVG 240

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            G    T   + L+A+ R E  P+AP  GL  + VEY
Sbjct: 241 SGARDVTYPVQILRARSRSEAAPIAPAHGLTLEGVEY 277


>gi|83816613|ref|YP_444802.1| tRNA pseudouridine synthase A [Salinibacter ruber DSM 13855]
 gi|123726203|sp|Q2S4S9|TRUA_SALRD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83758007|gb|ABC46120.1| tRNA pseudouridine synthase A [Salinibacter ruber DSM 13855]
          Length = 265

 Score =  128 bits (321), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 88/250 (35%), Positives = 131/250 (52%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G+ + GWQ Q    ++QG++E+A+  V G    V G+GRTD+GVHA  Q
Sbjct: 1   MPRYRLLVEYDGTDFHGWQIQPTVPTVQGALEEAVDTVVGTACRVTGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL     P  L  +LN      D +++  +      FHAR+ A RR Y Y + T+ 
Sbjct: 61  VAHVDLPETRDPYRLRGSLNGL--TPDAVAVRRVERAPDDFHARYDARRRRYHYHLHTQ- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF---DV 177
            P AL +     +    D   +R A   L+GRH+F++F     +  + + T+ H    D 
Sbjct: 118 -PCALGRRARTPVRPVPDFGRIRAATPDLLGRHNFSSFCLTQSETENRVCTLTHLRWVDE 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G    + VV   FLH  +R+ VG+L  +G  K  +  L   L A+DR+  GP  PPE
Sbjct: 177 ARRG-CWRVEVVGTRFLHGMVRALVGTLVEIGHEKRAADALPAVLAARDRRAAGPSMPPE 235

Query: 238 GLYFDSVEYS 247
           GL  ++V Y 
Sbjct: 236 GLVLEAVRYE 245


>gi|224079884|ref|XP_002194368.1| PREDICTED: similar to MGC80334 protein [Taeniopygia guttata]
          Length = 427

 Score =  128 bits (321), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 89/264 (33%), Positives = 132/264 (50%), Gaps = 30/264 (11%)

Query: 12  GSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE- 69
           G G    +  +    +Q  +EKA   L     +  H + RTD+GVHAL   AH D+ R  
Sbjct: 138 GGGVMETKSDQALVGVQNYLEKAAERLKPSAPIKFHISSRTDAGVHALANAAHLDIQRPP 197

Query: 70  ----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-----RQ 120
               +    L + LN +L+  + I IL+   V   FHARF A+ R+Y+YR++       Q
Sbjct: 198 GKAPFSGQQLVQGLNHHLR-PEPIRILSAQRVSSTFHARFCALSRTYIYRLLLGCAHHSQ 256

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDV 177
            P+  E+   W      LD   MR AAQ L+G HDF++FRS+H +A+  SP+RT+    +
Sbjct: 257 IPV-FEQDLCWAPAGGPLDVAAMREAAQFLLGTHDFSSFRSLHAEAAAQSPVRTLQQLQL 315

Query: 178 NSFGNLI------------EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                 +            E++V +RSFL+ Q+R  VG+L  VG G+     L + L+ +
Sbjct: 316 QPAPGFLQQHYLHSGLEFWEVKVKSRSFLYRQVRRMVGALVAVGQGRLAPVQLRELLELR 375

Query: 226 DRKECGP--LAPPEGLYFDSVEYS 247
           D     P  +AP  GL+   VEYS
Sbjct: 376 DPHAFPPHAMAPAAGLFLQRVEYS 399



 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 61/120 (50%), Gaps = 15/120 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY +  +Y G+ Y      +  + +  + E+   L     +  H + RTD+GVHAL   A
Sbjct: 7   RYLVFFQYLGTRY------RIIAELTRAAER---LKPSAPIKFHISSRTDAGVHALANAA 57

Query: 63  HFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           H D+ R      +    L + LN +L+  + I IL+   V   FHARF A+ R+Y+YR++
Sbjct: 58  HLDIQRPPGKAPFSSQQLVQGLNHHLR-PEPIRILSAQRVSSTFHARFCALSRTYIYRLL 116


>gi|270294324|ref|ZP_06200526.1| tRNA pseudouridine synthase A [Bacteroides sp. D20]
 gi|270275791|gb|EFA21651.1| tRNA pseudouridine synthase A [Bacteroides sp. D20]
          Length = 250

 Score =  127 bits (320), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 120/248 (48%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDSPLDTVFMTDKLNRLLPPD--ISVYRLRAVKPDAHARFDATARMYKYYVTTAK 118

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +P   + + R +  P   D E M  AAQ L    DFT+F  +H    +    I H     
Sbjct: 119 SPFNRQYRCRLFQTP---DFERMNEAAQTLFDYTDFTSFSKLHTDVKTNNCKIMHAAWTR 175

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             ++  +  + A  FL   +R+ VG+L  VG GK +     + ++ +DR + G   P   
Sbjct: 176 VDDVTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVEGFRRVIEQKDRCQAGTSVPGNA 235

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 236 LFLVDVAY 243


>gi|212704912|ref|ZP_03313040.1| hypothetical protein DESPIG_02979 [Desulfovibrio piger ATCC 29098]
 gi|212671683|gb|EEB32166.1| hypothetical protein DESPIG_02979 [Desulfovibrio piger ATCC 29098]
          Length = 264

 Score =  127 bits (320), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 126/270 (46%), Gaps = 38/270 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R  +++ Y+GS Y GWQ Q       ++Q ++E A+  + G  V V G+GRTD+GVHA 
Sbjct: 8   MRLRLLLAYDGSRYCGWQIQDIPTPPPTVQAAVEAAVGRIAGRPVRVFGSGRTDAGVHAH 67

Query: 59  RQVAHFDLVR----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            QVAH D+ R    +W       ALNA L     + +L        FHAR SA+R++Y+Y
Sbjct: 68  GQVAHCDVPRRPGLDWR-----HALNALLPAD--VRVLYWQEAAPDFHARISALRKTYVY 120

Query: 115 R-------IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
                   +  R AP     G        LD E MR A   L+GRHDF +F++   +  S
Sbjct: 121 DFWQEKGFVPPRLAPFVWRSG-------PLDAEAMRAALPFLLGRHDFASFQNAGTEMES 173

Query: 168 PIRTIDHFDVNSFGNL---------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            +R +    +     +         + + V A  FL   +R+  G L   G  K     +
Sbjct: 174 TVRELQAATLTELPPVEFMPPCLPCLRLTVTANGFLKQMVRNMAGLLAAYGRHKLRPDQI 233

Query: 219 EKALQAQDRKEC-GPLAPPEGLYFDSVEYS 247
              L+A DR+    P APP+GL    VEY 
Sbjct: 234 PAILEAADRRALPSPTAPPQGLALAHVEYP 263


>gi|53712218|ref|YP_098210.1| tRNA pseudouridine synthase A [Bacteroides fragilis YCH46]
 gi|253563743|ref|ZP_04841200.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_2_5]
 gi|62901264|sp|Q64XV0|TRUA_BACFR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52215083|dbj|BAD47676.1| tRNA pseudouridine synthase A [Bacteroides fragilis YCH46]
 gi|251947519|gb|EES87801.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_2_5]
          Length = 252

 Score =  127 bits (320), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 122/246 (49%), Gaps = 6/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQ Q NG SIQ  + KA+     +   V GAGRTD+GVHA   VA
Sbjct: 5   RYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRKDTEVIGAGRTDAGVHASLMVA 64

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD   E + V  + + LN  L     IS+  +  V    HARF A  R+Y Y I T + 
Sbjct: 65  HFDYEGEPLDVDKVAEKLNRLL--PQDISVYKVCRVKPDAHARFDATARTYKYYITTVKF 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +     
Sbjct: 123 P--FNRQYRYRIHNPLDFQKMNEAALTLFHYSDFTSFSKLHTDVKTNICKIMHAEWTQED 180

Query: 182 NLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               +  + A  FL   +R+ VG+L  VG GK +  D  K ++ Q+R + G  AP   L+
Sbjct: 181 EYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVVDFRKIIEQQNRCKAGTSAPGNALF 240

Query: 241 FDSVEY 246
             +VEY
Sbjct: 241 LVNVEY 246


>gi|15612730|ref|NP_241033.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Bacillus halodurans C-125]
 gi|8134764|sp|Q9Z9J0|TRUA_BACHD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|4512436|dbj|BAA75303.1| truA homologue (identity of 62% to B. subtilis ) [Bacillus
           halodurans]
 gi|10172779|dbj|BAB03886.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Bacillus halodurans C-125]
          Length = 263

 Score =  127 bits (320), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 125/245 (51%), Gaps = 13/245 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R  + + Y+G+ + G+Q Q N  ++QG +E  +  +  G  + V  +GRTD+GVHA  
Sbjct: 1   MKRIGLKVAYDGTDFAGYQIQPNERTVQGELESVLKNIHKGMSIRVTASGRTDTGVHARG 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           Q+ HFD      V  W P+ L   L A       I +L  + V   FHAR+SA  + Y Y
Sbjct: 61  QIVHFDTSLSFPVDRW-PIALNSQLPA------DICVLEAADVPADFHARYSAKTKEYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R++T        +   + +   LD E M+ AA  L+G HDF++F +   +    +RTI+ 
Sbjct: 114 RVLTSAQADVFRRNYTYHVRYPLDVEAMQRAAVQLLGTHDFSSFCAAKAEVEDKVRTIED 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G+ +   +    FL+  +R  VG+L  +G GK ++ ++ K L A+ R+  G  A
Sbjct: 174 VALWREGDELIFSIRGNGFLYNMVRIIVGTLLEIGAGKRSAEEVAKILAARSREAAGKTA 233

Query: 235 PPEGL 239
           P  GL
Sbjct: 234 PGHGL 238


>gi|163787684|ref|ZP_02182131.1| putative tRNA pseudouridine synthase A [Flavobacteriales bacterium
           ALC-1]
 gi|159877572|gb|EDP71629.1| putative tRNA pseudouridine synthase A [Flavobacteriales bacterium
           ALC-1]
          Length = 252

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 125/249 (50%), Gaps = 12/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  Y GWQ Q N  S+Q  +EKA+  +    V V GAGRTD+GVHA +  
Sbjct: 1   MRFFIELSYNGKEYHGWQNQPNAISVQEVLEKALSTILKAEVSVMGAGRTDAGVHASQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +E+    +   LN+YL     I++  +  V    HARF A  R+Y Y+I T + 
Sbjct: 61  AHFDFEKEFEYKDVVYKLNSYL--PKDIAVSTIFEVKPDAHARFEAKSRTYHYKISTSKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
               +   A+ +   LD E M  A + L    DF  F     ++++ ++T +     +F 
Sbjct: 119 --VFDYDFAYQVQLPLDVEAMNTACKILFEYKDFQCF----SKSNTDVKTYNCDIKEAFW 172

Query: 181 ---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +   + A  FL   +R+ VG++  +G GK    DL K + +++R E G   P  
Sbjct: 173 TQNSNQLIFTITADRFLRNMVRAIVGTMVNIGLGKLKPEDLHKIIASKNRSEAGFSVPAH 232

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 233 GLYLAKIVY 241


>gi|90962375|ref|YP_536291.1| tRNA pseudouridine synthase A [Lactobacillus salivarius UCC118]
 gi|301300240|ref|ZP_07206452.1| tRNA pseudouridine synthase A [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|123391325|sp|Q1WSC1|TRUA_LACS1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|90821569|gb|ABE00208.1| tRNA pseudouridine synthase A [Lactobacillus salivarius UCC118]
 gi|300215017|gb|ADJ79433.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Lactobacillus salivarius
           CECT 5713]
 gi|300852181|gb|EFK79853.1| tRNA pseudouridine synthase A [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 256

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 126/249 (50%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQ 60
           R+ + + Y+G+ + G+Q Q N  ++Q  +EKAI  ++   E + V+G+GRTDSGVHAL Q
Sbjct: 4   RFKVTLAYDGTNFAGFQAQPNQRTVQFVLEKAINKMSKKDEYITVYGSGRTDSGVHALGQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD         + + LN+ L +     +++  IV   FH+R++   + YLYR+   +
Sbjct: 64  VVHFDFPHPISAKGMLRGLNSMLPLD--CEVVDCKIVPNDFHSRYTTHGKRYLYRVSRGE 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++         LD E ++ A   + G HD+++F +   QA S +RTI    V  +
Sbjct: 122 FVNPFKRLYTGHYKYPLDIEKIKEAMPDVEGTHDYSSFVASGSQAKSHVRTIYEAKVYED 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + I        FL+ Q+R  V +L  +G+GK    D  +  + +DR +    AP  G
Sbjct: 182 KVNDEIVFEFYGNGFLYNQVRIMVATLLEIGNGKRPVHDFLRLYEVKDRSQARQTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLKEVYYD 250


>gi|329768896|ref|ZP_08260324.1| tRNA pseudouridine synthase A [Gemella sanguinis M325]
 gi|328837259|gb|EGF86896.1| tRNA pseudouridine synthase A [Gemella sanguinis M325]
          Length = 262

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +I  Y+GS Y G+Q Q N +++Q  IEK++  +  + V ++ +GRTDSGVHA  QV
Sbjct: 1   MRVVLICRYDGSRYHGFQIQPNNNTVQEEIEKSLRKIHKKNVRIYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           KA+NA   I   I I++  +V+ +FH R+++I+++Y Y++   + 
Sbjct: 61  LHFDTDLNIPTDGWVKAINAM--IPKDIRIVSAKVVNDEFHVRYNSIKKTYSYKLYLGRE 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV---N 178
                         + + +  + A ++ +G HDF++F S +      +RTI  F +   N
Sbjct: 119 IDPFLINYVGQHKFNFNFDKAKEALKYFIGEHDFSSFCSKNTSVEDKVRTIYSFKMDRDN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N+I   +    FL+  +R  +G+++ V  GK+    +++ L  ++R   GP A   G
Sbjct: 179 QNDNIINFEITGNGFLYNMVRIIIGTVQDVAAGKYEPEYIQEILAKKERSFSGPKADASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLKEVLYD 247


>gi|291533595|emb|CBL06708.1| pseudouridylate synthase I [Megamonas hypermegale ART12/1]
          Length = 256

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 126/242 (52%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y+G+ Y G+QRQ    ++Q  +E A+F + G+ + +  AGRTD+GVHA+ QV +F 
Sbjct: 18  LTLSYDGTNYHGFQRQTKVVAVQNVLEGALFKLFGDSIELAAAGRTDAGVHAIGQVVNF- 76

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                +P+  + +A N  L   D I +L     D+ F A  S   + Y+Y++   +    
Sbjct: 77  FTDGTIPIQNVVRAGNRLL--PDDIVLLKAEEADRDFSALHSVKSKIYIYKVFENELADP 134

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                 W + K L+ E+M+ A +++ G HDF++FRS     +SPIR I         N+ 
Sbjct: 135 FMSRFYWHVNKKLNLEDMQEALKYIEGEHDFSSFRSAGGNDTSPIREIYEASCTKENNVY 194

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             +     FL+  +R+ +G +  +G G+    ++ K ++A++R   G +AP  GLY   V
Sbjct: 195 TFKFWGSGFLYHMVRNIMGLMINIGLGRVDKHEVPKIIEAKNRALAGKMAPANGLYLQKV 254

Query: 245 EY 246
            Y
Sbjct: 255 YY 256


>gi|323699460|ref|ZP_08111372.1| tRNA pseudouridine synthase A [Desulfovibrio sp. ND132]
 gi|323459392|gb|EGB15257.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans ND132]
          Length = 251

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 118/249 (47%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y G+ + GWQ Q    ++QG +E+A+  + G  V VHG+GRTD+GVHAL Q
Sbjct: 3   MTRIRLTLAYEGTDFCGWQVQPADRTVQGEVERALATILGRAVRVHGSGRTDAGVHALGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + LN  L     + +L+ + V   FHAR+ A+ ++Y Y +   +
Sbjct: 63  VVHFDCPDGRTGFPWQRGLNGILPRD--VRVLDAAEVPDDFHARYGAVSKTYEYCLWHER 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++ R       +D   M  AA  L+G HDF  F+++     S +RT+     ++ 
Sbjct: 121 GFCLPQRRRFVWNCGPVDFARMEAAAGLLLGEHDFAAFQNVGTDVDSTVRTVTEISRHAG 180

Query: 181 GNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               E   R  A  FL   +R+ VG L   G GK     +   L+A DR       PP+G
Sbjct: 181 PTAHESVWRFTADGFLKQMVRNLVGCLVACGRGKLDLDGVRVILEAGDRTLAPATVPPQG 240

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 241 LTLVRVAYG 249


>gi|166367993|ref|YP_001660266.1| tRNA pseudouridine synthase A [Microcystis aeruginosa NIES-843]
 gi|166090366|dbj|BAG05074.1| tRNA pseudouridine synthase 1 [Microcystis aeruginosa NIES-843]
          Length = 276

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 120/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ +  S+Q  IEKA+  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 8   RIALVIQYVGTNFHGWQRQPDHRSVQEEIEKALADILGHDVTLHGAGRTDSGVHAAAQVA 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+      P    K LNA  ++ D I I     V  ++HARFSA+ R Y Y + T   P
Sbjct: 68  HFEQQSPIPPSHWAKVLNA--RLDDDIVIRASGRVPDRWHARFSALWRRYRYTLYTDPIP 125

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W    + LD + M  A + L+G+H    F   +         +   +    G
Sbjct: 126 NLFVSPFSWHYYHRPLDADVMARALKPLLGKHHLAAFHRANSSRDHSWVEVQGVECYRQG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +++ + A  FL+  +R  VG L  VG G+ +  +       Q R+     AP +GL  
Sbjct: 186 PFVQMEIQANGFLYGMVRLLVGMLVEVGTGERSLENFTDIWVNQRRELVKYAAPAKGLCL 245

Query: 242 DSVEYS 247
             V Y+
Sbjct: 246 LRVGYA 251


>gi|160891004|ref|ZP_02072007.1| hypothetical protein BACUNI_03451 [Bacteroides uniformis ATCC 8492]
 gi|317480950|ref|ZP_07940030.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_1_36]
 gi|156859225|gb|EDO52656.1| hypothetical protein BACUNI_03451 [Bacteroides uniformis ATCC 8492]
 gi|316902843|gb|EFV24717.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_1_36]
          Length = 250

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 119/248 (47%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDSPLDTVFMTDKLNRLLPPD--ISVYRLRAVKPDAHARFDATARMYKYYVTTAK 118

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P   + + R +  P   D E M  AAQ L    DFT+F  +H    +    I H     
Sbjct: 119 MPFNRQYRCRLFQTP---DFERMNEAAQTLFDYTDFTSFSKLHTDVKTNNCKIMHAAWTR 175

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             ++  +  + A  FL   +R+ VG+L  VG GK +     + ++ +DR + G   P   
Sbjct: 176 VDDVTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVESFRRVIEQKDRCQAGTSVPGNA 235

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 236 LFLVDVAY 243


>gi|229027990|ref|ZP_04184143.1| tRNA pseudouridine synthase A [Bacillus cereus AH1271]
 gi|228733378|gb|EEL84207.1| tRNA pseudouridine synthase A [Bacillus cereus AH1271]
          Length = 235

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 80/235 (34%), Positives = 117/235 (49%), Gaps = 9/235 (3%)

Query: 17  GWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVAHFDL---VREWVP 72
           G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  QV HFD    + EW  
Sbjct: 5   GYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKGQVIHFDTPLSLEEWQ- 63

Query: 73  VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWL 132
                ALN  L   D I I  +    ++FHAR+   R+ Y YR++  +      +   + 
Sbjct: 64  --WSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRVLLSKTADVFRRNYVYQ 119

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARS 192
            P  L+  ++R A  + +G HDFT+F S        +RTI   ++    + +  R V   
Sbjct: 120 YPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIEQDDELIFRFVGNG 179

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GLY   V Y+
Sbjct: 180 FLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGLYLWQVNYN 234


>gi|325675475|ref|ZP_08155159.1| tRNA pseudouridine synthase A [Rhodococcus equi ATCC 33707]
 gi|325553446|gb|EGD23124.1| tRNA pseudouridine synthase A [Rhodococcus equi ATCC 33707]
          Length = 296

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 82/251 (32%), Positives = 129/251 (51%), Gaps = 11/251 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ    ++ G IE+ +  +    V++  AGRTD+GVHA  QV
Sbjct: 21  VRLRLDISYDGTDFSGWARQPGRRTVCGEIEEKLSAIVRTPVLLTVAGRTDAGVHASGQV 80

Query: 62  AHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH D+  + +P    + +    + +   + +  +S   + F ARFSAIRR Y YR+ T  
Sbjct: 81  AHVDVPADMIPEEPSRLVRRLARFLPRDVRVKAVSFAPEHFDARFSAIRRHYEYRLTT-- 138

Query: 121 APLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           AP   E  R     AW  PK +D + MR A+  L+G HDF  F     + ++ +R +  F
Sbjct: 139 APYGAEPLRARDTVAW--PKDVDVDAMRKASSRLLGLHDFAAF-CKRREGATTVRELQRF 195

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D    G+ +   V A +F  + +RS VG+   VG+G+ T   +   L  ++R     +AP
Sbjct: 196 DWEQSGHELTAFVSADAFCWSMVRSLVGAALAVGEGRRTVEWMAGLLAERERASAVAVAP 255

Query: 236 PEGLYFDSVEY 246
             GL    V+Y
Sbjct: 256 AHGLSLIRVDY 266


>gi|301161932|emb|CBW21476.1| putative tRNA pseudouridine synthase A [Bacteroides fragilis 638R]
          Length = 252

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 122/246 (49%), Gaps = 6/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQ Q NG SIQ  + KA+     +   V GAGRTD+GVHA   VA
Sbjct: 5   RYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRKDTEVIGAGRTDAGVHASLMVA 64

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD   E + V  + + LN  L     IS+  +  V    HARF A  R+Y Y I T + 
Sbjct: 65  HFDYEGEPLDVDKVAEKLNRLL--PQDISVYKVCRVKPDAHARFDATARTYKYYITTVKF 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +     
Sbjct: 123 P--FNRQYRYRIHNPLDFQKMNEAALTLFHYSDFTSFSKLHTDVKTNICKIMHAEWTQKD 180

Query: 182 NLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               +  + A  FL   +R+ VG+L  VG GK +  D  K ++ Q+R + G  AP   L+
Sbjct: 181 EYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDDFRKIIEQQNRCKAGTSAPGNALF 240

Query: 241 FDSVEY 246
             +VEY
Sbjct: 241 LVNVEY 246


>gi|60680398|ref|YP_210542.1| tRNA pseudouridine synthase A [Bacteroides fragilis NCTC 9343]
 gi|265765551|ref|ZP_06093826.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_16]
 gi|81316532|sp|Q5LGZ6|TRUA_BACFN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|60491832|emb|CAH06590.1| putative tRNA pseudouridine synthase A [Bacteroides fragilis NCTC
           9343]
 gi|263254935|gb|EEZ26369.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_16]
          Length = 252

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 122/246 (49%), Gaps = 6/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQ Q NG SIQ  + KA+     +   V GAGRTD+GVHA   VA
Sbjct: 5   RYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRKDTEVIGAGRTDAGVHASLMVA 64

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD   E + V  + + LN  L     IS+  +  V    HARF A  R+Y Y I T + 
Sbjct: 65  HFDYEGEPLDVDKVAEKLNRLL--PQDISVYKVCRVKPDAHARFDATARTYKYYITTVKF 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +     
Sbjct: 123 P--FNRQYRYRIHNPLDFQKMNEAALTLFHYSDFTSFSKLHTDVKTNICKIMHAEWTQED 180

Query: 182 NLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               +  + A  FL   +R+ VG+L  VG GK +  D  K ++ Q+R + G  AP   L+
Sbjct: 181 EYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDDFRKIIEQQNRCKAGTSAPGNALF 240

Query: 241 FDSVEY 246
             +VEY
Sbjct: 241 LVNVEY 246


>gi|298209267|ref|YP_003717446.1| putative tRNA pseudouridine synthase A [Croceibacter atlanticus
           HTCC2559]
 gi|83849194|gb|EAP87063.1| putative tRNA pseudouridine synthase A [Croceibacter atlanticus
           HTCC2559]
          Length = 258

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 122/245 (49%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I YNG  Y G+QRQ    S+Q  +E AI +   + V + GAGRTD+GVH  + +
Sbjct: 1   MRYFLDIAYNGKPYHGFQRQPEDISVQEVLEDAIAVYFQKAVTIFGAGRTDTGVHGKQLI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             LN  L   D++++ ++ +V+ + HARF A+ R Y Y + TR+ 
Sbjct: 61  AHFDSDTTINESQFLYKLNKLL--PDSVAVRDVYLVNSEAHARFDAMAREYEYVVTTRKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E   A  I K LD E M  AA+ L+   DF  F  +     +    I +   +  G
Sbjct: 119 PFLSES--ALYIIKPLDVEAMNTAAKVLLEYTDFECFSKVKTDVKTFNCKITYAHWSQHG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +   + A  FL   +R+ VG+L  VG GK     +   + +++R E G     +GLY 
Sbjct: 177 HKLVFTIRADRFLRNMVRAIVGTLLEVGLGKRLPGSIHDIIASKNRGEAGKSVAAQGLYL 236

Query: 242 DSVEY 246
             V Y
Sbjct: 237 TKVLY 241


>gi|159027087|emb|CAO89272.1| truA [Microcystis aeruginosa PCC 7806]
          Length = 271

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 119/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ +  S+Q  IEKA+  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 8   RIALVIQYVGTNFHGWQRQPHHRSVQEEIEKALADILGHAVTLHGAGRTDSGVHAAAQVA 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF       P    K LNA  ++ D I I   + V  ++HARFSA+ R Y Y + T   P
Sbjct: 68  HFQQQSPIPPAHWAKVLNA--RLDDDIVIRASAQVPDRWHARFSALWRRYRYTLYTDPIP 125

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W    + LD + M  A   L+G+H    F   +         +   +    G
Sbjct: 126 NLFVSPFSWHYYHRPLDADLMARALAPLLGKHHLAAFHRANSSRDHSWVEVQGVECYRQG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +++ + A  FL+  +R  VG L  VG G+ +  +       Q R+     AP +GL  
Sbjct: 186 PFVQMEIQANGFLYGMVRLLVGMLVEVGTGERSLENFTDIWVNQRRELVKYAAPAKGLCL 245

Query: 242 DSVEYS 247
             V Y+
Sbjct: 246 LRVGYA 251


>gi|118101049|ref|XP_417580.2| PREDICTED: similar to MGC80334 protein [Gallus gallus]
          Length = 291

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 91/275 (33%), Positives = 145/275 (52%), Gaps = 31/275 (11%)

Query: 3   RYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHAL 58
           RY +  +Y G+ Y G  +   +++G  +Q  +EKA   +   + +  H + RTDSGVHAL
Sbjct: 7   RYLVFFQYWGTKYSGVMQTSAEQSGIGVQNYLEKAAQNLKPVVPIKFHISSRTDSGVHAL 66

Query: 59  RQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      +   +L   LN +LK  + I IL+   V   FHARFSA+ R+Y+
Sbjct: 67  CNSAHLDIQRAPGKPAFQERVLIGCLNHHLK-PEPIRILSAYRVTNNFHARFSALSRTYI 125

Query: 114 YRII---TRQAPLAL-EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQAS-- 166
           YR++   T  + + + E+   W  P   L+   M+ AAQ L+G HDF+TF S++ +    
Sbjct: 126 YRLLMGCTHHSEIPVFERDLCWAPPGGYLNVPAMQDAAQFLLGTHDFSTFCSLNSETPFR 185

Query: 167 SPIRTIDHFDVNSFGNLI------------EIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           SP++TI   D+      +            E++  +RSFL+ Q+R  VG+L  VG GK  
Sbjct: 186 SPVKTILQADIQPSSGFLSHHYEYRGLQFWELKFKSRSFLYRQVRRMVGALVAVGQGKLA 245

Query: 215 STDLEKALQAQDRK--ECGPLAPPEGLYFDSVEYS 247
              +++ L+ +D +      +AP  GL+  SVEY+
Sbjct: 246 PHHIKELLEMKDARAFPAFAMAPSSGLFLKSVEYN 280


>gi|227891575|ref|ZP_04009380.1| tRNA pseudouridine synthase A [Lactobacillus salivarius ATCC 11741]
 gi|227866722|gb|EEJ74143.1| tRNA pseudouridine synthase A [Lactobacillus salivarius ATCC 11741]
          Length = 256

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 126/249 (50%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQ 60
           R+ + + Y+G+ + G+Q Q N  ++Q  +EKAI  ++   E + V+G+GRTDSGVHAL Q
Sbjct: 4   RFKVTLAYDGTNFAGFQAQPNQRTVQFVLEKAINKMSKKDEYITVYGSGRTDSGVHALGQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD         + + LN+ L +     +++  IV   FH+R++   + YLYR+   +
Sbjct: 64  VVHFDFPHPISAKGMLRGLNSMLPLD--CEVVDCKIVPNDFHSRYTTHGKRYLYRVSRGE 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++         LD E ++ A   + G HD+++F +   QA S +RTI    V  +
Sbjct: 122 FVNPFKRLYTGHYKYPLDIEKIKEAMPDVEGTHDYSSFVASGSQAKSHVRTIYEAKVYED 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + I        FL+ Q+R  V +L  +G+GK    D  +  + +DR +    AP  G
Sbjct: 182 KVNDEIVFEFYGNGFLYNQVRIMVATLLEIGNGKRPVHDFLRLYKVKDRSQARQTAPASG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLKEVYYD 250


>gi|329767334|ref|ZP_08258859.1| tRNA pseudouridine synthase A [Gemella haemolysans M341]
 gi|328836023|gb|EGF85714.1| tRNA pseudouridine synthase A [Gemella haemolysans M341]
          Length = 265

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 78/253 (30%), Positives = 133/253 (52%), Gaps = 13/253 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS Y G+Q Q N ++IQ  IEK++  +  + V ++ +GRTDSGVHA  QV
Sbjct: 1   MRIALLCRYDGSNYHGFQIQPNNNTIQEEIEKSLKKINKKDVRLYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI-ITRQ 120
            HFD       V   KALNA   I   I I+  + V + FH R+++ +++Y Y++ I R+
Sbjct: 61  LHFDTDLNIPDVAWVKALNA--TIPKDIRIVGATTVSEDFHVRYNSTQKTYYYKLYIGRE 118

Query: 121 -APLALEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             P  L     ++   S D   E  + + ++ +G HDF++F S +      +RTI    +
Sbjct: 119 IDPFLLN----YVGKHSFDFNFEKAQESLKYFIGEHDFSSFCSKNSSVEDKVRTIYSLTM 174

Query: 178 NS---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                  N++   +    FL+  +R  +G+++ V  GK+ +  +++ L  ++R+  GP A
Sbjct: 175 GKDPINPNIVNFEITGNGFLYNMVRIIIGTIQNVAAGKYEADYIKEILDKKERQFAGPKA 234

Query: 235 PPEGLYFDSVEYS 247
              GLY   V Y 
Sbjct: 235 DAAGLYLKEVVYD 247


>gi|260881651|ref|ZP_05404943.2| tRNA pseudouridine synthase A [Mitsuokella multacida DSM 20544]
 gi|260848088|gb|EEX68095.1| tRNA pseudouridine synthase A [Mitsuokella multacida DSM 20544]
          Length = 264

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 126/243 (51%), Gaps = 6/243 (2%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G+ Y G+QRQ     ++Q  +E+ +  + G+ + +  AGRTD+GVHA  QV +F  
Sbjct: 20  VAYDGTAYHGFQRQTPPIVAVQNILEEKLQTIFGDTIELAAAGRTDAGVHAYGQVVNF-F 78

Query: 67  VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
               +PV  + +A N+ L   D I +      D  F AR SA  ++Y+YRI   + P  +
Sbjct: 79  TDGRIPVDRIARAANSLL--PDDIVVRAAGEADTDFSARHSAKSKTYVYRIQQGEVPDPM 136

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSFGNLI 184
               AW I + LD   MR A   ++G HDF+ FR+      SP+RT+    +  + G  +
Sbjct: 137 TARYAWYIRRPLDVAAMREALGAILGTHDFSAFRASGGAPMSPVRTMYEATIEEAAGQQL 196

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+    FL+  +R+ +G+L  VG G  T     + L+ +DR +    AP  GLY + V
Sbjct: 197 ICRIHGSGFLYHMVRNIIGTLANVGLGVLTPARFGEILEGRDRTKASATAPACGLYLEHV 256

Query: 245 EYS 247
           +Y 
Sbjct: 257 DYG 259


>gi|302670312|ref|YP_003830272.1| tRNA pseudouridine synthase A TruA2 [Butyrivibrio proteoclasticus
           B316]
 gi|302394785|gb|ADL33690.1| tRNA pseudouridine synthase A TruA2 [Butyrivibrio proteoclasticus
           B316]
          Length = 265

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 125/249 (50%), Gaps = 9/249 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
           Y  II Y+G+ Y GW+++ +   +IQG +E  +  +     TGE+ ++ GAGRTD+GVHA
Sbjct: 20  YKFIISYDGTRYHGWEKKPDLEMTIQGKLEGVLNRMIGAEGTGEVNLI-GAGRTDAGVHA 78

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
               A   L        +   +N YL   + IS+  + +   +FHAR++AI ++Y Y   
Sbjct: 79  RAMTASAVLDTHLSEAEIQSYMNTYL--PEDISVNEVKVCSDRFHARYNAIGKTYRYTCW 136

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                   ++    ++ +  + + MR AA+ L+G HDF +F        S +R +D  ++
Sbjct: 137 YGDGKPVFDRKYVTVLDREPNVDMMRKAAELLIGEHDFRSFCGNSKMKKSTVRVLDTINI 196

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              GN I        FL   +R   G+L  VG G  +   ++  L+A DRK+ GP A PE
Sbjct: 197 EKNGNYIRFYFHGNGFLQNMVRILTGTLLEVGYGNISPEKIQDILKACDRKKAGPTARPE 256

Query: 238 GLYFDSVEY 246
           GL    V+Y
Sbjct: 257 GLCMMKVDY 265


>gi|199598865|ref|ZP_03212276.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus HN001]
 gi|199590277|gb|EDY98372.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus HN001]
          Length = 247

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + +A+N+ + +   I IL   IV   FHAR+SA  + Y YR+   
Sbjct: 61  QVISFDYPGNIPAESMLRAMNSLMPLD--IEILKAEIVAADFHARYSAKGKRYRYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEE 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   + +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  
Sbjct: 179 DPAADELIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|78780010|ref|YP_398122.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9312]
 gi|123768929|sp|Q318K9|TRUA_PROM9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78713509|gb|ABB50686.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9312]
          Length = 268

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS Y GWQRQKN +++Q ++E+A+F +T ++V    AGRTD+GVHA  Q
Sbjct: 1   MKRIALLVQYDGSNYSGWQRQKNATTVQETLERALFKITHQVVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF++            LN  L     I IL    V   +H+ +SA+ R Y Y I   +
Sbjct: 61  VVHFNIDCVIPANSYSDILNGLL--PSAIRILESVEVKDSWHSCYSAMYRHYRYVINNSK 118

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    K LD   M  A++ + G HDF  F+    Q  + I  I + ++  
Sbjct: 119 FPNLFINNWSWHRYQKILDEVLMSNASKLMEGEHDFFAFQKSGSQRKNSITKIKNVEIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +          Q + +    AP +GL
Sbjct: 179 VEDLILVDIKATGFLYGMVRLIVGQLVLVGEKKISPEIFTDIWVNQKKNDVKESAPAKGL 238

Query: 240 YFDSVEY 246
            F +  Y
Sbjct: 239 CFVNAVY 245


>gi|291460751|ref|ZP_06600141.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
 gi|291416710|gb|EFE90429.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
          Length = 266

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/244 (32%), Positives = 124/244 (50%), Gaps = 7/244 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R  + I Y+G+ Y GWQ Q+  S+I+G + +A+  L+ GE + + GA RTD+GVHA +
Sbjct: 1   MRRIRLDIAYDGTNYHGWQYQEGQSTIEGELRRALSELLPGEEIGLTGASRTDAGVHARQ 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             A FD            ALN   ++ + I IL      + FH RFS  ++ Y YRI   
Sbjct: 61  NTACFDTKSRIPGANFSMALNC--RLPEDIRILRSMEAGEDFHPRFSPHKKVYEYRIGRS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ----ASSPIRTIDHF 175
           + P  L++   +     L    MR+AA+ LVG HDF +F +   Q      + +RT+   
Sbjct: 119 RIPDPLKRLYCFPFSFPLSLSEMRLAAEELVGEHDFRSFANPDSQVLMHGGAAVRTLYEL 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   G  + +      FL+  IR   G+L  +G G+  + ++ + L A+DR+  G  AP
Sbjct: 179 SLREEGEELILHFEGSGFLYHMIRILTGTLLEIGSGRRRAAEIPEILAARDRRRAGFTAP 238

Query: 236 PEGL 239
            +GL
Sbjct: 239 AKGL 242


>gi|219849858|ref|YP_002464291.1| tRNA pseudouridine synthase ACD [Chloroflexus aggregans DSM 9485]
 gi|254789611|sp|B8G6P6|TRUA_CHLAD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219544117|gb|ACL25855.1| tRNA pseudouridine synthase A [Chloroflexus aggregans DSM 9485]
          Length = 278

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 123/250 (49%), Gaps = 14/250 (5%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +++ Y+G+ + G Q Q +  ++QG+IE A   +T E   +  AGRTD+GVHA  QVAH 
Sbjct: 5   ALLLAYDGTDFAGSQWQTDIRTVQGAIEAAWEALTQEQRRIVLAGRTDAGVHASGQVAHV 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + + LNA+L     +++ N+    + FHAR+SAI R Y Y I     PL 
Sbjct: 65  QTATRHSLATIWRGLNAHLPTD--VTVQNVGEAVRDFHARYSAIEREYRYLIDCAPVPLP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--------DHFD 176
             + +A     +LD   M  A + L G HDF  F +      S +RT+          FD
Sbjct: 123 QLRHQALHYAGTLDVTAMATALKLLEGTHDFAAFTTATPSQRSTVRTMYWTRIVERVWFD 182

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 L+ I + A +FL   +R  VG+L LVG G+ T     + L  +DR+  GP AP 
Sbjct: 183 ----RRLLAIELAANAFLQHMVRMIVGTLLLVGRGRMTVDQFGEVLAGRDRRLAGPTAPA 238

Query: 237 EGLYFDSVEY 246
            GL   +V Y
Sbjct: 239 HGLTLTAVRY 248


>gi|284929586|ref|YP_003422108.1| pseudouridylate synthase I [cyanobacterium UCYN-A]
 gi|284810030|gb|ADB95727.1| pseudouridylate synthase I [cyanobacterium UCYN-A]
          Length = 281

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 117/245 (47%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +II+Y+G+ + GWQRQ    ++Q  IE  I    G  V +HGAGRTD+GVHA  QVA
Sbjct: 13  RIALIIQYSGNRFHGWQRQPYRRTVQADIENTITKSLGYKVSIHGAGRTDAGVHATGQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD      P  L + LN YL   + I I N   V   +HARFSA  R Y Y + T    
Sbjct: 73  HFDYAGPIPPKSLARVLNRYL--PEDILIRNSKEVSINWHARFSAQWRRYRYTLYTNNDC 130

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             L K  +W   +  L  ++M  A + L+G H  T FR    Q +     I   +    G
Sbjct: 131 NLLIKSYSWHYYRYPLKVKSMLDALKSLLGTHHLTAFRKKGSQRNHSWVEIQDVECYRKG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+  +R  +G L  VG  K +  +  +  + Q R+     AP  GL  
Sbjct: 191 AFIHIEIQANGFLYGMVRLLMGMLVEVGIDKLSLANFNQIWRDQKREYVRHSAPANGLCL 250

Query: 242 DSVEY 246
             V Y
Sbjct: 251 LGVGY 255


>gi|78357749|ref|YP_389198.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|123754841|sp|Q30XU3|TRUA_DESDG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78220154|gb|ABB39503.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
          Length = 278

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 92/273 (33%), Positives = 133/273 (48%), Gaps = 29/273 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ---------KNGSSIQGSIEKAIFLVTGEIVVVHGAGRT 51
           M R  +II Y G+ Y GWQ Q             ++Q ++E A   + G  V VHGAGRT
Sbjct: 1   MARLKLIIAYAGTRYAGWQIQCLPAGRPHAVQQPTVQQAVEDAAKAILGSAVRVHGAGRT 60

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           DSGVHA  QVAH D+      V   +ALNA  K+ + IS+L  ++V   FHARF A+++ 
Sbjct: 61  DSGVHAEGQVAHLDIPDAKAAVDWRRALNA--KLPEDISVLQAAVVPDGFHARFDAVKKR 118

Query: 112 YLYRIITRQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y YRI   +A   L + R ++ +   LD   M  AA  + G HDF +F++   + ++ +R
Sbjct: 119 YTYRIWLTRA-FVLPQRRPFVHMTGPLDIAAMDAAAAFMTGTHDFASFQNAGTELATTVR 177

Query: 171 TI-----------DHF----DVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           T+           D F    D      L +     A  FL   +R+ +G L   G G+  
Sbjct: 178 TVYSITRTPGLAPDDFPRSHDTTPRAPLELAWHFEADGFLKQMVRNMMGLLLWTGTGRCA 237

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             D+   + A+DR+   P AP  GL  + V Y 
Sbjct: 238 PEDVPAIIAARDRRLSAPTAPACGLTMERVFYP 270


>gi|241890020|ref|ZP_04777318.1| tRNA pseudouridine synthase A [Gemella haemolysans ATCC 10379]
 gi|241863642|gb|EER68026.1| tRNA pseudouridine synthase A [Gemella haemolysans ATCC 10379]
          Length = 265

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 78/253 (30%), Positives = 132/253 (52%), Gaps = 13/253 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS Y G+Q Q N ++IQ  IEK++  +  + V ++ +GRTDSGVHA  QV
Sbjct: 1   MRVVLLCRYDGSNYHGFQIQPNNNTIQEEIEKSLKKINKKDVRLYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI-ITRQ 120
            HFD           KALNA   I   I I+  +   + FH R+++ +++Y Y++ I R+
Sbjct: 61  LHFDTDLNIPDEAWVKALNA--TIPKDIRIVGATSASEDFHVRYNSTQKTYYYKLHIGRE 118

Query: 121 A-PLALEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             P  L     ++   S D   E  + A Q+ +G HDF++F S +      +RTI    +
Sbjct: 119 VDPFLLN----YVGKHSFDFNFEKAQEALQYFIGEHDFSSFCSKNSSVEDKVRTIYSLTM 174

Query: 178 NS---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                  N++   +    FL+  +R  +G+++ V  GK+ +  +++ L+ ++R+  GP A
Sbjct: 175 EKDLINPNIVNFEITGNGFLYNMVRIIIGTIQNVAAGKYEANYVKEILEKKERQFAGPKA 234

Query: 235 PPEGLYFDSVEYS 247
              GLY   V Y 
Sbjct: 235 DAAGLYLKEVLYD 247


>gi|218296263|ref|ZP_03497019.1| tRNA pseudouridine synthase A [Thermus aquaticus Y51MC23]
 gi|218243335|gb|EED09865.1| tRNA pseudouridine synthase A [Thermus aquaticus Y51MC23]
          Length = 259

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 123/250 (49%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ+ G  ++QG +EKA+  + G +     AGRTD+GVHAL 
Sbjct: 1   MRRILLLTEYDGTHFAGLQRQRQGLRTVQGELEKALPHI-GALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H DL     P  + +ALN  L   + + ++    V   FHAR  A+ R+Y YR++ R
Sbjct: 60  MPFHIDLQSPIPPEKVPEALNRLL--PEDLKVVAAREVAPDFHARKDALWRAYRYRVLLR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
             P  L + R   + + LD + M  A   L+GRH+F  F     +           +V  
Sbjct: 118 PHPSPLLRHRVLWLRRPLDLKAMEEALPLLLGRHNFLGFAKEETREGVRELLEARLEVLE 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  +      RSFL  Q+R  VG+L  VG G+ +   ++  L+  DR+  G  AP  
Sbjct: 178 GEMGPEVRFYFKGRSFLRGQVRGMVGTLLEVGLGRRSPESVKAILETADRRLAGQSAPAT 237

Query: 238 GLYFDSVEYS 247
           GLYF    Y 
Sbjct: 238 GLYFLEAAYP 247


>gi|326932368|ref|XP_003212291.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Meleagris
           gallopavo]
          Length = 292

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 91/275 (33%), Positives = 144/275 (52%), Gaps = 31/275 (11%)

Query: 3   RYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHAL 58
           RY +  +Y G+ Y G      +++G  +Q  +EKA   +   + +  H + RTDSGVHAL
Sbjct: 7   RYLVFFQYWGTKYSGVMHTSAEQSGVGVQNYLEKAAQNLKPVVPIKFHISSRTDSGVHAL 66

Query: 59  RQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      +   +L   LN +LK  + I IL+   V   FHARFSA+ R+Y+
Sbjct: 67  CNSAHLDIQRAPGKPAFQEKMLIGCLNHHLK-PEPIRILSAYRVTNNFHARFSALSRTYI 125

Query: 114 YRII---TRQAPLAL-EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQAS-- 166
           YR++   T  + + + E+   W      L+   M+ AAQ L+G HDF+TF S++ +    
Sbjct: 126 YRLLMGCTHHSEIPVFERDLCWAPTGGYLNVPAMQDAAQFLLGTHDFSTFCSLNSETPFR 185

Query: 167 SPIRTIDHFDVNSFGNLI------------EIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           SP++TI   D+      +            E++  +RSFL+ Q+R  VG+L  VG GK  
Sbjct: 186 SPVKTILQADIQPSSGFLSHHYEYRGLQFWELKFKSRSFLYRQVRRMVGALVAVGQGKLA 245

Query: 215 STDLEKALQAQDRKECGP--LAPPEGLYFDSVEYS 247
              +++ L+ +D +   P  +AP  GL+  SVEY+
Sbjct: 246 PYHIKELLEMKDARAFPPFAMAPSSGLFLKSVEYN 280


>gi|193214164|ref|YP_001995363.1| tRNA pseudouridine synthase A [Chloroherpeton thalassium ATCC
           35110]
 gi|193087641|gb|ACF12916.1| tRNA pseudouridine synthase A [Chloroherpeton thalassium ATCC
           35110]
          Length = 265

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 83/244 (34%), Positives = 122/244 (50%), Gaps = 7/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           M++EY+G+ + GWQRQ       +IQG IE  +  V  E V +  AGRTD+GVHA  QVA
Sbjct: 23  MLLEYDGTDFAGWQRQPQNLHQKTIQGEIESVLCRVLQEPVELIAAGRTDAGVHAKAQVA 82

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F          L  ALN  L     I I+ +    + F+ARF A  R+Y Y ++TR + 
Sbjct: 83  NFLTENSLSISRLKHALNGLL--PSQIKIIEIEDAPENFNARFDAKSRTYRYFLLTRYS- 139

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            AL      +     D   M    Q ++G+HDFT+F     Q  + I TI+        N
Sbjct: 140 -ALLSRFTGIYRYDFDARAMNACCQEILGQHDFTSFSKAGSQTKTRICTIEKARWYQRKN 198

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A  FLH+ +R  VG++  VG+G+ +  D +    A+D       A P+GL+  
Sbjct: 199 GLMLEIRANRFLHSMVRLLVGTMIKVGNGELSVQDFDAIFSAKDVCLAATSAQPQGLFLW 258

Query: 243 SVEY 246
            VEY
Sbjct: 259 HVEY 262


>gi|89100313|ref|ZP_01173178.1| pseudouridylate synthase I [Bacillus sp. NRRL B-14911]
 gi|89084934|gb|EAR64070.1| pseudouridylate synthase I [Bacillus sp. NRRL B-14911]
          Length = 245

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 117/247 (47%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R+   I Y+GS + G+Q Q    ++Q  +E+A+  +  G  V +  +GRTD+GVHA  
Sbjct: 1   MQRFKCKIAYDGSQFSGYQVQPGKRTVQLEVERALAKIHKGNPVKIFASGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L     I++ +     + FHARF A  + Y Y I   
Sbjct: 61  QVIHFDSPLAIPEDRWVTALNSLL--PKDIAVESTEKAAEGFHARFDACGKEYRYFIYRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     E+  ++  P  LD   MR AA+HL+G HDF++F +        +R I    V  
Sbjct: 119 KIRSPFERHYSYHYPHPLDIRAMREAAEHLLGTHDFSSFCASRTDVEDKVREIRKVHVEE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E+      FL+  +R   G+L   G G        + +  +DR   G  AP EGL
Sbjct: 179 AGEMLELHFTGSGFLYNMVRILTGTLLEAGAGTRDPGSFPEVISGRDRSLAGKTAPAEGL 238

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 239 YLWKVFY 245


>gi|228470580|ref|ZP_04055437.1| tRNA pseudouridine synthase A [Porphyromonas uenonis 60-3]
 gi|228307707|gb|EEK16683.1| tRNA pseudouridine synthase A [Porphyromonas uenonis 60-3]
          Length = 262

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 121/245 (49%), Gaps = 10/245 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y GWQ Q  G S+Q  +E+A+ ++  + + V GAGRTD+GVHA   +AH DL 
Sbjct: 12  VAYDGTNYCGWQVQPRGVSVQSELERALSMLFRQPISVTGAGRTDAGVHAYSMMAHADLP 71

Query: 68  REWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
               P+  + + L   L+    IS+ +++ V    HARF A  R Y Y I     P   +
Sbjct: 72  IPHPPLAQIQRGLCGILR--GGISVRSVTPVIPTAHARFDATSRRYHYYISACSNPFWGD 129

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-----DHFDVNSFG 181
               W      D E M  A +H +G HDFT+F  +H Q      T+     +  ++    
Sbjct: 130 Y--CWERRTLPDMELMNEACRHFIGEHDFTSFSKLHTQTKHNRCTVYTAHWEQVEMPGLW 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +   V A  FLH  +R+ VG+L  VG G+ T   + + +Q +DR   G  AP   L+F
Sbjct: 188 DAMRYEVCANRFLHGMVRTMVGTLLEVGYGQRTPDSIAELIQREDRTLAGSAAPARALFF 247

Query: 242 DSVEY 246
               Y
Sbjct: 248 VEATY 252


>gi|253681679|ref|ZP_04862476.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
 gi|253561391|gb|EES90843.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
          Length = 245

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 123/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + I+Y+G+ Y GWQ+  +  ++IQ  IE  +  + GE V +  +GRTD+GVHA  Q+A+F
Sbjct: 6   LTIQYDGTRYKGWQKLGDADNTIQYKIESVLNELLGEEVSLIASGRTDAGVHANMQIANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + K    YL     I I N+S   + FH+R++  ++ Y Y I        
Sbjct: 66  KTNSNVTNDTILKHCYKYL--PQDIVITNISDASENFHSRYNVKKKIYTYNIYNNPVHDV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  ++ I ++LD + M+ A++  +G HDF +F ++  +  S ++TID        N I
Sbjct: 124 FTRKYSYHIKETLDIKKMKEASKLFIGEHDFKSFTALKSKKKSTVKTIDSITFKKKDNNI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           EI      FL+  IR  VGSL  VG GK T  DL+  +  +DR      AP  GL    V
Sbjct: 184 EIIFTGNGFLYKMIRILVGSLINVGLGKLTIEDLQNIMNKKDRSIAPETAPAHGLILTEV 243

Query: 245 EY 246
           +Y
Sbjct: 244 KY 245


>gi|282877805|ref|ZP_06286618.1| tRNA pseudouridine synthase A [Prevotella buccalis ATCC 35310]
 gi|281300121|gb|EFA92477.1| tRNA pseudouridine synthase A [Prevotella buccalis ATCC 35310]
          Length = 243

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 82/253 (32%), Positives = 129/253 (50%), Gaps = 17/253 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG+S+Q  +++A+ ++  E +V  GAGRTD+GVHA + 
Sbjct: 1   MHRYFICFRYDGTAYHGWQVQPNGNSVQAELQQAMSVILREPIVTVGAGRTDAGVHARKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD   E         LN  L     IS+LN+  + +  HARFSA  R+Y Y I   +
Sbjct: 61  FAHFDFHAEIDTKQFTYKLNRLL--PRDISVLNVFSLSEDMHARFSAKWRTYHYYIHLSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +  +P  LD   M  AA HL+   DF  F    C++++ ++T     V + 
Sbjct: 119 NPFL--RHYSCQLPYQLDFSLMNEAASHLLKVEDFGAF----CKSNTDVKTTLCHVVQA- 171

Query: 181 GNLIEIR-------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              +E+        + A  FL   +R+ VG+L  VG  + T  + +  +++ +R + G  
Sbjct: 172 -EWVEVGEDAWYFVIKANRFLRNMVRAVVGTLIEVGRHRMTLDEFDAVVRSGNRTKAGES 230

Query: 234 APPEGLYFDSVEY 246
            P   L+ + VEY
Sbjct: 231 MPANALFLEDVEY 243


>gi|302874184|ref|YP_003842817.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|307689556|ref|ZP_07632002.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|302577041|gb|ADL51053.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
          Length = 245

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/244 (32%), Positives = 127/244 (52%), Gaps = 7/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IE++GS Y GWQ QK+   ++QG IE  +  +TGE + V G  R D+G HA   +A+F
Sbjct: 6   LTIEFDGSRYKGWQNQKDKEQTVQGKIETVLSKMTGEEIEVIGCERIDTGAHADGYIANF 65

Query: 65  DLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
               E    + C A++ YL   + + I +  +  VD++FHAR++A  + Y Y I      
Sbjct: 66  KTNCE----LSCTAISIYLYEFLPEDILVKFIEEVDERFHARYNAKAKVYEYVINNNNLR 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  ++ I   L+ E M  AA+   G+HDF  F ++   A S +RT++   +     
Sbjct: 122 NVFNRKYSYHIDIDLNIEEMLKAAEAFKGKHDFKAFTNLKSSAKSTVRTVEDILIKKDNG 181

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI+I ++A  FL    R  VG+L  VG G   +T++ K L+   + E  P+A  + L+  
Sbjct: 182 LIKIELIADDFLLNMERIIVGTLIEVGKGNVKATNVFKMLKDGKKIETIPMAQAKALFLK 241

Query: 243 SVEY 246
            V Y
Sbjct: 242 KVIY 245


>gi|229552739|ref|ZP_04441464.1| tRNA-pseudouridine synthase I [Lactobacillus rhamnosus LMS2-1]
 gi|229313945|gb|EEN79918.1| tRNA-pseudouridine synthase I [Lactobacillus rhamnosus LMS2-1]
          Length = 242

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 121/244 (49%), Gaps = 5/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL QV  F
Sbjct: 1   MTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALGQVISF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D         + +A+N+ + +   I IL   IV   FHAR+SA  + Y YR+        
Sbjct: 61  DYPGNIPAESMLRAMNSLMPLD--IEILKAEIVAADFHARYSAKGKRYRYRVARGYYTNP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--NSFGN 182
             +      P  LD + + +A + LVG HDFT+F +        +RTI    V  +   N
Sbjct: 119 FNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEEDPATN 178

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  GLY  
Sbjct: 179 ELIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPASGLYLK 238

Query: 243 SVEY 246
            V Y
Sbjct: 239 EVYY 242


>gi|145294737|ref|YP_001137558.1| tRNA pseudouridine synthase A [Corynebacterium glutamicum R]
 gi|140844657|dbj|BAF53656.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 294

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 89/263 (33%), Positives = 133/263 (50%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW +Q      ++Q  +E  + +V  E V +  AGRTD+GVHA  
Sbjct: 6   VRIRLDLAYDGTDFHGWAKQGTSDLRTVQKVLEDNLSMVLRETVELTVAGRTDAGVHAAG 65

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+    +        P  L + L   L   D I +  +   +  F ARFSA+RR 
Sbjct: 66  QVAHFDIPAHALEQRSIDGDPSKLVRRLGRLL--PDDIRVHGVRFAEPGFDARFSAMRRH 123

Query: 112 YLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YRI T  A   P        W  PK ++ E M++AA  L+G HDF  F      A++ 
Sbjct: 124 YVYRITTHPAGALPTRRHDTAQW--PKPVELERMQLAADALLGLHDFVAFCKAKPHATT- 180

Query: 169 IRTIDHF---DVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R +  F   DV++     + E  VVA +F  + +RS VGS   VG+G+  S    + L 
Sbjct: 181 VRELQKFAWKDVSTDIEPQVYEAHVVADAFCWSMVRSLVGSCMAVGEGRRGSGFTTELLD 240

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A +R    P+AP +GL    V+Y
Sbjct: 241 ASERSPMVPVAPAKGLSLVGVDY 263


>gi|19551801|ref|NP_599803.1| tRNA pseudouridine synthase A [Corynebacterium glutamicum ATCC
           13032]
 gi|62389456|ref|YP_224858.1| tRNA pseudouridine synthase A [Corynebacterium glutamicum ATCC
           13032]
 gi|41324790|emb|CAF19272.1| PROBABLE TRNA PSEUDOURIDINE SYNTHASE A PROTEIN [Corynebacterium
           glutamicum ATCC 13032]
          Length = 294

 Score =  126 bits (317), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 89/263 (33%), Positives = 133/263 (50%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW +Q      ++Q  +E  + +V  E V +  AGRTD+GVHA  
Sbjct: 6   VRIRLDLAYDGTDFHGWAKQGTSDLRTVQKVLEDNLSMVLRETVELTVAGRTDAGVHAAG 65

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+    +        P  L + L   L   D I +  +   +  F ARFSA+RR 
Sbjct: 66  QVAHFDIPAHALEQRSIDGDPSKLVRRLGRLL--PDDIRVHGVRFAEPGFDARFSAMRRH 123

Query: 112 YLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YRI T  A   P        W  PK ++ E M++AA  L+G HDF  F      A++ 
Sbjct: 124 YVYRITTHPAGALPTRRHDTAQW--PKPVELERMQLAADALLGLHDFVAFCKAKPHATT- 180

Query: 169 IRTIDHF---DVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R +  F   DV++     + E  VVA +F  + +RS VGS   VG+G+  S    + L 
Sbjct: 181 VRELQKFAWKDVSTDIEPQVYEAHVVADAFCWSMVRSLVGSCMAVGEGRRGSGFTAELLD 240

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A +R    P+AP +GL    V+Y
Sbjct: 241 ASERSPMVPVAPAKGLSLVGVDY 263


>gi|238927931|ref|ZP_04659691.1| tRNA-pseudouridine synthase I [Selenomonas flueggei ATCC 43531]
 gi|238884264|gb|EEQ47902.1| tRNA-pseudouridine synthase I [Selenomonas flueggei ATCC 43531]
          Length = 256

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 123/243 (50%), Gaps = 3/243 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
            + I Y+G+ Y G+QRQ     ++Q  +E A+  + GE+V +  AGRTD+GVHA  QV +
Sbjct: 10  ALTIAYDGTNYHGFQRQTPPVLAVQNVLEGALAKICGEMVELAAAGRTDAGVHAYGQVVN 69

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F          L +A+N  L     +S        ++F AR SA  ++Y+YRI   + P 
Sbjct: 70  FFTDGRIPTEHLPRAVNGLLPPDIVVS--QAWEAPREFSARHSATGKAYVYRIEECRVPN 127

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
              +  AW + + LD E M      L G HD+++FR+      SP+RT+D   +      
Sbjct: 128 PFTRNYAWQVFQPLDHEAMHAVLLLLKGTHDYSSFRAAGGAPMSPVRTLDEIRLTEEEGR 187

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + I V    FL+  +R+ V +   VG G+ + +   +   A+DR+   P AP  GLY  +
Sbjct: 188 LSIYVHGTGFLYHMVRNIVSTAAAVGMGRISPSRFAEIFAARDRRLAPPTAPACGLYLLA 247

Query: 244 VEY 246
           V+Y
Sbjct: 248 VDY 250


>gi|313895792|ref|ZP_07829346.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 137 str.
           F0430]
 gi|312975217|gb|EFR40678.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 137 str.
           F0430]
          Length = 266

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 128/243 (52%), Gaps = 6/243 (2%)

Query: 8   IEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G+ Y G+QRQ     ++Q  +EK +  V GE V +  AGRTD+GVHA  QV +F  
Sbjct: 20  LSYDGTRYHGFQRQSLPVVAVQNVLEKVLAEVCGESVELAAAGRTDTGVHAYGQVVNF-F 78

Query: 67  VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
               +PV  L +A+N  L     I+++     ++ F AR S+  ++YLYRI     P   
Sbjct: 79  TDGRIPVAQLPRAVNGLLP--PDIAVMAAWEAERDFSARHSSTGKAYLYRIERCTVPNPF 136

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFGNLI 184
            +  AW I + LD   MR   + LVG HD+++FR+      SP+RT+D   ++   G  +
Sbjct: 137 TRNYAWQIFRPLDVAAMRTVLRLLVGTHDYSSFRAAGGAPMSPVRTLDEIRLDEEEGGQL 196

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
              +    FL+  +R+ + ++  VG G+ ++    +   A DR+   P AP  GLY   V
Sbjct: 197 SCYMHGNGFLYHMVRNIMSTVVHVGLGRISTDRFTEIFAAHDRRLASPTAPACGLYLLHV 256

Query: 245 EYS 247
           +Y+
Sbjct: 257 DYA 259


>gi|297829238|ref|XP_002882501.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297328341|gb|EFH58760.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 323

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 131/255 (51%), Gaps = 14/255 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T     E+ ++ GAGRTD+GVHA 
Sbjct: 42  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELHLI-GAGRTDAGVHAW 100

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF     +  +     ALN  L     I +  LS    +FHARFSA  + Y Y+I 
Sbjct: 101 GQVAHFVTPFNYTSLDSFHAALNGLLP--KDIRVRELSAAVPEFHARFSAHSKVYRYQIY 158

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHF 175
                   ++  A+     L+   MR AA   VG HDF+ F +   +     P++TI  F
Sbjct: 159 NDTFMDPFQRHWAYHCAYKLNASKMREAANLFVGMHDFSAFANATREDGLPDPLKTISRF 218

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL-- 233
           DV   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR+       
Sbjct: 219 DVIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTT 278

Query: 234 --APPEGLYFDSVEY 246
             APP GL   SV+Y
Sbjct: 279 LPAPPHGLCLVSVKY 293


>gi|111220576|ref|YP_711370.1| tRNA pseudouridine synthase A [Frankia alni ACN14a]
 gi|111148108|emb|CAJ59776.1| tRNA pseudouridine synthase A (Pseudouridylate synthase I)
           (Pseudouridine synthase I) (Uracil hydrolyase) [Frankia
           alni ACN14a]
          Length = 288

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 94/262 (35%), Positives = 131/262 (50%), Gaps = 30/262 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALR 59
           ++R  + I Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA  
Sbjct: 19  LVRLRLDIAYDGTPFAGWARQPGQRTVQGDVEDALIRVARLAAVRLTVAGRTDSGVHAAG 78

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL  + VP+  L + LN  L  S  + +  L+     F ARFSA+ R Y+YRI  
Sbjct: 79  QVAHVDLPTD-VPLGGLARRLNGVLDRS--VRVTGLAPAPAGFDARFSALSRRYVYRIT- 134

Query: 119 RQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIR 170
             AP   E  R     AW  P+ LD   M  AA  LVG HDF  F    C   + ++ +R
Sbjct: 135 -DAPFGAEPLRRFDTLAW--PRPLDVPAMASAALLLVGEHDFAAF----CRRREGATTVR 187

Query: 171 TIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQ 225
           T+   DV      ++   V A +F H+ +R+ VG+L  VG+G+    W +  L + L   
Sbjct: 188 TLLRLDVLRRPDGVVVADVEADAFCHSMVRALVGALLAVGEGRRPPQWPAAVLRRGL--- 244

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R     +AP  GL    V Y 
Sbjct: 245 -RDPAVTVAPAHGLTLVEVRYP 265


>gi|156743919|ref|YP_001434048.1| tRNA pseudouridine synthase ACD [Roseiflexus castenholzii DSM
           13941]
 gi|189029997|sp|A7NR34|TRUA_ROSCS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|156235247|gb|ABU60030.1| tRNA pseudouridine synthase A [Roseiflexus castenholzii DSM 13941]
          Length = 270

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 90/252 (35%), Positives = 128/252 (50%), Gaps = 12/252 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ + G Q Q NG S+QG++E A   +TGE   +  AGRTD+GVHA  Q
Sbjct: 1   MRNIALRIEYDGTDFVGSQWQTNGRSVQGALEAAWQQLTGERRRMILAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+           + + LN  L   + I IL    V ++FHAR+SA+RR Y Y I   +
Sbjct: 61  VANVSTNTRHSLATIIRGLNGVLP--EDIGILAAWEVPEEFHARYSAVRREYRYVIDNGR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P  L +  A  +P+ LD   M  A Q ++G HDF    S   Q  S +R    +D    
Sbjct: 119 TPSPLLRRHAAYVPRRLDVAAMDRAIQQVIGTHDFAPL-SDGPQEGSTVRIC--YDARCT 175

Query: 180 ----FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +G  L+ I V A +FL   +R+ VG+L  VG+G+  +      L   +R+    LA
Sbjct: 176 CTEVWGQPLVLIDVAANAFLRHMVRNLVGTLIQVGEGRIDADGFAAVLAGANRR-ARVLA 234

Query: 235 PPEGLYFDSVEY 246
           P  GLY  +V Y
Sbjct: 235 PAHGLYLMAVRY 246


>gi|298243939|ref|ZP_06967746.1| tRNA pseudouridine synthase A [Ktedonobacter racemifer DSM 44963]
 gi|297556993|gb|EFH90857.1| tRNA pseudouridine synthase A [Ktedonobacter racemifer DSM 44963]
          Length = 264

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 87/252 (34%), Positives = 125/252 (49%), Gaps = 16/252 (6%)

Query: 8   IEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           IEY+G+ Y G+QRQ   +G ++QG++E A+  ++G  + V GAGRTD GVHA  QV HF 
Sbjct: 7   IEYDGTDYHGFQRQSASHGPTVQGTLEAAVTQISGVQITVMGAGRTDVGVHASGQVIHFR 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                   +  +ALNA L    T+ +     + + FHARFSA  RSY Y I     P AL
Sbjct: 67  TESRLTVEVWRRALNAVLP--STVVVRWAKEMPEGFHARFSAQSRSYRYTIWNECFPTAL 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF----- 180
               A+   + LD   M  A ++L+GR DF  F       S+P++   H  + +      
Sbjct: 125 RARYAYHCSRELDVTLMDDACRYLLGRKDFGAF-GHSPNDSNPLKPGPHHCIRTMLEARC 183

Query: 181 ------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                   LI     A +FL  Q+R  VG+L LVG  + +  +  + +Q  ++   G  A
Sbjct: 184 LRDHQQAELIYCDFTADAFLTGQVRRMVGTLLLVGQQRLSVAEFAEIVQRAEKTHPGSAA 243

Query: 235 PPEGLYFDSVEY 246
           P  GL    VEY
Sbjct: 244 PSLGLCLVRVEY 255


>gi|315655839|ref|ZP_07908737.1| tRNA pseudouridine synthase A [Mobiluncus curtisii ATCC 51333]
 gi|315489903|gb|EFU79530.1| tRNA pseudouridine synthase A [Mobiluncus curtisii ATCC 51333]
          Length = 314

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 90/276 (32%), Positives = 135/276 (48%), Gaps = 32/276 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW  Q    ++QG++E A+ ++  + V +  AGRTD+GVHA  Q
Sbjct: 17  VMRIRLDIRYDGTPFHGWAAQPGLPTVQGALESALAVIYRQTVELTVAGRTDAGVHASGQ 76

Query: 61  VAHFDLV----REWVPVILCKALNAYLK---------------------ISDTISILNLS 95
           VAHF +     R   P  L   L A L+                       D + +    
Sbjct: 77  VAHFTVPEVGDRIVPPDTLAPRLGAVLRAVLSGNLASPLPDSPAAYPPNAVDALVVTTAM 136

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
           +V + F ARFSA+ R Y+YRI+   A   PL   +   W  P  LD   M  +A  L+G 
Sbjct: 137 VVPETFDARFSALARHYVYRIVDDLAVRNPLC--RNYCWWYPTPLDAAAMNASAAVLLGE 194

Query: 153 HDFTTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           HDF  F     + ++ IRT+   + + +   ++EIRV A +F H+ +RS VG+L  VG  
Sbjct: 195 HDFAAFCKPR-EGATTIRTLQQLETLRTAPGMMEIRVRADAFCHSMVRSLVGALTEVGRA 253

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           K  +  L  AL A+ R    P+AP  GL    V+Y 
Sbjct: 254 KRDTVWLADALAAKARIPEIPVAPALGLTLTQVDYP 289


>gi|332300500|ref|YP_004442421.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica DSM
           20707]
 gi|332177563|gb|AEE13253.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica DSM
           20707]
          Length = 262

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 123/250 (49%), Gaps = 10/250 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ Y GWQ Q  G S+Q  +E+A+ ++  + + V GAGRTD+GVHA   +A
Sbjct: 7   RVFLEVAYDGTNYCGWQVQPRGVSVQSELERALSMLFRQSISVTGAGRTDAGVHAYSMMA 66

Query: 63  HFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           H DL     P+  + + L   L+    IS+ +++ V    HARF A  R Y Y I     
Sbjct: 67  HADLPIPHPPLAQIQRGLCGILR--GGISVRSVTPVIPTAHARFDATSRRYHYYISACSN 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-----DHFD 176
           P   +    W      D   M  A +H +G HDFT+F  +H Q      T+     +  +
Sbjct: 125 PFWSDY--CWERRTLPDMALMNEACRHFIGEHDFTSFSKLHTQTKHNRCTVYTAHWEQVE 182

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +   V A  FLH  +R+ VG+L  VG G+ T   + + +Q++DR   G  AP 
Sbjct: 183 MPGLWDAMRYEVCANRFLHGMVRTMVGTLLEVGYGQRTPDSIAELIQSEDRSLAGSAAPA 242

Query: 237 EGLYFDSVEY 246
             L+F    Y
Sbjct: 243 RALFFVEATY 252


>gi|261415083|ref|YP_003248766.1| tRNA pseudouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371539|gb|ACX74284.1| tRNA pseudouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302325886|gb|ADL25087.1| tRNA pseudouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 250

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 127/254 (50%), Gaps = 16/254 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           +RY    EY GS ++GWQ Q  G      ++Q ++E+A+       + V G+GRTD+GVH
Sbjct: 1   MRYRFRCEYLGSAFYGWQEQNCGGKLRFVTVQSTLEEALSTALRAPIRVVGSGRTDTGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  Q  HFD   E  P  + +++N   K    I I +L      F+AR+ A+ R Y Y I
Sbjct: 61  ARGQCVHFDFDGELDPQKVVRSVNGLTK--RLIRIRDLEPCASDFNARYDAVLRYYQYTI 118

Query: 117 ITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
            TR  P+AL +   W     +LD E M   AQ  +G HDF  F        S + T+  F
Sbjct: 119 FTR--PVALMRDFGWECGSLNLDIEAMGREAQSFLGEHDFIDFCIPRNDGKSTLCTLSEF 176

Query: 176 ---DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
               +N +  +  I+     FLH Q+R+ VG+L  VG G++    + +  +   + E   
Sbjct: 177 RLERLNDWSCMFHIK--GNRFLHRQVRAMVGTLFDVGRGRYPEGTVNQIFEKNFKGE-RT 233

Query: 233 LAPPEGLYFDSVEY 246
            APP+GL  ++VEY
Sbjct: 234 WAPPQGLVLENVEY 247


>gi|225018926|ref|ZP_03708118.1| hypothetical protein CLOSTMETH_02877 [Clostridium methylpentosum
           DSM 5476]
 gi|224948306|gb|EEG29515.1| hypothetical protein CLOSTMETH_02877 [Clostridium methylpentosum
           DSM 5476]
          Length = 250

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 119/239 (49%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I YNG+ Y GWQ QKN  ++Q  ++ A+  + G    V G  RTD+GVHA     +    
Sbjct: 10  IAYNGAAYHGWQVQKNALTVQEVVQDAVEKLFGRREDVVGCSRTDTGVHANEYFFNMHTE 69

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           ++     + + +N  L   D +++L  + V++ FHAR+    + Y+Y+I   ++      
Sbjct: 70  KDIPCRSVMRGMNTLL--PDDVAVLGCTEVEEDFHARYCCTGKEYIYKIWNAESRNPFLH 127

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            +    P  LD + +  A +  +G HDF+ F S        +RTI     +  G+L+ + 
Sbjct: 128 RQCLRYPFPLDIQLLNRAMERFLGTHDFSAFCSAGSDVEDRVRTITQAHASREGDLVTLT 187

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           V    FL+  +R  VG+L  V +GK +  D+   + ++DR   G  APP GL+ + V Y
Sbjct: 188 VRGDGFLYNMVRILVGTLIEVQEGKLSPDDIPSVIASRDRSRAGKTAPPCGLFLNRVFY 246


>gi|293190229|ref|ZP_06608725.1| tRNA pseudouridine synthase A [Actinomyces odontolyticus F0309]
 gi|292821045|gb|EFF79998.1| tRNA pseudouridine synthase A [Actinomyces odontolyticus F0309]
          Length = 302

 Score =  126 bits (316), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 90/277 (32%), Positives = 134/277 (48%), Gaps = 37/277 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW  Q    ++QG +E A+ + + E VV   AGRTD+GVHA  QV 
Sbjct: 5   RLRLDLGYDGTDFRGWAAQPGLRTVQGEVEAALAMASREDVVTTVAGRTDAGVHARHQVC 64

Query: 63  HFDLVR---------------EWVPVILCKALN----------------AYLKISDTISI 91
           H D+                 + V   + + LN                A  + +  + I
Sbjct: 65  HADISEAAWARLSPRGGESDEQAVASAIVRRLNKILSGRYGERARGRDLAVARGTCDVRI 124

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
            + ++VD  F ARFSA+ RSY YR+  R  PL     R W + + LD   M  A   L+G
Sbjct: 125 YSAAVVDPSFDARFSALGRSYAYRVSDRPEPLG-RWDRLW-VEEPLDEAAMNEAGAALLG 182

Query: 152 RHDFTTFRSIHCQASSPIRTIDHF--DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
            HDF  F     + ++ IRT+     + ++ G L+  RV A +F H+ +RS VG+L LVG
Sbjct: 183 EHDFLGFCRPR-EGATTIRTLRTLLAERDAEGTLV-FRVEADAFCHSMVRSLVGALLLVG 240

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            G        + L+A+ R E  P+AP  GL  + VEY
Sbjct: 241 SGARDVAYPVQILRARSRSEAAPIAPAHGLTLEGVEY 277


>gi|282882119|ref|ZP_06290760.1| tRNA pseudouridine synthase A [Peptoniphilus lacrimalis 315-B]
 gi|281298149|gb|EFA90604.1| tRNA pseudouridine synthase A [Peptoniphilus lacrimalis 315-B]
          Length = 243

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 79/239 (33%), Positives = 118/239 (49%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y G+Q Q    +I+G + KAI     +   ++ AGRTD GVHAL Q  +F   
Sbjct: 7   VTYDGTNYHGYQVQNKLKTIEGELSKAINNTLKKETKIYSAGRTDRGVHALGQYVNFYTD 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L + +N +L   D IS+++   V   FHARFSA  + Y Y +   +   A+  
Sbjct: 67  TTIDLGNLPRVINFHL--PDDISVISAKEVPFDFHARFSAKEKIYRYVVYNNKYRNAIYH 124

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            RA+  P SLD   M  + ++L+G+ DF +F          IRTI    V      I   
Sbjct: 125 NRAYQYPFSLDLSLMNESFKYLIGQKDFKSFMGRDAIVKDTIRTIYSIKVKKDNKFIYFD 184

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
              +SFL   IR  +G+   +G GK     +++ L+ Q+RK  GP AP  GLY  ++ Y
Sbjct: 185 FQGKSFLKNMIRIIMGTAIEIGRGKKDPIFMKEVLEKQNRKYAGPTAPSCGLYLMNILY 243


>gi|42559832|sp|Q8NSV0|TRUA_CORGL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21323332|dbj|BAB97960.1| Pseudouridylate synthase (tRNA psi55) [Corynebacterium glutamicum
           ATCC 13032]
          Length = 289

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 89/263 (33%), Positives = 133/263 (50%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW +Q      ++Q  +E  + +V  E V +  AGRTD+GVHA  
Sbjct: 1   MRIRLDLAYDGTDFHGWAKQGTSDLRTVQKVLEDNLSMVLRETVELTVAGRTDAGVHAAG 60

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+    +        P  L + L   L   D I +  +   +  F ARFSA+RR 
Sbjct: 61  QVAHFDIPAHALEQRSIDGDPSKLVRRLGRLL--PDDIRVHGVRFAEPGFDARFSAMRRH 118

Query: 112 YLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YRI T  A   P        W  PK ++ E M++AA  L+G HDF  F      A++ 
Sbjct: 119 YVYRITTHPAGALPTRRHDTAQW--PKPVELERMQLAADALLGLHDFVAFCKAKPHATT- 175

Query: 169 IRTIDHF---DVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R +  F   DV++     + E  VVA +F  + +RS VGS   VG+G+  S    + L 
Sbjct: 176 VRELQKFAWKDVSTDIEPQVYEAHVVADAFCWSMVRSLVGSCMAVGEGRRGSGFTAELLD 235

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A +R    P+AP +GL    V+Y
Sbjct: 236 ASERSPMVPVAPAKGLSLVGVDY 258


>gi|312140887|ref|YP_004008223.1| tRNA pseudouridine synthase a [Rhodococcus equi 103S]
 gi|311890226|emb|CBH49544.1| tRNA pseudouridine synthase A [Rhodococcus equi 103S]
          Length = 274

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 126/245 (51%), Gaps = 11/245 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + GW RQ    ++ G +E+ +  +    V++  AGRTD+GVHA  QVAH D+ 
Sbjct: 5   ISYDGTDFSGWARQPGRRTVCGEVEEKLSAIVRTPVLLTVAGRTDAGVHASGQVAHVDVP 64

Query: 68  REWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            + +P    + +    + +   + +  +S   + F ARFSAIRR Y YR+ T  AP   E
Sbjct: 65  ADMIPEEPSRLVRRLARFLPRDVRVKAVSFAPEHFDARFSAIRRHYEYRLTT--APYGAE 122

Query: 127 KGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             R     AW  PK +D + MR A+  L+G HDF  F     + ++ +R +  FD    G
Sbjct: 123 PLRARDTVAW--PKDVDVDAMREASSRLLGLHDFAAF-CKRREGATTVRELQRFDWEQSG 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +   V A +F  + +RS VG+   VG+G+ T   +   L  ++R     +AP  GL  
Sbjct: 180 HELTAFVSADAFCWSMVRSLVGAALAVGEGRRTVEWMAGLLAERERASAVAVAPAHGLSL 239

Query: 242 DSVEY 246
             V+Y
Sbjct: 240 IRVDY 244


>gi|317418864|emb|CBN80902.1| tRNA pseudouridine synthase-like 1 [Dicentrarchus labrax]
          Length = 285

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 95/274 (34%), Positives = 140/274 (51%), Gaps = 31/274 (11%)

Query: 3   RYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHA 57
           RY +  +Y G+ Y G  +    Q     +Q  +E AI  L+    V +  + RTD GVHA
Sbjct: 6   RYLIFFQYIGTKYSGVVKVPPHQLPSKGVQDHLEDAIRKLMPLNPVSLSVSSRTDRGVHA 65

Query: 58  LRQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           L   AHFDL R+     +   IL +ALN YLK ++ I I N   V   FHAR+ A  R+Y
Sbjct: 66  LSNSAHFDLQRKNNLPPFTEGILIEALNFYLK-TEQIRITNAHRVPDDFHARYQAQSRTY 124

Query: 113 LYRI---ITRQAPLALEKGR-AW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS- 166
           +YRI   I  Q  L L + +  W L    LD   MR AA  LVG HDF++FR++  + + 
Sbjct: 125 VYRIALGIPNQLLLPLTELKFCWSLRNTELDVGAMRKAAALLVGNHDFSSFRAVSTEMAF 184

Query: 167 -SPIRTIDHFDVNSFGNLI-----------EIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
            +P++ +D   +   G+ +           E+   ARSFL+ Q+R   G+L  VG G+ +
Sbjct: 185 KNPVKVLDVASIQPGGSFVQSHFQREVLFWEVTFKARSFLYKQVRRMTGALVAVGQGRLS 244

Query: 215 STDLEKALQAQDRKECGP--LAPPEGLYFDSVEY 246
              L++ L+A+D        +AP  GL+   V+Y
Sbjct: 245 VPQLKEILEARDTMAYPKNLVAPAHGLFLTRVDY 278


>gi|294783832|ref|ZP_06749154.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
 gi|294479644|gb|EFG27423.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
          Length = 246

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 82/243 (33%), Positives = 122/243 (50%), Gaps = 13/243 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA +QV++F    +
Sbjct: 12  YDGSRYYGFQRQPDKVTVQGEIEKILKIVTKEDINLISAGRTDRGVHANQQVSNFYTSSN 71

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL         I IL++  VDK F+AR  A  R Y+Y I   + P   
Sbjct: 72  IPVEKYKYLLTRAL------PKDIDILSVEEVDKNFNARHDAKMREYIYIISWEKNP--F 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
           E      +   +D E ++      +G HDF  FR   C +   IR I   D+N F  N +
Sbjct: 124 EARYCKFVKNKIDVEKLKKIFSSFLGIHDFRNFRLSDCVSKITIREIYSIDINYFSENKL 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG+   V  G      +E  L    +     L   EGLY + +
Sbjct: 184 KIYIRGSAFLKSQVRIMVGTALEVYYGNLPENHIELMLNDFSKDYKKNLVEAEGLYLNKI 243

Query: 245 EYS 247
            YS
Sbjct: 244 YYS 246


>gi|302342258|ref|YP_003806787.1| tRNA pseudouridine synthase A [Desulfarculus baarsii DSM 2075]
 gi|301638871|gb|ADK84193.1| tRNA pseudouridine synthase A [Desulfarculus baarsii DSM 2075]
          Length = 279

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 80/239 (33%), Positives = 114/239 (47%), Gaps = 4/239 (1%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           YNG+G+ GWQ Q  G +IQG +E+ +  + G  V +  AGRTD+GVHA  QVA F     
Sbjct: 43  YNGAGFAGWQIQARGRTIQGQVERELSRLCGHAVRLWAAGRTDAGVHAFGQVASFQTDSR 102

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
                + +AL A L     I +  L    + FHARF A  ++Y Y +  +  P     G 
Sbjct: 103 LEEGRMAQALAAMLP--PDIWLRRLGRAPEGFHARFDAAGKTYEYYLWPKARPGVFLDGL 160

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVN-SFGNLIEIR 187
            W +   LD E M   A  L+G  D   F +   +   P +R I    V  + G +I +R
Sbjct: 161 CWPLACDLDMEAMARGAAFLLGEVDLAAFAAHSSEVEGPTVRRISEATVTPAEGGMILVR 220

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +    FL   +R+ VG+L  +G  +     + + L A  R   GP APP GLY   + Y
Sbjct: 221 LSGSGFLRHVVRNVVGTLTQIGQHRLEPEAVGRMLAAGRRIYPGPKAPPGGLYLGQIYY 279


>gi|313205364|ref|YP_004044021.1| tRNA pseudouridine synthase a [Paludibacter propionicigenes WB4]
 gi|312444680|gb|ADQ81036.1| tRNA pseudouridine synthase A [Paludibacter propionicigenes WB4]
          Length = 251

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 119/246 (48%), Gaps = 7/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY +   Y G+ Y GWQ Q NG S+Q  + +A+  +    + + GAGRTD+GVHA   VA
Sbjct: 4   RYFIYFSYKGTAYHGWQMQPNGISVQEVLTRALCTILRTNLEIVGAGRTDAGVHAKLMVA 63

Query: 63  HFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           HFD     +P    L   LN++L     ISI  ++ V    HARF AI R Y Y I T +
Sbjct: 64  HFDF-ETALPSEFDLVAKLNSFL--PGDISIYKIAEVKPDAHARFDAISRRYEYHIFTNK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E   A      LD E M +AA+ L    DFT+F  +H    +    I H +    
Sbjct: 121 NVFKNE--LAVRESDKLDFEAMNLAAKTLTKFKDFTSFSKLHTDVKTNNCQIHHAEWTQQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+     + A  FL   +R+ VG+L  VG  K  + +    + A++R + G   P  GLY
Sbjct: 179 GDEWVFTIEADRFLRNMVRAIVGTLFEVGRRKMNTDEFATVIAAKNRCKAGVSVPAHGLY 238

Query: 241 FDSVEY 246
              ++Y
Sbjct: 239 LVDIKY 244


>gi|298491424|ref|YP_003721601.1| tRNA pseudouridine synthase A ['Nostoc azollae' 0708]
 gi|298233342|gb|ADI64478.1| tRNA pseudouridine synthase A ['Nostoc azollae' 0708]
          Length = 275

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 122/250 (48%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ    ++Q  IE AI  + G  V +HGAGRTD+GVHA  Q+A
Sbjct: 12  RVALVIQYRGTHFRGWQRQSCQRTVQEEIETAIATILGYHVTLHGAGRTDAGVHAAAQIA 71

Query: 63  HFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD        +W  V     LN+YL     I I   + V+  +HARFSA+ R Y Y I 
Sbjct: 72  HFDATGFIPAHKWATV-----LNSYLP--PDILIRASASVNDFWHARFSAVSRRYRYTIY 124

Query: 118 TRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           T   P       +W      LD   ++ A + L+G+H    F       S     +   +
Sbjct: 125 TEVLPNLFVNPFSWHYYYAPLDESVIQAALKPLLGKHHLAAFHRAGSARSHSWVEVQVAE 184

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +  G  I I + A  FL+  +R  VG L  +G G+ T  +  +  + + R++    APP
Sbjct: 185 CHRSGPFIHIEIQANGFLYGMVRLLVGMLVQLGSGQVTLDNFTEIWKEERREKVKYAAPP 244

Query: 237 EGLYFDSVEY 246
           +GL    VEY
Sbjct: 245 QGLCLLRVEY 254


>gi|258647412|ref|ZP_05734881.1| tRNA pseudouridine synthase A [Prevotella tannerae ATCC 51259]
 gi|260852780|gb|EEX72649.1| tRNA pseudouridine synthase A [Prevotella tannerae ATCC 51259]
          Length = 256

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 123/246 (50%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y+G  Y GWQ+Q N  S+Q  + KAI  +    + + GAGRTD+ V+A R V
Sbjct: 1   MRYFLYFSYDGGNYHGWQQQPNAISVQEVLNKAISTLLQSAISLVGAGRTDTSVNAKRMV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD     +P      LN  L     I++L++  V+K  HARF A+ R+Y Y I  ++ 
Sbjct: 61  AHFDFCCT-LPDKFTFRLNRLL--PPDIAVLDIKQVNKDAHARFDALSRTYHYYIYKKKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNSF 180
           P        +L    LD   M  AA+ L+   DFT+F  +H    + I  +   + +   
Sbjct: 118 PFKRHYATRYL--AELDYTAMNQAAKLLLQVEDFTSFSKLHTDTRTKICHVTKAEWIQEK 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +L    + A  FL   +R+ VG+L  VG G+ +  +  K +Q ++R       P E L+
Sbjct: 176 EDLWRFEITADRFLRNMVRAIVGTLIEVGRGRMSIEEFSKVIQQKNRCAAAESVPGEALF 235

Query: 241 FDSVEY 246
             +++Y
Sbjct: 236 LVNIKY 241


>gi|15672468|ref|NP_266642.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281490978|ref|YP_003352958.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           KF147]
 gi|13878837|sp|Q9CI80|TRUA_LACLA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|12723367|gb|AAK04584.1|AE006284_2 tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281374736|gb|ADA64256.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           KF147]
 gi|326406013|gb|ADZ63084.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           CV56]
          Length = 253

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 83/256 (32%), Positives = 130/256 (50%), Gaps = 17/256 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+Q Q N  ++Q  IEK +  L + E V++ G+GRTDSGVHA  
Sbjct: 1   MTRYKATIAYDGTDFAGFQSQTNQRTVQKEIEKILTKLNSFEPVILQGSGRTDSGVHAFG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--- 116
           QV HFDL +  V  +         +    I++  + +V   +HAR+    ++Y Y +   
Sbjct: 61  QVIHFDL-KGKVRDLERLRFGLDTQTPADIAVKKVELVPDDWHARYQKHEKTYEYYLENS 119

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH-- 174
           ITR +P        +  P  L+ E M+ A   LVG HDFT F +        +RTI    
Sbjct: 120 ITR-SPFQRHSKAYFRYP--LNFERMQEAMSKLVGEHDFTGFTASGSSVDDKVRTIYQAE 176

Query: 175 ---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
               D  +F  +         FL+ Q+R+ VG++  +G+ +   + ++K L +++R   G
Sbjct: 177 IIRLDEENFKFIFR----GNGFLYKQVRNMVGTVIKIGNDRMPVSQIDKILTSKNRDFAG 232

Query: 232 PLAPPEGLYFDSVEYS 247
           P A PEGLY   V+Y+
Sbjct: 233 PTAAPEGLYLKEVKYA 248


>gi|206901950|ref|YP_002250733.1| tRNA pseudouridine synthase A [Dictyoglomus thermophilum H-6-12]
 gi|238057728|sp|B5YDX5|TRUA_DICT6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|206741053|gb|ACI20111.1| tRNA pseudouridine synthase A [Dictyoglomus thermophilum H-6-12]
          Length = 245

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 124/248 (50%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MI + + + Y G  ++G+Q+Q    ++QG +EK + L+  E + V GAGRTD+GVHAL Q
Sbjct: 1   MINWKVELSYIGKDFWGFQKQPGKRTVQGELEKVLKLLFDEDIKVIGAGRTDAGVHALGQ 60

Query: 61  VAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V +F     + +    L K LN  L     I I  + IVD  FHAR+SA RR Y+Y I  
Sbjct: 61  VVNFKTKESKNFSCDKLYKVLNKLL--PGDIKIKKVEIVDDNFHARYSAKRRWYIYVIYN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +   W I K LD + + ++A    G HDF  F  I    ++ +   + F   
Sbjct: 119 NEEKNLFLRDYCWWINKPLDKDLLNLSANLFKGIHDFRNFCVIENYDNTNVEIYESFWYF 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+   V A  FL   +R  VGS+  VG  K    DLEK L+ +  +     AP  G
Sbjct: 179 K-EDLLIYFVSAPFFLRKMVRFIVGSMVEVGLKKKELEDLEKYLKDRKEERFSSPAPASG 237

Query: 239 LYFDSVEY 246
           LY   ++Y
Sbjct: 238 LYLFKIDY 245


>gi|145225544|ref|YP_001136222.1| tRNA pseudouridine synthase A [Mycobacterium gilvum PYR-GCK]
 gi|145218030|gb|ABP47434.1| tRNA pseudouridine synthase A [Mycobacterium gilvum PYR-GCK]
          Length = 298

 Score =  125 bits (315), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 83/261 (31%), Positives = 127/261 (48%), Gaps = 18/261 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            +R  + I Y+G+ + GW  Q    ++ G I+ A+  V    V+   AGRTDSGVHA  Q
Sbjct: 19  FVRLRLDIAYDGTDFAGWATQAGQRTVAGVIDDALSTVFRTPVLTRAAGRTDSGVHATGQ 78

Query: 61  VAHFDLVREWVPVILCKALNAYLK------------ISDTISILNLSIVDKQFHARFSAI 108
           VAH D+  + +P    + + A               +++ + +  +      F ARFSA+
Sbjct: 79  VAHADIPTDALPHAYPRTVRAGEPEFGPLVRRLGRMLTEDVRVRGIVRAAPGFDARFSAL 138

Query: 109 RRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           RR Y+YR+ T  AP  +E   A  +   P+ LD + M  AAQ+++G HDF  F   H   
Sbjct: 139 RRHYVYRLTT--APYGVEPAEARFVTAWPRPLDVDAMAGAAQNVLGLHDFAAF-CRHRDG 195

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           ++ IR +   D    G+ I + V A +F    +RS VG+L  VG+ +   T   + L A+
Sbjct: 196 ATTIRELQRLDCVRDGDRISVHVSADAFCWNMVRSLVGALLAVGEHRRDDTWCVQLLHAR 255

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
            R      AP  GL    V+Y
Sbjct: 256 HRSSDFAAAPARGLTLVGVDY 276


>gi|86739325|ref|YP_479725.1| tRNA pseudouridine synthase A [Frankia sp. CcI3]
 gi|123737799|sp|Q2JFE6|TRUA_FRASC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|86566187|gb|ABD09996.1| tRNA pseudouridine synthase A [Frankia sp. CcI3]
          Length = 274

 Score =  125 bits (314), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 92/262 (35%), Positives = 133/262 (50%), Gaps = 30/262 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           ++R  + + Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA+ 
Sbjct: 5   LVRLRLDLSYDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDSGVHAVG 64

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL  + VP+  L + LN  L  +  + I+ L+     F ARFSA+ R Y+YRI  
Sbjct: 65  QVAHVDLPDD-VPLGGLARRLNGVLDRA--VRIIGLAPAPPGFDARFSALSRRYVYRIT- 120

Query: 119 RQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIR 170
             AP   E  R     AW  P+ LD   M  AA  LVG HDF  F    C   + ++ +R
Sbjct: 121 -DAPYGAEPLRRFDTLAW--PRPLDVPAMAAAALFLVGEHDFAAF----CRRREGATTVR 173

Query: 171 TIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQ 225
           T+   DV      ++   V A +F H+ +R+ VG+L  VG+G+    W +  L + +   
Sbjct: 174 TLLRLDVLRRPEGVVVADVEADAFCHSMVRALVGALLAVGEGRKPPQWPAAVLHRGV--- 230

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R     +AP  GL    V Y 
Sbjct: 231 -RDPAVTVAPAHGLTLVDVRYP 251


>gi|320530646|ref|ZP_08031695.1| tRNA pseudouridine synthase A [Selenomonas artemidis F0399]
 gi|320137097|gb|EFW29030.1| tRNA pseudouridine synthase A [Selenomonas artemidis F0399]
          Length = 258

 Score =  125 bits (314), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 127/243 (52%), Gaps = 6/243 (2%)

Query: 8   IEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G+ Y G+QRQ     ++Q  +EK +  V GE V +  AGRTD+GVHA  QV +F  
Sbjct: 12  LSYDGTRYHGFQRQSLPVVAVQNVLEKVLAEVCGEPVELAAAGRTDTGVHAYGQVVNF-F 70

Query: 67  VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
               +PV  L +A+N  L     I+++      + F AR S+  ++YLYRI     P   
Sbjct: 71  TDGRIPVAQLPRAVNGLLP--PDIAVMAAWEAGRDFSARHSSTGKAYLYRIERCTVPNPF 128

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFGNLI 184
            +  AW I + LD   MR   + LVG HD+++FR+      SP+RT+D   ++   G  +
Sbjct: 129 TRNYAWQIFRPLDVAAMRTVLRLLVGTHDYSSFRAAGGAPMSPVRTLDEIRLDEEEGGQL 188

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
              +    FL+  +R+ + ++  VG G+ ++    +   A DR+   P AP  GLY   V
Sbjct: 189 SCYMHGNGFLYHMVRNIMSTVVHVGLGRISTDRFTEIFAAHDRRLASPTAPACGLYLLHV 248

Query: 245 EYS 247
           +Y+
Sbjct: 249 DYA 251


>gi|239994150|ref|ZP_04714674.1| tRNA pseudouridine synthase A [Alteromonas macleodii ATCC 27126]
          Length = 242

 Score =  125 bits (314), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 77/226 (34%), Positives = 111/226 (49%), Gaps = 12/226 (5%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL-----VREWVPVILCKALN 80
           S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV HF+       R W        L 
Sbjct: 5   SVQEHLEKALSTVANEPIEVQCAGRTDAGVHATGQVVHFNCDAPRSERAWT-------LG 57

Query: 81  AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCE 140
               + +++++     V   FHARFSA  R Y Y I   +   A+       I + LD +
Sbjct: 58  VNANLPNSVAVTWAKNVSDDFHARFSATHRRYRYVIHNAKMRPAILHSGVTHIHRELDEK 117

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
            M +AAQ L+G  DFT+FR+  CQ+ +P R +    V   G  + I + A +FLH  +R+
Sbjct: 118 KMHVAAQALLGEQDFTSFRAALCQSKTPFRNVTDVSVYRQGRYVIIDIRANAFLHHMVRN 177

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             G+L  +G G+     +   L  +DR +    A P GLY   V Y
Sbjct: 178 ITGALVEIGAGEQDVNWIAHLLSLKDRSKSAATAKPNGLYLVDVTY 223


>gi|6729002|gb|AAF26999.1|AC016827_10 putative tRNA pseudouridine synthase [Arabidopsis thaliana]
          Length = 298

 Score =  125 bits (314), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 131/255 (51%), Gaps = 14/255 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T     E+ ++ GAGRTD+GVHA 
Sbjct: 17  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELQLI-GAGRTDAGVHAW 75

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF     +  +     ALN  L     I +  LS    +FHARFSA  + Y Y+I 
Sbjct: 76  GQVAHFVTPFNYTSLDSFHAALNGLL--PKDIRVRELSAAVPEFHARFSASSKVYRYQIY 133

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHF 175
                   ++  A+     L+   MR AA   VG+HDF+ F +   +     P++TI  F
Sbjct: 134 NDTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFANATREDGVPDPLKTISRF 193

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR----KECG 231
           DV   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR    K   
Sbjct: 194 DVIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTS 253

Query: 232 PLAPPEGLYFDSVEY 246
             A P GL   SV+Y
Sbjct: 254 LPASPHGLCLVSVKY 268


>gi|237721333|ref|ZP_04551814.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_2_4]
 gi|229449129|gb|EEO54920.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_2_4]
          Length = 260

 Score =  125 bits (314), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 83/240 (34%), Positives = 118/240 (49%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   VAHFD  
Sbjct: 1   MAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLMVAHFDSD 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  +   LN  L     ISI  +  V    HARF A  R+Y Y + T + P    +
Sbjct: 61  ELLDTTSVTDKLNRLLPPD--ISIYRVCRVRPDTHARFDATARTYKYYVTTSKYP--FNR 116

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
              W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +     +   + 
Sbjct: 117 QYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQEEDATWVF 176

Query: 188 VV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L+  +VEY
Sbjct: 177 TIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQALFLVNVEY 236


>gi|188997613|ref|YP_001931864.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932680|gb|ACD67310.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 243

 Score =  125 bits (314), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 124/246 (50%), Gaps = 11/246 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + I Y G+ Y GWQRQKNG  IQ  IE  +  +  E + + GAGRTD+GVHALRQVA+
Sbjct: 6   YKLEISYIGTNYNGWQRQKNGIGIQQVIEDLLSELLEEKITLIGAGRTDAGVHALRQVAN 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F   +      +   LNA  K+   ISIL +  V   F+ARFSA  ++YLY+I T+  P 
Sbjct: 66  FKTKKHKNTKTIYTYLNA--KLPRDISILKVEEVPLSFNARFSAKGKTYLYKINTKPDPF 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT-IDHFDVNSF-- 180
             +   AW   K LD   M      +    D ++      +A   IR  ID  ++  +  
Sbjct: 124 LFK--LAWYYDKKLDLIKMVEGINLIKQYKDLSSL----AKAGDYIRKEIDLRELKLYFD 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I I + A  FL   +R   G L  +G G  +  +L+  ++ +        APPEGLY
Sbjct: 178 GKIITIEITASHFLRNMVRRIAGHLVALGRGSLSLEELKDIIEKKSPSHGKFTAPPEGLY 237

Query: 241 FDSVEY 246
             +V Y
Sbjct: 238 LKAVYY 243


>gi|313887179|ref|ZP_07820875.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|312923408|gb|EFR34221.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica
           PR426713P-I]
          Length = 262

 Score =  125 bits (314), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 123/250 (49%), Gaps = 10/250 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ Y GWQ Q  G S+Q  +E+A+ ++  + + V GAGRTD+GVHA   +A
Sbjct: 7   RVFLEVAYDGTNYCGWQVQSRGVSVQSELERALSILFRQPISVTGAGRTDAGVHAYSMMA 66

Query: 63  HFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           H DL     P+  + + L   L+    IS+ +++ V    HARF A  R Y Y I     
Sbjct: 67  HADLPIPHPPLAQIQRGLCGILR--GGISVRSVTPVIPTAHARFDATSRRYHYYISACSN 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-----DHFD 176
           P   +    W      D   M  A +H +G HDFT+F  +H Q      T+     +  +
Sbjct: 125 PFWGDY--CWERRTLPDMALMNEACRHFIGEHDFTSFSKLHTQTKHNRCTVYTAHWEQVE 182

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + +   V A  FLH  +R+ VG+L  VG G+ T   + + +Q++DR   G  AP 
Sbjct: 183 MPGLWDAMRYEVCANRFLHGMVRTMVGTLLEVGYGQRTPDSIAELIQSEDRSLAGSAAPA 242

Query: 237 EGLYFDSVEY 246
             L+F    Y
Sbjct: 243 RALFFVEATY 252


>gi|323345677|ref|ZP_08085900.1| tRNA pseudouridine synthase A [Prevotella oralis ATCC 33269]
 gi|323093791|gb|EFZ36369.1| tRNA pseudouridine synthase A [Prevotella oralis ATCC 33269]
          Length = 243

 Score =  125 bits (314), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG+S+Q  ++ A+ ++  + V V GAGRTD+GVHA   
Sbjct: 1   MQRYFVYFAYDGTAYHGWQVQPNGNSVQVELQNALSVLLRQPVEVVGAGRTDAGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD       V L   LN  L     IS+  +  VD   HARFSA+ R+Y Y +  R+
Sbjct: 61  AAHFDFDTPVDEVQLAYKLNRLL--PKDISVDRVVAVDSSMHARFSAVSRTYHYYVHCRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTIDHFDVNS 179
            P   ++  ++ +   LD   M   AQHL+   DF  F   H  + + + R      V  
Sbjct: 119 NP--FKRAYSYELHYQLDFRAMNEVAQHLLQVEDFGAFCKSHNDSKTTLCRVTRALWVQD 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  VG  + +  +  K ++ ++R   G   P   L
Sbjct: 177 DADSWHFVITANRFLRNMVRAVVGTLIDVGRHRISKEEFIKIVERRNRTGAGESMPAHAL 236

Query: 240 YFDSVEY 246
           + + ++Y
Sbjct: 237 FLEDIKY 243


>gi|42522098|ref|NP_967478.1| pseudouridylate synthase I [Bdellovibrio bacteriovorus HD100]
 gi|51316639|sp|Q6MQH6|TRUA_BDEBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|39574629|emb|CAE78471.1| pseudouridylate synthase I [Bdellovibrio bacteriovorus HD100]
          Length = 262

 Score =  125 bits (314), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 131/247 (53%), Gaps = 12/247 (4%)

Query: 8   IEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + Y+G+G+ GWQ+QK  +  S+   IE+A+  V  E + +  +GRTD+GVHAL QV HF 
Sbjct: 9   VAYDGTGFCGWQKQKPEDQISVAQVIEEALSKVFNEKITLFASGRTDAGVHALNQVCHFS 68

Query: 66  LVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
             R+  P     LC ALN++L  S  I      I    FHA  SA  ++Y Y I+ +  P
Sbjct: 69  THRKIDPNKKWDLCWALNSHLPPS--IVAKKAWIAPDDFHATLSATHKTYRYLIVNKPRP 126

Query: 123 LA-LEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
            A L +   W+ +P  +D E+++ ++++L+G  DF +F+S+       +R I   D    
Sbjct: 127 SAHLNRYADWVRLP--IDIEHLQESSKYLLGNQDFKSFQSVGTPVPDTVREIYKADWEWR 184

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              +++  +    FL   +R+ VG+   +       + +++ + AQDR + GP AP +GL
Sbjct: 185 KPGVMQFTITGSGFLKQMVRNIVGTSLFLERKGLDPSKMQEIIAAQDRMKAGPPAPAQGL 244

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 245 YLMKVYY 251


>gi|159904194|ref|YP_001551538.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9211]
 gi|226741290|sp|A9BCM2|TRUA_PROM4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|159889370|gb|ABX09584.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9211]
          Length = 289

 Score =  125 bits (314), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 127/247 (51%), Gaps = 6/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  ++I+YNGSG+ GWQRQK G+S+Q  +E+A+  L   + + V  AGRTDSGVHA  QV
Sbjct: 17  RIALLIQYNGSGFCGWQRQKEGNSVQSILEEAVSSLDPFQPIKVVAAGRTDSGVHASGQV 76

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD    ++P      ALN   ++   I +   ++    +HA FSA  R Y Y I    
Sbjct: 77  AHFD-CSGFIPANRWAAALNG--RLPKAIRVRYSALRPITWHACFSATYRRYRYTIYNGC 133

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P        W   +  LD   M +A Q + G HDFT F+       + + T++   +  
Sbjct: 134 KPNLFLSPWCWHRYQFRLDENLMNLALQGIKGFHDFTAFQRAGSNRPNALTTVEDVHLFR 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ I + A  FL+  +R  VG L  VG+ + +  + E+  + + R+E    APP GL
Sbjct: 194 QGDLVSIDIQATGFLYGMVRLLVGQLVAVGEHRISVAEFERRWKLKLREEVREAAPPNGL 253

Query: 240 YFDSVEY 246
               V Y
Sbjct: 254 SLIRVGY 260


>gi|300814956|ref|ZP_07095184.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300510926|gb|EFK38198.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 243

 Score =  125 bits (313), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 79/239 (33%), Positives = 118/239 (49%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y G+Q Q    +I+G + KAI     +   ++ AGRTD GVHAL Q  +F   
Sbjct: 7   VTYDGTNYHGYQIQNKLKTIEGELSKAINDTLKKETKIYSAGRTDRGVHALGQYVNFYTD 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L + +N +L   D IS+++   V   FHARFSA  + Y Y +   +   A+  
Sbjct: 67  TTIDLGNLPRVINFHL--PDDISVISAKEVPFDFHARFSAREKIYRYVVYNNKYRNAIYH 124

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            RA+  P SLD   M  + ++L+G+ DF +F          IRTI    V      I   
Sbjct: 125 NRAYQYPFSLDLSLMNESFKYLIGQKDFKSFMGRDAIVKDTIRTIYSIKVKKDNKFIYFD 184

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
              +SFL   IR  +G+   +G GK     +++ L+ Q+RK  GP AP  GLY  ++ Y
Sbjct: 185 FQGKSFLKNMIRIIMGTAIEIGRGKKDPIFMKEVLEKQNRKYAGPTAPSCGLYLMNILY 243


>gi|110737769|dbj|BAF00823.1| putative tRNA pseudouridine synthase [Arabidopsis thaliana]
          Length = 323

 Score =  125 bits (313), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 131/255 (51%), Gaps = 14/255 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T     E+ ++ GAGRTD+GVHA 
Sbjct: 42  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELQLI-GAGRTDAGVHAW 100

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF     +  +     ALN  L     I +  LS    +FHARFSA  + Y Y+I 
Sbjct: 101 GQVAHFVTPFNYTSLDSFHAALNGLLP--KDIRVRELSAAVPEFHARFSASSKVYRYQIY 158

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHF 175
                   ++  A+     L+   MR AA   VG+HDF+ F +   +     P++TI  F
Sbjct: 159 NDTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFANATREDGVPDPLKTISRF 218

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR----KECG 231
           DV   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR    K   
Sbjct: 219 DVIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTS 278

Query: 232 PLAPPEGLYFDSVEY 246
             A P GL   SV+Y
Sbjct: 279 LPASPHGLCLVSVKY 293


>gi|332665403|ref|YP_004448191.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
 gi|332334217|gb|AEE51318.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
          Length = 249

 Score =  125 bits (313), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 83/252 (32%), Positives = 127/252 (50%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG+ YFGWQRQ    S+Q ++E +I  + G  + + G GRTD+GVHA + 
Sbjct: 1   MQRYFIELAYNGTQYFGWQRQPGKISVQQTLEDSINTILGTELEITGCGRTDTGVHARQY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD   E+ P    + LN +L     I++  +  V+ + HARF A  RSY Y +  R+
Sbjct: 61  FAHFDFEGEF-PAEFVRRLNKFL--PKDIAVYQIIAVEPEAHARFDAYERSYEYHLSFRK 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P        +   +  D   M+ AA  L+   +F  F    C+++   +T+      S 
Sbjct: 118 NPFTEHLAYFYPYVQQPDPVLMQDAAAFLLQYQEFEPF----CKSNHDAKTMVCKLTRSE 173

Query: 180 -FGNLIEIRVV----ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              +L E R V    +  FL   +R  VG    VG G+ +  +L+ A++ Q R +    A
Sbjct: 174 WIFDLKEQRAVFHITSNRFLRGMVRLIVGMCIGVGTGQISMEELKTAMEQQSRLKKATSA 233

Query: 235 PPEGLYFDSVEY 246
           PPEGLY   ++Y
Sbjct: 234 PPEGLYLGGIKY 245


>gi|311111942|ref|YP_003983164.1| tRNA pseudouridine synthase A [Rothia dentocariosa ATCC 17931]
 gi|310943436|gb|ADP39730.1| tRNA pseudouridine synthase A [Rothia dentocariosa ATCC 17931]
          Length = 327

 Score =  125 bits (313), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 89/271 (32%), Positives = 130/271 (47%), Gaps = 35/271 (12%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y G+ + GW RQ N  ++QG +E A+ LV      V  AGRTD+GVHA  Q  H D+  E
Sbjct: 41  YEGTWFSGWARQPNLVTVQGVLEDALELVLRAHHRVTVAGRTDAGVHAQAQTIHLDIAAE 100

Query: 70  -WVPVI-----------LCKALNAYLK-------------------ISDTISILNLSIVD 98
            W  +            L + ++  LK                   +  ++ +  +  V 
Sbjct: 101 TWQKLTGRDGLADPAESLKRKVSGALKRTLAQAEHTLGIPERMRGLLQGSLVLHQVQPVP 160

Query: 99  KQFHARFSAIRRSYLYRIITRQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           + F ARFSA  R Y YRI+  Q  +P  L +  AW IP+SLD E++  AA  L G HDF 
Sbjct: 161 QDFDARFSATGRRYTYRILDGQGSSPDPLRRAYAWCIPESLDLEDLNKAAHELTGLHDFL 220

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +F     + ++ IR +    +    + +IE  V A +F H  +RS +G+L L G GK T 
Sbjct: 221 SFCKPR-EGATTIRELRRIYLTRHDDGVIEATVEADAFCHHMVRSLIGALVLYGTGKRTQ 279

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           T L + L+   R     +APP GL    ++Y
Sbjct: 280 TWLRERLENPQRDASLIMAPPHGLALAHIDY 310


>gi|30680075|ref|NP_187351.2| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|119360081|gb|ABL66769.1| At3g06950 [Arabidopsis thaliana]
 gi|332640958|gb|AEE74479.1| tRNA pseudouridine synthase A [Arabidopsis thaliana]
          Length = 323

 Score =  125 bits (313), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 131/255 (51%), Gaps = 14/255 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T     E+ ++ GAGRTD+GVHA 
Sbjct: 42  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELQLI-GAGRTDAGVHAW 100

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF     +  +     ALN  L     I +  LS    +FHARFSA  + Y Y+I 
Sbjct: 101 GQVAHFVTPFNYTSLDSFHAALNGLLP--KDIRVRELSAAVPEFHARFSASSKVYRYQIY 158

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHF 175
                   ++  A+     L+   MR AA   VG+HDF+ F +   +     P++TI  F
Sbjct: 159 NDTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFANATREDGVPDPLKTISRF 218

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR----KECG 231
           DV   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR    K   
Sbjct: 219 DVIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTS 278

Query: 232 PLAPPEGLYFDSVEY 246
             A P GL   SV+Y
Sbjct: 279 LPASPHGLCLVSVKY 293


>gi|149196320|ref|ZP_01873375.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
 gi|149140581|gb|EDM28979.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
          Length = 276

 Score =  125 bits (313), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 82/254 (32%), Positives = 129/254 (50%), Gaps = 12/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+++G+ +FGWQ Q +  ++Q  IEKA+  L     + + G+GRTD+GVHA  
Sbjct: 1   MNSYKLSIQFDGTTWFGWQSQNDFEAVQEQIEKALNTLYNCSEIKIDGSGRTDAGVHAFG 60

Query: 60  QVAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             A F    + ++    L K LNA L +S  I I +    +  FHARFS I ++Y+Y I 
Sbjct: 61  LCATFTEPKISKFTSDTLRKGLNALLPVS--IRIRSALQCETDFHARFSCIGKTYVYFID 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----RSIHCQASSPIRTID 173
                  +    +W + K L+ E MR + QHL G+HDF+ F    +++   A   IRT+ 
Sbjct: 119 NSTTSSPILAPYSWHMRKKLNREKMRQSLQHLEGKHDFSAFTVDRKNLQGHA---IRTVF 175

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             ++   G+++ +      FL+  +RS  G +  VG           AL++  R E G  
Sbjct: 176 KAELIEIGHIVALLFTGDGFLYRMVRSMAGEVVNVGMEFQNPQHTLDALESHQRSEAGVT 235

Query: 234 APPEGLYFDSVEYS 247
           AP +GL+     YS
Sbjct: 236 APAKGLFLGQCYYS 249


>gi|19704921|ref|NP_602416.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|42559836|sp|Q8R601|TRUA_FUSNN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|19712818|gb|AAL93715.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 247

 Score =  125 bits (313), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 123/242 (50%), Gaps = 13/242 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F    +
Sbjct: 14  YDGSSYYGFQRQPNKITVQGEIEKVLRIVTKEEINLISAGRTDRGVHANHQVSNFYTSSN 73

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I   + P   
Sbjct: 74  IPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKMREYIYIISWEKNP--F 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
           E      + + +  E +       +G HDF  FR   C +   +R I   +V  FG N I
Sbjct: 126 EARYCKFVKEKIVAEKLEKIFSDFIGVHDFKNFRLSDCVSKVTVREIYQIEVKYFGENKI 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   EGLY + +
Sbjct: 186 KIYIKGSAFLKSQVRIMVGTALEIYYGRLLENHIRLMLNDFTKEYKKNLVEAEGLYLNKI 245

Query: 245 EY 246
           EY
Sbjct: 246 EY 247


>gi|283781972|ref|YP_003372727.1| tRNA pseudouridine synthase A [Pirellula staleyi DSM 6068]
 gi|283440425|gb|ADB18867.1| tRNA pseudouridine synthase A [Pirellula staleyi DSM 6068]
          Length = 285

 Score =  125 bits (313), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 81/253 (32%), Positives = 126/253 (49%), Gaps = 10/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + + Y+G+ + GWQ Q N  ++Q  +EKA+  +TG       +GRTD+GVHAL Q
Sbjct: 1   MRTFKLTLAYDGTNFGGWQWQPNRRTVQDELEKAVETITGVRSRFVASGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F       P  L K LNA  K+ D I I ++  V   FH    A+R+ Y Y  + + 
Sbjct: 61  VAAFSSETGIDPAGLLKGLNA--KVPDDIFIFDVVEVPLAFHPIRDAVRKRYRY--VVQD 116

Query: 121 APLA--LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            PL    ++  AW + + LD + M  A++ L+G HDF +F++      +  R +    V 
Sbjct: 117 GPLRDIFDRQYAWHVRQPLDEQAMLEASRLLLGEHDFASFQTSGSSRLTTERNVLDISVE 176

Query: 179 SFGNL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                    + + V A  FL   +R+ VG+L  VG G        + L+++DR+  G  A
Sbjct: 177 RVDGARTSRVHVEVEADGFLFNMVRNIVGTLVEVGKGTRPVAWTREVLESRDRRRAGMTA 236

Query: 235 PPEGLYFDSVEYS 247
           P +GL+   V Y 
Sbjct: 237 PAQGLFMIGVHYD 249


>gi|296329175|ref|ZP_06871676.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
 gi|296153531|gb|EFG94348.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
          Length = 247

 Score =  125 bits (313), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 123/242 (50%), Gaps = 13/242 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F    +
Sbjct: 14  YDGSSYYGFQRQPNKITVQGEIEKVLRIVTKEEINLISAGRTDRGVHANHQVSNFYTSSN 73

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I   + P   
Sbjct: 74  IPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKMREYIYIISWEKNP--F 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
           E      + + +  E +       +G HDF  FR   C +   +R I   +V  FG N I
Sbjct: 126 EARYCKFVKEKIVAEKLEKIFSDFIGVHDFKNFRLSDCVSKVTVREIYQIEVKYFGENKI 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   EGLY + +
Sbjct: 186 KIYIKGSAFLKSQVRIMVGTALEIYYGRLLENHIRLMLNDFTKEYKKNLVEAEGLYLNKI 245

Query: 245 EY 246
           EY
Sbjct: 246 EY 247


>gi|289550174|ref|YP_003471078.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis HKU09-01]
 gi|289179706|gb|ADC86951.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis HKU09-01]
          Length = 267

 Score =  124 bits (312), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 115/243 (47%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q  G ++Q   EK +  +    V +H + RTD GVHAL Q 
Sbjct: 1   MRILVNICYQGSNFLGFQIQNQGRTVQQQFEKILKRMHRHDVRIHPSSRTDRGVHALEQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I +  +  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELKIADSQWQYAMNSAL--PDDIYVKEVKQVDSDFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    +P+ L+ E M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 KNPFESGLKTYVPQQLNIERMNEAAQKFIGTHDFTGFCSQKTEVESKVRTLYQSEIEMTT 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  +  L  VG G  +  ++   L+ ++R      AP EGLY 
Sbjct: 179 YGFDYIVTGSGFLYNMVRVLMAFLIEVGKGNRSPEEVTALLEQKNRDNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|292670303|ref|ZP_06603729.1| tRNA pseudouridine synthase A [Selenomonas noxia ATCC 43541]
 gi|292648034|gb|EFF66006.1| tRNA pseudouridine synthase A [Selenomonas noxia ATCC 43541]
          Length = 260

 Score =  124 bits (312), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 81/242 (33%), Positives = 125/242 (51%), Gaps = 6/242 (2%)

Query: 8   IEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           I Y+G+ Y G+QRQ     ++Q ++E A+  V GE V +  AGRTD+GVHA  QV +F  
Sbjct: 13  IAYDGTRYHGFQRQSPPVVAVQNALEAALAEVCGETVELAAAGRTDAGVHACGQVVNF-F 71

Query: 67  VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
               +P   L +A+N  L     I++ +     + F AR SA  ++Y+YR+     P   
Sbjct: 72  TDGRIPTERLPRAVNGLLP--PDIAVTDAWEAARDFSARHSAKGKAYVYRMEQCTVPNPF 129

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LI 184
            +  AW I + LD E MR A   LVG HD+++FR+      SP+RTID   +   G   +
Sbjct: 130 TRNYAWQIFRPLDVEAMRAALAMLVGTHDYSSFRAAGGAPMSPVRTIDEIRLEDEGEGRL 189

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
              +    FL+  +R+ + ++  VG  + +     +   A+DR+   P AP  GLY   V
Sbjct: 190 SCYLHGNGFLYHMVRNIMSTVVSVGQERISVGRFAEIFAARDRRLASPTAPACGLYLLHV 249

Query: 245 EY 246
           +Y
Sbjct: 250 DY 251


>gi|296168687|ref|ZP_06850436.1| tRNA pseudouridine synthase A [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896596|gb|EFG76237.1| tRNA pseudouridine synthase A [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 302

 Score =  124 bits (312), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 84/263 (31%), Positives = 129/263 (49%), Gaps = 22/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G +++A+  +    + +  AGRTD+GVHA  QV
Sbjct: 27  VRLRLDIAYDGTEFAGWATQAGQRTVAGVLDEALTTLFRAPMRLRAAGRTDTGVHATGQV 86

Query: 62  AHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           AH D+  + +P              + L + L  +L     + +L ++     F ARFSA
Sbjct: 87  AHVDVPPDALPNAYPRAPRVGEPEFLPLVRRLGRFLPTD--VRVLGIARAPAGFDARFSA 144

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           +RR Y YR+ T  AP  +E  RA  +   P+ LD + M  A++ LVG HDF  F   H  
Sbjct: 145 LRRHYTYRLST--APYGVEPQRARYVTAWPRPLDVDAMAAASRDLVGLHDFAGF-CRHRP 201

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            ++ IR +   D +  G LI   V A +F  + +RS VG+L  VG+ +   +     L A
Sbjct: 202 NATTIRDLQGLDWSRDGELITAHVTADAFCWSMVRSLVGALLAVGEHRRPVSWCRGLLTA 261

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
             R      APP GL    V+Y 
Sbjct: 262 TSRSSDFAAAPPHGLTLVGVDYP 284


>gi|315445896|ref|YP_004078775.1| pseudouridylate synthase I [Mycobacterium sp. Spyr1]
 gi|315264199|gb|ADU00941.1| pseudouridylate synthase I [Mycobacterium sp. Spyr1]
          Length = 291

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 82/261 (31%), Positives = 127/261 (48%), Gaps = 18/261 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            +R  + I Y+G+ + GW  Q    ++ G I+ A+  V    ++   AGRTDSGVHA  Q
Sbjct: 12  FVRLRLDIAYDGTDFAGWATQAGQRTVAGVIDDALSTVFRTPMLTRAAGRTDSGVHATGQ 71

Query: 61  VAHFDLVREWVPVILCKALNAYLK------------ISDTISILNLSIVDKQFHARFSAI 108
           VAH D+  + +P    + + A               +++ + +  +      F ARFSA+
Sbjct: 72  VAHVDIPTDALPHAYPRTVRAGEAEFGPLVRRLGRMLTEDVRVRGIVRAAPGFDARFSAL 131

Query: 109 RRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           RR Y+YR+ T  AP  +E   A  +   P+ LD + M  AAQ+++G HDF  F   H   
Sbjct: 132 RRHYVYRLTT--APYGVEPSEARFVTAWPRPLDVDAMAGAAQNVLGLHDFAAF-CRHRDG 188

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           ++ IR +   D    G+ I + V A +F    +RS VG+L  VG+ +   T   + L A+
Sbjct: 189 ATTIRELQRLDCVRDGDRISVHVSADAFCWNMVRSLVGALLAVGEHRRDDTWCVQLLHAR 248

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
            R      AP  GL    V+Y
Sbjct: 249 HRSSDFAAAPARGLTLVGVDY 269


>gi|307154816|ref|YP_003890200.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7822]
 gi|306985044|gb|ADN16925.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7822]
          Length = 284

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 80/246 (32%), Positives = 121/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ N  ++Q  IE AI  V G  + +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYLGTHFHGWQRQPNRRTVQEEIETAIAQVLGYPITLHGAGRTDAGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD +    P      LN+  ++ D I +     V   +HARFSA+ R Y Y I T + P
Sbjct: 72  HFDQMSLIPPYRWATILNS--RLPDDIVVRASHKVCDTWHARFSALWRRYRYTIYTDKQP 129

Query: 123 LALEKGRAWLIPKSLDCEN-MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               K  +W   +    E+ M+ A + L+G+H    F   +   +     +        G
Sbjct: 130 NLFVKPFSWHYYQYPLSESLMQAALEPLLGKHHLAAFHRANSARTHSWVEVQAVQCYRSG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  +G L  VG+ + + ++     + Q R+E    AP +GL  
Sbjct: 190 PFIHVEIQANGFLYGMVRLLMGMLIEVGNQQRSLSEFTNIWKNQRREEVKYAAPAKGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|86132219|ref|ZP_01050814.1| Pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85817138|gb|EAQ38321.1| Pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 263

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 120/249 (48%), Gaps = 8/249 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G  Y GWQRQ N  ++Q +IEKA+  +  + V++ GAGRTD+GVHA +  
Sbjct: 8   VRYFIELSYFGKDYHGWQRQPNAVTVQETIEKALSTILRKPVLIMGAGRTDAGVHATQMY 67

Query: 62  AHF----DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           AHF    DL  +     L   LN +L     I+I  +  V  + H RF A  RSYLYRI 
Sbjct: 68  AHFDWDDDLSLDNKLRNLTYKLNRFLPPD--IAIDRIFNVRDEAHTRFDATSRSYLYRIA 125

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R+ P + E+  A  I   +D   M  AA  L+   DF  F     + ++ +  I     
Sbjct: 126 KRKNPFSTEQAHA--IAYDIDLSLMNEAAAALLDYSDFECFSKSKTEVNTYLCDITRAQW 183

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               +     + A  FL   +R+ VG+L  +G GK   + +   ++ + R   G   P  
Sbjct: 184 LETEDEYHFHITANRFLRNMVRAIVGTLLEIGQGKKPVSWIHDVVKGKSRSRAGSSVPGH 243

Query: 238 GLYFDSVEY 246
           GLY   + Y
Sbjct: 244 GLYLTEIIY 252


>gi|213962633|ref|ZP_03390894.1| tRNA pseudouridine synthase A [Capnocytophaga sputigena Capno]
 gi|213954628|gb|EEB65949.1| tRNA pseudouridine synthase A [Capnocytophaga sputigena Capno]
          Length = 250

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 120/245 (48%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + + G  Y GWQ Q    S+Q  +E+ +  +    + V GAGRTDSGVHA +  
Sbjct: 1   MRYFIELSFFGKNYHGWQSQPKAISVQEVLEQGLSTILRTPISVVGAGRTDSGVHASQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD V E +P      LNA+L     I++ N+  +    H RF A++R+Y Y I T++ 
Sbjct: 61  AHFD-VTEPLPTNFVHRLNAFL--PKDIAVHNIYEMKPNAHTRFDALKRTYQYHISTQKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A +   A     +L+   M  AAQ L+   DF  F   H    + I  I         
Sbjct: 118 VFAYD--YAMFFTHTLNIAIMNEAAQILLDYSDFQCFSKTHTDVKTFICKIYKAHWEKID 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   ++A  FL   +R+ VG+L  VG  K + TD E  + +++R + G   P  GL+ 
Sbjct: 176 KQLVFTIIADRFLRNMVRAIVGTLIDVGLQKLSLTDFEDIILSKNRSKAGASVPACGLFL 235

Query: 242 DSVEY 246
             +EY
Sbjct: 236 THIEY 240


>gi|319901295|ref|YP_004161023.1| tRNA pseudouridine synthase A [Bacteroides helcogenes P 36-108]
 gi|319416326|gb|ADV43437.1| tRNA pseudouridine synthase A [Bacteroides helcogenes P 36-108]
          Length = 250

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 115/248 (46%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGESVQECLMKALATLLRCDVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSAAPLDAAFMVDKLNRLLPPD--ISVYRLRAVKSDAHARFDATTRMYKYYVTTAK 118

Query: 121 APLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P     + R +  P   D E M  AAQ L    DFT+F  +H    +    I H     
Sbjct: 119 IPFDRWYRCRLFQTP---DFERMNEAAQTLYDYTDFTSFSKLHTDVKTNNCKIMHAVWTQ 175

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +  +  + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G   P   
Sbjct: 176 QDEVTWVFTIKADRFLRNMVRAIVGTLLEVGRGKLTVEGFRRVIEQQDRCQAGTSVPGNA 235

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 236 LFLVDVSY 243


>gi|313905811|ref|ZP_07839169.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
 gi|313469325|gb|EFR64669.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
          Length = 252

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 124/250 (49%), Gaps = 9/250 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTG----EIVVVHGAGRTDSGVHAL 58
           Y M I Y+G+ +FGW+ Q K   +IQG +E  +  + G    + V V GAGRTD+GVHA 
Sbjct: 5   YKMKISYDGTRFFGWEHQPKQEMTIQGKLETVLSRMVGAPEDQPVTVIGAGRTDAGVHAK 64

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             +A+  L        +   +N YL   + IS+  L +   +FH+RF A  ++Y Y    
Sbjct: 65  EMIANVLLDTRMSEEEIQTYMNRYL--PEDISVNELKVCADRFHSRFKAKGKTYCYSFWY 122

Query: 119 RQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               +    ++    ++ K  + + MR AA+ +VG  DF +F        S +R +D  +
Sbjct: 123 ADGGVRPTFDRKYVTVLDKRPNVDRMRKAAEEIVGMRDFKSFCGNSHMKKSTVRLVDSIE 182

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I I +    FL   +R   G+L  VG GK T   + + ++A+DRK  GP AP 
Sbjct: 183 FKIRGPYIRIYIHGSGFLQNMVRIIAGTLLEVGYGKRTPESIAELIEARDRKLAGPTAPA 242

Query: 237 EGLYFDSVEY 246
           +GL    V+Y
Sbjct: 243 QGLCLIKVDY 252


>gi|300173999|ref|YP_003773165.1| tRNA pseudouridine synthase A [Leuconostoc gasicomitatum LMG 18811]
 gi|299888378|emb|CBL92346.1| tRNA pseudouridine synthase A [Leuconostoc gasicomitatum LMG 18811]
          Length = 255

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 92/258 (35%), Positives = 134/258 (51%), Gaps = 14/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIFLV----TGEIVVVHGAGRT 51
           M RY  I+ Y+GS +FG+Q Q KNG     ++QG + KA+  +    T  I VV GA RT
Sbjct: 1   MPRYKAIVSYDGSDFFGFQVQTKNGVERQRTVQGELNKAVNQMAKNPTPAIKVV-GASRT 59

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D+GVHA  QV HFDL  +   + + K LN  L     I I ++  V   FHARF+   + 
Sbjct: 60  DTGVHAFGQVVHFDLPFDINVIGVRKGLNTLL--PKDIIIQSVDQVANDFHARFNTHAKR 117

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y+YR+ T+      ++         LD E ++IA   L+G HDF +F +   Q  + IRT
Sbjct: 118 YVYRVSTQDFTDPFKRFYTGHFQWQLDVERIKIALPDLLGEHDFASFAASGNQTITTIRT 177

Query: 172 IDHFD--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           I   D  VN+    +       +FL+ QIR  VG L  +G+G+    D+ + +  +DR++
Sbjct: 178 ITRADLKVNNDEQELVFTFEGNAFLYNQIRIMVGVLLEIGNGRRDVHDIIRLIAVKDREQ 237

Query: 230 CGPLAPPEGLYFDSVEYS 247
               AP  GLY D + Y 
Sbjct: 238 ARFTAPASGLYLDEIYYD 255


>gi|331269740|ref|YP_004396232.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
 gi|329126290|gb|AEB76235.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
          Length = 245

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 123/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + I+Y+G+ Y GWQ+  N  ++IQ  +E  +  + GE + +  +GRTD+GVHA  Q+A+F
Sbjct: 6   LTIQYDGTRYKGWQKLGNTDNTIQCKVENVLNELLGEEISLIASGRTDAGVHANMQIANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + K    YL     I + N++   + FH+R++  ++ Y Y I        
Sbjct: 66  KTDSNVSNDTILKHCYKYL--PHDIVVTNVADASENFHSRYNVKKKIYTYNICNNPVHDV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  ++ + ++LD + M+ A++  +G HDF +F ++  +  S ++TID        N I
Sbjct: 124 FTRKYSYHVKETLDIKKMKEASKLFIGEHDFKSFTALKSKKKSTVKTIDSISFKKKDNNI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E+      FL+  IR  VGSL  VG GK T  DLE  +  +DR      AP  GL    V
Sbjct: 184 EVIFTGNGFLYKMIRILVGSLINVGLGKLTIEDLENIMNEKDRSIAPETAPAHGLILTEV 243

Query: 245 EY 246
           +Y
Sbjct: 244 KY 245


>gi|281355314|ref|ZP_06241808.1| tRNA pseudouridine synthase A [Victivallis vadensis ATCC BAA-548]
 gi|281318194|gb|EFB02214.1| tRNA pseudouridine synthase A [Victivallis vadensis ATCC BAA-548]
          Length = 272

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 126/248 (50%), Gaps = 6/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           RY + I Y+G+ Y GWQ Q +  ++Q  +++ +  +  G+ + + G+ RTD+GVHA R  
Sbjct: 13  RYLLEIAYDGTNYSGWQIQPHRVAVQQRVQEILTKMYNGQPIHLIGSSRTDAGVHAQRFA 72

Query: 62  A-HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           A +   VR  +P   + +A+N   ++   I +  +  V  +FHAR+ A+ ++Y Y ++  
Sbjct: 73  ASYLTPVRPDIPTDKILRAVNR--QLPGDIKLRTVREVPLEFHARYDALGKAYTY-VLNL 129

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P        W     +D E +R A+Q L G HD+++F          +RTI   DV  
Sbjct: 130 GDPSPFTDRYTWRPIHRMDVEKIRAASQVLTGTHDYSSFVVERSLIDEAVRTIYRIDVQE 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG    +  V   FL+  IR  +G+L+  G GK +   + + L+A DR      APP GL
Sbjct: 190 FGQFCCVTFVGNGFLYKMIRCLMGTLEAAGAGKLSPEAVRRILEACDRTVAPETAPPNGL 249

Query: 240 YFDSVEYS 247
           +   V Y+
Sbjct: 250 FLMKVFYT 257


>gi|329965278|ref|ZP_08302208.1| tRNA pseudouridine synthase A [Bacteroides fluxus YIT 12057]
 gi|328523298|gb|EGF50398.1| tRNA pseudouridine synthase A [Bacteroides fluxus YIT 12057]
          Length = 288

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 84/245 (34%), Positives = 117/245 (47%), Gaps = 5/245 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   VA
Sbjct: 31  RYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLMVA 90

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD         +   LN  L     IS+ +L  V  + HARF A  R Y Y + T + P
Sbjct: 91  HFDSETPLDVTFMADKLNRLL--PPDISVYSLRAVKPEAHARFDATARMYKYYVTTAKVP 148

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               + R  L  ++ D E M  AA+ L    DFT+F  +H    +    I H        
Sbjct: 149 FN-RRYRCRLF-QTPDFERMNEAAKTLFDYTDFTSFSKLHTDVKTNNCRIMHAAWTQLDE 206

Query: 183 LIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   L+ 
Sbjct: 207 VTWVFTVQADRFLRNMVRAIVGTLLEVGRGKLTVEGFRRVIEQKDRCRAGTSVPGNALFL 266

Query: 242 DSVEY 246
             V Y
Sbjct: 267 VDVAY 271


>gi|304438671|ref|ZP_07398609.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 149 str.
           67H29BP]
 gi|304368320|gb|EFM22007.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 149 str.
           67H29BP]
          Length = 275

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 126/245 (51%), Gaps = 6/245 (2%)

Query: 5   CMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
            + + Y+G+ Y G+QRQ     ++Q  +E A+  V GE V +  AGRTD+GVHA  QV +
Sbjct: 10  ALKVAYDGTNYHGFQRQTPPIRAVQNVLEAALAQVCGETVELASAGRTDAGVHAYGQVVN 69

Query: 64  FDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +P   L +A+N  L     I +       + F AR SA  ++Y+YR+   + P
Sbjct: 70  F-FTDGRIPTERLPRAVNGLLPPD--IVVSEAWEAARDFSARHSATGKAYVYRMKECRVP 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG- 181
               +  AW I + LD + MR A   L G HD+++FR+      SP+RT+D   + + G 
Sbjct: 127 DPFTRSYAWQIFQPLDYDAMRAALHLLEGTHDYSSFRAAGGAPMSPVRTLDTIRLTAEGE 186

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + +    FL+  +R+ V +   VG G+ +     +   A+DR+   P AP  GLY 
Sbjct: 187 GRLSLYIHGTGFLYHMVRNIVSTAVAVGTGRISKDRFAEIFAARDRRLAPPTAPAGGLYL 246

Query: 242 DSVEY 246
            +V+Y
Sbjct: 247 LAVDY 251


>gi|303237649|ref|ZP_07324209.1| tRNA pseudouridine synthase A [Prevotella disiens FB035-09AN]
 gi|302482101|gb|EFL45136.1| tRNA pseudouridine synthase A [Prevotella disiens FB035-09AN]
          Length = 255

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 127/270 (47%), Gaps = 41/270 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG S+Q  +EKA+  +    + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIKFSYDGTNYHGWQIQPNGISVQEVLEKALSTLLRTKMSVTGAGRTDAGVHARLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAHFD    W   I  + L   L   +   +S++++  V+ + HARFSA  R+Y Y +  
Sbjct: 61  VAHFD----WEAPIDGQQLAYKLNRMLPRDVSVISVEAVENELHARFSATSRTYHYYMHR 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P +  +  ++ +P  LD E M  AA++L+G  DF  F    C+A    +T       
Sbjct: 117 GRNPFS--RAYSYEMPYELDFERMNEAAKYLIGERDFKCF----CKAGGDNKT------- 163

Query: 179 SFGNLIEIR----------------------VVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           +  NL E R                      + A  FL   +R+ VG+L  VG G+ T  
Sbjct: 164 TICNLTEARWQHCNTEIAIHEAEKAEEWCFVITANRFLRNMVRAVVGTLVEVGRGRITID 223

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  K +    R + G   P   L+   V Y
Sbjct: 224 EFRKIVDNGTRSDAGESMPGNALFLWDVTY 253


>gi|307610015|emb|CBW99548.1| transfer RNA-pseudouridine synthase I [Legionella pneumophila 130b]
          Length = 253

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 71/204 (34%), Positives = 109/204 (53%), Gaps = 12/204 (5%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSI-----VDKQFH 102
           AGRTD+GVHA  QV HFD  ++       +++ A++  ++T    ++ +     + + FH
Sbjct: 38  AGRTDTGVHATNQVIHFDCEKD-------RSIRAWIHGANTFLPKDICVKWGKEMPENFH 90

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           AR+SA+ R Y Y I        L +G      + LD   M+   Q L+G +DFT+FRS+ 
Sbjct: 91  ARYSAVSRRYRYVIYNGAIRPGLLRGNVTWQYRQLDHRLMQQGGQCLLGENDFTSFRSVE 150

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           CQ+++P+R I    V   G+L+ + + A +FLH  +R+  G L  VG GK     ++  L
Sbjct: 151 CQSNTPMRNIHQLQVTRHGDLVVLDITANAFLHHMVRNIAGVLIAVGSGKHPVGWVKDVL 210

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
            A+DRK     AP  GLY   V Y
Sbjct: 211 NAKDRKLGAETAPSYGLYLVQVTY 234


>gi|159901453|ref|YP_001547700.1| tRNA pseudouridine synthase ACD [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159894492|gb|ABX07572.1| tRNA pseudouridine synthase A [Herpetosiphon aurantiacus ATCC
           23779]
          Length = 272

 Score =  124 bits (311), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 86/248 (34%), Positives = 125/248 (50%), Gaps = 11/248 (4%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +  EY G+ + G Q Q  G ++Q  +E A   +T E      AGRTD+GVHAL QVAH 
Sbjct: 6   ALCFEYLGTAFCGSQWQPGGRAVQTELETAWQRLTSETGRWIFAGRTDAGVHALAQVAHI 65

Query: 65  --DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
             D  R      + KA+NA       IS+     +   FHARFSA +R+Y Y   +  AP
Sbjct: 66  VSDTPRSLD--TIAKAINAI--TPPDISVHEAWEMPTGFHARFSARQRTYRYVFDSAPAP 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS--- 179
            A   GR   +   LD   M+ A   L+G HDF  F     + S+  RT     +     
Sbjct: 122 SATLSGRVLRLDHQLDWAAMQAALDTLIGTHDFAAFAGAGHEGST-TRTCMLAQLRPAEW 180

Query: 180 FGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            G  + +  + A +FL   +R+ VG+L +VGDG+ +    +  + ++DR+  GP APP+G
Sbjct: 181 LGRPVTVLHLQANAFLKHMVRNIVGTLLMVGDGRLSLEAWQAIIASRDRRNAGPTAPPQG 240

Query: 239 LYFDSVEY 246
           LY +S+ Y
Sbjct: 241 LYLESIGY 248


>gi|269122416|ref|YP_003310593.1| tRNA pseudouridine synthase A [Sebaldella termitidis ATCC 33386]
 gi|268616294|gb|ACZ10662.1| tRNA pseudouridine synthase A [Sebaldella termitidis ATCC 33386]
          Length = 244

 Score =  124 bits (310), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 81/241 (33%), Positives = 117/241 (48%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++ EY+GS + G+QRQ N  ++QGSIE+ I     E V +  +GRTD GVHAL QV++F 
Sbjct: 6   IVYEYDGSKFSGFQRQLNKKTVQGSIEEVIKNYFNEEVNLLSSGRTDKGVHALGQVSNFF 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           + +   P I+   LN  L  S  I + +    D  FHARFSA  R+YLY +  +      
Sbjct: 66  MEKSISPDIIKGILNRAL--SGKIRVTDAKEADSDFHARFSAKTRTYLYIMKLKDEITPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E      +   +  E ++   +  +GRH+F +FR       +P R I++         + 
Sbjct: 124 ESSYVSALDGKIIPEKLQKIMEPFIGRHNFDSFRKKDKDNKNPEREINNIRCYEEDKRLF 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I +  +SFL T IR  +GS   V   K     +   L   D      LAP EGLY   V 
Sbjct: 184 IEIEGKSFLKTMIRIMIGSALAVYFEKRNPDYICDKLDNPDSDGEKILAPSEGLYLYKVN 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|224538364|ref|ZP_03678903.1| hypothetical protein BACCELL_03255 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224519993|gb|EEF89098.1| hypothetical protein BACCELL_03255 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 279

 Score =  124 bits (310), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 117/248 (47%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + +A+  +    V V GAGRTD+GVHA   
Sbjct: 29  MQRYFIYLAYDGTAYHGWQIQPNGDSVQECLMRALATLMRREVEVIGAGRTDAGVHASLM 88

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD             LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 89  VAHFDSDEPLDTAFFTDKLNRLLPPD--ISVYRLRAVKPDAHARFDATARMYKYYVTTAK 146

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +P   + + R +  P   D E M  AA+ L    DFT+F  +H    +    I H     
Sbjct: 147 SPFNRQYRCRLFQTP---DFERMNEAARSLFDYTDFTSFSKLHTDVKTNNCRIMHAAWTQ 203

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             ++  +  + A  FL   +R+ VG+L  VG GK T     + ++ +DR + G   P   
Sbjct: 204 IDDVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTVDGFRRVIEQKDRCKAGTSVPGNA 263

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 264 LFLVDVTY 271


>gi|28377870|ref|NP_784762.1| tRNA pseudouridine synthase A [Lactobacillus plantarum WCFS1]
 gi|254556054|ref|YP_003062471.1| tRNA pseudouridine synthase A [Lactobacillus plantarum JDM1]
 gi|308180048|ref|YP_003924176.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ST-III]
 gi|38258756|sp|Q88XU9|TRUA_LACPL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|28270703|emb|CAD63609.1| pseudouridylate synthase A [Lactobacillus plantarum WCFS1]
 gi|254044981|gb|ACT61774.1| tRNA pseudouridine synthase A [Lactobacillus plantarum JDM1]
 gi|308045539|gb|ADN98082.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ST-III]
          Length = 262

 Score =  124 bits (310), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 128/250 (51%), Gaps = 7/250 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           RY +++ Y+G+ + G+QRQ +  +++  + KA+  +     E +V++GAGRTD+GVHA  
Sbjct: 4   RYKVVLAYDGTNFAGFQRQPHQRTVEQVVTKAVNKMAKDPVEPIVIYGAGRTDAGVHAFG 63

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFDL  E  P  + + LN+ L + DTI +  +SIV   FHAR+  + + Y YR    
Sbjct: 64  QTLHFDLPYEINPEGVRRGLNSMLPM-DTI-VKAVSIVPNDFHARYDTVGKRYWYRAYQN 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++        + D + ++ A   L GRHDF+TF +   QA   +R I      +
Sbjct: 122 EFVDPFKRHYTGHFKFAADIDRIQQAIGDLEGRHDFSTFVASGSQAHDHVREIYSAKAWA 181

Query: 180 FGNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +  EI+       FL+ Q+R  V  L  +G G+     +   L A+DR++    AP  
Sbjct: 182 LPDEREIQFEFCGSGFLYNQVRIMVAVLMEIGQGRRAVDCIPALLAAKDREQARGTAPAA 241

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 242 GLYMKKVYYE 251


>gi|300767857|ref|ZP_07077767.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|300494842|gb|EFK30000.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
          Length = 273

 Score =  124 bits (310), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 128/250 (51%), Gaps = 7/250 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           RY +++ Y+G+ + G+QRQ +  +++  + KA+  +     E +V++GAGRTD+GVHA  
Sbjct: 15  RYKVVLAYDGTNFAGFQRQPHQRTVEQVVTKAVNKMAKDPVEPIVIYGAGRTDAGVHAFG 74

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFDL  E  P  + + LN+ L + DTI +  +SIV   FHAR+  + + Y YR    
Sbjct: 75  QTLHFDLPYEINPEGVRRGLNSMLPM-DTI-VKAVSIVPNDFHARYDTVGKRYWYRAYQN 132

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++        + D + ++ A   L GRHDF+TF +   QA   +R I      +
Sbjct: 133 EFVDPFKRHYTGHFKFAADIDRIQQAIGDLEGRHDFSTFVASGSQAHDHVREIYSAKAWA 192

Query: 180 FGNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +  EI+       FL+ Q+R  V  L  +G G+     +   L A+DR++    AP  
Sbjct: 193 LPDEREIQFEFCGSGFLYNQVRIMVAVLMEIGQGRRAVDCIPALLAAKDREQARGTAPAA 252

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 253 GLYMKKVYYE 262


>gi|315659196|ref|ZP_07912060.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis M23590]
 gi|315495621|gb|EFU83952.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis M23590]
          Length = 264

 Score =  124 bits (310), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 115/243 (47%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q  G ++Q   EK +  +    V +H + RTD GVHAL Q 
Sbjct: 1   MRILVNICYQGSNFLGFQIQNQGRTVQQQFEKILKRMHRHDVRIHPSSRTDRGVHALEQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I +  +  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELKIADGQWQYAMNSAL--PDDIYVKEVKQVDSDFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    +P+ L+ E M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 KNPFESGLKTYVPQQLNIERMNEAAQKFIGTHDFTGFCSQKTEVESKVRTLYQSEIEMTT 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  +  L  VG G  +  ++   L+ ++R      AP EGLY 
Sbjct: 179 YGFDYIVTGSGFLYNMVRVLMAFLIGVGKGNRSPEEVTALLEQKNRDNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|300742028|ref|ZP_07072049.1| tRNA pseudouridine synthase A [Rothia dentocariosa M567]
 gi|300381213|gb|EFJ77775.1| tRNA pseudouridine synthase A [Rothia dentocariosa M567]
          Length = 316

 Score =  124 bits (310), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 88/271 (32%), Positives = 130/271 (47%), Gaps = 35/271 (12%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+G+ + GW RQ N  ++QG +E A+ LV      V  AGRTD+GVHA  Q  H D+  E
Sbjct: 12  YDGTWFSGWARQPNLVTVQGVLEDALELVLRTHHRVTVAGRTDAGVHAQAQTIHLDIATE 71

Query: 70  -WVPVI-----------LCKALNAYLK-------------------ISDTISILNLSIVD 98
            W  +            L + ++  LK                   +  ++ +  +  V 
Sbjct: 72  TWQKLTGRDGLADPAESLKRKVSGALKRTLAQAEHTLGIPERMRGLLQGSLVLHQVQPVP 131

Query: 99  KQFHARFSAIRRSYLYRIITRQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           + F ARFSA  R Y YRI+  Q  +P  L +  AW IP+SLD E++  AA  L G HDF 
Sbjct: 132 QDFDARFSATGRRYTYRILDGQGSSPDPLHRAYAWCIPESLDLEDLNKAAHELTGLHDFL 191

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +F     + ++ IR +    +    + +IE  V A +F H  +RS +G+L L G GK T 
Sbjct: 192 SFCKPR-EGATTIRELRRIYLTRHDDGVIEATVEADAFCHHMVRSLIGALVLYGTGKRTQ 250

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             L + L+   R     +APP GL    ++Y
Sbjct: 251 AWLRERLENPQRDASLIMAPPHGLALAHIDY 281


>gi|261409491|ref|YP_003245732.1| tRNA pseudouridine synthase A [Paenibacillus sp. Y412MC10]
 gi|329922021|ref|ZP_08277814.1| tRNA pseudouridine synthase A [Paenibacillus sp. HGF5]
 gi|261285954|gb|ACX67925.1| tRNA pseudouridine synthase A [Paenibacillus sp. Y412MC10]
 gi|328942404|gb|EGG38668.1| tRNA pseudouridine synthase A [Paenibacillus sp. HGF5]
          Length = 263

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 87/259 (33%), Positives = 126/259 (48%), Gaps = 18/259 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    M + Y+G+ Y G+Q Q  G +IQ  +E+AI  ++GE + +  +GRTD+GVHA  Q
Sbjct: 1   MRNLLMKVSYDGTDYNGFQTQPGGHTIQDYLEEAIRRLSGEQLKITASGRTDAGVHARAQ 60

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V +F      +PV   C ALN +L   + I + +   V  +FH+R +A R++Y + I   
Sbjct: 61  VFNF-YTASPIPVERWCMALNTWL--PEDIVVSDAMEVPMEFHSRHAAKRKTYRFTINAN 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           Q P    +         LD   M     HL+G HDFTTF S      S +RTI  FD   
Sbjct: 118 QYPDLFNRRYQIHHHGKLDIAAMEQGLSHLIGTHDFTTFASRKSTKPSHVRTI--FDAWI 175

Query: 178 ----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                          +I   V    FL   +R  +G+L  VG+GK    D++  L+AQ+R
Sbjct: 176 EKDTSMCRPGTRDQGIIHTYVSGNGFLQHMVRIIMGTLIEVGEGKRHPDDMKVILEAQNR 235

Query: 228 KECGPLAPPEGLYFDSVEY 246
              GP A  +GL    V+Y
Sbjct: 236 AAAGPTAMGKGLMLWEVDY 254


>gi|227871757|ref|ZP_03990163.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
 gi|227842397|gb|EEJ52621.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
          Length = 265

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 127/249 (51%), Gaps = 7/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + + Y G+ Y G+Q+Q+  S+I G++E+ +  L   ++    GA RTD GVHAL  +
Sbjct: 11  RIVLKLAYEGTSYHGFQKQEGLSTIAGTVEEQLRNLFPWKMENFIGASRTDQGVHALGNL 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD   +     + +ALN+YL   + I ++    V + FH RF+  R++Y Y I   + 
Sbjct: 71  LSFDTEGKVSGEQILRALNSYL--PEDIRVMEAYSVQQDFHPRFTPHRKAYRYSICRSKV 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA----SSPIRTIDHFDV 177
              L +  A+     LDC  +    + L G HDF +F +   Q+     S +R I  F +
Sbjct: 129 ENPLRRRTAYHYTFPLDCGKISEGMELLKGEHDFRSFANPKAQSLLQGGSSVREIYRFSM 188

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ +   V    FL+  IR   G+L  +G G+ + + LE+ L+ +DR   GP AP +
Sbjct: 189 EEEGDYLHFSVEGNGFLYHMIRILAGTLLELGRGRISLSQLEEILEKKDRTLAGPTAPAK 248

Query: 238 GLYFDSVEY 246
           GL   +++Y
Sbjct: 249 GLCLMNLDY 257


>gi|269216172|ref|ZP_06160026.1| tRNA pseudouridine synthase A [Slackia exigua ATCC 700122]
 gi|269130431|gb|EEZ61509.1| tRNA pseudouridine synthase A [Slackia exigua ATCC 700122]
          Length = 331

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 91/256 (35%), Positives = 131/256 (51%), Gaps = 19/256 (7%)

Query: 8   IEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + Y+G+ + G+ RQ     +++QG +E+ + ++    V    AGRTD+GVHAL QV  FD
Sbjct: 78  VAYDGAPFAGFARQAESHVTTVQGELERVLSVLYRRAVDTVCAGRTDAGVHALGQVVSFD 137

Query: 66  LVREWV---PV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           L  E     P+  L K++NA   + + I++         F ARF A  R Y Y I T  A
Sbjct: 138 LTEEEFASRPLRTLMKSMNAL--VDERITVTCAEERPAGFSARFDATSREYRYFIATGNA 195

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTF----RSIHCQAS--SPIRTIDH 174
              L     W L    LD + M  AA+ LVG HDF +F     ++H +    S  R +  
Sbjct: 196 RPVLIARSVWHLRGAPLDVDAMNTAARFLVGEHDFKSFCVASSALHLEGEGRSTCRRVIE 255

Query: 175 FDVNS---FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            DV S    G  ++E+R+V  +FLH+ IR  VG+L  VG G+  ++ +   L A+DR   
Sbjct: 256 ADVRSTHVMGTPVVEVRIVGNAFLHSMIRIIVGTLVAVGQGRRDASWVADVLAARDRTAA 315

Query: 231 GPLAPPEGLYFDSVEY 246
           G  AP  GL F SV Y
Sbjct: 316 GETAPACGLTFWSVRY 331


>gi|194477033|ref|YP_002049212.1| tRNA pseudouridine synthase A [Paulinella chromatophora]
 gi|171192040|gb|ACB43002.1| tRNA pseudouridine synthase A [Paulinella chromatophora]
          Length = 252

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 119/248 (47%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R  + ++Y GS Y GWQRQ+N  S+Q  +E+A+  L   + ++   AGRTD+GVHA  
Sbjct: 1   MKRIALCLQYEGSSYCGWQRQRNALSVQEVLEEALLALGCDKPIISFAAGRTDAGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN YL  S  I  L  + V   +HA +SA+ R Y Y ++  
Sbjct: 61  QVVHFDTNSPIPTDSWASALNGYLPSS--IRALKATSVPNNWHACYSAVYRRYRYTLLNS 118

Query: 120 QAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           + P       +W      LD   MR +    +G HDF+ F+       S   TI    + 
Sbjct: 119 REPDLFIAPYSWHRYDTVLDENAMRRSLLTFLGTHDFSAFQRSGSDRISTRTTIQEVSLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +   I + + A  FL+  +R  V  L  VG+G+ T ++LE+  +   R +    AP +G
Sbjct: 179 RYDEKITLEIQASGFLYGMVRLMVAQLVEVGEGRLTESNLEQRWRQHCRGQIKEAAPAQG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLLQVGY 246


>gi|167765202|ref|ZP_02437315.1| hypothetical protein BACSTE_03590 [Bacteroides stercoris ATCC
           43183]
 gi|167696830|gb|EDS13409.1| hypothetical protein BACSTE_03590 [Bacteroides stercoris ATCC
           43183]
          Length = 251

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 84/248 (33%), Positives = 118/248 (47%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       + +   LN  L     IS+  L  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSETPLDVIFMMDKLNRLLPPD--ISVYRLRAVRPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P   + + R +  P   D E M  AA+ L    DFT+F  +H    +    I H     
Sbjct: 119 MPFNRQYRCRLFQTP---DFERMNEAARTLFEYTDFTSFSKLHTDVKTNNCKIMHAAWTQ 175

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +  +  + A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   
Sbjct: 176 VDEVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTIGGFRRVIEQKDRCRAGTSVPGNA 235

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 236 LFLVDVAY 243


>gi|302346677|ref|YP_003814975.1| tRNA pseudouridine synthase A [Prevotella melaninogenica ATCC
           25845]
 gi|302150885|gb|ADK97146.1| tRNA pseudouridine synthase A [Prevotella melaninogenica ATCC
           25845]
          Length = 253

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 83/268 (30%), Positives = 126/268 (47%), Gaps = 37/268 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E A+  +  E + + GAGRTD+GVH    
Sbjct: 1   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLEHALSTILRESIAITGAGRTDAGVHGRMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD    +    L   +N  L     +S+  +  V +  HARFSA  R+Y Y + T +
Sbjct: 61  VAHFDTELSFDCAQLVYKVNRLLPRD--VSVSRIEPVGEDLHARFSATSRTYHYYVHTGK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P + +   A  +  SLD + M  AA +L+G  DF  F    C+A + ++T       + 
Sbjct: 119 QPFSRQYSCA--LHYSLDFDKMNEAAAYLIGEKDFKCF----CKAGADVKT-------TI 165

Query: 181 GNLIEIR----------------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            NL E R                      + A  FL   +R+ VG+L  VG G+ +  + 
Sbjct: 166 CNLTEARWIPTNDEFALATDDTVTNWCFVITANRFLRNMVRAVVGTLVEVGRGRLSLDEF 225

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +K +    R + G   P   L+   V+Y
Sbjct: 226 KKIVDGGTRSDAGESMPGNALFLWEVKY 253


>gi|168186842|ref|ZP_02621477.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
 gi|169295253|gb|EDS77386.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
          Length = 245

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + I+Y+G+ Y GWQ+   N ++IQ  IE  +  + GE V +  +GRTD+GVHA  QVA+F
Sbjct: 6   LTIQYDGTRYKGWQKLGNNDTTIQHKIESVLNELLGEKVSLMASGRTDAGVHANMQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     + K L  YL     I + +++     FH+R++   + Y YRI   +    
Sbjct: 66  KTDSEISNDEIFKYLYKYL--PQDIVVTSVNNASDNFHSRYNVKEKVYTYRIHNSEVHDV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  ++ I + LD + M+ A++  +G HDF +F ++  +  S ++ I+        N I
Sbjct: 124 FTRKYSYHIKEKLDLKKMKEASKLFIGEHDFKSFTALKSKKKSTVKAINSITFRKKENDI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           EI      FL+  IR  VG+L   G  K +  +++  +  +DR      AP  GL    V
Sbjct: 184 EIVFSGNGFLYKMIRILVGTLIQAGLNKISLDEIQNIMDKKDRNIAPETAPAHGLTLTEV 243

Query: 245 EY 246
           +Y
Sbjct: 244 KY 245


>gi|226496511|ref|NP_001146958.1| pseudouridylate synthase [Zea mays]
 gi|195605848|gb|ACG24754.1| pseudouridylate synthase [Zea mays]
          Length = 386

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 75/218 (34%), Positives = 116/218 (53%), Gaps = 14/218 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V 
Sbjct: 66  RYLVAVEYIGTRFSGSQKQPNQRTVTGVLEEAFHRFIGQPVSIIFSSRTDAGVHALSNVC 125

Query: 63  HFDLVR-----------EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L K    I + ++  V   FHAR+ ++ R
Sbjct: 126 HVDVERISKRKPGEVLTPHEPGVVKRAVNHFLLKSEGDIMVTDVCCVAPDFHARYKSLER 185

Query: 111 SYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YR++   ++    EK   W I + LD ++M+ A   LVG HDF++FR+  CQA+SP+
Sbjct: 186 TYHYRLLAGPESTSVFEKNSVWHISEDLDIQSMKKACSILVGHHDFSSFRAAGCQANSPV 245

Query: 170 RTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLK 206
           RT+D   V   F  +     V RS L     S V S K
Sbjct: 246 RTLDELSVTEVFPFMFFPSSVERSELELSNVSLVYSRK 283



 Score = 50.1 bits (118), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ARSFL+ Q+R  VG LK VG G  T+ D+E+ L A+       +AP  GLY  +V+Y
Sbjct: 326 ARSFLYHQVRLMVGLLKSVGTGDLTTADVERILDAKTVTAAPSMAPSCGLYLANVKY 382


>gi|282879881|ref|ZP_06288608.1| tRNA pseudouridine synthase A [Prevotella timonensis CRIS 5C-B1]
 gi|281306275|gb|EFA98308.1| tRNA pseudouridine synthase A [Prevotella timonensis CRIS 5C-B1]
          Length = 243

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ+Q N  S+Q  ++KA+  +  E +VV GAGRTD+GVHA + 
Sbjct: 1   MQRYFIYFSYDGTSYHGWQQQPNSHSVQAELQKALSTILREPIVVVGAGRTDTGVHARKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+        L   LN  L     IS+  +  V    HARFSA  R+Y Y + + +
Sbjct: 61  VAHFDIEAVIDGEQLAYKLNRLL--PRDISVAGVKPVQADMHARFSAKWRTYHYYVHSHK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNS 179
            P    +  +  +P  LD   M  AA HL+   DF  F   H    + +  +   + V +
Sbjct: 119 NPFL--RHYSCQLPFQLDYPLMNQAANHLLSVTDFGAFCKTHTDVKTTLCEVVRAEWVQT 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  VG  + T    +  +++ +R   G   P   L
Sbjct: 177 GEDSWYFVIKANRFLRNMVRAVVGTLIEVGRHRMTLEQFDAVIRSGNRSNAGESMPAHAL 236

Query: 240 YFDSVEY 246
           + + +EY
Sbjct: 237 FLEEIEY 243


>gi|254525991|ref|ZP_05138043.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
 gi|221537415|gb|EEE39868.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
          Length = 268

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 120/247 (48%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+G  Y GWQ+QKN +++Q  +E A+F +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGYHYSGWQKQKNATTVQEILESALFKITNHTVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN  L    TI IL    V   +HA +SA+ R Y Y I   +
Sbjct: 61  VVHFDIDSVIPGFSYSNILNNLL--PSTIRILESVEVKNSWHACYSAVYRHYRYVINNGK 118

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    K LD   M  A++ + G HDF  F+       + +  I + D+  
Sbjct: 119 FPNLFINNWSWHRYQKVLDEVLMLRASKTMKGEHDFFAFQKSGSNRRNSVTKIKNIDIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +S         + + +    AP +GL
Sbjct: 179 VEDLIFVDIKATGFLYGMVRLIVGQLVLVGEKKISSDIFIDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEY 246
            F +  Y
Sbjct: 239 CFVNAVY 245


>gi|254302141|ref|ZP_04969499.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148322333|gb|EDK87583.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 247

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 125/242 (51%), Gaps = 13/242 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F    +
Sbjct: 14  YDGSRYYGFQRQPNKITVQGEIEKVLRIVTKEEINLISAGRTDRGVHANHQVSNFYTSSN 73

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I   + P   
Sbjct: 74  IPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKMREYVYIISWEKNP--F 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LI 184
           E      + + +  E +       +G HDF  FR   C +   IR I   +V  FG+  I
Sbjct: 126 EARHCKFVKEKIVAEKLEKIFSDFIGVHDFKNFRLSDCVSKVTIREIYQIEVKYFGDSKI 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG++  +  G+     ++  L    R+    L   EGLY + +
Sbjct: 186 KIYIKGSAFLKSQVRIMVGTVLEIYYGRLPENHIKLMLNDFTREYKKNLVEAEGLYLNKI 245

Query: 245 EY 246
           +Y
Sbjct: 246 KY 247


>gi|295694868|ref|YP_003588106.1| tRNA pseudouridine synthase A [Bacillus tusciae DSM 2912]
 gi|295410470|gb|ADG04962.1| tRNA pseudouridine synthase A [Bacillus tusciae DSM 2912]
          Length = 277

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 121/245 (49%), Gaps = 14/245 (5%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y G+QRQ    ++QG +E A+  + G  V + GAGRTD+GVHA  QV  F   
Sbjct: 7   VGYDGTDYHGFQRQPGLRTVQGVLEGALGELAGREVSIVGAGRTDAGVHARGQVIAF--- 63

Query: 68  REWVPVILCK--ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
            EW   I  +        ++ + + + NL    + FH RFSA+ + Y Y +     P   
Sbjct: 64  -EWPGPIPWQRLERVLLRRLPEDLVVSNLEPAPESFHPRFSAVGKCYRYTLDQGVYPSVF 122

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVNSFG 181
            +   W +P  +D  +MR AA    G HD+T+F    C AS+P    +RT+    +    
Sbjct: 123 LRRYTWHVPTQMDLGSMRRAALAAAGTHDYTSF----CAASTPVQNKVRTVYAIRLAEEP 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + V    FL+  +R  VG+L  VG GK +   +   L A+DR+  G  AP +GL  
Sbjct: 179 PFVHLYVFGNGFLYQMVRILVGTLVEVGIGKRSVESISGILAARDRRAAGVTAPAKGLTL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 WDVYY 243


>gi|189467951|ref|ZP_03016736.1| hypothetical protein BACINT_04345 [Bacteroides intestinalis DSM
           17393]
 gi|189436215|gb|EDV05200.1| hypothetical protein BACINT_04345 [Bacteroides intestinalis DSM
           17393]
          Length = 253

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 84/248 (33%), Positives = 118/248 (47%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + +A+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGDSVQECLMRALATLMRREVEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V     LN  L     ISI  +  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDEPLDTVFFTDKLNRLLPPD--ISIYRIRAVKPDAHARFDATARMYKYYVTTVK 118

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +P   + + R +  P   D E M  AA+ L    DFT+F  +H    +    I H     
Sbjct: 119 SPFNRQYRCRLFQAP---DFERMNEAARILFDYTDFTSFSKLHTDVKTNNCRIMHAAWTQ 175

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             ++  +  + A  FL   +R+ VG+L  VG GK T     + ++ +DR + G   P   
Sbjct: 176 VDDVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTVEGFRRVIEQKDRCKAGTSVPGNA 235

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 236 LFLVDVTY 243


>gi|315919940|ref|ZP_07916180.1| tRNA pseudouridine synthase A [Bacteroides sp. D2]
 gi|313693815|gb|EFS30650.1| tRNA pseudouridine synthase A [Bacteroides sp. D2]
          Length = 260

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/240 (34%), Positives = 116/240 (48%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   VAHFD  
Sbjct: 1   MAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLMVAHFDSD 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  +   LN  L     ISI  +  V    H RF A  R+Y Y + T + P    +
Sbjct: 61  ELLDTTSVTDKLNRLLPPD--ISIYRVCRVRPDAHVRFDATARTYKYYVTTSKYP--FNR 116

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
              W +   L+ E M  AA  L   +DFT+F  +H    + I  I H +     +   + 
Sbjct: 117 QYRWRLYNQLNYERMNEAAHILFEYNDFTSFSKLHTDVKTNICHITHAEWTQEEDATWVF 176

Query: 188 VV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L+  +VEY
Sbjct: 177 TIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQALFLVNVEY 236


>gi|157414138|ref|YP_001485004.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9215]
 gi|166991165|sp|A8G737|TRUA_PROM2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157388713|gb|ABV51418.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9215]
          Length = 268

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 120/247 (48%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+G  Y GWQ+QKN +++Q  +E A+F +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGYHYSGWQKQKNATTVQEILESALFKITNHTVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN  L    TI IL    V   +HA +SA+ R Y Y I   +
Sbjct: 61  VVHFDIDSVIPGFSYSNILNNLL--PSTIRILESVEVKNSWHACYSAVYRHYRYVINNGK 118

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    K LD   M  A++ + G HDF  F+       + +  I + D+  
Sbjct: 119 FPNLFINNWSWHRYQKVLDEVLMLHASKTMEGEHDFFAFQKSGSNRRNSVTLIKNIDIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +S         + + +    AP +GL
Sbjct: 179 VEDLILVDIKATGFLYGMVRLIVGQLVLVGEKKISSDIFIDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEY 246
            F +  Y
Sbjct: 239 CFVNAVY 245


>gi|160934132|ref|ZP_02081519.1| hypothetical protein CLOLEP_02995 [Clostridium leptum DSM 753]
 gi|156866805|gb|EDO60177.1| hypothetical protein CLOLEP_02995 [Clostridium leptum DSM 753]
          Length = 251

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 118/243 (48%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I Y+G  Y GWQ Q+N  S+Q   + A+  V G+   V G  RTDSGVHA +      
Sbjct: 8   LTIAYDGRAYHGWQIQENALSVQEVFQGALRQVIGDDFDVKGCSRTDSGVHANQYCISLK 67

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    L  ALN +L +   +++     V   FHAR+S   + Y Y I         
Sbjct: 68  TGHRIPCERLVAALNRFLPMD--MAVKGCRSVSLDFHARYSCKGKEYQYLIWNDPVRNPF 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSFGNLI 184
             GRA+     LD + +  AAQ  VG+HDFT+F ++ H +  +  R +    V+  G+L+
Sbjct: 126 LDGRAFHYWYPLDTDMLNQAAQAFVGKHDFTSFCTLDHRERDNMERMVKCCSVSREGSLV 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             RV A  FL+  +R  VG+L  +  GK     +   L+A+DR + GP A   GLY + V
Sbjct: 186 TFRVEADGFLYNMVRIMVGTLLRIAQGKIPEDGIPAILEAKDRSKAGPTARACGLYLNRV 245

Query: 245 EYS 247
            Y 
Sbjct: 246 FYE 248


>gi|256028207|ref|ZP_05442041.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289766139|ref|ZP_06525517.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289717694|gb|EFD81706.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
          Length = 245

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 123/243 (50%), Gaps = 15/243 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F     
Sbjct: 12  YDGSRYYGFQRQPNKITVQGEIEKILRIVTKEEINLISAGRTDRGVHANHQVSNF-YTSS 70

Query: 70  WVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +P+     +L +AL      S  I IL++  VD+ F+AR +A  R Y+Y I   + P  
Sbjct: 71  TIPIEKYKYLLTRAL------SKDIDILSVEEVDENFNARHNAKMREYIYIISWEKNP-- 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NL 183
            E      + + +D   +       VG HDF  FR   C +   IR I   +V  FG + 
Sbjct: 123 FEARYCKFVKEKIDVRKLEKIFSDFVGVHDFKNFRLNDCVSKVTIREIYQIEVKYFGESK 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I+I +   +FL +Q+R  VG+   +  G+     ++  L    R+    L   EGLY + 
Sbjct: 183 IKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIKLMLNDFTREYKKNLVEAEGLYLNK 242

Query: 244 VEY 246
           + Y
Sbjct: 243 INY 245


>gi|297180263|gb|ADI16482.1| pseudouridylate synthase [uncultured bacterium HF4000_05M23]
          Length = 273

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 119/248 (47%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ +++EY+G+ + G Q Q N  ++QG IE A+  +  E + VH A RTDSGVHA  QV
Sbjct: 1   MRFGLVVEYDGTNFHGSQLQSNARTVQGEIESALLQIFSEKIRVHFASRTDSGVHARGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD--KQFHARFSAIRRSYLYRIITR 119
             FD   +  P  + KALN +      I    L + D    F  R  A  R+Y+Y     
Sbjct: 61  GRFDAETDMPPDQIRKALNFHTTTDVRIRCAQL-VEDGPDGFDPRGDASARTYVYTFNDA 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS-PIRTIDHFDVN 178
            +  AL++     + K LD   M  A+Q LVG HDF +F        +  +R ++     
Sbjct: 120 PSEPALDRHYVTHVRKPLDEIAMNDASQALVGLHDFASFAGPKAPHDALTMRNVETASTT 179

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ IE ++ A +FLH QIR   G L  VG G      +   L   +R     + P +G
Sbjct: 180 RIGDSIEFKITANAFLHQQIRRIAGVLCDVGTGGSPVAVVGDLLATAERGAASHVMPAQG 239

Query: 239 LYFDSVEY 246
           L  + + Y
Sbjct: 240 LCLEKIAY 247


>gi|125623329|ref|YP_001031812.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|166228735|sp|A2RIH1|TRUA_LACLM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|124492137|emb|CAL97066.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|300070076|gb|ADJ59476.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 253

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/256 (31%), Positives = 130/256 (50%), Gaps = 17/256 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+Q Q N  ++Q  IEK +  L + E V++ G+GRTDSGVHA  
Sbjct: 1   MTRYKATIAYDGTDFAGFQSQTNQRTVQEEIEKVLSKLNSFEPVILQGSGRTDSGVHAFG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--- 116
           QV HFDL  +   +   +      +    I++  + +V   +HAR+    ++Y Y +   
Sbjct: 61  QVIHFDLNGKARDLERLR-FGLDTQTPADIAVKKVELVPDDWHARYQKHEKTYEYYLENS 119

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH-- 174
           +TR +P        +  P  L+ E M+ A   LVG+HDFT F +        +RTI    
Sbjct: 120 VTR-SPFHRHSKAYFRYP--LNFERMQGAMVKLVGQHDFTGFTASGSSVDDKVRTIYQAE 176

Query: 175 ---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
               D  +F  +         FL+ Q+R+ VG++  +G+ +   + ++K L +++R   G
Sbjct: 177 IIQLDKENFKFIFR----GNGFLYKQVRNMVGTVIKIGNDRMPVSQIDKILTSKNRNFAG 232

Query: 232 PLAPPEGLYFDSVEYS 247
           P A PEGLY   V+Y 
Sbjct: 233 PTAAPEGLYLKEVKYE 248


>gi|303230129|ref|ZP_07316898.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-134-V-Col7a]
 gi|302515190|gb|EFL57163.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-134-V-Col7a]
          Length = 261

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 127/245 (51%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+   G+Q+Q    G ++QG++EKA+ ++  E + ++GA RTD+GVHA  QV  
Sbjct: 6   LIVAYDGTDLAGYQKQPADKGITVQGALEKALSIICAEPIQIYGASRTDAGVHARFQVCA 65

Query: 64  FDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +PV  + +A  A+L     I +     +   +  R +   + Y+Y I  R+  
Sbjct: 66  FQ-TSGSIPVKNIPRATIAHL--PKDIVVTEAVEIPLDWKPRHNIFGKEYIYSIYNREIA 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             + +   W + K LD E MR A + L G HDF+T +  +     P++TI    +     
Sbjct: 123 DPMGQRYHWHVKKPLDVEAMRQAGKALEGTHDFSTLKGANTTPVDPVKTIYAIGIKEKAG 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I+I VV   FL+  +R+  G L  +G G+ +   + + L A+DRK  G  AP +GL  +
Sbjct: 183 RIDISVVGDGFLYHMVRNIAGLLVDIGLGRKSVARIPELLAAKDRKRIGKTAPAQGLVLE 242

Query: 243 SVEYS 247
            + ++
Sbjct: 243 EIFFT 247


>gi|320353071|ref|YP_004194410.1| tRNA pseudouridine synthase A [Desulfobulbus propionicus DSM 2032]
 gi|320121573|gb|ADW17119.1| tRNA pseudouridine synthase A [Desulfobulbus propionicus DSM 2032]
          Length = 274

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 84/253 (33%), Positives = 123/253 (48%), Gaps = 14/253 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           ++I Y+G  Y GWQRQ+ G ++IQ  +E+ +  +  E + +HGAGRTD+GVHAL  VAHF
Sbjct: 7   LLIAYDGGNYCGWQRQRQGEATIQEELEQRLSHLCEEPITLHGAGRTDAGVHALGMVAHF 66

Query: 65  DLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
              R  +PV+   K LNA L     I IL        FH+RFSA+ ++Y Y   T     
Sbjct: 67  H-TRAAIPVVAFFKGLNALL--PPDIRILAAEEASATFHSRFSALGKTYRYDFFTGAVQC 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI------RTIDHFDV 177
              +      P   D + +R A   LVGRHDF++F     +  + I      RT+     
Sbjct: 124 PSTRLHRAHFPGPFDPKRLRTALTQLVGRHDFSSFERSGSRDKTAIDGRGAVRTLYEIRC 183

Query: 178 N---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +      +   + V    FL   +R   G+L  +G GK     +   L A+DR + G  A
Sbjct: 184 SPRLGCEDFWSLHVTGDGFLRQMVRILAGTLIEIGHGKRPEEAIAAILAARDRTQAGLTA 243

Query: 235 PPEGLYFDSVEYS 247
           P  GL+ + + Y 
Sbjct: 244 PACGLFLERLYYP 256


>gi|296119322|ref|ZP_06837890.1| tRNA pseudouridine synthase A [Corynebacterium ammoniagenes DSM
           20306]
 gi|295967714|gb|EFG80971.1| tRNA pseudouridine synthase A [Corynebacterium ammoniagenes DSM
           20306]
          Length = 297

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 89/263 (33%), Positives = 130/263 (49%), Gaps = 22/263 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           ++R    I Y+G+ + GW  QK    ++QG +E+ + ++    + +  AGRTD+GVHA  
Sbjct: 14  LVRLRFDIAYDGTDFHGWASQKGQLRTVQGVLEQCLTMILRHPIELTVAGRTDAGVHAAG 73

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAH D+  E +        P  L + L     + D I I ++S   + F ARFSA+RR 
Sbjct: 74  QVAHADVPVESLQQRSIDGEPAKLVRRLAKL--VDDDIRIHSVSFAPEGFDARFSALRRH 131

Query: 112 YLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YRI T +A   P  L     W  P  +D + M+ AA  LVG HDF  F      A++ 
Sbjct: 132 YVYRITTEEAGALPTRLRDTATWTRP--VDIDLMQQAATTLVGLHDFAAFCKAKPHATT- 188

Query: 169 IRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           IR +  F        S  NL E  V A +F  + +RS VG    VG+G+     +E  L 
Sbjct: 189 IRDLQEFYWVDASTPSEPNLYEAHVSADAFCWSMVRSLVGCCLAVGEGRRDINFVEAMLG 248

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
             +R    P+A  +GL    V+Y
Sbjct: 249 ESERSSSIPVAAAKGLSLVGVDY 271


>gi|329957112|ref|ZP_08297679.1| tRNA pseudouridine synthase A [Bacteroides clarus YIT 12056]
 gi|328523380|gb|EGF50479.1| tRNA pseudouridine synthase A [Bacteroides clarus YIT 12056]
          Length = 251

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 117/247 (47%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  L  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSEVPLDVTFMADKLNRLLPPD--ISVYRLRAVRPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    + R  L  ++ D E M  AAQ L    DFT+F  +H    +    I H      
Sbjct: 119 MPFD-RRYRCRLF-QTPDFERMNEAAQTLFEYTDFTSFSKLHTDVKTNNCKIMHAAWTQV 176

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +  +  + A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   L
Sbjct: 177 DEVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTIEGFRRVIEQKDRCRAGTSVPGNAL 236

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 237 FLVDIAY 243


>gi|162446996|ref|YP_001620128.1| tRNA pseudouridine synthase A [Acholeplasma laidlawii PG-8A]
 gi|161985103|gb|ABX80752.1| pseudouridylate synthase [Acholeplasma laidlawii PG-8A]
          Length = 240

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 119/245 (48%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY  I  Y+G+ Y G+Q+Q N   IQ  IEKA  L+T   +    A RTD GVHAL QV
Sbjct: 1   MRYKAIFSYDGTNYSGYQKQINQLGIQTVIEKAFRLMTQIDIETFAASRTDKGVHALHQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E        ALN   ++   I ++ ++ V   FHAR SA  + Y+Y+I   + 
Sbjct: 61  LHFDSDIELTSDQWVDALNK--RLPTDIRLMKVTPVKDNFHARHSAKSKRYIYKIA--KQ 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  + +G   L  K  D + ++     +VG HDF+ F S + +   PI+TI  FD     
Sbjct: 117 PSTVFRGNHELYVKHFDIDLVKDHLHTIVGTHDFSGF-SPNKEHKPPIKTIYSFDYKETK 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                 +   SFL   +R  +G++  V   K     LE  L+ ++R+     A  +GLY 
Sbjct: 176 THYIFSIHGNSFLRYMVRIIMGNVIAVATNKKPQNQLEILLETKNRELSAKTADAKGLYL 235

Query: 242 DSVEY 246
             + Y
Sbjct: 236 KHIYY 240


>gi|328948028|ref|YP_004365365.1| tRNA pseudouridine synthase A [Treponema succinifaciens DSM 2489]
 gi|328448352|gb|AEB14068.1| tRNA pseudouridine synthase A [Treponema succinifaciens DSM 2489]
          Length = 261

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 84/256 (32%), Positives = 128/256 (50%), Gaps = 12/256 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK---NGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M    + + Y+G+ + GWQRQ    NGS   ++QG IE A+F +    V + G+GRTDSG
Sbjct: 1   MTNILLTVSYDGTDFCGWQRQDKSDNGSPVRTVQGEIENALFKMLKVPVKLSGSGRTDSG 60

Query: 55  VHALRQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           VHA  Q A+F+   + +P     +ALN  L     I IL    V+K F +RF A  R Y 
Sbjct: 61  VHAAGQAANFESPIDTIPCENYVRALNGIL--PQDIRILKARKVEKDFSSRFCATSRLYR 118

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I T+  P A E    W I    + + +      L G  D  +F +    + S  R ID
Sbjct: 119 YFIQTKNPPFASESRYRWFISFRPEIDLLNEMCSCLRGEIDCASFAASGDSSLSTKRYID 178

Query: 174 H---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +   F      +L+  ++ A +FL   +RS  G+L  +   K +  + +K L+++DR + 
Sbjct: 179 NAFFFWNKENPDLLVFQIEANAFLWKMVRSITGTLIQLAQKKCSPNEFKKILESRDRTKA 238

Query: 231 GPLAPPEGLYFDSVEY 246
           G  APP GL+   V++
Sbjct: 239 GITAPPTGLFLWEVKF 254


>gi|237743728|ref|ZP_04574209.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
 gi|229432759|gb|EEO42971.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
          Length = 245

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 122/243 (50%), Gaps = 15/243 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GSGY+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F     
Sbjct: 12  YDGSGYYGFQRQPNKITVQGEIEKILRIVTKEEINLISAGRTDRGVHANHQVSNF-YTSS 70

Query: 70  WVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +P+     +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I   + P  
Sbjct: 71  TIPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKMREYVYIISWEKNP-- 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NL 183
            E      + + +D   +       VG HDF  FR   C +   IR I   +V  FG + 
Sbjct: 123 FEARYCKFVKEKIDVRKLEKIFSDFVGVHDFKNFRLNDCVSKVTIREIYQIEVKYFGESK 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I+I +   +FL +Q+R  VG    +  G+     +   L    R+    L   EGLY + 
Sbjct: 183 IKIYIKGSAFLKSQVRIMVGIALEIYYGRLPENHIRLMLNDFTREYKKNLVEAEGLYLNK 242

Query: 244 VEY 246
           + Y
Sbjct: 243 INY 245


>gi|123969273|ref|YP_001010131.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. AS9601]
 gi|166228750|sp|A2BTB3|TRUA_PROMS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123199383|gb|ABM71024.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. AS9601]
          Length = 268

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 120/247 (48%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS Y GWQ+QKN ++IQ  ++KA+  +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGSHYSGWQKQKNANTIQEILDKALLKITNHTVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN+ L    TI IL    V   +HA +SA  R Y Y I   +
Sbjct: 61  VIHFDIDCVIPGNSYSDVLNSLL--PSTIRILESVEVKDSWHACYSASYRHYRYVINNSK 118

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    K LD   M  A++ + G HDF  F+       + I  I + DV  
Sbjct: 119 FPNLFINNWSWHRYQKVLDEVLMLNASKKMEGEHDFFAFQKSGSNRQNSITKIKNIDVKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +          + + +    AP +GL
Sbjct: 179 VEDLILVDIKATGFLYGMVRLIVGQLVLVGEKKISPEIFTDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEY 246
            F +  Y
Sbjct: 239 CFVNAVY 245


>gi|260495597|ref|ZP_05815722.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_33]
 gi|260196939|gb|EEW94461.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_33]
          Length = 245

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 122/243 (50%), Gaps = 15/243 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F     
Sbjct: 12  YDGSRYYGFQRQPNKITVQGEIEKILRIVTKEEINLISAGRTDRGVHANHQVSNF-YTSS 70

Query: 70  WVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +P+     +L +AL       + I IL++  VDK F+AR +A  R Y+Y I   + P  
Sbjct: 71  TIPIEKYKYLLTRAL------PNDIDILSVEEVDKNFNARHNAKMREYVYIISWEKNP-- 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NL 183
            E      + + +D   +       VG HDF  FR   C +   IR I   +V  FG + 
Sbjct: 123 FEARYYKFVKEKIDVRKLEKIFSDFVGVHDFKNFRLNDCVSKVTIRKIYQIEVKYFGESK 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I+I +   +FL +Q+R  VG+   +  G+     +   L    R+    L   EGLY + 
Sbjct: 183 IKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLNDFTREYKKNLVEAEGLYLNK 242

Query: 244 VEY 246
           + Y
Sbjct: 243 INY 245


>gi|270307870|ref|YP_003329928.1| pseudouridylate synthase [Dehalococcoides sp. VS]
 gi|270153762|gb|ACZ61600.1| pseudouridylate synthase [Dehalococcoides sp. VS]
          Length = 246

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  + 
Sbjct: 1   MVIEYEGTMYSGFQIQDKGATIQGELETAIQKLTNEKTRVSGSGRTDAGVHAAYQVVSYL 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +   LN YL     I++  +  V + F  R  AI R Y Y I+  +    L
Sbjct: 61  SESSLGLEKIKGGLNYYLPTD--IAVKEVYFVAENFDVRRRAISREYSYHILNSKTRSPL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
            + +AW +P  LD + M  A + L G HDF  F  S+  +    +R ++   ++   + +
Sbjct: 119 ARLQAWQVPYKLDTKLMEQAFKMLEGEHDFVAFASSLGPEIKKTVRRVNWTRLDIAEDRL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+ A SFL  Q+R+ +G+L  +G G  +  +     +A+     GP AP  GL    V
Sbjct: 179 VFRIEANSFLTHQVRNTIGTLVELGRGILSMREFGALFEAKTPGLAGPAAPACGLSLVRV 238

Query: 245 EY 246
            Y
Sbjct: 239 NY 240


>gi|78045100|ref|YP_361085.1| tRNA pseudouridine synthase A [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77997215|gb|ABB16114.1| tRNA pseudouridine synthase A [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 246

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 126/254 (49%), Gaps = 19/254 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +  + + I Y+G+ + G+Q+QKN   +IQG +E+ +  +  E V V GAGRTD+GVHAL 
Sbjct: 4   LPNFKLTIAYDGTNFAGFQKQKNTPQTIQGILEEKLHKILKEPVKVIGAGRTDAGVHALG 63

Query: 60  QVAHFDLVREW------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           QV +F     W      +P IL   L         I +L   IV   FHAR+SA ++ Y 
Sbjct: 64  QVVNFSA--PWKAPVDKIPEILNNTL------PTAIRVLEAEIVPDDFHARYSARKKEYR 115

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y +     P    +  AW +P+ LD E +  A ++L+G HDF+ F +      +PI+T+ 
Sbjct: 116 YYLY-YGPPSPFYERYAWALPQKLDREKVAKALEYLIGTHDFSGFGAAGSSGKNPIKTMF 174

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG-DGKWTSTDLEKALQAQDRKECGP 232
                  G L     VA SFL+   R   G+L  +G +G      + + L   ++K  G 
Sbjct: 175 EASYREDGFLGYFTFVADSFLYKMARILTGTLVEIGLNGH--PERVREILTTGNKKLAGK 232

Query: 233 LAPPEGLYFDSVEY 246
            AP  GL+   V Y
Sbjct: 233 TAPAHGLFLVKVFY 246


>gi|283853830|ref|ZP_06371050.1| tRNA pseudouridine synthase A [Desulfovibrio sp. FW1012B]
 gi|283570781|gb|EFC18821.1| tRNA pseudouridine synthase A [Desulfovibrio sp. FW1012B]
          Length = 270

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 83/253 (32%), Positives = 120/253 (47%), Gaps = 8/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+G+ + GWQ Q    G ++QG +E+A+  + GE V + GAGRTDSGVHA+
Sbjct: 1   MPRLRLTLAYDGTAFAGWQLQAPGRGRTVQGCLEEALATLCGEPVRIFGAGRTDSGVHAM 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   KALNA L     +S+    +V   FHARF A  + Y Y + T
Sbjct: 61  AQVAHVDVPEGRAAIPWQKALNALLPAD--MSVAGAELVPDGFHARFCATGKVYHYTLWT 118

Query: 119 RQAP-LALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                L   +   W + +   LD   M   A    G HDF  F++      +  R +   
Sbjct: 119 EPGHVLPWRRPYVWDVGRYGRLDVAAMDACAACFAGFHDFAAFQNAGSDVKTTTRLVHGV 178

Query: 176 D-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             + + G  +  R  A  FL   +R+ +G+L  VG GK +  D+   L    R+     A
Sbjct: 179 TRLATGGPEMVWRFHAEGFLKQMVRNLMGALVAVGRGKVSPEDIRSVLTQGQRRLAPQTA 238

Query: 235 PPEGLYFDSVEYS 247
           P  GL    VEY 
Sbjct: 239 PASGLCLVVVEYG 251


>gi|160942942|ref|ZP_02090181.1| hypothetical protein FAEPRAM212_00419 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445843|gb|EDP22846.1| hypothetical protein FAEPRAM212_00419 [Faecalibacterium prausnitzii
           M21/2]
          Length = 254

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 122/249 (48%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + + + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL   
Sbjct: 1   MNFLLTLAYDGTNYCGFQVQPNGRSVAATFQDALEAVLGSRPDIKGCSRTDAGVHALGFR 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F       P  L  ALN +L     I +L    V + FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPPQKLPLALNQHLPPD--IRVLAAQTVPEDFHARYAAHTKTYLYRIHNHPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDVN 178
               +      +P+ LD   M+ AAQ  VG HDF    +    A      +RTI    V 
Sbjct: 119 DSPFDAAYYTRVPRRLDEAAMQAAAQQFVGTHDFLALCAAGSSAAAHGDTVRTITDCHVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ ++I V A  +L+  +R   G+L  VG G+  + D+   L ++DR   GP  P +G
Sbjct: 179 RRGDEVDIEVTADGYLYNMVRILAGTLCEVGAGRLRAADIPAILASRDRSRAGPTLPAKG 238

Query: 239 LYFDSVEYS 247
           L+   V+Y 
Sbjct: 239 LFLKCVDYP 247


>gi|255536203|ref|YP_003096574.1| tRNA pseudouridine synthase A [Flavobacteriaceae bacterium 3519-10]
 gi|255342399|gb|ACU08512.1| tRNA pseudouridine synthase A [Flavobacteriaceae bacterium 3519-10]
          Length = 245

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 125/250 (50%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y+G  YFG+Q Q    +IQ  +EKA+  +    +   GAGRTD+GVHA +  
Sbjct: 1   MRYFIEFSYHGKNYFGYQIQPREITIQQELEKALSTLLRAEIKTTGAGRTDTGVHAKKMY 60

Query: 62  AHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           AHFD    V + +P      LN++L     I++  +  V    HARF A  R+Y Y I  
Sbjct: 61  AHFDTEIAVEDNLPY----RLNSFL--PQDIAVSRIFKVKDDLHARFDATFRTYEYYISL 114

Query: 119 RQAPLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            + P +  +  +W I  ++L+   M  A + L    DFT+F  +H    +    I     
Sbjct: 115 AKNPFS--QDFSWQIRNRTLEIGKMNEACRILFEYEDFTSFSKLHTDNKTNNCKIYKAFW 172

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              GN ++  V A  FL   +R+ VG++  +G+GK    DL K ++A+DR   G  AP +
Sbjct: 173 EQNGNELKFTVSADRFLRNMVRAIVGTMVEIGNGKIQPMDLRKIIEAKDRSFAGTSAPAQ 232

Query: 238 GLYFDSVEYS 247
           GL+   V Y 
Sbjct: 233 GLFLVDVGYD 242


>gi|300932964|ref|ZP_07148220.1| tRNA pseudouridine synthase A [Corynebacterium resistens DSM 45100]
          Length = 324

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 88/264 (33%), Positives = 132/264 (50%), Gaps = 26/264 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + + Y+G+ + GW  Q    ++QG +E+ + LVT   V +  AGRTD+GVHA  Q
Sbjct: 40  MVRVRLDVAYDGTDFHGWAAQFGLRTVQGVLEEKLSLVTRHAVQLTVAGRTDAGVHADGQ 99

Query: 61  VAHFDLVREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           VAHFD+            P  L + L+  L     + +   S     F ARFSA+RR Y+
Sbjct: 100 VAHFDVPATTFTQRSLQRPGDLVRRLSRMLPAD--VRVHGASEAPVGFDARFSALRRHYV 157

Query: 114 YRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           YR+ T  A   P+ +     W  P  +D + ++ A++ LVG +DF  F    C+A     
Sbjct: 158 YRVTTATAGPRPVRVRDTARWRRP--IDLDKVKAASEVLVGLNDFAAF----CKAREGAT 211

Query: 171 TIDH------FDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           TI        FDV++       E RV A +F  + +RS VG++  VG+GK       + L
Sbjct: 212 TIRELQQFQWFDVSTPAEPETYEARVAADAFCWSMVRSLVGAVLTVGEGKRDGDFTAELL 271

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
           +  +R    P+AP EGL    V+Y
Sbjct: 272 KQNERSSKVPVAPAEGLNLVQVDY 295


>gi|182415339|ref|YP_001820405.1| tRNA pseudouridine synthase A [Opitutus terrae PB90-1]
 gi|177842553|gb|ACB76805.1| tRNA pseudouridine synthase A [Opitutus terrae PB90-1]
          Length = 268

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 128/245 (52%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+  +  Y+G  + GWQ Q +G+S+Q +IE  +  + G  V +HG+GRTD+GVHAL QV 
Sbjct: 10  RWKCVCAYDGGHFAGWQSQVSGASVQDAIEARLREMFGREVRIHGSGRTDAGVHALGQVF 69

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD      P  L  AL A  ++   I I  +  V  +FHARF A  + Y YR+    A 
Sbjct: 70  HFDAHWRHGPEKLLAALRA--RLPSAIQIKTVCAVTPEFHARFQASGKRYTYRLHLGDAD 127

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVNSFG 181
               +  +W + + LD   M  AA  L GRHDF  F +++  A    +R +   DV   G
Sbjct: 128 -PFTRPYSWPVFRPLDLAAMNAAAAVLRGRHDFRAFTALNGPARVDTVRDLRRLDVRRRG 186

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I   A  FL+  +RS VG L  VG+GK T  D+   L ++ R      APP+GL+ 
Sbjct: 187 RVIRIIAEADGFLYKMVRSLVGVLVAVGEGKLTVHDVRAILASRQRTAVVQTAPPQGLFL 246

Query: 242 DSVEY 246
             V Y
Sbjct: 247 VRVFY 251


>gi|303231239|ref|ZP_07317977.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-049-V-Sch6]
 gi|302514146|gb|EFL56150.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-049-V-Sch6]
          Length = 261

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 125/248 (50%), Gaps = 12/248 (4%)

Query: 6   MIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+   G+Q+Q    G ++QG++EKA+ ++  E + ++GA RTD+GVHA  QV  
Sbjct: 6   LIVAYDGTDLAGYQKQPADKGITVQGALEKALSIICAEPIQIYGASRTDAGVHARFQVCA 65

Query: 64  FD----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           F     +  E +P      L   + +++ I I         +  R +   + Y+Y I  R
Sbjct: 66  FQTSGSIPVENIPRATIAHLPKDIVVTEAIEI------PLDWKPRHNIFGKEYIYSIYNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +   W + K LD E M  A + L G HDF+T +  +     P++TI    +  
Sbjct: 120 EIADPMGQRYHWHVKKPLDVEAMHQAGKALEGTHDFSTLKGANTTPVDPVKTIYAIGIKE 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I+I VV   FL+  +R+  G L  VG G+ +   + + L A+DRK  G  AP +GL
Sbjct: 180 KAGRIDISVVGDGFLYHMVRNIAGLLVDVGLGRKSVAQIPELLAAKDRKRIGKTAPAQGL 239

Query: 240 YFDSVEYS 247
             + + ++
Sbjct: 240 VLEEIFFT 247


>gi|313145437|ref|ZP_07807630.1| tRNA pseudouridine synthase A [Bacteroides fragilis 3_1_12]
 gi|313134204|gb|EFR51564.1| tRNA pseudouridine synthase A [Bacteroides fragilis 3_1_12]
          Length = 255

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 119/246 (48%), Gaps = 6/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQ Q NG SIQ  + KA+         V GAGRTD+GVHA   VA
Sbjct: 8   RYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRRDTEVIGAGRTDAGVHASLMVA 67

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD   E +    + + LN  L     IS+  +  V    HARF A  R+Y Y I T + 
Sbjct: 68  HFDYEGEVLDTDKVTEKLNRLL--PQDISVYKVCRVRPDAHARFDATARTYKYYITTVKY 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +     
Sbjct: 126 P--FNRQYRYRIHNPLDFQKMNEAALTLFHYTDFTSFSKLHTDVKTNICKIMHAEWTQED 183

Query: 182 NLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               +  + A  FL   +R+ VG+L  VG GK +     + ++ QDR + G  AP   L+
Sbjct: 184 EYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDGFRRIIEQQDRCKAGTSAPGNALF 243

Query: 241 FDSVEY 246
             +VEY
Sbjct: 244 LVNVEY 249


>gi|158334430|ref|YP_001515602.1| tRNA pseudouridine synthase A [Acaryochloris marina MBIC11017]
 gi|158304671|gb|ABW26288.1| tRNA pseudouridine synthase A [Acaryochloris marina MBIC11017]
          Length = 292

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 85/256 (33%), Positives = 118/256 (46%), Gaps = 15/256 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ    S+Q  IE  +  +    V +HGAGRTDSGVHA  QVA
Sbjct: 10  RVALVIQYLGTHFHGWQRQPQHRSVQADIEDTLAEIVQHPVTLHGAGRTDSGVHAAAQVA 69

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+            LNA  ++   I I   ++V   +HARFSA  R Y Y + T   P
Sbjct: 70  HFDVESPIPAHRWASVLNA--RLPQDILIRGSALVPSDWHARFSATWRRYRYTLYTDPCP 127

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID-------- 173
               +  +W    + LD + M+ A   L+GRH    F      +S P   +D        
Sbjct: 128 NLFLRPYSWHYYYQPLDVQRMQAALDPLIGRHHLAAFHR--AGSSRPHSWVDVHEATCVQ 185

Query: 174 --HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
               +      LI+I V A  FL+  +R  VG L  VG G  +     +  QA+ R +  
Sbjct: 186 RPTVEAKDSSPLIQIEVQASGFLYGMMRLLVGLLVQVGRGLRSPDSFTELWQAERRDQVK 245

Query: 232 PLAPPEGLYFDSVEYS 247
             AP +GL    V Y 
Sbjct: 246 YSAPAKGLCLLRVGYP 261


>gi|116493132|ref|YP_804867.1| pseudouridylate synthase [Pediococcus pentosaceus ATCC 25745]
 gi|116103282|gb|ABJ68425.1| Pseudouridylate synthase [Pediococcus pentosaceus ATCC 25745]
          Length = 248

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 128/253 (50%), Gaps = 13/253 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +RY +I+ Y+G+ + G+Q Q N  +++G +++ +  +    T EI V +G+GRTD+GVHA
Sbjct: 1   MRYKIILAYDGTNFAGFQMQPNQRTVEGVLKRIVNKIAKNPTPEISV-YGSGRTDAGVHA 59

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV HFDL  E     +  ALN+ L +   + +  + IVD+ FHARF+   + Y YR+ 
Sbjct: 60  LGQVVHFDLSIEMSERSMLHALNSQLPLD--MQVKKVEIVDETFHARFTTHGKKYQYRMA 117

Query: 118 TRQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
             Q   P        W  P ++    ++ A + L G HDF++F +        +RTI   
Sbjct: 118 LGQFVDPFKRNYTGHWKFPINIGL--IQKAIKDLEGTHDFSSFVASGSTVKDHVRTIYEA 175

Query: 176 DV--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            V  +   N I        FL+  +R  V  L  +G  +  + D+ +  + +DR +    
Sbjct: 176 KVWEDKKQNEIVFEFYGNGFLYNMVRIMVAVLVEIGSKRRPADDIPRLFEVKDRNQARGT 235

Query: 234 APPEGLYFDSVEY 246
           AP  GLY   V+Y
Sbjct: 236 APASGLYLKEVDY 248


>gi|212550510|ref|YP_002308827.1| tRNA pseudouridine synthase A [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|229557952|sp|B6YQE4|TRUA_AZOPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|212548748|dbj|BAG83416.1| tRNA pseudouridine synthase A [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
          Length = 249

 Score =  122 bits (307), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 119/246 (48%), Gaps = 4/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  Y GWQ Q NG ++Q  I++ + ++  + V + GAGRTD+GVHA   
Sbjct: 1   MNRYFIYLAYNGRNYCGWQIQPNGITVQQRIQQCLSILLRKSVTIIGAGRTDAGVHANLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD         L K LN  L     I I  +  V K  HARF AI R Y Y I  ++
Sbjct: 61  TAHFDWEEILSTTSLTKRLNGILPCD--ILIYKIIPVKKNAHARFDAISRKYKYYITYQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E+   + + + L+   M  A+  L    DFT+F  +H    + +  I   + N+ 
Sbjct: 119 NPFRNEQ--LFRLKQPLNKHLMNEASNILSEYSDFTSFCKLHSNTRTNVCRISKAEWNTV 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +    + A  FL   +RS VG++  +G  K + TD  K +++++        P   L+
Sbjct: 177 QGIDIFTIKADRFLRNMVRSIVGTMIDIGKNKLSITDFRKIIESKNHIMLKSSVPAHALF 236

Query: 241 FDSVEY 246
              +EY
Sbjct: 237 LTDIEY 242


>gi|255007737|ref|ZP_05279863.1| tRNA pseudouridine synthase A [Bacteroides fragilis 3_1_12]
          Length = 252

 Score =  122 bits (307), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 119/246 (48%), Gaps = 6/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQ Q NG SIQ  + KA+         V GAGRTD+GVHA   VA
Sbjct: 5   RYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRRDTEVIGAGRTDAGVHASLMVA 64

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD   E +    + + LN  L     IS+  +  V    HARF A  R+Y Y I T + 
Sbjct: 65  HFDYEGEVLDTDKVTEKLNRLL--PQDISVYKVCRVRPDAHARFDATARTYKYYITTVKY 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +     
Sbjct: 123 P--FNRQYRYRIHNPLDFQKMNEAALTLFHYTDFTSFSKLHTDVKTNICKIMHAEWTQED 180

Query: 182 NLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               +  + A  FL   +R+ VG+L  VG GK +     + ++ QDR + G  AP   L+
Sbjct: 181 EYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDGFRRIIEQQDRCKAGTSAPGNALF 240

Query: 241 FDSVEY 246
             +VEY
Sbjct: 241 LVNVEY 246


>gi|296111462|ref|YP_003621844.1| tRNA pseudouridine synthase A [Leuconostoc kimchii IMSNU 11154]
 gi|295832994|gb|ADG40875.1| tRNA pseudouridine synthase A [Leuconostoc kimchii IMSNU 11154]
          Length = 256

 Score =  122 bits (307), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 89/257 (34%), Positives = 133/257 (51%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIFLVTG---EIVVVHGAGRTD 52
           M RY  I+ Y+GSG+FG+Q Q KNG     ++QG + KA+  +     E + V GA RTD
Sbjct: 1   MPRYKAIVSYDGSGFFGFQVQTKNGIERQRTVQGELTKAVNQMAKNPTEPIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL  +     + K LN  L     + I  +  V   FHARF+   + Y
Sbjct: 61  TGVHAFGQVVHFDLPFDINENGVRKGLNTLLPRD--MLIKQVDKVTPDFHARFNTHAKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YR+ T+      ++         LD E ++ A   L+G HDF +F +   Q ++ IRTI
Sbjct: 119 IYRVSTQDFTDPFKRQYTGHFQWHLDIERIKSALPDLLGEHDFASFAASGNQTATTIRTI 178

Query: 173 DHFDVNSFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              DV    +  E+       +FL+ QIR  VG L  +G+G+    D+ + +  +DR++ 
Sbjct: 179 TRADVTIKPDDQELVFTFEGNAFLYNQIRIMVGVLLEIGNGRRDVHDILRLITVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
              AP  GLY D + Y+
Sbjct: 239 RFTAPASGLYLDQIYYN 255


>gi|297736816|emb|CBI26017.3| unnamed protein product [Vitis vinifera]
          Length = 326

 Score =  122 bits (307), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 129/254 (50%), Gaps = 11/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ ++I Y G+ Y GWQ Q++  +IQ  +EKA+   T    E + + GA RTD+GVHA  
Sbjct: 46  KWRLVIAYEGTRYSGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTDTGVHAWG 105

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +  +  +  ALN  L     I +  +S    +FHARFS   + Y Y+I  
Sbjct: 106 QVAHFLTPFNYDGLESIHAALNGLL--PPDIRVREISPAVPEFHARFSVKSKIYHYKIYN 163

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFD 176
                   +   +     L+   MR AA+H  G+HDF+ F   S + ++ +P++ I  FD
Sbjct: 164 DAVMDPFLRHYVYHSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKNIFRFD 223

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL--- 233
           VN  G L+++ V    FL+ Q+R+ V  L  +G        +   L  +DRKE       
Sbjct: 224 VNEMGALLQLEVEGSGFLYRQVRNMVALLLQIGREAIPPNIVPWILATRDRKELAKYALS 283

Query: 234 APPEGLYFDSVEYS 247
           APP GL   SV+Y+
Sbjct: 284 APPHGLCLMSVKYN 297


>gi|116511297|ref|YP_808513.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           SK11]
 gi|123320604|sp|Q031N1|TRUA_LACLS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116106951|gb|ABJ72091.1| Pseudouridylate synthase [Lactococcus lactis subsp. cremoris SK11]
          Length = 253

 Score =  122 bits (307), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 81/256 (31%), Positives = 130/256 (50%), Gaps = 17/256 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+Q Q N  ++Q  IEK +  L + E V++ G+GRTDSGVHA  
Sbjct: 1   MTRYKATIAYDGTDFAGFQSQTNQRTVQEEIEKVLSKLNSFEPVILQGSGRTDSGVHAFG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--- 116
           QV HFDL  +   +   +      +    I++  + +V   +HAR+    ++Y Y +   
Sbjct: 61  QVIHFDLNGKARDLERLR-FGLDTQTPADIAVKKVELVPDDWHARYQKHEKTYEYYLENS 119

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH-- 174
           +TR +P        +  P  L+ E M+ A   LVG+HDFT F +        +RTI    
Sbjct: 120 VTR-SPFHRHSKAYFRYP--LNFELMQGAMAKLVGQHDFTGFTASGSSVDDKVRTIYQAE 176

Query: 175 ---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
               D  +F  +         FL+ Q+R+ VG++  +G+ +   + ++K L +++R   G
Sbjct: 177 IIQLDKENFKFIFR----GNGFLYKQVRNMVGTVIKIGNDRMPVSQIDKILTSKNRNFAG 232

Query: 232 PLAPPEGLYFDSVEYS 247
           P A PEGLY   V+Y 
Sbjct: 233 PTAAPEGLYLKEVKYE 248


>gi|225432191|ref|XP_002275097.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 336

 Score =  122 bits (307), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 129/254 (50%), Gaps = 11/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ ++I Y G+ Y GWQ Q++  +IQ  +EKA+   T    E + + GA RTD+GVHA  
Sbjct: 56  KWRLVIAYEGTRYSGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTDTGVHAWG 115

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +  +  +  ALN  L     I +  +S    +FHARFS   + Y Y+I  
Sbjct: 116 QVAHFLTPFNYDGLESIHAALNGLL--PPDIRVREISPAVPEFHARFSVKSKIYHYKIYN 173

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFD 176
                   +   +     L+   MR AA+H  G+HDF+ F   S + ++ +P++ I  FD
Sbjct: 174 DAVMDPFLRHYVYHSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKNIFRFD 233

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL--- 233
           VN  G L+++ V    FL+ Q+R+ V  L  +G        +   L  +DRKE       
Sbjct: 234 VNEMGALLQLEVEGSGFLYRQVRNMVALLLQIGREAIPPNIVPWILATRDRKELAKYALS 293

Query: 234 APPEGLYFDSVEYS 247
           APP GL   SV+Y+
Sbjct: 294 APPHGLCLMSVKYN 307


>gi|289523335|ref|ZP_06440189.1| tRNA pseudouridine synthase A [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289503027|gb|EFD24191.1| tRNA pseudouridine synthase A [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 268

 Score =  122 bits (307), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 125/247 (50%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQ 60
           R+  ++ Y+GS + G+QRQK+  +++ ++E+A+ L+   G  V V GAGRTD GVHAL Q
Sbjct: 6   RFAALLSYDGSAFHGFQRQKDLPTVELALEEALNLLDKKGRRVKVTGAGRTDRGVHALGQ 65

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+     P  L KAL A L  S  I +  +  VD  FHAR SA+ R Y Y I    
Sbjct: 66  VVHFDISWPHGPTALRKALEANLPSS--IGVYEVVPVDFAFHARRSALWRKYAYFIWKGD 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             L       W   +  D +  +     + G HDF  F     + S   RTI    +   
Sbjct: 124 CRLPHLGRYVWWNRRGWDMDLAKKFLTMIEGFHDFGAFCRKADRPSDARRTIMEARIEEK 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+++ V  RSFL   +R  VG++  +  G+ +  ++ + L    R E GP AP +GL+
Sbjct: 184 GPLLKVSVTGRSFLTNMVRIIVGTMDEIATGRKSLEEVCRLLDGGSRGEAGPTAPAKGLF 243

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 244 LWEVRYD 250


>gi|288928084|ref|ZP_06421931.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330918|gb|EFC69502.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 244

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 123/250 (49%), Gaps = 15/250 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY +   Y+G+ Y GWQ Q N +S+Q  +++A+ L+    V + GAGRTD+GVHA   VA
Sbjct: 4   RYFIYFSYDGTSYHGWQIQPNANSVQAEMQRAMSLLLRHPVELVGAGRTDTGVHARTMVA 63

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+      V L   LN  L     I+I  +  VD   HARFSA +R+Y Y I   + P
Sbjct: 64  HFDVDTPIDAVQLTYKLNRVLPFD--ITINAIKAVDADMHARFSATKRTYHYYIHLDRDP 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI------RTIDHFD 176
               +  ++ + ++ D + M  AA+ L+   DF  F   H  A + +      R I   D
Sbjct: 122 FC--RAYSYALHQAPDFQLMNEAAEILLSHKDFGAFCKSHSDAKTTLCEVYEARWIKLSD 179

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                    +R+ A  FL   +R+ VG+L  VG  K T       L ++ R++ G   P 
Sbjct: 180 TK-----WHLRISANRFLRNMVRAIVGTLLDVGWHKITLEQFVDILHSKSRQQAGESVPG 234

Query: 237 EGLYFDSVEY 246
             L+ + V+Y
Sbjct: 235 HALFLEDVQY 244


>gi|282890956|ref|ZP_06299470.1| hypothetical protein pah_c032o038 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499171|gb|EFB41476.1| hypothetical protein pah_c032o038 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 254

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 124/246 (50%), Gaps = 7/246 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +II Y+G  + GWQ+   G SI+ ++E  +  +  E +++  A RTD+GVHA  QV +F 
Sbjct: 6   LIISYDGGRFLGWQKTSMGPSIEENLENVLHQILQEPIILQAASRTDAGVHAHEQVVNFF 65

Query: 66  LVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
             +   P+ L K  N+  + +   I +L+  I    FH     + + Y Y I T      
Sbjct: 66  TEK---PIDLNKITNSLNRLLPKDIVVLDAQIAPDHFHPTLDCLSKEYRYYISTGPIQPP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFDVN-SFG 181
             +  AW  P  LD E ++ AA+ LVG HDF+ F ++    S    +R + +  ++ +  
Sbjct: 123 NHRFYAWHCPGHLDKELIKKAAEQLVGTHDFSAFCNLKPSESYTHHVREVLNIQIHETDA 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +    +V+ +SFL+  +R+ VG+L  VG GK    D+   L  +DR + G  AP  GL  
Sbjct: 183 HHFYFQVMGKSFLYKMVRNIVGTLIFVGKGKLRCEDIPLLLSCRDRTKIGMTAPAHGLTL 242

Query: 242 DSVEYS 247
             + Y+
Sbjct: 243 YRLNYA 248


>gi|120402449|ref|YP_952278.1| tRNA pseudouridine synthase A [Mycobacterium vanbaalenii PYR-1]
 gi|119955267|gb|ABM12272.1| tRNA pseudouridine synthase A [Mycobacterium vanbaalenii PYR-1]
          Length = 299

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 87/262 (33%), Positives = 125/262 (47%), Gaps = 22/262 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G+I+ A+  V    VV   AGRTDSGVHA  QV
Sbjct: 21  VRLRLDIAYDGTDFAGWATQAGQRTVAGAIDDALSTVFRTPVVTRAAGRTDSGVHATGQV 80

Query: 62  AHFDLVREWVPVI--------------LCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           AH D+  + +P                L + L   L   + + +  ++     F ARFSA
Sbjct: 81  AHVDVPADALPYAYPRTTRPGEAEFGPLVRRLGRMLP--EDVRVREITRAAPGFDARFSA 138

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           +RR YLYR+ T  AP  +E   A  +   P+ LD   M  AA+ LVG HDF  F   H  
Sbjct: 139 LRRHYLYRLST--APYGVEPAEARFVTPWPRPLDVAAMAAAARELVGLHDFAAF-CRHRD 195

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            ++ IR +   D    G+ +E+ V A +F    +RS VG+L  VG+ +  +      L A
Sbjct: 196 GATTIRELQRLDCVRDGDRVEVHVSADAFCWNMVRSLVGALLAVGEHRRDAAWCAALLDA 255

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
             R      AP  GL    V+Y
Sbjct: 256 TGRSSDFAAAPARGLTLVGVDY 277


>gi|73748346|ref|YP_307585.1| tRNA pseudouridine synthase A [Dehalococcoides sp. CBDB1]
 gi|289432394|ref|YP_003462267.1| tRNA pseudouridine synthase A [Dehalococcoides sp. GT]
 gi|73660062|emb|CAI82669.1| tRNA pseudouridine synthase A [Dehalococcoides sp. CBDB1]
 gi|288946114|gb|ADC73811.1| tRNA pseudouridine synthase A [Dehalococcoides sp. GT]
          Length = 246

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  + 
Sbjct: 1   MVIEYEGTRYSGFQIQDKGATIQGELETAIRKLTSEQTRVSGSGRTDAGVHAAYQVVSYL 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +   LN YL     I++  +  V + F  R  AI R Y Y I+  +    L
Sbjct: 61  TESSLGLEKIKGGLNYYL--PPDIAVKEVHFVAENFDVRRRAISREYSYHILNSKTRSPL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
            + +AW +P  LD + M  A + L G HDF  F  S+  +    +R ++   ++   + +
Sbjct: 119 ARLQAWQVPYKLDIKLMEQAFKMLEGEHDFIAFASSLGPEIKKTVRRVNWTRLDIVEDRL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +R+ A SFL  Q+R+ +G L  +G G  +  +     +A+     GP AP  GL    V
Sbjct: 179 ILRIEANSFLTHQVRNTIGVLVELGRGTISMGEFGALFEAKTPGLAGPAAPACGLSLVRV 238

Query: 245 EY 246
            Y
Sbjct: 239 NY 240


>gi|255693609|ref|ZP_05417284.1| tRNA pseudouridine synthase A [Bacteroides finegoldii DSM 17565]
 gi|260620585|gb|EEX43456.1| tRNA pseudouridine synthase A [Bacteroides finegoldii DSM 17565]
          Length = 254

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 122/248 (49%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +  A+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMNALSTFLRREIEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  +  V  + HARF A  R+Y Y + T +
Sbjct: 61  VAHFDYDEPLDTESVADKLNRLLPPD--ISVYRVCRVRPEAHARFDATARTYKYYVTTAK 118

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P   + + R +     LD E M  AA+ L    DFT+F  +H    + I  I H +   
Sbjct: 119 YPFNRQYRCRVY---SPLDYERMNEAAKVLFEYTDFTSFSKLHTDVKTNICHITHAEWTR 175

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             +   +  + A  FL   +R+ VG+L  VG GK +     + ++ +DR + G  AP + 
Sbjct: 176 EEDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLSIEGFRRIIEQKDRCKAGTSAPGQA 235

Query: 239 LYFDSVEY 246
           L+  +VEY
Sbjct: 236 LFLVNVEY 243


>gi|218129428|ref|ZP_03458232.1| hypothetical protein BACEGG_01005 [Bacteroides eggerthii DSM 20697]
 gi|317477530|ref|ZP_07936755.1| tRNA pseudouridine synthase A [Bacteroides eggerthii 1_2_48FAA]
 gi|217988158|gb|EEC54481.1| hypothetical protein BACEGG_01005 [Bacteroides eggerthii DSM 20697]
 gi|316906331|gb|EFV28060.1| tRNA pseudouridine synthase A [Bacteroides eggerthii 1_2_48FAA]
          Length = 251

 Score =  122 bits (306), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 116/248 (46%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDAPLDVDFMADKLNRLLPPD--ISVYRLRAVRPDAHARFDATARMYKYYVTTAK 118

Query: 121 APLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P   + + R +  P   D E M  AAQ L    DFT+F  +H    +    I H     
Sbjct: 119 MPFDRQYRCRLFQTP---DFERMNEAAQTLFEYTDFTSFSKLHTDVKTNNCKIMHAAWTQ 175

Query: 180 FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +  +  + A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   
Sbjct: 176 VDEVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTVEGFRRIIEQKDRCRAGTSVPGNA 235

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 236 LFLVDVTY 243


>gi|57234742|ref|YP_181248.1| tRNA pseudouridine synthase A [Dehalococcoides ethenogenes 195]
 gi|57225190|gb|AAW40247.1| tRNA pseudouridine synthase A [Dehalococcoides ethenogenes 195]
          Length = 248

 Score =  122 bits (306), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 122/243 (50%), Gaps = 3/243 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            ++IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  +
Sbjct: 2   LLVIEYEGTRYSGFQVQDKGATIQGELETAIRKLTSEQTRVSGSGRTDAGVHAAYQVVSY 61

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I++  +  V + F  R  AI R Y Y+I+  +    
Sbjct: 62  LSESSLGLDKIKGGLNFYL--PPDIAVKEVHFVAESFDVRRRAISREYSYQILNSKTRSP 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNL 183
           L + +AW +P  LD + M  A + L G HDF  F  S+  +    +R ++   +    + 
Sbjct: 120 LARLQAWQVPYKLDIKLMEQAFKMLEGEHDFIAFASSLGPEIKKTVRRVNWTRLGIREDR 179

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   + A SFL  Q+R+ +G+L  +G G  + ++ E   +A+     GP AP  GL    
Sbjct: 180 LIFNIEANSFLTHQVRNTIGTLVELGRGTMSMSEFEALFEAKTPGLAGPAAPACGLSLVR 239

Query: 244 VEY 246
           V Y
Sbjct: 240 VNY 242


>gi|288924968|ref|ZP_06418904.1| tRNA pseudouridine synthase A [Prevotella buccae D17]
 gi|288338158|gb|EFC76508.1| tRNA pseudouridine synthase A [Prevotella buccae D17]
          Length = 261

 Score =  122 bits (305), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 85/257 (33%), Positives = 123/257 (47%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  +EKA+ L+      + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLNYDGTNYHGWQIQPNGNSVQEELEKALSLLLRTKTEIVGAGRTDAGVHARLM 60

Query: 61  VAHFDL----------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           VAHFD            ++     LC  LN  L     ISI  +  V +  HARFSA+ R
Sbjct: 61  VAHFDYEVGTTTEGQAAKDIDCPQLCYKLNRLL--PRDISIRKIIPVAQDMHARFSAVAR 118

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           +Y Y I T + P   E+  ++ +P +LD + MR   + L  + DF  F        S   
Sbjct: 119 TYHYYIHTGKMP--FERHYSYQMPYALDFDAMREGCELLKRQTDFAAFCKAGADNKSTCC 176

Query: 171 TIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           T+     V +        + A  FL   +R+ VG+L  +G  K T       ++A  R +
Sbjct: 177 TVTEARWVKTSPGTWYFEITANRFLRNMVRAVVGTLVDLGRHKITLEQFRHIVEAGRRSD 236

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+ + VEY
Sbjct: 237 AGESMPGHALFLERVEY 253


>gi|315608004|ref|ZP_07882997.1| tRNA pseudouridine synthase A [Prevotella buccae ATCC 33574]
 gi|315250473|gb|EFU30469.1| tRNA pseudouridine synthase A [Prevotella buccae ATCC 33574]
          Length = 284

 Score =  122 bits (305), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 85/257 (33%), Positives = 123/257 (47%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  +EKA+ L+      + GAGRTD+GVHA   
Sbjct: 24  MQRYFIYLSYDGTNYHGWQIQPNGNSVQEELEKALSLLLRTKTEIVGAGRTDAGVHARLM 83

Query: 61  VAHFDL----------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           VAHFD            ++     LC  LN  L     ISI  +  V +  HARFSA+ R
Sbjct: 84  VAHFDYEVGTTTEGQEAKDIDCPQLCYKLNRLL--PRDISIRKIIPVAQDMHARFSAVAR 141

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           +Y Y I T + P   E+  ++ +P +LD + MR   + L  + DF  F        S   
Sbjct: 142 TYHYYIHTGKMP--FERHYSYQMPYALDFDAMREGCELLKRQTDFAAFCKAGADNKSTCC 199

Query: 171 TIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           T+     V +        + A  FL   +R+ VG+L  +G  K T       ++A  R +
Sbjct: 200 TVTEARWVKTSPETWYFEITANRFLRNMVRAVVGTLVDLGRHKITLDQFRHIVEAGRRSD 259

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+ + VEY
Sbjct: 260 AGESMPGHALFLERVEY 276


>gi|38233160|ref|NP_938927.1| tRNA pseudouridine synthase A [Corynebacterium diphtheriae NCTC
           13129]
 gi|38199419|emb|CAE49063.1| tRNA pseudouridine synthase A [Corynebacterium diphtheriae]
          Length = 295

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 89/263 (33%), Positives = 130/263 (49%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ +    ++Q  IE  + LV    + +  AGRTD+GVHA  
Sbjct: 13  VRIRLDLAYDGTDFHGWARQGDSDLRTVQKIIEDTLTLVLQRPIDLTVAGRTDAGVHATG 72

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+    +        P  L + L   +   D + I N+S V  +F ARFSA+RR 
Sbjct: 73  QVAHFDVDPAALETRSIAGDPARLIRRLARLMP--DDVRIHNMSFVPAEFDARFSALRRH 130

Query: 112 YLYRIITRQ---APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YR+ T      P        W  P+S+D   M+ AA  L+G HDF  F   + + +S 
Sbjct: 131 YVYRVTTHPRGALPTRARDTAHW--PRSVDISAMQAAADALIGMHDFAAF-CKYREGAST 187

Query: 169 IRTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           IR +  F   DV++     L E  V A +F  + +RS VG+  +VG+GK      E  L 
Sbjct: 188 IRDLQEFTWHDVSTPQEPQLYEAHVTADAFCWSMVRSLVGACLVVGEGKRADGFTEHLLG 247

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
              R    P+A   GL    V+Y
Sbjct: 248 ETKRSSSIPVAAACGLSLVGVDY 270


>gi|332702220|ref|ZP_08422308.1| tRNA pseudouridine synthase A [Desulfovibrio africanus str. Walvis
           Bay]
 gi|332552369|gb|EGJ49413.1| tRNA pseudouridine synthase A [Desulfovibrio africanus str. Walvis
           Bay]
          Length = 266

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 118/247 (47%), Gaps = 6/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y G+ + G Q Q    ++QG +E  +  +    V +  A RTDSGVHAL Q
Sbjct: 1   MPRLKLTLAYTGTRFAGLQIQPGCRTVQGEVEAVLARMLNGPVRIDMAARTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           V H D+    + +   KA+NA L   D + +  + +V  +FH+RFSA  + Y Y I +  
Sbjct: 61  VVHLDVPESKMRIPWRKAINALL--PDDVCVTEVEVVPPEFHSRFSATSKVYAYTIWSEL 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  L   K   W +   L+   M  A QH VGRHDF +F+++        RT+  F    
Sbjct: 119 EFILPQRKPFVWRM-AGLNQTAMDKAMQHFVGRHDFKSFQNVGTPIRDTRRTVARFWREP 177

Query: 180 FGNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                E   R+ A  FL   +R+ +G L  VG GK    D+   +  +DR    P AP  
Sbjct: 178 GQTQWETVYRIQADGFLKQMVRNIIGCLVAVGRGKLCPNDIPALIAVRDRSLAPPTAPSR 237

Query: 238 GLYFDSV 244
           GL  + +
Sbjct: 238 GLCLERI 244


>gi|269798518|ref|YP_003312418.1| tRNA pseudouridine synthase A [Veillonella parvula DSM 2008]
 gi|269095147|gb|ACZ25138.1| tRNA pseudouridine synthase A [Veillonella parvula DSM 2008]
          Length = 261

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 129/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+   G+Q+Q N  G ++QG +E  +  +  E + ++GA RTD+GVHA  QV  
Sbjct: 6   IIVAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAKFQVCT 65

Query: 64  FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +PV  + +A+ A+  I   I ++    +   +  R++   + Y+Y I  +   
Sbjct: 66  FQ-TSGTIPVENIPRAMIAH--IPKDIVVIEAIEIPLDWKPRWNIYGKEYVYTIHNQLIA 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L +   W + K LD + M+ A   LVG HDFTT +  +   + P++TI    V + G+
Sbjct: 123 DPLTQRYHWHVKKPLDIDRMQAAGNELVGTHDFTTLKGTNSTPADPVKTIMGIRVEARGS 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + I VV   FL+  +R+  G L  VG G+    D++  L A+DR+  G  AP +GL  +
Sbjct: 183 QVTISVVGDGFLYHMVRNIAGLLVDVGLGRRKVEDIKGYLAAKDRRVIGKTAPAQGLCLE 242

Query: 243 SVEYS 247
            + ++
Sbjct: 243 EIFFT 247


>gi|282857331|ref|ZP_06266568.1| tRNA pseudouridine synthase A [Pyramidobacter piscolens W5455]
 gi|282584831|gb|EFB90162.1| tRNA pseudouridine synthase A [Pyramidobacter piscolens W5455]
          Length = 247

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 119/247 (48%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  +I Y+G  + GWQ Q NG+++Q S+E+ + L+ G  V V GAGRTD+GVHA  Q
Sbjct: 1   MPRYSCVISYDGGKFCGWQTQPNGATVQESLERVLSLLNGSPVKVTGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A F L REW P  L  ALNA L     ++ +    +   F AR  A+ R Y + +    
Sbjct: 61  TASFLLDREWEPRRLLLALNANLPEGAAVASVRERPIG--FDARRDALWREYAFFVWRGP 118

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               + K   W   K   D + +R     L GRHDF+ F        + +R +       
Sbjct: 119 FCYPMMKPYVWWKKKDDWDHDLIRRGCALLEGRHDFSAFCRAGDLPENAVRRMHFVRYIR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L   R+   +FL   +R  +G+L  V  G+ T + LE  L    R +    APP GL
Sbjct: 179 RGRLSAFRIRGDAFLTNMVRIMIGNLDAVASGRRTLSWLEGLLDGASRGDSAMTAPPNGL 238

Query: 240 YFDSVEY 246
           +F  V Y
Sbjct: 239 FFWKVGY 245


>gi|255324781|ref|ZP_05365895.1| tRNA pseudouridine synthase A [Corynebacterium tuberculostearicum
           SK141]
 gi|255298256|gb|EET77559.1| tRNA pseudouridine synthase A [Corynebacterium tuberculostearicum
           SK141]
          Length = 297

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 90/263 (34%), Positives = 132/263 (50%), Gaps = 24/263 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW +QK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 21  VRLRLDLAYDGTDFHGWAKQKGGLRTVQGVLEEKLAMIARTEVPLTVAGRTDAGVHARGQ 80

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+  E +        P  L + L   L   + + +         F ARFSA+RR Y
Sbjct: 81  VAHVDVPTEMLAQRSVAGEPGKLVRRLAKLL--PEDVRVHGCEFAPAGFDARFSALRRHY 138

Query: 113 LYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YRI T      P        W+ P  +D + M+ AA  LVG HDF  F      A++ I
Sbjct: 139 VYRITTNPRGALPTRARDTAEWIKP--VDIDAMQEAATALVGLHDFAAFCKAKPNATT-I 195

Query: 170 RTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA-LQ 223
           R +  F   DV++     L E RV A +F  + +RS VG    VG+G+   TD   A LQ
Sbjct: 196 RELQEFSWRDVSTPEEPELYEARVSADAFCWSMVRSLVGCCLRVGEGR-RDTDFAAALLQ 254

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
              R    P+AP +GL   +V+Y
Sbjct: 255 ETKRSSSIPVAPAKGLSLVAVDY 277


>gi|42559717|sp|P60349|TRUA_CORDI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 288

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 89/263 (33%), Positives = 130/263 (49%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ +    ++Q  IE  + LV    + +  AGRTD+GVHA  
Sbjct: 6   VRIRLDLAYDGTDFHGWARQGDSDLRTVQKIIEDTLTLVLQRPIDLTVAGRTDAGVHATG 65

Query: 60  QVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+    +        P  L + L   +   D + I N+S V  +F ARFSA+RR 
Sbjct: 66  QVAHFDVDPAALETRSIAGDPARLIRRLARLMP--DDVRIHNMSFVPAEFDARFSALRRH 123

Query: 112 YLYRIITRQ---APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YR+ T      P        W  P+S+D   M+ AA  L+G HDF  F   + + +S 
Sbjct: 124 YVYRVTTHPRGALPTRARDTAHW--PRSVDISAMQAAADALIGMHDFAAF-CKYREGAST 180

Query: 169 IRTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           IR +  F   DV++     L E  V A +F  + +RS VG+  +VG+GK      E  L 
Sbjct: 181 IRDLQEFTWHDVSTPQEPQLYEAHVTADAFCWSMVRSLVGACLVVGEGKRADGFTEHLLG 240

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
              R    P+A   GL    V+Y
Sbjct: 241 ETKRSSSIPVAAACGLSLVGVDY 263


>gi|329945764|ref|ZP_08293451.1| putative tRNA pseudouridine synthase A [Actinomyces sp. oral taxon
           170 str. F0386]
 gi|328528212|gb|EGF55190.1| putative tRNA pseudouridine synthase A [Actinomyces sp. oral taxon
           170 str. F0386]
          Length = 308

 Score =  121 bits (304), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 131/277 (47%), Gaps = 34/277 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GW  Q    +++G +  A+  V  E V +  AGRTD+GVHA  Q
Sbjct: 14  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTSALATVLREPVRLAVAGRTDAGVHAAAQ 73

Query: 61  VAHFDLVRE-WVPV-----------ILCKALNAYLKISDT-----------ISILNLSIV 97
           V H D+  E W  +           +L +      + + T           + +    IV
Sbjct: 74  VVHLDVSPEAWAALPGRSDRLPEAALLTRMAGVLAREAQTSLPRTPRGAGDVVVTGARIV 133

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRA---WLIPKSLDCENMRIAAQHLVGRHD 154
            + F ARF A+ R Y YRI    AP    + RA   WL P  LD E M  +A+ L+G HD
Sbjct: 134 PEAFDARFGALSRRYTYRIADADAPRNPAR-RATVLWL-PDRLDVEAMEASAKPLLGEHD 191

Query: 155 FTTFRSIHCQASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           F ++     Q ++ IRT+   +           L+ + VVA +F H+ +RS VG+   VG
Sbjct: 192 FLSYCKPR-QGATTIRTLRALEWRRVAAGPDAGLVTLSVVADAFCHSMVRSLVGAGLAVG 250

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            G+  +   ++ L A+ R    P+APP GL  + V Y
Sbjct: 251 QGRRPAAWPDELLAARSRDGAAPVAPPHGLTLEEVVY 287


>gi|307565293|ref|ZP_07627786.1| tRNA pseudouridine synthase A [Prevotella amnii CRIS 21A-A]
 gi|307345962|gb|EFN91306.1| tRNA pseudouridine synthase A [Prevotella amnii CRIS 21A-A]
          Length = 257

 Score =  121 bits (304), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 134/263 (50%), Gaps = 25/263 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NGSS+Q ++EKA+ ++  + + + GAGRTD+GVHA   
Sbjct: 3   MQRYFITLSYDGNNYHGWQIQPNGSSVQETLEKALTILLRQPISIIGAGRTDTGVHARMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+  ++  + +   LN  L     IS+ ++  V    HARFSAI+R+Y Y +  ++
Sbjct: 63  VAHFDMKSKFDNMQISYRLNRLL--PHDISVSSIIPVSNDMHARFSAIKRTYHYYLHLQK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  +  +  +L+ + M  AA +L+G+ DF  F    C+  + ++T       ++
Sbjct: 121 D--IYNRQYSCYVGYNLNFDLMNEAALYLIGKKDFKCF----CKTGADVKTTICNITEAY 174

Query: 181 GNLI----------EIR-------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
              I          +I+       + A  FL   +R+ VG+L  VG GK + T  +  + 
Sbjct: 175 WKPIYPELSTLSSTDIKPTNWCFIISANRFLRNMVRAIVGTLIAVGRGKMSITKFKTIVD 234

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
              R + G   P   L+   +EY
Sbjct: 235 TGSRSDAGESMPGNALFLWDIEY 257


>gi|313893105|ref|ZP_07826682.1| tRNA pseudouridine synthase A [Veillonella sp. oral taxon 158 str.
           F0412]
 gi|313442458|gb|EFR60873.1| tRNA pseudouridine synthase A [Veillonella sp. oral taxon 158 str.
           F0412]
          Length = 261

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 124/244 (50%), Gaps = 4/244 (1%)

Query: 6   MIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+   G+Q+Q N  G ++QG +E  +  +  E + ++GA RTD+GVHA  QV  
Sbjct: 6   IIVAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSKICNEPIQIYGASRTDAGVHAKFQVCT 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F          + +A+ A+  I   I +L    +   +  R++   + Y+Y I  +    
Sbjct: 66  FQTSGAIPAENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYVYTIHNQLIAN 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
            L K   W + K L+ E M+ A   L+G HDFTT +  +   + P++TI    V   G  
Sbjct: 124 PLTKRYHWHVKKPLNIELMQAAGNELLGTHDFTTLKGTNSTPADPVKTIMGIQVEGEGPH 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + I VV   FL+  +R+  G L  VG G+    D++  L A+DR+  G  AP +GL  + 
Sbjct: 184 VTISVVGDGFLYHMVRNIAGLLVDVGLGRRKVEDIKGYLAAKDRRVIGKTAPAQGLCLEE 243

Query: 244 VEYS 247
           + ++
Sbjct: 244 IFFT 247


>gi|171910331|ref|ZP_02925801.1| putative tRNA pseudouridylate synthase I [Verrucomicrobium spinosum
           DSM 4136]
          Length = 258

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 127/265 (47%), Gaps = 31/265 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I Y+G  + GWQ Q N  ++Q  +E A+  +TG  V V G+GRTD+GVHAL QVA
Sbjct: 5   RLKLTIAYDGRPWRGWQSQANSVTVQDQVETALRDLTGTQVNVQGSGRTDAGVHALAQVA 64

Query: 63  HFD------LVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           H D      + RE WV     +ALN  +++  +I +++      +FHARF A+ + Y YR
Sbjct: 65  HADVPDALKMGREAWV-----RALN--VRLPQSIRVMDCEDAAGEFHARFDAVGKIYCYR 117

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---------QAS 166
           +         E+GRAW +  +LD + +   A  L G H+F    +             A 
Sbjct: 118 LWRGDVMSPFEQGRAWHVYGALDLDLLHHGAGILTGTHNFARLSANRGGMSEDERREDAE 177

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKAL 222
           +  RT+   D+   G +I I      FL+  +R   GSL  V  G+    W S DL    
Sbjct: 178 ALTRTVRRIDIIPEGEVIRIEFEGDGFLYKMVRLMTGSLVQVARGRERLEWLS-DLVGDP 236

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
                 +C   AP +GLY   V Y+
Sbjct: 237 SGLKSNQC---APADGLYLVKVFYA 258


>gi|147669126|ref|YP_001213944.1| tRNA pseudouridine synthase A [Dehalococcoides sp. BAV1]
 gi|146270074|gb|ABQ17066.1| tRNA pseudouridine synthase A [Dehalococcoides sp. BAV1]
          Length = 246

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  + 
Sbjct: 1   MVIEYEGTRYSGFQIQDKGATIQGELETAIRKLTSEQTRVSGSGRTDAGVHAAYQVVSYL 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +   LN YL     I++  +  V + F  R  AI R Y Y I+  +    L
Sbjct: 61  TESSLGLEKIKGGLNYYL--PPDIAVKEVHFVAENFDVRRRAISREYSYHILNSKTRSPL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFGNLI 184
            + +AW +P  LD + M  A + L G HDF  F S +  +    +R ++   ++   + +
Sbjct: 119 ARLQAWQVPYKLDIKLMEQAFKMLEGEHDFIAFASGLGPEIKKTVRRVNWTRLDIAEDRL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +R+ A SFL  Q+R+ +G L  +G G  +  +     +A+     GP AP  GL    V
Sbjct: 179 ILRIEANSFLTHQVRNTIGVLVELGRGTISMGEFGALFEAKTPGLAGPAAPACGLSLVRV 238

Query: 245 EY 246
            Y
Sbjct: 239 NY 240


>gi|320160443|ref|YP_004173667.1| tRNA pseudouridine synthase A [Anaerolinea thermophila UNI-1]
 gi|319994296|dbj|BAJ63067.1| tRNA pseudouridine synthase A [Anaerolinea thermophila UNI-1]
          Length = 259

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 129/249 (51%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+QRQ    ++Q  +EKA+  L  GE  ++  +GRTD+GVHA  
Sbjct: 1   MARYKVILAYDGTHFQGFQRQAGARTVQAEVEKALRSLGWGEESLL-SSGRTDTGVHASG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FDL        L  ALNA  ++ + ++   +  V   FH RF+AI R+YLYRII  
Sbjct: 60  QVIAFDLDWRHSLEALRNALNA--RLPEDVAAKQVEEVPGDFHPRFNAIERAYLYRIIVA 117

Query: 120 QAPLALEKGRAWLIPKSLDC-ENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +    L +  AW +   L+  E ++ AAQ L G HDF+ F +   +  S +R I   +  
Sbjct: 118 ETRDPLRERYAWRLWPPLEAPEALQSAAQALCGTHDFSAFGTPPVEGGSTLRHIYQAEWR 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+     V   +FL+  +R  V +   VG  + +  D  +A+Q Q R     LAP  G
Sbjct: 178 ENGDEWLFEVRGNAFLYHMVRRMVWAQVQVGLNRLSLADFLEAVQ-QARPLPPGLAPAHG 236

Query: 239 LYFDSVEYS 247
           L    V Y+
Sbjct: 237 LVLTGVRYA 245


>gi|295132840|ref|YP_003583516.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
 gi|294980855|gb|ADF51320.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
          Length = 250

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 14/250 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ Y GWQ Q    S+Q  +++A+  +  + + V GAGRTD+GVHA +  
Sbjct: 1   MRYFIDLAYLGTAYHGWQIQPEAVSVQQVLQEALSKILQQNIEVVGAGRTDAGVHATQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD         L   LN++L     ISI  L  V  Q HARF A  RSY Y I+  + 
Sbjct: 61  AHFDADLNCDEKTLQFKLNSFL--PKDISIRQLFKVQSQAHARFDACSRSYEYHIVNFKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID-----HFD 176
           P  ++   A+ + K  D E M  AA  L    D+T F+    ++ + ++T +      F 
Sbjct: 119 PFKID--LAYYLLKQPDIEKMNHAAAML---KDYTNFKCF-SKSRTDVKTYNCNITAAFW 172

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             S   LI   + A  FL   +R+ VG+L  +G GK +   L++ L+++DR   G   P 
Sbjct: 173 EQSKDELI-FHITADRFLRNMVRAIVGTLLDIGLGKNSVEFLKEILKSEDRSMAGTSVPA 231

Query: 237 EGLYFDSVEY 246
            GLY   +EY
Sbjct: 232 HGLYLTRIEY 241


>gi|168009447|ref|XP_001757417.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691540|gb|EDQ77902.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 299

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 87/244 (35%), Positives = 121/244 (49%), Gaps = 23/244 (9%)

Query: 18  WQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV 73
           WQ QKN  SIQ  +E A+   T     E+ +V GAGRTD+GVHA  QVAHF       P 
Sbjct: 36  WQIQKNYVSIQEKVEDALSKFTRLPRDELKLV-GAGRTDAGVHAWGQVAHFT-----TPT 89

Query: 74  ILC------KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
             C       +LN  L     I IL +S V   FHAR+SA R++Y Y+          + 
Sbjct: 90  CFCDLEPLHTSLNGILP--PDIRILEVSSVQPDFHARYSACRKTYQYKAYVSPVMDPFQH 147

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS--PIRTIDHFDVNSFGNLIE 185
             A+ I  S++   M  AA + VG H+F+ F +     +S   +R +  F V+S G  + 
Sbjct: 148 AYAYHIKNSVNIAAMEEAASYFVGTHNFSAFANHSADTASRDTLRDLLSFTVSSIGPQLL 207

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG---PLAPPEGLYFD 242
             V  +SF++ Q+R+ VG L  VG      + +   L  +DR+E     P+AP  GLY  
Sbjct: 208 FEVEGKSFMYKQVRNMVGLLVQVGKELVPPSMVRTILLTEDRRELAKISPVAPAHGLYLM 267

Query: 243 SVEY 246
           SV Y
Sbjct: 268 SVGY 271


>gi|241895121|ref|ZP_04782417.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
 gi|241871617|gb|EER75368.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
          Length = 249

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 123/251 (49%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           M RY   I Y+G+ +FGWQ Q N  ++Q  +E  +  +     E + V G+GRTD+ VHA
Sbjct: 1   MPRYKATIAYDGTDFFGWQVQPNKRTVQAEMELVVNKMAKNPAEHIRVQGSGRTDARVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QVAHFDL  +     + K L+  L     I I  +  V   FHA+F+A  ++Y YR  
Sbjct: 61  KGQVAHFDLPFDIPADAVRKGLSTMLPYD--IGIKKVEKVSDDFHAQFNAHNKTYFYRFS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHF 175
           T +     ++       + L+ E M+ A    VG HD+ +F +   Q  + +RT+     
Sbjct: 119 TSEYIDPFKRNYTGHWHRRLNPELMQQAIGDYVGEHDWLSFVASGYQQKTTVRTVYSAKM 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V      I        FL+ QIR  VG L  +G+G     D+++  + +DR++    AP
Sbjct: 179 WVKPEEEEIWFEFSGNGFLYNQIRIMVGVLLEIGNGVRPVDDIKRLFEVKDRQQAQFTAP 238

Query: 236 PEGLYFDSVEY 246
            +GLY   V+Y
Sbjct: 239 AQGLYLMDVKY 249


>gi|160879036|ref|YP_001558004.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
 gi|160427702|gb|ABX41265.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
          Length = 248

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 120/245 (48%), Gaps = 5/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +IIEY+GS Y GWQ+Q       +IQ  +E  +  +  E V V GA RT++GVHA +QVA
Sbjct: 6   LIIEYDGSRYDGWQKQAGNQKSITIQDKLEDVLNKMENETVTVIGAARTEAGVHAYKQVA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F    +     + + LN +L     I++L    V ++FHA F+A    Y Y+I   + P
Sbjct: 66  SFMTNSKLKVYEIKQYLNRFL--PRDIAVLEALEVPERFHASFNAGSFEYEYKISIGEVP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   +   K  D   M+ AA++LVG+HDF  F        S  R I   ++     
Sbjct: 124 SVFERKYNYYCFKRPDIAKMKEAAKYLVGKHDFKAFSDNKRMKKSTEREIYSLEIYGDEK 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I I V    F    +R  VG+L  VG  K    D+++ L+++DR + G     +GL+  
Sbjct: 184 EIVITVHGDDFWPHMVRIMVGTLLDVGLSKIEPMDIKRILESKDRDKAGETIEAKGLFLT 243

Query: 243 SVEYS 247
            V Y 
Sbjct: 244 EVHYK 248


>gi|255086349|ref|XP_002509141.1| predicted protein [Micromonas sp. RCC299]
 gi|226524419|gb|ACO70399.1| predicted protein [Micromonas sp. RCC299]
          Length = 452

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 108/229 (47%), Gaps = 59/229 (25%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI------------------VV 44
           RY + ++Y+G+ + G+QRQ N  ++QG +E A+    G                    +V
Sbjct: 64  RYLLRVQYDGTNFHGFQRQANARTVQGCVEDALDAFAGGGGGGGGGGGGDGADTMRSSIV 123

Query: 45  VHGAGRTDSGVHALRQVAHFDLV-----REWV-------PVILCKALNAYLK---ISDTI 89
            HG+ RTD+GVHAL    H DL      RE         P ++  ALN +LK     D  
Sbjct: 124 THGSSRTDAGVHALDNTMHVDLPPRVSRREPTRALPPHEPHVVASALNHFLKKRGAPDVA 183

Query: 90  SILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL-EKGRAWLIPK------------- 135
               + +    FHARFSA  R+Y YR+     P +L E+GR W +               
Sbjct: 184 VTRCIRVDPNAFHARFSATGRTYHYRMHVSPTPPSLFERGRVWHVCSGAGDRDAAGGGAD 243

Query: 136 ------------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
                        LD + MR+AA HLVG HDF+TFR+  CQASSP+RT+
Sbjct: 244 GCHENAGHDGRWGLDVDAMRVAAAHLVGTHDFSTFRASGCQASSPVRTL 292



 Score = 37.7 bits (86), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 31/63 (49%)

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + +  V  SFL+ Q+R  V +L+ VG G+     +   L A+  +    +AP  GLY   
Sbjct: 371 VVVTAVGPSFLYHQVRLMVATLRAVGAGEIDPASVPALLAARTPRAVPAMAPAHGLYLGR 430

Query: 244 VEY 246
           V Y
Sbjct: 431 VHY 433


>gi|288802284|ref|ZP_06407724.1| tRNA pseudouridine synthase A [Prevotella melaninogenica D18]
 gi|288335251|gb|EFC73686.1| tRNA pseudouridine synthase A [Prevotella melaninogenica D18]
          Length = 253

 Score =  121 bits (304), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 81/268 (30%), Positives = 124/268 (46%), Gaps = 37/268 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E A+  +  E + + GAGRTD+GVH    
Sbjct: 1   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLEHALSTILRESIAITGAGRTDAGVHGRMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD    +    L   +N  L     +S+  +  V +  HARFSA  R+Y Y + T +
Sbjct: 61  VAHFDTELSFDSAQLVYKVNRLLPRD--VSVSRIEPVGEDLHARFSATSRTYHYYVHTGK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P +  +  +     +LD + M  AA +L+G  DF  F    C+  + ++T       + 
Sbjct: 119 QPFS--RQYSCEFRYALDFDKMNEAAAYLIGEKDFKCF----CKTGADVKT-------TI 165

Query: 181 GNLIEIR----------------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            NL E R                      + A  FL   +R+ VG+L  VG G+ +  D 
Sbjct: 166 CNLTEARWIPANEEFALTTDNTVTNWCFVITANRFLRNMVRAVVGTLVEVGRGRLSLDDF 225

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +K +    R + G   P   L+   V+Y
Sbjct: 226 KKIVDGGTRSDAGESMPGNALFLWEVKY 253


>gi|42527777|ref|NP_972875.1| tRNA pseudouridine synthase A [Treponema denticola ATCC 35405]
 gi|51316703|sp|Q73KE3|TRUA_TREDE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|41818605|gb|AAS12794.1| tRNA pseudouridine synthase A [Treponema denticola ATCC 35405]
 gi|325474992|gb|EGC78178.1| tRNA pseudouridine synthase A [Treponema denticola F0402]
          Length = 268

 Score =  121 bits (303), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 8/247 (3%)

Query: 6   MIIEYNGSGYFGWQRQ-KNGS----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + I Y+G+ + GWQ+Q K G+    ++QG +EKA+  +    +  +G+GRTDSGVHA RQ
Sbjct: 12  LTISYDGTNFCGWQKQTKEGAETFRTVQGELEKALTKIHKHPIETNGSGRTDSGVHAARQ 71

Query: 61  VAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             +F   ++         ALN+ L     I +++ + V    HARF+A+ R+Y Y+I   
Sbjct: 72  AVNFFCDIKSMRASNFLPALNSIL--PKDIRVMDAAEVSPLLHARFNALSRTYRYKIKCG 129

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   A E+   W I +  D   +   A  L G  D T F +   Q+ S  R I       
Sbjct: 130 KTIFAHEQPYTWHIRRYPDIAALNEMASCLSGELDCTAFSAAGDQSISKSRYIKKAVFFI 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +   + A +FL   +RS VG+L  + +   +  D +  L+++ R++ GP APP+GL
Sbjct: 190 ENDYLIFEICANAFLWKMVRSIVGTLLHLDEIGASKKDFKDILESKMREKAGPTAPPQGL 249

Query: 240 YFDSVEY 246
           +  S+EY
Sbjct: 250 FLWSIEY 256


>gi|261879379|ref|ZP_06005806.1| tRNA pseudouridine synthase A [Prevotella bergensis DSM 17361]
 gi|270333946|gb|EFA44732.1| tRNA pseudouridine synthase A [Prevotella bergensis DSM 17361]
          Length = 244

 Score =  121 bits (303), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I ++G+ Y GWQ Q NG S+Q  +++ +  +  + + V GAGRTD+GVHA R  
Sbjct: 1   MRYFVWISFDGTAYHGWQIQPNGMSVQEKLQQGLTTLLRQPIEVTGAGRTDAGVHARRMA 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+ RE     L   LN  L     IS   +  V+ + HARFSA +R+Y Y I T++ 
Sbjct: 61  AHFDIDRELNCEQLAYRLNRIL--PRDISCEKVVRVNDEMHARFSATKRTYRYFIHTQRN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNSF 180
           P   E+  +  +   LD E M  AA  L+   DF  F   H    + +  +     V + 
Sbjct: 119 P--FERFFSVEMNWQLDFEQMNQAAAILLETDDFKAFCKAHADNKTTLCKVTTARWVQTG 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
                  + A  FL   +R+ VG+L  VG    T     + ++   R + G   PP GL+
Sbjct: 177 PATYYFEISANRFLRNMVRAVVGTLIDVGRHNITLQQFSEIVEKGSRSDAGQSMPPHGLF 236

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 237 LWDIEYE 243


>gi|221195458|ref|ZP_03568513.1| tRNA pseudouridine synthase A [Atopobium rimae ATCC 49626]
 gi|221184645|gb|EEE17037.1| tRNA pseudouridine synthase A [Atopobium rimae ATCC 49626]
          Length = 281

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 90/249 (36%), Positives = 120/249 (48%), Gaps = 19/249 (7%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--DLV 67
           Y G+ + G+  Q    ++ G +++A+  V    V +  AGRTD+GV AL Q      D  
Sbjct: 26  YRGAAFSGFAEQPKQRTVAGDLKQALTTVLRRPVELTCAGRTDAGVSALAQYVSVPVDAH 85

Query: 68  REWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            E +P   L ++L A     D ISI  +      F ARF A+ RSY YRI     P+ L 
Sbjct: 86  EEKIPKRQLLRSLTAL--TDDDISIQEIYKAQSGFSARFDALARSYRYRISAGLRPV-LA 142

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG----- 181
              AW    +LD   M  AAQ  VG HDF +F    C+A S +    H  V S       
Sbjct: 143 WDHAWWYNGALDVAAMNEAAQIFVGEHDFKSF----CKALSAVDKPTHRYVESIQVAEIQ 198

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                LI I +V  +FLHT +R+ VG+L  VG G   +    + L A DRK+ GP AP +
Sbjct: 199 EAGEKLIAIDIVGNAFLHTMVRTMVGTLVEVGRGHRATNWTREVLLACDRKKAGPTAPAK 258

Query: 238 GLYFDSVEY 246
           GL F  V Y
Sbjct: 259 GLVFTGVLY 267


>gi|296121106|ref|YP_003628884.1| tRNA pseudouridine synthase A [Planctomyces limnophilus DSM 3776]
 gi|296013446|gb|ADG66685.1| tRNA pseudouridine synthase A [Planctomyces limnophilus DSM 3776]
          Length = 305

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 122/265 (46%), Gaps = 27/265 (10%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I Y+G+ Y GWQ Q NG SIQ ++ +AI   T E  V++ AGRTD+GVHA+ QV  F 
Sbjct: 10  LTIAYDGTAYCGWQTQPNGVSIQSTLMQAIQEFTAETPVLYAAGRTDAGVHAVGQVVSFS 69

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       AL  +L   D I I  +  V   FHA+F A  R   YR +   AP+  
Sbjct: 70  TTSPVPAANFRPALQRFLP--DDIVIRQVEDVQPGFHAQFHA--RLKTYRYLFHNAPVWS 125

Query: 126 EKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI----------- 172
              R + +     LD + M  A + +VG  DF +  +      + +RT+           
Sbjct: 126 PFYRQYALWHRTRLDEQAMDFAIRQIVGTFDFRSLETQWPNRKTSVRTVIKASVQRIRNW 185

Query: 173 ----------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
                     +   ++  G  + + + A  FL+  +R+  G+L  +G GKW    L + +
Sbjct: 186 NLLGENGPPSEECQLDPEGEFLCMEITANGFLYNMVRTIAGTLIHIGRGKWGPEKLREIV 245

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
             QDR+  G  AP  GLY   V+Y+
Sbjct: 246 DLQDRRRAGETAPAHGLYLWHVDYA 270


>gi|126433747|ref|YP_001069438.1| tRNA pseudouridine synthase A [Mycobacterium sp. JLS]
 gi|126233547|gb|ABN96947.1| tRNA pseudouridine synthase A [Mycobacterium sp. JLS]
          Length = 299

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 84/263 (31%), Positives = 125/263 (47%), Gaps = 22/263 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + R  + + Y+G+ + GW  Q    ++ G I++A+  V    V V  AGRTD+GVHA  Q
Sbjct: 22  LTRLRLDVSYDGTDFAGWAPQTGQRTVAGLIDEALTTVFRTPVTVRAAGRTDAGVHATGQ 81

Query: 61  VAHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           VAH D+  + +P              + L + L  +L     + I ++      F ARFS
Sbjct: 82  VAHVDVPDDALPHAYPRSARPDEPEFLPLVRRLGRFLPAD--VRIRDIIRAPTGFDARFS 139

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A+RR Y YR+ T  AP  +E   A  +   P+ LD E M  A   LVG  DF  F   H 
Sbjct: 140 ALRRHYTYRLGT--APYGVEPQSARFVTPWPRPLDVEAMNDAGSQLVGLRDFAAF-CRHR 196

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           + ++ IR +   +    G+L+   V A +F  + +RS VG+L  VG+ +         L 
Sbjct: 197 EGATTIRDLQRLEWTRDGDLVTAYVSADAFCWSMVRSLVGALIAVGEHRREPEWCAGLLS 256

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A  R      APP+GL    V+Y
Sbjct: 257 ATRRSSEFAAAPPQGLTLVGVDY 279


>gi|313892355|ref|ZP_07825947.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
 gi|329121372|ref|ZP_08249998.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
 gi|313119214|gb|EFR42414.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
 gi|327469781|gb|EGF15247.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
          Length = 266

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 125/247 (50%), Gaps = 7/247 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y+G+ Y G+QRQ+NG ++Q ++EK +  +TG    ++   RTD+GVHA  Q   F 
Sbjct: 6   ITVSYDGTEYAGFQRQENGFTVQEALEKVLKKLTGVHTTIYFVARTDAGVHAYGQECTFY 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       A+N+ L     I +L    + + F  R +   ++Y Y +   +     
Sbjct: 66  TESSIPSERFKNAMNSLLPCD--IRVLKSKEMYEDFSVRKTNYGKTYAYILSEDKDINPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   W   + LD + M+  A+ L G+HDFT+FR  +   + P+R I+   +    +LI 
Sbjct: 124 LRKYVWYTGRKLDLQKMKEVAKVLEGKHDFTSFRGNNSVPADPVRFINEVRIIRKNSLIF 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL-----Y 240
           + V    FL+  +R+ VG+    G G  T   +++ L+A+DRK+ G  APP+GL     Y
Sbjct: 184 VYVTGEGFLYHMVRNMVGAFVDAGRGIMTPERIKEILKAKDRKKLGVTAPPQGLALLKVY 243

Query: 241 FDSVEYS 247
           F+ + + 
Sbjct: 244 FEPISHE 250


>gi|269218953|ref|ZP_06162807.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 848 str.
           F0332]
 gi|269212064|gb|EEZ78404.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 848 str.
           F0332]
          Length = 310

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 83/262 (31%), Positives = 131/262 (50%), Gaps = 19/262 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW  Q    +++G++ +A+ L+TG    +  AGRTD+GVHA  QVA
Sbjct: 8   RLRLRMSYDGTDFHGWAVQPGLRTVEGTVTEALNLITGGSHALTVAGRTDAGVHARGQVA 67

Query: 63  HFDLVREWVPVIL------CKA----LNAYL-------KISDTISILNLSIVDKQFHARF 105
           H D+    +          C+A    L+A L       K S  +++  +      F ARF
Sbjct: 68  HVDVSENELARAARRAGDPCQAIMRRLSALLARESPGPKGSSDVAVTGVDFAPAGFDARF 127

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y YR+    A     + R  L + + LD E M  AA+ L G HDF ++     +
Sbjct: 128 SALSRTYSYRVCDDPARFDPLRRRDVLWLREPLDVEAMGAAARKLTGEHDFISYCKPR-E 186

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            ++ IR +    V   G L+E+   A +F H+ +R+ VGSL  VG G+       + L+ 
Sbjct: 187 GATTIRELLELKVERKGGLVEVTARADAFCHSMVRTLVGSLLKVGAGRRDEEWPARRLEE 246

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
           + R     +APP  L  +SVEY
Sbjct: 247 RSRNGEVAVAPPHPLTLESVEY 268


>gi|15606137|ref|NP_213514.1| pseudouridine synthase I [Aquifex aeolicus VF5]
 gi|3929394|sp|O66953|TRUA_AQUAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2983318|gb|AAC06908.1| pseudouridine synthase I [Aquifex aeolicus VF5]
          Length = 241

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 125/244 (51%), Gaps = 5/244 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + + + G+ ++GWQ Q N  ++QG I+KA+  +  E V V G  RTDSGVHAL  
Sbjct: 1   MPNYLLRLAFVGTNFYGWQVQPNLRTVQGEIQKALSQILCEDVKVTGCCRTDSGVHALDY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A+F   +++    L KALN  L     + +  +  V ++F+AR+S   + YLY+I   +
Sbjct: 61  IANFKTQKDFPEEKLLKALNGIL--PKDVGVYAVKKVSEEFNARYSVKGKVYLYKIWNSE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    +W + + ++ E +R   +   G HDF     +  + ++ I  ++   +N  
Sbjct: 119 VRNPFLYPFSWQVKREINTEVLRNILKKFEGTHDFRALTKLEEERNTVI-NLEEVSLNVE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LIEIR+ A  FL   +R  VG+   +  G ++   LE+ LQ +        APP+GL+
Sbjct: 178 YPLIEIRLKASHFLRYMVRRIVGTAVKISLGLYSEEVLEELLQGKGNSPYT--APPQGLH 235

Query: 241 FDSV 244
            + V
Sbjct: 236 LEKV 239


>gi|229489482|ref|ZP_04383345.1| tRNA pseudouridine synthase A [Rhodococcus erythropolis SK121]
 gi|229323579|gb|EEN89337.1| tRNA pseudouridine synthase A [Rhodococcus erythropolis SK121]
          Length = 294

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 126/250 (50%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW RQ +  ++ G IE  +  V    V +  AGRTD+GVHA  Q
Sbjct: 20  LVRLRLDISYDGTDFSGWARQTDLRTVCGEIEDKLGTVLRRPVQLTVAGRTDAGVHATGQ 79

Query: 61  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D+  E +P    + +    + +   + +  +S+V   F ARFSA+RR Y YR+   
Sbjct: 80  VAHVDVPGELLPDDPSRLVRRLARFLPKDVRVKQISVVPGDFDARFSAMRRYYEYRVT-- 137

Query: 120 QAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            A   +E  RA      PK LD   M+ A+  L+G H+F  F     + ++ +R +  FD
Sbjct: 138 NAAFGVEPLRARDTVSYPKPLDLGAMQEASNRLLGLHNFAAF-CKRREGATTVRELQRFD 196

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G +    V A +F  + +RS VG++  VG+G+ T+  +   L    R     +AP 
Sbjct: 197 WTQVGTVFTAYVNADAFCWSMVRSLVGAVLSVGEGRRTADWVAGLLDETSRSSSILVAPA 256

Query: 237 EGLYFDSVEY 246
            GL    V+Y
Sbjct: 257 HGLSLVRVDY 266


>gi|282859476|ref|ZP_06268581.1| tRNA pseudouridine synthase A [Prevotella bivia JCVIHMP010]
 gi|282587704|gb|EFB92904.1| tRNA pseudouridine synthase A [Prevotella bivia JCVIHMP010]
          Length = 255

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 86/259 (33%), Positives = 128/259 (49%), Gaps = 17/259 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+GS Y GWQ Q NGSS+Q ++EKAI ++  E + + GAGRTD+GVHA   
Sbjct: 1   MQRYFITLSYDGSKYHGWQIQPNGSSVQETLEKAISVLLREPIAIIGAGRTDAGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  +  V    HARFSA RR+Y Y + T++
Sbjct: 61  VAHFDFTGSVDCHQMVYRLNRLLP--HDISVSKIEPVTNDLHARFSASRRTYHYYLHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-------RSIHCQASS----PI 169
                ++  +  +  +LD + M  AAQ+L+G  DF  F       ++  C+ +     PI
Sbjct: 119 N--IYQRQYSCYMSYALDFDLMNEAAQYLIGTKDFKCFCKAGADVKTTICELTEARWVPI 176

Query: 170 RTIDHFDVNSFGNLIE--IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           R      ++S     +    + A  FL   +R+ VG+L  VG GK +    +  +    R
Sbjct: 177 RAELSMPLSSKEQPTDWCFIISANRFLRNMVRAVVGTLVDVGRGKLSLEAFKAIVDGGTR 236

Query: 228 KECGPLAPPEGLYFDSVEY 246
            + G   P   L+   V Y
Sbjct: 237 SDAGESMPGNALFLWEVIY 255


>gi|332638011|ref|ZP_08416874.1| tRNA pseudouridine synthase A [Weissella cibaria KACC 11862]
          Length = 249

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 79/251 (31%), Positives = 126/251 (50%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           M RY   I Y+G+ ++GWQ Q    ++Q  +EK +  +     + + V G+GRTD+ VHA
Sbjct: 1   MPRYKATISYDGTEFYGWQVQPGKRTVQLEMEKVVNKMAKDPADHIRVQGSGRTDARVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV HFDL  +     + K L+  L     I I ++  VD+ FHA+FSA  ++Y YR+ 
Sbjct: 61  QGQVVHFDLPFDIPNEAVRKGLSTMLPYD--IGIKSVEKVDESFHAQFSAHNKTYRYRLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T +     ++       + +D   M+ A    VG HD+ +F +   Q  + +RT+    +
Sbjct: 119 TTEFIDPFKRNYTGHWHRRIDTSLMQQAIGDYVGEHDWLSFVASGFQQKTTVRTVYSAKM 178

Query: 178 NSFGNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  EI        FL+ QIR  VG L  +G+G     D+++    +DR++    AP
Sbjct: 179 WEKPEEDEIWFEFTGNGFLYNQIRIMVGVLLEIGNGSRPVDDIQRLFAVKDRQQARFTAP 238

Query: 236 PEGLYFDSVEY 246
            +GLY  SV+Y
Sbjct: 239 AQGLYLMSVDY 249


>gi|254412106|ref|ZP_05025881.1| tRNA pseudouridine synthase A [Microcoleus chthonoplastes PCC 7420]
 gi|196181072|gb|EDX76061.1| tRNA pseudouridine synthase A [Microcoleus chthonoplastes PCC 7420]
          Length = 283

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 82/251 (32%), Positives = 118/251 (47%), Gaps = 13/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ +  ++Q  IE+ +  V G+ V +HGAGRTD+GVHA  QVA
Sbjct: 11  RIALVIQYLGTKFSGWQRQPHHRTVQAEIEQVLSTVEGKPVTLHGAGRTDTGVHAAAQVA 70

Query: 63  HFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HF+  R      W+P+     LN+  ++ + I I   + V   +HARFSAI R Y Y I 
Sbjct: 71  HFNSSRPIPGERWMPI-----LNS--RLPEDILIRASAPVPANWHARFSAIWRRYRYSIY 123

Query: 118 TRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           T   P    +   W      LD   ++ A   L G+H    F   +        T+    
Sbjct: 124 TDACPNLFVRPFCWHYYHAPLDEHRIQEALNPLWGKHHLAAFHRANSGRKHSWVTVQDTH 183

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G+ I I + A  FL+  +R  VG L  VG G     +  +    Q R+     AP 
Sbjct: 184 CYRNGSFIHIEIQADGFLYGMVRLLVGMLVEVGRGNLNPHEFTQLWVNQQRERIKYSAPA 243

Query: 237 EGLYFDSVEYS 247
           +GL    V Y 
Sbjct: 244 KGLCLLRVGYP 254


>gi|317484413|ref|ZP_07943328.1| tRNA pseudouridine synthase A [Bilophila wadsworthia 3_1_6]
 gi|316924332|gb|EFV45503.1| tRNA pseudouridine synthase A [Bilophila wadsworthia 3_1_6]
          Length = 269

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 94/260 (36%), Positives = 124/260 (47%), Gaps = 17/260 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--KNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + I Y G+ Y GWQ Q  KN S   +IQ  IE A+  V GE V VHGAGRTD+GV
Sbjct: 1   MPRLKLTIAYVGTQYHGWQTQARKNASPLPTIQNIIEDAVAHVLGERVHVHGAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+      +    ALN  L     I I +  +V   FHA+ SA+R++Y YR
Sbjct: 61  HAEAQVAHLDVPESRARMDWQLALNTLL--PRDIRIADAVLVPDTFHAQHSAVRKTYEYR 118

Query: 116 --IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
             +  R  P  L     W     +D E M   +++L+G+ DF + ++      + +RTI 
Sbjct: 119 LWLSKRYTPPQLFP-FVWAC-GPVDVERMDEGSRYLLGKRDFASLKNAGTDLRTTVRTIL 176

Query: 174 HFDVNSFGNLIE------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                  G L E       R  A  FL   +R+ +G L  VG GK    D+   L A DR
Sbjct: 177 SITRTPEGQLPEDCLELTWRFEADGFLKQMVRNTMGLLVAVGRGKLEPADIPGILDACDR 236

Query: 228 KECGPLAPPEGLYFDSVEYS 247
           +     AP  GL    V Y 
Sbjct: 237 RIAPLTAPACGLTMKKVWYD 256


>gi|315605929|ref|ZP_07880960.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 180 str.
           F0310]
 gi|315312211|gb|EFU60297.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 180 str.
           F0310]
          Length = 299

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 88/277 (31%), Positives = 128/277 (46%), Gaps = 34/277 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GW  Q    ++QG IE A+ + + E V    AGRTD+GVHA  Q
Sbjct: 1   MRRLRLDLGYDGTDFRGWAAQPGLRTVQGEIEAALAMASREEVTTTVAGRTDAGVHARHQ 60

Query: 61  VAHFDLVRE-WVPVI-------------LCKALNAYL----------------KISDTIS 90
           V H DL  E W  +              + + LN  L                + +  + 
Sbjct: 61  VCHVDLSDEAWARLAPRGERSEDDAATSIVRRLNKILSGRYGERSRTRGMGVARGTCDVR 120

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           I    +VD  F ARFSA+ R Y YR+     PLA    R W + + LD + M  AA  L+
Sbjct: 121 IFAARVVDASFDARFSALARRYTYRVSDAPDPLA-RWDRLW-VDEPLDDQAMNDAAAPLL 178

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           G+HDF  +     + ++ IR +     V      +  RV A +F H+ +RS VG+L LVG
Sbjct: 179 GQHDFLGYCRPR-EGATTIRALRTLRAVREADGTLAFRVEADAFCHSMVRSLVGALLLVG 237

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            G        + L A+ R    P+AP  GL  + V+Y
Sbjct: 238 SGARNIDYPARVLGARSRASAAPIAPAHGLTLEGVDY 274


>gi|108798087|ref|YP_638284.1| tRNA pseudouridine synthase A [Mycobacterium sp. MCS]
 gi|119867183|ref|YP_937135.1| tRNA pseudouridine synthase A [Mycobacterium sp. KMS]
 gi|108768506|gb|ABG07228.1| tRNA pseudouridine synthase A [Mycobacterium sp. MCS]
 gi|119693272|gb|ABL90345.1| tRNA pseudouridine synthase A [Mycobacterium sp. KMS]
          Length = 299

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 84/263 (31%), Positives = 125/263 (47%), Gaps = 22/263 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + R  + + Y+G+ + GW  Q    ++ G I++A+  V    V V  AGRTD+GVHA  Q
Sbjct: 22  VTRLRLDVSYDGTDFAGWAPQTGQRTVAGLIDEALTTVFRTPVTVRAAGRTDAGVHATGQ 81

Query: 61  VAHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           VAH D+  + +P              + L + L  +L     + I ++      F ARFS
Sbjct: 82  VAHVDVPDDALPHAYPRSARPDEPEFLPLVRRLGRFLPAD--VRIRDIIRAPTGFDARFS 139

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A+RR Y YR+ T  AP  +E   A  +   P+ LD E M  A   LVG  DF  F   H 
Sbjct: 140 ALRRHYTYRLGT--APYGVEPQSARFVTPWPRPLDVEAMNDAGSQLVGLRDFAAF-CRHR 196

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           + ++ IR +   +    G+L+   V A +F  + +RS VG+L  VG+ +         L 
Sbjct: 197 EGATTIRDLQRLEWTRDGDLVTAYVSADAFCWSMVRSLVGALIAVGEHRREPEWCAGLLS 256

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A  R      APP+GL    V+Y
Sbjct: 257 ATRRSSEFAAAPPQGLTLVGVDY 279


>gi|255326873|ref|ZP_05367949.1| tRNA pseudouridine synthase A [Rothia mucilaginosa ATCC 25296]
 gi|255296090|gb|EET75431.1| tRNA pseudouridine synthase A [Rothia mucilaginosa ATCC 25296]
          Length = 321

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 92/274 (33%), Positives = 125/274 (45%), Gaps = 41/274 (14%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS + GW  Q N  ++QG+IE A+ L+      V  AGRTD+GVHA  Q  H DL  E
Sbjct: 27  YDGSLFSGWAAQPNLVTVQGAIENALELILRAPHRVVVAGRTDAGVHAEAQTLHCDLNDE 86

Query: 70  -WV-----------PVILCKALNAYLK-------------------ISDTISILNLSIVD 98
            W               L + L   L+                   +   I I  +S V 
Sbjct: 87  DWTRLQGRTGEDDPTAALGRRLTGALQRCLYDAEEQLNLPKNVRGILQGAIQIHRVSEVS 146

Query: 99  KQFHARFSAIRRSYLYRIITRQAP--LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            +F ARFSA  R Y+YRI    A     L +   W +P+ LDC ++  +AQ L+G  DF 
Sbjct: 147 FEFDARFSATGRRYVYRIADGAANGLNPLHRTYTWAVPEHLDCADLNQSAQQLLGLRDFL 206

Query: 157 TFRSIHCQASSPIRTIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +F    C+      TI      SF      LIE+RVVA +F H  +RS VG+L L G GK
Sbjct: 207 SF----CKPREGATTIRELRELSFTRTESGLIEVRVVADAFCHHMVRSLVGALVLYGTGK 262

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             +  L + ++   R+    LAPP  L    + Y
Sbjct: 263 RDAAWLRERIENPGREASLTLAPPHALALAEIYY 296


>gi|311740028|ref|ZP_07713862.1| tRNA pseudouridine synthase A [Corynebacterium pseudogenitalium
           ATCC 33035]
 gi|311305101|gb|EFQ81170.1| tRNA pseudouridine synthase A [Corynebacterium pseudogenitalium
           ATCC 33035]
          Length = 297

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 85/262 (32%), Positives = 126/262 (48%), Gaps = 22/262 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW +QK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 21  VRLRLDLAYDGTDFHGWAKQKGGLRTVQGVLEEKLAMIARTEVPLTVAGRTDAGVHARGQ 80

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+  E +        P  L + L   L   + + +         F ARFSA+RR Y
Sbjct: 81  VAHVDVPTEMLAQRSVAGEPGKLVRRLAKLL--PEDVRVHGCEFAPAGFDARFSALRRHY 138

Query: 113 LYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YRI T      P        W+ P  +D + M+ AA  LVG HDF  F      A++ I
Sbjct: 139 VYRITTNPRGALPTRARDTAEWIKP--VDIDAMQEAATALVGLHDFAAFCKAKPNATT-I 195

Query: 170 RTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           R +  F            L E RV A +F  + +RS VG    VG+G+  +      LQ 
Sbjct: 196 RELQEFSWRDASTPEEPELFEARVSADAFCWSMVRSLVGCCLRVGEGRRDADFAAALLQE 255

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
             R    P+AP +GL   +V+Y
Sbjct: 256 TKRSSSIPVAPAKGLSLVAVDY 277


>gi|108804942|ref|YP_644879.1| tRNA pseudouridine synthase A [Rubrobacter xylanophilus DSM 9941]
 gi|108766185|gb|ABG05067.1| tRNA pseudouridine synthase A [Rubrobacter xylanophilus DSM 9941]
          Length = 257

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 116/246 (47%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   ++EY+G+G+ GW RQ    +++G + +A+  V    V +  AGRTD+GVHA  QV
Sbjct: 1   MRLAGLVEYDGAGFSGWARQPGRRTVEGELSRALETVLRHPVRLTAAGRTDAGVHASGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD      P  L    +A L  S+ +++         F AR  A  RSY YRI+    
Sbjct: 61  VSFDARDGTDPGTLAYKASAVL--SEDVALRRCVAAPPGFDARRDAASRSYEYRIVNAPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L + RA  +   LD   +  AA+ ++G HDF  F           R +        G
Sbjct: 119 RSPLRRRRAVHVGYRLDERLLGEAARRVLGVHDFRAFTPAKSHHVRFERAVSESRWERCG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+  R+ A +FL+  +R+ VG++  V  G+      E+ L    R E GP AP  GL  
Sbjct: 179 DLLVYRITADAFLYNMVRALVGTMLEVARGRRDLASFEELLGGARRAEGGPTAPARGLTL 238

Query: 242 DSVEYS 247
             V Y+
Sbjct: 239 VRVRYA 244


>gi|294792824|ref|ZP_06757971.1| tRNA pseudouridine synthase A [Veillonella sp. 6_1_27]
 gi|294456723|gb|EFG25086.1| tRNA pseudouridine synthase A [Veillonella sp. 6_1_27]
          Length = 261

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 129/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+   G+Q+Q N  G ++QG +E  +  +  E + ++GA RTD+GVHA  QV  
Sbjct: 6   IIVAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAKFQVCT 65

Query: 64  FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +PV  + +A+ A+  I   I +L    +   +  R++   + Y+Y I  +   
Sbjct: 66  FQ-TSGTIPVENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYIYTIHNQLIA 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L +   W + K L+   M+ A   LVG HDFTT +  +  ++ P++TI    V + G+
Sbjct: 123 DPLTQRYHWHVKKPLNIARMQAAGNELVGTHDFTTLKGTNSTSADPVKTIMGIRVEARGS 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + I V+   FL+  +R+  G L  +G G+    D++  L A+DR+  G  AP +GL  +
Sbjct: 183 QVTISVIGDGFLYHMVRNIAGLLVDIGLGRRKVEDIKGYLAAKDRRAIGKTAPAQGLCLE 242

Query: 243 SVEYS 247
            + ++
Sbjct: 243 EIFFT 247


>gi|289805625|ref|ZP_06536254.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 225

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 77/211 (36%), Positives = 108/211 (51%), Gaps = 4/211 (1%)

Query: 38  VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV 97
           +  E + V  AGRTD+GVH   QV HF+             +NA L     I++  +  V
Sbjct: 1   MANEPINVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANL--PGDIAVRWVKTV 58

Query: 98  DKQFHARFSAIRRSYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
              FHARFSA  R Y Y I   R  P  L KG      + LD E M  AAQ L+G +DFT
Sbjct: 59  PDDFHARFSATARRYRYIIYNHRLRPAVLAKGVTHYY-EPLDAERMHRAAQCLLGENDFT 117

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           +FR++ CQ+ +P R + H +V   G  + + + A +F+H  +R+ VGSL  VG      +
Sbjct: 118 SFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLLEVGAHNQPES 177

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + + L A+DR      A  EGLY  +V+Y 
Sbjct: 178 WIAELLAARDRTLAAATAKAEGLYLVAVDYP 208


>gi|315649669|ref|ZP_07902753.1| tRNA pseudouridine synthase A [Paenibacillus vortex V453]
 gi|315274857|gb|EFU38233.1| tRNA pseudouridine synthase A [Paenibacillus vortex V453]
          Length = 266

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 86/262 (32%), Positives = 127/262 (48%), Gaps = 22/262 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    M + Y+G+ Y G+Q Q  G +IQ  +E AI  ++GE + +  +GRTD+GVHA  Q
Sbjct: 1   MRNLLMRVSYDGTDYNGFQTQPGGHTIQDYLEDAIHRLSGEQLKIIASGRTDAGVHARAQ 60

Query: 61  VAHFDLVREWVPVIL---CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           V +F       P+ L   C ALN +L   + I + +   V  +FH+R +A R++Y Y I 
Sbjct: 61  VFNFYTAS---PIPLERWCMALNTWL--PEDIVVSDAMEVPMEFHSRHAAKRKTYRYTIN 115

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             Q P    +         LD   M    +HL+G +D+TTF S     SS +RTI  FD 
Sbjct: 116 ANQHPDLFNRRYQIHHYGQLDIPAMEQGLRHLIGTYDYTTFASRKSTKSSHVRTI--FDA 173

Query: 178 ------------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                            +I   +    FL   +R  +G+L  VG+GK    D++  L+A+
Sbjct: 174 WFERDTSMCRPGTRDQGVIHTYLSGNGFLQHMVRIIMGTLIEVGEGKRHPDDMKIILEAK 233

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R   GP A  +GL    VEY 
Sbjct: 234 NRAAAGPTAMGKGLMLWEVEYD 255


>gi|320537307|ref|ZP_08037262.1| tRNA pseudouridine synthase A [Treponema phagedenis F0421]
 gi|320145772|gb|EFW37433.1| tRNA pseudouridine synthase A [Treponema phagedenis F0421]
          Length = 261

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 85/252 (33%), Positives = 125/252 (49%), Gaps = 22/252 (8%)

Query: 8   IEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           I Y+G+ + GWQ+Q KNG     +IQG IEKA   +  +   + GAGRTD+GVHA+ Q A
Sbjct: 11  ISYDGTFFSGWQKQVKNGIETFPTIQGEIEKAASKIHKQKKEIIGAGRTDTGVHAIGQAA 70

Query: 63  HFDL------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +F         + ++P     A N+ L     I +++   V  Q HARFSA  R+Y Y I
Sbjct: 71  NFFTEIQTIEAKSFIP-----AFNSLL--PKQIRVVDAQEVSPQLHARFSAQARTYRYFI 123

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DH 174
              +   A E+   W I +  D   +   A  L G  D T+F     Q++S  R I   H
Sbjct: 124 QCAKREFAHEQAYCWQIKRYPDISTLNRYAAVLRGELDCTSFSFAKDQSASKSRYIFSAH 183

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           F +    + +   + A +FL   +RS  G+L       +T  D +K L+ +DR   GP A
Sbjct: 184 FFIEK--DFLVFEISANAFLWRMVRSLTGTLLRCEKEHYTQNDFKKILELKDRGLAGPTA 241

Query: 235 PPEGLYFDSVEY 246
           PP+GL+   + Y
Sbjct: 242 PPQGLFLWHITY 253


>gi|282849896|ref|ZP_06259279.1| tRNA pseudouridine synthase A [Veillonella parvula ATCC 17745]
 gi|282580333|gb|EFB85733.1| tRNA pseudouridine synthase A [Veillonella parvula ATCC 17745]
          Length = 261

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 128/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+   G+Q+Q N  G ++QG +E  +  +  E + ++GA RTD+GVHA  QV  
Sbjct: 6   IIVAYDGTDLVGYQKQSNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAKFQVCT 65

Query: 64  FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +PV  + +A+ A+  I   I +L    +   +  R++   + Y+Y I  +   
Sbjct: 66  FQ-TSGTIPVENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYVYTIHNQLIA 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L +   W + K L+   M+ A   LVG HDFTT +  +   + P++TI    V + G+
Sbjct: 123 DPLTQRYHWHVKKPLNIARMQAAGNELVGTHDFTTLKGTNSTPADPVKTIMGIRVEARGS 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + I V+   FL+  +R+  G L  +G G+    D++  L A+DR+  G  AP +GL  +
Sbjct: 183 QVTISVIGDGFLYHMVRNIAGLLVDIGLGRRKVEDIKGYLAAKDRRAIGKTAPAQGLCLE 242

Query: 243 SVEYS 247
            + ++
Sbjct: 243 EIFFT 247


>gi|306835272|ref|ZP_07468304.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49726]
 gi|304568865|gb|EFM44398.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49726]
          Length = 293

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 88/262 (33%), Positives = 131/262 (50%), Gaps = 22/262 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW +QK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 17  VRLRLDLAYDGTNFHGWAKQKGGLRTVQGVLEEQLAMIVRTEVPLTVAGRTDAGVHARGQ 76

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+ +E +        P  + + L   L   + + +       + F ARFSA+RR Y
Sbjct: 77  VAHVDVPQEMLEQRSVAGDPGTIVRRLAKLL--PEDVRVHGCEFAPEGFDARFSALRRHY 134

Query: 113 LYRIIT--RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YRI T  R A P        W  P  +D + M+ AA  LVG HDF  F      A++ I
Sbjct: 135 VYRITTSPRGALPTRARDTAEWFKP--VDIDAMQDAATALVGLHDFAAFCKAKPNATT-I 191

Query: 170 RTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           R +  F   DV++     L E RV A +F  + +RS VG    VG+G+         LQ 
Sbjct: 192 RELQEFSWQDVSTPEEPQLFEARVTADAFCWSMVRSLVGCCLSVGEGRRDVDFAAALLQE 251

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
             R    P+AP +GL    V+Y
Sbjct: 252 TKRSSRIPVAPAKGLSLVQVDY 273


>gi|126663837|ref|ZP_01734832.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BAL38]
 gi|126624101|gb|EAZ94794.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BAL38]
          Length = 248

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/245 (31%), Positives = 119/245 (48%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG  + G+Q Q + SS+Q ++EKA+  +  E + + GAGRTDSGVHA +  
Sbjct: 1   MRYFIEFAYNGKNFHGFQSQPDASSVQETLEKALSTLFREKIAIVGAGRTDSGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+   E         LN++L  S  I +  +  V    HARF A  R+Y Y + T + 
Sbjct: 61  AHFETELELDSEYWSHKLNSFLPPS--IVVYRIFKVTDNAHARFDASSRTYEYYMHTFKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +   +W     L+ + M  A   L   +DF  F  +H   ++    I        G
Sbjct: 119 AFITDG--SWYHSHQLNLDKMNEACAILFEYNDFECFSKVHTDVNTFNCKISEAHWKQVG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG++  +G GK    DL   +++++R + G   P  GLY 
Sbjct: 177 NQLIFTITADRFLRNMVRAIVGTMVNIGLGKIEVADLRTIIESKNRGKAGFSVPAHGLYL 236

Query: 242 DSVEY 246
            +V Y
Sbjct: 237 VNVRY 241


>gi|226305372|ref|YP_002765330.1| tRNA pseudouridine synthase TruA [Rhodococcus erythropolis PR4]
 gi|226184487|dbj|BAH32591.1| tRNA pseudouridine synthase TruA [Rhodococcus erythropolis PR4]
          Length = 294

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 127/250 (50%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW RQ +  ++ G IE  +  V  + V +  AGRTD+GVHA  Q
Sbjct: 20  LVRLRLDISYDGTDFSGWARQTDLRTVCGEIEDKLGTVLRQPVQLTVAGRTDAGVHATGQ 79

Query: 61  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D+  E +P    + +    + +   + +  +S+V   F ARFSAIRR Y YR+   
Sbjct: 80  VAHVDVPGELLPDDPSRLVRRLARFLPKDVRVKQISVVPGDFDARFSAIRRYYEYRVT-- 137

Query: 120 QAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            A   +E  RA      PK LD   M+ A+  L+G H+F  F     + ++ +R +  FD
Sbjct: 138 NAAFGVEPLRARDTVSYPKPLDLAAMQEASNRLLGLHNFAAF-CKRREGATTVRELQRFD 196

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G +    V A +F  + +RS VG++  VG+G+ T+  +   L    R     +AP 
Sbjct: 197 WAQEGTVFTAYVNADAFCWSMVRSLVGAVLSVGEGRRTADWVAGLLDETLRSSSILVAPA 256

Query: 237 EGLYFDSVEY 246
            GL    V+Y
Sbjct: 257 HGLSLVRVDY 266


>gi|310777852|ref|YP_003966185.1| tRNA pseudouridine synthase A [Ilyobacter polytropus DSM 2926]
 gi|309747175|gb|ADO81837.1| tRNA pseudouridine synthase A [Ilyobacter polytropus DSM 2926]
          Length = 243

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 81/239 (33%), Positives = 121/239 (50%), Gaps = 5/239 (2%)

Query: 9   EYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           EY+GSG+FG+QRQ +  ++QG IE A+ +V  E + +  +GRTD GVHA  QV++F    
Sbjct: 9   EYDGSGFFGFQRQPSARTVQGEIESALKVVLKEEINLASSGRTDRGVHAYMQVSNF-FTS 67

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
             +P+   +     L I + I I ++  V ++FHARFSA  R+Y Y  I      A E  
Sbjct: 68  SKIPLDRLEFAVKNL-IPEDIKIHSMKNVSEEFHARFSAKSRAYEY--IMGWDRTAFETK 124

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLIEIR 187
               I   +D E +    + +VGRH+F  FR   C   +P+R I        G N + + 
Sbjct: 125 YVSGIKGKVDPEKLYKILEPIVGRHNFEGFRLTDCSGKNPVRDISEIRCYPKGENKLAVY 184

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +   +FL +QIR  +G+   V   K     L   L+  D K+   +A   GLY   +EY
Sbjct: 185 IKGNAFLKSQIRIIMGTALAVYFEKRPKNYLINKLKNPDSKDEKIVADGSGLYLCDIEY 243


>gi|227502701|ref|ZP_03932750.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49725]
 gi|227076431|gb|EEI14394.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49725]
          Length = 293

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/262 (34%), Positives = 130/262 (49%), Gaps = 22/262 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW RQK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 17  VRIRLDLAYDGTDFHGWARQKGGLRTVQGVLEEQLAMIARTEVPLTVAGRTDAGVHARGQ 76

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+ +E +        P  L + L   L   + + +       + F ARFSA+RR Y
Sbjct: 77  VAHVDVPQEMLEQRSVANDPGKLVRRLAKLL--PEDVRVHGCDFAPEGFDARFSALRRHY 134

Query: 113 LYRIIT--RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YRI T  R A P        W  P  +D   M+ AA  LVG HDF  F      A++ I
Sbjct: 135 VYRITTSPRGALPTRARDTAEWFKP--VDIGAMQDAANALVGLHDFAAFCKAKPNATT-I 191

Query: 170 RTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           R +  F   DV++     L E RV A +F  + +RS VG    VG+G+         LQ 
Sbjct: 192 RELQEFSWQDVSTPEEPQLFEARVTADAFCWSMVRSLVGCCLSVGEGRRDVDFAAALLQE 251

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
             R    P+AP +GL    V+Y
Sbjct: 252 TKRSSRIPVAPAKGLSLVQVDY 273


>gi|160878286|ref|YP_001557254.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
 gi|160426952|gb|ABX40515.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
          Length = 264

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 86/252 (34%), Positives = 127/252 (50%), Gaps = 15/252 (5%)

Query: 6   MIIEYNGSGYFGWQR---QKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +II Y+G+ Y GWQR     NG  SIQG +E+ +  V  E + + G+GRTD+GVHAL QV
Sbjct: 13  LIISYDGTNYSGWQRIPKAANGDHSIQGLLEEFLSKVLLEPIKLIGSGRTDTGVHALGQV 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F         I+ + +N  L   + I IL  + VD  FH+RF A+ + Y Y I T++ 
Sbjct: 73  ANFYSRSNLDVNIIRQKMNQVL--PEDIKILQANEVDLNFHSRFDAVEKIYQYIIDTKER 130

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV---- 177
                +  ++   K LD E MR AA+ L+G  D+ +F +      S IRTI    +    
Sbjct: 131 ESVFFRKYSYSCGKDLDIEAMRQAAKLLIGTMDYKSFCTDRKDGKSTIRTISEITIEELR 190

Query: 178 ---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              N  G +   R     FLH  IR   G+L  VG  + +   + +A+  + R+  G   
Sbjct: 191 QNRNQQGIIFTFR--GNGFLHHMIRIISGTLLEVGTQERSVESVRQAILGKKREYAGITL 248

Query: 235 PPEGLYFDSVEY 246
            P+GL+   V Y
Sbjct: 249 YPQGLFLKQVIY 260


>gi|294673952|ref|YP_003574568.1| tRNA pseudouridine synthase A [Prevotella ruminicola 23]
 gi|294472804|gb|ADE82193.1| tRNA pseudouridine synthase A [Prevotella ruminicola 23]
          Length = 244

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 121/247 (48%), Gaps = 9/247 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQ Q NG S+QG +++ +  +  + + + GAGRTD+GVHA    A
Sbjct: 4   RYFIWLSYDGTNYHGWQVQPNGISVQGELQRVLSTLLRQDISITGAGRTDAGVHARVMAA 63

Query: 63  HFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           HF++  +    I CK L   +   +   I I  +  V    HARFSA  R+Y Y I TR+
Sbjct: 64  HFEIEAD----IDCKQLAYKMNRMLPQDIVIDRIEEVSLDMHARFSATERTYHYYIHTRK 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E+  +  I   LD E M  A + L    DF  F   H    + +  +   +    
Sbjct: 120 CP--FERHYSCEIHYPLDFEKMNEAGRILCTYEDFGAFCKAHSDVKTTLCNVTRAEWIQT 177

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G+     V+ A  FL   +R+ VG+L  VG G+ +  +    ++ + R + G   P   L
Sbjct: 178 GDTTWYFVITANRFLRNMVRAVVGTLVDVGRGRLSLDEFRSVIEGKRRSDAGESMPGNAL 237

Query: 240 YFDSVEY 246
           + + V+Y
Sbjct: 238 FLEDVKY 244


>gi|164686559|ref|ZP_02210587.1| hypothetical protein CLOBAR_00126 [Clostridium bartlettii DSM
           16795]
 gi|164604428|gb|EDQ97893.1| hypothetical protein CLOBAR_00126 [Clostridium bartlettii DSM
           16795]
          Length = 201

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 71/202 (35%), Positives = 106/202 (52%), Gaps = 3/202 (1%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           V  +GRTD+GVHAL QVA+F    +     L  ALNA  K+   ISI++   VD  FHAR
Sbjct: 3   VTASGRTDAGVHALGQVANFKTESKIPADRLPDALNA--KLPKDISIISCEEVDIDFHAR 60

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           ++A  ++Y Y I  +     L K  ++ +   LD + +R+ A+ L+G HDF  F S    
Sbjct: 61  YNACGKTYRYLIYNKPYRSPLYKDLSYHVRYDLDLDKIRLEAKSLIGTHDFGGFMSSGSS 120

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
               +RTI   D+     +I I V    FL+  +R  VG+L  +G G+    ++E+ + +
Sbjct: 121 VKDTVRTIYDVDIQENDGMISIEVSGNGFLYNMVRIIVGTLVDIGRGRIKH-NMEEIINS 179

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
           + R  CG  AP  GL+   V Y
Sbjct: 180 KSRSMCGHTAPAHGLFLKKVNY 201


>gi|270291103|ref|ZP_06197326.1| tRNA pseudouridine synthase A [Pediococcus acidilactici 7_4]
 gi|304385383|ref|ZP_07367728.1| tRNA pseudouridine synthase A [Pediococcus acidilactici DSM 20284]
 gi|270280499|gb|EFA26334.1| tRNA pseudouridine synthase A [Pediococcus acidilactici 7_4]
 gi|304328590|gb|EFL95811.1| tRNA pseudouridine synthase A [Pediococcus acidilactici DSM 20284]
          Length = 248

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 77/252 (30%), Positives = 126/252 (50%), Gaps = 11/252 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHAL 58
           +RY + + Y+G+ + G+Q Q N  +++G +++A+  +       + + G+GRTD+GVHA 
Sbjct: 1   MRYKITMAYDGTNFAGFQAQPNQRTVEGVLKRAVNKIAKNPQPEIPIFGSGRTDAGVHAF 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFDL  E     +  ALN+ L + DT  +  + IVD+ FHARF+   + Y YR+  
Sbjct: 61  GQVVHFDLPIEMTANNMLHALNSILPL-DT-QVKKVEIVDEDFHARFTTHGKRYQYRMAL 118

Query: 119 RQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +   P        W  P S++   ++ A + L G HDF++F +    A + +RTI    
Sbjct: 119 GEFVDPFKRNYTGHWKFPISIEL--IQQAIKDLEGTHDFSSFVASGSTAKNHVRTIYEAK 176

Query: 177 V--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              +   N I        FL+  +R  V  L  +G  +    D+ + L  +DR +    A
Sbjct: 177 AWKDEAQNEIIFEFYGNGFLYNMVRIMVAVLVEIGSKRRPVDDIPRLLAVKDRNQARGTA 236

Query: 235 PPEGLYFDSVEY 246
           P  GLY   V+Y
Sbjct: 237 PASGLYLKEVDY 248


>gi|187734897|ref|YP_001877009.1| tRNA pseudouridine synthase A [Akkermansia muciniphila ATCC
           BAA-835]
 gi|238691867|sp|B2UNB6|TRUA_AKKM8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|187424949|gb|ACD04228.1| tRNA pseudouridine synthase A [Akkermansia muciniphila ATCC
           BAA-835]
          Length = 265

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 85/258 (32%), Positives = 117/258 (45%), Gaps = 15/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R      Y+G  Y GWQ Q  G ++Q  +E+A   + G    +HG+GRTD+GVHAL Q
Sbjct: 1   MTRIRFTAAYDGRPYLGWQSQPGGRTVQDVLERAFSGLFGTTCRIHGSGRTDAGVHALGQ 60

Query: 61  VAHFDLV-REWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V H D      +P      ALN   ++  TI I +   V   FHARFSA  ++Y Y I  
Sbjct: 61  VFHADAPDTHRIPADKWPAALNT--RLPRTIRITHAEYVPPGFHARFSATGKTYRYCI-- 116

Query: 119 RQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI------R 170
            +AP+    + G AW  P +   + +  A     G HDFT F ++      PI      R
Sbjct: 117 SRAPILNPFDAGLAWHRPLAWSVDILEQAVHLFRGTHDFTAFAALRGNEPRPIPEGYFRR 176

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           TI    V   G  + I      FL+  +R   G+      GK T  +L + + A    + 
Sbjct: 177 TITQTQVAQTGEHVFITFTGTGFLYKMVRLMTGAAHEAARGKITLEELARLINAPLPDDK 236

Query: 231 GPL-APPEGLYFDSVEYS 247
            P  APP+GL    V Y 
Sbjct: 237 SPFCAPPDGLTLMRVHYP 254


>gi|303247874|ref|ZP_07334142.1| tRNA pseudouridine synthase A [Desulfovibrio fructosovorans JJ]
 gi|302490775|gb|EFL50676.1| tRNA pseudouridine synthase A [Desulfovibrio fructosovorans JJ]
          Length = 265

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 83/254 (32%), Positives = 119/254 (46%), Gaps = 9/254 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+G+ + GWQ Q  G   ++QG +E+A+  + GE   VHGAGRTD+GVHA+
Sbjct: 1   MTRVRLTVAYDGTRFAGWQLQAPGMGRTVQGCLEEALARLCGEAARVHGAGRTDAGVHAV 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   +ALNA L    ++    +   D  FHARF A  + Y Y + T
Sbjct: 61  AQVAHVDVPEARAGLPWQRALNALLPDDVSVVDAAVVPPD--FHARFDASGKIYQYTLWT 118

Query: 119 RQAP-LALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           R    L   +   W + +   LD   M   A    G HDF  F++      +  R +   
Sbjct: 119 RPGSILPWRRPYVWDVGRFSPLDVAAMDACAALFAGYHDFAAFQNAGSSVKTSTRLVHGV 178

Query: 176 DVNSFGNLIEI--RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                 N  E+  R  A  FL   +R+ +G+L  VG GK    D+   L    R+     
Sbjct: 179 SRLPQANSDEMVWRFHAEGFLKQMVRNLMGALVEVGRGKAAPEDIRSVLTLGQRRHAPRT 238

Query: 234 APPEGLYFDSVEYS 247
           AP  GL   +VEY 
Sbjct: 239 APAGGLCLMAVEYG 252


>gi|317498140|ref|ZP_07956442.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894617|gb|EFV16797.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 206

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 69/175 (39%), Positives = 99/175 (56%), Gaps = 5/175 (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  NFHTDCMMSVNEIKNYLTKYLP-SD-IGIVEVSEASERFHSRLNAKEKTYLYRIAIPGVS 124

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
              E+   W  P++LD + M  AA  L+G HDF  F SI     S +RTI + ++
Sbjct: 125 NVFERKYLWYFPETLDIKKMEEAASLLIGTHDFKGFSSIKKTKKSTVRTIYNIEI 179


>gi|257126804|ref|YP_003164918.1| tRNA pseudouridine synthase A [Leptotrichia buccalis C-1013-b]
 gi|257050743|gb|ACV39927.1| tRNA pseudouridine synthase A [Leptotrichia buccalis C-1013-b]
          Length = 251

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 125/247 (50%), Gaps = 8/247 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++ +Y+GS + G+QRQ    ++QG IEK I     + + +  +GRTD GVHA+ QV++F 
Sbjct: 8   IVYQYDGSKFCGFQRQMGIKTVQGEIEKVISKTFFQNINMISSGRTDKGVHAIEQVSNF- 66

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           ++ + +P+  + + LN  LK    I IL++  +D++F++RF A  R+YLY +        
Sbjct: 67  MIDQNIPLNAIKRQLNKRLK--GEIKILDIEEMDEKFNSRFDAQNRTYLYIMKVEDEITP 124

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID----HFDVNSF 180
            E      I + +D +  +      +G+HDF++F        +P+R I     ++D N  
Sbjct: 125 FETNYITGIKEMIDIDKFQKIMLEFIGKHDFSSFMKKDKAYRNPVREIFFINCYYDKNGK 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I +    FL T +R  +GS   V  GK     ++K L+  D      LA  EGLY
Sbjct: 185 EKQINIEICGNGFLKTMVRIMIGSALAVYFGKEEKNYIKKKLENPDADGKKILAGSEGLY 244

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 245 LYKVSYE 251


>gi|237739188|ref|ZP_04569669.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
 gi|229423788|gb|EEO38835.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
          Length = 246

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 120/244 (49%), Gaps = 15/244 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F     
Sbjct: 12  YDGSRYYGFQRQPNKETVQGEIEKILKIVTKEDINLISAGRTDRGVHANHQVSNF-YTSS 70

Query: 70  WVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +PV     +L +AL         I IL++  VD++F+AR  A  R Y+Y I   + P  
Sbjct: 71  TIPVEKYKYLLTRAL------PKDIDILSVEEVDEKFNARHDAKMREYVYIISWEKNP-- 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NL 183
            E      +   +D E +       +G HDF  FR   C +   +R I   DV  F  N 
Sbjct: 123 FEARYCKFVKDKIDAERLEKIFSSFLGIHDFRNFRLSDCMSKVTVREIYSIDVKYFSENK 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           ++I +   +FL +Q+R  VG+   V         ++  L    ++    L   EGLY + 
Sbjct: 183 LKICIRGSAFLKSQVRIMVGTALEVYYKNLPKNHIDLMLNDFSKEYKKSLVEAEGLYLNR 242

Query: 244 VEYS 247
           + YS
Sbjct: 243 INYS 246


>gi|317505831|ref|ZP_07963676.1| tRNA pseudouridine synthase [Segniliparus rugosus ATCC BAA-974]
 gi|316255913|gb|EFV15138.1| tRNA pseudouridine synthase [Segniliparus rugosus ATCC BAA-974]
          Length = 293

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 92/259 (35%), Positives = 131/259 (50%), Gaps = 25/259 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHAL 58
           +R  + I Y+G+ + GW RQ    ++ G+IE A+   F    ++ V   AGRTDSGVHA 
Sbjct: 21  VRLRLDIAYDGTEFSGWARQPGRRTVAGTIEAALGRLFQAPAQLTV---AGRTDSGVHAT 77

Query: 59  RQVAHFDLVREWV-----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            QVAH D+  E V     P  L + L A +  SD + +L    V KQF ARFSA+RR Y 
Sbjct: 78  GQVAHVDVSAELVSGRLPPDKLVRKL-ARMLPSD-VRVLAAREVSKQFDARFSALRRHYR 135

Query: 114 YRIITRQAPLALEKGRA-WLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQ---ASS 167
           Y+I   +AP   +  RA  ++P  + LD   +  A+  LVG HDF  F    C+    S+
Sbjct: 136 YQIT--RAPHGADPLRAREVVPWGRPLDLGLLNAASAALVGLHDFAAF----CRPRPGST 189

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            IR +  FD    G L+  R+ A +F  +  RS +G++  V +G+         L A  R
Sbjct: 190 TIRELQRFDWTEDGPLLTARISADAFCWSMCRSLIGAVTAVAEGRREPGWAAALLTAPSR 249

Query: 228 KECGPLAPPEGLYFDSVEY 246
                +AP  GL    V+Y
Sbjct: 250 SSEIAVAPGHGLCLTGVDY 268


>gi|148655308|ref|YP_001275513.1| tRNA pseudouridine synthase ACD [Roseiflexus sp. RS-1]
 gi|166229831|sp|A5USG0|TRUA_ROSS1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148567418|gb|ABQ89563.1| tRNA pseudouridine synthase A [Roseiflexus sp. RS-1]
          Length = 270

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 121/250 (48%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ + G Q Q NG S+QG +E A   +TGE   +  AGRTD+GVHA  Q
Sbjct: 1   MRNIALRIEYDGADFVGSQWQTNGRSVQGVLEAAWQQLTGERRRMTLAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+           + + LN  L   + + +L        FHAR+SA+RR Y Y I   +
Sbjct: 61  VANVRTDTRHTISTIVRGLNGILP--EDVGVLAAWEAPDDFHARYSAVRREYRYVIDNGR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH---FDV 177
            P  L +  A  +P+ LD   M    + ++G HDF    S   Q  S +R          
Sbjct: 119 TPSPLLRRHAAYVPRRLDTAAMDAVVRQVIGTHDFAPL-SDGPQEGSTVRICYEARCTRT 177

Query: 178 NSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             +G  L+ I + A +FL   +R+ VG+L  VG+G+  +      L   DR+    LAP 
Sbjct: 178 EVWGQPLVLIDIAANAFLRHMVRNLVGTLIQVGEGRIDADRFAAVLAGDDRR-ARVLAPA 236

Query: 237 EGLYFDSVEY 246
            GLY  +V Y
Sbjct: 237 HGLYLMAVRY 246


>gi|256846563|ref|ZP_05552020.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
 gi|256718332|gb|EEU31888.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
          Length = 245

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 121/242 (50%), Gaps = 13/242 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ    ++QG IEK + +VT E + +  AGRTD GVHA  QV++F    +
Sbjct: 12  YDGSRYYGFQRQPKKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAYHQVSNFYTSSN 71

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I   + P   
Sbjct: 72  IPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKMREYIYIISWEKNP--F 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
           E      + + +  E +       VG HDF  FR   C +   IR I   +V  FG N I
Sbjct: 124 EARYCKFVKEKIVVEKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVKYFGENKI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   EGLY + +
Sbjct: 184 KIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLTDFTKEYKKNLVEAEGLYLNKI 243

Query: 245 EY 246
            Y
Sbjct: 244 SY 245


>gi|260911484|ref|ZP_05918073.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 472 str.
           F0295]
 gi|260634413|gb|EEX52514.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 472 str.
           F0295]
          Length = 244

 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 11/248 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY +   Y+G+ Y GWQ Q N +S+Q  +++A+ L+    V + GAGRTD+GVHA   VA
Sbjct: 4   RYFIYFSYDGTAYHGWQIQPNANSVQAEMQRAMSLLLRHPVELVGAGRTDTGVHARTMVA 63

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD       V L   LN  L     I+I  +  +D   HARFSA +R+Y Y +   + P
Sbjct: 64  HFDEEEPIDTVQLTYKLNRVLPFD--ITINQIKPIDGGLHARFSATKRTYHYYVHLDRDP 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  ++ + +  D + M  AAQ L+   DF  F   H  A + +  +         N
Sbjct: 122 FC--RAYSYALHQVPDFQLMNDAAQILLSHKDFGAFCKSHSDAKTTLCDVYEARWIRLSN 179

Query: 183 L-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK---ALQAQDRKECGPLAPPEG 238
                R+ A  FL   +R+ VG+L  VG   W    LE+    L ++ R++ G   P   
Sbjct: 180 TKWHFRISANRFLRNMVRAIVGTLLDVG---WHKVSLEQFVDILHSKSRQQAGESVPGHA 236

Query: 239 LYFDSVEY 246
           L+ + V+Y
Sbjct: 237 LFLEDVQY 244


>gi|227512894|ref|ZP_03942943.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227523022|ref|ZP_03953071.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227083894|gb|EEI19206.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227089840|gb|EEI25152.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 255

 Score =  119 bits (298), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 120/244 (49%), Gaps = 11/244 (4%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQVAHFDL 66
           Y+G+ + G++RQ N  +I+G + + + ++       ++++G+GRTD+GVHA+ QVAHFD 
Sbjct: 2   YDGTNFSGFERQPNRRTIEGVLTQKVNVMAKLPEPPIIIYGSGRTDAGVHAVAQVAHFDF 61

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII--TRQAPLA 124
             +     + + LN+ L +   + I  +  V   FHAR+    + Y YR+     Q P  
Sbjct: 62  PFDLSAEAIYRGLNSMLPLD--MEITKVEKVSNDFHARYDVSGKKYFYRMYLGEFQNPFK 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVNSFGN 182
                 W  P  +D E +  A   LVG HDF++F +    A S IRTI      ++   N
Sbjct: 120 RNYTGHWKFP--IDMEKVNHALADLVGEHDFSSFVASGSTARSNIRTIYSASAKLDQAEN 177

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + +      FL+  +R  VG +  +G G    +D+ +  + +DR +     P  GLY  
Sbjct: 178 EVHLEFYGNGFLYNMVRIMVGVVAEIGSGMRPESDVLRLFEVKDRDQARRTMPASGLYLK 237

Query: 243 SVEY 246
            V Y
Sbjct: 238 RVFY 241


>gi|227509961|ref|ZP_03940010.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227190567|gb|EEI70634.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 255

 Score =  119 bits (298), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 120/244 (49%), Gaps = 11/244 (4%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQVAHFDL 66
           Y+G+ + G++RQ N  +I+G + + + ++       ++++G+GRTD+GVHA+ QVAHFD 
Sbjct: 2   YDGTNFSGFERQPNRRTIEGVLTQKVNVMAKMPEPPIIIYGSGRTDAGVHAVAQVAHFDF 61

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII--TRQAPLA 124
             +     + + LN+ L +   + I  +  V   FHAR+    + Y YR+     Q P  
Sbjct: 62  PFDLSTEAIYRGLNSMLPLD--MEITKVEKVSNDFHARYDVSGKKYFYRMYLGEFQNPFK 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVNSFGN 182
                 W  P  +D E +  A   LVG HDF++F +    A S IRTI      ++   N
Sbjct: 120 RNYTGHWKFP--IDMEKVNHALADLVGEHDFSSFVASGSTARSNIRTIYSASAKLDQAEN 177

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + +      FL+  +R  VG +  +G G    +D+ +  + +DR +     P  GLY  
Sbjct: 178 EVHLEFYGNGFLYNMVRIMVGVVAEIGSGMRPESDVLRLFEVKDRDQARRTMPASGLYLK 237

Query: 243 SVEY 246
            V Y
Sbjct: 238 RVFY 241


>gi|257457999|ref|ZP_05623158.1| tRNA pseudouridine synthase A [Treponema vincentii ATCC 35580]
 gi|257444712|gb|EEV19796.1| tRNA pseudouridine synthase A [Treponema vincentii ATCC 35580]
          Length = 265

 Score =  119 bits (298), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 82/248 (33%), Positives = 125/248 (50%), Gaps = 14/248 (5%)

Query: 8   IEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           I Y+G+ + GWQ+Q     ++  ++QG +E+A+ L+    V + G+GRTD+GVHA  Q A
Sbjct: 16  ISYDGTRFHGWQKQLQHGEESFRTVQGEVERALALLHKHPVELFGSGRTDAGVHACGQAA 75

Query: 63  HF--DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           HF  D+ R   P     ALN+ L     + I+  + V    HARFSA  R+Y Y +   +
Sbjct: 76  HFFTDIAR-IKPESFVPALNSALP--KDVRIIEAAHVSDNLHARFSARSRTYRYFVHCGK 132

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVN 178
              A +    W I +  D   +   A  L G  D TTF +   Q+ S  R I   HF  +
Sbjct: 133 TAFAHQLPYCWHIRREPDINLLNRMAGVLSGELDCTTFSAAGDQSKSKSRYIYTAHFFTD 192

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + +   + A +FL   +RS  G+L        T  D E  L+++DR+  G  APP+G
Sbjct: 193 R--DFLVFEISANAFLWRMVRSVTGTLLHYEQQNGTKEDFEAVLRSKDRRNAGETAPPQG 250

Query: 239 LYFDSVEY 246
           L+  S++Y
Sbjct: 251 LFLWSIDY 258


>gi|149279607|ref|ZP_01885736.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
 gi|149229643|gb|EDM35033.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
          Length = 283

 Score =  119 bits (298), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 123/249 (49%), Gaps = 10/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG+ Y GWQ Q N  ++Q  ++KA+ +   + V   G GRTD+GVHA +   
Sbjct: 36  RYFIELSYNGTEYHGWQIQPNAVTVQEDLDKALSVFFRQPVATVGCGRTDTGVHATQFFV 95

Query: 63  HFDLVREWV----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           HFDL  E      P      +N+ L  S  I+I  +  VD + HARF A  R+Y Y +  
Sbjct: 96  HFDLPAETASTLDPGRAVTGINSLL--SYQIAIGRIFAVDNEAHARFGATARAYHYHLHF 153

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDV 177
            + P  L   R+WL   SLD E M  AA  ++   DF+ F   + Q  ++  + ++ +  
Sbjct: 154 HKDPFKLN--RSWLYKGSLDVEAMNQAAAAILEYTDFSCFSKSNTQTFTNNCKVVEAYFT 211

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            + G L +  + A  FL   +R+ VG+L  VG  +    +  + + +  R   G   P  
Sbjct: 212 LTDGGL-QFTIRADRFLRNMVRAIVGTLIKVGKKEINLNEFREIIASGSRSNAGQSVPAC 270

Query: 238 GLYFDSVEY 246
           GLY  +V Y
Sbjct: 271 GLYLVNVVY 279


>gi|33866624|ref|NP_898183.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8102]
 gi|42559753|sp|Q7TTT1|TRUA_SYNPX RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33633402|emb|CAE08607.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8102]
          Length = 299

 Score =  119 bits (297), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 114/239 (47%), Gaps = 4/239 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y GS + GWQRQ+NG+S+Q  +E AI  L     +    AGRTD+GVHA  QV
Sbjct: 17  RIALSLQYEGSAFCGWQRQRNGNSVQAQLEAAIEQLDPYRPIQTFAAGRTDTGVHAAGQV 76

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     ALN  L    TI +    +  K +HA +SA  R Y Y I   + 
Sbjct: 77  VHFDCGDRIPPAKWAPALNGRLPF--TIRVRESVLRPKDWHACYSATYRRYRYTIHNGRR 134

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P       +W      LD   MR A   ++G HDF+ F     + +    T+   D+   
Sbjct: 135 PNLFLAPWSWHRYQLRLDESRMRDALNGMLGLHDFSAFMRAGSRRAHARTTVQEVDLVRQ 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G+++ + + A  FL+  +R  +  L  VG+ + +  D E+  + + R E    AP  GL
Sbjct: 195 GDMVRVEIQASGFLYGMVRLLIAQLVAVGEHRLSVQDFEQRWRQRRRHEVREAAPGHGL 253


>gi|89890586|ref|ZP_01202096.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BBFL7]
 gi|89517501|gb|EAS20158.1| tRNA  pseudouridine synthase A [Flavobacteria bacterium BBFL7]
          Length = 251

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 119/244 (48%), Gaps = 4/244 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQRQ    ++Q  +E+ +  +  E + V GAGRTD+GVHA   VA
Sbjct: 6   RYFIELAYDGTAYHGWQRQPQSITVQEVLEEGLHKMLREQIKVQGAGRTDAGVHAAYMVA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD         L   LN +L     I++  +  V    HARF A +RSY Y  + R  P
Sbjct: 66  HFDYSGAIDLDHLVYRLNRWL--PKDIAVYEVKPVVNNAHARFHAYKRSYEYHFLLRPDP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             + +  A+++ +  D + M+ AA  L    DF  F   +    + +  +         +
Sbjct: 124 FQVMQ--AYVLFRKPDFKLMQEAAAILPEYKDFECFSRSNTDVKTYVCDLTEAYFEFKDH 181

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +   + A  FL   +R+ VG+L  +G GK T  DL + + ++DR   G  AP  GL+  
Sbjct: 182 KVIFHITANRFLRNMVRAVVGTLLDIGYGKKTIEDLREIIASKDRSNAGASAPAGGLFLT 241

Query: 243 SVEY 246
            + Y
Sbjct: 242 KIHY 245


>gi|54022806|ref|YP_117048.1| tRNA pseudouridine synthase A [Nocardia farcinica IFM 10152]
 gi|62901243|sp|Q5Z1K7|TRUA_NOCFA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54014314|dbj|BAD55684.1| putative tRNA pseudouridine synthase [Nocardia farcinica IFM 10152]
          Length = 257

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 81/234 (34%), Positives = 122/234 (52%), Gaps = 8/234 (3%)

Query: 16  FGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVIL 75
            GW RQ    ++QG +E A+  V  E + +  AGRTD+GVHA  QVAHFD   E+    L
Sbjct: 1   MGWARQPGLRTVQGVLEDALGKVLREPIQLTVAGRTDAGVHAEGQVAHFDTAAEFDGPQL 60

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW-LIP 134
              L  +L     + +    +V   F ARFSAIRR Y+YR+ T  AP   E   A  ++P
Sbjct: 61  VHRLARFLP--KDVRVKRADVVPPDFDARFSAIRRHYVYRLTT--APYGAEPLAARSVVP 116

Query: 135 --KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARS 192
              ++D + MR A+  L+G HDF  F     + ++ +R +  FD    G+L+   V A +
Sbjct: 117 CKSAVDVDAMRRASGLLLGLHDFAAF-CRRREGATTVRELQRFDWERQGDLLLAHVSADA 175

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           F  + +RS VG++  VG+G+ +   +   L+   R     +AP  GL   +V+Y
Sbjct: 176 FCWSMVRSLVGAVLAVGEGRRSPEWVAGLLRETQRSSSVTVAPAHGLSLVAVDY 229


>gi|254430842|ref|ZP_05044545.1| tRNA pseudouridine synthase A [Cyanobium sp. PCC 7001]
 gi|197625295|gb|EDY37854.1| tRNA pseudouridine synthase A [Cyanobium sp. PCC 7001]
          Length = 306

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 78/251 (31%), Positives = 117/251 (46%), Gaps = 8/251 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
           R  + ++Y+G  + GWQRQ N  S+Q ++E AI ++              AGRTD+GVHA
Sbjct: 13  RIALCLQYDGGAFHGWQRQHNAPSVQAALEDAIAILDPPAARPRPPRTWAAGRTDTGVHA 72

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV HFD           KALN   ++  TI ++  S V   +HA +SA  R Y Y I 
Sbjct: 73  AAQVVHFDSCGPIPAGRWPKALNG--RLPPTIRVMAASQVPPDWHACYSATYRRYRYTIF 130

Query: 118 TRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             +AP       +W      LD   M  A Q ++G HDF+ F+    +      T+    
Sbjct: 131 NGRAPNLFLAPWSWHRYQYRLDENAMVQALQGMLGEHDFSAFQRTGSRRRHARTTLQDVL 190

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+L+ + + A  FL+  +R  +G L  VG+G+ +     +  + +DR      APP
Sbjct: 191 LEREGDLLRVELQASGFLYGMVRLVLGQLVAVGEGRLSPEAFARRWRHRDRGAVKEAAPP 250

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 251 HGLCLLRVGYP 261


>gi|288574694|ref|ZP_06393051.1| tRNA pseudouridine synthase A [Dethiosulfovibrio peptidovorans DSM
           11002]
 gi|288570435|gb|EFC91992.1| tRNA pseudouridine synthase A [Dethiosulfovibrio peptidovorans DSM
           11002]
          Length = 247

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 122/248 (49%), Gaps = 7/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++Y + + Y G+ + GWQ Q +  ++Q  +E+A+ ++ G  V V GAGRTDSGVHA  QV
Sbjct: 1   MKYALELSYEGNHFSGWQLQPDSITVQEVLEEALTVLEGAPVKVSGAGRTDSGVHARGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A F+L + W P  L  A+NA L   + +S++  S V   F AR SA+ R Y Y +    +
Sbjct: 61  ASFELSKTWDPYRLTLAVNANLP--EHVSVMRASAVPDDFDARRSALWREYAYFVWHGPS 118

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +   W   +   D + +    + LVG HDF  F  +     + +RT+  F V   
Sbjct: 119 CFPHVRDMVWWRKRDDWDMDAVDGCCRALVGEHDFGAFCRLSECPENAVRTL--FSVRHI 176

Query: 181 --GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G L   R+  + FL   +R  +G++  V  GK      E+ L    R +    AP  G
Sbjct: 177 RRGRLSIFRIRGKGFLTNMVRIILGNIDAVATGKKRLEWFERLLLGGTRVDSATTAPASG 236

Query: 239 LYFDSVEY 246
           L+F  V Y
Sbjct: 237 LFFWRVGY 244


>gi|318042539|ref|ZP_07974495.1| tRNA pseudouridine synthase A [Synechococcus sp. CB0101]
          Length = 294

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 117/247 (47%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y+G+ Y GWQRQ    S+Q ++E+AI  L     + V  AGRTD+GVHA  QV
Sbjct: 23  RIALCLQYDGAPYCGWQRQPRDPSVQETLERAIAALDPRRPLSVQAAGRTDTGVHAAAQV 82

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            ALN  L  S  I +   + V   +HA FSA  R Y Y +   + 
Sbjct: 83  VHFDAEGPIPAQRWPAALNGRLPAS--IRVRAGAEVPADWHACFSASYRRYRYTLYNARL 140

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P       +W      LD + MR A + ++G HDF  F       S    T+    V   
Sbjct: 141 PNLFLAPWSWHRYQLRLDEQLMRQALEGMLGEHDFAAFERAGSSRSHSRTTLQEVTVERR 200

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LIE+ + A  FL+  +R  +G L  VG+ + +    E+  +++ R E    APP GL 
Sbjct: 201 GDLIEVELQASGFLYGMVRLVMGQLVAVGEQRLSLAAFERRWRSRARDEVKEAAPPHGLT 260

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 261 LLRVGYP 267


>gi|225010595|ref|ZP_03701066.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
 gi|225005424|gb|EEG43375.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
          Length = 218

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 75/217 (34%), Positives = 116/217 (53%), Gaps = 6/217 (2%)

Query: 31  IEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTIS 90
           +E+A  L+    + + GAGRTD+GVHA + VAHFD    +   I+   LNA+L  +  IS
Sbjct: 1   MEQAFSLLLATPIELMGAGRTDAGVHAKKMVAHFDTELGFDKQIIKDRLNAFL--AADIS 58

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           I  +  V ++ HARF+A  R+Y Y ++ ++ P   +   A  + + LD ++M  AAQ L+
Sbjct: 59  IDQILAVTQETHARFTATSRTYEYIVVNQKDPF--QHHGAHYVFQPLDIQSMNKAAQILL 116

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           G  DF  F   +    + I  I H   V + G L+   + A  FL   +R+ VG+L  +G
Sbjct: 117 GEKDFECFSKSNSDVHTFICDITHAKWVATKGQLV-FTITANRFLRNMVRAIVGTLLEIG 175

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            GK   TD+   L+ + R + GP  P +GLY   + Y
Sbjct: 176 TGKRPVTDIPLLLETKSRSKAGPSVPAKGLYLTQINY 212


>gi|312199990|ref|YP_004020051.1| tRNA pseudouridine synthase A [Frankia sp. EuI1c]
 gi|311231326|gb|ADP84181.1| tRNA pseudouridine synthase A [Frankia sp. EuI1c]
          Length = 297

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 87/255 (34%), Positives = 126/255 (49%), Gaps = 20/255 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQV 61
           R  + + Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTD+GVHA RQV
Sbjct: 30  RLRIDLAYDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDAGVHAARQV 89

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH D+  E     L + LN  L  +  + IL +      F ARFSA+ R Y YRI    A
Sbjct: 90  AHVDIPDEVPLGGLARRLNGVLDRA--VRILGIGPAPVGFDARFSALSRRYNYRI--SDA 145

Query: 122 PLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIRTID 173
           P   +  R     AW  P+ LD   MR+AA  L+G HDF  F    C   + ++ +RT+ 
Sbjct: 146 PYGADPLRRHDTLAW--PRPLDPAVMRLAALALLGEHDFAAF----CRRREGATTVRTLL 199

Query: 174 HFDVNSFGNLIEIR-VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             DV    + + +  V A +F H+ +R+ VG+L  VG+G+     + + L    R     
Sbjct: 200 RLDVRRGPDGVLVADVEADAFCHSMVRALVGALVGVGEGRQPPGWIPQMLARAVRSPGVT 259

Query: 233 LAPPEGLYFDSVEYS 247
           + P  GL    V Y 
Sbjct: 260 VLPAHGLTLVEVRYP 274


>gi|308178101|ref|YP_003917507.1| tRNA pseudouridylate synthase A [Arthrobacter arilaitensis Re117]
 gi|307745564|emb|CBT76536.1| tRNA pseudouridylate synthase A [Arthrobacter arilaitensis Re117]
          Length = 311

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 86/261 (32%), Positives = 127/261 (48%), Gaps = 19/261 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           IR  M++ Y+G+ Y GW RQ N   +Q  +E+A+ ++    V V  AGRTD+GVHA RQV
Sbjct: 25  IRMRMVLGYDGAAYSGWARQPNVLGVQQLVEEALEMLIRRQVRVVVAGRTDAGVHARRQV 84

Query: 62  AHFDLVREWVPVI-----------LCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            HFDL  E    +           L + +N  L   D  + +       + F ARFSA+ 
Sbjct: 85  VHFDLTEEEYTSLPRKAPLAPGPALVRRINGILGRQDGAVWVHEAERAPEGFDARFSALA 144

Query: 110 RSYLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           R Y YRI   Q    PL  +    W   + LD E M   A+ ++GRHDF T+      A+
Sbjct: 145 RRYSYRIADGQQRWDPLTRQLT-TWHR-EELDVEAMNREARSVLGRHDFLTYCKPRPHAT 202

Query: 167 SPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           + IRT+  F      + L+   + A +F H  +R+ +G+  +VGDG+     L + L+  
Sbjct: 203 T-IRTLQEFTFTRGADGLVLAHLKADAFCHNMVRALIGAAMMVGDGREQPGFLAERLELM 261

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
            R     L+ P  L  + V Y
Sbjct: 262 VRDSKTKLSHPRALVLEEVYY 282


>gi|299140694|ref|ZP_07033832.1| tRNA pseudouridine synthase A [Prevotella oris C735]
 gi|298577660|gb|EFI49528.1| tRNA pseudouridine synthase A [Prevotella oris C735]
          Length = 243

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+GS Y GWQ Q NG S+Q  +++A+  +  + + + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLSYDGSAYHGWQIQPNGISVQEKLQEALSKLLRQKIEIVGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  +      L   LN  L     I+I  +  V+   HARFSA  R+Y Y I T++
Sbjct: 61  VAHFDFPKSIEEEQLRYRLNRLL--PRDITINKVIPVEADMHARFSAKWRTYRYYIHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNS 179
              A  +  ++  P  LD + M   A+ L    DF  F        S + TI     V +
Sbjct: 119 D--AFLRHYSYESPYKLDYQLMNQGAELLKSHTDFAAFCKTGADNKSTLCTIRESKWVQT 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L L+G    +  DL+  LQ  DR   G   P   L
Sbjct: 177 SAISWYFEITANRFLRNMVRATVGTLFLLGRHHISLDDLDYILQEGDRSNAGESMPGHAL 236

Query: 240 YFDSVEY 246
           + +++EY
Sbjct: 237 FLENIEY 243


>gi|261749109|ref|YP_003256794.1| putative tRNA pseudouridine synthase A [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
 gi|261497201|gb|ACX83651.1| putative tRNA pseudouridine synthase A [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
          Length = 247

 Score =  119 bits (297), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 122/246 (49%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  Y GWQ Q   +S++G +E  +  +    + + GAGRTD GVHA +  
Sbjct: 1   MRFFIELSYNGKSYHGWQIQSEVNSVEGQLEYCLSKLLNTSINIVGAGRTDRGVHAKQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD   E +     K LN +L    +I + N+  V K  HARF+A+RR+Y Y + + + 
Sbjct: 61  AHFDF-EEKISNNFVKRLNLFL--PKSIYVSNIFPVKKHIHARFNALRRTYKYYLKSEKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +  +W     LD + M +A+Q L+   DF++F        + I  I H D +   
Sbjct: 118 PFF--QDFSWHCFYPLDIQRMNLASQILMKYKDFSSFCKKRKDKKNNICDIYHADWSRNK 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAPPEGLY 240
                 + A  FL   +RS +G+L  VG GK +     + ++ ++   C  P  P  GL+
Sbjct: 176 IHFCFTIEANRFLRNMVRSIIGTLIDVGRGKISINQFIEIIELKNPNTCSSPSVPACGLF 235

Query: 241 FDSVEY 246
              + Y
Sbjct: 236 LTKILY 241


>gi|253582682|ref|ZP_04859903.1| tRNA pseudouridine synthase A [Fusobacterium varium ATCC 27725]
 gi|251835552|gb|EES64092.1| tRNA pseudouridine synthase A [Fusobacterium varium ATCC 27725]
          Length = 246

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 83/246 (33%), Positives = 120/246 (48%), Gaps = 10/246 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           IRY     ++GS ++G+QRQ    ++QG IEK + +V  E V +  AGRTD GVHAL QV
Sbjct: 10  IRY----RFDGSMFYGFQRQPGKRTVQGEIEKLLEVVLREKVNMISAGRTDRGVHALEQV 65

Query: 62  AHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           ++F      +PV   K ALN  L +   I I  +  VD  F++RF A  R Y Y I   +
Sbjct: 66  SNF-FTTSPIPVEKLKYALNKGLPLD--IEIFEVEEVDMNFNSRFFAKNRGYKYIISWVK 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E     L+ + +D E      + L+G HDF  FR   C + + IR I    V   
Sbjct: 123 NP--FESRYVTLVREKIDKEIFFKILEPLIGVHDFNNFRLSDCGSKTSIREIYSIVVEEK 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N + + +   SFL +QIR  +G+   +  G +    L   L+   +     +A P GLY
Sbjct: 181 ENKLIVEIKGNSFLKSQIRIIIGTALDIYFGNYDENHLRDMLENPKKDFLKKVADPYGLY 240

Query: 241 FDSVEY 246
              + Y
Sbjct: 241 LSEINY 246


>gi|221632949|ref|YP_002522172.1| tRNA pseudouridine synthase A [Thermomicrobium roseum DSM 5159]
 gi|221155520|gb|ACM04647.1| tRNA pseudouridine synthase A [Thermomicrobium roseum DSM 5159]
          Length = 279

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 88/258 (34%), Positives = 129/258 (50%), Gaps = 16/258 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY +   Y G+ + G QRQ    ++QG +E+A+  + GE V V  AGRTD+GVHA+ QVA
Sbjct: 5   RYRLDFGYEGTAFSGSQRQPGLRTVQGVLEEALARLAGEPVRVALAGRTDAGVHAVGQVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            FDL        L +AL A+L   + + +  ++ +   FHAR  A+ R Y YRI   + P
Sbjct: 65  SFDLCWRHDEATLARALQAWL--PEDVVVYRVARMPAGFHARRGAVDREYRYRIWQGEQP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSP-IRTIDHFD-- 176
               +   W     LD   M+ AAQ  +G HDF +F        +A++P +RTI   +  
Sbjct: 123 PLFLRRFVWRFAGLLDLRAMQEAAQFFLGSHDFRSFAGHGLGGPKATTPRVRTITMAEWH 182

Query: 177 --------VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                   V +   ++E RV A  FL   +R+ V +L  VG G    + + + L+  DR+
Sbjct: 183 LLSPVVEPVGTGAQIVEFRVRANGFLPQMVRTMVSALVRVGTGAAEPSWISELLERCDRR 242

Query: 229 ECGPLAPPEGLYFDSVEY 246
              P APP GL    V Y
Sbjct: 243 AAPPPAPPGGLVLWRVRY 260


>gi|118473191|ref|YP_885908.1| tRNA pseudouridine synthase A [Mycobacterium smegmatis str. MC2
           155]
 gi|118174478|gb|ABK75374.1| tRNA pseudouridine synthase A [Mycobacterium smegmatis str. MC2
           155]
          Length = 291

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 84/263 (31%), Positives = 124/263 (47%), Gaps = 22/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G I++A+  V    VV   AGRTD+GVHA  QV
Sbjct: 11  VRLRLDIAYDGTDFAGWAVQAGQRTVAGVIDEALTTVFRTPVVTRVAGRTDTGVHATGQV 70

Query: 62  AHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           AH D+  E +P                L + L  +L     + + ++      F ARFSA
Sbjct: 71  AHVDVPAEALPHAYPRHTRPTDAEFTPLVRRLAGFLPAD--VRVRDIVRAPAGFDARFSA 128

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           +RR Y+YR+ T  AP   E      +    + LD + M  AAQ L+G +DF  F      
Sbjct: 129 LRRHYVYRLTT--APYGPEPHETRFVTPWTRPLDVDAMNAAAQELLGLNDFAAFCRYRAG 186

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           A++ IR +   +    G  I   V A +F    +RS VG+L  VG+G+ +     + L A
Sbjct: 187 ATT-IRDLQRLEWVRNGFYINAYVTADAFCWNMVRSLVGALLKVGEGRRSPEWTAELLGA 245

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
             R    P AP  GL   +V+Y 
Sbjct: 246 TSRSSEFPAAPARGLTLAAVDYP 268


>gi|289449823|ref|YP_003475752.1| tRNA pseudouridine synthase A [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
 gi|289184370|gb|ADC90795.1| tRNA pseudouridine synthase A [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
          Length = 274

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 78/245 (31%), Positives = 122/245 (49%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++ E++G+ Y GWQ Q N  +IQ +++KA+  +  + V+V+G  RTD+GVHA   V++F 
Sbjct: 7   ILTEWDGTAYGGWQIQANAPTIQENLQKALEKLCHKSVLVNGCSRTDAGVHARGHVSNFH 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +  ALNA L   + I++   + +   F+ARF A  + Y Y I   +   AL
Sbjct: 67  FDSSIPVANIPLALNAMLP--EDIAVQAATEMPLDFNARFDACGKQYSYYICNTKLRHAL 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF----G 181
               +    + L    MR AA ++ G HDF  F +   Q  S +RT+   D+ S+    G
Sbjct: 125 YSRYSCCEARPLSAAAMREAAGYIEGTHDFACFMASGGQVKSTVRTVYSVDLVSYPICGG 184

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +  I V    FL+  +R   G+L  VG  K    D+ + L++  R E G   P  GL+ 
Sbjct: 185 AIWRIIVRGNGFLYNMVRIIAGTLLYVGLNKLNPQDVREVLRSGHRSEAGKTLPACGLFL 244

Query: 242 DSVEY 246
           D V Y
Sbjct: 245 DRVFY 249


>gi|281425834|ref|ZP_06256747.1| tRNA pseudouridine synthase A [Prevotella oris F0302]
 gi|281400095|gb|EFB30926.1| tRNA pseudouridine synthase A [Prevotella oris F0302]
          Length = 243

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+GS Y GWQ Q NG S+Q  +++A+  +  + + + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLSYDGSAYHGWQIQPNGISVQEKLQEALSKLLRQEIEIVGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  +      L   LN  L     I+I  +  V+   HARFSA  R+Y Y I T++
Sbjct: 61  VAHFDFPKSIEEEQLRYRLNRLL--PRDITINKVIPVEADMHARFSAKWRTYRYYIHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNS 179
              A  +  ++  P  LD + M   A+ L    DF  F        S + TI     V +
Sbjct: 119 D--AFLRHYSYESPYKLDYQLMNQGAELLKSHTDFAAFCKTGADNKSTLCTIRESKWVQT 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L L+G    +  DL+  LQ  DR   G   P   L
Sbjct: 177 SAISWYFEITANRFLRNMVRATVGTLFLLGRHHISLDDLDYILQEGDRSNAGESMPGHAL 236

Query: 240 YFDSVEY 246
           + +++EY
Sbjct: 237 FLENIEY 243


>gi|167752124|ref|ZP_02424251.1| hypothetical protein ALIPUT_00366 [Alistipes putredinis DSM 17216]
 gi|167660365|gb|EDS04495.1| hypothetical protein ALIPUT_00366 [Alistipes putredinis DSM 17216]
          Length = 390

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 84/248 (33%), Positives = 120/248 (48%), Gaps = 8/248 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQRQ +  S+Q +IE AI  +  E +++ GAGRTD+GV+A   V
Sbjct: 126 MRYFIELRYNGGAYCGWQRQPDMPSVQQTIEGAISTLLREPILLTGAGRTDTGVNASYYV 185

Query: 62  AHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD       P  +   LN  L     I++  +  V    HARFSA  R Y Y I  R+
Sbjct: 186 AHFDTSSPVADPEQVVFKLNHMLP--GDIAVSRIVPVAADAHARFSAREREYRYYIEPRK 243

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--VN 178
            P        + +P  LD   M  AA  L+   DFT+F  ++    + I  +   D  V 
Sbjct: 244 NPFTRAASWQYYVP--LDVAAMNRAADVLMEYEDFTSFAKLNSDNKTNICHLKRADWTVG 301

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G L    + A  FL   +R+ VG+L  VG G++T       + ++D       AP +G
Sbjct: 302 RDGTLC-FTIRADRFLRNMVRAIVGTLVDVGRGRYTVEQFRDIVASRDLSRSSAGAPAQG 360

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 361 LFLSDVLY 368


>gi|169630847|ref|YP_001704496.1| tRNA pseudouridine synthase A [Mycobacterium abscessus ATCC 19977]
 gi|169242814|emb|CAM63842.1| tRNA pseudouridine synthase A [Mycobacterium abscessus]
          Length = 294

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 84/263 (31%), Positives = 130/263 (49%), Gaps = 22/263 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW  Q N  ++ G + +A   + G+ V ++ AGRTD+GVHA  Q
Sbjct: 15  LVRLRLDIAYDGTDFAGWATQVNQRTVAGVLGEAFTTIVGDSVQLYAAGRTDAGVHATGQ 74

Query: 61  VAHFDLVREWVPVI--------------LCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           VAH D+    +P +              L + L+ +L  SD + +L++S     F ARFS
Sbjct: 75  VAHLDVPVACLPGLRGRYRPAGAPEFDRLVRRLSRFLP-SD-VRVLDISRAPAHFDARFS 132

Query: 107 AIRRSYLYRIITRQ---APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A+RR Y YR+ T      PLA      W  P  LD + M  A+++L+G  DF  F   H 
Sbjct: 133 ALRRHYEYRLSTASFGVLPLARHDVVGWHRP--LDVDAMNEASRNLLGLRDFAAF-CRHR 189

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           + ++ IR +  FD    G  +   V A +F  + +RS VG++  VG+G+         L 
Sbjct: 190 EGATTIRELQRFDWGVDGQRLTAYVSADAFCWSMVRSLVGAVLAVGEGRRPVQWCVDLLN 249

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
            + R      AP  GL    V+Y
Sbjct: 250 KERRSSDFAAAPARGLTLVGVDY 272


>gi|22297651|ref|NP_680898.1| tRNA pseudouridine synthase A [Thermosynechococcus elongatus BP-1]
 gi|34222849|sp|Q8CWM6|TRUA_THEEB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|22293828|dbj|BAC07660.1| tRNA-pseudouridine synthase I [Thermosynechococcus elongatus BP-1]
          Length = 284

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 117/247 (47%), Gaps = 7/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ    ++Q  IE+AI  V    V V  AGRTD+GVHA  QVA
Sbjct: 13  RLALLIQYQGTHFHGWQRQVGQRTVQEVIEQAIASVVNHPVSVVAAGRTDTGVHAAGQVA 72

Query: 63  HFDLVREWVPVILCKA-LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           H   V   +PV      LNA  ++   + I   + V   +HARFSA+ R Y Y + T   
Sbjct: 73  HVT-VNSPIPVHRWPGILNA--RLPADVVIRAAAAVPPDWHARFSALWRRYRYTLYTDPC 129

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
           P    +   W      LD   M    Q LVGRH  + F RS   +A S +  +       
Sbjct: 130 PNIFLRPWTWHYYYAPLDVAKMAAVLQPLVGRHHLSAFHRSGSNRAHSWVE-VQAVSCQR 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L+EI V A  FL+  +R  VG L  VG G+ +     +  Q + R      APP GL
Sbjct: 189 RGALVEIEVQASGFLYGMMRLLVGLLVQVGQGQRSPASFTEIWQQEQRHLVKYAAPPSGL 248

Query: 240 YFDSVEY 246
               V Y
Sbjct: 249 CLLGVGY 255


>gi|237741391|ref|ZP_04571872.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
 gi|229430923|gb|EEO41135.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
          Length = 245

 Score =  118 bits (296), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 78/242 (32%), Positives = 123/242 (50%), Gaps = 13/242 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F    +
Sbjct: 12  YDGSRYYGFQRQPDKITVQGEIEKILRIVTKEEINLISAGRTDRGVHANHQVSNFYTSSN 71

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I  ++ P   
Sbjct: 72  IPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKMREYIYIISWKKNP--F 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
           E      + + +  + +       VG HDF  FR   C +   IR I   +V  FG N I
Sbjct: 124 EARYCKFVKEKIIAKKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVKYFGENKI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   EGLY + +
Sbjct: 184 KIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLTDFTKEYKKNLVEAEGLYLNKI 243

Query: 245 EY 246
            Y
Sbjct: 244 SY 245


>gi|325105198|ref|YP_004274852.1| tRNA pseudouridine synthase A [Pedobacter saltans DSM 12145]
 gi|324974046|gb|ADY53030.1| tRNA pseudouridine synthase A [Pedobacter saltans DSM 12145]
          Length = 258

 Score =  118 bits (296), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 78/253 (30%), Positives = 127/253 (50%), Gaps = 19/253 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + + Y+G  Y GWQ Q N  ++Q  ++ A+    GE +   G GRTD+GVHA +  A
Sbjct: 6   RFFIELSYHGLQYHGWQYQPNAITVQEKLDNALSTFFGEKIESLGCGRTDTGVHATQFYA 65

Query: 63  HFDLVREW---VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           HFD  +E+     +   K +N+ L     I++ +L  V +  HARF AIRRSY Y I   
Sbjct: 66  HFDTEKEFSENSEIRFLKGINSLLPYD--IAVKHLHQVHEDAHARFDAIRRSYEYHIHFN 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID------ 173
           + P   +   +WL  + L+ + M I A +++   DF  F    C+A++   T +      
Sbjct: 124 KNP--FKTYTSWLHKEPLNVDAMNIGASYILDYEDFGAF----CKANAGNFTNNCIVSRA 177

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            ++V + G  I   + A  FL   +R+ VG+L  +G GK+    ++  ++++ R   G  
Sbjct: 178 EWEVKNDG--IIFHITANRFLRNMVRAIVGTLTDIGKGKYAPEHIKHIIESKKRSSAGAS 235

Query: 234 APPEGLYFDSVEY 246
            P  GL    V Y
Sbjct: 236 VPACGLLLTEVCY 248


>gi|254495151|ref|ZP_05108075.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
 gi|85819501|gb|EAQ40658.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
          Length = 241

 Score =  118 bits (296), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 123/246 (50%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQ Q +  S+Q  +  A+  +  + + V GAGRTD+GVHA +  
Sbjct: 1   MRYFIELSYNGKNYHGWQIQPDVISVQEKLNSALSTIFQQDIQVVGAGRTDTGVHASQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+ +        K LN+ L     I +  + +VD + HARF A+ RSY Y+I   + 
Sbjct: 61  AHFDVDKNLKGDFAFK-LNSIL--PKDIVVYKVFLVDDEKHARFDAVSRSYEYKIWLGRN 117

Query: 122 PLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P  L+   +W I  +  D + M  AA+ L    DF TF  +  +  +    +        
Sbjct: 118 PFLLD--FSWQIHSQKPDLKLMNEAAKLLTEYTDFQTFSKVKTEVYTFNCDVTEAFWEQK 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +   + A  FL   +R+ VG+L  VG GK +  D    +++++R   G   P +GL+
Sbjct: 176 GEELTFHISANRFLRNMVRAIVGTLLDVGFGKISIDDFRNIIESKNRGNAGLSVPAKGLF 235

Query: 241 FDSVEY 246
              ++Y
Sbjct: 236 LTQIKY 241


>gi|284035717|ref|YP_003385647.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
 gi|283815010|gb|ADB36848.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
          Length = 252

 Score =  118 bits (295), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 125/254 (49%), Gaps = 20/254 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ Y GWQ Q NG SIQ ++E A+    G+ V + G+GRTD+GVHA +Q 
Sbjct: 1   MRYFIELSYRGTAYHGWQTQANGISIQITLEAALSQRLGKPVYIMGSGRTDAGVHAKQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHFD      P+ + ++L   L   + + I+I  +  V  + HARFSAI R Y Y  ITR
Sbjct: 61  AHFDSEE---PLDITESLIYSLNCMLPEDIAIHAIFPVSDKTHARFSAISRYYQYH-ITR 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-------IHCQASSPIRTI 172
           Q   A +    +     L+ + M  A   L+   +F +F          HCQ        
Sbjct: 117 QKD-AFQGTLTYHFRPQLNVDRMNEACTLLLRHTNFQSFSKARANVTHFHCQLEFAYWRY 175

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            + D  +F       + A  FL   +R+ VG++  +G  + +    EK + A+DRK  G 
Sbjct: 176 TNVDCLTF------HIKANRFLWGMVRTIVGTMLEIGQERMSLEQFEKIILARDRKIAGR 229

Query: 233 LAPPEGLYFDSVEY 246
            AP  GLY   V Y
Sbjct: 230 AAPANGLYLVEVGY 243


>gi|262039471|ref|ZP_06012775.1| tRNA pseudouridine synthase A [Leptotrichia goodfellowii F0264]
 gi|261746538|gb|EEY34073.1| tRNA pseudouridine synthase A [Leptotrichia goodfellowii F0264]
          Length = 249

 Score =  118 bits (295), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 125/244 (51%), Gaps = 6/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+ +Y+GS ++G+QRQKN  ++QG IEK I     + + +  +GRTD GVHAL QV++F 
Sbjct: 9   MVYQYDGSKFYGFQRQKNKKTVQGEIEKVILKNFSQKINMISSGRTDKGVHALGQVSNF- 67

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            + E +P+  + + +N  L     I IL++  + ++F++RF A  R+YLY +   +    
Sbjct: 68  FIDEKIPLEAIKRQINKNL--YGEIKILSVEEIKREFNSRFDAKSRTYLYIMKKEEEITP 125

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DVNSFGN 182
            E      I   ++ E  +   +   G++DF++F        + +R I +   +      
Sbjct: 126 FESNYITGIKNDINIEQFQKIMEIFKGKYDFSSFMKKDKAIRNTMREIYNIKCEYEEREK 185

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + +   SFL T IR  +GS   +  GK     ++  L+  D  +   LAP EGLY  
Sbjct: 186 KIYVEICGSSFLKTMIRIMIGSAMAIYFGKEREDYIKMRLENPDADKPKILAPSEGLYLY 245

Query: 243 SVEY 246
            V+Y
Sbjct: 246 RVDY 249


>gi|238018655|ref|ZP_04599081.1| hypothetical protein VEIDISOL_00490 [Veillonella dispar ATCC 17748]
 gi|237865126|gb|EEP66416.1| hypothetical protein VEIDISOL_00490 [Veillonella dispar ATCC 17748]
          Length = 261

 Score =  118 bits (295), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 129/245 (52%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           +I+ Y+G+   G+Q+Q +  G ++QG +E  +  +  E + ++GA RTD+GVHA  QV  
Sbjct: 6   IIVAYDGTDLAGYQKQPDDKGLTVQGCLEYGLSKICNEPIQIYGASRTDAGVHAKFQVCT 65

Query: 64  FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +PV  + +A+ A+  I   I +L    +   +  R++   + Y+Y I  +   
Sbjct: 66  FQTSGS-IPVENIPRAMIAH--IPKDIVVLEALEIPLDWKPRWNIYGKEYVYTIHNQLIA 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L K   W + K L+ + M+ A   L+G HDFTT +  +   + P++TI    V + G+
Sbjct: 123 NPLTKRYHWHVKKPLNIDLMQAAGNELLGTHDFTTLKGTNSTPADPVKTIIGIHVEAEGS 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + I VV   FL+  +R+  G L  VG G+    D++  L A+DR+  G  AP +GL  +
Sbjct: 183 HVTISVVGDGFLYHMVRNIAGLLVDVGLGRRKVEDIKGYLAAKDRRVIGKTAPAQGLCLE 242

Query: 243 SVEYS 247
            + ++
Sbjct: 243 EIFFT 247


>gi|257064823|ref|YP_003144495.1| pseudouridylate synthase I [Slackia heliotrinireducens DSM 20476]
 gi|256792476|gb|ACV23146.1| pseudouridylate synthase I [Slackia heliotrinireducens DSM 20476]
          Length = 271

 Score =  118 bits (295), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 87/256 (33%), Positives = 131/256 (51%), Gaps = 21/256 (8%)

Query: 8   IEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + Y+G+ + G+ RQ       ++QG +E A+ ++    V    AGRTD+GVHA+ QV  F
Sbjct: 21  VAYDGAPFAGFARQAECDRVMTVQGELEHALRVLYRRDVRTTCAGRTDAGVHAIGQVVSF 80

Query: 65  DLVREW----VPVILCKALNAYLKISDTISILNLSIVDKQ---FHARFSAIRRSYLYRII 117
           D+  +      P  L ++LNA   + D +S+   S+V+++   F ARF A  R Y YRI 
Sbjct: 81  DVTEDEFASRTPRSLLRSLNAL--VDDHMSV---SVVEEKPFGFSARFDAKWREYRYRIS 135

Query: 118 TRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTI 172
           T  A   L     W L    LD + M  AA HL+G HDF +F         P    +  +
Sbjct: 136 TAAARPVLIMPLVWHLGGVDLDIDAMNRAAVHLIGEHDFKSFCVAASAVGKPTCRNVMEL 195

Query: 173 DHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           + F+    G  +  +RVV  +FLH+ +R+ VG+L  VG G+     +   L+A++R   G
Sbjct: 196 EVFEEEILGQQVATVRVVGNAFLHSMVRTIVGTLVEVGRGRRNPEWVCDVLEARNRGAAG 255

Query: 232 PLAPPEGLYFDSVEYS 247
             AP +GL F  VEY 
Sbjct: 256 QNAPAQGLVFWHVEYE 271


>gi|260592560|ref|ZP_05858018.1| tRNA pseudouridine synthase A [Prevotella veroralis F0319]
 gi|260535606|gb|EEX18223.1| tRNA pseudouridine synthase A [Prevotella veroralis F0319]
          Length = 253

 Score =  118 bits (295), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 122/265 (46%), Gaps = 31/265 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E+++  +  E V + G GRTD+GVH    
Sbjct: 1   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLERSLSTLLREEVSITGGGRTDAGVHGRMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAHFD  +     I C+ L   L   +   +S+  +  V +  HARFSA  R+Y Y + T
Sbjct: 61  VAHFDTDK----TIACQQLVYKLNRLLPRDVSVSQIVPVSEDLHARFSATSRTYHYYVHT 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-----------------RSI 161
            + P + +       P  LD + M  AA +L+G  DF  F                 R I
Sbjct: 117 TKQPFSRQYSCEIHYP--LDFDKMNEAADYLIGEKDFKCFCKTGADVKTTICNLTEARWI 174

Query: 162 HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            C+A   + T D      F       + A  FL   +RS VG+L  VG G+ +  + +  
Sbjct: 175 PCKAEQALVTSDRITNWCF------VISANRFLRNMVRSVVGTLVDVGRGRLSLEEFQAI 228

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           +    R + G   P   L+   ++Y
Sbjct: 229 VNNGSRSDAGESMPGNALFLWDIKY 253


>gi|50955536|ref|YP_062824.1| tRNA pseudouridine synthase A [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|62901288|sp|Q6AD25|TRUA_LEIXX RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|50952018|gb|AAT89719.1| tRNA pseudouridine synthase A [Leifsonia xyli subsp. xyli str.
           CTCB07]
          Length = 288

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 86/268 (32%), Positives = 132/268 (49%), Gaps = 29/268 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA---IFLVTGEIVVVHGAGRTDSGVHALR 59
           R+ + I Y G+ + GW RQ +  ++QG++E+A   IF  +GE   +  AGRTD+GVHA  
Sbjct: 7   RFRLDIAYQGTDFAGWARQPDLRTVQGTLEEALATIFRCSGEPPSLTVAGRTDAGVHATG 66

Query: 60  QVAHFDLVREWVPVI---------------LCKALNAYLKISDTISILNLSIVDKQFHAR 104
           QVAH DL  E V ++               L + +N  L     + +   +     F AR
Sbjct: 67  QVAHVDLSPEQVALLRRPHGKREPQLAHDALKRRVNGVLGPVPDVLVSRATEAPAGFDAR 126

Query: 105 FSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R Y YR+  R A    L++ R   +P +LD + M   A  ++G HDF ++    C
Sbjct: 127 FSALWRRYEYRVADRIALRDPLQRHRTAWVPNTLDVDAMDRGAHGMLGLHDFASY----C 182

Query: 164 QA---SSPIRTIDHFD--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
           +A   ++ IRT+  F    ++ G L+   V A +F H+ +R+ VG+   VG+GK    DL
Sbjct: 183 KAREGATTIRTLQAFSWRRDAEGVLLG-EVAADAFCHSMVRALVGACVEVGEGKLRPGDL 241

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
                 + R     + P  GL    V Y
Sbjct: 242 VTLRDERQRTSAFKVMPARGLTLREVGY 269


>gi|89893262|ref|YP_516749.1| hypothetical protein DSY0516 [Desulfitobacterium hafniense Y51]
 gi|89332710|dbj|BAE82305.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 271

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 121/246 (49%), Gaps = 6/246 (2%)

Query: 5   CMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           C+ + Y+G+ Y G+QRQ   +G +IQG++E     +  E V ++ AGRTD+GVHA  QV 
Sbjct: 8   CLKVAYDGTYYHGFQRQPEFHGPTIQGTLEAVWAKLVEEEVTLNTAGRTDTGVHAAGQVV 67

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           +F      +PV  + KA N+ L     I IL      + FHARFSA  + Y YRI     
Sbjct: 68  NFR-TGARIPVDKIPKAFNSLL--PRDIRILAAQEAAENFHARFSAKWKRYDYRIDNHPV 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  +   P  LD + M+  AQ+LVGRH+F  F +    + +  RT+    V    
Sbjct: 125 ADVFTRLYSLHEPVRLDWQRMQQGAQYLVGRHNFKAFSAAGGTSKTFERTLYLCQVAENQ 184

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I  +   FL+  +R   G+L  VG  +    ++   L + DRK  G  A P+GL  
Sbjct: 185 GHLRITCIGDGFLYNMVRIIAGTLVYVGKNRIQPGEIPDILASLDRKRGGVTATPQGLTL 244

Query: 242 DSVEYS 247
             V Y 
Sbjct: 245 SYVHYG 250


>gi|12045035|ref|NP_072845.1| tRNA pseudouridine synthase A [Mycoplasma genitalium G37]
 gi|255660331|ref|ZP_05405740.1| tRNA pseudouridine synthase A [Mycoplasma genitalium G37]
 gi|1351308|sp|P47428|TRUA_MYCGE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3844778|gb|AAC71401.1| tRNA pseudouridine synthase A [Mycoplasma genitalium G37]
 gi|166078658|gb|ABY79276.1| tRNA pseudouridine synthase A [synthetic Mycoplasma genitalium
           JCVI-1.0]
          Length = 244

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 120/248 (48%), Gaps = 8/248 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  I+ Y+GS + GW  Q N ++IQG +E++  L+ G  + V G+GRTD GVHA+ Q
Sbjct: 1   MARYLGIVSYDGSYFKGWAIQPNLATIQGLLEQSFSLIIGRKIKVIGSGRTDKGVHAINQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             H D+  E    +L + +N  +K    +  L L  V+  FHARF    + Y Y +I   
Sbjct: 61  TFHVDINGEINLNLLIRKINQLIKPHCIVKTLVL--VNDSFHARFQVKTKVYEY-LINCG 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
               L+    W + + LD E ++  A   +G+ +F +F  SIH   +  IRTI    +  
Sbjct: 118 NLNPLQFNYVWQLNQQLDLEKLKADATLFLGKKNFLSFSSSIH---TDSIRTISKITIQK 174

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N L+ +      FL +Q+R  V  L  +   K     + K  +   +  C   AP  G
Sbjct: 175 ETNQLVRLTFFGSGFLRSQVRMIVACLVNLNTNKMALETVAKLFEHPKKGSCVVKAPSCG 234

Query: 239 LYFDSVEY 246
           LY  +V Y
Sbjct: 235 LYLKTVVY 242


>gi|213582886|ref|ZP_03364712.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 214

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 74/200 (37%), Positives = 103/200 (51%), Gaps = 4/200 (2%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           GRTD+GVH   QV HF+             +NA L     I++  +  V   FHARFSA 
Sbjct: 1   GRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSAT 58

Query: 109 RRSYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R Y Y I   R  P  L KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +
Sbjct: 59  ARRYRYIIYNHRLRPAVLAKGVTHYY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRT 117

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           P R + H +V   G  + + + A +F+H  +R+ VGSL  VG      + + + L A+DR
Sbjct: 118 PWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAARDR 177

Query: 228 KECGPLAPPEGLYFDSVEYS 247
                 A  EGLY  +V+Y 
Sbjct: 178 TLAAATAKAEGLYLVAVDYP 197


>gi|227505250|ref|ZP_03935299.1| tRNA pseudouridine synthase A [Corynebacterium striatum ATCC 6940]
 gi|227198149|gb|EEI78197.1| tRNA pseudouridine synthase A [Corynebacterium striatum ATCC 6940]
          Length = 285

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/268 (33%), Positives = 133/268 (49%), Gaps = 34/268 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW RQK    ++QG +E  + ++    V +  AGRTD+GVH+  Q
Sbjct: 4   VRLRLDLAYDGTDFHGWARQKGDLRTVQGVLEDNLSMILRHDVELTVAGRTDAGVHSAGQ 63

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAHFD+  E +        P  L + L   L   + + +   +   + F ARFSA++R Y
Sbjct: 64  VAHFDVPSEALDQRSIDGDPAKLVRRLAKLLP--EDVRVHACTAAPEGFDARFSALQRHY 121

Query: 113 LYRIIT--RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YRI T  R A P        W  PK +D + M+ AA  LVG HDF  F    C+A    
Sbjct: 122 VYRITTHPRGALPTRARDTAQW--PKPVDIDAMQEAATTLVGLHDFAAF----CKAKPHA 175

Query: 170 RTIDHFDVNSF----------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            TI   D++SF            L E RV A +F  + +RS VG    VG+G     D  
Sbjct: 176 TTI--RDLHSFEWVDVSTPTEPQLYEARVCADAFCWSMVRSLVGCCLRVGEGA-RDVDFA 232

Query: 220 KALQAQDRKECG-PLAPPEGLYFDSVEY 246
            A+ A+ ++    PLAP +GL    V+Y
Sbjct: 233 TAMLAESQRSSQIPLAPAKGLSLVRVDY 260


>gi|257470657|ref|ZP_05634747.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|317064863|ref|ZP_07929348.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|313690539|gb|EFS27374.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
          Length = 242

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 121/246 (49%), Gaps = 10/246 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           IRY     ++GS ++G+QRQ    ++QG IEK + +V  E V +  AGRTD GVHAL QV
Sbjct: 6   IRY----RFDGSMFYGFQRQPGKRTVQGEIEKLLDIVLREKVNMISAGRTDRGVHALEQV 61

Query: 62  AHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           ++F L    +PV   K ALN  L +   I I  +   D  F++RF A  R+Y Y I   +
Sbjct: 62  SNF-LTSSPIPVEKLKHALNKGLPLD--IEIFEVEDADIDFNSRFMAKDRAYRYVISWIK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E     L+ + +D  N     + LVG +DF  FR   C + + IR I        
Sbjct: 119 NP--FESRYVTLVNEKIDKNNFVKILEPLVGVNDFNNFRLSDCGSKTSIREIYSITAEEK 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N + I +   SFL +QIR  +G+   V  G      L+  L+  ++     +A P GLY
Sbjct: 177 ENKLIINIKGNSFLKSQIRIMMGTALDVYFGNRDENYLKNMLKNPNKDFIKKVADPYGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LSEVNY 242


>gi|163783710|ref|ZP_02178697.1| pseudouridine synthase I [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881035|gb|EDP74552.1| pseudouridine synthase I [Hydrogenivirga sp. 128-5-R1-1]
          Length = 239

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 127/244 (52%), Gaps = 7/244 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + + + G+ Y GWQ Q    ++QG++++A+  V GE + V G  RTD+GVHA   
Sbjct: 1   MNNYMLRLAFVGTNYSGWQIQPGVPTVQGTLKEALETVFGEEIRVIGCCRTDAGVHAEDY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F  ++E     L +ALN+ L     I +  + +VD+ F++R+S   ++YLYR+    
Sbjct: 61  VANFRSIKELECEKLLRALNSLL--PKDIGVYEVKLVDENFNSRYSVKGKTYLYRLWNSF 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    +W + + +D   +  A + + GRHDF  F  +    ++ I       V+  
Sbjct: 119 VRNPFLYPFSWSVTRRVDLNLLSEALEIVSGRHDFRGFAKLEEDKTTVIELETKLAVS-- 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LIE+R  A  FL   +R  VG++    +GK ++ +L + L+    K C   AP +GL 
Sbjct: 177 GDLIELRFTASHFLRYMVRRLVGAIVKRAEGKVSTGELYEYLKG---KHCPHTAPAKGLT 233

Query: 241 FDSV 244
            + V
Sbjct: 234 LERV 237


>gi|72382942|ref|YP_292297.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. NATL2A]
 gi|72002792|gb|AAZ58594.1| tRNA pseudouridine synthase [Prochlorococcus marinus str. NATL2A]
          Length = 276

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 81/251 (32%), Positives = 121/251 (48%), Gaps = 14/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  ++I+Y+GSG+ GWQ QK+  ++QG++E+ I  L     V    AGRTDSGVHA  QV
Sbjct: 4   RIALVIQYDGSGFRGWQNQKDSITVQGTLEEKIAELDPIRPVKAIAAGRTDSGVHASGQV 63

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      + +W       ALN  L  S  I +L    V K +HA +SA  R Y Y I
Sbjct: 64  VHFDCSGPIPIHKW-----ASALNGRLPAS--IKVLEAVGVPKVWHACYSAKYRRYRYSI 116

Query: 117 ITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                P    +  +W   +  LD   M+ A   L+G HDF  F+      S+ + T+   
Sbjct: 117 FNGSYPNLFLQNISWHKYRFMLDINLMKHALNDLLGLHDFAAFQKAGSNRSNSLTTVQDV 176

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            ++ +G+++ + + A  FL+  +R  +G L  VG+ + +        +   R E    AP
Sbjct: 177 SISRYGDIVTVEIQASGFLYGMVRLLMGQLVAVGEKRLSLEKFRYRWRKGLRSEVKEAAP 236

Query: 236 PEGLYFDSVEY 246
             GL    V Y
Sbjct: 237 AHGLCLIRVGY 247


>gi|34762680|ref|ZP_00143671.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|27887637|gb|EAA24715.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
          Length = 245

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 78/242 (32%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F    +
Sbjct: 12  YDGSRYYGFQRQPDKITVQGEIEKILRIVTKEEINLISAGRTDRGVHANHQVSNFYTSSN 71

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I   + P   
Sbjct: 72  IPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKMREYVYIISWEKNP--F 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
           E      + + +  + +       VG HDF  FR   C +   IR I   +V  FG N I
Sbjct: 124 EARYCKFVKEKIIAKKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVKYFGENKI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   EGLY + +
Sbjct: 184 KIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLNDFTKEYKKNLVEAEGLYLNKI 243

Query: 245 EY 246
            Y
Sbjct: 244 SY 245


>gi|262066902|ref|ZP_06026514.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
 gi|291379371|gb|EFE86889.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
          Length = 248

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 120/244 (49%), Gaps = 15/244 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F     
Sbjct: 14  YDGSRYYGFQRQPNKITVQGEIEKILKIVTKEDINLISAGRTDRGVHANHQVSNF-YTSS 72

Query: 70  WVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +PV     +L +AL         I IL++  V++ F+AR  A  R Y+Y I   + P  
Sbjct: 73  SIPVGKYKYLLTRAL------PKDIDILSVEEVNEDFNARHDAKMREYVYIISWDKNP-- 124

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NL 183
            E      +   +D E +       +G HDF  FR   C +   +R I   DV  F  N 
Sbjct: 125 FETRYCKFVKDKIDAEKLERIFSSFLGVHDFKNFRLSDCVSKVTVREIYSIDVKYFSENK 184

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           ++I +   +FL +Q+R  VG+   V     +   +E  L    ++    L   EGLY + 
Sbjct: 185 LKIFIRGSAFLKSQVRIMVGTALEVYYKNLSENHIELMLNNFSKEYKKYLVEAEGLYLNK 244

Query: 244 VEYS 247
           + YS
Sbjct: 245 INYS 248


>gi|116334238|ref|YP_795765.1| pseudouridylate synthase [Lactobacillus brevis ATCC 367]
 gi|122269080|sp|Q03PY8|TRUA_LACBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116099585|gb|ABJ64734.1| Pseudouridylate synthase [Lactobacillus brevis ATCC 367]
          Length = 265

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 124/256 (48%), Gaps = 15/256 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHA 57
           M RY + + Y+G+ + G+QRQ N  +++ ++   +  +  +    +V++G+GRTD+GVHA
Sbjct: 1   MQRYKVTLMYDGTNFAGFQRQPNKRTVESTLTDVVNKMAKQPDPAIVIYGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV HFD         + K LN+ L +   + +L +  V   FHAR+    + Y YR+ 
Sbjct: 61  LAQVVHFDFPFLIPADNMRKGLNSMLPMD--MEVLKVEEVAPTFHARYDVSGKQYQYRMD 118

Query: 118 TRQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID-- 173
             +   P        W  P  +D   + +A   LVG HD+T+F +   Q  + +RTI   
Sbjct: 119 MGEFRNPFKRNYTGHWKFP--VDLAKINVALADLVGEHDYTSFVASGAQTRTFVRTIYEA 176

Query: 174 --HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
             H D  +   + E       F++ Q+R  VG L  +G G     D+ +  + +DRK+  
Sbjct: 177 TCHIDEANHELVFEF--YGNGFMYNQVRIMVGVLVEIGSGTRPVHDVLRLYEVKDRKQAR 234

Query: 232 PLAPPEGLYFDSVEYS 247
              P  GLY   V Y 
Sbjct: 235 RTVPAAGLYLKHVYYQ 250


>gi|115730971|ref|XP_781664.2| PREDICTED: similar to MGC80334 protein [Strongylocentrotus
           purpuratus]
 gi|115939533|ref|XP_001190679.1| PREDICTED: similar to MGC80334 protein [Strongylocentrotus
           purpuratus]
          Length = 306

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 92/283 (32%), Positives = 139/283 (49%), Gaps = 38/283 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSS-------IQGSIEKAIFLVTGEIVV-VHGAGRTD 52
           M R+ +  +Y G+ Y G  R  + S+       +Q  IE A+  +   I V +H + RTD
Sbjct: 1   MGRFLIYFQYIGTRYRGVVRATSLSASGEKFVGVQDVIEGALDELKPVIPVKLHVSSRTD 60

Query: 53  SGVHALRQVAHFDLV---------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           +GVHAL   AHFD++         R+ +   +  A+N  L+  D I I+    V   FH+
Sbjct: 61  TGVHALCNTAHFDMIFKSKRTGEPRDILAESITAAVNKKLEDHD-IRIIKTLRVQDSFHS 119

Query: 104 RFSAIRRSYLYRIIT--RQAPLAL-EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR- 159
           +  A+ R+YLYR+    RQ  L + EK R+W   + LD  +M+ A+   VG HDFT FR 
Sbjct: 120 QHLAMGRTYLYRLAMGCRQIELPVFEKNRSWAFDQRLDIPSMKEASGRFVGTHDFTAFRN 179

Query: 160 -SIHCQASSPIRTIDHFDV-----------NSFGNL--IEIRVVARSFLHTQIRSFVGSL 205
            S+     SPI+TID  +            N    L  +E+   +RSFL+ QIR   G+L
Sbjct: 180 SSMDDDKKSPIKTIDMIEFRRTRGFLYHHCNKMAQLEFLELTFHSRSFLYKQIRRMTGAL 239

Query: 206 KLVGDGKWTSTDLEKALQAQDRKEC--GPLAPPEGLYFDSVEY 246
             VG G+   + +   L+++D        +AP  GLY   + Y
Sbjct: 240 VAVGLGRIAPSHITTILESRDNSHMHRTTMAPAHGLYLKEISY 282


>gi|219666536|ref|YP_002456971.1| tRNA pseudouridine synthase A [Desulfitobacterium hafniense DCB-2]
 gi|219536796|gb|ACL18535.1| tRNA pseudouridine synthase A [Desulfitobacterium hafniense DCB-2]
          Length = 271

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 121/246 (49%), Gaps = 6/246 (2%)

Query: 5   CMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           C+ + Y+G+ Y G+QRQ   +G +IQG++E     +  E V ++ AGRTD+GVHA  QV 
Sbjct: 8   CLKVAYDGTYYHGFQRQPEFHGPTIQGTLETVWAKLVEEQVTLNTAGRTDTGVHAAGQVV 67

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           +F      +PV  + KA N+ L     I IL      + FHARFSA  + Y YRI     
Sbjct: 68  NF-RTGARIPVDKIPKAFNSLL--PRDIRILAAQEAAEDFHARFSAKWKRYDYRIDNHPV 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  +   P  LD + M+  AQ+LVGRH+F  F +    + +  RT+    V    
Sbjct: 125 ADVFTRLYSLHEPVRLDWQRMQQGAQYLVGRHNFKAFSAAGGTSKTFERTLYLCQVAENQ 184

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I  +   FL+  +R   G+L  VG  +    ++   L + DRK  G  A P+GL  
Sbjct: 185 GHLRITCIGDGFLYNMVRIIAGTLVYVGKNRIQPGEIPDILASLDRKRGGVTATPQGLTL 244

Query: 242 DSVEYS 247
             V Y 
Sbjct: 245 SYVHYG 250


>gi|294784150|ref|ZP_06749451.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
 gi|294488220|gb|EFG35565.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
          Length = 245

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 78/242 (32%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF----D 65
           Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA  QV++F    +
Sbjct: 12  YDGSRYYGFQRQPDKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAYHQVSNFYTSSN 71

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +L +AL       + I IL++  VD+ F+AR +A  R Y+Y I   + P   
Sbjct: 72  IPIEKYKYLLTRAL------PNDIDILSVEEVDENFNARHNAKIREYIYIISWEKNP--F 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
           E      + + +  + +       VG HDF  FR   C +   IR I   +V  FG N I
Sbjct: 124 EARYCKFVKEKIIAKKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVKYFGENKI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   EGLY + +
Sbjct: 184 KIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLTDFTKEYKKNLVEAEGLYLNKI 243

Query: 245 EY 246
            Y
Sbjct: 244 SY 245


>gi|217967401|ref|YP_002352907.1| tRNA pseudouridine synthase A [Dictyoglomus turgidum DSM 6724]
 gi|226708649|sp|B8E1G5|TRUA_DICTD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217336500|gb|ACK42293.1| tRNA pseudouridine synthase A [Dictyoglomus turgidum DSM 6724]
          Length = 245

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 123/248 (49%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + I Y G  ++G+Q+Q    +IQG +EK +  +  E + V GAGRTD+GVHAL Q
Sbjct: 1   MTNWKLEISYIGKDFYGFQKQPGKRTIQGELEKVLSFLFDEEIRVIGAGRTDTGVHALGQ 60

Query: 61  VAHFDLV--REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V +F     + +    L K LN  L   + I I  + IVD  FHAR+SA RR Y+Y +  
Sbjct: 61  VVNFKSRGHKGFSCDKLHKVLNRLL--PEDIKIKKVEIVDDSFHARYSAKRRWYIYVVYN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                   K  +W I + ++ E +  +A    G HDF  F     +  + I   + F   
Sbjct: 119 NDERDLFLKDYSWWISREINRELLIFSANLFKGVHDFKNFCVTEDEDQTVIEVYESFWYF 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+   + A  FL   +R  VGS+  +  G+ +  +LE  L+ + ++     APP G
Sbjct: 179 K-KDLLIYFISAPFFLRKMVRFIVGSMVEIALGRKSLIELEDYLKEERKERFSVPAPPWG 237

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 238 LYLFRVDY 245


>gi|258646098|ref|ZP_05733567.1| tRNA pseudouridine synthase A [Dialister invisus DSM 15470]
 gi|260403476|gb|EEW97023.1| tRNA pseudouridine synthase A [Dialister invisus DSM 15470]
          Length = 265

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 110/234 (47%), Gaps = 2/234 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y G+ Y G+QRQ+N  ++Q  +E A+  +TG    ++ A RTD+GVHA  Q   F 
Sbjct: 6   ITLAYEGTAYSGFQRQENSITVQEILETALQKLTGTKTTLYFAARTDAGVHAYGQECTFY 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN  L     I +     V   F  R +   ++Y Y +   +     
Sbjct: 66  TESSIPGDRFIFALNILL--PPDIRVTESREVPYDFSVRRNNYGKTYGYLLTEEKDCPPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            K   W   + LD   M  AA+ L G HDFT+FR  +   +SP+RTI    +    +   
Sbjct: 124 FKRYTWQTGRKLDISKMEKAAEVLSGTHDFTSFRGNNSVPASPVRTIHDIRIIKKHHFFH 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           I V    FL+  +R+  G+L   G GK T  DL + L+A+DRK  G  AP  GL
Sbjct: 184 IFVTGEGFLYHMVRNIAGALADAGTGKLTPKDLREILEAKDRKFLGATAPAHGL 237


>gi|150025482|ref|YP_001296308.1| tRNA pseudouridine synthase A [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772023|emb|CAL43499.1| tRNA-pseudouridine synthase I [Flavobacterium psychrophilum
           JIP02/86]
          Length = 250

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 78/252 (30%), Positives = 119/252 (47%), Gaps = 18/252 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG+ Y GWQ Q N +S+Q ++ K    +  E + + GAGRTD+GVHA +  
Sbjct: 1   MRYFIEFAYNGTQYHGWQYQPNATSVQETLNKVFSTLLQEKIDIMGAGRTDAGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N++L     I I N+  V  Q HARF A  R+Y Y I T + 
Sbjct: 61  GHFDTDISIDNAKFIHKANSFL--PKDIVIFNIIPVHNQAHARFDATSRTYNYHISTYKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-------RSIHCQASSPIRTIDH 174
                   AW   K +D   M  AA+ L+   DF  F        + +C+ +    +I+ 
Sbjct: 119 --VFTNNLAWYSSKKIDVIAMNEAAKVLLKFTDFKCFSKTNTDVNTYNCKITEAFWSIEK 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                   LI   + A  FL   +R+ VG+L  +G  K T  +  + +++Q+R+  G   
Sbjct: 177 ------EQLI-FTITADRFLRNMVRAIVGTLINIGLHKITIENFIQIIESQNRENAGFSV 229

Query: 235 PPEGLYFDSVEY 246
           P  GL+  ++EY
Sbjct: 230 PAHGLFLTNIEY 241


>gi|218132910|ref|ZP_03461714.1| hypothetical protein BACPEC_00771 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991783|gb|EEC57787.1| hypothetical protein BACPEC_00771 [Bacteroides pectinophilus ATCC
           43243]
          Length = 256

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 78/259 (30%), Positives = 123/259 (47%), Gaps = 16/259 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+GS Y GWQR     ++I+  +  AI   TGE   + G+GRTD+GVHAL 
Sbjct: 1   MNNYRLTIQYDGSRYNGWQRLNDTDNTIEQILTDAIIKSTGEKTKLIGSGRTDAGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A+F   +    +   + LN+ L   + I +     V   FH+R SA  + Y+YRI   
Sbjct: 61  QTANFRCRQRLDEMHFTEELNSML--PEDIRVNLTKRVPPDFHSRHSATGKYYVYRIEIS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +W      D + M  AAQ ++G HDF  F +        ++T+  +D+N 
Sbjct: 119 EPANPFRRRYSWKPDGIPDVKLMCEAAQRMIGEHDFKAFCTDAKLMPYTVKTV--YDINI 176

Query: 180 FGN-----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
             +           +IE+      FL+  +R   G++   G G+++  D++  L    R 
Sbjct: 177 HKDYSCLWNREEPGIIELEFHGSGFLYNMVRIMAGTIVDAGLGRFSPADIDAMLNGGTRS 236

Query: 229 ECGPLAPPEGLYFDSVEYS 247
             G LAP  GL+    EYS
Sbjct: 237 MSGQLAPARGLFLKKAEYS 255


>gi|327288532|ref|XP_003228980.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Anolis
           carolinensis]
          Length = 293

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 94/277 (33%), Positives = 139/277 (50%), Gaps = 37/277 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSS---IQGSIEKAI----FLVTGEIVVVHGAGRTDSGV 55
           RY +  +Y+G+ Y G        +   +Q  +EKA      LV  + V+   + RTD+GV
Sbjct: 7   RYLISFQYSGTMYSGVMETPPHQATLGVQNYLEKAAEKLRPLVPVKFVI---SSRTDTGV 63

Query: 56  HALRQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           HAL   AH D+ R      +   +L +ALN  LK  + I +L    V   FHARFSA+ R
Sbjct: 64  HALCNTAHIDIERSGGKPPFSESVLVQALNRNLK-HEPIRVLAARRVSDTFHARFSALSR 122

Query: 111 SYLYRIITR-QAPLAL---EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQ- 164
           +Y+YR++T    P  L   E+   W+  +  LD   M+ AA  LVG HDF+TFRS   + 
Sbjct: 123 TYVYRVVTGCSCPSDLPVFERNLCWVTQRGHLDLTAMQEAAGLLVGTHDFSTFRSASSEL 182

Query: 165 -ASSPIRTIDHFDVN-SFGNLI-----------EIRVVARSFLHTQIRSFVGSLKLVGDG 211
            A +P++TID  ++  S G L+           E+   +RSFL+ Q+R   G L  VG  
Sbjct: 183 PAKNPVKTIDQLEIRPSSGFLMHHVKSSDLKFWELEFTSRSFLYKQVRRMAGVLVAVGQH 242

Query: 212 KWTSTDLEKALQAQDRKECGP--LAPPEGLYFDSVEY 246
           +     ++  L  +D     P  +AP  GL+  +VEY
Sbjct: 243 RLDPECVKTLLDIRDLMAYPPSTIAPACGLFLKNVEY 279


>gi|256544630|ref|ZP_05472002.1| tRNA pseudouridine synthase A [Anaerococcus vaginalis ATCC 51170]
 gi|256399519|gb|EEU13124.1| tRNA pseudouridine synthase A [Anaerococcus vaginalis ATCC 51170]
          Length = 252

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 120/245 (48%), Gaps = 11/245 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I+Y+GS + G+Q QKN  ++Q  +E AI  VTGE   +  +GRTDSGVHA     +F   
Sbjct: 10  IQYDGSLFEGFQIQKNKRTVQKELEDAIRKVTGEENRIIASGRTDSGVHANEMYINFLTA 69

Query: 68  REWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +    +I     + +LK  + D I  L    VDK FHARFS   ++Y Y I   +    +
Sbjct: 70  K----IIRADKFHFHLKKYLPDDILALESKKVDKNFHARFSVKTKTYKYVISLDKILHPI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTID--HFDVNSFGN 182
            +     I   LD + ++   + L G HDF  F  S      + IR ID  +F +N   N
Sbjct: 126 YRNYMEQITYKLDFDKLKQGMEILKGEHDFKAFMLSEKNDIINTIRKIDDCYFVLNE--N 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + +   A SFLH Q+R   GSL  +  GK +  D +      + +   P     GLY D
Sbjct: 184 RLYLYFKAESFLHNQVRIMAGSLIELSRGKISLDDFKYYFNKNNTRRANPTLKAGGLYLD 243

Query: 243 SVEYS 247
           S++YS
Sbjct: 244 SIDYS 248


>gi|210615874|ref|ZP_03290836.1| hypothetical protein CLONEX_03055 [Clostridium nexile DSM 1787]
 gi|210150077|gb|EEA81086.1| hypothetical protein CLONEX_03055 [Clostridium nexile DSM 1787]
          Length = 247

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 118/244 (48%), Gaps = 6/244 (2%)

Query: 6   MIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + IEY+GS Y GWQR    ++ ++I   I + I  +T E + +    RT+ GVHA  Q A
Sbjct: 6   LTIEYDGSRYQGWQRLGKDESTNTIANKITEVIKKMTNEDIELFCGSRTEVGVHAYGQAA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F    +   + +   LN YL +   I+I ++    ++FHA  +A  + Y+YRI   + P
Sbjct: 66  SFKTTTDMTLIEIQHYLNRYLPMD--IAITDIEEKPERFHASLNATSKIYMYRISVSEVP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   +   K  D + M+ AA  LVG+HDF  F ++    S+ ++ I   DV   G 
Sbjct: 124 SVFERKYVYHSFKRPDVDLMKQAAILLVGKHDFKKFSTVKKNKST-VKEIYDIDVYDDGE 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            ++I +    FLH   R  +G+L  +G G     D+E    +         A P+GLY  
Sbjct: 183 ELQITLHGNDFLHNMARMILGTLLDIGVGNRKKEDIELIFDSNSDVAASAPADPKGLYLQ 242

Query: 243 SVEY 246
            V Y
Sbjct: 243 EVLY 246


>gi|307128564|ref|YP_003880594.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri CARI]
 gi|306483026|gb|ADM89896.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri CARI]
          Length = 252

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 80/252 (31%), Positives = 132/252 (52%), Gaps = 14/252 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R+ + I Y+G+ ++GWQ Q    S+Q +IEK + FL+   I ++ GAGRTD+GVHA++ 
Sbjct: 1   MRFFLEISYHGALFYGWQIQNKNISVQETIEKCLSFLLKKNIKII-GAGRTDAGVHAIQM 59

Query: 61  VAHFDLVREWVPV--ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            AHFD  +  + +   +   LN +L ++  I I N+  V  + HARF+ + R Y YRI  
Sbjct: 60  FAHFDFNQNLLLIDKNIKFKLNYFLPLN--IKIKNIFSVKNKIHARFNVLSRVYEYRIFL 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT-IDHFDV 177
            + P  L+    WL  K +  + +   A+ L    D+++F    C+  S  +T I H   
Sbjct: 118 EKNPFYLDTSWQWLYKKKIKIKILNKGAKLLKKYKDYSSF----CKKKSNNKTYICHIFY 173

Query: 178 NSF---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +      +   + A  FL   +RS VG+L  +G  K T  D  + ++A++R   G  A
Sbjct: 174 AKWILKKKKLFFYIEANRFLRNMVRSIVGTLIELGIKKITLKDFIQIIEAKNRHLAGISA 233

Query: 235 PPEGLYFDSVEY 246
           P +GL+   + Y
Sbjct: 234 PAKGLFLIKINY 245


>gi|296130457|ref|YP_003637707.1| tRNA pseudouridine synthase A [Cellulomonas flavigena DSM 20109]
 gi|296022272|gb|ADG75508.1| tRNA pseudouridine synthase A [Cellulomonas flavigena DSM 20109]
          Length = 306

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 90/271 (33%), Positives = 135/271 (49%), Gaps = 32/271 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----TGEIVV-VHGAGRTDSGV 55
           +R  + + Y+G G+ GW RQ    ++QG +E A+  V      GE    V  AGRTD+GV
Sbjct: 12  VRLRLDLAYDGGGFAGWARQPGLRTVQGELEDALATVLRSGPRGEPRPRVTVAGRTDAGV 71

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDT--ISILNLSIV-------DKQFHARFS 106
           HA  QVAH D+V + +     ++  A + +  T    IL   +V        + F ARFS
Sbjct: 72  HARGQVAHVDVVPDALAAARGRSDRAAVDVLGTRLAGILPPDVVVHAVRHAPEGFDARFS 131

Query: 107 AIRRSYLYRIITRQA---PLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSI 161
           A+RR Y YR+   +    PL     R W++   ++LD   M  AA+ LVGRHDF  +   
Sbjct: 132 ALRRRYAYRVCDSEGTRDPLR----RGWVLWHRRALDVAAMDAAARSLVGRHDFAAYCKP 187

Query: 162 HCQASSPIRTIDHF------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
              A++ IRT++ F      D    G L+   V A +F H+ +R+ VG+   VG+G+   
Sbjct: 188 RPDATT-IRTLEEFTWTRPVDGPDAG-LVVAHVQADAFCHSMVRALVGASLAVGEGRRPV 245

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           T     L A+ R+    +  P+GL  + V Y
Sbjct: 246 TWPRDLLDARTRQGGATVVAPQGLTLEDVGY 276


>gi|314935862|ref|ZP_07843214.1| tRNA pseudouridine synthase A [Staphylococcus hominis subsp.
           hominis C80]
 gi|313656427|gb|EFS20167.1| tRNA pseudouridine synthase A [Staphylococcus hominis subsp.
           hominis C80]
          Length = 267

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 116/243 (47%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G G+ G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA  Q 
Sbjct: 1   MRILVNIAYQGHGFLGFQIQQQGRTVQQQFEKILKRMHRRHVRIHPSSRTDRGVHAYEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   + I + ++  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIEPKQWIYAMNSAL--PEDIYVNSVKQVDDTFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    I   LD + M  AA+H +G HDFT F S   +  S  RT+   +V    
Sbjct: 119 RNPFESGLKTFIKDDLDLDKMNEAAKHFIGTHDFTGFCSQKTEVESKERTLYQSEVVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+A++R      AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLVEVGKGKRQPNEVPELLKAKNRDNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|281420165|ref|ZP_06251164.1| tRNA pseudouridine synthase A [Prevotella copri DSM 18205]
 gi|281405965|gb|EFB36645.1| tRNA pseudouridine synthase A [Prevotella copri DSM 18205]
          Length = 247

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 82/252 (32%), Positives = 121/252 (48%), Gaps = 14/252 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y+G+ Y GWQ Q N +S+Q  +++A+ ++  + + V GAGRTD+GVHA    
Sbjct: 1   MRYFIFFGYDGTNYHGWQIQPNANSVQQELQRALSILLRKEMEVVGAGRTDTGVHARHMA 60

Query: 62  AHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD  R    P  L   LN  L     I++  +  V  + HARFSAI R+Y Y I T++
Sbjct: 61  AHFDTDRIPMEPDQLVYRLNRILPRD--IAVYEVMEVAPEMHARFSAISRTYHYYIHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR-TIDHFD--- 176
            P   E+  +  +   L+ E M  AAQH +   D+  F    C+A    + TI H     
Sbjct: 119 DP--FERHYSLQMNYPLNFEKMNEAAQHFLHHEDYAAF----CKAGGDNKTTICHVTAAR 172

Query: 177 -VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            + +        + A  FL   +R+ VG+L  VG  K T       L    R + G   P
Sbjct: 173 WIQTSPTTWYFEITANRFLRNMVRAVVGTLIDVGREKITMEQFLDILHNGSRSDAGESMP 232

Query: 236 PEGLYFDSVEYS 247
              L+ + V Y 
Sbjct: 233 GNALFLEDVGYD 244


>gi|292557750|gb|ADE30751.1| tRNA pseudouridine synthase [Streptococcus suis GZ1]
          Length = 222

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 72/216 (33%), Positives = 111/216 (51%), Gaps = 5/216 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  L +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQPHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   + S+ I ++++  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTSEDIDVVSVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTITVASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           +     +        FL+ Q+R+ VG+L  +G+G+ 
Sbjct: 179 DQQRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRM 214


>gi|225013075|ref|ZP_03703490.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-2A]
 gi|225002803|gb|EEG40784.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-2A]
          Length = 248

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 119/247 (48%), Gaps = 7/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G+ Y GWQRQ N  S+Q  +E A+  +  E + +  +GRTD+GVHA +  
Sbjct: 1   MRYFLEFSYAGTNYHGWQRQPNAVSVQEVLEHALSTLLKETISLLASGRTDTGVHARQMF 60

Query: 62  AHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHFD  L  E    ++ + LN +L     I + +L  V  + HARF A+ RSY Y I   
Sbjct: 61  AHFDGKLSLETFQQLVYQ-LNQFL--PQDIVVHSLREVKAEAHARFDALSRSYEYHIALG 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P        + I + LD E M  AA  L+   DF  F        + +  I +   + 
Sbjct: 118 KTPFG--NSMHYRINQDLDLEAMNEAAAILLEYEDFECFSKSRTDVKTFLCDISYAQWSK 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N     + A  FL   +R+ VG+L  +G  K    DL   ++++ R + G   P +GL
Sbjct: 176 TKNGYIFTITANRFLRNMVRAIVGTLIEIGLKKKEIEDLRGIIKSKSRSKAGFSVPAQGL 235

Query: 240 YFDSVEY 246
           +   +EY
Sbjct: 236 FLTRIEY 242


>gi|254282596|ref|ZP_04957564.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR51-B]
 gi|219678799|gb|EED35148.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR51-B]
          Length = 222

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 73/205 (35%), Positives = 104/205 (50%), Gaps = 14/205 (6%)

Query: 48  AGRTDSGVHALRQVAHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFH 102
           AGRTD+GVH   Q+ HFD       + WV       +     +  T+ +     V+  FH
Sbjct: 6   AGRTDTGVHGFAQIVHFDDPVGRSEKAWV-------MGTNSALPSTVRVHWAHPVEDDFH 58

Query: 103 ARFSAIRRSYLYRII-TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFSA  R+Y Y I  TR  P  L     W + ++LD + M  AAQ LVG HDF+ FR+ 
Sbjct: 59  ARFSAELRTYRYVIANTRVHPAQLAGLVTW-VRRALDADVMNKAAQALVGEHDFSAFRAA 117

Query: 162 HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            C A++P+R ++   +   G+L+ I + A +FLH  +R+  GSL +VG G  T+      
Sbjct: 118 SCGANTPMRRVEQISITRRGDLVVIEIAANAFLHHMVRNIAGSLIMVGSGLRTADWFRDI 177

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
            + +DR      A   GLY   V Y
Sbjct: 178 FRGRDRTVAADTAAAAGLYLIHVSY 202


>gi|94987504|ref|YP_595437.1| tRNA pseudouridine synthase A [Lawsonia intracellularis PHE/MN1-00]
 gi|123082124|sp|Q1MPG1|TRUA_LAWIP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|94731753|emb|CAJ55116.1| Pseudouridylate synthase [Lawsonia intracellularis PHE/MN1-00]
          Length = 257

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 88/266 (33%), Positives = 127/266 (47%), Gaps = 28/266 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R    + Y G+ Y GWQ Q+  S     +IQ ++EK I  + G+ V V GAGRTD+GV
Sbjct: 1   MPRLKFTLAYVGTAYHGWQTQRRKSLPELPTIQSTLEKVIASIIGKPVRVCGAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+    + +     LNA L     I +++   V+  FHA+  A+++ Y YR
Sbjct: 61  HAEGQVAHVDIPESKLKLDWQLVLNASL--PKNIRVVHSLYVEDTFHAQHDAVQKLYAYR 118

Query: 116 IITRQA-------PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           +            P     GR       LD E M  A+  L+G H+F + ++   +  S 
Sbjct: 119 LWLNHRYTPPVLYPFVWSCGR-------LDLEAMDKASTFLLGTHNFVSLQNRGTKLLST 171

Query: 169 IRTIDHF--DVNSFGNLIEIRVV-----ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           +RTI     + + F +L E   V     A  FL   +R+ +G L LVG  K     +   
Sbjct: 172 VRTISALYREPSQFFSLNESHEVTWFFKADGFLKQMVRNIMGLLVLVGRRKIQPEKIPYI 231

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
           L+A+DR+   P AP  GL    V YS
Sbjct: 232 LEAKDRRHSAPTAPAHGLTLKKVFYS 257


>gi|331702049|ref|YP_004399008.1| tRNA pseudouridine synthase A [Lactobacillus buchneri NRRL B-30929]
 gi|329129392|gb|AEB73945.1| tRNA pseudouridine synthase A [Lactobacillus buchneri NRRL B-30929]
          Length = 267

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 74/255 (29%), Positives = 123/255 (48%), Gaps = 15/255 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHAL 58
           IRY + + Y+G+ + G++RQ    +I+G + + + ++       +VV+G+GRTD+GVHAL
Sbjct: 4   IRYKVTLAYDGTLFSGFERQPKRRTIEGVLTQKVNIMAKNPDPPIVVYGSGRTDAGVHAL 63

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   +     + + LN+ L +   + I     V   FHAR+    + Y+YR+  
Sbjct: 64  GQVVHFDFPFDLPTKAIYRGLNSLLPLD--MEIKKAEKVSNTFHARYDVSGKRYVYRLDL 121

Query: 119 RQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +   P        W  P  +D E ++ A    VG HDF++F +    A S +RTI  ++
Sbjct: 122 GEFKDPFKRNYTGNWRFP--IDIERVQTAMNDFVGEHDFSSFVASGSTARSNVRTI--YE 177

Query: 177 VNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            N+      N I +      FL+  +R  VG +  +G       D+ +  + +DR +   
Sbjct: 178 ANAILDKSANEIRLEFYGNGFLYNMVRIMVGVVVEIGSQMRPEHDILRLYEVKDRDQARR 237

Query: 233 LAPPEGLYFDSVEYS 247
             P  GLY   V Y 
Sbjct: 238 TMPASGLYLKKVYYE 252


>gi|170077660|ref|YP_001734298.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7002]
 gi|238689046|sp|B1XJI2|TRUA_SYNP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169885329|gb|ACA99042.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7002]
          Length = 274

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 115/246 (46%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ    ++Q  IE+ I  V G+ + +HGAGRTDSGVHA  Q A
Sbjct: 11  RIALVIQYIGTHFCGWQRQTAERTVQAVIEETISTVVGQKITIHGAGRTDSGVHAAGQFA 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+           K LN   ++   I+I     V + +HA+FSA  R Y Y I T   P
Sbjct: 71  HFECESLIPGYKWAKILND--RLPPDINIRGACEVSQDWHAQFSAQWRRYRYTIYTHPTP 128

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  AW      LD   ++ A   L+G H    F+    + S     +   + +  G
Sbjct: 129 NLFIQPYAWHYYQAPLDETLIQAALTPLLGEHHLAAFQRTGSKRSHAWVNVQAAECSRRG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A  FL+  +R  VG L  +G GK +    +   + + R      AP +GL  
Sbjct: 189 SFIHIEIQANGFLYGMVRLLVGMLVDIGQGKLSLAQFQDIWKNEKRHLVKYSAPAKGLCL 248

Query: 242 DSVEYS 247
             V Y 
Sbjct: 249 LRVGYP 254


>gi|57867747|ref|YP_189363.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis RP62A]
 gi|293368464|ref|ZP_06615088.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|62901168|sp|Q5HM30|TRUA_STAEQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57638405|gb|AAW55193.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis RP62A]
 gi|291317422|gb|EFE57844.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329737018|gb|EGG73273.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU045]
          Length = 267

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 118/243 (48%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVNETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDKNRNNVPLTAPPDGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|294794578|ref|ZP_06759714.1| tRNA pseudouridine synthase A [Veillonella sp. 3_1_44]
 gi|294454908|gb|EFG23281.1| tRNA pseudouridine synthase A [Veillonella sp. 3_1_44]
          Length = 254

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 125/243 (51%), Gaps = 6/243 (2%)

Query: 8   IEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + Y+G+   G+Q+Q N  G ++QG +E  +  +  E + ++GA RTD+GVHA  QV  F 
Sbjct: 1   MAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAKFQVCTFQ 60

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                +PV  + +A+ A+  I   I +L    +   +  R++   + Y+Y I  +     
Sbjct: 61  -TSGTIPVENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYVYTIHNQLIADP 117

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L K   W + K LD + M+ A   L+G HDFTT +  +   + P++TI    V      +
Sbjct: 118 LTKRYHWHVKKPLDIDRMQAAGNELLGTHDFTTLKGTNSTPADPVKTILGIHVKVKEAHV 177

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I VV   FL+  +R+ VG L  VG G+    D++  L A+DR+  G  AP +GL  + +
Sbjct: 178 TISVVGDGFLYHMVRNIVGLLVDVGLGRRKVEDIKGYLVAKDRRVIGKTAPAQGLCLEEI 237

Query: 245 EYS 247
            ++
Sbjct: 238 FFT 240


>gi|27468710|ref|NP_765347.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis ATCC
           12228]
 gi|32130291|sp|Q8CML6|TRUA_STAES RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|27316258|gb|AAO05433.1|AE016750_38 tRNA pseudouridine synthase A [Staphylococcus epidermidis ATCC
           12228]
 gi|329731249|gb|EGG67619.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU144]
          Length = 267

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 118/243 (48%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVNETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDKNRNNVPLTAPPDGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|227872273|ref|ZP_03990632.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
 gi|227841885|gb|EEJ52156.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
          Length = 249

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 125/247 (50%), Gaps = 5/247 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALRQ 60
           Y +I+ Y+GS YFG+++QK+  ++IQG +E     + G  E V + GA RTD+GVHA   
Sbjct: 5   YKLIVAYDGSRYFGFEKQKDQEATIQGKLEGVFSRIPGNEEGVEIIGASRTDAGVHARGM 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+  L  E     +    N YL   + I+I+++  V  +FHAR++A+ + Y Y     +
Sbjct: 65  CANVFLDTELSEEEILDYGNRYL--PEDIAIVSVKKVSPRFHARYNALGKIYRYSCYIGR 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++     + +  D E M+ AA+ L+G+ DF +F        S IR+I    +   
Sbjct: 123 TKPVFDRKILLHLEEEPDLEAMQEAAKFLIGKQDFKSFCGNPKMKKSTIRSISSIRIQKS 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            NL+        FL  QIR  VG+L  VG  K  + D+   + A+DR++ G   P +GL 
Sbjct: 183 QNLLRFYFEGSGFLQYQIRIMVGTLLEVGYHKRKAGDIPGIIDAKDRQQAGYTVPAKGLC 242

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 243 LMKVLYD 249


>gi|269128483|ref|YP_003301853.1| tRNA pseudouridine synthase A [Thermomonospora curvata DSM 43183]
 gi|268313441|gb|ACY99815.1| tRNA pseudouridine synthase A [Thermomonospora curvata DSM 43183]
          Length = 288

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 78/250 (31%), Positives = 126/250 (50%), Gaps = 4/250 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           ++R  + I Y+G+ + GW RQ +  ++QG IE+A+   L       +  AGRTD+GVHA 
Sbjct: 6   LVRLRLDIGYDGTDFSGWARQPDRRTVQGVIEEALGRVLRLDPPPALTVAGRTDAGVHAR 65

Query: 59  RQVAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH D+       +  + ++     +   + +  +++  + F ARFSA+ R Y+YR+ 
Sbjct: 66  GQVAHVDVPERAYAAVSNRLVHRLAGLLPPDVRVWRIAVAPRGFDARFSALWRRYVYRVC 125

Query: 118 TRQAPLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            R+A +   + R  L  P+ LD + M  AA  L+G HDF  F      A++  R + +  
Sbjct: 126 DREAGVDPLRRREVLWHPRPLDLDRMNEAAARLLGEHDFAAFCRRREGATTIRRLLRYEW 185

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 L    VVA +F H+ +R+ VG+L  VGDG+       + L A  R     +AP 
Sbjct: 186 RREEPALAAATVVADAFCHSMVRALVGALLAVGDGRREVDWPARVLAAGVRDSAVNVAPA 245

Query: 237 EGLYFDSVEY 246
            GL  + + Y
Sbjct: 246 HGLSLEEIGY 255


>gi|332712143|ref|ZP_08432071.1| pseudouridylate synthase I [Lyngbya majuscula 3L]
 gi|332348949|gb|EGJ28561.1| pseudouridylate synthase I [Lyngbya majuscula 3L]
          Length = 277

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 77/245 (31%), Positives = 114/245 (46%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ ++GWQRQ    S+Q  IE  +  V    + ++GAGRTD+GVHA  QVA
Sbjct: 11  RIALVIQYLGNNFYGWQRQPQHRSVQSEIETVLSSVQQRAITLYGAGRTDTGVHAAAQVA 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             LN+  ++ + I +   ++V + +HARFSAI R Y Y I T   P
Sbjct: 71  HFNATGPIPAHRWAAILNS--RLPEDILVRASALVSQDWHARFSAIWRRYRYTIYTDACP 128

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +   W      LD   ++ A + L+G+H    F   +   S     +   +    G
Sbjct: 129 NLFVQPFCWHYYQAPLDESLIQAALKPLLGKHHLAAFHRSNSGRSHSWVNVQAAECYRNG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+  +R  VG L  VG GK T          Q R +    +P +GL  
Sbjct: 189 PFIHIEIQANGFLYGMVRLLVGMLVQVGIGKLTPEQFTDIWVNQQRDKVKHASPAKGLCL 248

Query: 242 DSVEY 246
             V Y
Sbjct: 249 LRVGY 253


>gi|310658388|ref|YP_003936109.1| tRNA pseudouridine synthase a [Clostridium sticklandii DSM 519]
 gi|308825166|emb|CBH21204.1| tRNA pseudouridine synthase A 2 (tRNA-uridine isomerase I 2) (tRNA
           pseudouridylate synthase I 2) [Clostridium sticklandii]
          Length = 245

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 116/240 (48%), Gaps = 3/240 (1%)

Query: 8   IEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           ++Y G+ Y GWQR K+  ++IQG +E  +  +T E V V G  RTD GVHA   +A+F  
Sbjct: 8   LQYEGTRYLGWQRLKDQDNTIQGKLEDLLNKMTDEEVQVIGCSRTDKGVHAKSLIANFHT 67

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
             +     +   +N YL   + I +  +   D +FHAR +A  + Y + I          
Sbjct: 68  NSKMTLHEIQTYMNYYL--PEDIRVTYIEEADDKFHARHNAKTKVYRFTIDNNSFADVFT 125

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +  A   PK LD + M  AA +L+G HD+  F ++  +  S  ++I    +    N + +
Sbjct: 126 RKTAIHQPKQLDIKAMEKAANYLIGTHDYDAFTTMKSKKKSCRKSIKSIAITKKNNYVYL 185

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                 FLH  IR   G+L  VG G+ +  +L   L ++DR   GP+   +GL    V Y
Sbjct: 186 EFEGEGFLHNMIRIITGTLIRVGTGEISPEELANILASKDRSLSGPMVEGKGLMLMQVNY 245


>gi|228474552|ref|ZP_04059283.1| tRNA pseudouridine synthase A [Staphylococcus hominis SK119]
 gi|228271215|gb|EEK12583.1| tRNA pseudouridine synthase A [Staphylococcus hominis SK119]
          Length = 267

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 116/243 (47%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G G+ G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA  Q 
Sbjct: 1   MRILVNIAYQGHGFLGFQIQQQGRTVQQQFEKILKRMHRRHVRIHPSSRTDRGVHAYEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   + I + ++  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIEPKQWKYAMNSAL--PEDIYVNSVKQVDDTFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    I   LD + M  AA+H +G HDFT F S   +  S  RT+   +V    
Sbjct: 119 RNPFESGLKTFIKDDLDLDKMNEAAKHFIGTHDFTGFCSQKTEVESKERTLYQSEVVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+A++R      AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLVEVGKGKRQPNEVPELLKAKNRDNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|32472096|ref|NP_865090.1| tRNA pseudouridine synthase A [Rhodopirellula baltica SH 1]
 gi|42559754|sp|Q7TU07|TRUA_RHOBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|32397468|emb|CAD72774.1| tRNA pseudouridine synthase A [Rhodopirellula baltica SH 1]
          Length = 276

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 78/256 (30%), Positives = 125/256 (48%), Gaps = 14/256 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + + Y+G+ Y GWQ Q    SIQ  +E+ I  + G  V V G+GRTD+GVHA+ QVA 
Sbjct: 10  FHLTVAYDGTEYCGWQVQPEQRSIQSELERVIRPLAGRPVRVLGSGRTDAGVHAIGQVAR 69

Query: 64  FDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
             L V +   V L +A+N+  K+ + I +  +    ++FH    A  + Y Y +    + 
Sbjct: 70  CVLPVWKADTVALQRAINS--KLPNDIRVKAVRETRERFHPIADATGKQYQYLVQVGGSR 127

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT------IDHFD 176
                     +   +D   M+ AA   VGRHDF  F+    +  S +RT      I    
Sbjct: 128 DPFANRFVNRVGGPIDHSAMQSAAAKFVGRHDFKAFQGTGAERPSTVRTIHSARWIPRVA 187

Query: 177 VNSFGNLIE-----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
               G  +E       +    FL+  +R+ +G++  VG GK +   +++ L ++DRK  G
Sbjct: 188 TGPTGAELEGEHWCFEIDGEGFLYNMVRNLMGTMLEVGRGKKSPNWIDEVLASRDRKMAG 247

Query: 232 PLAPPEGLYFDSVEYS 247
           P APP+GL+   V+Y 
Sbjct: 248 PTAPPQGLFLCRVDYP 263


>gi|256380565|ref|YP_003104225.1| tRNA-pseudouridine synthase I [Actinosynnema mirum DSM 43827]
 gi|255924868|gb|ACU40379.1| tRNA-pseudouridine synthase I [Actinosynnema mirum DSM 43827]
          Length = 314

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 83/258 (32%), Positives = 129/258 (50%), Gaps = 28/258 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW RQ N  ++ G +E  +  V  E VV+  AGRTD+GVHA  QV
Sbjct: 37  VRVRLDLAYDGTEFSGWARQPNRRTVCGVLEDTMSTVLREDVVLTVAGRTDAGVHAAGQV 96

Query: 62  AHFDLVR----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           AH DL        +P  L +AL A       + + +  +V   F ARF+A+RR Y YR+ 
Sbjct: 97  AHVDLPEAADVAGLPKRLARALPA------DVRVFSARVVPAAFDARFAALRRHYEYRVT 150

Query: 118 TRQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
              AP      R     AW  P+ LD   M  A+  ++G  DF  +     + ++ IR +
Sbjct: 151 --DAPFGAHPLRRLDTLAW--PRQLDVAAMNAASGLMLGERDFCAY-CRRREGATTIREL 205

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRK 228
              +    G+L+   V A +F H+ +RS VG+L  VG+G+    W ++ L    ++ +  
Sbjct: 206 QRLEWVREGDLLTAFVSADAFCHSMVRSLVGALLAVGEGRKPVEWPASLLSLHSRSSEVT 265

Query: 229 ECGPLAPPEGLYFDSVEY 246
               +APP GL    V+Y
Sbjct: 266 ----VAPPHGLSLVRVDY 279


>gi|168333393|ref|ZP_02691673.1| tRNA pseudouridine synthase A [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 259

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 86/254 (33%), Positives = 123/254 (48%), Gaps = 20/254 (7%)

Query: 7   IIEYNGSGYFGWQRQKN----GSSIQ---GSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           I+ Y G+ Y G+ RQ      GS IQ     +E AI  +T + V + GAGRTD+GVHAL 
Sbjct: 12  IVAYKGTRYNGFARQAGDKVVGSGIQTISAELELAIEKITQQQVRIVGAGRTDAGVHALA 71

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV   ++  +     L  ALN  L +   I I ++   ++ FH  FS  R+ Y Y+I+  
Sbjct: 72  QVCIANIDTQIGNSGLLLALNNKLPVD--IVIKSIEDAEEGFHPTFSGKRKMYRYQILNT 129

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----RSIHCQASSPIRTIDHF 175
                      +  P  LD E M++AA  LVG HDF  F     ++  + SS +RTI  F
Sbjct: 130 TVSCPFVAEFVYHFPHKLDVEEMKVAAXELVGTHDFRAFCAAKSNVLKKGSSTVRTI--F 187

Query: 176 DV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           D+        +I+I V    FL+  +R   G+  L+  G      + K L+ ++RK  G 
Sbjct: 188 DIVVARGDDEIIKIDVTGDGFLYNMVRIIAGT--LIDKGLGRGMPIAKILEMRERKNAGK 245

Query: 233 LAPPEGLYFDSVEY 246
            AP  GL    VEY
Sbjct: 246 TAPASGLTMIGVEY 259


>gi|332297806|ref|YP_004439728.1| tRNA pseudouridine synthase A [Treponema brennaborense DSM 12168]
 gi|332180909|gb|AEE16597.1| tRNA pseudouridine synthase A [Treponema brennaborense DSM 12168]
          Length = 257

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 77/248 (31%), Positives = 120/248 (48%), Gaps = 9/248 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGS------SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           + + Y+G+ + GWQRQ +        ++Q  +E+A+ ++    V + G+GRTDSGVHA  
Sbjct: 6   LTVSYDGTDFCGWQRQDHADRGEPVRTVQAELERALRIMLKTPVALTGSGRTDSGVHAFA 65

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           Q A+F    + VP      ALN+ L     + +     V   FHARF A  R+Y Y +  
Sbjct: 66  QAANFLSPFDSVPPENYVPALNSSLPPD--VRVTAAREVPPGFHARFDARMRTYRYFLYC 123

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P A E    W I +  D   +   A  L G  D TTF +      S  R ++     
Sbjct: 124 GATPPAHETRYVWPIRRYPDIARLNRMASCLYGEIDCTTFAAAGDPCESKKRYLEKAVFY 183

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + G+ +   + A +FL   +RS VGSL         +    + L+A+DR+  GP APP+G
Sbjct: 184 ADGDKLVFEIAANAFLWKMVRSVVGSLVYYEQKGKDADFFAEILRARDRRSAGPTAPPQG 243

Query: 239 LYFDSVEY 246
           L+  +V++
Sbjct: 244 LFLWNVDF 251


>gi|227832275|ref|YP_002833982.1| tRNA pseudouridine synthase A [Corynebacterium aurimucosum ATCC
           700975]
 gi|262183869|ref|ZP_06043290.1| tRNA pseudouridine synthase A [Corynebacterium aurimucosum ATCC
           700975]
 gi|227453291|gb|ACP32044.1| tRNA pseudouridine synthase A [Corynebacterium aurimucosum ATCC
           700975]
          Length = 286

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 95/268 (35%), Positives = 129/268 (48%), Gaps = 34/268 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW RQK G  ++Q ++E+ + +V    V +  AGRTD+GVHA  Q
Sbjct: 5   VRLRLDLAYDGTDFHGWARQKGGLRTVQQTVEEKLSMVLRHPVELTVAGRTDAGVHASGQ 64

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAHFD  R  +        P  L + L   L +   + +   + V   F ARFSA+RR Y
Sbjct: 65  VAHFDTTRAALSQRSIDGEPHKLVRRLAKLLPVD--VRVHACTEVSPDFDARFSALRRHY 122

Query: 113 LYRIIT--RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YRI T  R A P        WL P  LD   M+ AA  LVG +DF  F    C+A    
Sbjct: 123 VYRITTHPRGALPTRARDTATWLKPVDLDL--MQAAADRLVGLNDFVAF----CKAKPHA 176

Query: 170 RTIDHF------DVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            TI         DV++     L E  V A +F  + +R  VG    VG+G   S D+E A
Sbjct: 177 TTIRELLAFEWKDVSTPAEPQLYEAHVSADAFCWSMVRCLVGCCLRVGEG---SRDVEFA 233

Query: 222 ---LQAQDRKECGPLAPPEGLYFDSVEY 246
              L    R    PLAP  GL    V+Y
Sbjct: 234 GQMLNETSRSSQIPLAPAAGLSLVGVDY 261


>gi|288801196|ref|ZP_06406651.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288331807|gb|EFC70290.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 245

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 80/252 (31%), Positives = 124/252 (49%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG+++Q  ++KA+ L+    + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYFAYDGTNYHGWQIQPNGNTVQEELQKALSLILRCNINVVGAGRTDTGVHARSM 60

Query: 61  VAHFDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAHFD+  E V    +L   LN  L     I +  +  V +  HARFSA  R+Y Y +  
Sbjct: 61  VAHFDISTEIVFDAELLSGKLNRLL--PPDIVVFAIKPVAEDMHARFSATWRTYHYYVHK 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--- 175
            + P    +  ++   + LD   M  AA++L+   DF  F   H  A + +  +      
Sbjct: 119 GKDPFV--RNYSYSYYRDLDFTLMNEAARYLLEVEDFEAFCKSHSDAKTTLCNVTKAQWI 176

Query: 176 -DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            D ++  + +   + A  FL   +R+ VG+L  VG  K T  + +  +  + R   G   
Sbjct: 177 QDDDTHWHFV---IKANRFLRNMVRAVVGTLVEVGQHKITIEEFKNIVDQRKRIGAGESM 233

Query: 235 PPEGLYFDSVEY 246
           P   L+ + VEY
Sbjct: 234 PAHALFLEKVEY 245


>gi|88801321|ref|ZP_01116849.1| tRNA pseudouridine synthase A [Polaribacter irgensii 23-P]
 gi|88781979|gb|EAR13156.1| tRNA pseudouridine synthase A [Polaribacter irgensii 23-P]
          Length = 241

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 79/246 (32%), Positives = 123/246 (50%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG+ Y GWQ Q +  S+Q  +  AI  V    V V GAGRTD+GVHA++  
Sbjct: 1   MRYFIELSYNGTKYHGWQIQPDMVSVQEKLNNAISTVLQSKVEVVGAGRTDTGVHAVQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+     +       LN+ L   + IS+  +  V +  HARF A  RSY YRI   + 
Sbjct: 61  AHFN-TEILIENNFVHKLNSIL--PNDISVDKVLEVLEDKHARFDAKSRSYEYRIWLGRN 117

Query: 122 PLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P  L+   +W I  +  D   M  AA  L+   +F TF  +  +  +    +        
Sbjct: 118 PFLLD--FSWQIHSQKPDLSKMNAAAILLLEYENFQTFSKVKTEVHTFNCNVTAAFWRQE 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GNL+   + A  FL   +R+ VG+L  VG GK +  +  + +++++R   G   P +GL+
Sbjct: 176 GNLLIFHISANRFLRNMVRAIVGTLVDVGLGKISIAEFRQIIESKNRSNAGLSVPAKGLF 235

Query: 241 FDSVEY 246
              ++Y
Sbjct: 236 LTQIKY 241


>gi|251812078|ref|ZP_04826551.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|282875373|ref|ZP_06284246.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis SK135]
 gi|251804412|gb|EES57069.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|281296138|gb|EFA88659.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis SK135]
 gi|329736438|gb|EGG72706.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU028]
          Length = 267

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 118/243 (48%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVYETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 KGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDKNRNNVPLTAPPDGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|303328364|ref|ZP_07358802.1| tRNA pseudouridine synthase A [Desulfovibrio sp. 3_1_syn3]
 gi|302861694|gb|EFL84630.1| tRNA pseudouridine synthase A [Desulfovibrio sp. 3_1_syn3]
          Length = 226

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 74/223 (33%), Positives = 111/223 (49%), Gaps = 14/223 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R  +++ Y G+GY GWQ Q+  S   +IQG +E A+ ++ G  V VHG+GRTD+GVHA 
Sbjct: 1   MRLKLLLAYLGTGYSGWQIQEKPSPPPTIQGELEAALRVLAGAPVRVHGSGRTDAGVHAH 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   ++LNA L     I IL        FHAR  A+R++Y+Y+   
Sbjct: 61  GQVAHCDVPDAKAGLRWQRSLNALL--PPEIRILAAEPAAADFHARKDALRKTYVYQFWQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +A +  +    +     LD E MR A  HL+G HDF   ++      S  RT+   +++
Sbjct: 119 ERAFVPPQLAPFFWNCGPLDVEAMRAALPHLLGEHDFAGLQNAGTDMESTTRTVFRAELD 178

Query: 179 ---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
                         + + V A  FL   +R+  G L   G GK
Sbjct: 179 IPPPCEFYPPHAPGLRLTVTANGFLKQMVRNMAGLLAACGQGK 221


>gi|124516114|gb|EAY57622.1| Pseudouridylate synthase [Leptospirillum rubarum]
          Length = 268

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 82/254 (32%), Positives = 119/254 (46%), Gaps = 11/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  ++ Y+G G+ GWQ Q  G+++Q  IE+A   +T + V + G+GRTD+GV A  Q
Sbjct: 1   MPRFAFVVSYDGRGFQGWQSQIRGNAVQDHIEEAFCRLTRQDVRISGSGRTDTGVSAAGQ 60

Query: 61  VAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT- 118
           V H D+    W P  L + LN +L  S  I IL  + V   FHAR   +R+ Y YR ++ 
Sbjct: 61  VFHCDIAGPGWTPDSLSRGLNHFL--SPAIRILQAAAVAPDFHARHDVVRKIYRYRWVSL 118

Query: 119 ----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
               R+ P   +       P  +D   ++ A + L G +DFT F           R+ID 
Sbjct: 119 SRKAREVPPTEDPFCGIFFP-PVDWTLLQQATKLLEGANDFTRFTVQKSCPEDARRSIDA 177

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL- 233
               +  N +++ V  R FLH  IR    +L   G  K T    +  L          L 
Sbjct: 178 IQWIAGPNTLDLWVAGRGFLHMMIRYLAMALLETGQQKRTLKSFQDLLLPGSLPPVPALH 237

Query: 234 -APPEGLYFDSVEY 246
            APP+GL    V Y
Sbjct: 238 PAPPQGLSLMRVFY 251


>gi|260891283|ref|ZP_05902546.1| tRNA pseudouridine synthase A [Leptotrichia hofstadii F0254]
 gi|260858959|gb|EEX73459.1| tRNA pseudouridine synthase A [Leptotrichia hofstadii F0254]
          Length = 250

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 123/246 (50%), Gaps = 8/246 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           MI +Y+GS + G+QRQK   ++QG IE+A+F    + + +  +GRTD GVHA+ QV++F 
Sbjct: 8   MIYQYDGSKFCGFQRQKKMKTVQGEIERAVFKTFNQEINMISSGRTDKGVHAMEQVSNF- 66

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           ++ E +P+  + + +N  LK    + +L +    K F+ARF A  R+YLY +   +    
Sbjct: 67  VIDENIPIEAIKRQINKCLK--GEVKVLEVEEAGKDFNARFDAKSRTYLYIMRNEEDITP 124

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID----HFDVNSF 180
            E      +  S+  E  +      VG++DF++F        +P+R I     ++D    
Sbjct: 125 FEANYVTGLRASVSVEKFQEIMNDFVGKYDFSSFMKKDKAYRNPVREIVYIKCYYDEKIG 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + +    FL T +R  +GS   V  G      +++ L+  +  +   LA  EGLY
Sbjct: 185 QKQLNVEICGNGFLKTMVRIMIGSALAVYFGNVEEDYIKRRLENPNADDKKILAASEGLY 244

Query: 241 FDSVEY 246
              V Y
Sbjct: 245 LYKVNY 250


>gi|111023127|ref|YP_706099.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110822657|gb|ABG97941.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 297

 Score =  116 bits (290), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 126/248 (50%), Gaps = 7/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I Y+G+ + GW RQ    ++ G IE+ +  V    + +  AGRTD+GVHA  QVA
Sbjct: 27  RLRLDIAYDGTDFSGWARQNGLRTVCGEIEEKLGAVLRTPLQLTVAGRTDAGVHATGQVA 86

Query: 63  HFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-- 119
           H D+  + +P    + +    + +   + I  ++   + F ARFSA+RR Y YR+ +   
Sbjct: 87  HVDVPVDALPDDPSRLVRRLARFLPKDVRIKRIAFAPEHFDARFSAMRRHYEYRLTSAVY 146

Query: 120 -QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              PL      ++  PK LD E MR A+  L+G HDF  F     + ++ +R +  FD  
Sbjct: 147 GADPLRARDTVSY--PKVLDLELMRSASATLLGLHDFAAF-CKRREGATTVRDLQRFDWE 203

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G++    V A +F  + +RS VG++  VG+G+     +E  LQ + R     +AP  G
Sbjct: 204 RDGDVFTAFVSADAFCWSMVRSLVGAVLAVGEGRRDLGWIEGLLQEKSRSSSILVAPAHG 263

Query: 239 LYFDSVEY 246
           L    V+Y
Sbjct: 264 LSLVRVDY 271


>gi|319400595|gb|EFV88820.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis FRI909]
          Length = 267

 Score =  115 bits (289), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 118/243 (48%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVYETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDRNRNNVPLTAPPDGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|42559799|sp|Q83G11|TRUA_TROWT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 267

 Score =  115 bits (289), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 81/246 (32%), Positives = 119/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ + GW  Q    ++ G I  A+ L+  E   +  A RTD+GVHAL+QV 
Sbjct: 5   RYRLDVAYDGANFCGWAPQPGLRTVGGLILDALRLICSEPPDIVVAARTDAGVHALQQVC 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H DL+    PV L   L + LK    + IL+       FHARFSAI R Y+YR+I +++ 
Sbjct: 65  HVDLISSPDPVWLLHRLRSLLKSETDLHILSAVKAPVNFHARFSAIGRRYVYRVIDKRSS 124

Query: 123 -LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSF 180
                +   + +   L    MR AA  L+G  DF  F     +  S +R +  F+V    
Sbjct: 125 WYPQNRYFVYRVNAFLQDYRMRRAASGLIGLKDFGAFCKPR-RMGSTVRHLRQFEVIRQP 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I   + + +F H+ +R+ VGSL  VG G  T  DL    +   R    P  PP  L 
Sbjct: 184 DGQIHFFLESDAFCHSMVRNLVGSLIEVGRGALTLQDLFCYTKIAKRTPKIPTLPPHALT 243

Query: 241 FDSVEY 246
              ++Y
Sbjct: 244 LIGIDY 249


>gi|300770580|ref|ZP_07080459.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33861]
 gi|300763056|gb|EFK59873.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33861]
          Length = 257

 Score =  115 bits (289), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 119/249 (47%), Gaps = 10/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + I Y G+ Y GWQ Q N  S+Q  +   +  +  + +   GAGRTD+GVHA +   
Sbjct: 7   RFFLEIAYQGTAYHGWQIQHNAVSVQEKLNDVLKTLLRKDIETIGAGRTDTGVHARQLFV 66

Query: 63  HFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           HFD + E +   P     +LNA L     I++  L  VD Q HARF A  RSY Y +  +
Sbjct: 67  HFDAIPEGLLLQPDKFVHSLNALL--PHDIAVYRLLPVDDQAHARFDATSRSYEYHLHFK 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           + P  +    +WL     D   M  A Q+L+GR DF  F   + Q  +    I   +   
Sbjct: 125 KDPFLINA--SWLTRDIPDVVKMNEACQYLLGRQDFECFSKSNTQVFTNFCDISRAEWLW 182

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N+  +L+   + A  FL   +R+ VG+L  +G        +++ + ++ R + G   P  
Sbjct: 183 NTDDHLV-FHISADRFLRNMVRAIVGTLLEIGLKGKEPVYIQEVIASKSRSKAGTSVPAH 241

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 242 GLYLTEVVY 250


>gi|28493493|ref|NP_787654.1| tRNA pseudouridine synthase A [Tropheryma whipplei str. Twist]
 gi|28476535|gb|AAO44623.1| pseudouridylate synthase I [Tropheryma whipplei str. Twist]
          Length = 315

 Score =  115 bits (289), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 119/247 (48%), Gaps = 3/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ + GW  Q    ++ G I  A+ L+  E   +  A RTD+GVHAL+QV 
Sbjct: 53  RYRLDVAYDGANFCGWAPQPGLRTVGGLILDALRLICSEPPDIVVAARTDAGVHALQQVC 112

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H DL+    PV L   L + LK    + IL+       FHARFSAI R Y+YR+I +++ 
Sbjct: 113 HVDLISSPDPVWLLHRLRSLLKSETDLHILSAVKAPVNFHARFSAIGRRYVYRVIDKRSS 172

Query: 123 -LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSF 180
                +   + +   L    MR AA  L+G  DF  F     +  S +R +  F+V    
Sbjct: 173 WYPQNRYFVYRVNAFLQDYRMRRAASGLIGLKDFGAFCKPR-RMGSTVRHLRQFEVIRQP 231

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I   + + +F H+ +R+ VGSL  VG G  T  DL    +   R    P  PP  L 
Sbjct: 232 DGQIHFFLESDAFCHSMVRNLVGSLIEVGRGALTLQDLFCYTKIAKRTPKIPTLPPHALT 291

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 292 LIGIDYP 298


>gi|226365626|ref|YP_002783409.1| tRNA pseudouridine synthase TruA [Rhodococcus opacus B4]
 gi|226244116|dbj|BAH54464.1| tRNA pseudouridine synthase TruA [Rhodococcus opacus B4]
          Length = 270

 Score =  115 bits (289), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 124/245 (50%), Gaps = 11/245 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ + GW RQ    ++ G IE+ +  V    + +  AGRTD+GVHA  QVAH D+ 
Sbjct: 5   VAYDGTDFSGWARQNGLRTVCGEIEEKLGAVLRSPLQLTVAGRTDAGVHATGQVAHVDVP 64

Query: 68  REWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR---QA 121
            E +   P  L + L  +L     + I  +S   + F ARFSA+RR Y YR+ +      
Sbjct: 65  VEALPDEPSRLVRRLARFLP--KDVRIKQISFAPEHFDARFSAMRRHYEYRLTSAVYGAD 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           PL      ++  PK LD E MR A+  L+G HDF  F     + ++ +R +  FD    G
Sbjct: 123 PLRARDTVSY--PKILDLELMRSASATLLGLHDFAAF-CKRREGATTVRDLQRFDWERDG 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++    V A +F  + +RS VG++  VG+G+     +E  L+   R     +AP  GL  
Sbjct: 180 DVFTAFVSADAFCWSMVRSLVGAVLAVGEGRRDLDWIEGLLRETSRSSSILVAPAHGLCL 239

Query: 242 DSVEY 246
             V+Y
Sbjct: 240 VRVDY 244


>gi|255530580|ref|YP_003090952.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
 gi|255343564|gb|ACU02890.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
          Length = 261

 Score =  115 bits (289), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 78/261 (29%), Positives = 122/261 (46%), Gaps = 19/261 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q N +++Q  ++ A+ +   + V   G GRTD+GVHA + 
Sbjct: 1   MQRYFIELSYDGTPYHGWQIQPNATTVQEYLDSALTVYFRQPVSTLGCGRTDTGVHASQF 60

Query: 61  VAHFDLVRE-------WVPVILC-------KALNAYLKISDTISILNLSIVDKQFHARFS 106
            AHFDL  E        +P   C         +NA L     I++  +  V    HARF 
Sbjct: 61  FAHFDLQTEAEQSEATGIPASKCPDPLRSVNGINALLPYQ--IAVKRVFEVANTAHARFD 118

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA- 165
           A  R+Y Y I   + P  L   R+W     LD + M  AA  L+   DF+ F   H Q  
Sbjct: 119 ATARAYHYHIHFHKNPFKL--NRSWFHKGELDMDAMNRAASILLAHSDFSCFSKSHTQTF 176

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           ++  +  + F        +   + A  FL   +R+ VG+L  +G  +    + E+ ++++
Sbjct: 177 TNNCKITEAFFEEMEDGALRFTIRADRFLRNMVRAIVGTLIRIGKNELNLAEFEQIIKSK 236

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
           +R   G   P  GLY  +V Y
Sbjct: 237 NRSNAGQSVPACGLYLVNVIY 257


>gi|300857811|ref|YP_003782794.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300685265|gb|ADK28187.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302205546|gb|ADL09888.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           C231]
 gi|308275782|gb|ADO25681.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           I19]
          Length = 291

 Score =  115 bits (289), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 83/263 (31%), Positives = 131/263 (49%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ      ++Q  +E ++ L+    + +  AGRTD+GVHA  
Sbjct: 8   VRIRLDLAYDGTHFHGWARQGTSQLRTVQRVLEDSLELILRHPIQLTVAGRTDAGVHAAG 67

Query: 60  QVAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+          +  P  L + L   L   + + +   ++  + F ARFSA+RR 
Sbjct: 68  QVAHFDVPAIALDTRSIDGDPRNLVRRLARLLP--EDVRVHACTLAPEGFDARFSALRRH 125

Query: 112 YLYRIITRQ---APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YR+ T      P        W  PK +D + M+ AA  L+G HDF  F   H + ++ 
Sbjct: 126 YVYRLTTHPRGALPTRATDTAHW--PKRIDIDAMQAAADVLIGLHDFAAF-CKHREGATT 182

Query: 169 IRTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           IR +  F   DV++     L E  V A +F  + +RS VGS  ++G+GK     ++  L 
Sbjct: 183 IRDLQEFTWHDVSTSLEPQLYEAHVTADAFCWSMVRSLVGSCLVIGEGKRPEGFVDSLLT 242

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
              R    P+AP +GL    V+Y
Sbjct: 243 ETSRSSQVPVAPAKGLSLVGVDY 265


>gi|28572394|ref|NP_789174.1| tRNA pseudouridine synthase A [Tropheryma whipplei TW08/27]
 gi|42559794|sp|Q820Z2|TRUA_TROW8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|28410525|emb|CAD66911.1| tRNA pseudouridine synthase A [Tropheryma whipplei TW08/27]
          Length = 267

 Score =  115 bits (289), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 81/246 (32%), Positives = 119/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ + GW  Q    ++ G I  A+ L+  E   +  A RTD+GVHAL+QV 
Sbjct: 5   RYRLDVAYDGANFCGWAPQPGLRTVGGLILDALRLICSEPPDIVIAARTDAGVHALQQVC 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H DL+    PV L   L + LK    + IL+       FHARFSAI R Y+YR+I +++ 
Sbjct: 65  HVDLISSPDPVWLLHRLRSLLKSETDLHILSAVKAPVNFHARFSAIGRRYVYRVIDKRSS 124

Query: 123 -LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSF 180
                +   + +   L    MR AA  L+G  DF  F     +  S +R +  F+V    
Sbjct: 125 WYPQNRYFVYRVNAFLQDYRMRRAASGLIGLKDFGAFCKPR-RMGSTVRHLRQFEVIRQP 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I   + + +F H+ +R+ VGSL  VG G  T  DL    +   R    P  PP  L 
Sbjct: 184 DGQIHFFLESDAFCHSMVRNLVGSLIEVGRGALTLQDLFCYTKIAKRTPKIPTLPPHALT 243

Query: 241 FDSVEY 246
              ++Y
Sbjct: 244 LIGIDY 249


>gi|113476553|ref|YP_722614.1| tRNA pseudouridine synthase A [Trichodesmium erythraeum IMS101]
 gi|110167601|gb|ABG52141.1| tRNA pseudouridine synthase A [Trichodesmium erythraeum IMS101]
          Length = 272

 Score =  115 bits (289), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 83/246 (33%), Positives = 116/246 (47%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ N  ++Q  IEK I     E V +HGAGRTD+GVHA  QVA
Sbjct: 10  RVALVIQYQGTHFHGWQRQPNQRTVQEEIEKTIASFINEPVTLHGAGRTDAGVHAAAQVA 69

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+            LN+  ++++ I I   + +D  +H+RF+AI R Y Y I T + P
Sbjct: 70  HFDVSGPIPAHKWATILNS--RLANDILIRGSARIDYAWHSRFTAIWRRYRYTIYTDKQP 127

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSF 180
                   W     SLD + ++ A   L+G H    F R+  C+  S +  +        
Sbjct: 128 NLFVMPFVWHYYQASLDPQLIQAALNPLIGHHHLAAFQRAGSCRPHSWV-DVQEVMCERK 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I V A  FL+  +R  VG L  VG  + +          Q R      AP  GL 
Sbjct: 187 GPFIYIEVQASGFLYGMMRLLVGLLIQVGTEELSLESFTDIWVNQRRDIVKHSAPASGLC 246

Query: 241 FDSVEY 246
              V Y
Sbjct: 247 LLRVGY 252


>gi|65317910|ref|ZP_00390869.1| COG0101: Pseudouridylate synthase [Bacillus anthracis str. A2012]
          Length = 175

 Score =  115 bits (288), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 63/159 (39%), Positives = 95/159 (59%), Gaps = 3/159 (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 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAF 157


>gi|260438877|ref|ZP_05792693.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
 gi|292808716|gb|EFF67921.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
          Length = 249

 Score =  115 bits (288), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 5/243 (2%)

Query: 8   IEYNGSGYFGWQRQKNGS-SIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           I ++G+ YFGW+ Q N   +IQG IE  +   + + ++  V G GRTD+GVHA   +A+ 
Sbjct: 9   IMFDGTRYFGWEHQPNTDLTIQGKIETVLQRMVSSEKVPEVIGCGRTDAGVHAKAMIANA 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            L  +     +   +N YL   D I +L +    ++FH+R+ A+ ++Y Y   T      
Sbjct: 69  FLETDMSTDAIRDYMNRYL--PDDICVLEVKEAAERFHSRYKAVGKTYCYTCYTGPLKPV 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            ++   + I ++ D   M  AA+ L+G HD+ +F S      S +R +D   +   G  I
Sbjct: 127 FDRKYVYYIEETPDIGKMEEAAKLLIGIHDYASFCSNPKMKKSTVREVDSIQIIKKGQYI 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                   FL   +R   G+L  VG GK   + + +  +A+DR   G  AP  GL    V
Sbjct: 187 RFTYHGTGFLQHMVRILTGTLLEVGFGKRDVSSIPELFEAKDRSLAGFTAPASGLCMMQV 246

Query: 245 EYS 247
           +Y+
Sbjct: 247 DYN 249


>gi|255022149|ref|ZP_05294152.1| tRNA pseudouridine synthase A [Acidithiobacillus caldus ATCC 51756]
 gi|254968413|gb|EET25972.1| tRNA pseudouridine synthase A [Acidithiobacillus caldus ATCC 51756]
          Length = 206

 Score =  115 bits (288), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 69/185 (37%), Positives = 97/185 (52%), Gaps = 2/185 (1%)

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD       +   + +N YL    +IS+L    V + FHARF+A+ R Y Y I+ R   
Sbjct: 3   HFDAPVTRPALAWTRGVNRYLP--SSISVLWARPVPRDFHARFAAVGRRYRYCILNRSER 60

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            AL  GRA  +P+ L  E M+ AA  L+GRHDF+ FR+  CQA  PIR +    V+  G+
Sbjct: 61  SALYAGRAAWVPRPLAVEPMQEAASLLLGRHDFSAFRAAACQAKHPIRELRQLRVSRQGD 120

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + +   A +FLH  +R+ VG L  +G G        + L ++ R   G  AP EGLYF 
Sbjct: 121 WVFVDAEANAFLHHMVRNLVGVLLGIGWGDRPPHWAAEVLASRKRALAGVTAPAEGLYFV 180

Query: 243 SVEYS 247
           +  Y 
Sbjct: 181 AALYP 185


>gi|302330101|gb|ADL20295.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           1002]
          Length = 319

 Score =  115 bits (288), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 83/263 (31%), Positives = 131/263 (49%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ      ++Q  +E ++ L+    + +  AGRTD+GVHA  
Sbjct: 36  VRIRLDLAYDGTHFHGWARQGTSQLRTVQRVLEDSLELILRHPIQLTVAGRTDAGVHAAG 95

Query: 60  QVAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+          +  P  L + L   L   + + +   ++  + F ARFSA+RR 
Sbjct: 96  QVAHFDVPAIALDTRSIDGDPRNLVRRLARLLP--EDVRVHACTLAPEGFDARFSALRRH 153

Query: 112 YLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           Y+YR+ T      P        W  PK +D + M+ AA  L+G HDF  F   H + ++ 
Sbjct: 154 YVYRLTTHPRGALPTRATDTAHW--PKRIDIDAMQAAADVLIGLHDFAAF-CKHREGATT 210

Query: 169 IRTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           IR +  F   DV++     L E  V A +F  + +RS VGS  ++G+GK     ++  L 
Sbjct: 211 IRDLQEFTWHDVSTSLEPQLYEAHVTADAFCWSMVRSLVGSCLVIGEGKRPEGFVDSLLT 270

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
              R    P+AP +GL    V+Y
Sbjct: 271 ETSRSSQVPVAPAKGLSLVGVDY 293


>gi|305664970|ref|YP_003861257.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
 gi|88707800|gb|EAR00040.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
          Length = 224

 Score =  115 bits (288), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 111/220 (50%), Gaps = 4/220 (1%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS 86
           +Q  +E AI  +    + V GAGRTD+GVHA    AHFD         L   +NA+L   
Sbjct: 1   MQEVLENAISKLLRSPISVVGAGRTDAGVHAREMFAHFDFKDSIDSKDLVYRMNAFLPAD 60

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAA 146
             I++  + +V+ + HARF A  R+Y Y I  ++ P   +  RA  +  +LD + M  AA
Sbjct: 61  --IAVSQIYLVNGEAHARFDATERTYEYWITQKKNPFYFD--RAHFVKNTLDVKAMNDAA 116

Query: 147 QHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
              +GR DF  F   +    + +  +         + +   +VA  FL   +R+ VG+L 
Sbjct: 117 NLFLGRKDFECFSKSNTDVHTYLCDVRKTIWTEEEDKLVFTIVADRFLRNMVRAVVGTLI 176

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            VG GK +  D+++ L+++DR + G   P +GLY   +EY
Sbjct: 177 DVGTGKTSLADIQRILESKDRTKAGASVPAKGLYLTKIEY 216


>gi|332877177|ref|ZP_08444927.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332684920|gb|EGJ57767.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 268

 Score =  115 bits (287), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 82/253 (32%), Positives = 117/253 (46%), Gaps = 11/253 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  ++KA+  +  + V + GAGRTD+GVHA   
Sbjct: 1   MQRYFLYLAYDGTNYHGWQIQPNGISVQEVLQKALATLLRQPVSITGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPV------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAHFD      PV       L   LN  L     ISI     V    HARF A+ R+Y Y
Sbjct: 61  VAHFDFEYADDPVRRIDGRWLTDKLNRLLPPD--ISIYKTVPVAADAHARFDALSRTYHY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTID 173
            +   ++P    +  +  + + LD E M  AA  L    DFT+F  ++    ++  R + 
Sbjct: 119 YLHFGKSPFL--RAYSCRLYRMLDFEKMNEAAAALFDYTDFTSFSKVNTDTKTNNCRIMQ 176

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                         + A  FL   +R+ VG+L  VG GK T       ++ +DR   G  
Sbjct: 177 ARWTELAPGEWRFEIQADRFLRNMVRAIVGTLVEVGRGKLTPEGFRAVIEGKDRCRAGES 236

Query: 234 APPEGLYFDSVEY 246
            P   L+   V Y
Sbjct: 237 MPGNALFLVDVAY 249


>gi|289641136|ref|ZP_06473304.1| tRNA pseudouridine synthase A [Frankia symbiont of Datisca
           glomerata]
 gi|289509077|gb|EFD30008.1| tRNA pseudouridine synthase A [Frankia symbiont of Datisca
           glomerata]
          Length = 279

 Score =  115 bits (287), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 86/255 (33%), Positives = 125/255 (49%), Gaps = 31/255 (12%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTD+GVHA  QVAH D+  
Sbjct: 16  YDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDAGVHARGQVAHVDIPD 75

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
           +     L + LN  L  +  + I  L+     F ARFSA+ R Y+YRI    AP  ++  
Sbjct: 76  DVPLGGLARRLNGVLDRA--VRITALAPAPPGFDARFSALSRRYVYRI--GDAPYGVDPL 131

Query: 129 R-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIRTIDHFDV--- 177
           R     AW  P+ LD E M  AA  LVG  DF  F    C   + ++ +RT+   DV   
Sbjct: 132 RRHDTLAW--PRPLDAERMADAALALVGERDFAAF----CRRREGATTVRTLLRLDVARV 185

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRKECGP 232
            +    ++   V A +F H+ +R+ VG+L  VG+G+    W +  L + +    R     
Sbjct: 186 PDGHDGVVVADVEADAFCHSMVRALVGALLAVGEGRRPHHWPADVLARGV----RDPAVT 241

Query: 233 LAPPEGLYFDSVEYS 247
           +A P GL    V Y 
Sbjct: 242 VAAPHGLTLVEVRYP 256


>gi|319442992|ref|ZP_07992148.1| tRNA pseudouridine synthase A [Corynebacterium variabile DSM 44702]
          Length = 283

 Score =  115 bits (287), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 130/265 (49%), Gaps = 24/265 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M+R  + + Y+G+ + GW RQK       ++QG +E+ + LV    V +  AGRTD+GVH
Sbjct: 4   MVRVRLDVAYDGTDFHGWARQKGPQEALRTVQGVLEEKLSLVFRTPVELTVAGRTDAGVH 63

Query: 57  ALRQVAHFDLVREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           A  QVAH D+            P  L + L+  L     + +   S     F ARFSA+R
Sbjct: 64  ATGQVAHVDVPASAFGQRSLEQPSDLVRRLSRMLPAD--VRLHGASAAAPGFDARFSALR 121

Query: 110 RSYLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           R Y+YR+ T  A   PL +     W    S+D   +++A+  LVG HDF  F   + + S
Sbjct: 122 RHYVYRVTTSMAGPSPLRVRDTAQWR--HSVDLSAVQLASDVLVGLHDFAAF-CKYREGS 178

Query: 167 SPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           + +R +  F+       +     E  VVA +F  + +RS VG++  VG+G+         
Sbjct: 179 TTVRELQSFEWRDISTPTEPETYEASVVADAFCWSMVRSLVGAVLTVGEGRRDEGFASCL 238

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           LQ + R    P+AP  GL   +V+Y
Sbjct: 239 LQERSRSSKVPVAPACGLNLVAVDY 263


>gi|238916468|ref|YP_002929985.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
 gi|238871828|gb|ACR71538.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
          Length = 245

 Score =  115 bits (287), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 126/249 (50%), Gaps = 7/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M  Y + IEY+G  Y GWQR     + ++I+  + + I  +TGE V ++   RT+ GVHA
Sbjct: 1   MYNYRIEIEYDGGRYDGWQRLGKDASTNTIESRLCEIIARMTGETVDMYAGSRTEKGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L Q A+F L +E   + +   LN YL     I++++++  D++FH++ +A  + Y YR+ 
Sbjct: 61  LCQTANFKLEKEVKAIEIKNYLNRYL--PRDIAVMSVTEADERFHSQLNAKSKIYEYRLD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T        +  A+      D + MR AA +  G+HDF  F +   ++ S  +TI    V
Sbjct: 119 TGNVANVFRRKYAYHTFDKPDFDAMRKAAGYFEGKHDFKAFTTAK-KSKSTEKTIKKISV 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G    IR+ A  FLH   R  +G +  VG+G     D+++ L  ++ +   P A   
Sbjct: 178 EYEGARAYIRIEADDFLHNMARYIIGMMLDVGNGIKKPEDVKRCLDGENIQMSLP-AESY 236

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 237 GLFLVKVVY 245


>gi|33241136|ref|NP_876078.1| tRNA pseudouridine synthase A [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|42559767|sp|Q7V9Y7|TRUA_PROMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33238666|gb|AAQ00731.1| Pseudouridylate synthase [Prochlorococcus marinus subsp. marinus
           str. CCMP1375]
          Length = 289

 Score =  115 bits (287), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 116/251 (46%), Gaps = 14/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + I+Y GS + GWQRQK G +IQ  +E AIF L + +   V  AGRTD+GVHA  QV
Sbjct: 17  RIALSIQYQGSNFSGWQRQKVGHTIQAILEDAIFSLDSSKPAKVVAAGRTDAGVHAAGQV 76

Query: 62  AHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      V  W P  L   L   +++ D++           +HA  SA+ R Y Y I
Sbjct: 77  VHFDSFGPIPVHRW-PSALNGRLPEAIRVRDSVE------QSLDWHACHSAVYRRYRYII 129

Query: 117 ITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                P        W      LD E M  AA+ L+G HDF+ F+      +    TI   
Sbjct: 130 YNGCTPNLFLNPWTWHKYQYQLDEELMEEAAKGLIGMHDFSAFQRSGSNRTHAFTTIQEV 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   G+L+   + A  FL+  +R  VG L  +G+ + +  D E   + + R E    AP
Sbjct: 190 KLVRHGDLLVFDIQASGFLYGMVRLLVGQLVSIGEHRLSINDFETRWKLKLRSEVKEAAP 249

Query: 236 PEGLYFDSVEY 246
             GL F    Y
Sbjct: 250 ARGLCFIRAGY 260


>gi|242243978|ref|ZP_04798421.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis W23144]
 gi|242232611|gb|EES34923.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis W23144]
          Length = 267

 Score =  115 bits (287), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 117/243 (48%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+    + +  
Sbjct: 119 RNPFKSGTETFVYETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSKIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDRNRNNVPLTAPPDGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|303288620|ref|XP_003063598.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454666|gb|EEH51971.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 261

 Score =  115 bits (287), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 84/267 (31%), Positives = 127/267 (47%), Gaps = 36/267 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHALR 59
           Y + + Y+G  Y G+Q Q ++  ++QG +EKA+  +TGE    + +  +GRTD+GVHA  
Sbjct: 3   YALTLAYDGENYLGFQYQPRDAKTVQGEVEKALTKITGEDRDFLGIQASGRTDAGVHARG 62

Query: 60  QVAHF-------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           QV HF       DL R        +++N  L     + ++        FHARF A+R++Y
Sbjct: 63  QVLHFYARRPIEDLAR------FQRSMNGVL--PRDVRVMKAIRPHPAFHARFHAVRKTY 114

Query: 113 LYRIITR--QAPL----ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
            Y + TR    P     AL  G  W  P   D E +R  A+  VG  DF+ F +     +
Sbjct: 115 HYYLDTRLTMDPFLRRHALHVG--WNPP---DVEKLRRGAECFVGTRDFSAFSNKPRDKT 169

Query: 167 ---SPIRTIDHFDVNSF--GNLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEK 220
               P+RTI  FDVN      L+ + V    F++ Q+R+ VG++       K    D+  
Sbjct: 170 LVRDPVRTIYRFDVNELKGDGLLRLEVEGNGFMYKQVRNMVGAMITAATSKKMQPADIAA 229

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            L+ +DR      AP  GL+   V Y 
Sbjct: 230 MLEGKDRGVAPMGAPAHGLFLHDVVYP 256


>gi|311258299|ref|XP_003127542.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Sus scrofa]
          Length = 306

 Score =  115 bits (287), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 136/273 (49%), Gaps = 30/273 (10%)

Query: 3   RYCMIIEYNGSGYFGW---QRQKNGSSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHAL 58
           RY +  +Y G+ + G    +  ++   +Q  +E+A   +   + V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYLGTDFNGVAAVRGPQHAVGVQNYLEEAAERLNSVVPVKFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR++A  R+YL
Sbjct: 73  SNAAHLDIQRRSGQPPFSPEVLTEALNTHLR-HPAIRVLQAFRVPSHFHARYAATSRTYL 131

Query: 114 YRIIT---RQAPLAL-EKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T   R   L++ E+ R W L    LD   M+ AAQHL+G HDF+ F+S    A+SP
Sbjct: 132 YRLATGCPRPDHLSVFERNRCWPLRADCLDVAAMQEAAQHLLGTHDFSAFQSTGSPATSP 191

Query: 169 IRTIDHFDVNSFGN-------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V+   +                +   ++SFL+ Q+R     L  VG G  T 
Sbjct: 192 VRTLRRASVSPEPSSPLVLPGESRGLRFWSLEFESQSFLYRQVRRMTAVLVAVGLGALTP 251

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             ++  L+++D   +    +AP  GL+  SV Y
Sbjct: 252 AQVKMILESRDPLGRHQSRVAPAHGLFLKSVLY 284


>gi|189501513|ref|YP_001957230.1| tRNA pseudouridine synthase A [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189496954|gb|ACE05501.1| tRNA pseudouridine synthase A [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 253

 Score =  114 bits (286), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 81/251 (32%), Positives = 123/251 (49%), Gaps = 11/251 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y G+ Y GWQ Q+N +S+Q  I+K +  +    + + G+ RTD+GVHA +Q 
Sbjct: 1   MRYFLEIAYQGTHYHGWQIQQNATSVQAVIQKKLTQLLSTNIEIVGSSRTDTGVHAQQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH D+        L   LN  L +   I+IL +  V    H+RF A+ R+Y+Y+I   + 
Sbjct: 61  AHVDMPFTIDIDKLKYKLN--LIVPSDIAILGIHPVLPTAHSRFDALSRTYVYKISCTKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-----HCQASSPIRTID-HF 175
           P    +   ++  + LD E M  AA  L    +F +F  +     H    +    I+ H+
Sbjct: 119 PFM--QATTYVFRRVLDLEKMNEAAAILKIYKNFESFSKVGSITDHTLYPNLCNIIEAHW 176

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              S   LI  ++ A  FL   +R+ VG+L  VG GK +  D E  L  +DR     L P
Sbjct: 177 STGSNDQLI-FQITANRFLRGMVRAIVGNLLEVGLGKCSVKDFEYTLVQKDRNLAASLVP 235

Query: 236 PEGLYFDSVEY 246
             GL   +V Y
Sbjct: 236 ACGLTLVNVTY 246


>gi|167629501|ref|YP_001680000.1| tRNA pseudouridine synthase a [Heliobacterium modesticaldum Ice1]
 gi|167592241|gb|ABZ83989.1| tRNA pseudouridine synthase a [Heliobacterium modesticaldum Ice1]
          Length = 259

 Score =  114 bits (286), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 122/244 (50%), Gaps = 13/244 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ Y G+Q Q+N +  +IQ ++ +AI ++TGE V V+ AGRTD+GVHA  Q
Sbjct: 5   RLKLTVAYDGTCYHGFQTQENPALPTIQDALVRAIKVLTGEEVKVNCAGRTDAGVHARGQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F             A+NA L     ++++    V   FH+RF A+ + Y Y I   +
Sbjct: 65  VVDFVTSSPIPDDRFPFAMNAIL--PPDVAVVAAKTVPLAFHSRFGALGKHYRYTIYNHR 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFD 176
            P    +  +  +   L  E M  AAQ  VG HDF  F    C   SP    +RT+   D
Sbjct: 123 IPSPFHRRYSHQVFPPLQFEAMAAAAQCFVGTHDFRGF----CATGSPVKDFVRTVYRCD 178

Query: 177 VN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +     + + + V+   FL+  IR   G+L  VG GK    ++   + ++DR   G  AP
Sbjct: 179 LTRQEEHRLVLDVMGNGFLYNMIRIIAGTLIDVGKGKIALEEIPAIIASRDRTRAGMTAP 238

Query: 236 PEGL 239
           P+GL
Sbjct: 239 PQGL 242


>gi|256827610|ref|YP_003151569.1| pseudouridylate synthase I [Cryptobacterium curtum DSM 15641]
 gi|256583753|gb|ACU94887.1| pseudouridylate synthase I [Cryptobacterium curtum DSM 15641]
          Length = 273

 Score =  114 bits (286), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 89/259 (34%), Positives = 127/259 (49%), Gaps = 16/259 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    ++I YNG+ + G+ RQ+    ++QGS+E+A+ L+    V    AGRTD+GVHA  
Sbjct: 1   MATIALLISYNGAPFHGFARQEGDLLTVQGSLEEALSLLYRREVETVCAGRTDTGVHARG 60

Query: 60  QVAHFDLVREWV----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           QV  F++  E +    P  L ++LNA     D I I  L      F ARF A  R Y Y 
Sbjct: 61  QVVTFEVTPEELASHTPHSLIRSLNALTH--DAIGIRQLRRAPDGFSARFDAKSRHYRYF 118

Query: 116 IITRQAPLALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR--- 170
           I     P  + +   W +    SLD   M  AA +LVG HDF +F      A  P R   
Sbjct: 119 ISDGSVPPLVMRDFCWQVRGGVSLDANAMTAAAAYLVGEHDFKSFCLAVSAAGKPTRREV 178

Query: 171 ---TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
              T++  +V     ++ I ++  SFLH+ +R+  G+L  VG G    + + + L A DR
Sbjct: 179 LSLTVERIEVLG-DEVVCIDIIGSSFLHSMVRTIAGTLVAVGRGLRPPSWMAEVLAACDR 237

Query: 228 KECGPLAPPEGLYFDSVEY 246
              G  AP  GL F  V+Y
Sbjct: 238 TAAGEKAPAAGLVFWDVDY 256


>gi|126697063|ref|YP_001091949.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9301]
 gi|166228747|sp|A3PF23|TRUA_PROM0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|126544106|gb|ABO18348.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9301]
          Length = 268

 Score =  114 bits (286), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 122/247 (49%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS Y GWQ+QKN +++Q  +++A+  +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGSHYSGWQKQKNATTVQEILDRALLKITNHTVQTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D+            LN+ L  S  I IL    V   +HA +SA+ R Y Y I   +
Sbjct: 61  VVHCDVDCVVPGNSYSDVLNSLLPSS--IRILESIEVKDSWHACYSALYRHYRYVINNSK 118

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    K LD   M  A++ ++G HDF  F+      ++ I  I + D+  
Sbjct: 119 FPNLFIDNWSWHRYQKVLDEVLMLNASRQMIGEHDFFAFQKTGSNRTNSITKIKNIDIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  +G L LVG+ K +          + + +    AP +GL
Sbjct: 179 VEDLIFVDIKATGFLYGMVRLIIGQLVLVGENKISPEIFTDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEY 246
            F +  Y
Sbjct: 239 CFVNAVY 245


>gi|307701658|ref|ZP_07638674.1| tRNA pseudouridine synthase A [Mobiluncus mulieris FB024-16]
 gi|307613161|gb|EFN92414.1| tRNA pseudouridine synthase A [Mobiluncus mulieris FB024-16]
          Length = 340

 Score =  114 bits (286), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 93/308 (30%), Positives = 132/308 (42%), Gaps = 64/308 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R    I Y+G  + GW RQ    ++QG++E A+ ++  + V +  AGRTD+GVHA  Q
Sbjct: 1   MTRIRFDIRYDGRPFHGWARQPGLPTVQGALETALTVLFRQPVTLTVAGRTDAGVHATGQ 60

Query: 61  VAHFDL--------VREWVPVILCKALNAYLKISDTISILNLSI---------------- 96
           VAHFDL        +R+        +L A +  S+   I N  +                
Sbjct: 61  VAHFDLPDQFSGDWLRDARDTDFAASLGAIVAASNPPGIANFQLSTGFHRRLDSVLRLVT 120

Query: 97  -----------VDKQ----------------------FHARFSAIRRSYLYRII---TRQ 120
                      +D Q                      F ARFSA+ R Y Y +I   T +
Sbjct: 121 SGNTPTIPGINLDDQPIYPPEANGAIVVTAACPVLDAFDARFSALARHYEYLVIDEPTAR 180

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL   +   W     LD   M  A+  L+G HDF  F     + ++ IRT+    V+  
Sbjct: 181 NPLT--RNTCWWYGAPLDVARMHEASAGLLGTHDFAAFCKPR-EGATTIRTLKQLGVSRL 237

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I   V A +F H+ +RS VG+L  VG GK  +  LE+AL +  R    PLAP +GL
Sbjct: 238 APGEIRFDVAADAFCHSMVRSLVGALTEVGRGKRDADWLEQALHSAVRIPEIPLAPAQGL 297

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 298 TLVRVDYP 305


>gi|172040043|ref|YP_001799757.1| tRNA pseudouridine synthase A [Corynebacterium urealyticum DSM
           7109]
 gi|171851347|emb|CAQ04323.1| tRNA pseudouridine synthase A [Corynebacterium urealyticum DSM
           7109]
          Length = 324

 Score =  114 bits (286), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 88/264 (33%), Positives = 132/264 (50%), Gaps = 27/264 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  M + Y+G+ + GW  QK G  ++QG +E+ + LV    V +  AGRTD+GVHA  Q
Sbjct: 50  VRVRMDVSYDGTDFHGWAAQKGGLRTVQGVLEEKLTLVCRTPVELTVAGRTDAGVHADGQ 109

Query: 61  VAHFDLVREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           V H D+  E         P  L + L+  L   + I +       + F ARFSA+RR Y+
Sbjct: 110 VCHADIPAEAFTHRSLARPEDLVRRLSRMLP--EDIRLNAAVAAPEGFDARFSALRRHYV 167

Query: 114 YRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SS 167
           YR+ T      P  +     W  P  +D E ++IAA  LVG ++F  +    C+A   ++
Sbjct: 168 YRVCTAPGGPLPRRVRDTARWRRP--VDLEKVQIAADALVGLNNFAAY----CKAREGAT 221

Query: 168 PIRTIDHF---DVNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
            IR +  F   DV++       E  VVA +F  + +RS VG+   VG+GK       + L
Sbjct: 222 TIRELQEFTWKDVSTPAEPQTYEAHVVADAFCWSMVRSIVGACLTVGEGKRPEGFTAELL 281

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
           +  +R    P+AP EGL    V+Y
Sbjct: 282 ELDERSSQVPVAPAEGLNLVGVDY 305


>gi|120603116|ref|YP_967516.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris DP4]
 gi|166228695|sp|A1VF73|TRUA_DESVV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120563345|gb|ABM29089.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris DP4]
          Length = 297

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 88/292 (30%), Positives = 127/292 (43%), Gaps = 48/292 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + I Y G+   GWQ Q++ +     ++QG +E  +  + GE V +H AGRTD+GV
Sbjct: 1   MARLRLTIAYKGTDLHGWQVQEHATRPRPRTVQGVLEPIVSRMAGEQVRLHAAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+    + V   KA+NA  ++ D I IL++      FHARF A+ + Y YR
Sbjct: 61  HADGQVAHVDIPDHKLDVDWQKAINA--QLPDDICILDVRRAADDFHARFDALGKRYTYR 118

Query: 116 I-ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           + +TR+       G+ W     LD   M  AA+HL G HDF  F++     +S +RT+  
Sbjct: 119 LWLTRRFIPPKLHGQVWAT-GPLDVYAMDRAARHLAGTHDFAAFQNQGTDVTSTVRTVHA 177

Query: 175 FDVNSFGNL-----------------------------------IEIRVV----ARSFLH 195
                 G L                                   I + +V       FL 
Sbjct: 178 IRRCPSGTLPAGALLTYGEPYTSWRCTGTHPDQPPATAGHPLAGIGLELVWSFEGDGFLK 237

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +R+ +G L  VG G   + D+   +   DR      AP  GL    V Y 
Sbjct: 238 QMVRNMMGLLVAVGRGALAADDVPGIMATLDRSRAPATAPACGLTLSEVYYP 289


>gi|312129758|ref|YP_003997098.1| tRNA pseudouridine synthase a [Leadbetterella byssophila DSM 17132]
 gi|311906304|gb|ADQ16745.1| tRNA pseudouridine synthase A [Leadbetterella byssophila DSM 17132]
          Length = 251

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 77/248 (31%), Positives = 120/248 (48%), Gaps = 11/248 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y G+ + GWQ Q    ++QG +EKA+  V    + + G+ RTD+GVHA +Q 
Sbjct: 1   MRYFIEISYLGTHFHGWQIQPGADTVQGELEKALSTVLNAPISIMGSSRTDTGVHARQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH DL +E +     + LN +L     I+I N   +  + HARF A  R Y+YRI+  + 
Sbjct: 61  AHVDLPQE-IHAGYIQRLNRFL--PKDITIKNFYPLSDEAHARFDATGRKYIYRILHSKD 117

Query: 122 PLALEKGRAWL---IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  + W+     +  D + M  AA+ L    D+ +F  +    ++   TI      
Sbjct: 118 SF-----QQWICAHYSRRPDVDAMNKAAKILFLHTDYQSFSKVKTDVTTFDCTITEAVWR 172

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                +E  + A  FL   +R+ VG+L  VG GK    + E  + A+DR + G     EG
Sbjct: 173 YVDERLEFHISANRFLRGMVRAVVGTLLEVGYGKIGLQEFENIILAKDRTKAGTAVKAEG 232

Query: 239 LYFDSVEY 246
           L  + V Y
Sbjct: 233 LTLERVYY 240


>gi|311744771|ref|ZP_07718567.1| tRNA pseudouridine synthase A [Aeromicrobium marinum DSM 15272]
 gi|311311888|gb|EFQ81809.1| tRNA pseudouridine synthase A [Aeromicrobium marinum DSM 15272]
          Length = 262

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/249 (32%), Positives = 120/249 (48%), Gaps = 8/249 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW  Q    ++QG IE A+   L       +  AGRTD+GVHA  
Sbjct: 1   MRLRIDLAYDGTDFRGWAVQPGQRTVQGVIESALGTMLRLDPTPTLTCAGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH DL  +  P +L + L  YL   D I I ++      F ARF+A  R Y+YR+   
Sbjct: 61  QVAHVDL--DTHPGVLERRLRRYL--PDDIRIKSVVEAPPGFDARFAATERRYVYRMTDH 116

Query: 120 QA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            A P  L +      P+ L  + M  AA+HL+G+HDF  F      A++ IRT+      
Sbjct: 117 PAGPDPLARRMIVHHPRPLSVDLMNAAAEHLLGQHDFAAFCKKRAGATT-IRTLLALRTI 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I   V A +F H  +RS +G L  VG+ ++      + L  + R     +  P G
Sbjct: 176 RGGETIATTVRADAFCHAMVRSLMGCLVAVGERRFPPEFAAEVLSGRVRDGRVKVMEPHG 235

Query: 239 LYFDSVEYS 247
           L  + V Y 
Sbjct: 236 LVLEEVSYP 244


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

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 120/240 (50%), Gaps = 14/240 (5%)

Query: 8   IEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + Y+G+ Y G+Q Q+   N  +IQ  + +AI ++TGE V +  AGRTD+GVHA  QV  F
Sbjct: 1   MSYDGTSYHGFQTQEDPTNLPTIQDELMRAIQVLTGEEVKITCAGRTDAGVHARGQVVDF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                        A+N+ L     I+++    V + FH+RF A+ + Y Y I   +    
Sbjct: 61  LTTSRIPDEKFPLAMNSLLP--KDIAVVKAETVAEDFHSRFGALGKHYRYSIYNHRIHSP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI----RTIDHFDVN-S 179
                ++ +   L    M+ AA + VG HDF  F    C   SP+    RTI H  +  +
Sbjct: 119 FHHRYSYQVYPPLHVAAMQEAAGYFVGTHDFRGF----CATGSPVKDFVRTIWHCTLTVT 174

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             NL+ + V+   FL+  +R   G+L  VG GK     + + + ++DR + G  APP+GL
Sbjct: 175 EENLLLMDVMGDGFLYNMVRIITGTLVDVGKGKIAPESIPQIIASRDRTQAGTTAPPQGL 234


>gi|193212885|ref|YP_001998838.1| tRNA pseudouridine synthase A [Chlorobaculum parvum NCIB 8327]
 gi|193086362|gb|ACF11638.1| tRNA pseudouridine synthase A [Chlorobaculum parvum NCIB 8327]
          Length = 238

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/242 (33%), Positives = 112/242 (46%), Gaps = 5/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M IEY+G+ Y GWQRQ     ++QG IE+ +  +T E V + GAGRTD GVHA  QVA F
Sbjct: 1   MQIEYDGTDYSGWQRQPGDVVTVQGEIERVLGRITQEPVSIDGAGRTDRGVHARGQVASF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +  E     +  + N+ L    TI I ++  V + FHARFSA  R Y Y ++ R  P A
Sbjct: 61  AVASEMPLGRMMHSANSLLP--STIRITSMRQVPESFHARFSATSREYRYVLLER--PSA 116

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           ++   A       D   M   A  LVG HDF  F          + T+        G   
Sbjct: 117 IDSRFAGCSHGKPDVVLMNRLAAMLVGTHDFAAFSKETPDQQGTLCTVTEARWYRSGRFH 176

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+ A  FL + +R  V  +  VG G+ +  +  + L    R      A P GL+   V
Sbjct: 177 VFRIEANRFLRSMVRFLVAGMIEVGMGRLSEEEFSRMLVDGGRPASLVPADPAGLFLWKV 236

Query: 245 EY 246
            Y
Sbjct: 237 RY 238


>gi|302338166|ref|YP_003803372.1| tRNA pseudouridine synthase A [Spirochaeta smaragdinae DSM 11293]
 gi|301635351|gb|ADK80778.1| tRNA pseudouridine synthase A [Spirochaeta smaragdinae DSM 11293]
          Length = 247

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 113/243 (46%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           MI+ Y+G  + GWQ Q+   ++QG IE A+  +  + V V  AGRTDSGVHA  QV HFD
Sbjct: 1   MIVAYDGRKFSGWQVQREDRTVQGVIEAALESMEKQKVRVFAAGRTDSGVHARGQVVHFD 60

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                +       ALNA L     + I+    V   FHAR+SA  RSY Y +        
Sbjct: 61  TSLSSIEADKFAPALNAILPAD--VRIVGSYAVPDDFHARYSAKARSYRYFLYPGVCVSP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L +   +          +  A   L+G HDF++F +    + S +R I          +I
Sbjct: 119 LLRPYCYARRSLPSIGALNRAVSPLLGSHDFSSFSASGDPSPSKVRVIYQAVFLQHRGMI 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E R+   +FL   +RS VG+   V   +  +  +   L  +DR   G  AP  GL+F  V
Sbjct: 179 EFRITGNAFLWRMVRSIVGTALEVASAEEPARAMRLILDEKDRSLAGTTAPARGLFFWRV 238

Query: 245 EYS 247
            Y+
Sbjct: 239 HYT 241


>gi|76637689|ref|XP_875031.1| PREDICTED: pseudouridylate synthase-like 1 [Bos taurus]
 gi|297484219|ref|XP_002694181.1| PREDICTED: pseudouridylate synthase-like 1 [Bos taurus]
 gi|296479092|gb|DAA21207.1| pseudouridylate synthase-like 1 [Bos taurus]
          Length = 303

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 92/273 (33%), Positives = 134/273 (49%), Gaps = 30/273 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHAL 58
           RY +  +Y G+ + G    +       +Q  +E+A   +   + V    + RTD+GVHAL
Sbjct: 9   RYLVYFQYLGTDFNGVAAVRGVQRAVGVQNYLEEAAERLNSVMPVKFTISSRTDAGVHAL 68

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +LK    I +L    V   FHAR +AI R+YL
Sbjct: 69  SNAAHLDIQRRSDLPPFSPEVLTEALNTHLK-HPAIRVLQAFRVPSHFHARHAAISRTYL 127

Query: 114 YRIIT---RQAPLAL-EKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T   R   L + E+ R W L    LD   M+ AAQHL+G HDF+ F+S    ASSP
Sbjct: 128 YRLATGCPRPDRLPVFERNRCWALQADCLDVAAMQEAAQHLLGTHDFSAFQSAGSPASSP 187

Query: 169 IRTIDHFDV-----NSFGNLIEIRVV--------ARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V     + F    E R +        ++SFL+ Q+R     L  VG G    
Sbjct: 188 VRTLRRASVSPDPASPFVLPEESRQLQFWSMEFESQSFLYKQVRRMTAVLVAVGLGALMP 247

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             ++  L+++D   K    +AP  GL+  SV Y
Sbjct: 248 AQVKAILESRDPLGKHQSRVAPAHGLFLKSVLY 280


>gi|222630953|gb|EEE63085.1| hypothetical protein OsJ_17893 [Oryza sativa Japonica Group]
          Length = 279

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 74/209 (35%), Positives = 113/209 (54%), Gaps = 10/209 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG----EIVVVHGAGRTDSGVHAL 58
           ++ M+I Y+G+ + GWQ Q +  +IQ SIE A+  +T     E+ +V GAGRTD+GVHA 
Sbjct: 64  KWRMVIAYDGTKFKGWQYQPSPPTIQCSIENALTRITKLDRKELCLV-GAGRTDTGVHAW 122

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF     +  +  +  A+N  L     I +  +S    +FHAR S   + Y Y+I 
Sbjct: 123 GQVAHFTTPFSYHCLDSMHSAINGLLP--HEIRVREISAAKPEFHARTSTRSKIYHYKIY 180

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHC-QASSPIRTIDHF 175
                       A+     L+ + MR AA+H VG HDFT+F  ++H  +  SPI+ I  F
Sbjct: 181 NGPVMDPFHNHYAYHSAYKLNSQAMREAAKHFVGTHDFTSFANAVHNDRVRSPIKKIMRF 240

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
           DV   G ++++ +    FL+ Q+R+  GS
Sbjct: 241 DVIEMGAILQLEIEGTGFLYRQVRNMAGS 269


>gi|151554108|gb|AAI49177.1| PUSL1 protein [Bos taurus]
          Length = 312

 Score =  114 bits (285), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 91/274 (33%), Positives = 134/274 (48%), Gaps = 32/274 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHAL 58
           RY +  +Y G+ + G    +       +Q  +E+A   +   + V    + RTD+GVHAL
Sbjct: 34  RYLVYFQYLGTDFNGVAAVRGVQRAVGVQNYLEEAAERLNSVMPVKFTISSRTDAGVHAL 93

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +LK    I +L    V   FHAR +AI R+YL
Sbjct: 94  SNAAHLDIQRRSDLPPFSPEVLTEALNTHLK-HPAIRVLQAFRVPSHFHARHAAISRTYL 152

Query: 114 YRIIT-----RQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           YR+ T      + P+  E+ R W L    LD   M+ AAQHL+G HDF+ F+S    ASS
Sbjct: 153 YRLATGCPRPDRLPV-FERNRCWALQADCLDVAAMQEAAQHLLGTHDFSAFQSAGSPASS 211

Query: 168 PIRTIDHFDV-----NSFGNLIEIRVV--------ARSFLHTQIRSFVGSLKLVGDGKWT 214
           P+RT+    V     + F    E R +        ++SFL+ Q+R     L  VG G   
Sbjct: 212 PVRTLRRASVSPDPASPFVLPEESRQLQFWSMEFESQSFLYKQVRRMTAVLVAVGLGALM 271

Query: 215 STDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
              ++  L+++D   K    +AP  GL+  SV Y
Sbjct: 272 PAQVKAILESRDPLGKHQSRVAPAHGLFLKSVLY 305


>gi|46579324|ref|YP_010132.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|51316681|sp|Q72DL8|TRUA_DESVH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46448738|gb|AAS95391.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|311233151|gb|ADP86005.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris RCH1]
          Length = 297

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 88/292 (30%), Positives = 127/292 (43%), Gaps = 48/292 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + I Y G+   GWQ Q++ +     ++QG +E  +  + GE V +H AGRTD+GV
Sbjct: 1   MARLRLTIAYKGTDLHGWQVQEHATRPRPRTVQGVLEPIVSRMAGEQVRLHAAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+    + V   KA+NA  ++ D I IL++      FHARF A+ + Y YR
Sbjct: 61  HADGQVAHVDIPDHKLGVDWQKAINA--QLPDDICILDVRRAADDFHARFDALGKRYTYR 118

Query: 116 I-ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           + +TR+       G+ W     LD   M  AA+HL G HDF  F++     +S +RT+  
Sbjct: 119 LWLTRRFIPPKLHGQVWAT-GPLDVYAMDRAARHLAGTHDFAAFQNQGTDVTSTVRTVHA 177

Query: 175 FDVNSFGNL-----------------------------------IEIRVV----ARSFLH 195
                 G L                                   I + +V       FL 
Sbjct: 178 IRRCPSGTLPAGALLTCSEPYTSWRCTGTHPDQPPATAGHPLAGIGLELVWSFEGDGFLK 237

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +R+ +G L  VG G   + D+   +   DR      AP  GL    V Y 
Sbjct: 238 QMVRNMMGLLVAVGRGALAADDVPGIMATLDRSRAPATAPACGLTLSEVYYP 289


>gi|329938203|ref|ZP_08287654.1| tRNA pseudouridine synthase A [Streptomyces griseoaurantiacus M045]
 gi|329302692|gb|EGG46582.1| tRNA pseudouridine synthase A [Streptomyces griseoaurantiacus M045]
          Length = 288

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 123/254 (48%), Gaps = 11/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHA 57
            +R  + + Y+G+G+ GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA
Sbjct: 9   FVRVRLDLSYDGTGFSGWAKQAGGRRTVQGEIEDALRTVTRSRETFELTVAGRTDAGVHA 68

Query: 58  LRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
             QVAH DL RE W      L K L    ++   + +  L      F ARFSA+ R Y Y
Sbjct: 69  RGQVAHVDLPREVWAEHHGKLLKRLAG--RLPRDVRVWALREAPAGFDARFSAVWRRYAY 126

Query: 115 RIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+      +  L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+ 
Sbjct: 127 RVTDNPGGVDPLLRGHVLWHDWPLDVDAMNEAARGLLGEHDFAAY-CKKREGATTIRTLQ 185

Query: 174 HFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              +   G+ ++   V A +F H  +RS +G+L  VGDG        K L A  R     
Sbjct: 186 ELSLARGGDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRAPDWPAKVLAAGVRDSAVH 245

Query: 233 LAPPEGLYFDSVEY 246
           +  P GL  + V Y
Sbjct: 246 VVRPHGLTLEEVGY 259


>gi|156538761|ref|XP_001607889.1| PREDICTED: similar to CG34140-PA [Nasonia vitripennis]
          Length = 298

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 89/284 (31%), Positives = 131/284 (46%), Gaps = 42/284 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVH 56
           RY + + Y G+ Y G Q+  N +     +IQG+IE ++       I  +  AGRTD+GVH
Sbjct: 7   RYLLKLSYIGTSYRGSQKHVNNAVVDIDTIQGAIEYSMRRFNFSNIPTISLAGRTDAGVH 66

Query: 57  ALRQVAHFDLVREWV--PVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYL 113
           AL   AH DL          L + +N  L   +  I I++   V K FHAR+SA  R+YL
Sbjct: 67  ALCTSAHVDLEHSGTLDTEYLVRMMNRNLINANHEIRIMSAHEVSKDFHARYSAKSRTYL 126

Query: 114 YRIITRQAPLA-----LEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTF------- 158
           YR+I  + PL       E  R+  +   P++ D E +R   +   G  DF TF       
Sbjct: 127 YRLIIPKDPLDHRFPIAEANRSLFLNMYPQNFDIERLRSGIKLFCGTKDFMTFSARKRDR 186

Query: 159 -----------RSIHC--QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
                      R++H   + + P+ + D    N   +   +   +RSFL+ QIR  VGSL
Sbjct: 187 NPEFEMRRNFVRTLHVTMKEAGPLMSFDPLSKNL--DYWHLEFTSRSFLYNQIRRIVGSL 244

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
             +G  K +  D++  +Q        P    A P GLY  +VEY
Sbjct: 245 IALGSHKVSEEDIQTMIQVPSHHNWNPHVTPAAPRGLYLKNVEY 288


>gi|327539206|gb|EGF25829.1| tRNA pseudouridine synthase A [Rhodopirellula baltica WH47]
          Length = 276

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 77/257 (29%), Positives = 124/257 (48%), Gaps = 16/257 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + + Y+G+ Y GWQ Q    SIQ  +E+ I  + G  V V G+GRTD+GVHA+ QVA 
Sbjct: 10  FHLTVAYDGTEYCGWQVQPEQRSIQSELERVIRPLAGRPVRVLGSGRTDAGVHAIGQVAR 69

Query: 64  FDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             ++  W    V L +A+N+  K+ + I +  +    ++FH    A  + Y Y +    +
Sbjct: 70  C-VLPAWKANTVALQRAINS--KLPNDIRVKAVRETRERFHPIADATGKQYQYLVQVGGS 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT------IDHF 175
                      +   +D   M+ AA   VGRHDF  F+    +  S +RT      I   
Sbjct: 127 RDPFANRFVNRVGGPIDHSAMQSAAAKFVGRHDFKAFQGTGAERPSTVRTIHLARWIPRV 186

Query: 176 DVNSFGNLIE-----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                G  +E       +    FL+  +R+ +G++  VG GK     +++ L ++DRK  
Sbjct: 187 ATGPTGAELEGEHWCFEIDGEGFLYNMVRNLMGTMLEVGRGKKPLDWIDEVLASRDRKMA 246

Query: 231 GPLAPPEGLYFDSVEYS 247
           GP APP+GL+   V+Y 
Sbjct: 247 GPTAPPQGLFLCRVDYP 263


>gi|283457578|ref|YP_003362161.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
 gi|283133576|dbj|BAI64341.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
          Length = 348

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 90/274 (32%), Positives = 122/274 (44%), Gaps = 41/274 (14%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS + GW  Q N  ++QG IE A+ L+      V  AGRTD+GVHA  Q  H DL  E
Sbjct: 54  YDGSLFSGWAAQPNLVTVQGVIENALELILRAPHRVVVAGRTDAGVHAEAQTLHCDLSDE 113

Query: 70  -WV-----------PVILCKALNAYLK-------------------ISDTISILNLSIVD 98
            W               L + L   L+                   +   I I  ++ V 
Sbjct: 114 DWTRLQGRTGEDDPTAALGRRLTGALQRCLYDAEEQLNLPKNVRGILQGAIQIHRVAEVP 173

Query: 99  KQFHARFSAIRRSYLYRIITRQAP--LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
             F ARFSA  R Y+YRI    A     L +   W +P+ LDC ++  +AQ L+G  DF 
Sbjct: 174 FDFDARFSATGRRYVYRIADGAADGLNPLHRTYTWAVPEHLDCADLNESAQQLLGLRDFL 233

Query: 157 TFRSIHCQASSPIRTIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +F    C+      TI      SF      LIE+ VVA +F H  +RS VG+L L G GK
Sbjct: 234 SF----CKPREGATTIRELRELSFTRTESALIEVCVVADAFCHHMVRSLVGALVLYGTGK 289

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             +  L + ++   R+    LAPP  L    + Y
Sbjct: 290 RDAAWLRERIENPGREASLTLAPPHALALAEIYY 323


>gi|269976928|ref|ZP_06183902.1| tRNA pseudouridine synthase A [Mobiluncus mulieris 28-1]
 gi|269934759|gb|EEZ91319.1| tRNA pseudouridine synthase A [Mobiluncus mulieris 28-1]
          Length = 326

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 96/306 (31%), Positives = 135/306 (44%), Gaps = 60/306 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R    I Y+G  + GW RQ    ++QG++E A+ ++  + V +  AGRTD+GVHA  Q
Sbjct: 1   MTRIRFDIRYDGRPFHGWARQPGLPTVQGALETALTVLFRQPVTLTVAGRTDAGVHATGQ 60

Query: 61  VAHFDLVRE----WV---------------------PVI--------LCKALNAYLKI-- 85
           VAHFDL  +    W+                     P I        L + L++ L++  
Sbjct: 61  VAHFDLPDQFSGDWLRDAHDTDFAASLGAIVAASNPPGIANFQLSTGLHRRLDSVLRLVT 120

Query: 86  ---SDTISILNLS-------------------IVDKQFHARFSAIRRSYLYRIITRQ-AP 122
              + TI  LNL                     V   F ARFSA+ R Y Y +I    A 
Sbjct: 121 SGNTPTIPGLNLDDQPIYPPEANGAIVVTTARPVPDAFDARFSALARHYEYLVIDEPTAR 180

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG- 181
             L +   W     L+   M  A+  L+G HDF  F      A++ IRT+    V+    
Sbjct: 181 NPLTRNTCWWYGAPLNVARMHEASAGLLGTHDFAAFCKPREGATT-IRTLKQLGVSRLAP 239

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I   V A +F H+ +RS VG+L  VG GK  +  LE+AL +  R    PLAP +GL  
Sbjct: 240 GEIRFDVAADAFCHSMVRSLVGALTEVGRGKRDADWLEQALHSAVRIPEIPLAPAQGLTL 299

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 300 VRVDYP 305


>gi|325847073|ref|ZP_08169899.1| tRNA pseudouridine synthase A [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481045|gb|EGC84090.1| tRNA pseudouridine synthase A [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 252

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 120/244 (49%), Gaps = 11/244 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I+Y+GS + G+Q QK+  ++Q  +E+AI  VTGE   +  +GRTDSGVHA     +F   
Sbjct: 10  IQYDGSLFEGFQIQKDKRTVQKELEEAIRKVTGEKNRIIASGRTDSGVHANEMYINFLTA 69

Query: 68  REWVPVILCKALNAYLKISDTISILNLS--IVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           ++    I     + +LK      IL LS   VDK FHARFS   ++Y Y I   +    +
Sbjct: 70  KD----IRADKFHFHLKKYLPADILALSSKKVDKNFHARFSVKTKTYKYVISLEKILHPI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF---GN 182
            +     I   LD + ++   + L G HDF  F  +  + +  I TI   D   +    N
Sbjct: 126 YRNYMEQITYKLDFDKLKQGMEILKGEHDFRAF--MLSEKNDIINTIRKIDDCYYILDNN 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           ++ +   A SFLH Q+R   GSL  +  GK +  D +      ++K   P     GLY D
Sbjct: 184 ILFLYFKAESFLHNQVRIMAGSLIELSRGKISLDDFKFYFDKNNKKRANPTLKAGGLYLD 243

Query: 243 SVEY 246
           S++Y
Sbjct: 244 SIDY 247


>gi|225020488|ref|ZP_03709680.1| hypothetical protein CORMATOL_00495 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224946877|gb|EEG28086.1| hypothetical protein CORMATOL_00495 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 290

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/267 (31%), Positives = 121/267 (45%), Gaps = 31/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           IR  + + Y+G+ + GW RQ +    ++Q  +E A+ LV  + + +  AGRTD+GVHA+ 
Sbjct: 4   IRIRLDLAYDGTHFHGWARQGHSELRTVQQVLEDALTLVLRQPIALTVAGRTDAGVHAVA 63

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT--------------ISILNLSIVDKQFHARF 105
           QVAHFD        +   AL+      D               + +   +I    F ARF
Sbjct: 64  QVAHFD--------VPAAALDTRSIAGDPGRLVRRLARLLPTDVRVHAATIAPPDFDARF 115

Query: 106 SAIRRSYLYRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+RR Y+YR+ T  +  L          PK +D   M+  A  L+G HDF  F   H  
Sbjct: 116 SALRRHYVYRLTTHPRGALPTRVTDTAHHPKPVDLAAMQACAAELIGLHDFAAF-CRHRD 174

Query: 165 ASSPIRTIDHFDVNSFGNLI-----EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            ++ IR +  F  N     I     E  V A +F  + +RS VG   +VG+GK  +    
Sbjct: 175 GATTIRDLQEFTWNDISTPIEPDTFEAHVTADAFCWSMVRSLVGCCLVVGEGKRPAGFAT 234

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEY 246
             L    R    P+AP  GL    V+Y
Sbjct: 235 SLLAETSRSALVPVAPAAGLSLVGVDY 261


>gi|332290819|ref|YP_004429428.1| tRNA pseudouridine synthase A [Krokinobacter diaphorus 4H-3-7-5]
 gi|332168905|gb|AEE18160.1| tRNA pseudouridine synthase A [Krokinobacter diaphorus 4H-3-7-5]
          Length = 257

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 115/250 (46%), Gaps = 9/250 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G  Y GWQRQ N  ++Q +IEKA+ ++  + V + GAGRTD+GVHA +  
Sbjct: 1   MRYFIELSYFGKHYHGWQRQPNAVTVQETIEKALSMILRKPVQIMGAGRTDAGVHATQMY 60

Query: 62  AHFDLVREWVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AHFD   E          L    N  L     I+   +  V  + H RF A  RSY+YRI
Sbjct: 61  AHFDWDGEQFTTQESIEKLTHKFNRLL--PKDIAFKRIFQVADKAHTRFDATSRSYVYRI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              + P   +   A  +   +  E M  AA  L+   DF  F   +   ++ +  I    
Sbjct: 119 GKEKNPFTSD--HAPTVRNEVHIEAMNKAAAILLDYSDFECFSKSNTDVNTYLCDITRAT 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                +     + A  FL   +R+ VG+L  +G+GK   T + + +  + R + G   P 
Sbjct: 177 WIETEDEYHFHITANRFLRNMVRAIVGTLLEIGEGKRDITWMHEVITGKSRSQAGKSVPG 236

Query: 237 EGLYFDSVEY 246
            GLY   + Y
Sbjct: 237 RGLYLTEILY 246


>gi|330685169|gb|EGG96833.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU121]
          Length = 267

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 120/243 (49%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+ + G+Q Q+ G ++Q   EK +  +    + +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIEYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHIRIHPSSRTDRGVHAYQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I + ++  VD+ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELQIENSKWQYAMNSAL--PDDIYVKSVQHVDEDFHCRYDCVGKRYRYKVYQAKH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I  SLD   M  AA+  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTYIADSLDLNQMNEAAKRFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK +  ++ + L+ ++R +    AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLIEVGKGKRSPEEIPQLLEEKNRNKIPFTAPSEGLYL 238

Query: 242 DSV 244
           + V
Sbjct: 239 EKV 241


>gi|21223110|ref|NP_628889.1| tRNA pseudouridine synthase A [Streptomyces coelicolor A3(2)]
 gi|289769686|ref|ZP_06529064.1| tRNA pseudouridine synthase A [Streptomyces lividans TK24]
 gi|8134769|sp|O86776|TRUA_STRCO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3449243|emb|CAA20387.1| putative pseudouridylate synthase [Streptomyces coelicolor A3(2)]
 gi|289699885|gb|EFD67314.1| tRNA pseudouridine synthase A [Streptomyces lividans TK24]
          Length = 284

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/254 (33%), Positives = 122/254 (48%), Gaps = 11/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHA 57
            +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA
Sbjct: 9   FVRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSRETYELTVAGRTDAGVHA 68

Query: 58  LRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
             QVAH DL RE W    V L K L    ++   + +  L      F+ARFSA+ R Y Y
Sbjct: 69  RGQVAHVDLPREVWAEHHVKLLKRLAG--RLPRDVRVWALREAPSGFNARFSAVWRRYAY 126

Query: 115 RIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+      +  L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+ 
Sbjct: 127 RVTDNPGGVDPLLRGHVLWHDWPLDVDAMNAAARGLLGEHDFAAY-CKKREGATTIRTLQ 185

Query: 174 HFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
               V     ++   V A +F H  +RS +G+L  VGDG        K L A  R     
Sbjct: 186 ELSLVRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRGPEWPAKVLAAGVRDSAVH 245

Query: 233 LAPPEGLYFDSVEY 246
           +  P GL  + V Y
Sbjct: 246 VVRPHGLTLEEVGY 259


>gi|296268583|ref|YP_003651215.1| tRNA pseudouridine synthase A [Thermobispora bispora DSM 43833]
 gi|296091370|gb|ADG87322.1| tRNA pseudouridine synthase A [Thermobispora bispora DSM 43833]
          Length = 294

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 131/275 (47%), Gaps = 36/275 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALR 59
           +R+ + + Y+G+ + GW RQ    ++QG +E A+   L       +  AGRTD+GVHA  
Sbjct: 6   VRFRLDLGYDGTDFQGWARQPGLRTVQGELEAALATLLRLEAPPRLTVAGRTDAGVHARG 65

Query: 60  QVAHFDLVREWVPVI-----------------LCKALNAYLK--ISDTISILNLSIVDKQ 100
           QV H DL    + ++                 LC AL   L   +   + +  +S+    
Sbjct: 66  QVVHVDLPLAALAILEPRGRETATPPAERLPELCSALVRRLAAVLPPDVRVFAVSVPPDG 125

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTT 157
           F ARFSA+ R Y YR+    AP  ++  R   +   PK LD E M  A+  L+G HDF  
Sbjct: 126 FDARFSALCRRYCYRVC--DAPGGVDPLRRREVLWYPKPLDVELMNAASVRLLGEHDFAA 183

Query: 158 FRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK---- 212
           F     + ++ IR +  F+       +IE  VVA +F H+ +RS VG++  VG+GK    
Sbjct: 184 FCKKR-EGATTIRELRRFEWARRDDGIIEATVVADAFCHSMVRSLVGAVLAVGEGKRPVE 242

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           W +  L +A+    R     +AP  GL  + V Y 
Sbjct: 243 WPAEVLARAV----RDSAVRVAPAHGLTLEEVRYP 273


>gi|46446316|ref|YP_007681.1| putative tRNA-pseudouridine synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
 gi|51316630|sp|Q6MDE3|TRUA2_PARUW RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|46399957|emb|CAF23406.1| putative tRNA-pseudouridine synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 262

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 116/244 (47%), Gaps = 8/244 (3%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G  YFGWQ+   G S++ +++ ++  +    + +  A RTD GVHA  Q+ +F   
Sbjct: 22  IAYDGQAYFGWQKTPAGPSVEKTLQNSLEQILQHTISLQAASRTDKGVHARGQIVNFLTT 81

Query: 68  REWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
           +    +     +LN+ L     + IL+   +   FH   + + + Y Y I      L   
Sbjct: 82  KSITDLQKFILSLNSLLPTD--LRILSAEKMPSTFHPTLNCVAKEYCYYICYDFVQLPEY 139

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTID--HFDVNSFGN 182
           +  +W  P  L    M  A   L+G HDF+ F +   +   +  IR +   H +V +   
Sbjct: 140 RPYSWHCPFPLMLGKMTQAISVLIGEHDFSAFCNFKKNVNYTDYIRRVQAIHLEVLNHKR 199

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           L  IR+    FL+  +R+ VG+L  +G GK    D+   LQ+QDRK  G  AP  GL+  
Sbjct: 200 LC-IRIKGNHFLYKMVRNIVGTLIYIGKGKLMVEDIPSILQSQDRKMAGVTAPAHGLFLQ 258

Query: 243 SVEY 246
           +V Y
Sbjct: 259 TVLY 262


>gi|302757930|ref|XP_002962388.1| hypothetical protein SELMODRAFT_78854 [Selaginella moellendorffii]
 gi|300169249|gb|EFJ35851.1| hypothetical protein SELMODRAFT_78854 [Selaginella moellendorffii]
          Length = 268

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/261 (31%), Positives = 131/261 (50%), Gaps = 25/261 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ +++ Y+G+ + GWQ Q +  ++QG IE A+  +T    E +++  A RTD+GVHAL 
Sbjct: 1   KWRIVVSYDGTRFSGWQYQPDFPTVQGLIEDALTKLTRYTREELLMAAASRTDAGVHALG 60

Query: 60  QVAHF-------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           QVAHF       DL R      + + LN  L     I +  +S     FHA+  A  + Y
Sbjct: 61  QVAHFHSPACIGDLSR------IHRGLNGTL--PHEIRVREISPAKSSFHAQACARTKRY 112

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIR 170
            Y++        L +  A+ +P+ LD   M  A  + VG+HDF+TF   S      +P+R
Sbjct: 113 QYKLFVAPVMDPLLRLYAYHVPERLDVAAMAEACGYFVGKHDFSTFSNSSTLRPLQNPVR 172

Query: 171 TIDHFDV--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            I  FD+   + G ++   +    F H QIR+ VG +  +G G+  +  + + L  +DR+
Sbjct: 173 EILRFDLLEQASGPVLCFEIEGTGFFHKQIRNMVGLIVAIGKGEHEARVIPELLAMKDRQ 232

Query: 229 ECGPL---APPEGLYFDSVEY 246
           +   +   AP  GL   SV Y
Sbjct: 233 KLARVSITAPSRGLTLVSVHY 253


>gi|256785794|ref|ZP_05524225.1| tRNA pseudouridine synthase A [Streptomyces lividans TK24]
          Length = 275

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/253 (33%), Positives = 122/253 (48%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 1   MRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSRETYELTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QVAH DL RE W    V L K L    ++   + +  L      F+ARFSA+ R Y YR
Sbjct: 61  GQVAHVDLPREVWAEHHVKLLKRLAG--RLPRDVRVWALREAPSGFNARFSAVWRRYAYR 118

Query: 116 IITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +      +  L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+  
Sbjct: 119 VTDNPGGVDPLLRGHVLWHDWPLDVDAMNAAARGLLGEHDFAAY-CKKREGATTIRTLQE 177

Query: 175 FD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V     ++   V A +F H  +RS +G+L  VGDG        K L A  R     +
Sbjct: 178 LSLVRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRGPEWPAKVLAAGVRDSAVHV 237

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 238 VRPHGLTLEEVGY 250


>gi|331090989|ref|ZP_08339831.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330405211|gb|EGG84747.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 248

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 121/245 (49%), Gaps = 6/245 (2%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSS--IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + +EY+GS Y GWQR  KN SS  I   I + I  +T E V +    RT+ GVHA  Q+ 
Sbjct: 6   LTLEYDGSRYQGWQRLGKNESSNTIANKIIEVIKKMTNEDVELFCGARTEVGVHAYAQIV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F    +     + + LN YL +   I++ ++    ++FHA  +A  + Y+YR+   + P
Sbjct: 66  NFKTTSDMKLGEIKQYLNRYLPMD--IAVTDIEEKPERFHASLNATSKIYMYRMAIGEVP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   + + K  D + M+ AA  LVG+HDF  F ++  ++ S ++ I   D+ +   
Sbjct: 124 SVFERKYTYYVFKKPDVDVMKQAALLLVGKHDFKNFSTVK-KSKSTVKEIYDIDIYTDDE 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I+I + A  FLH   R  +G+L  +G G     ++E     +   +       +GLY  
Sbjct: 183 EIQITLHANDFLHNMARMVIGTLIDIGLGNRKKEEIEDIFNPESSVQASSPCDAKGLYLQ 242

Query: 243 SVEYS 247
            V Y 
Sbjct: 243 EVLYE 247


>gi|300727110|ref|ZP_07060529.1| tRNA pseudouridine synthase A [Prevotella bryantii B14]
 gi|299775654|gb|EFI72245.1| tRNA pseudouridine synthase A [Prevotella bryantii B14]
          Length = 259

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 88/266 (33%), Positives = 130/266 (48%), Gaps = 27/266 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI------FLVTG----EIVVVHGAGR 50
           M RY +I  Y+G+ Y GWQ Q NG+S+Q  ++ A+      FL+      EI VV GAGR
Sbjct: 1   MHRYFIIFAYDGTNYHGWQIQPNGNSVQAELQHALALSLRSFLLLKSNDFEIEVV-GAGR 59

Query: 51  TDSGVHALRQVAHFDLVREWVPVI---LCKALNAYLK--ISDTISILNLSIVDKQFHARF 105
           TD+GVHA +  AHF+L  E  P++    CK +   +   +   IS+ ++  V+   HARF
Sbjct: 60  TDAGVHARQMAAHFELSEEEFPLLDESKCKQIVYRINRILPRDISVSDVYPVESDMHARF 119

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           SA  R+Y Y I T + P           P  LD + M    + ++   DF  F    C+A
Sbjct: 120 SAKWRTYHYYIHTDKNPFLRFYSLETHYP--LDFDLMNEGGKIIMEHQDFAAF----CKA 173

Query: 166 SSPIRTI--DHFD---VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            +  +T   D  +   V +      + + A  FL   +R+ VG+L L+G  K T  DL  
Sbjct: 174 GADNKTTLCDVTECKWVQTSPTSWYLTITANRFLRNMVRAVVGTLFLLGRHKITLDDLRV 233

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEY 246
            L   +R + G   P   L+ + VEY
Sbjct: 234 ILHEGNRSKAGESMPGNALFLEKVEY 259


>gi|239636202|ref|ZP_04677206.1| tRNA pseudouridine synthase A [Staphylococcus warneri L37603]
 gi|239598218|gb|EEQ80711.1| tRNA pseudouridine synthase A [Staphylococcus warneri L37603]
          Length = 267

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 120/243 (49%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+ + G+Q Q+ G ++Q   EK +  +    + +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIEYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHISIHPSSRTDRGVHAYQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I + ++  VD+ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELQIENSKWQYAMNSAL--PDDIYVKSVKQVDEDFHCRYDCVGKRYRYKVYQAKH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I  SLD   M  AA+  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTYIADSLDLNQMNEAAKLFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK +  ++ + L+ ++R +    AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLIEVGKGKRSPEEIPQLLEEKNRNKIPFTAPSEGLYL 238

Query: 242 DSV 244
           + V
Sbjct: 239 EKV 241


>gi|158317762|ref|YP_001510270.1| tRNA pseudouridine synthase A [Frankia sp. EAN1pec]
 gi|158113167|gb|ABW15364.1| tRNA pseudouridine synthase A [Frankia sp. EAN1pec]
          Length = 275

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/255 (32%), Positives = 126/255 (49%), Gaps = 17/255 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           +IR  + + Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA  
Sbjct: 7   LIRLRLDLAYDGTAFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDSGVHAAG 66

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH D+  +     L + LN  L  +  + +  L+     F ARFSA+ R Y+YRI   
Sbjct: 67  QVAHVDIPDDTPVGGLARRLNGVLDRA--VRVKGLAPAPDGFDARFSALSRRYVYRIT-- 122

Query: 120 QAPLALEKGRAW---LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            AP   +  R +     P+ LD   M  AA  L+G HDF  F     + ++ +RT+   D
Sbjct: 123 DAPYGADPLRRFDTLASPRPLDVPAMAEAALLLLGEHDFAAF-CRRREGATTVRTLLRLD 181

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRKECGP 232
           V+   ++I   V A +F H+ +R+  G+L  VG+G+    W +  L + +    R     
Sbjct: 182 VSRSRDVILADVEADAFCHSMVRALAGALVAVGEGRRRPEWVAAVLGRGM----RDPAVT 237

Query: 233 LAPPEGLYFDSVEYS 247
           + P  GL    V Y 
Sbjct: 238 VLPAHGLTLVEVRYP 252


>gi|326799821|ref|YP_004317640.1| tRNA pseudouridine synthase A [Sphingobacterium sp. 21]
 gi|326550585|gb|ADZ78970.1| tRNA pseudouridine synthase A [Sphingobacterium sp. 21]
          Length = 255

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 120/251 (47%), Gaps = 14/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + ++G  Y GWQ Q+N  S+Q  + KA+  +    V   G GRTD+GVHA +  A
Sbjct: 7   RYFVELAFHGGAYHGWQIQENAISVQEVLNKALGTLLRVPVNTVGCGRTDTGVHAKQLFA 66

Query: 63  HFDLVREWVPVI------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           HFD   + V  I      +   LNA L     I++  L +V    HARF AI+RSY Y I
Sbjct: 67  HFD---DAVGAIEGNEERIVTGLNALLPTD--IAVKQLFVVAPNAHARFDAIKRSYEYHI 121

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              + P     G +W +    D E M  AA+H++   DF+ F   H Q  +    +   +
Sbjct: 122 HFGKNPFL--HGFSWQLRDRPDVEAMNEAARHMMKYKDFSCFSKSHTQVFTNNCQLTKAE 179

Query: 177 VNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G  +   + A  FL   +R+ VG+L  +G+GK     + + + +++R   G   P
Sbjct: 180 WQWLDGGRLVFYISADRFLRNMVRAIVGTLMEIGNGKRDLNYIHEVINSKNRSMAGVSVP 239

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


>gi|302764370|ref|XP_002965606.1| hypothetical protein SELMODRAFT_84331 [Selaginella moellendorffii]
 gi|300166420|gb|EFJ33026.1| hypothetical protein SELMODRAFT_84331 [Selaginella moellendorffii]
          Length = 269

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 81/262 (30%), Positives = 131/262 (50%), Gaps = 26/262 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ +++ Y+G+ + GWQ Q +  ++QG IE A+  +T    E +++  A RTD+GVHAL 
Sbjct: 1   KWRIVVSYDGTRFSGWQYQPDFPTVQGLIEDALTKLTRYTREELLMAAASRTDAGVHALG 60

Query: 60  QVAHF-------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           QVAHF       DL R      + + LN  L     I +  +S     FHA+  A  + Y
Sbjct: 61  QVAHFHSPACIGDLSR------IHRGLNGTL--PHEIRVREISPAKSSFHAQACARTKRY 112

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIR 170
            Y++        L +  A+ +P+ LD   M  A  + VG+HDF+TF   S      +P+R
Sbjct: 113 QYKLFVAPVMDPLLRLYAYHVPERLDVAAMAEACGYFVGKHDFSTFSNSSTLRPLQNPVR 172

Query: 171 TIDHFDV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            I  F++    S G ++   +    F H QIR+ VG +  +G G+  +  + + L  +DR
Sbjct: 173 EILRFELLEQASLGPVLCFEIEGTGFFHKQIRNMVGLIVAIGKGEHQARVIPELLAMKDR 232

Query: 228 KECGPL---APPEGLYFDSVEY 246
           ++   +   AP  GL   SV Y
Sbjct: 233 QKLARVSITAPSRGLTLVSVHY 254


>gi|23503259|ref|NP_699170.1| tRNA pseudouridine synthase-like 1 [Homo sapiens]
 gi|52783232|sp|Q8N0Z8|PUSL1_HUMAN RecName: Full=tRNA pseudouridine synthase-like 1; AltName:
           Full=tRNA pseudouridylate synthase-like 1; AltName:
           Full=tRNA-uridine isomerase-like 1
 gi|21706547|gb|AAH34304.1| Pseudouridylate synthase-like 1 [Homo sapiens]
 gi|22761287|dbj|BAC11527.1| unnamed protein product [Homo sapiens]
 gi|56204950|emb|CAI23172.1| pseudouridylate synthase-like 1 [Homo sapiens]
 gi|119576649|gb|EAW56245.1| pseudouridylate synthase-like 1 [Homo sapiens]
          Length = 303

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/276 (32%), Positives = 130/276 (47%), Gaps = 36/276 (13%)

Query: 3   RYCMIIEYNGSGYFGW---QRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G    +  +    +Q  +E+A   L + E V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYVGTDFNGVAAVRGTQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR +A  R+YL
Sbjct: 73  SNAAHLDVQRRSGRPPFPPEVLAEALNTHLR-HPAIRVLRAFRVPSDFHARHAATSRTYL 131

Query: 114 YRIIT----RQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T    R      E+   W +P   LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 132 YRLATGCHRRDELPVFERNLCWTLPADCLDMVAMQEAAQHLLGTHDFSAFQSAGSPVPSP 191

Query: 169 IRTIDHFDVNS----------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +RT+    V+                 F NL      ++SFL+ Q+R     L  VG G 
Sbjct: 192 VRTLRRVSVSPGQASPLVTPEESRKLRFWNL---EFESQSFLYRQVRRMTAVLVAVGLGA 248

Query: 213 WTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
                ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 249 LAPAQVKTILESQDPLGKHQTRVAPAHGLFLKSVLY 284


>gi|260435918|ref|ZP_05789888.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8109]
 gi|260413792|gb|EEX07088.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8109]
          Length = 293

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 113/244 (46%), Gaps = 14/244 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y GS + GWQRQ+NG S+Q  +E AI  L     V    AGRTD+GVHA  QV
Sbjct: 17  RIALSLQYEGSSFCGWQRQRNGRSVQAVLEDAIAQLDPHRPVQTFAAGRTDAGVHAAGQV 76

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R+W P     ALN   ++  TI +         +HA +SA  R Y Y I
Sbjct: 77  VHFDCSGPIPARKWAP-----ALNG--RLPSTIRVRESVARPMDWHACYSATYRRYRYTI 129

Query: 117 ITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              + P       +W      LD   MR A   ++G HDF+ F     + +    T+   
Sbjct: 130 HNGRRPNLFLSPWSWHRYQHRLDASRMRDALSTMLGLHDFSAFMKAGSRRAHARTTVQEV 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G+L+ + + A  FL+  +R  +  L  VG+ + +    E+  + + R E    AP
Sbjct: 190 LVERQGDLLRVEIQASGFLYGMVRLLMAQLVAVGEHRLSVAAFEQRWRERRRHEVKEAAP 249

Query: 236 PEGL 239
             GL
Sbjct: 250 ATGL 253


>gi|89953446|gb|ABD83318.1| Fgenesh protein 88 [Beta vulgaris]
          Length = 278

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 82/239 (34%), Positives = 119/239 (49%), Gaps = 11/239 (4%)

Query: 18  WQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV 73
           WQ Q +  ++Q +IEKA+  +T     E+ VV GAGRTD+GVHA  QVAHF     +  +
Sbjct: 26  WQYQASPPTVQCAIEKALTKITHLDRKELSVV-GAGRTDTGVHAWGQVAHFFTPFNYDSL 84

Query: 74  ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
               A    L  SD I +  +S    QFHARFSA  + Y Y I          +   +  
Sbjct: 85  DEVHAAFNGLLPSD-IRVREVSPASPQFHARFSAKGKIYRYSIYNSSFMDPFLRYHVYHS 143

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNSFGNLIEIRVVAR 191
              L+   M  AA++  G+HDFT F +   + +   PI+TI  FDV   G L+E+ V   
Sbjct: 144 TYKLNAAVMAEAARYFTGKHDFTAFANAIRNDRVRDPIKTISRFDVTERGPLLELEVEGS 203

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEYS 247
            FL+ Q+R+ V  L  +G        + + L+ ++R+E        PP GL   SV+Y+
Sbjct: 204 GFLYRQVRNMVALLLQIGREAIPPDIVPEILETKNRRELAKYTKSTPPHGLSLVSVKYN 262


>gi|258651414|ref|YP_003200570.1| tRNA pseudouridine synthase A [Nakamurella multipartita DSM 44233]
 gi|258554639|gb|ACV77581.1| tRNA pseudouridine synthase A [Nakamurella multipartita DSM 44233]
          Length = 305

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 80/265 (30%), Positives = 125/265 (47%), Gaps = 24/265 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I Y+G+ + GW  Q    ++ G +  A+  +    V +  AGRTD+GVHA  QVA
Sbjct: 27  RLRLDISYDGTDFAGWAIQPGLRTVAGELTSALTTIVRTPVRLVVAGRTDAGVHAAGQVA 86

Query: 63  HFDLVREWVPVILCK----------------ALNAYLKISDTISILNLSIVDKQFHARFS 106
           H DL +  +  ++ +                       +   + +  +    + F ARFS
Sbjct: 87  HVDLPQAALLTVIPRDRADHPDPERAGRLGLLRRLGGLLPPDVRVRAVLAAPEGFDARFS 146

Query: 107 AIRRSYLYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-- 163
           A+RR Y YRI T +  +     R  +   ++LD E M +AAQ LVG HDF  F    C  
Sbjct: 147 ALRRRYRYRIGTAEWGVEPADRRFVYARRRTLDVEAMTLAAQALVGLHDFHAF----CRP 202

Query: 164 -QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
            + ++ IR +    V   G+ + I VVA +F H+ +R+ VGSL  VG+ +  +    + L
Sbjct: 203 REGATTIRDLQKLTVTRAGDEVRIDVVADAFCHSMVRALVGSLLAVGELRMPTARPAELL 262

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
            A +R     +AP  GL    V+Y 
Sbjct: 263 AAGERTSAFAVAPAHGLSLVGVDYP 287


>gi|312150754|gb|ADQ31889.1| pseudouridylate synthase-like 1 [synthetic construct]
          Length = 303

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/276 (32%), Positives = 130/276 (47%), Gaps = 36/276 (13%)

Query: 3   RYCMIIEYNGSGYFGW---QRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G    +  +    +Q  +E+A   L + E V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYVGTDFNGVAAVRGTQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR +A  R+YL
Sbjct: 73  SNAAHLDVQRRSGRPPFPPEVLAEALNTHLR-HPAIRVLRAFRVPSDFHARHAATSRTYL 131

Query: 114 YRIIT----RQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T    R      E+   W +P   LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 132 YRLATGCHRRDELPVFERNLCWTLPADCLDMVAMQEAAQHLLGTHDFSAFQSAGSPVPSP 191

Query: 169 IRTIDHFDVNS----------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +RT+    V+                 F NL      ++SFL+ Q+R     L  VG G 
Sbjct: 192 VRTLRRVSVSPGQASPLVTPEESRKLRFWNL---EFESQSFLYRQVRRMTAVLVAVGLGA 248

Query: 213 WTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
                ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 249 LAPAQVKTILESQDPLGKHQTRVAPAHGLFLKSVLY 284


>gi|147903104|ref|NP_001085529.1| tRNA pseudouridine synthase-like 1 [Xenopus laevis]
 gi|82236585|sp|Q6GQ53|PUSL1_XENLA RecName: Full=tRNA pseudouridine synthase-like 1; AltName:
           Full=tRNA pseudouridylate synthase-like 1; AltName:
           Full=tRNA-uridine isomerase-like 1
 gi|49115069|gb|AAH72895.1| MGC80334 protein [Xenopus laevis]
          Length = 298

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 82/274 (29%), Positives = 135/274 (49%), Gaps = 33/274 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG-----AGRTDSGVHA 57
           RY +  +Y G+ Y G        S+ G ++  + +   ++  V       + RTDSGVHA
Sbjct: 7   RYLVFFQYYGTKYSGVMETPITQSVLG-VQNYLEVAAQKLRPVGTIKFFISSRTDSGVHA 65

Query: 58  LRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +  +AH D+ R      +   IL +A+N +L+  + I +L    V   FHAR +A+ R+Y
Sbjct: 66  ICNLAHVDIERAKGKPPFTEEILVQAMNHHLQ-PEPIRLLKAIRVCDNFHARHNALSRTY 124

Query: 113 LYRI---ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--S 167
           +YR+    +R      E    W I   L+   +  A++ L+G H+F+ FRS + + +  S
Sbjct: 125 VYRVAAGCSRPELPVFEGNLCWAIQDGLNVTAINEASKMLLGTHNFSAFRSANSENAFKS 184

Query: 168 PIRTIDHFDVNSFGNLI------------EIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           PI+T+   D+N    ++            +    ARSFL+ Q+R   G+L  VG G+ T 
Sbjct: 185 PIKTLQQADINPSCGILTHHWQSRNLQFWDFTFRARSFLYKQVRRMTGALVAVGQGRLTP 244

Query: 216 TDLEKALQAQDRKEC---GPLAPPEGLYFDSVEY 246
             +++ L+ QD   C     +APP GL+   VEY
Sbjct: 245 QQIKEFLENQD-PNCFLGNFVAPPHGLFLKDVEY 277


>gi|227876165|ref|ZP_03994281.1| tRNA-pseudouridine synthase I [Mobiluncus mulieris ATCC 35243]
 gi|306819440|ref|ZP_07453147.1| tRNA pseudouridine synthase A [Mobiluncus mulieris ATCC 35239]
 gi|227843126|gb|EEJ53319.1| tRNA-pseudouridine synthase I [Mobiluncus mulieris ATCC 35243]
 gi|304647732|gb|EFM45050.1| tRNA pseudouridine synthase A [Mobiluncus mulieris ATCC 35239]
          Length = 326

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 97/308 (31%), Positives = 136/308 (44%), Gaps = 64/308 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R    I Y+G  + GW RQ    ++QG++E A+ ++  + V +  AGRTD+GVHA  Q
Sbjct: 1   MTRIRFDIRYDGRPFHGWARQPGLPTVQGALETALTVLFRQPVTLTVAGRTDAGVHATGQ 60

Query: 61  VAHFDLVRE----WV---------------------PVI--------LCKALNAYLKI-- 85
           VAHFDL  +    W+                     P I        L + L + L++  
Sbjct: 61  VAHFDLPDQFSGDWLRDAHDTEFAASLGAIVAASNPPGIANFQLSTGLHRRLESVLRLVT 120

Query: 86  ---SDTISILNLS-------------------IVDKQFHARFSAIRRSYLYRII---TRQ 120
              + TI  LNL                     V   F ARFSA+ R Y Y +I   T +
Sbjct: 121 SGNTPTIPGLNLDDQPIYPPEANGAIVVTAARPVPDAFDARFSALARHYEYLVIDEPTAR 180

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL   +   W     L+   M  A+  L+G HDF  F      A++ IRT+    V+  
Sbjct: 181 NPLT--RNTCWWYGAPLNVARMHEASAGLLGTHDFAAFCKPREGATT-IRTLKQLGVSRL 237

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I   V A +F H+ +RS VG+L  VG GK  +  LE+AL +  R    PLAP +GL
Sbjct: 238 APGEIRFDVAADAFCHSMVRSLVGALTEVGRGKRDADWLEQALHSAVRIPEIPLAPAQGL 297

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 298 TLVRVDYP 305


>gi|153815016|ref|ZP_01967684.1| hypothetical protein RUMTOR_01233 [Ruminococcus torques ATCC 27756]
 gi|145847584|gb|EDK24502.1| hypothetical protein RUMTOR_01233 [Ruminococcus torques ATCC 27756]
          Length = 260

 Score =  112 bits (281), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/262 (32%), Positives = 120/262 (45%), Gaps = 17/262 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ +   +IQG +E+ +    G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGTNYQGWQRQSDTDRTIQGILEETLENCIGYQVQIDGSGRTDAGVHASG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +    +  + +N  L     I IL++ +V   FHAR SA+ + Y YRI T 
Sbjct: 61  QTASVVLPGKVDTALFTEKMNGCLPPD--IRILDVELVKNGFHARKSAVGKVYEYRIDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----------RSIHC----QA 165
                  +  +   P   D   MR AA +L G H F  +          R+I+       
Sbjct: 119 IKQDVFTRKYSGHFPGEPDLARMREAAGYLTGTHFFAEYTDKKDNRSVRRTIYSIMIRDE 178

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                     D    GN I IR     FL+  +R   G+L  VG  + T+  +++AL   
Sbjct: 179 RKDFLPCGKSDQIGNGNCIVIRYDGTGFLYHMVRILTGTLLEVGMRERTAESVKEALLTG 238

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           DR + G LAP  GL+   V Y 
Sbjct: 239 DRSKAGFLAPAGGLFLREVRYE 260


>gi|209527116|ref|ZP_03275630.1| tRNA pseudouridine synthase A [Arthrospira maxima CS-328]
 gi|209492456|gb|EDZ92797.1| tRNA pseudouridine synthase A [Arthrospira maxima CS-328]
          Length = 278

 Score =  112 bits (281), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/249 (34%), Positives = 121/249 (48%), Gaps = 8/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +II+Y+G+ + GWQRQ N  ++Q  IE AI  ++  E V +H AGRTDSGVHA  QV
Sbjct: 6   RIALIIQYDGTHFHGWQRQPNQRTVQEDIETAIGKVLKQERVPLHAAGRTDSGVHAAAQV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             LN+  ++   + I   + V K +HARF A  R Y Y + T   
Sbjct: 66  AHFDAPAHIPAYRWATILNS--RLPADVLIRASAPVAKDWHARFDAQWRRYRYSLYTDAR 123

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +   W    + LD   M  A + L+G H  + F+     +S P   +D  DV  +
Sbjct: 124 PNLFIRRFTWHYYHQRLDESLMLAALKPLLGYHHLSAFQR--AGSSRPHAWVDVQDVQCW 181

Query: 181 GN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +   I I V A  FL+  +R  VG L  VG G+ +  + +     + R+     APP+G
Sbjct: 182 RSEAFIHIEVQASGFLYGMMRLLVGLLVQVGAGERSLENFQDIWVNERREIVKSAAPPQG 241

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 242 LCLLRVGYP 250


>gi|189500072|ref|YP_001959542.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides BS1]
 gi|189495513|gb|ACE04061.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides BS1]
          Length = 233

 Score =  112 bits (281), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 116/242 (47%), Gaps = 10/242 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M IEY+G+ + GWQ+Q  G  ++QG +E  +  +  E VV+  AGRTD GVHA  QVA+F
Sbjct: 1   MTIEYDGTDFSGWQKQPEGVVTVQGVLETTLSRIVQEEVVMTAAGRTDRGVHARGQVANF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     L  +LNA L    T+ I ++  V   FHAR+SA+ R Y Y  +  + P A
Sbjct: 61  RTASCLSTGRLLHSLNALL--PSTVCIRDMQEVPDSFHARYSALFREYRYFFL--EKPSA 116

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L K  A +    LD + +   A  LVGRHDF+ +     Q  S   T+           +
Sbjct: 117 LGKRYAGVYGGRLDVDRLNRCAGELVGRHDFSAYAKEDAQNGSTFCTVFGASWGRQDEKV 176

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+ A  FL T +R  V +    G G+ T    E+  +    K   P A P GL+   V
Sbjct: 177 VFRIAANRFLRTMVRFLVSAQLEAGPGELT----ERLRRGNVLKNIVP-ADPAGLFLWKV 231

Query: 245 EY 246
            Y
Sbjct: 232 LY 233


>gi|326383234|ref|ZP_08204922.1| tRNA pseudouridine synthase A [Gordonia neofelifaecis NRRL B-59395]
 gi|326197984|gb|EGD55170.1| tRNA pseudouridine synthase A [Gordonia neofelifaecis NRRL B-59395]
          Length = 296

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 87/263 (33%), Positives = 129/263 (49%), Gaps = 28/263 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + R  ++I Y+G+ + GW  Q    ++  +IE+A+  V    + +  AGRTD+GVHA  Q
Sbjct: 14  LCRLRLLIGYDGTDFSGWATQPGRRTVCETIEQALGTVLRAPIRLTVAGRTDAGVHAAGQ 73

Query: 61  VAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+    +        P  L + L   L   D + +  +  V + F ARFSA+ R+Y
Sbjct: 74  VAHCDVPAASLRTRSIDGDPARLVRRLAKMLP--DDVRVKRIEAVSEDFDARFSALARTY 131

Query: 113 LYRIITRQAPLALEKGRA-----WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            YR+    AP   E   A     W  P  LD E M  A+  LVG +DF  F   + + S+
Sbjct: 132 EYRLT--DAPWGAEPTLARITADWTRP--LDVEAMNTASAGLVGLNDFAAF-CRYREGST 186

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQ 223
            IR +  FD    G ++   V+A +F  + +RS VG++  VGDG+    W  TDL   L 
Sbjct: 187 TIRELQRFDWRREGPVVVGTVIADAFCWSMVRSLVGAVASVGDGRRSLGW-CTDL---LD 242

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
            + R    P+A   GL    V+Y
Sbjct: 243 QRARSAQVPVAQARGLSLIGVDY 265


>gi|229829433|ref|ZP_04455502.1| hypothetical protein GCWU000342_01523 [Shuttleworthia satelles DSM
           14600]
 gi|229791864|gb|EEP27978.1| hypothetical protein GCWU000342_01523 [Shuttleworthia satelles DSM
           14600]
          Length = 325

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 82/299 (27%), Positives = 123/299 (41%), Gaps = 52/299 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI------------FLVTGEIVVVHGA 48
           M  Y + I Y+G+ Y GW+ Q    +IQG +E+A+            F+     V + GA
Sbjct: 27  MQNYRLKIAYDGTRYAGWEHQPGQETIQGKLEQALARMCGLAMDERDFMRPDTPVKLIGA 86

Query: 49  GRTDSGVHALRQVAHF-------------------------------------DLVREWV 71
           GRTD+GVHA   VA                                        L R   
Sbjct: 87  GRTDAGVHARGMVASIAFEAPAYRPGPWERRESKGRDRGNQPGNMTWQAEPSAQLTRRNQ 146

Query: 72  P-VILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
           P  + C+ +  YL   + D IS++       +FHAR+ A+ ++Y Y     +      + 
Sbjct: 147 PRSMTCQEMQDYLNHYLPDDISVVAFKEAAARFHARYKAVGKTYQYTAFDGRVKPVFNRR 206

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
               + + LD   M+ AA  L+G HDF +F        S +R +D  ++      +    
Sbjct: 207 YYTPLEEELDVSAMQEAANCLLGEHDFRSFCGNPKMKKSTVRRVDRIEIRRSKGYVYFSF 266

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
               FL   +R  VG+L  VG  +    D+EK L+A+DRK  GP AP  GL    V+Y 
Sbjct: 267 HGTGFLQNMVRILVGTLMEVGWHRMRPQDVEKILEARDRKAAGPTAPARGLCLIRVDYD 325


>gi|70725835|ref|YP_252749.1| tRNA pseudouridine synthase A [Staphylococcus haemolyticus
           JCSC1435]
 gi|123735013|sp|Q4L882|TRUA_STAHJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|68446559|dbj|BAE04143.1| tRNA pseudouridine synthase A [Staphylococcus haemolyticus
           JCSC1435]
          Length = 267

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 114/243 (46%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA  Q 
Sbjct: 1   MRILVNISYQGSQFLGFQIQQQGRTVQQQFEKILKRMHRRHVRIHPSSRTDRGVHAYEQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   D I +  +  VD  FH R+  + + Y Y++     
Sbjct: 61  FHFDTDLNIEPKQWKYAMNSAL--PDDIYVKEVQQVDDHFHCRYDCLGKRYRYKVYQATH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    I + L+   M  AA+H +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RNPFESGLKTFIKEDLNYSKMNEAAKHFIGTHDFTGFCSQKTEVESKVRTLYQSEIIQTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK  ++++   L  ++R      AP EGLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRHASEVSTLLNEKNRDSVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|317501544|ref|ZP_07959740.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088594|ref|ZP_08337505.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 3_1_46FAA]
 gi|316897055|gb|EFV19130.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407551|gb|EGG87051.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 260

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 84/262 (32%), Positives = 120/262 (45%), Gaps = 17/262 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ +   +IQG +E+ +    G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGTNYQGWQRQSDTDRTIQGILEETLENCIGYQVQIDGSGRTDAGVHASG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +    +  + +N  L     I IL++ +V   FHAR SA+ + Y YRI T 
Sbjct: 61  QTASVVLPGKVDTALFTEKMNGCLPPD--IRILDVELVKNGFHARKSAVGKVYEYRIDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----------RSIHC----QA 165
                  +  +   P   D   MR AA +L G H F  +          R+I+       
Sbjct: 119 IKQDVFTRKYSGHFPGEPDLARMREAAGYLTGTHFFAGYTDKKDNRSVRRTIYSIMIRDE 178

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                     D    GN I IR     FL+  +R   G+L  VG  + T+  +++AL   
Sbjct: 179 RKDFLPCGKSDQIGNGNCIVIRYDGTGFLYHMVRILTGTLLEVGMRERTAESVKEALLTG 238

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           DR + G LAP  GL+   V Y 
Sbjct: 239 DRSKAGFLAPAGGLFLREVRYE 260


>gi|224373193|ref|YP_002607565.1| tRNA pseudouridine synthase A [Nautilia profundicola AmH]
 gi|223588941|gb|ACM92677.1| tRNA pseudouridine synthase A [Nautilia profundicola AmH]
          Length = 223

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 107/228 (46%), Gaps = 6/228 (2%)

Query: 19  QRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA 78
           Q+Q +  ++QGSIE A+  +     V+H AGRTD GVHAL QV  F L   W    L   
Sbjct: 2   QKQPDKITVQGSIENALKRLNINSDVLH-AGRTDRGVHALNQVVSFKLPSFWNQNKLLTE 60

Query: 79  LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD 138
           LN  L     I I     V+  F+ RF A +RSY Y +     P +      +  P  ++
Sbjct: 61  LNKIL--HPNIHIKKFYNVNDDFNPRFDAKKRSYRYILNPNFNPFSANYTTYY--PHKIN 116

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
              ++ A +   G HDF  F       ++ IR I   DV  + N   I++V   FL  QI
Sbjct: 117 ISLLKKALKEFEGIHDFEYFAKTGSDVNNYIREIYKTDVYKYKNFTVIKIVGNGFLRAQI 176

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           R  V  +  + + K T  DL+K L  Q+      LAPP GLY D + Y
Sbjct: 177 RLIVDFVLKINENKLTVQDLQKQLSKQEL-ISKHLAPPNGLYLDRIWY 223


>gi|305680135|ref|ZP_07402945.1| tRNA pseudouridine synthase A [Corynebacterium matruchotii ATCC
           14266]
 gi|305660755|gb|EFM50252.1| tRNA pseudouridine synthase A [Corynebacterium matruchotii ATCC
           14266]
          Length = 290

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 81/259 (31%), Positives = 118/259 (45%), Gaps = 15/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           IR  + + Y+G+ + GW RQ +    ++Q  +E A+ LV  + + +  AGRTD+GVHA  
Sbjct: 4   IRIRLDLAYDGTHFHGWARQGHSELRTVQQVLEDALTLVLRQPIALTVAGRTDAGVHAAA 63

Query: 60  QVAHFDL------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           QVAHFD+       R                +   + +   +I    F ARFSA+RR Y+
Sbjct: 64  QVAHFDVPAAALDTRSIAGDPGRLVRRLARLLPTDVRVHAATIAPPDFDARFSALRRHYV 123

Query: 114 YRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+ T  +  L          PK +D   M+  A  L+G HDF  F   H   ++ IR +
Sbjct: 124 YRLTTHPRGALPTRVTDTAHHPKPVDLAAMQACAAELIGLHDFAAF-CRHRDGATTIRDL 182

Query: 173 DHFDVNSFGNLI-----EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             F  N     I     E  V A +F  + +RS VG   +VG+GK  +      L    R
Sbjct: 183 QEFTWNDISTPIEPDTFEAHVTADAFCWSMVRSLVGCCLVVGEGKRPAGFATSLLAETSR 242

Query: 228 KECGPLAPPEGLYFDSVEY 246
               P+AP  GL    V+Y
Sbjct: 243 SALVPVAPAAGLSLVGVDY 261


>gi|260188510|ref|ZP_05765984.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis CPHL_A]
 gi|289449159|ref|ZP_06438903.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289422117|gb|EFD19318.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           CPHL_A]
          Length = 256

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 77/238 (32%), Positives = 122/238 (51%), Gaps = 22/238 (9%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP------------- 72
           ++ G ++ A+  +    V +  AGRTD+GVHA  QVAH D+  + +P             
Sbjct: 5   TVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQVAHVDVPADALPNAYPRAGHVGDPE 64

Query: 73  -VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
            + L + L  +L     + IL+++     F ARFSA+RR Y+YR+ T  AP  +E  +A 
Sbjct: 65  FLPLLRRLGRFLPAD--VRILDITRAPAGFDARFSALRRHYVYRLST--APYGVEPQQAR 120

Query: 132 LI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
            I   P+ LD + M  A++ L+G HDF  F   H + ++ IR +   D +  G+L+   V
Sbjct: 121 YITAWPRELDLDAMTAASRDLMGLHDFAAF-CRHREGATTIRDLQRLDWSRAGSLVTAHV 179

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            A +F  + +RS VG+L  VG+ +  +T   + L A  R     +AP  GL    V+Y
Sbjct: 180 TADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRSSDFAVAPAHGLTLIQVDY 237


>gi|210631184|ref|ZP_03296795.1| hypothetical protein COLSTE_00680 [Collinsella stercoris DSM 13279]
 gi|210160151|gb|EEA91122.1| hypothetical protein COLSTE_00680 [Collinsella stercoris DSM 13279]
          Length = 281

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 115/243 (47%), Gaps = 6/243 (2%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+G+G+ G+  Q +  ++ G   +A+       + +  AGRTD+GVHA+ Q       RE
Sbjct: 30  YDGAGFSGFAEQPDVRTVAGEARRALETFLRRPIDMTCAGRTDAGVHAISQYVSVPAHRE 89

Query: 70  WVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
            + +   + + A   +  D I++  +      F ARF A  R+Y YRI T  A   L + 
Sbjct: 90  ELAIEHRRWMRAMAALLPDDIALSGVYHAAPGFSARFDARSRTYTYRIATGDARPLLTRN 149

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVNSFG-NL 183
             W     LD E M   A HLVG HDF +F  +      P    + ++      + G + 
Sbjct: 150 VTWWHRLPLDVEAMEAGAVHLVGEHDFKSFCKMSSAVGKPTCRNVISVSFAREQALGEDH 209

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   +   +FLH+ +R+ VG+L  VG G+     + + L A DR+  GP AP  GL F  
Sbjct: 210 LAFTITGNAFLHSMVRTIVGTLVEVGAGRRDPAWVVEVLAACDRRAAGPTAPARGLCFMD 269

Query: 244 VEY 246
           V Y
Sbjct: 270 VAY 272


>gi|78211903|ref|YP_380682.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9605]
 gi|123743387|sp|Q3AMQ5|TRUA_SYNSC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78196362|gb|ABB34127.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9605]
          Length = 293

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 115/246 (46%), Gaps = 14/246 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           + R  + ++Y+GS + GWQRQ+NG S+Q  +E AI  L     V    AGRTD+GVHA  
Sbjct: 15  LQRIALSLQYDGSSFCGWQRQRNGRSVQAVLEDAIAQLDPHRPVQTFAAGRTDAGVHAAG 74

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD       R+W P     ALN   ++  TI +         +HA +SA  R Y Y
Sbjct: 75  QVVHFDCSGPIPARKWAP-----ALNG--RLPSTIRVRESVARPLDWHACYSATYRRYRY 127

Query: 115 RIITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
            I   + P       +W      LD   MR A   ++G HDF+ F     + +    T+ 
Sbjct: 128 TIHNGRRPNLFLSPWSWHCYQHRLDESRMRDALSSMLGLHDFSAFMKAGSRRAHARTTVQ 187

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V   G+L+ + + A  FL+  +R  +  L  VG+ + +    E+  + + R E    
Sbjct: 188 EVLVERQGDLLRVEIQASGFLYGMVRLLMAQLVAVGEHRLSVAAFEQRWRERRRHEVKEA 247

Query: 234 APPEGL 239
           AP  GL
Sbjct: 248 APAAGL 253


>gi|223042638|ref|ZP_03612687.1| tRNA pseudouridine synthase A [Staphylococcus capitis SK14]
 gi|222444301|gb|EEE50397.1| tRNA pseudouridine synthase A [Staphylococcus capitis SK14]
          Length = 267

 Score =  112 bits (281), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 114/243 (46%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H   RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHVRIHPTSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N +L   D I + N+  V++ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIDNQQWQYAMNRFL--PDDIYVKNVQTVEENFHCRYDCVGKRYRYKVYQGEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I   LD   M  AA H +G HDFT F S   +  S +RT+   +V    
Sbjct: 119 RNPFKSGLETFINSDLDLSKMNEAAHHFIGTHDFTGFCSQKTEVESKVRTLYQSEVVQTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+ ++R      AP EGLY 
Sbjct: 179 TGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRQPDEVPQLLEEKNRNNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|218135248|ref|ZP_03464052.1| hypothetical protein BACPEC_03153 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990633|gb|EEC56644.1| hypothetical protein BACPEC_03153 [Bacteroides pectinophilus ATCC
           43243]
          Length = 196

 Score =  112 bits (280), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 63/177 (35%), Positives = 95/177 (53%), Gaps = 2/177 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q N  +I+G +  A+  + GE + V GA RTD+GVHAL  
Sbjct: 1   MRRIKLIVAYDGTKYSGWQVQNNADTIEGRLNAALSSICGENIRVIGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD            ALNA  ++ + I +     V   +H R  +  ++Y Y I+ R 
Sbjct: 61  IAVFDTESRIPAEKFAYALNA--RLPEDIVVQKSCEVPPDYHPRHCSTIKTYEYHILNRT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             L   +   +    +LD E M  AAQ+L+G HDF +F S++ QA + +RTI   +V
Sbjct: 119 FRLPQMRNNTFFCHYALDLETMNEAAQYLLGEHDFKSFCSVNTQAETTVRTIYSIEV 175


>gi|121639375|ref|YP_979599.1| tRNA pseudouridine synthase A [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148663320|ref|YP_001284843.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Ra]
 gi|215405494|ref|ZP_03417675.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis 02_1987]
 gi|215413368|ref|ZP_03422053.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis
           94_M4241A]
 gi|215428962|ref|ZP_03426881.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T92]
 gi|215432426|ref|ZP_03430345.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis EAS054]
 gi|215447792|ref|ZP_03434544.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T85]
 gi|218755231|ref|ZP_03534027.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis GM 1503]
 gi|219559524|ref|ZP_03538600.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T17]
 gi|224991871|ref|YP_002646560.1| tRNA pseudouridine synthase A [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|254552559|ref|ZP_05143006.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260202637|ref|ZP_05770128.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T46]
 gi|260206826|ref|ZP_05774317.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis K85]
 gi|289445055|ref|ZP_06434799.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T46]
 gi|289571689|ref|ZP_06451916.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T17]
 gi|289576191|ref|ZP_06456418.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis K85]
 gi|289752179|ref|ZP_06511557.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T92]
 gi|289755588|ref|ZP_06514966.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           EAS054]
 gi|289759618|ref|ZP_06518996.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T85]
 gi|289763637|ref|ZP_06523015.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis GM
           1503]
 gi|297636114|ref|ZP_06953894.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis KZN 4207]
 gi|297733114|ref|ZP_06962232.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis KZN R506]
 gi|306777802|ref|ZP_07416139.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu001]
 gi|306782521|ref|ZP_07420858.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu002]
 gi|306809459|ref|ZP_07446127.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu007]
 gi|313660445|ref|ZP_07817325.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis KZN
           V2475]
 gi|2104378|emb|CAB08721.1| PROBABLE TRNA PSEUDOURIDINE SYNTHASE A TRUA (PSEUDOURIDYLATE
           SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL
           HYDROLYASE) [Mycobacterium tuberculosis H37Rv]
 gi|31620228|emb|CAD95671.1| PROBABLE TRNA PSEUDOURIDINE SYNTHASE A TRUA (PSEUDOURIDYLATE
           SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL
           HYDROLYASE) [Mycobacterium bovis AF2122/97]
 gi|121495023|emb|CAL73509.1| Probable tRNA pseudouridine synthase A truA [Mycobacterium bovis
           BCG str. Pasteur 1173P2]
 gi|148507472|gb|ABQ75281.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Ra]
 gi|224774986|dbj|BAH27792.1| tRNA pseudouridine synthase A [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|289417974|gb|EFD15214.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T46]
 gi|289540622|gb|EFD45200.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis K85]
 gi|289545443|gb|EFD49091.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T17]
 gi|289692766|gb|EFD60195.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T92]
 gi|289696175|gb|EFD63604.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           EAS054]
 gi|289711143|gb|EFD75159.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis GM
           1503]
 gi|289715182|gb|EFD79194.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T85]
 gi|308213887|gb|EFO73286.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu001]
 gi|308324838|gb|EFP13689.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu002]
 gi|308344299|gb|EFP33150.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu007]
 gi|326905301|gb|EGE52234.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           W-148]
          Length = 256

 Score =  112 bits (280), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 77/238 (32%), Positives = 121/238 (50%), Gaps = 22/238 (9%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP------------- 72
           ++ G ++ A+  +    V +  AGRTD+GVHA  QVAH D+  + +P             
Sbjct: 5   TVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQVAHVDVPADALPNAYPRAGHVGDPE 64

Query: 73  -VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
            + L + L  +L     + IL+++     F ARFSA+RR Y+YR+ T  AP  +E  +A 
Sbjct: 65  FLPLLRRLGRFLPAD--VRILDITRAPAGFDARFSALRRHYVYRLST--APYGVEPQQAR 120

Query: 132 LI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
            I   P+ LD + M  A++ L+G HDF  F   H + ++ IR +   D +  G L+   V
Sbjct: 121 YITAWPRELDLDAMTAASRDLMGLHDFAAF-CRHREGATTIRDLQRLDWSRAGTLVTAHV 179

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            A +F  + +RS VG+L  VG+ +  +T   + L A  R     +AP  GL    V+Y
Sbjct: 180 TADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRSSDFAVAPAHGLTLIQVDY 237


>gi|296394888|ref|YP_003659772.1| tRNA pseudouridine synthase A [Segniliparus rotundus DSM 44985]
 gi|296182035|gb|ADG98941.1| tRNA pseudouridine synthase A [Segniliparus rotundus DSM 44985]
          Length = 278

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 122/254 (48%), Gaps = 15/254 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW RQ    ++ G IE+A+  +      +  AGRTD+GVHA  QV
Sbjct: 9   LRLRLDVAYDGTEFSGWARQPGRRTVAGVIEEALSTLLQSSAQLTVAGRTDAGVHATGQV 68

Query: 62  AHFDLVREWV-----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AH D+  + V     P  L + L   L     + +L+   V  QF ARFSA+RR Y Y  
Sbjct: 69  AHVDVRADLVSGRLPPEKLVRKLARMLPTD--VRVLSAQKVSAQFDARFSALRRHYRYH- 125

Query: 117 ITRQA----PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           ITR      PL   +   W  P  LD + +  A+  LVG HDF  F      A++ IR +
Sbjct: 126 ITRSVYGADPLRAREVVPWARP--LDFDVLNAASSALVGLHDFAAFCRPRPGATT-IREL 182

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             F+    G LI   + A +F  +  RS VG++  V +G+     +   L A  R     
Sbjct: 183 QRFEWAESGVLITASITADAFCWSMCRSLVGAVTAVAEGRRDLAWIRSLLTASSRASEIT 242

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GL    V+Y
Sbjct: 243 VAPAHGLCLVGVDY 256


>gi|325297315|ref|YP_004257232.1| tRNA pseudouridine synthase A [Bacteroides salanitronis DSM 18170]
 gi|324316868|gb|ADY34759.1| tRNA pseudouridine synthase A [Bacteroides salanitronis DSM 18170]
          Length = 268

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 117/247 (47%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY M + Y+G+ Y GWQ Q NG+S+Q  ++KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MARYFMYLGYDGTNYHGWQIQPNGASVQEELQKALSTLMRRPVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+       I    LN  L     I++  +  V    HARF A  R Y Y + T +
Sbjct: 61  VAHADIDALADAAIWVGKLNRLL--PPDIAVYRMRRVADDAHARFDATYRKYQYHVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  AW + + LD   M  AA  L    DFT+F  +H    +    I +      
Sbjct: 119 NPFL--RHYAWRVFQPLDFGRMNEAASVLFEYTDFTSFSKLHTDVKTNNCRILYARWEQT 176

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G +     + A  FL   +R+ VG+L  VG GK T     + ++A++R   G   P   L
Sbjct: 177 GADEWVFTIQADRFLRNMVRAVVGTLVEVGRGKLTIEGFRRVIEAKNRCSAGTSVPGNAL 236

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 237 FLVDVGY 243


>gi|296206475|ref|XP_002750239.1| PREDICTED: tRNA pseudouridine synthase-like 1-like, partial
           [Callithrix jacchus]
          Length = 301

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 132/273 (48%), Gaps = 30/273 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHAL 58
           RY + ++Y G+ + G    +       +Q  +E+A   L + E V    + RTD+GVHAL
Sbjct: 11  RYLVYLQYVGTDFNGVAAVRGAQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 70

Query: 59  RQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR +A  R+YL
Sbjct: 71  SNAAHLDVQRRSGRPPFPPEVLTEALNTHLR-HPAIRVLRAFRVPSDFHARHAATSRTYL 129

Query: 114 YRIIT---RQAPLAL-EKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR++T   R   L + E+   W L    LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 130 YRLVTGCHRSDELPVFERNLCWALRADRLDVAAMQEAAQHLLGTHDFSAFQSAGSPVPSP 189

Query: 169 IRTIDHFDVNS--FGNLI-----------EIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V+      L+            +   ++SFL+ Q+R     L  VG G    
Sbjct: 190 VRTLRRVSVSPGLTSPLVTPQESRKLQFWSLEFESQSFLYRQVRRMTAVLVAVGLGALAP 249

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             ++  L++QD   K    LAP  GL+  SV Y
Sbjct: 250 AQVKTILESQDPLGKHQTRLAPAHGLFLKSVVY 282


>gi|297568336|ref|YP_003689680.1| tRNA pseudouridine synthase A [Desulfurivibrio alkaliphilus AHT2]
 gi|296924251|gb|ADH85061.1| tRNA pseudouridine synthase A [Desulfurivibrio alkaliphilus AHT2]
          Length = 252

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 82/256 (32%), Positives = 116/256 (45%), Gaps = 14/256 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  + I Y+G+ + GWQRQ N  +IQ  +E+A+  + GE VV+HGAGRTD+GVHAL  
Sbjct: 1   MVKVKLTIAYDGTDFAGWQRQLNRPTIQAVVEEALARMLGEQVVLHGAGRTDAGVHALGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F+  R          LN+ L     I I+        FHARFSA  + Y Y   T  
Sbjct: 61  VASFNAPRRLPLAAYRLGLNSML--PPAIRIMAADEAADDFHARFSAKGKLYRYCFSTAA 118

Query: 121 A-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---------QASSPIR 170
             P      RA L P     E +R     ++G HDF+TF +                 + 
Sbjct: 119 VMPPCRRLYRAHL-PGPFAAERVRQLLPQMLGEHDFSTFEAAGSRDRDRAGGRGGVRRLN 177

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            +     +  G      +    FL   +R+ VG+L  +G G+  +  +   L  +DR   
Sbjct: 178 LLQLEQEDPAGQEFCFELGGDGFLRHMVRNIVGTLVAIGQGRPLAEPV-ALLVGRDRARA 236

Query: 231 GPLAPPEGLYFDSVEY 246
           GP AP  GL    V Y
Sbjct: 237 GPTAPACGLTLVKVIY 252


>gi|297201758|ref|ZP_06919155.1| tRNA pseudouridine synthase A [Streptomyces sviceus ATCC 29083]
 gi|197710867|gb|EDY54901.1| tRNA pseudouridine synthase A [Streptomyces sviceus ATCC 29083]
          Length = 289

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 87/254 (34%), Positives = 125/254 (49%), Gaps = 12/254 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHG---AGRTDSGVHA 57
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT    V +    AGRTD+GVHA
Sbjct: 10  VRVRLDLSYDGSDFSGWAKQAGGRRTVQGEIEDALRTVTRSKDVTYELTVAGRTDAGVHA 69

Query: 58  LRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
             QVAH DL    W      L K L    ++   + + +L      F+ARF+A+ R Y+Y
Sbjct: 70  RGQVAHVDLPEGLWAEHRDKLLKRLAG--RLPKDVRVWSLREAPAGFNARFAALWRRYVY 127

Query: 115 RIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+  +   +  L +         LD   M  AA+ LVG HDF  + +   + ++ IR I 
Sbjct: 128 RVGDQPGGVDPLLRNHVLWHDWELDVAVMDAAAKSLVGEHDFAAY-AKRREGATTIREIL 186

Query: 174 HFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            F V    + ++EI V A +F H Q+RS VG+L  VGDG        K L A  R     
Sbjct: 187 DFGVRRRADGVVEIEVRADAFCHNQVRSMVGALLFVGDGHRGVEWPRKVLDAGVRDSAVH 246

Query: 233 LAPPEGLYFDSVEY 246
           +  P GL  + V Y
Sbjct: 247 VVRPHGLTLEEVAY 260


>gi|314934267|ref|ZP_07841626.1| tRNA pseudouridine synthase A [Staphylococcus caprae C87]
 gi|313652197|gb|EFS15960.1| tRNA pseudouridine synthase A [Staphylococcus caprae C87]
          Length = 267

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 114/243 (46%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H   RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHVRIHPTSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N +L   D I + N+  V++ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIDNQQWQYAMNRFL--PDDIYVKNVHTVEENFHCRYDCVGKRYRYKVYQGEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I   LD   M  AA H +G HDFT F S   +  S +RT+   +V    
Sbjct: 119 RNPFKSGLETFINSDLDLSKMNEAAHHFIGTHDFTGFCSQKTEVESKVRTLYQSEVVQTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+ ++R      AP EGLY 
Sbjct: 179 TGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRQPDEVPQLLEEKNRNNVPFTAPAEGLYL 238

Query: 242 DSV 244
           + +
Sbjct: 239 EKI 241


>gi|124026684|ref|YP_001015799.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. NATL1A]
 gi|123961752|gb|ABM76535.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. NATL1A]
          Length = 276

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 79/251 (31%), Positives = 118/251 (47%), Gaps = 14/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  ++I+Y+G G+ GWQ QK+  ++QG++E+ I  L     V    AGRTDSGVHA  QV
Sbjct: 4   RIALVIQYDGLGFRGWQNQKDSITVQGTLEEKIAELDPIRPVKAIAAGRTDSGVHASGQV 63

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      + +W       ALN  L  S  I +L    V   +HA +SA  R Y Y I
Sbjct: 64  VHFDCSGPIPIHKW-----ASALNGRLPAS--IKVLEAVSVPSAWHACYSAKYRRYRYSI 116

Query: 117 ITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                P    +  +W   +  LD   M+ A   L+G HDF  F+      S+ + T+   
Sbjct: 117 FNGSYPNLFLQNISWHKYRFKLDINLMKQALNDLLGLHDFAAFQKAGSNRSNSLTTVQDV 176

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            ++  G+++ + + A  FL+  +R  +G L  VG+ + +        +   R E    AP
Sbjct: 177 SISRDGDIVTVEIQASGFLYGMVRLLMGQLVAVGEKRLSLEKFRYRWRKGLRSEVKEAAP 236

Query: 236 PEGLYFDSVEY 246
             GL    V Y
Sbjct: 237 AHGLCLIRVGY 247


>gi|302524024|ref|ZP_07276366.1| tRNA pseudouridine synthase A [Streptomyces sp. AA4]
 gi|302432919|gb|EFL04735.1| tRNA pseudouridine synthase A [Streptomyces sp. AA4]
          Length = 298

 Score =  112 bits (280), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 88/268 (32%), Positives = 131/268 (48%), Gaps = 29/268 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVV--VHGAGRTDSGVHA 57
           ++R  + + Y+G+ + GW RQ    ++Q  +E+A+     GE V   V  AGRTD+GVHA
Sbjct: 16  LVRLRLDVSYDGTDFSGWARQPGRRTVQAELEQALQRQPPGEAVPKSVVVAGRTDAGVHA 75

Query: 58  LRQVAHFDLVR------EWVPVI------LCKALNAYLKI-SDTISILNLSIVDKQFHAR 104
             QV H D+V         +PV       L +    + K+    + +LN  +    F AR
Sbjct: 76  TGQVVHVDVVPFAPGAPGRIPVDERGIPDLTRMRGRWNKLLPADVRVLNARVAPDGFDAR 135

Query: 105 FSAIRRSYLYRIITRQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
           FSAIRR Y YR+    AP  ++  R     AW  P  L  E M  AA  L+G  DF  + 
Sbjct: 136 FSAIRRHYRYRV--SDAPWGVDPLRRNDTLAWGRP--LSTERMNAAAAELLGLQDFAAY- 190

Query: 160 SIHCQASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               +  + IR +   +      +L+E+RV A +F H+ +RS VG L LVGDG+  +   
Sbjct: 191 CKQREGGTTIRELQRLEWTRIDEHLLEVRVSADAFCHSMVRSLVGVLLLVGDGRRGTGWP 250

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + L +  R     +AP  GL   +V+Y
Sbjct: 251 GEVLASGTRDSA--VAPAHGLTLTAVDY 276


>gi|326792524|ref|YP_004310345.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
 gi|326543288|gb|ADZ85147.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
          Length = 245

 Score =  112 bits (279), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 122/247 (49%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  + ++I+Y+GS Y G+Q Q++   ++Q  IE  +  +T E V + G  RTD GVHA  
Sbjct: 1   MRNFKIVIQYDGSRYKGFQLQRDTDLTVQAKIEAVLEKMTEEQVEIIGCDRTDVGVHAEN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA F    E      C     Y  + + I + ++  VD++FHAR++   ++Y Y I   
Sbjct: 61  YVASFKT--ECTLSTACMLDYLYEFLPEDIVVKSIEEVDERFHARYNVKAKTYEYTINCG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +     + ++ D ++M   A    G HDF +F S+     S ++TI+  ++  
Sbjct: 119 AQRNVFNRKYVHHMSENFDLKSMNEVAAVFKGTHDFQSFTSLKPNGKSTMQTINEIEIIQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++++IRV A  FL    R  +G++   G G  T+   ++ +  + R    P+A P+ L
Sbjct: 179 KGDILQIRVTADDFLLHMPRMIIGAIVEAGKGTITAQQTQEVMDKKQRATGYPMAKPKAL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 SLVEVKY 245


>gi|260062032|ref|YP_003195112.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
 gi|88783594|gb|EAR14765.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
          Length = 253

 Score =  112 bits (279), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 82/258 (31%), Positives = 126/258 (48%), Gaps = 30/258 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALR 59
           +R+ + I Y G+ Y GWQ+Q N  +IQ  +E  +   L  G I +V GAGRTD+GVHA +
Sbjct: 1   MRFFLEISYLGTAYHGWQKQPNALAIQEILEDRMGKLLGNGPIDLV-GAGRTDAGVHARQ 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             AHFD     +P      LNA+L     I++  +  V    HARF A  R+Y Y ++  
Sbjct: 60  LFAHFDR-DAALPSGFVHRLNAFLPAD--IAVKGVYEVAPNAHARFDATGRTYEYHLVRE 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +G A+     LD   M  AA  ++G  +F  F     ++ S ++T +      
Sbjct: 117 KDPF--REGLAYQFQGELDFGAMNRAAASMLGYGNFKAF----SRSKSDVKTYNC----- 165

Query: 180 FGNLIEIR-----------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
             +L E R           + A  FL   +R+ VG+L  VG G+  +  ++  +++QDR 
Sbjct: 166 --DLREARWEEGDGVWVFTISADRFLRNMVRAVVGTLLEVGKGRLDAEGVKTIIKSQDRS 223

Query: 229 ECGPLAPPEGLYFDSVEY 246
           E G   P +GLY   + Y
Sbjct: 224 EAGVSVPAKGLYLTRITY 241


>gi|324999254|ref|ZP_08120366.1| tRNA pseudouridine synthase a [Pseudonocardia sp. P1]
          Length = 268

 Score =  112 bits (279), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 124/251 (49%), Gaps = 21/251 (8%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + GW  Q    ++QG +  A+  V    + +  AGRTD+GVHA  QVAH D+ 
Sbjct: 5   IAYDGTDFSGWATQPTRRTVQGVLTDALSTVLRTPLRLTVAGRTDAGVHASGQVAHVDVP 64

Query: 68  REWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ---AP 122
            E  P +  L + LN +L     + +   + V + F ARFSA+RR Y YR+ T      P
Sbjct: 65  AELDPQLDGLLRRLNRFLPPD--VRVRATTRVPETFDARFSALRRHYRYRVTTASFGAEP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-- 180
           L   +  AW  P  LD   M  A+  +VG HDF  F     + ++ +R +  F+ +    
Sbjct: 123 LRARETVAW--PHPLDPALMNAASALMVGEHDFAAF-CKRREGATTVRALQRFEWDPAPG 179

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVG----DGKWTSTDLEKALQAQDRKECGPLAP 235
              ++   V A +F H+ +RS VG++  VG      +W +  L +  +A +      +AP
Sbjct: 180 EPGVLVASVSADAFCHSMVRSLVGAVFEVGRVHRPPEWPAELLSRTSRASEVT----VAP 235

Query: 236 PEGLYFDSVEY 246
           P GL    V+Y
Sbjct: 236 PHGLSLTGVDY 246


>gi|260579203|ref|ZP_05847093.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium ATCC 43734]
 gi|258602689|gb|EEW15976.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium ATCC 43734]
          Length = 328

 Score =  112 bits (279), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 131/265 (49%), Gaps = 27/265 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           ++R  + + Y+G+ + GW  Q  G  ++ G +++ + LVT   + +  AGRTD+GVHA  
Sbjct: 28  LVRVRLEVAYDGTDFHGWATQSGGLRTVAGVLQEKLSLVTRHPIELVVAGRTDAGVHASG 87

Query: 60  QVAHFDLVREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           QV H D+  +         P  L + L+  L  SD + +   S+  + F ARFSA+RR Y
Sbjct: 88  QVCHADIPADAFEQRSLTRPEDLVRRLSRMLP-SD-VRLHGASVAPQGFDARFSALRRHY 145

Query: 113 LYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---S 166
           +YR+ T  A   P+      AW  P  +D E  + A+  L+G +DF  F    C+A   +
Sbjct: 146 IYRVTTHPAGPVPVRARDTAAWRHP--IDLEKTQAASDALIGLNDFAAF----CKAREGA 199

Query: 167 SPIRTIDHF---DVNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           + +R +  F   DV++       E  V A +F  + +RS VG+   VG GK         
Sbjct: 200 TTVRELQEFRWVDVSTEAEPQTYEAHVTADAFCWSMVRSLVGAALTVGSGKRPDDFTPGL 259

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           L+   R    P+AP EGL    V+Y
Sbjct: 260 LKETKRSSAVPVAPAEGLNLVRVDY 284


>gi|288919692|ref|ZP_06414019.1| tRNA pseudouridine synthase A [Frankia sp. EUN1f]
 gi|288348881|gb|EFC83131.1| tRNA pseudouridine synthase A [Frankia sp. EUN1f]
          Length = 275

 Score =  112 bits (279), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 85/249 (34%), Positives = 122/249 (48%), Gaps = 23/249 (9%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA+ QVAH DL  
Sbjct: 16  YDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDSGVHAIGQVAHVDLPT 75

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
                 L + LN  L  +  + +  L+     F ARFSA+ R Y+YRI    AP   E  
Sbjct: 76  GTPVGGLARRLNGVLDRA--VRVKGLAPAPAGFDARFSALSRRYVYRIT--DAPFGAEPL 131

Query: 129 RAW---LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIRTIDHFDVNSFGN 182
           R +     P+ LD   M  AA  L+G HDF  F    C   + ++ +RT+   DV+    
Sbjct: 132 RRFDTLASPRPLDVPAMAEAALLLLGEHDFAAF----CRRREGATTVRTLLRLDVSRVEG 187

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEG 238
           +I   V A +F H+ +R+ VG+L  VG+G+    W +  L + +    R     + P  G
Sbjct: 188 VILADVEADAFCHSMVRALVGALVAVGEGRRRPEWAAAVLGRGV----RDSGVTVLPAHG 243

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 244 LTLVEVRYP 252


>gi|328884456|emb|CCA57695.1| tRNA pseudouridine synthase A [Streptomyces venezuelae ATCC 10712]
          Length = 285

 Score =  112 bits (279), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 86/251 (34%), Positives = 121/251 (48%), Gaps = 7/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G  + GW +Q  G  ++QG IE A+  VT   E   +  AGRTDSGVHA 
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQAQGQRTVQGDIEDALRTVTRSKETYELTVAGRTDSGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL  E       K L     ++S  + + +L+     F+ARFSAI R Y YR+ 
Sbjct: 70  GQVAHVDLPAELWAEHRDKLLRRLAGRLSHDVRVWSLAEAPSGFNARFSAIWRRYAYRVT 129

Query: 118 TRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                +  L +G       +LD + M  AA  LVG HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWALDMDAMNEAAAALVGEHDFAAY-CKRREGATTIRTLQELR 188

Query: 177 VNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                + ++E  V A +F H  +RS VG+L  VGDG        K L A  R     +  
Sbjct: 189 WERRPDGVLEATVKADAFCHNMVRSLVGALLFVGDGHRPVDWPGKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEY 246
           P GL  + V Y
Sbjct: 249 PHGLTLEEVGY 259


>gi|330998477|ref|ZP_08322301.1| tRNA pseudouridine synthase A [Paraprevotella xylaniphila YIT
           11841]
 gi|329568583|gb|EGG50388.1| tRNA pseudouridine synthase A [Paraprevotella xylaniphila YIT
           11841]
          Length = 256

 Score =  112 bits (279), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 81/253 (32%), Positives = 116/253 (45%), Gaps = 11/253 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  ++KA+  +  + V + GAGRTD+GVHA   
Sbjct: 1   MQRYFLYLAYDGTSYHGWQIQPNGISVQEVLQKALATLLRQPVSITGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPV------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAHFD      PV       L   LN  L     ISI     V    HARF A+ R+Y Y
Sbjct: 61  VAHFDFEYADDPVRRIDGRWLTDKLNRLLPPD--ISIYKTVPVAADAHARFDALSRTYHY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTID 173
            +   ++P    +  +  + + LD   M  AA  L    DFT+F  ++    ++  R + 
Sbjct: 119 YLHFGKSPFL--RAYSCRLYQMLDFGKMNEAAAALFDYTDFTSFSKVNTDTKTNNCRIMQ 176

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                         + A  FL   +R+ VG+L  VG GK T       ++ +DR   G  
Sbjct: 177 ARWTELAPGEWRFEIQADRFLRNMVRAIVGTLVEVGRGKLTPEGFRAVIEGKDRCRAGES 236

Query: 234 APPEGLYFDSVEY 246
            P   L+   V Y
Sbjct: 237 MPGNALFLVDVAY 249


>gi|169830000|ref|YP_001700158.1| tRNA pseudouridine synthase A [Lysinibacillus sphaericus C3-41]
 gi|238688163|sp|B1HMV0|TRUA_LYSSC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|168994488|gb|ACA42028.1| tRNA pseudouridine synthase A [Lysinibacillus sphaericus C3-41]
          Length = 246

 Score =  111 bits (278), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 123/250 (49%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R  +II Y+G+ + G+Q Q    ++Q  IE+ + ++   E V V  +GRTD+ VHA  
Sbjct: 1   MRRLKIIISYDGTHFSGYQVQPGERTVQAEIERVLAIMHKEEKVKVTASGRTDARVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           KALN  +++   I +L++  V   FHAR+S   + Y Y  I  
Sbjct: 61  QTLHFDTPLAIPTDKYRKALN--VQLPRDIRVLSVEEVAHDFHARYSVTGKRYRY--IWS 116

Query: 120 QAPLALEKGRAWLIPKS---LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             P+     R + +  +    D   M+ AAQ ++G HDF+ F + +      +RT+    
Sbjct: 117 CEPIQNPFRRHYTVDTNGVKPDVVAMQKAAQAIIGTHDFSCFCAANTSVQDKVRTVTSLQ 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  + + +    FL+  +R   G+L  VG  + T  ++   + ++DR + G  APP
Sbjct: 177 FEWHGEELHMVIEGNGFLYNMVRIIAGTLWEVGIDRRTIENIALVVASEDRDKAGKTAPP 236

Query: 237 EGLYFDSVEY 246
           +GLY + V Y
Sbjct: 237 QGLYLEKVFY 246


>gi|291457231|ref|ZP_06596621.1| tRNA pseudouridine synthase A [Bifidobacterium breve DSM 20213]
 gi|291381066|gb|EFE88584.1| tRNA pseudouridine synthase A [Bifidobacterium breve DSM 20213]
          Length = 303

 Score =  111 bits (278), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 138/285 (48%), Gaps = 40/285 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q    ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPELRTVQGTIEDALHKVLRVPVGDEREPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVREWVP-------VILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E +        V L +AL   LK  +   I I  ++I  + F AR
Sbjct: 61  GVHASHQVAHLDVSDETLARCQGHMDVPLTEALARRLKAVLPADIVIHGIAIAPQGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R + +    +G    + +SLD + M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLRVDESLDLDAMNAAAAMTIGLHDFGSFATPNP 180

Query: 164 QASS------------PIRTI--------DHFDVNSF-GNLIEIRVVARSFLHTQIRSFV 202
             ++            P+ ++        + +   S    L+   +VA +F    +RS V
Sbjct: 181 GGTTIREVKTAYWRRVPVASLVPDVLAENEAYRTPSLESGLVVFTIVADAFARNMVRSLV 240

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEY 246
           GS   VG G+ T       +    R+   GP+A P+GL  + +EY
Sbjct: 241 GSSIKVGSGRKTLEWFADKMANPVREGSSGPIA-PQGLTLEHIEY 284


>gi|319950123|ref|ZP_08024062.1| tRNA pseudouridine synthase A [Dietzia cinnamea P4]
 gi|319436208|gb|EFV91389.1| tRNA pseudouridine synthase A [Dietzia cinnamea P4]
          Length = 380

 Score =  111 bits (278), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 83/268 (30%), Positives = 127/268 (47%), Gaps = 31/268 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW RQ    ++ G +E  +  V    VV+  AGRTD+GVHA  QV 
Sbjct: 5   RIRLDVAYDGTDFSGWARQPGLRTVCGVLEAELSTVLRHPVVLTVAGRTDAGVHARAQVC 64

Query: 63  HFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           H D+   W+        P  L + L   L     I++++   V  +F ARFSA+RR Y Y
Sbjct: 65  HLDVDPAWLDQRSLDGRPEALVRRLARLLPAD--IAVMDGRWVPDEFDARFSALRRHYEY 122

Query: 115 RIITRQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           R+ T  AP   E  R     AW   ++ D E +R A++ L+G HDF  F     + ++ I
Sbjct: 123 RLTT--APWGAEPIRARDTAAWT--RTADLEAVRAASERLLGLHDFAAF-CRRREGATTI 177

Query: 170 RTIDHF-----------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
           R +  F           D      +    V A +F  + +RS VG++  VG+G+ +   +
Sbjct: 178 RELQRFEWRTEPDPRGPDAPGAAEVWTASVSADAFCWSMVRSLVGAVMAVGEGRRSLEWI 237

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
              L   +R    P+AP  GL    V+Y
Sbjct: 238 SGLLAETERSSAVPVAPACGLSLIGVDY 265


>gi|227539074|ref|ZP_03969123.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33300]
 gi|227241078|gb|EEI91093.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33300]
          Length = 257

 Score =  111 bits (278), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 118/249 (47%), Gaps = 10/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + I Y G+ Y GWQ Q N  S+Q  +   +  +  + +   GAGRTD+GVHA +   
Sbjct: 7   RFFLEIAYQGTAYHGWQIQHNAVSVQEKLNDVLKTLLRKDIETIGAGRTDTGVHARQLFV 66

Query: 63  HFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           HFD + E +   P     +LNA L     I++  L  V  + HARF A  RSY Y +  +
Sbjct: 67  HFDAIPEGLLLQPDKFVHSLNALL--PHDIAVYRLLPVVDEAHARFDATSRSYEYHLHFK 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           + P  +    +WL     D   M  A Q+L+GR DF  F   + Q  +    I   +   
Sbjct: 125 KDPFLIHA--SWLTRDIPDVAKMNEACQYLLGRQDFECFSKSNTQVFTNFCDISRAEWLW 182

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N+  +L+   + A  FL   +R+ VG+L  +G        +++ + ++ R + G   P  
Sbjct: 183 NTDDHLV-FHISADRFLRNMVRAIVGTLLEIGLKGKEPVYIQEVIASKSRSKAGTSVPAH 241

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 242 GLYLTEVVY 250


>gi|166032002|ref|ZP_02234831.1| hypothetical protein DORFOR_01704 [Dorea formicigenerans ATCC
           27755]
 gi|166028455|gb|EDR47212.1| hypothetical protein DORFOR_01704 [Dorea formicigenerans ATCC
           27755]
          Length = 310

 Score =  111 bits (278), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 124/247 (50%), Gaps = 13/247 (5%)

Query: 6   MIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQV 61
           + IEY+GS Y GW R    ++ ++I   I   +  +TGE  +    G RT+ GVHA  QV
Sbjct: 71  ITIEYDGSRYQGWTRLGKDESNNTISAKIIDVLGKMTGEKNIELNCGCRTEVGVHAYAQV 130

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          +   LN YL +   I+I  +  V  +FHA+ +A+ ++Y+YR+     
Sbjct: 131 ANFKTSSNLSTKDIQHYLNRYLPMD--IAITEVEEVPDRFHAQLNAVSKTYVYRMTIMDV 188

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E+   +   K+ D + M+ AA   +G HDF  F S   ++ +  R +  +D++ +G
Sbjct: 189 PSVFERKHTYHCFKTPDKKAMQQAALLFIGEHDFRNF-STAKKSKNTTREV--YDIDIYG 245

Query: 182 NLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           +  E++++  A  FLH   R  +G+L  +G G     D+E     +  K  G    P+GL
Sbjct: 246 DNEEMQILIQADDFLHNMARLMIGTLLDIGFGLRKKEDIEAIFNGE--KAVGNPCDPKGL 303

Query: 240 YFDSVEY 246
           Y   VEY
Sbjct: 304 YLQEVEY 310


>gi|284042832|ref|YP_003393172.1| tRNA pseudouridine synthase A [Conexibacter woesei DSM 14684]
 gi|283947053|gb|ADB49797.1| tRNA pseudouridine synthase A [Conexibacter woesei DSM 14684]
          Length = 261

 Score =  111 bits (278), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 115/243 (47%), Gaps = 8/243 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQVAHF 64
           + +EY+G  + GW RQ    +++ ++E+A+  V   + V +  AGRTD+GVHA  Q A +
Sbjct: 10  LTLEYDGRDFAGWARQPGRRTVEDALERALATVLRRDAVGLTVAGRTDAGVHAWAQEASY 69

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +      P      LNA L   D +++++       F AR  A  R+Y YR++ R++  A
Sbjct: 70  E-----GPPAAPHRLNALLP--DDVAVIDARPAPPGFSARHDATSRAYRYRVLVRRSRSA 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            E+GRA   P  LD + +   A  L G HDFT F           R + H    + G+++
Sbjct: 123 HERGRALWWPHRLDRDALDACAAALAGTHDFTAFTPTETDHVRFQREVMHASWRADGDML 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +  + A +F+    R  VG++  V   + +       L    R   G  APP GLY   V
Sbjct: 183 QFSIEADAFMRNMNRVLVGTMLEVAGERRSVEQFTALLDGAPRDRAGVTAPPHGLYLAGV 242

Query: 245 EYS 247
            Y 
Sbjct: 243 GYD 245


>gi|113954813|ref|YP_729642.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9311]
 gi|113882164|gb|ABI47122.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9311]
          Length = 299

 Score =  111 bits (277), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 118/248 (47%), Gaps = 16/248 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHA 57
           + R  + ++Y GS + GWQRQ  G   S+Q  +EKAI  L     +    AGRTDSGVHA
Sbjct: 17  LQRIAICLQYEGSFFCGWQRQTQGRGQSVQAVLEKAIAALDPHRPIKAIAAGRTDSGVHA 76

Query: 58  LRQVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
             QV HFD         W P +  + L A +++ + I    LS     +HA +SA  R Y
Sbjct: 77  SGQVVHFDCSGPIPASRWAPALNGR-LPACIRVREAIE-RPLS-----WHACYSASYRRY 129

Query: 113 LYRIITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
            Y I   + P       +W    K LD + M  A   L+G HDF  F+    + S    T
Sbjct: 130 RYTIYNGRRPNLFLAPWSWHRYHKRLDEQAMAQALAGLMGEHDFAAFQRAGSRRSHSRTT 189

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           I   ++   G+L+ + + A  FL+  +R  +G L  VG+ + T    E+  Q + R E  
Sbjct: 190 IQDVNIERDGDLLSVEIQASGFLYGMVRLLMGQLIAVGEHRLTPQQFEQRWQERRRDEVR 249

Query: 232 PLAPPEGL 239
             APP GL
Sbjct: 250 EAAPPHGL 257


>gi|68536845|ref|YP_251550.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium K411]
 gi|68264444|emb|CAI37932.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium K411]
          Length = 328

 Score =  111 bits (277), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 129/265 (48%), Gaps = 27/265 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           ++R  + + Y+G+ + GW  Q  G  ++ G +++ + LVT   + +  AGRTD+GVHA  
Sbjct: 28  LVRVRLEVAYDGTDFHGWATQSGGLRTVAGVLQEKLSLVTRHPIELVVAGRTDAGVHASG 87

Query: 60  QVAHFDLVREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           QV H D+  +         P  L + L+  L     + +   S+  + F ARFSA+RR Y
Sbjct: 88  QVCHADIPVDAFEQRSLTRPEDLVRRLSRMLPAD--VRLHGASVAPQGFDARFSALRRHY 145

Query: 113 LYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---S 166
           +YR+ T  A   P+      AW  P  +D E  + A+  L+G +DF  F    C+A   +
Sbjct: 146 IYRVTTHPAGPVPVRARDTAAWRHP--IDLEKTQAASDALIGLNDFAAF----CKAREGA 199

Query: 167 SPIRTIDHF---DVNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           + +R +  F   DV++       E  V A +F  + +RS VG+   VG GK         
Sbjct: 200 TTVRELQEFRWVDVSTEAEPQTYEAHVTADAFCWSMVRSLVGAALTVGSGKRPDDFTPGL 259

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           L+   R    P+AP EGL    V+Y
Sbjct: 260 LKETKRSSAVPVAPAEGLNLVRVDY 284


>gi|331699143|ref|YP_004335382.1| tRNA pseudouridine synthase A [Pseudonocardia dioxanivorans CB1190]
 gi|326953832|gb|AEA27529.1| tRNA pseudouridine synthase A [Pseudonocardia dioxanivorans CB1190]
          Length = 263

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/257 (32%), Positives = 131/257 (50%), Gaps = 25/257 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y+G+ + GW  Q    ++ G +  A+  +    V +  AGRTD+GVHA  QV
Sbjct: 1   MRYRLDIAYDGTDFSGWAPQPGRRTVHGVLTDALQRLVRAPVALTVAGRTDAGVHASGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
           AH DL  E  P  L + L   L     + +  ++ V  +F ARFSA+RR Y+YR+ T   
Sbjct: 61  AHVDLSGELEPDRLVRRLARLLPPD--VRVRAVTAVPPEFDARFSALRRHYVYRVTTAPW 118

Query: 121 --APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIRTIDHF 175
              PL      AW  P  +D + +  A+  L+G HDF  F    C   + ++ IR +  F
Sbjct: 119 GADPLRARDTLAW--PHPIDLDAVARASTALLGEHDFAAF----CRRREGATTIRELLRF 172

Query: 176 --DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRKE 229
              V++ G ++   + A +F H+ +RS VG++  VG G+    W +  L++A +A D   
Sbjct: 173 AWSVDADG-VVRAELSADAFCHSMVRSLVGAMLDVGRGRRAVEWPAGLLDRAERASDVA- 230

Query: 230 CGPLAPPEGLYFDSVEY 246
              +AP  GL    V+Y
Sbjct: 231 ---VAPAHGLTLVGVDY 244


>gi|307328060|ref|ZP_07607241.1| tRNA pseudouridine synthase A [Streptomyces violaceusniger Tu 4113]
 gi|306886365|gb|EFN17370.1| tRNA pseudouridine synthase A [Streptomyces violaceusniger Tu 4113]
          Length = 288

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 116/251 (46%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
            +R  + + Y+G  + GW +Q+   ++QG +E A+  VT   E   +  AGRTD+GVHA 
Sbjct: 9   FVRVRLDLSYDGKDFSGWAKQRERRTVQGELESALRTVTRSSETFELTVAGRTDAGVHAR 68

Query: 59  RQVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL    W             ++   + +  ++     F+ARFSAI R Y YR+ 
Sbjct: 69  GQVAHVDLPEALWAEHRDRLLRRLAGRLPHDVRVWKVAQAPPGFNARFSAIWRRYAYRVT 128

Query: 118 TRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                +  L +G        LD   M  A++ L+G HDF  +      A++ IRT+   D
Sbjct: 129 DHPGGVDPLLRGHVLWHDWPLDVAAMNAASERLLGEHDFAAYCKKRDGATT-IRTLQRLD 187

Query: 177 -VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V     +I   V A +F H  +RS VG+L  VGDG        K L A  R     +  
Sbjct: 188 WVRGADGVITATVRADAFCHNMVRSLVGALLFVGDGHRPWDWPAKVLAAGVRDSAVHVVR 247

Query: 236 PEGLYFDSVEY 246
           P GL  + V Y
Sbjct: 248 PHGLTLEEVGY 258


>gi|161723265|ref|NP_302320.2| tRNA pseudouridine synthase A [Mycobacterium leprae TN]
          Length = 320

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 82/268 (30%), Positives = 127/268 (47%), Gaps = 34/268 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G +++A   V    V +  AGRTD+GVHA  QV
Sbjct: 44  VRLRLDIAYDGTDFAGWAVQAGQRTVAGVLDEAFTTVFRTPVRLRAAGRTDTGVHATGQV 103

Query: 62  AHFDLVREWVPVILCKALNAYLKISDT----------------ISILNLSIVDKQFHARF 105
           AH D+        L KA        D                 + +L+++     F ARF
Sbjct: 104 AHVDIPG----TALSKANPRSPHTGDPEFLPLLRRLSRLLPVDVRVLDIACAPVGFDARF 159

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           SA+RR Y YR+ T  AP  ++  +A  +   P+ LD ++M  A++ L+G  DF  F   H
Sbjct: 160 SALRRHYRYRLST--APYGVQPNQARYVTAWPRELDLDSMSAASRDLLGLRDFAVF-CRH 216

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDL 218
              ++ IR +   + +  G LI   + A +F  + +RS +G+L  VGD +    W    L
Sbjct: 217 RHGATTIRELQRLEWSREGYLITAHITADAFCWSMVRSLIGALLAVGDHRRTIGWCGELL 276

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
            KA ++ D       AP  GL F  V+Y
Sbjct: 277 TKASRSSDFTT----APAHGLTFIRVDY 300


>gi|118443953|ref|YP_878363.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
 gi|118134409|gb|ABK61453.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
          Length = 245

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 122/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + I+Y+G+ Y GWQ+   N ++IQ  IE  +  +  E V +  +GRTD+GVHA  QVA+F
Sbjct: 6   LTIQYDGTRYKGWQKLGNNDNTIQHKIESVLGELLKEEVALIASGRTDAGVHANMQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     + K L  YL     I + +++   + FH+R++   + Y YRI   +    
Sbjct: 66  KTDSRISNDEISKYLYKYL--PQDIVVKSVNEASENFHSRYNVKEKVYTYRIHNSEVHDV 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  ++ + + LD + M+ A++  +G HDF +F ++  +  S ++TI+        + I
Sbjct: 124 FTRKYSYHVREKLDLKKMKEASKLFIGEHDFKSFTALKSKKKSTVKTINSITFRKKEDDI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           EI      FL+  IR  VG+L  VG  K +  D++  +  +DR      AP  GL    V
Sbjct: 184 EIVFSGNGFLYKMIRILVGTLVEVGLNKISIDDVKDVMDKKDRSIAPETAPAHGLTLTEV 243

Query: 245 EY 246
           +Y
Sbjct: 244 KY 245


>gi|289547965|ref|YP_003472953.1| tRNA pseudouridine synthase A [Thermocrinis albus DSM 14484]
 gi|289181582|gb|ADC88826.1| tRNA pseudouridine synthase A [Thermocrinis albus DSM 14484]
          Length = 241

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 124/247 (50%), Gaps = 6/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y +I+ + G+ + GWQ Q +  ++QG +   +  +    +   G  RTD+GVHA   
Sbjct: 1   MFNYGLILSFVGTHFHGWQIQPSLRTVQGELSSCLSKIFDRTIKPIGCCRTDAGVHAKEY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F       P  L KALN+ L     I +  + + ++++++R+S   ++Y+YRI    
Sbjct: 61  AANFKAPTFIEPDKLLKALNSLL--PHDIGVKKVWLAEEKWNSRYSIKGKTYVYRIHMSH 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A     +   W IP +L  + MR  +Q LVG HDF+ F S      +PI  ++   +   
Sbjct: 119 ARDPFLEPFVWRIPYTLQVDKMREISQLLVGTHDFSGF-SKKEDDKNPIIDLEELVLLQE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ +   AR FL   +R  VG+L  VG  K    ++E+ L  ++   C   AP +GL 
Sbjct: 178 GDILILSFRARRFLRYMVRRMVGALVQVGLEKIGKEEIERYLSGEN---CPYTAPAKGLT 234

Query: 241 FDSVEYS 247
            + + +S
Sbjct: 235 LEKIHFS 241


>gi|116624080|ref|YP_826236.1| tRNA pseudouridine synthase A [Candidatus Solibacter usitatus
           Ellin6076]
 gi|122253167|sp|Q01WL4|TRUA_SOLUE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116227242|gb|ABJ85951.1| tRNA pseudouridine synthase A [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 240

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 122/250 (48%), Gaps = 14/250 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G  + GWQ Q   ++IQG +E+ +  + G+ V V G+GRTD+GVHAL Q
Sbjct: 1   MRRIRIYLAYDGGPFHGWQVQPGLATIQGILEEIVGGMEGKPVHVAGSGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA F  +   +PV  L +A+N  L     I IL    V   FH RF A+ ++Y YR+   
Sbjct: 61  VAAFS-IENPIPVENLRRAVNRLL--PPAIRILCAEEVQADFHPRFDAVAKTYEYRMFRD 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFD 176
           +     E    +  P  LD   M   A+   G HDFT F +      +  S +RTI    
Sbjct: 118 EVCSPFEWPYVYHHPYPLDEARMATLARAFEGEHDFTPFAASDARDAEGKSKVRTIFSST 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++     +  RV    FL   +R+ VG+L   G G     +   +L A+     G  AP 
Sbjct: 178 LDRTPQRLVYRVRGSGFLKHMVRNIVGTLIEAGRGNIADLN---SLPAR----SGATAPA 230

Query: 237 EGLYFDSVEY 246
           +GL+  SVEY
Sbjct: 231 KGLFQVSVEY 240


>gi|319956627|ref|YP_004167890.1| tRNA pseudouridine synthase a [Nitratifractor salsuginis DSM 16511]
 gi|319419031|gb|ADV46141.1| tRNA pseudouridine synthase A [Nitratifractor salsuginis DSM 16511]
          Length = 242

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 87/249 (34%), Positives = 124/249 (49%), Gaps = 10/249 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHAL 58
           M R   +I Y+GS + G+QRQK    ++QG++E+A+  L  G  +V  G+GRTD+GVHA 
Sbjct: 1   MQRIKAVIAYDGSAFEGFQRQKRTPRTVQGALERALASLGIGTPIV--GSGRTDAGVHAT 58

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFDL   W    L +      +  D I   +L+ V   FHAR+ A  R  +YR I 
Sbjct: 59  GQVIHFDLPPHWAKQPLDELQIHLNRRLDAIRFKHLTPVPADFHARYDAKER--IYRYIF 116

Query: 119 RQAPLALEKGRAWLIPKSL-DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           R+ P   E  R ++   ++ D   +  A +   GRHDF+ F     + +  IRTI     
Sbjct: 117 RREPSIFE--RKYVAGLAIADEAKLSEALKTFQGRHDFSHFLKTGSETAHNIRTITRAYF 174

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G    I   A  FL  Q+R  V +   V +G+ +   L++ L+   R     LAPPE
Sbjct: 175 LRRGKYGYIYFHADGFLRAQVRMMVHAAAAVANGELSLEQLKEQLELGKRYTTR-LAPPE 233

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 234 GLYLARVIY 242


>gi|153854831|ref|ZP_01996054.1| hypothetical protein DORLON_02059 [Dorea longicatena DSM 13814]
 gi|149752533|gb|EDM62464.1| hypothetical protein DORLON_02059 [Dorea longicatena DSM 13814]
          Length = 245

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 126/247 (51%), Gaps = 13/247 (5%)

Query: 6   MIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQV 61
           + IEY+GS Y GW R    ++G++I   I + +  +T E  +    G RT+ GVHA  Q+
Sbjct: 6   LTIEYDGSRYQGWTRLGKDESGNTISNKITEVLKKMTEEDDLELFCGCRTEVGVHAYAQI 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          +   LN YL +   I+I+++  V ++FHA+ +A  ++Y+YR+     
Sbjct: 66  ANFKTSSSTTTQNIKHYLNRYLPMD--IAIIDVKEVPERFHAQLNATSKTYVYRMTIDDV 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   ++   +   +  D   M+ AA+ L GRHDF  F S   +  S +R I  FD++ +G
Sbjct: 124 PSVFDRKYTYHCYRIPDKRLMQQAAEKLTGRHDFRNFSSAK-KTKSTVREI--FDIDIYG 180

Query: 182 NLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           ++ E++++  A  FLH   R  VG+L  +G G  +  D++         E      P+GL
Sbjct: 181 DIEEMQILIHADDFLHNMARIIVGTLMDIGLGNRSVQDIDDIFAGI--LEASAPCDPKGL 238

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 239 YLQEITY 245


>gi|139438880|ref|ZP_01772340.1| Hypothetical protein COLAER_01344 [Collinsella aerofaciens ATCC
           25986]
 gi|133775591|gb|EBA39411.1| Hypothetical protein COLAER_01344 [Collinsella aerofaciens ATCC
           25986]
          Length = 274

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/256 (31%), Positives = 123/256 (48%), Gaps = 28/256 (10%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ-----VA 62
           + Y+GS Y G+  Q   +++ G + +AI  +    + +  AGRTD+GVHA+ Q     V 
Sbjct: 21  VAYDGSSYSGFAEQPGQATVAGELRRAIETLLRRPIDLTCAGRTDAGVHAVAQYISVPVT 80

Query: 63  HFDLV---REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             +L    R W+     +A++A L     I+I  +    K F ARF A  R+Y YRI  R
Sbjct: 81  DAELALTRRRWL-----RAMDALLP--KDIAINEVYRARKGFSARFDARSRTYTYRIADR 133

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
            A   L +G  W     LD E M  A   L+G  DF +F    C+ +S +    H  V  
Sbjct: 134 DARPVLSRGAVWWHRYPLDVEAMSAACPALLGEQDFKSF----CKVASAVGKPTHRCVMR 189

Query: 179 -------SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                  +FG +++   +   +FLH+ +R+ VG+L  +G  +     + + + A DR   
Sbjct: 190 AEFGHEVAFGEDILTFTIEGNAFLHSMVRTIVGTLVEIGMHRRKPEWMREVIDACDRTAA 249

Query: 231 GPLAPPEGLYFDSVEY 246
           GP AP  GL F  V+Y
Sbjct: 250 GPTAPACGLTFMGVDY 265


>gi|294630922|ref|ZP_06709482.1| tRNA pseudouridine synthase A [Streptomyces sp. e14]
 gi|292834255|gb|EFF92604.1| tRNA pseudouridine synthase A [Streptomyces sp. e14]
          Length = 284

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/253 (33%), Positives = 122/253 (48%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGSAFHGWAKQAGGKRTVQGEIEDALRTVTRSQETYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QVAH DL  + W      L K L    ++   + +  L      F+ARFSA+ R Y YR
Sbjct: 70  GQVAHVDLPEQVWREHHEKLLKRLAG--RLPRDVRVWALRPAPSGFNARFSAVWRRYAYR 127

Query: 116 IITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +      +  L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+  
Sbjct: 128 VTDNPGGVDPLLRGHVLWHDWPLDVDAMNEAARRLLGEHDFAAY-CKKREGATTIRTLQE 186

Query: 175 FDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             +    + +I   V A +F H  +RS +G+L  VGDG  T     K L A  R     +
Sbjct: 187 LSLRRGADGIITATVRADAFCHNMVRSLIGALLFVGDGHRTPDWPGKVLAAGVRDSAVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVGY 259


>gi|227501274|ref|ZP_03931323.1| tRNA-pseudouridine synthase I [Anaerococcus tetradius ATCC 35098]
 gi|227216507|gb|EEI81913.1| tRNA-pseudouridine synthase I [Anaerococcus tetradius ATCC 35098]
          Length = 246

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 82/250 (32%), Positives = 121/250 (48%), Gaps = 8/250 (3%)

Query: 1   MIRYCMI-IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MIR  ++   Y+G+ + G+Q QK+  S++  I+KA+  VTGE   +   GRTDSGVHA  
Sbjct: 1   MIRNVLVETAYDGTNFAGFQYQKDQRSVEEEIKKALVKVTGEDNRIVSCGRTDSGVHAKS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSI--VDKQFHARFSAIRRSYLYRII 117
              +F    +  P    KA + +L++     IL LS   VD  FHARFS   + Y Y I 
Sbjct: 61  HFFNFLTASKIDP----KAFSYHLQVHLPADILALSSREVDLSFHARFSCKSKLYKYVIY 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFD 176
             +    + +     I   LD + +    + L G HDF +F R     + + +R ID   
Sbjct: 117 RGKGMHPIYRNYKEEISYKLDLKRLEEGLKLLCGEHDFRSFMREDKDLSINTVRKIDQAY 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G+ +EI   A SFLH Q+R  VGSL  +  GK +  D ++      +    P    
Sbjct: 177 FLENGDDLEIYFKAESFLHNQVRIMVGSLVELSRGKLSLDDYKRFFDEDYKIRANPALGA 236

Query: 237 EGLYFDSVEY 246
           +GLY   VE+
Sbjct: 237 QGLYLWRVEF 246


>gi|302558965|ref|ZP_07311307.1| tRNA pseudouridine synthase A [Streptomyces griseoflavus Tu4000]
 gi|302476583|gb|EFL39676.1| tRNA pseudouridine synthase A [Streptomyces griseoflavus Tu4000]
          Length = 285

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/255 (32%), Positives = 122/255 (47%), Gaps = 12/255 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVH 56
            +R  + + Y+G+ + GW RQ  G  ++QG IE A+  VT   G +  +  AGRTD+GVH
Sbjct: 9   FVRVRLDLSYDGAEFSGWARQAGGRRTVQGEIEDALRTVTRSGGTVYELTVAGRTDAGVH 68

Query: 57  ALRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           A  QVAH DL RE W      L K L    ++   + +  L      F+ARFSA+ R Y 
Sbjct: 69  ARGQVAHVDLPREVWAEHHTKLLKRLAG--RLPRDVRVWALREAPAGFNARFSAVWRRYA 126

Query: 114 YRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+      +  L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+
Sbjct: 127 YRVTDNPGGVDPLLRGHVLWHDWPLDVDAMNEAARGLLGEHDFAAY-CKRREGATTIRTL 185

Query: 173 DHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                +     ++   V A +F H  +RS +G+L  VGDG        + L A  R    
Sbjct: 186 QELSLLRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRPPHWPAEVLAAGVRDSAV 245

Query: 232 PLAPPEGLYFDSVEY 246
            +  P GL  + V Y
Sbjct: 246 HVVRPHGLTLEEVGY 260


>gi|189346490|ref|YP_001943019.1| tRNA pseudouridine synthase A [Chlorobium limicola DSM 245]
 gi|238692218|sp|B3EIU9|TRUA_CHLL2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189340637|gb|ACD90040.1| tRNA pseudouridine synthase A [Chlorobium limicola DSM 245]
          Length = 243

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 81/242 (33%), Positives = 112/242 (46%), Gaps = 9/242 (3%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           +EY+G+ + GWQRQ  G  ++QG +E  +  +  E + +  AGRTD GVHA  QV +F  
Sbjct: 8   VEYDGTDFCGWQRQPGGIQTLQGELEAQLGRILQENISLTAAGRTDKGVHARLQVVNFMT 67

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                   +  ALN+ L   DT+ + N  +V   FHARFSA  R Y Y ++  + P AL 
Sbjct: 68  GSAMELSKMAHALNSLL--PDTVRVSNPHVVPLDFHARFSAKEREYRYFLL--EEPSALR 123

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
                    SL    M+ AA  LVG HDF           +P+  I   +      +   
Sbjct: 124 CRFTGCSKGSLHIGVMQDAAGLLVGEHDFLLLSKEPADKKNPVCLIKECEWQEENGVFVF 183

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP--PEGLYFDSV 244
           R+ A  FL + +R  VG +  VG G+    DL   L   D     PL P  P GL+   V
Sbjct: 184 RIRANRFLRSMVRYLVGVMIAVGRGRAVPEDLGMLL--DDGLMTFPLFPAEPNGLFLWDV 241

Query: 245 EY 246
            Y
Sbjct: 242 SY 243


>gi|256420466|ref|YP_003121119.1| tRNA pseudouridine synthase A [Chitinophaga pinensis DSM 2588]
 gi|256035374|gb|ACU58918.1| tRNA pseudouridine synthase A [Chitinophaga pinensis DSM 2588]
          Length = 250

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 120/245 (48%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ + G+Q Q N  ++Q  I+ AI  +    +V  G+ RTD+GVHA +  
Sbjct: 1   MRYFIEVAYKGTSFGGFQIQDNVETVQSVIDHAISTLMRGAIVTTGSSRTDAGVHARQNF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+ +   P  L K +NA L     + + N+  V    H+RF+A+ RSY Y +   + 
Sbjct: 61  LHFDMEQPLHPQFLYK-VNAIL--PPDVVMRNIYRVADDAHSRFAALSRSYEYTLYMEKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   ++G  +  P +L  E +  AA  L    +F TF   + Q  +    I   +     
Sbjct: 118 PFMRDRG--YFFPYTLHPELLHEAASVLREYENFMTFSKRNTQVKTYNCNIMSSEWEVGE 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  RV A  FL   +R  VG++  VG GK T     +A+++++        PP+GL+ 
Sbjct: 176 DRIVYRVTANRFLRGMVRGMVGTMLRVGRGKLTMDGFREAIESRNCVNADFAVPPQGLFL 235

Query: 242 DSVEY 246
             V Y
Sbjct: 236 MKVAY 240


>gi|257784931|ref|YP_003180148.1| tRNA pseudouridine synthase A [Atopobium parvulum DSM 20469]
 gi|257473438|gb|ACV51557.1| tRNA pseudouridine synthase A [Atopobium parvulum DSM 20469]
          Length = 294

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 115/245 (46%), Gaps = 10/245 (4%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH---FDL 66
           Y G+ + G+  Q    S+ G + +A+  V    V +  AGRTD+GVHA  Q      +D 
Sbjct: 44  YRGAAFCGFAEQPTQRSVAGDLRRALETVLRREVELTCAGRTDAGVHAQVQYVSLPVYDA 103

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
              +    L ++L A     D ISI  L    + F ARF A  RSY YRI    A   L 
Sbjct: 104 DLSFSGEKLVRSLTAL--TDDDISIRQLFRAPQGFSARFDAQARSYRYRICADSARPILG 161

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGN--- 182
               W     LD + M  AAQ LVG HDF +F ++I  +     R ++   V        
Sbjct: 162 WDHVWWYNGHLDADLMDKAAQALVGEHDFKSFCKAISAEGKPTHRFVERLSVEEIEEAGE 221

Query: 183 -LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ VG+L  +G G      +++ L A++R   G  AP +GL F
Sbjct: 222 KLIAVDITGNAFLHNMVRTIVGTLVEIGRGHRPVEWIDEVLAAKNRIAAGSCAPAQGLTF 281

Query: 242 DSVEY 246
            +V Y
Sbjct: 282 VNVRY 286


>gi|300867109|ref|ZP_07111775.1| tRNA pseudouridine synthase A [Oscillatoria sp. PCC 6506]
 gi|300334864|emb|CBN56941.1| tRNA pseudouridine synthase A [Oscillatoria sp. PCC 6506]
          Length = 265

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/250 (34%), Positives = 116/250 (46%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++I+Y G+   GWQRQ +  ++Q  IE  I  V    V +HGAGRTDSGVHA  Q
Sbjct: 1   MQRIALVIQYIGTDLHGWQRQPHQRTVQEEIETTISTVLQRPVTLHGAGRTDSGVHAAAQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAHFD     VP    +  LN+  ++   I I   + V+  +HARFSA  R Y Y + T 
Sbjct: 61  VAHFDAEGP-VPAHRWQDILNS--RLPKDILIRASAKVEPTWHARFSATWRRYRYTLYTD 117

Query: 120 QAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
             P    +  AW      LD   ++ A   L+GR     F             +   +  
Sbjct: 118 PVPNLFVRPFAWHYYHAPLDESLIQAALTPLIGRFHLAAFHRAGSSRPHSWVDVQVAECQ 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL-APPE 237
            FG  I I V A  FL+  +R  VG L  VG G+  S +  K +  Q+R+E     AP  
Sbjct: 178 RFGPFIHIEVQASGFLYGMMRLLVGLLVQVGRGE-RSLENFKDIWVQERREMVKYSAPAH 236

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 237 GLCLLRVGYP 246


>gi|320459238|dbj|BAJ69859.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. infantis
           ATCC 15697]
          Length = 303

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 84/288 (29%), Positives = 137/288 (47%), Gaps = 46/288 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPADDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPAGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R + +    +G    + +SLD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEIDPRLRGCVLTVDESLDLELMNRAAALTIGLHDFGSFATPNP 180

Query: 164 QASS------------PIRTI--------DHFDVNSF-GNLIEIRVVARSFLHTQIRSFV 202
             ++            PI  +        + +   S    L+   +VA +F    +RS V
Sbjct: 181 GGTTIREVKTAYWRRVPITPLVPDAMASHEAYRTPSLESGLVVFTIVADAFARNMVRSLV 240

Query: 203 GSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           GS   VG G+    W +  +   ++       GP+A P+GL  + + Y
Sbjct: 241 GSCIKVGSGRKSLEWFAGKMADPVR---EGSSGPIA-PQGLTLEHIAY 284


>gi|226227135|ref|YP_002761241.1| tRNA pseudouridine synthase A [Gemmatimonas aurantiaca T-27]
 gi|226090326|dbj|BAH38771.1| tRNA pseudouridine synthase A [Gemmatimonas aurantiaca T-27]
          Length = 259

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/250 (31%), Positives = 119/250 (47%), Gaps = 14/250 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH-GAGRTDSGVHALRQVAHF 64
           ++ +Y+G  + GWQRQ +  ++QG +E+ +  ++G + V   GAGRTD+GVHA  Q    
Sbjct: 8   LVTQYDGGRFAGWQRQPDVRTVQGDMERVLGRLSGGLYVPAVGAGRTDAGVHAHGQGVGV 67

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ-APL 123
            +  +W    L +A+NA L   D I +     ++ +FH R+SA  R Y Y I T + A  
Sbjct: 68  RMPPQWTAPRLRRAMNALLP--DDIWVAAAYQMEPEFHPRYSATARRYGYLIGTDELASS 125

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI----RTIDHFD--V 177
              +   W + + LD E +   A  L+G H F  F   H   ++P+    R I H    V
Sbjct: 126 PFRRRHEWALHRPLDVEALHGEAAELLGEHTFRAFAIAH---TAPVDDHHRCIIHHAAWV 182

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  +   V A  FLH  +R  VG++  V  G+     + + L   D  +  P AP  
Sbjct: 183 PREGGWV-FEVSANRFLHHMVRFLVGTMVDVALGRRPRGTIARLLVTPDNADTSPPAPAH 241

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 242 GLSLREVTYP 251


>gi|325972112|ref|YP_004248303.1| tRNA pseudouridine synthase A [Spirochaeta sp. Buddy]
 gi|324027350|gb|ADY14109.1| tRNA pseudouridine synthase A [Spirochaeta sp. Buddy]
          Length = 281

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 112/247 (45%), Gaps = 8/247 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M + Y+GS Y GWQ+Q N  S+   IE+ +  +  E V V G+GRTDSGVHAL QV H D
Sbjct: 23  MTVSYHGSHYSGWQKQSNAKSVAEIIEQTLKQILDEEVQVVGSGRTDSGVHALAQVCHMD 82

Query: 66  LVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +    +       ALN  L     I IL+    D  FHAR++ + R+Y Y         A
Sbjct: 83  IANTRIKGEKFALALNRLLPAD--IRILDSCETDGTFHARYTTMARTYRYYYKRECDMTA 140

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH----FDVNSF 180
            +      + +    E +   A  + G HDFTTF +      S  R I       +++ F
Sbjct: 141 FDDKLVAKVKQFPSLELLNEYACSIRGTHDFTTFTASGDLCPSRFRDIYESYWRLEIDRF 200

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G  L+   +   +FL+  +RS VGS+           +    L ++DR   G  A   GL
Sbjct: 201 GKELLSYTICGNAFLYKMVRSLVGSMMEFATKDLPVEEFRHILASKDRSRSGRTASACGL 260

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 261 YLYRISY 267


>gi|213693060|ref|YP_002323646.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 15697]
 gi|213524521|gb|ACJ53268.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 305

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 84/288 (29%), Positives = 137/288 (47%), Gaps = 46/288 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 3   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPADDAAEPLRLTVAGRTDT 62

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 63  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPAGFDAR 122

Query: 105 FSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R + +    +G    + +SLD E M  AA   +G HDF +F + + 
Sbjct: 123 FSALERTYVYRVADRSSEIDPRLRGCVLTVDESLDLELMNRAAALTIGLHDFGSFATPNP 182

Query: 164 QASS------------PIRTI--------DHFDVNSF-GNLIEIRVVARSFLHTQIRSFV 202
             ++            PI  +        + +   S    L+   +VA +F    +RS V
Sbjct: 183 GGTTIREVKTAYWRRVPITPLVPDAMASHEAYRTPSLESGLVVFTIVADAFARNMVRSLV 242

Query: 203 GSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           GS   VG G+    W +  +   ++       GP+A P+GL  + + Y
Sbjct: 243 GSCIKVGSGRKSLEWFAGKMADPVR---EGSSGPIA-PQGLTLEHIAY 286


>gi|206602902|gb|EDZ39382.1| Pseudouridylate synthase [Leptospirillum sp. Group II '5-way CG']
          Length = 268

 Score =  110 bits (274), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 82/255 (32%), Positives = 117/255 (45%), Gaps = 13/255 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  ++ Y+G G+ GWQ Q  G+++Q  IE+A   +T + V + G+GRTD+GV A  Q
Sbjct: 1   MQRFAFVVSYDGRGFQGWQSQIRGNAVQDHIEEAFCRLTRQDVRISGSGRTDTGVSAAGQ 60

Query: 61  VAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL    W P  L + LN +L  S  I IL  + V   FHAR   +R+ Y YR ++R
Sbjct: 61  VFHCDLAGPGWTPDSLSRGLNHFL--SPAIRILQAAAVAPDFHARHDVVRKIYRYRWVSR 118

Query: 120 Q------APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
                   P        +L P  +    ++ A + L G +DFT F           RTID
Sbjct: 119 SRKMREVGPTEDPFCGTFLPP--VHWTLLQQATKLLEGSNDFTRFTVQKSCPEDARRTID 176

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                +    +++ V  R FLH  IR    +L   G  K +    +  L          L
Sbjct: 177 AIQWIAGPYTLDLWVAGRGFLHMMIRYLAMALLETGQQKRSLKSFQDLLLTGSLPPVPAL 236

Query: 234 --APPEGLYFDSVEY 246
             APP+GL    V Y
Sbjct: 237 HPAPPQGLSLVRVLY 251


>gi|134103229|ref|YP_001108890.1| tRNA pseudouridine synthase A [Saccharopolyspora erythraea NRRL
           2338]
 gi|291007979|ref|ZP_06565952.1| tRNA pseudouridine synthase A [Saccharopolyspora erythraea NRRL
           2338]
 gi|133915852|emb|CAM05965.1| tRNA pseudouridine synthase A [Saccharopolyspora erythraea NRRL
           2338]
          Length = 296

 Score =  110 bits (274), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/272 (30%), Positives = 139/272 (51%), Gaps = 37/272 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
           ++R  + + Y+G+ +FGW +Q +  ++QG +E A+        V   +VV   AGRTD+G
Sbjct: 13  LVRLRLEVSYDGTDFFGWAKQPDRRTVQGLLEDALRKQPPGRSVPRSVVV---AGRTDTG 69

Query: 55  VHALRQVAHFDLV-------------REWVPVILCKALNAYLKI-SDTISILNLSIVDKQ 100
           VHA  QV H D+V                +P  L +  + + +I    + +L   +    
Sbjct: 70  VHATGQVVHVDVVPSAPDEGGRLPLDEHGIP-DLDRMRHRWNRILPGDVRVLGARVAPAG 128

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDF 155
           F ARFSA+RR Y Y++    AP  ++  R     +W  P  LD + +  A++ L+G +DF
Sbjct: 129 FDARFSAMRRHYRYQVS--DAPWGVDPLRRRDTLSWNRP--LDVDALNAASEDLLGLNDF 184

Query: 156 TTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             F     + ++ +R +  F    +  +L+  RV A +F H+ +RS VG+L +VGDG+ +
Sbjct: 185 AAF-CKQREGATTVRELQRFSWERAEPHLLVARVSADAFCHSMVRSLVGALLMVGDGRRS 243

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            T   +AL+A +R     +AP  GL    V+Y
Sbjct: 244 RTWPAEALRAAERTST--VAPAHGLTLVGVDY 273


>gi|317483422|ref|ZP_07942412.1| tRNA pseudouridine synthase A [Bifidobacterium sp. 12_1_47BFAA]
 gi|316915108|gb|EFV36540.1| tRNA pseudouridine synthase A [Bifidobacterium sp. 12_1_47BFAA]
          Length = 303

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 138/288 (47%), Gaps = 46/288 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPTDDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R + +    +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 180

Query: 164 QASS------------PIRTIDHFDVNSF---------GNLIEIRVVARSFLHTQIRSFV 202
             ++            PI  +   ++ S            L+   +VA +F    +RS V
Sbjct: 181 GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSLV 240

Query: 203 GSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           GS   VG G+    W +  + + ++       GP+A P+GL  + + Y
Sbjct: 241 GSCIKVGSGRKSLEWFADKMAEPVR---EGSSGPIA-PQGLTLEHIAY 284


>gi|227546504|ref|ZP_03976553.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 55813]
 gi|227213053|gb|EEI80932.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 55813]
          Length = 305

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 138/288 (47%), Gaps = 46/288 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 3   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPTDDAAEPLRLTVAGRTDT 62

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 63  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 122

Query: 105 FSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R + +    +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 123 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 182

Query: 164 QASS------------PIRTIDHFDVNSF---------GNLIEIRVVARSFLHTQIRSFV 202
             ++            PI  +   ++ S            L+   +VA +F    +RS V
Sbjct: 183 GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSLV 242

Query: 203 GSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           GS   VG G+    W +  + + ++       GP+A P+GL  + + Y
Sbjct: 243 GSCIKVGSGRKSLEWFAGKMAEPVR---EGSSGPIA-PQGLTLEHIAY 286


>gi|23466158|ref|NP_696761.1| tRNA pseudouridine synthase A [Bifidobacterium longum NCC2705]
 gi|46190438|ref|ZP_00121526.2| COG0101: Pseudouridylate synthase [Bifidobacterium longum DJO10A]
 gi|189440597|ref|YP_001955678.1| pseudouridylate synthase [Bifidobacterium longum DJO10A]
 gi|239621038|ref|ZP_04664069.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|296454842|ref|YP_003661986.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp. longum
           JDM301]
 gi|312133902|ref|YP_004001241.1| trua [Bifidobacterium longum subsp. longum BBMN68]
 gi|322689901|ref|YP_004209635.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
 gi|42559815|sp|Q8CY46|TRUA_BIFLO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238692041|sp|B3DQE2|TRUA_BIFLD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|23326895|gb|AAN25397.1| tRNA pseudouridine synthase A [Bifidobacterium longum NCC2705]
 gi|189429032|gb|ACD99180.1| Pseudouridylate synthase [Bifidobacterium longum DJO10A]
 gi|239516139|gb|EEQ56006.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|291516444|emb|CBK70060.1| pseudouridylate synthase I [Bifidobacterium longum subsp. longum
           F8]
 gi|296184274|gb|ADH01156.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp. longum
           JDM301]
 gi|311773196|gb|ADQ02684.1| TruA [Bifidobacterium longum subsp. longum BBMN68]
 gi|320461237|dbj|BAJ71857.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
          Length = 303

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 138/288 (47%), Gaps = 46/288 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPTDDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R + +    +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 180

Query: 164 QASS------------PIRTIDHFDVNSF---------GNLIEIRVVARSFLHTQIRSFV 202
             ++            PI  +   ++ S            L+   +VA +F    +RS V
Sbjct: 181 GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSLV 240

Query: 203 GSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           GS   VG G+    W +  + + ++       GP+A P+GL  + + Y
Sbjct: 241 GSCIKVGSGRKSLEWFAGKMAEPVR---EGSSGPIA-PQGLTLEHIAY 284


>gi|322691842|ref|YP_004221412.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. longum
           JCM 1217]
 gi|320456698|dbj|BAJ67320.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. longum
           JCM 1217]
          Length = 303

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 138/288 (47%), Gaps = 46/288 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPADDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R + +    +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 180

Query: 164 QASS------------PIRTIDHFDVNSF---------GNLIEIRVVARSFLHTQIRSFV 202
             ++            PI  +   ++ S            L+   +VA +F    +RS V
Sbjct: 181 GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSLV 240

Query: 203 GSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           GS   VG G+    W +  + + ++       GP+A P+GL  + + Y
Sbjct: 241 GSCIKVGSGRKSLEWFAGKMAEPVR---EGSSGPIA-PQGLTLEHIAY 284


>gi|302553571|ref|ZP_07305913.1| tRNA pseudouridine synthase A [Streptomyces viridochromogenes DSM
           40736]
 gi|302471189|gb|EFL34282.1| tRNA pseudouridine synthase A [Streptomyces viridochromogenes DSM
           40736]
          Length = 284

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/253 (33%), Positives = 120/253 (47%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSKETYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QVAH DL RE W      L K L    ++   + +  L      F+ARFSA+ R Y YR
Sbjct: 70  GQVAHVDLPREVWAEHHQKLLKRLAG--RLPRDVRVWALREAPSGFNARFSAVWRRYAYR 127

Query: 116 IITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +      +  L +         LD + M  AA+ L+G HDF  +     + ++ IRT+  
Sbjct: 128 VTDNPGGVDPLLRNHVLWHDWPLDVDAMNEAARRLLGEHDFAAY-CKKREGATTIRTLQE 186

Query: 175 FD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V     +I   V A +F H  +RS +G+L  VGDG        K L A  R     +
Sbjct: 187 LSLVKGEDGIITATVRADAFCHNMVRSLIGALLFVGDGHRPPDWPGKVLAAGVRDSAVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVGY 259


>gi|290958122|ref|YP_003489304.1| tRNA-pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260647648|emb|CBG70753.1| putative tRNA-pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 287

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 122/254 (48%), Gaps = 13/254 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT  GE   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSGETYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLV----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            QVAH DL     RE    +L +      ++   + +  L      F+ARFSAI R Y Y
Sbjct: 70  GQVAHVDLPEAVWREHHEKLLKRLAG---RLPRDVRVWALREAPSGFNARFSAIWRRYAY 126

Query: 115 RIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+      +  L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+ 
Sbjct: 127 RVTDNPGGVDPLLRGHVLWHDWPLDVDAMNEAARLLLGEHDFAAY-CKRREGATTIRTLQ 185

Query: 174 HFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
               V     ++   V A +F H  +RS +G+L  VGDG   +    K L A  R     
Sbjct: 186 ELSLVRGDDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRGADWPGKVLAAGVRDSAVH 245

Query: 233 LAPPEGLYFDSVEY 246
           +  P GL  + V Y
Sbjct: 246 VVRPHGLTLEEVGY 259


>gi|325479638|gb|EGC82730.1| tRNA pseudouridine synthase A [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 246

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 118/248 (47%), Gaps = 4/248 (1%)

Query: 1   MIRYCMI-IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MI+  ++   Y+G+ + G+Q QK+  S++  + KAI  VTGE   +   GRTDSGVHA  
Sbjct: 1   MIKNILLETSYDGALFSGFQYQKDQRSVEEELTKAIRKVTGEENRIVSCGRTDSGVHAKS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              +F    +  P+ +   +  +L   D I  ++   VD  FHARFSA  + Y Y I   
Sbjct: 61  HFVNFLTASDINPIGIKFQIQPHL--PDDILAISSREVDLNFHARFSAKSKLYKYVICRS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVN 178
           +    + +     +   LD + +      LVG HDF  F       S + +RTI+     
Sbjct: 119 KDMHPIYRNYKEHVTYKLDLKKLEEGLNLLVGTHDFRLFMMEDKNLSINTVRTIEEAYFI 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +EI     SFLH Q+R  VGSL  +  G+ +  D EK    ++ K   P    EG
Sbjct: 179 ENGADLEIYFKGESFLHNQVRIMVGSLIELARGRISLDDYEKFFDKENTKRANPALGAEG 238

Query: 239 LYFDSVEY 246
           LY   VE+
Sbjct: 239 LYLWRVEF 246


>gi|118616627|ref|YP_904959.1| tRNA pseudouridine synthase A [Mycobacterium ulcerans Agy99]
 gi|118568737|gb|ABL03488.1| pseudouridine synthase a, TruA [Mycobacterium ulcerans Agy99]
          Length = 260

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 123/243 (50%), Gaps = 22/243 (9%)

Query: 21  QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP-------- 72
           Q    ++ G +++A+  V    V +  AGRTD+GVHA  QVAH D+  + +P        
Sbjct: 2   QTGQRTVAGVLDEALTTVLRTPVRLRAAGRTDAGVHATGQVAHADVPVDALPNAYSRSAR 61

Query: 73  ------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                 + L + L  +L     + +L+++     F ARFSA+RR Y+YR+ T  AP  +E
Sbjct: 62  AGDPEFLPLVRRLARFLPAD--LRVLDIARAPTAFDARFSALRRHYVYRLST--APYGVE 117

Query: 127 KGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
             +A  +   P+ LD + M +A+Q L+G H+F  F     + ++ IR +   D +  G+L
Sbjct: 118 PQQARYVTVWPRELDIDAMTVASQELLGLHNFAAF-CRRREGATTIRDLQRLDWSRNGHL 176

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  +V A +F  + +RS VG+L  VG+ + T     + L A  R      AP  GL    
Sbjct: 177 VTAQVSADAFCWSMVRSLVGALLAVGEHRRTPDWCRELLTATARSSDFAAAPAHGLVLAK 236

Query: 244 VEY 246
           V+Y
Sbjct: 237 VDY 239


>gi|282933805|ref|ZP_06339157.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
 gi|281302070|gb|EFA94320.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
          Length = 223

 Score =  109 bits (272), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 70/211 (33%), Positives = 109/211 (51%), Gaps = 5/211 (2%)

Query: 40  GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVD 98
           G+ +VVHG+GRTD+GVHAL QV HFD   + +P   +  ALN+ +     I   +  IV+
Sbjct: 2   GQRIVVHGSGRTDAGVHALGQVIHFDFPNDNIPANRMVLALNSMMPTD--IIFKDAEIVN 59

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           + FH ++S   + Y Y +   +     ++      P  L+   M+ AA  L+G HDFT+F
Sbjct: 60  EDFHVQYSTHGKWYRYIVNQDRFVDPFKRFYTGHYPYKLNVSKMQEAALDLLGEHDFTSF 119

Query: 159 RSIHCQASSPIRTIDHFDV--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
            +   Q    +RTI +  +   S  N I    +   FL+  +R  VG+L  +G+ +    
Sbjct: 120 AASGGQIIDKVRTIYYVKIWQKSEENEIIFDFIGNGFLYNMVRIMVGALLEIGNERRPVH 179

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           DL++ + A+DR+E    AP  GLY   V Y 
Sbjct: 180 DLKRVILAKDRQEVINTAPASGLYLYHVFYE 210


>gi|323357344|ref|YP_004223740.1| pseudouridylate synthase [Microbacterium testaceum StLB037]
 gi|323273715|dbj|BAJ73860.1| pseudouridylate synthase [Microbacterium testaceum StLB037]
          Length = 285

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 84/262 (32%), Positives = 125/262 (47%), Gaps = 18/262 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ    ++QG +E+A+  + G    +  AGRTD+GVHA  QV
Sbjct: 1   MRLRLDISYDGTHFRGWARQPGLRTVQGVLEEALARILGGDPRLVVAGRTDAGVHASGQV 60

Query: 62  AHFDL---VREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           AH DL    +  +P              L   +   L     +++   S   + F ARFS
Sbjct: 61  AHLDLDDAQQARLPRRRREGDEGDAVAALAGRVRGVLGAYPDVTVHRSSCAPEGFDARFS 120

Query: 107 AIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R Y YRI   QA    LE+ R   +  SLD + M  AAQ L+G HDF  +     +A
Sbjct: 121 AVWRRYSYRIADAQAGYEPLERLRTTSVRASLDVDAMHAAAQRLIGLHDFAAYCKAREEA 180

Query: 166 SSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           ++ IRT+  +D     + I I  V A +F H+ +R+ VG+   VG+G+    D+ K    
Sbjct: 181 TT-IRTLLEYDWRRGDDGILIANVRADAFCHSMVRALVGACVAVGEGRLEVDDVIKIRDE 239

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
             R     +    GL    V Y
Sbjct: 240 GRRTADSKVLAARGLVLAEVGY 261


>gi|303284649|ref|XP_003061615.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456945|gb|EEH54245.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 390

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 73/207 (35%), Positives = 105/207 (50%), Gaps = 37/207 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH---GAGRTDSGVHALR 59
           RY + I+Y+G  + G+QRQ N  ++QG +E+A+   TG    VH   G+ RTD+GVHAL 
Sbjct: 7   RYLLRIQYDGGAFHGFQRQANARTVQGCVEEAMAKFTGVEGGVHAITGSSRTDAGVHALD 66

Query: 60  QVAHFDLVREWVPV----------ILCKALNAYL-KISDTISILNLS-IVDKQFHARFSA 107
             AH D+                  + KA+N YL K +   SI + + +  + FHAR+ A
Sbjct: 67  ATAHVDIDDGDAGDAPPPPPHSARTVMKAVNHYLRKTAPMASIASCARVCPETFHARYCA 126

Query: 108 IRRSYLYRI-ITRQAPLALEKGRAWLI---------------PKS------LDCENMRIA 145
             R+Y Y I + R  P   ++G+AW +               P        LD + M  A
Sbjct: 127 TARTYRYLIYLGRDEPSVFDRGKAWHVYDGRNASGAGVNTHEPSGGCALGGLDVDAMNAA 186

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTI 172
           A+  VG HDF+ FR+  CQASSPIR +
Sbjct: 187 ARRFVGEHDFSAFRANGCQASSPIRRL 213



 Score = 47.0 bits (110), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA-QDRKECGPLAPPEGLYFD 242
           I I   A SFL+ Q+R  VG+L+ VG G+ +  D+   L+   D     P+AP  GLY +
Sbjct: 286 IVITARAPSFLYHQVRLMVGTLRAVGAGELSPDDVTDLLEGTTDASRAPPMAPAHGLYLE 345

Query: 243 SVEY 246
            V Y
Sbjct: 346 RVHY 349


>gi|282601160|ref|ZP_05980960.2| tRNA pseudouridine synthase A [Subdoligranulum variabile DSM 15176]
 gi|282570067|gb|EFB75602.1| tRNA pseudouridine synthase A [Subdoligranulum variabile DSM 15176]
          Length = 249

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 116/249 (46%), Gaps = 7/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y + I Y G+ Y G+Q Q N  ++   ++ A+  V G    V G  RTD+GVHA R  
Sbjct: 1   MTYLLWITYKGTNYAGFQVQPNAPTVCAVLQDAMQAVLGSRPDVKGCSRTDAGVHARRFA 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F          +  ALNA+L     I  L +  V + FHAR++A  ++Y Y I+  + 
Sbjct: 61  LSFCYTGRVPAEKIVPALNAHLPPD--IRALAVQAVPEGFHARYAAHEKTYCYHILNARI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----RSIHCQASSPIRTIDHFDV 177
                      + + LD   M+ AA   VG HDF        S+     + +RTI    V
Sbjct: 119 DDPFTLDTCHRVAQPLDLAAMQAAAAQFVGTHDFLALCASGSSVAAHGDT-VRTISRCTV 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G+   I V A  +L+  +R   G+L   G  K T   +   LQ++DR++ GP  P +
Sbjct: 178 SRCGDRFVITVTADGYLYNMVRILAGTLVEAGLHKRTPDSIPALLQSRDRRQAGPTLPAK 237

Query: 238 GLYFDSVEY 246
           GL+ + V Y
Sbjct: 238 GLFLEDVAY 246


>gi|301788920|ref|XP_002929883.1| PREDICTED: LOW QUALITY PROTEIN: tRNA pseudouridine synthase-like
           1-like [Ailuropoda melanoleuca]
          Length = 290

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 89/275 (32%), Positives = 136/275 (49%), Gaps = 35/275 (12%)

Query: 3   RYCMIIEYNGSGYFGW---QRQKNGSSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHAL 58
           RY +  +Y G+ + G    +  +   + Q  +E+A   +   + V    + RTD+GVHAL
Sbjct: 11  RYLVYFQYLGTDFNGVAAVRGSQRAVAXQNYLEEAAKRLNSVVPVKFTISSRTDAGVHAL 70

Query: 59  RQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALNA+L+    I IL    V   FHAR +A  R+YL
Sbjct: 71  CNAAHLDVQRRSGQPPFSPEVLAEALNAHLR-HPAIRILQAFRVPSDFHARHAATSRTYL 129

Query: 114 YRIIT---RQAPLAL-EKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR++T   R   L++ E+ R W L    LD + M+ AAQHL+G HDF+ F+S    A+S 
Sbjct: 130 YRLVTGCHRPDQLSVFERNRCWPLRAGCLDVDAMQEAAQHLLGTHDFSAFQSAGSPAASS 189

Query: 169 IRTIDHFDVNS---------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           +RT+    V+                F NL      ++SFL+ Q+R     L  VG G  
Sbjct: 190 VRTLRRASVSPDPGSPFVLPQENRLRFWNL---EFESQSFLYRQVRRMTAVLVAVGLGAL 246

Query: 214 TSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
               ++  L+++D   +    +AP  GL+  SV Y
Sbjct: 247 MPAQVKVILESRDPLGRHQARVAPAHGLFLKSVLY 281


>gi|297192674|ref|ZP_06910072.1| tRNA pseudouridine synthase A [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197721671|gb|EDY65579.1| tRNA pseudouridine synthase A [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 286

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 87/254 (34%), Positives = 121/254 (47%), Gaps = 11/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHA 57
            +R  + + Y+G  + GW +Q  G  ++QG IE A+  VT  G    +  AGRTD+GVHA
Sbjct: 9   FVRVRLDLSYDGKDFSGWAKQAGGRRTVQGEIEDALRTVTRSGTTYELTVAGRTDAGVHA 68

Query: 58  LRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
             QVAH DL  E W      L K L    ++S  + I +++   + F+ARFSAI R Y Y
Sbjct: 69  RGQVAHVDLPSELWAEHREKLLKRLAG--RLSRDVRIWSVAEAPEGFNARFSAIWRRYAY 126

Query: 115 RIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+      +  L +G        LD   M  A+  LVG HDF  +      A++ IRT+ 
Sbjct: 127 RVTDNPGGVDPLLRGHVLWHDWPLDVAAMNEASAGLVGEHDFAAYCKKRDGATT-IRTLQ 185

Query: 174 HFDVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                     +I   V A +F H  +RS VG+L  VGDG   +    K L A  R     
Sbjct: 186 QLSWERDPSGVITATVKADAFCHNMVRSLVGALLFVGDGHRPAEWPAKVLAAGVRDSAVH 245

Query: 233 LAPPEGLYFDSVEY 246
           +  P GL  + V Y
Sbjct: 246 VVRPHGLTLEEVGY 259


>gi|229815740|ref|ZP_04446065.1| hypothetical protein COLINT_02789 [Collinsella intestinalis DSM
           13280]
 gi|229808656|gb|EEP44433.1| hypothetical protein COLINT_02789 [Collinsella intestinalis DSM
           13280]
          Length = 292

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/257 (34%), Positives = 123/257 (47%), Gaps = 29/257 (11%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV----A 62
           + Y+G+ + G+  Q  G  ++ G + +A+  +    V +  AGRTD+GVHA+ Q     A
Sbjct: 38  LGYDGAAFSGFAEQPEGLRTVAGEVRRALETILRRPVDLTCAGRTDAGVHAVSQYVSIPA 97

Query: 63  HFDLVR----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           H D +      W+     +A+ A L  SD I++  +      F ARF A  R+Y YRI+T
Sbjct: 98  HADELAITHARWM-----RAMAALLP-SD-IALNAVYHARPGFSARFDARSRTYTYRIVT 150

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR--TIDHFD 176
             A   L +   W     LD + M  AA  LVG HDF +F    C+ SS I   T  +  
Sbjct: 151 GDARPLLTRSVTWWHRLPLDMDAMERAAACLVGEHDFKSF----CKTSSAIDKPTCRNVI 206

Query: 177 VNSFGNL-------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
             SF          I   +   +FLH+ +R+ VGSL  VG G+     L  AL A DR+ 
Sbjct: 207 AVSFERASALGEEHIAFTITGNAFLHSMVRTIVGSLVEVGAGRRDERWLSDALAACDRRA 266

Query: 230 CGPLAPPEGLYFDSVEY 246
            GP AP  GL F  V Y
Sbjct: 267 AGPTAPARGLCFMDVAY 283


>gi|242371866|ref|ZP_04817440.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W1]
 gi|242350373|gb|EES41974.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W1]
          Length = 267

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 113/243 (46%), Gaps = 2/243 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H   RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHVRIHPTSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N +L   + I + ++  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNQQWQYAMNRFL--PNDIYVKSVQTVDENFHCRYDCVGKRYRYKVYQGAH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I   LD   M  AA H +G HDFT F S   +  S +RT+   +V    
Sbjct: 119 RDPFKSGLETFIDNDLDLAKMNEAAHHFIGTHDFTGFCSQKTEVESKVRTLYQSEVVQTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+ ++R      AP EGLY 
Sbjct: 179 AGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRNPDEVPQLLEEKNRNNVPFTAPSEGLYL 238

Query: 242 DSV 244
           + V
Sbjct: 239 EKV 241


>gi|332261432|ref|XP_003279774.1| PREDICTED: LOW QUALITY PROTEIN: tRNA pseudouridine synthase-like
           1-like [Nomascus leucogenys]
          Length = 287

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 81/239 (33%), Positives = 115/239 (48%), Gaps = 25/239 (10%)

Query: 32  EKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKIS 86
           E A  L + E V    + RTD+GVHAL   AH D+ R      + P +L +ALN +L+  
Sbjct: 31  EAAERLNSVEPVRFTISSRTDAGVHALSNAAHLDVQRRSGRPPFPPEVLTEALNTHLR-H 89

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIIT----RQAPLALEKGRAWLIPKS-LDCEN 141
             I +L    V   FHAR +A  R+YLYR+ T    R      E+   W +P   LD   
Sbjct: 90  PAIRVLRAFRVPNDFHARHAATSRTYLYRLATGCNRRDELPVFERNLCWALPADCLDVVA 149

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS--FGNLI----------EIRVV 189
           M+ AAQHL+G HDF+ F+S      SP+RT+    V+      L+           +   
Sbjct: 150 MQEAAQHLLGTHDFSAFQSTGSPVPSPVRTLRRVSVSPGQASPLVTQESRKLRFWSLEFE 209

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
           ++SFL+ Q+R     L  VG G      ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 210 SQSFLYRQVRRMTAVLVAVGLGALAPAQVKTILESQDPLGKHQTRVAPAHGLFLKSVLY 268


>gi|299541963|ref|ZP_07052286.1| tRNA pseudouridine synthase A [Lysinibacillus fusiformis ZC1]
 gi|298725701|gb|EFI66342.1| tRNA pseudouridine synthase A [Lysinibacillus fusiformis ZC1]
          Length = 246

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 123/250 (49%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R  +II Y+G+ + G+Q Q    ++Q  +E+ + ++  GE V V  +GRTD+ VHA  
Sbjct: 1   MRRLKVIISYDGTLFSGYQVQPGERTVQAELERVLAIMHKGEQVKVTASGRTDAKVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           KALN  +++   I +L++  V   FHAR+    + Y Y  I  
Sbjct: 61  QTLHFDTSLAIPAEKYRKALN--VQLPRDIRVLSVEEVAHDFHARYDVAGKRYRY--IWS 116

Query: 120 QAPLALEKGRAWLIPKS---LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             P+     R + +  +    + E M+ AA+ + G HDF+ F + +      +RT+    
Sbjct: 117 CEPIQSPFRRYYTVETNGVKPNVEAMQEAAKAITGTHDFSCFCAANTSVKDKVRTVTLLQ 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  + + +    FL+  +R   G+L  VG G+    ++ + + + +R + G  APP
Sbjct: 177 FEWHGEELHMVIEGNGFLYNMVRIIAGTLWEVGIGRRKVDNVSQVVASGNRDKAGKTAPP 236

Query: 237 EGLYFDSVEY 246
           +GLY + V Y
Sbjct: 237 QGLYLEKVFY 246


>gi|302336349|ref|YP_003801556.1| tRNA pseudouridine synthase A [Olsenella uli DSM 7084]
 gi|301320189|gb|ADK68676.1| tRNA pseudouridine synthase A [Olsenella uli DSM 7084]
          Length = 284

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 79/256 (30%), Positives = 120/256 (46%), Gaps = 21/256 (8%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y G+G+ G+  Q    ++ G +  A+  +    V +  AGRTD+GV+AL Q     + 
Sbjct: 24  LGYRGAGFAGFAEQPGQRTVAGELRTALETLLHRPVDLTCAGRTDAGVNALAQYVSLPVT 83

Query: 68  REWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
           R  +     + +++ + ++ D +S+  L   D  F ARF A+ R Y YR+    A   L 
Sbjct: 84  RGELEREGRRLVSSLVALTPDDLSVRGLYKADVSFSARFDALERGYRYRVACGSARPVLS 143

Query: 127 KGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----------IRTIDH 174
            G  W +     LD + M  AA  L+G HDF +F    C+ASS            R +  
Sbjct: 144 WGHTWWLRSVADLDVDAMGEAASALLGEHDFRSF----CKASSAGLLEADGRSTCRRLSA 199

Query: 175 FDV----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
             V     +   L+ I V   +FLH  +R   G+L  VG G   ++ + +AL A DR   
Sbjct: 200 VSVVRAREAGEELVAIDVRGNAFLHNMVRVIAGTLVEVGRGHRDASWVARALAAHDRSAA 259

Query: 231 GPLAPPEGLYFDSVEY 246
           GP AP  GL F+ V Y
Sbjct: 260 GPTAPAHGLTFEWVGY 275


>gi|226325156|ref|ZP_03800674.1| hypothetical protein COPCOM_02948 [Coprococcus comes ATCC 27758]
 gi|225206504|gb|EEG88858.1| hypothetical protein COPCOM_02948 [Coprococcus comes ATCC 27758]
          Length = 255

 Score =  108 bits (271), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 111/217 (51%), Gaps = 6/217 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+GS Y G+  +K  +SI+  +  AI  VTG+   +  A +T+ GVHA  Q
Sbjct: 12  MTTIKLTIEYDGSRYPGFSTKKKSTSIESKLTLAIRDVTGQSTQLFAAVKTEPGVHAAHQ 71

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           +  F L +E       +L   LNA L     I++ +L I D++F A  +    +Y  RI 
Sbjct: 72  IVSFQLEKESFSDNTELLKMKLNAALPAD--IAVTSLEIADERFVASLAVKSCTYTCRIA 129

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T  A     +    ++ +SLD E+M+ AAQ L G HDF  F +   + S+ +RT++   +
Sbjct: 130 TDPAAALFSRPYTCVVTESLDLESMQQAAQLLTGTHDFAAFSNGRTRKST-VRTVETIKI 188

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           N    LI+I++ A SFL    +   G++   G  K T
Sbjct: 189 NREDQLIQIQLTANSFLRHMPQLLAGTILTAGKEKKT 225


>gi|301165600|emb|CBW25171.1| tRNA pseudouridine synthase A [Bacteriovorax marinus SJ]
          Length = 256

 Score =  108 bits (271), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 87/260 (33%), Positives = 127/260 (48%), Gaps = 18/260 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHA 57
           M  Y +I+ Y G+ Y GWQ+Q + S +IQG +EKA+  ++   EI  + G+GRTDSGVHA
Sbjct: 1   MSFYKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTI-GSGRTDSGVHA 59

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV    +  E  P+ L KALN++L   + I  ++     + F+  F A  ++Y Y   
Sbjct: 60  LGQVVRVQIPLELEPLSLLKALNSHL--PNDIECIHSENSSELFNPVFDAKDKTYKYLFS 117

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID---- 173
                 AL       + + +D E MR A +  +G HDF  F ++    SS +R I     
Sbjct: 118 LNGRRNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKL 177

Query: 174 HFDVNSFGNLIEI-------RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           H +    G L E+        V    FL   +R  VG+L  +G GK    DL+ AL +  
Sbjct: 178 HLEKQQ-GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPS 236

Query: 227 RKECGPLAPPEGLYFDSVEY 246
             +   +AP  GLY   V Y
Sbjct: 237 GAKLAAVAPSNGLYLCEVNY 256


>gi|308814270|ref|XP_003084440.1| TRUA1_PARUW tRNA pseudouridine synthase A 1 (ISS) [Ostreococcus
           tauri]
 gi|116056325|emb|CAL56708.1| TRUA1_PARUW tRNA pseudouridine synthase A 1 (ISS) [Ostreococcus
           tauri]
          Length = 705

 Score =  108 bits (270), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 82/259 (31%), Positives = 122/259 (47%), Gaps = 18/259 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHALR 59
           Y M I Y+G+ Y G+QRQ  + +S+Q  +E+ +  +TGE    + + G+GRTD GVHA  
Sbjct: 17  YAMTISYDGTNYKGFQRQGADVASVQRELERCLTRLTGEGRDALRLGGSGRTDGGVHARG 76

Query: 60  QVAHFDLVREWVPV---ILC-KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           QV HF   ++W        C KA+N  L     +           FHARF A R++Y Y 
Sbjct: 77  QVVHFYSEKDWRSAEDFARCVKAMNGMLPRD--VRCERFWRPHPAFHARFHATRKTYAYY 134

Query: 116 IITRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTF------RSIHCQASSP 168
           +  R       +  A     ++ D + +R A Q+ VG  DF  F      +    +  + 
Sbjct: 135 VDARSPHDVFARAYACQCGWRACDVDALRRACQYFVGTRDFRAFANTSRDKPTSDEDLNT 194

Query: 169 IRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            RTI  FDV      LI +      FL+ Q+R+ VG+  +V  G+     +   L + DR
Sbjct: 195 TRTIFRFDVFEQADGLIRLECEGDGFLYRQVRNMVGAALVVASGREKPEWILDLLASGDR 254

Query: 228 KECGPLAPPEGLYFDSVEY 246
           +     AP  GL+  SVEY
Sbjct: 255 RRVPTAAPARGLFLQSVEY 273


>gi|282890286|ref|ZP_06298816.1| hypothetical protein pah_c014o179 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499943|gb|EFB42232.1| hypothetical protein pah_c014o179 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 231

 Score =  108 bits (270), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 72/223 (32%), Positives = 107/223 (47%), Gaps = 4/223 (1%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKI 85
           +IQ  +EK I  +  + V V  +GRTD+GVHA  QVAHF    E        ++N  L  
Sbjct: 2   AIQEIVEKEIGKIVRQPVRVVASGRTDAGVHARGQVAHFSTNAEIDLRRFLVSINGLL-- 59

Query: 86  SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIA 145
              I + ++  V   FHA++S   ++Y Y +   +      +  AW I + LD   +++A
Sbjct: 60  PKDIRVKDICQVPPDFHAQYSVSGKAYHYHLTLSRVQSPFSRFYAWHIRQKLDLSQLQVA 119

Query: 146 AQHLVGRHDFTTF--RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVG 203
           AQ  VG HDFT+F   +      + +RTI   DV        +      FL+  +R+ VG
Sbjct: 120 AQLFVGTHDFTSFANEAHREHPQNAVRTIKRVDVIMEDEGCRLEFEGDGFLYKMVRNMVG 179

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            L  V  G    TD+     A+DRK+ G  APP GL+   V +
Sbjct: 180 ILIEVATGYRPITDIPAIFAAKDRKKAGKAAPPHGLFLHQVNF 222


>gi|150390096|ref|YP_001320145.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
 gi|149949958|gb|ABR48486.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
          Length = 248

 Score =  108 bits (270), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 77/252 (30%), Positives = 128/252 (50%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y M+I Y+G  Y G+ + K+    SIQG +E  +  +  E V V  A  TD+GVH+ 
Sbjct: 1   MQNYKMMIAYDGRKYTGYNKSKDNLEKSIQGKLELILSKLYEEEVEVISAVSTDAGVHSK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            Q+ +F      +     K +  Y +  ++D I IL++   D++FH+R+     +Y YR+
Sbjct: 61  GQIVNFIAPNSRLD---EKEIFDYFEKYLTDDIIILSVETADERFHSRYLMKSATYEYRL 117

Query: 117 ITRQAP--LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
             + AP     E+    L+ +++D   ++ A ++LVG HDF  F + + + +  I+T+  
Sbjct: 118 WKKDAPNRPLFERQYVNLMNQTVDVTKIKKAGKYLVGEHDFLAF-TTNRKTTKSIKTMVS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            DV    N I I + A  FL    R  VG+L  +G G+     +EKA ++++  + G  A
Sbjct: 177 LDVMETRNEIIITMTANGFLLNMERVIVGTLIQIGLGQLPMNTIEKAFESKNMNDVGHKA 236

Query: 235 PPEGLYFDSVEY 246
               L   SVEY
Sbjct: 237 SAGALCLLSVEY 248


>gi|119484807|ref|ZP_01619289.1| tRNA pseudouridine synthase A [Lyngbya sp. PCC 8106]
 gi|119457625|gb|EAW38749.1| tRNA pseudouridine synthase A [Lyngbya sp. PCC 8106]
          Length = 279

 Score =  108 bits (270), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 114/245 (46%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ NG ++Q  IE AI  V    V +HGAGRTD+GVHA  QVA
Sbjct: 5   RIALVIQYQGTRFNGWQRQPNGRTVQEEIETAIANVVDSPVTLHGAGRTDTGVHAAAQVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF++            LN   ++   I +   + VD  +HARFSA+ R Y Y + T   P
Sbjct: 65  HFEVTGPIPGYRWATILNH--RLPHDILVRASAQVDPSWHARFSAVWRRYRYLLYTDSRP 122

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W      LD + M+ A   L+GRH  + F+    +       +        G
Sbjct: 123 NLFVRPWSWHYYHAPLDEKLMQAALIPLLGRHHLSAFQRAGTRRPHAWVDVQDVSCQRQG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I+I V A  FL+  +R  +G L  VG    +  +       + R+     AP  GL  
Sbjct: 183 PFIQIEVQASGFLYGMMRLLLGLLVEVGAQARSLENFTDIWVHERRELVKYSAPARGLCL 242

Query: 242 DSVEY 246
             V Y
Sbjct: 243 LRVGY 247


>gi|269796221|ref|YP_003315676.1| pseudouridylate synthase I [Sanguibacter keddieii DSM 10542]
 gi|269098406|gb|ACZ22842.1| pseudouridylate synthase I [Sanguibacter keddieii DSM 10542]
          Length = 287

 Score =  108 bits (270), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 81/270 (30%), Positives = 122/270 (45%), Gaps = 34/270 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +IR  + + Y G+ + GW  Q    ++QG++E+ +  V      +  AGRTD+GVH+  Q
Sbjct: 4   VIRIRLDVSYRGTDFAGWAVQPGLRTVQGTLEEGLARVLRADTRLTVAGRTDAGVHSRGQ 63

Query: 61  VAHFDLVRE-WVPV----------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           V H D+ RE W  V           L   +   L     + +  +S+    F ARFSA+ 
Sbjct: 64  VTHLDVPREVWDTVSGRGHRTGEQALLSRMTGVLPTD--VVVRAVSVAPPGFDARFSALS 121

Query: 110 RSYLYRIITRQA---PLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           R Y YRI+ R A   PL  +    W++   + LD + M+ A Q LVG  DF  F    C+
Sbjct: 122 RRYRYRIVDRHALRDPLRAD----WVLWSKRPLDVDAMQAAVQPLVGVRDFKAF----CR 173

Query: 165 ASSPIRTIDHF--------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                 TI H         D      L+   V + +F H  +R+ VG+   VG G+    
Sbjct: 174 PRPGATTIRHLQELTWERVDGGPDDGLVVASVRSDAFCHNMVRALVGASMAVGHGQRPVG 233

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
              + L+  +R     + PP GL  + VEY
Sbjct: 234 WPAEVLRRGERDPLAGVVPPHGLTLEEVEY 263


>gi|220917510|ref|YP_002492814.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219955364|gb|ACL65748.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 272

 Score =  108 bits (270), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 83/257 (32%), Positives = 125/257 (48%), Gaps = 20/257 (7%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + + Y+G  + G+QRQ    ++Q ++E+A+  + G    +H A RTD+GVHAL QV  
Sbjct: 6   YALRLAYDGGRFRGFQRQPGLPTVQQALEEALERL-GVRAQLHVAARTDAGVHALAQVVS 64

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       PV L   LN  L   + I +L+ + V   FHAR SAI R+Y+Y ++    P+
Sbjct: 65  FSARAALDPVALRGGLNEGLP--EGILVLDAARVGPSFHARGSAIARTYVY-LVGAPPPV 121

Query: 124 ALEKGRAWLIPKS-----------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            L +  AW +P +           LD   MR A  H VG HDF  F     Q  + +RT+
Sbjct: 122 GL-RPYAWTLPDARAFPDLAEVPPLDAAAMREALGHAVGEHDFVGFARPGEQRGT-VRTL 179

Query: 173 DHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              +V   G   L+ + +  + FL   +R+ VG+    G G+    D+ + L A   +  
Sbjct: 180 LRAEVIEAGWAPLVAVVLEGKGFLRAMVRNLVGTAVAAGLGR-APPDVIRTLLATRGRYR 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           G  AP  GL   +V Y 
Sbjct: 239 GVRAPGWGLTLAAVRYP 255


>gi|291567810|dbj|BAI90082.1| tRNA pseudouridine synthase A [Arthrospira platensis NIES-39]
          Length = 278

 Score =  108 bits (269), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 118/249 (47%), Gaps = 8/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +II+Y+G+ + GWQRQ N  ++Q  IE AI  ++  E V +H AGRTDSGVHA  QV
Sbjct: 6   RIALIIQYDGTHFHGWQRQPNQRTVQEDIETAISKVLKQERVPLHAAGRTDSGVHAAAQV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             LN   ++   + I   + V   +HARF A  R Y Y + T   
Sbjct: 66  AHFDAPAHIPAYRWATILNG--RLPADVLIRASAPVPSDWHARFDAQWRRYRYSLYTDAR 123

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +   W    + LD   M  A + L+G H  + F+     +S P   +D  DV  +
Sbjct: 124 PNLFIRQFTWHYYHQRLDESLMLAALKPLLGYHHLSAFQR--AGSSRPHAWVDVQDVECW 181

Query: 181 GN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +   I I V A  FL+  +R  VG L  VG  + +  + +     + R+     APP+G
Sbjct: 182 RSEAFIHIEVQASGFLYGMMRLLVGLLVQVGAKERSLENFQDIWVNERREIVKSAAPPQG 241

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 242 LCLLRVGYP 250


>gi|284053328|ref|ZP_06383538.1| tRNA pseudouridine synthase A [Arthrospira platensis str. Paraca]
          Length = 278

 Score =  108 bits (269), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 118/249 (47%), Gaps = 8/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +II+Y+G+ + GWQRQ N  ++Q  IE AI  ++  E V +H AGRTDSGVHA  QV
Sbjct: 6   RIALIIQYDGTHFHGWQRQPNQRTVQEDIETAISKVLKQERVPLHAAGRTDSGVHAAAQV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             LN   ++   + I   + V   +HARF A  R Y Y + T   
Sbjct: 66  AHFDAPAHIPAYRWATILNG--RLPADVLIRASAPVPSDWHARFDAQWRRYRYSLYTDAR 123

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +   W    + LD   M  A + L+G H  + F+     +S P   +D  DV  +
Sbjct: 124 PNLFIREFTWHYYHQRLDESLMLAALKPLLGYHHLSAFQR--AGSSRPHAWVDVQDVECW 181

Query: 181 GN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +   I I V A  FL+  +R  VG L  VG  + +  + +     + R+     APP+G
Sbjct: 182 RSEAFIHIEVQASGFLYGMMRLLVGLLVQVGAKERSLENFQDIWVNERREIVKSAAPPQG 241

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 242 LCLLRVGYP 250


>gi|325262993|ref|ZP_08129729.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
 gi|324032087|gb|EGB93366.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
          Length = 244

 Score =  108 bits (269), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 121/244 (49%), Gaps = 8/244 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +++EY+G+ Y GWQR   G S   +   + + I  +T E V +    RT+ GVHA  QV 
Sbjct: 6   LVLEYDGARYQGWQRLGKGESTNTVANKLLEVIHKMTAEDVELFCGARTEVGVHAYGQVV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F    +     + + LN YL +   I++L+   + ++FHA  +A  R+Y YRI     P
Sbjct: 66  NFKTTSDMKTDEIRQYLNRYLPMD--IAVLSAEEMPERFHASLNAKSRTYQYRIAIGAVP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +   +   ++ D   M+ AA  L GRHDF  F ++  ++ S  + I + D+    +
Sbjct: 124 SVFNRKYTYYAFRTPDIGIMQQAALLLAGRHDFKNFSTVK-KSKSTEKEIYNIDIYGDTD 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I+I + A  FLH   R  +G+L  +G GK     +E   + ++  E      P+G++  
Sbjct: 183 EIQISLRANDFLHNMPRMIIGTLMDIGLGKRKMECIEAIFKGEE--EASAPCDPKGMFLK 240

Query: 243 SVEY 246
           +V Y
Sbjct: 241 NVGY 244


>gi|284033969|ref|YP_003383900.1| tRNA pseudouridine synthase A [Kribbella flavida DSM 17836]
 gi|283813262|gb|ADB35101.1| tRNA pseudouridine synthase A [Kribbella flavida DSM 17836]
          Length = 270

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/253 (32%), Positives = 126/253 (49%), Gaps = 15/253 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALR 59
           +R+ + + Y+G+ + GW RQ    ++QG++E+A+   L   +   V  AGRTD+GVHA  
Sbjct: 1   MRWRIDLRYDGTEFHGWARQDGLRTVQGALEEALGTVLRLPDRPAVTCAGRTDTGVHARG 60

Query: 60  QVAHFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV H DL    VPV    L + LN  L   D +++  ++     F ARFSA+ R Y+YR+
Sbjct: 61  QVTHVDLD---VPVTGRDLLRRLNGVL--PDDVAVTAVAEAADGFDARFSALARRYVYRL 115

Query: 117 ITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
                   PL   +    + P  LD + M  AA  L+G HDF  F      AS+    ++
Sbjct: 116 CDDAVGWDPLRRREVLRVVRP--LDVDRMNAAAAQLLGEHDFAAFCKKREGASTVRALLE 173

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           +  V     L++  V+A +F H+ +R+ VG+L  VGDG+         L  + R     +
Sbjct: 174 YSWVRVGPGLLDGTVIADAFCHSMVRALVGALIPVGDGRRDVDWPAAVLAGKMRDSAVAV 233

Query: 234 APPEGLYFDSVEY 246
            P  GL  + V Y
Sbjct: 234 LPAHGLTLEEVRY 246


>gi|78189343|ref|YP_379681.1| tRNA pseudouridine synthase A [Chlorobium chlorochromatii CaD3]
 gi|123757011|sp|Q3AQT7|TRUA_CHLCH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78171542|gb|ABB28638.1| tRNA pseudouridine synthase [Chlorobium chlorochromatii CaD3]
          Length = 243

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 114/240 (47%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           IEY+G+ + GWQRQ     ++QG+IEK +  +T E V+++GAGRTD GVHA +QVA   L
Sbjct: 8   IEYDGTDFAGWQRQSGTIPTVQGTIEKLLSQITQEEVLLNGAGRTDKGVHARQQVASCAL 67

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                   L  +LN  L    TI I N   V   FHARFSA  R+Y Y     + P AL 
Sbjct: 68  HSSMELSRLAHSLNCLLP--PTIRICNAVHVTDDFHARFSATERTYRY--FVSETPSALC 123

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
                     LD   M+  A  +VG HDFT F      + +    +     +    ++ +
Sbjct: 124 NRFTGCANALLDVGVMQQMAAMVVGEHDFTAFSREERDSPAKRCKVTSCRWHRLHGMVVL 183

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++ A  FL + +R  V ++   G G+   T  +  +++         AP  GL+   + Y
Sbjct: 184 QISANRFLRSMVRYLVHAMLQGGKGRLAPTLFQDMVESGTSSYRMVAAPASGLFLWRIGY 243


>gi|322374719|ref|ZP_08049233.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
 gi|321280219|gb|EFX57258.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
          Length = 163

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 63/163 (38%), Positives = 91/163 (55%), Gaps = 5/163 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGFAFAGFQRQPHARSVQEEIEKTLTRLNKGQAIAVHGAGRTDSGVHALE 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + I+ R
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEF-IVDR 117

Query: 120 QAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
             P   + +  A   P  LD E M+ A + L G HDFT  + +
Sbjct: 118 GRPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFTGLQHL 160


>gi|239929485|ref|ZP_04686438.1| tRNA pseudouridine synthase A [Streptomyces ghanaensis ATCC 14672]
 gi|291437810|ref|ZP_06577200.1| pseudouridylate synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291340705|gb|EFE67661.1| pseudouridylate synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 284

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/253 (32%), Positives = 119/253 (47%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G+G+ GW +Q  G  ++QG +E A+  VT  G    +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGAGFHGWAKQAGGRRTVQGEVEDALRTVTRSGTTYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDL-VREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QVAH DL    W      L K L    ++   + +  L      F ARFSA+ R Y YR
Sbjct: 70  GQVAHVDLPAGVWAEHKGKLLKRLAG--RLPKDVRVWALREAPAGFDARFSAVWRRYAYR 127

Query: 116 IITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +      +  L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+  
Sbjct: 128 VTDNPGGVDPLLRGHVLWHDWPLDVDAMNEAARGLLGEHDFAAY-CKRREGATTIRTLQE 186

Query: 175 FD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V     ++   V A +F H  +RS +G+L  VGDG        K L A  R     +
Sbjct: 187 LSLVRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRPPDWPGKVLAAGVRDSAVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVGY 259


>gi|301167543|emb|CBW27126.1| putative tRNA pseudouridine synthase [Bacteriovorax marinus SJ]
          Length = 267

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 118/253 (46%), Gaps = 15/253 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVA 62
           Y   + YNG  YFGWQ+QKN  +IQ +IE A+ ++   E +   G+ RTD+GVH+   V 
Sbjct: 5   YNAEVHYNGENYFGWQKQKNFKTIQDTIEDALRVIAPSEKIRTMGSSRTDTGVHSRANVC 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
              +  +  P  L K LN  L   + I I       + F   + A R+ YLY      + 
Sbjct: 65  FIQIQEDLEPHELTKKLNQEL--PNDIRITKCERTYRHFKVVYFAKRKQYLYIFKINNSD 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI---------D 173
            +        I ++LD E M+ AA+  +G HDF  F     +     R I         D
Sbjct: 123 HST---FYHSIEENLDIEKMKEAAKVFIGTHDFRNFCHKVSENVDKKREIFECKIIEDQD 179

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
               N+      + +    FL   +R  +GSL  +G GK T + +++AL + + K+ G +
Sbjct: 180 FISENNCHGSYALVIEGSGFLKQMVRIIMGSLINIGLGKTTLSQIQEALVSTEFKKTGFI 239

Query: 234 APPEGLYFDSVEY 246
           AP  GLY + +E+
Sbjct: 240 APGGGLYLNEIEF 252


>gi|41410333|ref|NP_963169.1| tRNA pseudouridine synthase A [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|51316707|sp|Q73S41|TRUA_MYCPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|41399167|gb|AAS06785.1| TruA [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 251

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 118/237 (49%), Gaps = 22/237 (9%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI------------ 74
           + G +++A+  V    V +  AGRTD+GVHA  QVAH D+    +P              
Sbjct: 1   MAGVLDEALTTVFRTPVRLRAAGRTDAGVHATGQVAHLDVPGTALPNAYPRAPHVGEAEF 60

Query: 75  --LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR--- 129
             L + L  +L     + +++++     F ARFSA+RR Y+YR+ T    +  ++ R   
Sbjct: 61  GPLLRRLGRFLPTD--VRVVDITRAPAGFDARFSALRRHYVYRLSTAPWGVLPQQARYVT 118

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           AW  P+ LD E M  A++ L+G HDF  F   H + ++ IR +   D    G+LI  RV 
Sbjct: 119 AW--PRPLDVEAMAAASRDLLGLHDFAAF-CRHRENATTIRDLQRLDWTRDGDLITARVS 175

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           A +F  + +RS VG+L  VG+ +   +   + L A +R      AP  GL    V+Y
Sbjct: 176 ADAFCWSMVRSLVGALLAVGENRRPVSWCRELLSATNRSSDYATAPAHGLTLVGVDY 232


>gi|320009073|gb|ADW03923.1| tRNA pseudouridine synthase A [Streptomyces flavogriseus ATCC
           33331]
          Length = 284

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 78/253 (30%), Positives = 124/253 (49%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVRE-WV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVAH DL  E W      L + +   L +   + I   +     F+ARFSA+ R Y YR+
Sbjct: 70  QVAHVDLPAEVWAEHEEKLLRRMAGRLPLD--VRIWRAAEAPAGFNARFSALWRRYAYRV 127

Query: 117 ITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID-- 173
             R   +  L +G      + LD + M  AA  + G HDF  +     + ++ IRT+   
Sbjct: 128 GDRPGGVDPLTRGHVLWHDRPLDLDAMNEAAALMTGEHDFAAY-CKKREGATTIRTLQRL 186

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           H+  ++   ++   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +
Sbjct: 187 HWVRDAESGVLTATVQADAFCHNMVRALIGAALFVGDGRRPAGWPAEVLAAKVRDPAVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVAY 259


>gi|291298744|ref|YP_003510022.1| tRNA pseudouridine synthase A [Stackebrandtia nassauensis DSM
           44728]
 gi|290567964|gb|ADD40929.1| tRNA pseudouridine synthase A [Stackebrandtia nassauensis DSM
           44728]
          Length = 300

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 80/257 (31%), Positives = 128/257 (49%), Gaps = 20/257 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++R  + I Y+G+ + GW  Q    ++ G +  A+  + G+   +  AGRTD+GVHA  Q
Sbjct: 21  LVRLRLDICYDGTDFAGWAFQPGQRTVAGEVFTALSALFGQPEGLTVAGRTDAGVHATGQ 80

Query: 61  VAHFDL-VREWV-----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAH D+    W      P+   + +     +   + I  ++ V  +F+ARFSA+ R Y+Y
Sbjct: 81  VAHVDVPAAAWARYRDRPLWRLRGI-----LPPDVRITAITEVSSEFNARFSALSRRYVY 135

Query: 115 RI---ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPI 169
           R+   +    PL      AW  P+ +D + M  AA  LVG HDF  F  R         +
Sbjct: 136 RVADTVWGVNPLRRLDTVAW--PRPVDLDVMNAAATVLVGEHDFAAFCKRREGATTVRAL 193

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           RT+  +D ++ G +    VVA +F H+ +RS VG++  VG+G+  +  L   L   +R  
Sbjct: 194 RTV-RWDRDADG-IARATVVADAFCHSMVRSLVGAMLAVGEGRRDAAWLAALLTRGERSG 251

Query: 230 CGPLAPPEGLYFDSVEY 246
              +AP  GL    VE+
Sbjct: 252 EVLVAPANGLTLVEVEF 268


>gi|194334164|ref|YP_002016024.1| tRNA pseudouridine synthase A [Prosthecochloris aestuarii DSM 271]
 gi|194311982|gb|ACF46377.1| tRNA pseudouridine synthase A [Prosthecochloris aestuarii DSM 271]
          Length = 237

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 79/244 (32%), Positives = 119/244 (48%), Gaps = 12/244 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MIIEY+G+ + GWQRQ    S++QG IE  +  +  E V + GAGRTD GVHA+ Q A F
Sbjct: 1   MIIEYDGTDFAGWQRQDGAVSTVQGEIEAVLRRILQEAVSITGAGRTDKGVHAMGQAASF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     LC +LN+ L  S  I I++L  VD  FHAR+SA+ R Y Y  + RQ   A
Sbjct: 61  MTGSSMEAGRLCHSLNSLLPSS--IRIMSLIDVDGDFHARYSALSRQYRY--MLRQRESA 116

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           + +  +     S D + +   A  L+GRHDF  F        +   T+           +
Sbjct: 117 IFRRFSGYDRASHDLDQLNSRASVLLGRHDFKAFSKSGSDTRTTCCTVSEAQWFREKEFL 176

Query: 185 EIRVVARSFLHTQIRSFV-GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             ++ A  FL + +R  V  +L+  G+      ++  AL ++   +    A P GL+   
Sbjct: 177 VFQISANRFLRSMVRYLVSATLRFSGE------EISYALVSRQPIKGLLPADPAGLFLWE 230

Query: 244 VEYS 247
           + Y+
Sbjct: 231 IGYA 234


>gi|88854648|ref|ZP_01129314.1| tRNA pseudouridine synthase A [marine actinobacterium PHSC20C1]
 gi|88815809|gb|EAR25665.1| tRNA pseudouridine synthase A [marine actinobacterium PHSC20C1]
          Length = 315

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 78/270 (28%), Positives = 131/270 (48%), Gaps = 30/270 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA---IFLVTGEIVVVHGAGRTDSGVHALR 59
           R  + I Y+G+ + GW +Q +  ++QG+IE A   IF   G +  +  AGRTD+GVHA  
Sbjct: 29  RMRLDIAYDGTDFAGWGKQPSLRTVQGTIEDALGVIFRRFGAVPSLVVAGRTDAGVHASG 88

Query: 60  QVAHFDLVREWV------------------PVILCKALNAYLKISDTISILNLSIVDKQF 101
           QVAH DL    +                  P  L + +N    +   I +   +I    F
Sbjct: 89  QVAHLDLTDAQLISLDRPRRGNLRGKRYDGPASLARRINGIAGLEADIFLSRSAIAADGF 148

Query: 102 HARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
            ARFS + R Y YRI    +P    ++      P +LD + M IA+  L+G HD+  +  
Sbjct: 149 DARFSPLWRRYEYRIADNASPRDPRQRNHTVWYPATLDVDAMNIASDELLGLHDWAAYCK 208

Query: 161 IHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
              + ++ +R+++ F+ V +   +I   + A +F H+ +RS VG+   VG GK    +++
Sbjct: 209 PR-EGATTVRSLERFNWVRNEEGIIVAELRADAFCHSMVRSLVGAGVFVGQGK---LEVD 264

Query: 220 KALQAQDRKECG---PLAPPEGLYFDSVEY 246
           + ++ +D +  G    + P +GL    V Y
Sbjct: 265 RPVEIRDERSKGSEYKVMPAKGLTLVEVGY 294


>gi|327398248|ref|YP_004339117.1| tRNA pseudouridine synthase A [Hippea maritima DSM 10411]
 gi|327180877|gb|AEA33058.1| tRNA pseudouridine synthase A [Hippea maritima DSM 10411]
          Length = 241

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 106/204 (51%), Gaps = 3/204 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RYC  I Y+G+ Y G+Q Q +  ++QG IEKA+  +    + ++ AGRTD+GVHA  QV
Sbjct: 1   MRYCACIAYDGTNYSGFQIQPDVKTVQGEIEKALKRIFKTDLRINFAGRTDAGVHAFEQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F ++ +     L KALN+ L   + I I ++ IVD  FH+R+SA  R Y+Y     + 
Sbjct: 61  IDFPVIADIETYSLKKALNSVL--PEDIRIKSVKIVDNSFHSRYSAKFREYVYFAFDGEY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                    W +   LD + MR+A++  VG  DF +F +   +  +  R +    +  + 
Sbjct: 119 LPPFLCRYVWHVKFKLDVDAMRLASRLFVGYKDF-SFVANEPEGKNCTREVYFLRIKRYR 177

Query: 182 NLIEIRVVARSFLHTQIRSFVGSL 205
             +   + A  FL   +R+ VG L
Sbjct: 178 EFVVFHIRAGGFLRGMVRNIVGLL 201


>gi|227487069|ref|ZP_03917385.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227541767|ref|ZP_03971816.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227093143|gb|EEI28455.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227182473|gb|EEI63445.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 284

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 83/256 (32%), Positives = 123/256 (48%), Gaps = 20/256 (7%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQVAHF 64
           I Y+G+ + GW  QK G  ++Q +IE+A+ LV    +   +  AGRTD+GVHA  QVA+ 
Sbjct: 9   IAYDGTNFHGWATQKGGLRTVQQTIEEALRLVLRLDDSYQLTVAGRTDAGVHATGQVANM 68

Query: 65  DLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            +    +        P  L + LN  L   D IS+L +S   + F ARF A+RR Y YR+
Sbjct: 69  VVPESCLEQRSIDGDPARLTRRLNKLLP--DDISLLAVSAAPEAFDARFGALRRYYEYRV 126

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
            TR   PL L +       K +D + +   A   VG HDF      H   ++ IRT++ F
Sbjct: 127 TTRPGGPLPLRRFDTATWKKPVDIDVVSACASAFVGLHDFAAL-CKHKPHATTIRTVETF 185

Query: 176 DVNSFGNLIE-----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                    E      +V A +F  + +RS VG+   VG+G+   +     L  ++R   
Sbjct: 186 TWEDISTPCEPQTYLAKVSADAFCWSMVRSLVGACLAVGEGRRDLSFAPHLLTLKERAAD 245

Query: 231 GPLAPPEGLYFDSVEY 246
            P+A   GL    V+Y
Sbjct: 246 VPVASACGLTLTGVDY 261


>gi|289706561|ref|ZP_06502911.1| tRNA pseudouridine synthase A [Micrococcus luteus SK58]
 gi|289556696|gb|EFD50037.1| tRNA pseudouridine synthase A [Micrococcus luteus SK58]
          Length = 297

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 83/263 (31%), Positives = 125/263 (47%), Gaps = 20/263 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW RQ    S+QG++E  +  +    V    AGRTD+GVHA  QV
Sbjct: 19  VRVRLDLAYDGGAFHGWARQPGLDSVQGALEDGLERILRRPVRTVVAGRTDAGVHARGQV 78

Query: 62  AHFDLVR-EWVPVI-----LCKALNAYLKISDTISILNLSIV-------DKQFHARFSAI 108
           AH DL   EW  +      L  A +   ++   +S    ++V          F ARFSA+
Sbjct: 79  AHLDLTETEWAGLTRGRPGLEPAASLTRRLGGVLSGWGGAVVVHGAGRAPAGFDARFSAL 138

Query: 109 RRSYLYRIITRQAPLALE---KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
            R Y YRI    AP A +   +G       +LD   M + A  ++G HDF +F      A
Sbjct: 139 WREYEYRID--DAPAARDPRTRGFTHWHGAALDDRLMALEADAVLGLHDFLSFCRPRAGA 196

Query: 166 SSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           ++ IR + H +V      ++ +R+ A +F H  +R+ VG+L  VG+G      L + +  
Sbjct: 197 TT-IREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVGEGAREPGWLARRVAR 255

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
             R     LAPP GL   +V Y 
Sbjct: 256 PARDSEVRLAPPGGLTLLAVGYP 278


>gi|24212680|sp|Q9X796|TRUA_MYCLE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 286

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/264 (30%), Positives = 127/264 (48%), Gaps = 27/264 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G +++A   V    V +  AGRTD+GVHA  QV
Sbjct: 11  VRLRLDIAYDGTDFAGWAVQAGQRTVAG-LDEAFTTVFRTPVRLRAAGRTDTGVHATGQV 69

Query: 62  AHFDLVREWV------------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+    +            P  L         +   + +L+++     F ARFSA+R
Sbjct: 70  AHVDIPGTALSKANPRSPHTGDPEFLPLLRRLSRLLPVDVRVLDIACAPVGFDARFSALR 129

Query: 110 RSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           R Y YR+ T  AP  ++  +A  +   P+ LD ++M  A++ L+G  DF  F   H   +
Sbjct: 130 RHYRYRLST--APYGVQPNQARYVTAWPRELDLDSMSAASRDLLGLRDFAVF-CRHRHGA 186

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKAL 222
           + IR +   + +  G LI   + A +F  + +RS +G+L  VGD +    W    L KA 
Sbjct: 187 TTIRELQRLEWSREGYLITAHITADAFCWSMVRSLIGALLAVGDHRRTIGWCGELLTKAS 246

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
           ++ D       AP  GL F  V+Y
Sbjct: 247 RSSDFTT----APAHGLTFIRVDY 266


>gi|115375174|ref|ZP_01462441.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
 gi|115367825|gb|EAU66793.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 221

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 68/200 (34%), Positives = 98/200 (49%), Gaps = 3/200 (1%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           AGRTDSGVHA  QV  FD  R+       + LN  L   + I+++    V   F  R  +
Sbjct: 4   AGRTDSGVHATGQVVCFDTERQLPLKAYHRGLNGLLP--EDIAVVRAEEVSAAFDPRRWS 61

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
             + Y YR+    +   L +   W I   L  E M  AA  L+GRHD++ FR+  CQA+ 
Sbjct: 62  RGKRYRYRVSNLPSRSPLRRHTHWEIYAPLQVEAMARAATSLLGRHDYSAFRASDCQAAH 121

Query: 168 PIRTIDHFDVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            +R +    V  + G+ +   V   +FL   +R+ VG+L  VG G+     + + L + D
Sbjct: 122 AVREVRRLSVEGTPGDAVAFVVEGTAFLKHMVRNLVGTLVEVGKGRRPEAWVAEVLASGD 181

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R   GP APP GL  + V Y
Sbjct: 182 RTLAGPTAPPHGLVLEEVFY 201


>gi|21673806|ref|NP_661871.1| tRNA pseudouridine synthase A [Chlorobium tepidum TLS]
 gi|42559829|sp|Q8KDR7|TRUA_CHLTE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21646936|gb|AAM72213.1| tRNA pseudouridine synthase A [Chlorobium tepidum TLS]
          Length = 247

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 109/242 (45%), Gaps = 5/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M IEY+G+GY GWQRQ     ++QG IE+ +  +  E V + GAGRTDSGVHA RQVA F
Sbjct: 10  MQIEYDGTGYSGWQRQPGDVVTVQGEIERVLERIMQEPVSIDGAGRTDSGVHARRQVASF 69

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     L  + N+ L    TI I  +    + FHARFSA  R Y Y ++  + P A
Sbjct: 70  ATCSPMPLGRLIYSANSLLP--STIRINAMRQAPESFHARFSATSREYRYFLL--EHPSA 125

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           ++   A       D   M   A  L+G HDF  F          + T+        G   
Sbjct: 126 IDSRFAGCSHGKPDVGAMNRLALMLIGTHDFAAFSKETPDQYGTLCTVTAARWYRSGRFH 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+ A  FL + +R  V  +  VG G+       + L++  R      A   GL+   V
Sbjct: 186 VFRIEANRFLRSMVRFLVAGMIEVGMGRLEEGAFARMLESGHRPPKLKPADAAGLFLWKV 245

Query: 245 EY 246
            Y
Sbjct: 246 RY 247


>gi|282860840|ref|ZP_06269906.1| tRNA pseudouridine synthase A [Streptomyces sp. ACTE]
 gi|282564576|gb|EFB70112.1| tRNA pseudouridine synthase A [Streptomyces sp. ACTE]
          Length = 284

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/253 (30%), Positives = 121/253 (47%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q    ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTGRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDL-VREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVAH DL V  W      L + +   L +   + I         F+ARFSA+ R Y YR+
Sbjct: 70  QVAHVDLPVEVWAEHREKLLRRMAGRLPLD--VRIWRAEEAPAGFNARFSALWRRYAYRV 127

Query: 117 ITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID-- 173
             R   +  L +G      + LD + M  AA  + G HDF  +     + ++ IRT+   
Sbjct: 128 GDRPGGVDPLTRGHVLWHDRPLDLDAMNEAAARMTGEHDFAAY-CKKREGATTIRTLQKL 186

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           H+  +    ++   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +
Sbjct: 187 HWVRDGESGVLTATVQADAFCHNMVRALIGAALFVGDGRRPAGWPAEVLAARVRDPAVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVAY 259


>gi|319654901|ref|ZP_08008976.1| tRNA pseudouridine synthase A [Bacillus sp. 2_A_57_CT2]
 gi|317393464|gb|EFV74227.1| tRNA pseudouridine synthase A [Bacillus sp. 2_A_57_CT2]
          Length = 269

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 115/229 (50%), Gaps = 9/229 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R+   I Y+G+ + G+Q Q    ++QG +E+A+  L  GE + V  +GRTD+GVHA  
Sbjct: 1   MQRFKCNITYDGTHFAGYQVQPGKRTVQGELERALKKLHKGEDIKVTASGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI-- 116
           QV HFD     +P+   + ALN+ L   D ++I+    V   FH RF A  + Y Y +  
Sbjct: 61  QVIHFDSPLN-IPIEKWEIALNSLL--PDEVAIVGAETVPDDFHVRFDAKGKEYRYFVHC 117

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +R+ P        +  P  L+ + ++ AA  L+G HDFT+F S   +    +R +   +
Sbjct: 118 SSRRDPFKRHYAYQYSYP--LNTDAIKQAAADLIGTHDFTSFCSAKTEVEDKVRELQEIE 175

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           V    +++  R     FL+  +R   G+L  VG G+     +   L+ +
Sbjct: 176 VQEKEDMLIFRFRGTGFLYNMVRILAGTLLEVGSGERDPDSMPSVLKEK 224


>gi|260906021|ref|ZP_05914343.1| pseudouridylate synthase I [Brevibacterium linens BL2]
          Length = 284

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 90/274 (32%), Positives = 130/274 (47%), Gaps = 38/274 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + + Y G+ + GW +Q    ++Q S+E  +  +TG  V    AGRTD+GVHA RQ
Sbjct: 1   MTRFRIDLGYRGTDFHGWAKQPGLRTVQDSLEAGLSRITGAEVATIVAGRTDAGVHARRQ 60

Query: 61  VAHFDLVREWVPVILCKA-----------LNAYLKISDT--ISILNLSIVDKQFHARFSA 107
           V H DL  E +  ++ K+           L   L + DT  I I  +S V + F ARFSA
Sbjct: 61  VVHIDLAEEGIEKLIGKSSRPAEAALLSRLRGVLTVDDTDDIVIHAVSEVPEDFDARFSA 120

Query: 108 IRRSYLYRIITRQA---PLALEKGRAWLIPK---SLDCENMRIAAQHLVGRHDFTTFRSI 161
           + R+Y YR+  R++   PL        + P+    LD E M  AA+   G HDF  F   
Sbjct: 121 LWRTYQYRLADRRSFIDPLLTP-----VTPRHKGELDAEAMAEAAREAQGLHDFIPF--- 172

Query: 162 HC---QASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
            C   + ++ IRT+   +V      +I I + A +F H  +R+ VG L  VG G W  T 
Sbjct: 173 -CKPREGATTIRTLHELEVTRDQEAVITIDLRADAFCHHMVRALVGGLIKVGSGTWPVTR 231

Query: 218 LEKALQAQDRKECGP-----LAPPEGLYFDSVEY 246
             + L   D     P     ++P  GL    V Y
Sbjct: 232 PAELLTEAD-SGVDPDVPMFVSPAHGLVLTGVGY 264


>gi|153824082|ref|ZP_01976749.1| tRNA pseudouridine synthase A [Vibrio cholerae B33]
 gi|126518399|gb|EAZ75622.1| tRNA pseudouridine synthase A [Vibrio cholerae B33]
          Length = 205

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 67/187 (35%), Positives = 94/187 (50%), Gaps = 4/187 (2%)

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           + HFD   E   V      NA   +   I++     V  +FHARFSA  R Y Y I    
Sbjct: 1   MVHFDTTAERQMVAWTMGANA--NLPKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHV 58

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V  
Sbjct: 59  YRPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTR 117

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGL
Sbjct: 118 HGRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGL 177

Query: 240 YFDSVEY 246
           Y  SV+Y
Sbjct: 178 YLVSVDY 184


>gi|194208171|ref|XP_001496445.2| PREDICTED: similar to LOC617640 protein [Equus caballus]
          Length = 389

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 123/246 (50%), Gaps = 29/246 (11%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR-----EWVPVILCKALN 80
           S Q + E+   +V  ++ +   + RTD+GVHAL   AH D+ R      + P +L KALN
Sbjct: 128 SPQEAAERLNSVVPVKLTI---SSRTDAGVHALSNAAHLDVQRRSGQPPFSPEVLAKALN 184

Query: 81  AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-QAPLAL---EKGRAW-LIPK 135
            +L+    I +L    V   FHAR+SA  R+YLYR+ T    P  L   E+ R W L   
Sbjct: 185 THLR-HPAIRVLQAFRVPSDFHARYSATSRTYLYRLATGCPQPDQLSVFEQNRCWALRAD 243

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-----NSFGNLIEIRVV- 189
           SLD   M  AAQHL+G HDF+ F+S     +S +RT+    V     + F    E R + 
Sbjct: 244 SLDVAAMEEAAQHLLGTHDFSAFQSAGSPTTSSVRTLRRASVSPDLPSPFVLPQESRRLR 303

Query: 190 -------ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLY 240
                  ++SFL+ Q+R     L  VG G  T   ++  L+++D   +    +AP  GL+
Sbjct: 304 FWSLEFESQSFLYRQVRRMTAVLVAVGLGALTPAQVKMILESRDPLGRHQTRVAPAHGLF 363

Query: 241 FDSVEY 246
             SV Y
Sbjct: 364 LKSVLY 369


>gi|153807552|ref|ZP_01960220.1| hypothetical protein BACCAC_01832 [Bacteroides caccae ATCC 43185]
 gi|149129914|gb|EDM21126.1| hypothetical protein BACCAC_01832 [Bacteroides caccae ATCC 43185]
          Length = 220

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/211 (36%), Positives = 105/211 (49%), Gaps = 12/211 (5%)

Query: 41  EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
           EI VV GAGRTD+GVHA   VAHFD       V + + LN  L     IS+  +  V  +
Sbjct: 11  EIEVV-GAGRTDAGVHASLMVAHFDYDGLLDTVSVAEKLNRLLPPD--ISVYRVCRVKPE 67

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
            HARF A  R+Y Y +   + P    +   W I  SLD E M  AA+ L    DFT+F  
Sbjct: 68  AHARFDATARTYKYYVTAVKYPF--NRQYRWRIYSSLDYERMNEAARTLFEYSDFTSFSK 125

Query: 161 IHCQASSPIRTIDHFDVNSFGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +H    + I  I H +     +     +  IR  A  FL   +R+ VG+L  VG GK + 
Sbjct: 126 LHTDVKTNICHITHAEWTKVTDDEATWVFTIR--ADRFLRNMVRAIVGTLIEVGRGKLSV 183

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            D  + ++ QDR + G  AP + L+  +VEY
Sbjct: 184 EDFRRIIEQQDRCKAGTSAPGQALFLVNVEY 214


>gi|294621109|ref|ZP_06700300.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|291599345|gb|EFF30371.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
          Length = 165

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 56/159 (35%), Positives = 91/159 (57%), Gaps = 3/159 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           +      +  A   P  LD E ++ A   L+G HDFT+F
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSF 157


>gi|325191328|emb|CCA26111.1| tRNA pseudouridine synthase A putative [Albugo laibachii Nc14]
          Length = 289

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/262 (32%), Positives = 131/262 (50%), Gaps = 23/262 (8%)

Query: 7   IIEYNGSGYFGWQRQ-KNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           II Y+G+ Y G+Q Q K G+ ++Q +IE AIF  TGE V +    RTD GVHA  QV  F
Sbjct: 30  IIAYDGTDYNGFQAQGKEGTITLQEAIEDAIFRTTGEAVRIRACSRTDRGVHARGQVIVF 89

Query: 65  DLVREWVPVILCKALNAYLKISDTISILN---LSIVDKQFHARFSAIRRSYLYRIITRQA 121
           D +       L  ALN+  ++ D I+ L    LSI   +   R  +I + Y YRI++   
Sbjct: 90  DTLCTADAEKLRDALNS--RLDDAIACLQVVPLSISSDRMDPRKLSIGKEYEYRIVSGGV 147

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRH--DFTTF---RSIHCQASSPIRTIDHFD 176
               E+ + W + + +D ++M+ AAQ L  R   D+ +F   R    + +    T+   D
Sbjct: 148 RPVHERFQVWFVRQLVDIKSMKQAAQLLFHREKRDYASFSGERDDAKEGTDTFCTLHALD 207

Query: 177 V-----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           +           +   + I IR+    FL+  +R+ VG+L  VG GK  +  +   L A+
Sbjct: 208 ITMDQPRQEVMNHGQQSCIRIRMSGDRFLYKMVRNIVGTLVDVGLGKIDALSIPDILLAR 267

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           DR++ G  AP +GL    V +S
Sbjct: 268 DRRQAGQGAPAKGLTLVRVYFS 289


>gi|148238745|ref|YP_001224132.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7803]
 gi|147847284|emb|CAK22835.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7803]
          Length = 297

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 116/244 (47%), Gaps = 14/244 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y GS + GWQRQ+ G+S+QG +E+AI  L     V    AGRTD+GVHA  QV
Sbjct: 23  RIAISLQYAGSFFCGWQRQRQGTSVQGVLEQAIADLDPHRPVHAVAAGRTDAGVHAAGQV 82

Query: 62  AHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD         W P     ALN  L  S  I +         +HA +SA  R Y Y +
Sbjct: 83  VHFDSSGPIPASRWAP-----ALNGRLPAS--IRVREAVERPLSWHACYSATYRRYRYTL 135

Query: 117 ITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              + P        W      LD + M  A + ++G HDF  F+    + +    TI   
Sbjct: 136 YNGRRPNLFLAPWTWHRYQARLDEQAMAAALEGMLGSHDFAAFQRAGSRRAHSRTTIQDV 195

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G+LI++ V A  FL+  +R  +G L  VG+ + T    E+  + + R E    AP
Sbjct: 196 SVQRRGDLIDLEVQASGFLYGMVRLMMGQLVAVGEHRLTPDQFERRWRERRRDEVKDGAP 255

Query: 236 PEGL 239
           P+GL
Sbjct: 256 PQGL 259


>gi|311115139|ref|YP_003986360.1| tRNA-pseudouridine synthase I [Gardnerella vaginalis ATCC 14019]
 gi|310946633|gb|ADP39337.1| tRNA-pseudouridine synthase I [Gardnerella vaginalis ATCC 14019]
          Length = 310

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 94/300 (31%), Positives = 137/300 (45%), Gaps = 68/300 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG-----------AGR 50
           +R  + + Y+G  ++GW RQ N  ++QG++E A++    +++ VH            AGR
Sbjct: 1   MRLRLDLAYDGGDFYGWARQPNLRTVQGTLEDALY----KVLRVHDGDSCFPLRLTVAGR 56

Query: 51  TDSGVHALRQVAHFDLVRE----------WVPVILCKALNAYLK--ISDTISILNLSIVD 98
           TD+GVHA  QV H D+  +            PV   KAL   L+  +   ISI ++SI  
Sbjct: 57  TDTGVHASYQVCHLDVEDDILQNCVGHTNLTPV---KALEYRLRGVLPKDISIHSVSIAP 113

Query: 99  KQFHARFSAIRRSYLYRI---ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
             F ARFSA+ R+Y+YRI     R+      +G    I   LD  +M  AAQ +VG HDF
Sbjct: 114 SGFDARFSALDRTYVYRISDAANRENLDPRMRGFVLQIDYDLDVNSMNQAAQMIVGLHDF 173

Query: 156 TTF-------RSIHC-----------QASSPIRTIDHFDVNSFGN-------LIEIRVVA 190
            +F        +I C              +P+ +       S GN       LIE  +VA
Sbjct: 174 GSFARPNPGGTTIRCVKKAVWNRVCLDGCAPVGS--SIASRSTGNIPPIEHGLIEFTIVA 231

Query: 191 RSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +F H  +RS V +   VG GK    W    +E  ++       GP+A   GL  + VEY
Sbjct: 232 DAFAHNMVRSLVQACVQVGCGKRSVDWFKDKIENPIR---EGSTGPIA-SNGLTLEYVEY 287


>gi|159469598|ref|XP_001692950.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158277752|gb|EDP03519.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 239

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 112/239 (46%), Gaps = 16/239 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHAL 58
           + Y +I+ Y+G+ Y GWQ Q    ++Q  +E A+  V  E   ++ V  AGRTDSGVHA 
Sbjct: 3   LSYRLILAYDGTDYCGWQLQPAAPTVQAKLEAALGTVLREDRGVLGVRAAGRTDSGVHAR 62

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV      R  +PV  L   LNA L     I ++ +      F    S I ++Y Y I 
Sbjct: 63  GQVRTGLTGRGGLPVDKLAYKLNAVL--PPDIRVMGVRRTAPDFSVTCSPIGKTYHYNIT 120

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-----SPIRTI 172
             +A   L    A+ + K LD   MR AA  LVG HDFT F +I  +       +P++T+
Sbjct: 121 NSEAHDPLRHRYAYHVRKPLDLAGMRAAAALLVGTHDFTQFSNIGEEGGRPRKRNPVKTL 180

Query: 173 DHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
              DV      +F   + I V    FL+  +R   G L  VG+ K     + + L+  D
Sbjct: 181 RRMDVVELDPAAFPGGVRIEVEGNGFLYKMVRHISGVLVAVGERKLPPGIVSEMLEVGD 239


>gi|87124988|ref|ZP_01080835.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9917]
 gi|86167308|gb|EAQ68568.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9917]
          Length = 274

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 113/239 (47%), Gaps = 14/239 (5%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           ++Y GS + GWQRQ+ G+S+QG +EKAI  L     V    AGRTD+GVHA  QV HFD 
Sbjct: 1   MQYEGSSFCGWQRQRQGTSVQGELEKAIAALDPHRPVQAVAAGRTDAGVHAAGQVVHFDC 60

Query: 67  -----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                 + W P     ALN   ++  TI +         +HA  SA  R Y Y I   + 
Sbjct: 61  CGPIPAQRWAP-----ALNG--RLPGTIRVREAVERPLHWHACHSASYRRYRYTIYNGRR 113

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P       +W      LD + MR     L+G HDF+ F     + +    T+    +   
Sbjct: 114 PNLFLAPWSWHRYHCRLDEDAMRRGLDGLIGSHDFSAFMRAGSRRAHARTTVQDVSLERQ 173

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G+++ + + A  FL+  +R   G L  VG+ +      E+  + + R+E    APP+GL
Sbjct: 174 GDVLILEIQASGFLYGMVRLLTGQLVAVGEHRLHPQAFEQRWRQRRRQEVKEAAPPQGL 232


>gi|118462566|ref|YP_883531.1| tRNA pseudouridine synthase A [Mycobacterium avium 104]
 gi|254776828|ref|ZP_05218344.1| tRNA pseudouridine synthase A [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|118163853|gb|ABK64750.1| tRNA pseudouridine synthase A [Mycobacterium avium 104]
          Length = 251

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 118/237 (49%), Gaps = 22/237 (9%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI------------ 74
           + G +++A+  V    V +  AGRTD+GVHA  QVAH D+    +P              
Sbjct: 1   MAGVLDEALTTVFRTPVRLRAAGRTDAGVHATGQVAHLDVPGTALPNAYPRAPHVGEAEF 60

Query: 75  --LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR--- 129
             L + L  +L     + +++++     F ARFSA+RR Y+YR+ T    +  ++ R   
Sbjct: 61  GPLLRRLGRFLPTD--VRVVDITRAPAGFDARFSALRRHYVYRLSTAPWGVLPQQARYVT 118

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           AW  P+ LD E M  A++ L+G HDF  F   H + ++ IR +   D    G+LI  RV 
Sbjct: 119 AW--PRPLDVEAMAAASRDLLGLHDFAAF-CRHRENATTIRDLQRLDWTRDGDLIIARVS 175

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           A +F  + +RS VG+L  VG+ +   +   + L A +R      AP  GL    V+Y
Sbjct: 176 ADAFCWSMVRSLVGALLAVGENRRPVSWCRELLSATNRSSDYATAPAHGLTLVGVDY 232


>gi|302543331|ref|ZP_07295673.1| tRNA pseudouridine synthase A [Streptomyces hygroscopicus ATCC
           53653]
 gi|302460949|gb|EFL24042.1| tRNA pseudouridine synthase A [Streptomyces himastatinicus ATCC
           53653]
          Length = 283

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 79/251 (31%), Positives = 117/251 (46%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
            +R  + + Y+G  + GW +Q+   ++QG +E A+  VT   E   +  AGRTD+GVHA 
Sbjct: 9   FVRVRLDLSYDGKDFSGWAKQRERRTVQGELESALGTVTRSSETPDLTVAGRTDAGVHAR 68

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL  E       K L     ++   + +  ++     F+ARFSAI R Y YR++
Sbjct: 69  GQVAHVDLPEELWAEHRDKLLRRLAGRLPHDVRVWRVAAAPPGFNARFSAIWRRYAYRVV 128

Query: 118 TRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                +  L +G        LD + M  A+  L+G HDF  +      A++ IRT+    
Sbjct: 129 DHPGGVDPLLRGHVLWHDWPLDVDAMNAASAPLLGEHDFAAYCKRRDGATT-IRTLQKLS 187

Query: 177 VNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                + +I   V A +F H  +RS VG+L   GDG        K L A  R     +  
Sbjct: 188 WERGADGVITATVRADAFCHNMVRSLVGALLFTGDGHRPVDWPGKVLAAGVRDSAVHVVR 247

Query: 236 PEGLYFDSVEY 246
           P GL  + V Y
Sbjct: 248 PHGLTLEEVGY 258


>gi|227549870|ref|ZP_03979919.1| tRNA-pseudouridine synthase I [Corynebacterium lipophiloflavum DSM
           44291]
 gi|227078125|gb|EEI16088.1| tRNA-pseudouridine synthase I [Corynebacterium lipophiloflavum DSM
           44291]
          Length = 285

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/266 (31%), Positives = 122/266 (45%), Gaps = 25/266 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           +R  + I Y+G+ + GW RQ+   +G+   ++Q +I+ A+  V    V +  AGRTD+GV
Sbjct: 6   LRLRLDIAYDGTDFHGWARQREQPDGTPTRTVQQTIQSALSTVLRTPVELTVAGRTDAGV 65

Query: 56  HALRQVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           HA  QVAH D+    +        P  L + L   L     + +  +S V   F ARFSA
Sbjct: 66  HASGQVAHADIPAASLDQRSIDGDPARLVRRLAKLLPAD--VRVYGVSAVSPLFDARFSA 123

Query: 108 IRRSYLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           + RSY+YR+ T  A   P        W  P  +D   M++AA   VG HDF  F      
Sbjct: 124 LTRSYVYRVTTHPAGALPTRARDTAVWRRP--VDIGAMQVAADAFVGLHDFAAFCRAKPH 181

Query: 165 ASSPIRTID----HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           A++  + ++            NL E  V A +F    +RS V +   VG+G    T +E 
Sbjct: 182 ATTVRKVVEMRWVEASTGEEPNLYEAHVTADAFCWNMVRSLVAACLQVGEGSKDPTWVEP 241

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEY 246
            L    R     LAP +GL    V Y
Sbjct: 242 LLGETTRHPHVLLAPAKGLTLVDVSY 267


>gi|29831498|ref|NP_826132.1| tRNA pseudouridine synthase A [Streptomyces avermitilis MA-4680]
 gi|38258718|sp|Q82DM1|TRUA_STRAW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|29608614|dbj|BAC72667.1| putative pseudouridine synthase [Streptomyces avermitilis MA-4680]
          Length = 285

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 85/255 (33%), Positives = 121/255 (47%), Gaps = 12/255 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVV-VHGAGRTDSGVH 56
            +R  + + Y+G+ + GW +Q  G  ++QG IE A+  VT  GE    +  AGRTD+GVH
Sbjct: 9   FVRVRLDLSYDGTEFSGWAKQAAGRRTVQGEIEDALRTVTRSGETTYELTVAGRTDAGVH 68

Query: 57  ALRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           A  QVAH DL  E W      L K L    ++   + + +L+     F+ARFSAI R Y 
Sbjct: 69  ARGQVAHVDLPGELWAEHQEKLLKRLAG--RLPKDVRVWSLTEAPSGFNARFSAIWRRYA 126

Query: 114 YRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+      +  L +         LD + M  AA+ LVG HDF  +     + ++ IRT+
Sbjct: 127 YRVTDNTGGVDPLLRSHVLWHDWPLDVDAMNEAARRLVGEHDFAAYCKKR-EGATTIRTL 185

Query: 173 DHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                V     +I   V A +F H  +RS +G+L  VGDG        K L    R    
Sbjct: 186 QELSLVRGDDGVITATVCADAFCHNMVRSLIGALLFVGDGHRGPDWPGKVLAVGVRDSAV 245

Query: 232 PLAPPEGLYFDSVEY 246
            +  P GL  + V Y
Sbjct: 246 HVVRPHGLTLEEVGY 260


>gi|297666734|ref|XP_002811665.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Pongo abelii]
          Length = 287

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 85/261 (32%), Positives = 120/261 (45%), Gaps = 35/261 (13%)

Query: 14  GYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR----- 68
           G     R   GS +Q + E+   L + E V    + RTD+GVHAL   AH D+ R     
Sbjct: 15  GPASLTRPPRGSVLQEAAER---LNSVEPVRFTISSRTDAGVHALSNAAHLDVQRRSGRP 71

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT----RQAPLA 124
            + P +L + LN +L+    I +L    V   FHAR +A  R YLYR+ T    R     
Sbjct: 72  PFPPEVLAEVLNRHLR-HPAIRVLRAFRVPSDFHARHAATSRIYLYRLATGCHRRDELPV 130

Query: 125 LEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS---- 179
            E+   W +P   LD   ++ AAQHL+G HDF+ F+S      SP+RT+    V+     
Sbjct: 131 FERNLCWALPADCLDVVAVQEAAQHLLGTHDFSAFQSTGSPVPSPVRTMRRVSVSPGQAS 190

Query: 180 ------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                       F NL      ++SFL+ Q+R     L  VG G      ++  L++QD 
Sbjct: 191 PLVTPEESRKLRFWNL---EFESQSFLYRQVRRMTAVLVAVGLGALAPAQVKTILESQDP 247

Query: 228 --KECGPLAPPEGLYFDSVEY 246
             K    +AP  GL+  SV Y
Sbjct: 248 LGKHQTRVAPAHGLFLKSVLY 268


>gi|195436014|ref|XP_002065973.1| GK25867, isoform B [Drosophila willistoni]
 gi|194162058|gb|EDW76959.1| GK25867, isoform B [Drosophila willistoni]
          Length = 313

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 97/303 (32%), Positives = 134/303 (44%), Gaps = 58/303 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLDQPRLDTNSVQGCLELALRVFRPTNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVR----EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTIHVDLERYDGQPYALTTLTGVLNRTLGKQRLPIRVLSTELVPDTFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPL----ALEKGRAWLIP------------KSLDCENMRIAAQH 148
            AI R+YLYR  + R +P+       +G    IP             S D E +R AA+ 
Sbjct: 120 HAIGRTYLYRFAVARNSPVDDGKLKNRGYEAFIPVEELDRCYFLQAASFDIERVRSAARL 179

Query: 149 LVGRHDFTTFRSIHCQASSP-------IRTIDHFDV--------NSFGNLI-------EI 186
            +G HDF TF S+  Q           +R ID  ++        N+   L        EI
Sbjct: 180 FLGIHDFRTFMSVSRQKGPSRDHPMFTVRKIDEINIRPGHSLALNAHAKLANETYDHWEI 239

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDS 243
            + A+SFL+ Q+R  VG+L  +G GK     + + L    +    P   LAP  GLY   
Sbjct: 240 EIKAKSFLYKQVRRIVGTLLALGTGKIDEKCIYQMLTIPSKNSWEPRILLAPACGLYLCQ 299

Query: 244 VEY 246
           V Y
Sbjct: 300 VHY 302


>gi|87300888|ref|ZP_01083730.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 5701]
 gi|87284759|gb|EAQ76711.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 5701]
          Length = 316

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 114/246 (46%), Gaps = 4/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y GS + GWQRQ +  S+Q ++E+A+  L     +    AGRTDSGVHA  QV
Sbjct: 12  RIALCLQYEGSSFCGWQRQPHQPSVQETLERALATLDPHRPIRAMAAGRTDSGVHAAGQV 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+            ALN  L  S  I +   + V   +HA FSA  R Y Y +   + 
Sbjct: 72  VHFEASGPIPSERWAAALNGRLPAS--IRVRAAAAVPSTWHACFSACYRRYRYTLYNGRR 129

Query: 122 PLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P       +W    + L+   M  A + L+G HDF+ F+    +       +    +   
Sbjct: 130 PNLFLSPWSWHRYRQRLNERAMATALRGLLGFHDFSAFQRAGSRRPHARTKVQAVSLERH 189

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ + + A  FL+  +R  +G L  VG+G+ +    E+  + + R E    AP  GL 
Sbjct: 190 GDLVVVEIQASGFLYGMVRLIMGQLVAVGEGQLSLAGFERRWRQRARSEVKEAAPAHGLC 249

Query: 241 FDSVEY 246
              V Y
Sbjct: 250 LLRVGY 255


>gi|315230173|ref|YP_004070609.1| tRNA pseudouridine synthase A [Thermococcus barophilus MP]
 gi|315183201|gb|ADT83386.1| tRNA pseudouridine synthase A [Thermococcus barophilus MP]
          Length = 266

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 121/250 (48%), Gaps = 27/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVHGAGRTDSGVHA 57
           +R  + I Y+GS ++G+QRQ    +++G I    +K   + + E     GA RTD GV A
Sbjct: 1   MRIALKIAYDGSKFYGFQRQPGLRTVEGEIIRVLQKLDVIESPENANFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L  V  F+   E   +   + LN +L+    I +L ++ V   FH RF A  + Y Y   
Sbjct: 61  LGNVIAFNT--ENPKLAQPRVLNHHLR---DIWVLGVAQVSDDFHPRFWAKSKIYRY--- 112

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +L+ +  D   M+  A+  VG HDF+ F  +  +   PIR ++  ++
Sbjct: 113 -------------YLVDEGFDVNAMKECARLFVGTHDFSAFARVE-KFKDPIREVNRLEI 158

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+LI I +  +SFL   +R  V +LKL G G   + D+ K L+ +  K+  P +PPE
Sbjct: 159 IPRGDLIIIEIEGKSFLWEMVRRIVTALKLCGFGIVETEDIRKMLEGRTDKKLPP-SPPE 217

Query: 238 GLYFDSVEYS 247
            L    ++Y 
Sbjct: 218 NLVLWEIKYE 227


>gi|302536280|ref|ZP_07288622.1| tRNA pseudouridine synthase A [Streptomyces sp. C]
 gi|302445175|gb|EFL16991.1| tRNA pseudouridine synthase A [Streptomyces sp. C]
          Length = 287

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/252 (32%), Positives = 121/252 (48%), Gaps = 10/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q+   ++QG +E A+  V    E V +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQRTLRTVQGELESALQTVMRLKEPVELTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVA FDL  E W      L + L    ++   I +   +   + F+ARFSAI R Y YR+
Sbjct: 70  QVAQFDLAEEVWAEHHDKLLRRLAG--RLPHDIRVWKAAEAPEGFNARFSAIWRRYAYRV 127

Query: 117 ITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              +A +  L +G        LD + M  AA  LVG HDF  +     + ++ IRT+   
Sbjct: 128 GDHRAGVDPLRRGHVLWHQWPLDVDAMNEAAAALVGEHDFAAY-CKKREGATTIRTLQQL 186

Query: 176 DVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                 + ++   V A +F H  +RS VG+L  VGDG        + L A  R     + 
Sbjct: 187 SWERGEDGVVTATVRADAFCHNMVRSLVGALLHVGDGHRPVEWPGQVLAAAVRDSSVHVV 246

Query: 235 PPEGLYFDSVEY 246
            P GL  + V Y
Sbjct: 247 KPHGLTLEEVGY 258


>gi|333026542|ref|ZP_08454606.1| putative tRNA pseudouridine synthase A [Streptomyces sp. Tu6071]
 gi|332746394|gb|EGJ76835.1| putative tRNA pseudouridine synthase A [Streptomyces sp. Tu6071]
          Length = 284

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/256 (32%), Positives = 126/256 (49%), Gaps = 17/256 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG-----EIVVVHGAGRTDSGV 55
           +R  + + Y+G+ + GW RQ  G  ++Q ++E+A+ +VT      E+ V   AGRTD+GV
Sbjct: 1   MRLRLDLSYDGTDFHGWARQPGGRRTVQETLEEALRVVTRAPAPYELTV---AGRTDAGV 57

Query: 56  HALRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           HA  QVAH  +  E W      L K L    ++   + +  ++   + F ARFSAI R Y
Sbjct: 58  HARGQVAHVGMADEVWAEHGEKLLKRLAG--RLPKDVRVWRVAPAPEGFEARFSAIWRRY 115

Query: 113 LYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
            YR+  +   +  L +G      + LD + M  AA+ L+G HDF  +     + ++ IR 
Sbjct: 116 AYRVADQAGGVDPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAY-CKKREGATTIRE 174

Query: 172 IDH-FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +   F       ++E  V A +F H  +RS VG+L  VGDG    +   K L A  R   
Sbjct: 175 MQQLFWTRRADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSA 234

Query: 231 GPLAPPEGLYFDSVEY 246
             +  P GL  + V Y
Sbjct: 235 VHVVRPVGLTLEEVGY 250


>gi|167758957|ref|ZP_02431084.1| hypothetical protein CLOSCI_01303 [Clostridium scindens ATCC 35704]
 gi|167663364|gb|EDS07494.1| hypothetical protein CLOSCI_01303 [Clostridium scindens ATCC 35704]
          Length = 245

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 126/247 (51%), Gaps = 13/247 (5%)

Query: 6   MIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQV 61
           + IEY+GS Y GW R   +++ +++   I + +  ++GE ++    G RT+ GVHA  Q+
Sbjct: 6   LTIEYDGSRYQGWTRLGKEESNNTVSNKIIEVLRKMSGEYLIELNCGCRTEVGVHAYAQI 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F    +   + +   LN YL +   I+I  +  V ++FHA+ +A  ++Y+YR+     
Sbjct: 66  ANFKTESKMDVLEIKHYLNRYLPMD--IAITEVEEVPERFHAQLNAASKTYVYRMTIDDV 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   ++   +   K  D   M+ AA  L+G HDF  F S   ++ S  R I  F++  +G
Sbjct: 124 PSVFDRKYTYHCFKIPDKRVMQQAAMLLIGTHDFKNF-STAKKSKSTERQI--FEIEVYG 180

Query: 182 NLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           +  E++++  A  FLH   R  +G+L  +G G     D+E+      R+       P+GL
Sbjct: 181 DTEEMQILIHADDFLHNMARLIIGTLMDIGFGTRRKEDIEEIFAG--RQLASAPCDPKGL 238

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 239 YLQEVAY 245


>gi|197122727|ref|YP_002134678.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
 gi|196172576|gb|ACG73549.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
          Length = 272

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 82/257 (31%), Positives = 124/257 (48%), Gaps = 20/257 (7%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + + Y+G  + G+QRQ    ++Q ++E+A+  + G    +H A RTD+GVHAL QV  
Sbjct: 6   YALRLAYDGGRFRGFQRQPGLPTVQQALEEALERL-GLRAQLHVAARTDAGVHALAQVVS 64

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P  L + LN  L   + I +L+ + V   FHAR SAI R+Y+Y ++    P 
Sbjct: 65  FSARAALDPAALRRGLNEGL--PEGILVLDAARVGPSFHARGSAIARTYVY-LVGAPPPE 121

Query: 124 ALEKGRAWLIPKS-----------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            L +  AW +P +           LD   MR A  H VG HDF  F     Q  + +RT+
Sbjct: 122 GL-RPYAWTLPDARAFPDLAEVPPLDAAAMREALGHAVGEHDFVGFARPGEQRGT-VRTL 179

Query: 173 DHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              +V   G   L+ + +  + FL   +R+ VG+    G G+    D+ + L A   +  
Sbjct: 180 LRAEVIEAGWAPLVAVVLEGKGFLRAMVRNLVGTAVAAGLGR-APPDVIRTLLATRGRYR 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           G  AP  GL   +V Y 
Sbjct: 239 GVRAPGWGLTLAAVRYP 255


>gi|326671566|ref|XP_683563.5| PREDICTED: tRNA pseudouridine synthase-like 1-like [Danio rerio]
          Length = 291

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 89/274 (32%), Positives = 134/274 (48%), Gaps = 32/274 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQG---SIEKAIF-LVTGEIVVVHGAGRTDSGVHAL 58
           RY +  +Y GS Y G  +     ++QG    +E A+  L     V V  + RTD+GVHAL
Sbjct: 7   RYLIFFQYTGSKYSGVMKAPAHQAVQGVGNHLENAVRKLKPVNEVCVSISSRTDTGVHAL 66

Query: 59  RQVAHFDLVR--EWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R  +  P+    L +ALN  LK  + I I     V   FHAR+ A  R+Y+
Sbjct: 67  CNSAHVDIQRRADKPPLSEQSLLEALNFQLK-EEPIRITRAYRVHSDFHARYQAQSRTYV 125

Query: 114 YRIIT-----RQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQA-- 165
           YR+          PL  EK   W +  + L+ + MR A+  L+G HDF+TFR++   A  
Sbjct: 126 YRLALGCQHHTLMPLT-EKDLCWALRDTRLNIDAMREASALLLGTHDFSTFRALSSDAPF 184

Query: 166 SSPIRTID--------HFDVNSFGNLI---EIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             P++T+D         F    F   I   E+   +RSFL+ Q+R   G L  +G G+ +
Sbjct: 185 KCPVKTLDLAQLEPGESFSQRHFQRDIQFWELTFKSRSFLYRQVRRMTGVLVAIGQGRLS 244

Query: 215 STDLEKALQAQDRK--ECGPLAPPEGLYFDSVEY 246
            + ++  L+A+D         AP  GL+  +V+Y
Sbjct: 245 VSKIQDLLEARDSLAFPNNLTAPAHGLFLTNVQY 278


>gi|239943606|ref|ZP_04695543.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 15998]
 gi|239990059|ref|ZP_04710723.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 11379]
 gi|291447073|ref|ZP_06586463.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 15998]
 gi|291350020|gb|EFE76924.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 15998]
          Length = 284

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 77/253 (30%), Positives = 123/253 (48%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVRE-WV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVAH DL    W      L + L   L +   + +   +     F+ARFSA+ R Y YR+
Sbjct: 70  QVAHVDLPEAVWAEHEEKLLRRLAGRLPLD--VRVWRAAPAPAGFNARFSALWRRYAYRV 127

Query: 117 ITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
             R   +  L +G      + LD ++M  AA  +VG HDF  +     + ++ IRT+   
Sbjct: 128 GDRPGGVDPLTRGHVLWHDRPLDLDSMNEAAALMVGEHDFAAY-CKKREGATTIRTLQKL 186

Query: 176 D--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
               +    ++   V A +F H  +R+ +G+   VGDG+  ++   + L A+ R     +
Sbjct: 187 SWVRDEESGVLTATVQADAFCHNMVRALIGAALFVGDGRRPASWPAEVLAAKVRDPGVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVAY 259


>gi|33864024|ref|NP_895584.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9313]
 gi|42559756|sp|Q7TUP1|TRUA_PROMM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33635608|emb|CAE21932.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9313]
          Length = 295

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 112/244 (45%), Gaps = 14/244 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y GS + GWQRQ    S+Q  +E AI  L     +    AGRTD+GVHA  QV
Sbjct: 17  RIGLSVQYEGSNFCGWQRQPQAVSVQQVLEDAISQLDPQRPIQAVAAGRTDAGVHAAGQV 76

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD         W P     ALN   ++  TI +         +HA  SAI R Y Y I
Sbjct: 77  VHFDCCGPIPAERWAP-----ALNG--RLPSTIRVREAVARPASWHACHSAIYRRYRYTI 129

Query: 117 ITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              + P       +W      LD   M+IA + L+G  DF+ F+    + +    TI   
Sbjct: 130 YNGRRPNLFLTPWSWHRYQVRLDETMMQIALEGLLGLQDFSAFQRTGSRRAHARTTIQEV 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   G+LI I + A  FL+  +R  +G L  +G+ +      E+  + + R+E    AP
Sbjct: 190 KIERQGDLIMIEIQASGFLYGMVRLLMGQLVALGEHRLNLETFERRWKEKRRQEVKEAAP 249

Query: 236 PEGL 239
            +GL
Sbjct: 250 AQGL 253


>gi|290999771|ref|XP_002682453.1| predicted protein [Naegleria gruberi]
 gi|284096080|gb|EFC49709.1| predicted protein [Naegleria gruberi]
          Length = 377

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 99/310 (31%), Positives = 140/310 (45%), Gaps = 73/310 (23%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-----GSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGV 55
           RY +I +Y G+ Y G+Q+Q N     G++IQ  IE ++     T +I +V G+ RTDSGV
Sbjct: 58  RYKLIFQYRGNNYDGYQKQNNKGEPRGNTIQKHIEGSLHKLFNTNDIYIV-GSSRTDSGV 116

Query: 56  HALRQVAHFDLVRE-------WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           HAL    HFD+  E       +    +   LN YLK  D I I +    D  FHAR    
Sbjct: 117 HALHNTCHFDVASEIIEKRENYTAKNVIFGLNFYLKDED-IVICSCEKKDMNFHARHRVK 175

Query: 109 RRSYLYRI-ITRQAP-LALE----KGRAWLI---------PK----SLD---------CE 140
            R Y YR+ +T   P LA +    + + W++         P     SLD          +
Sbjct: 176 EREYQYRVLLTGPKPDLAYKVPFIQDQYWIVNGAKYEQGGPTKQEISLDFRSLETYFRID 235

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQASSPIR----------TIDHFDVN----------SF 180
           ++R A Q+ +G H+F  F    C++  P R          T++  D+           S 
Sbjct: 236 DVREACQYFIGTHNFNNF----CKSDLPERVSRIKTINSVTVEEIDLQQDQTISPLFFST 291

Query: 181 GNLIEIRVVAR--SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK--ECGPLAPP 236
               EIR   R  SFLH Q+R  V +L  VG GK   T L   +Q  + +  E G  APP
Sbjct: 292 SKCKEIRFTIRGNSFLHNQVRIMVDALVKVGIGKMNPTYLRALVQNPNMRYPEKGS-APP 350

Query: 237 EGLYFDSVEY 246
            GL+  +V Y
Sbjct: 351 HGLFLTNVVY 360


>gi|73956519|ref|XP_546716.2| PREDICTED: similar to pseudouridylate synthase-like 1 [Canis
           familiaris]
          Length = 294

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 78/226 (34%), Positives = 114/226 (50%), Gaps = 31/226 (13%)

Query: 48  AGRTDSGVHALRQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFH 102
           + RTD+GVHAL   AH D+ R      + P +L +ALNA+++    I +L    V   FH
Sbjct: 60  SSRTDAGVHALSNAAHLDVQRRSGQPPFSPEVLAEALNAHVR-HPAIRVLQAFRVPSDFH 118

Query: 103 ARFSAIRRSYLYRIIT---RQAPLAL-EKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTT 157
           AR +A  R+YLYR++T   R   L++ E+ R W L    LD + M+ AAQHL+G HDF  
Sbjct: 119 ARHAATSRTYLYRLVTGCHRPDQLSVFERNRCWPLRADCLDVDAMQEAAQHLLGTHDFRA 178

Query: 158 FRSIHCQASSPIRTIDHFDVNS---------------FGNLIEIRVVARSFLHTQIRSFV 202
           F+S     +S +RT+    V+                F NL      +RSFL+ Q+R   
Sbjct: 179 FQSAGSPTTSSVRTLRRASVSPDPGSPFVLAQEKRLHFWNL---EFESRSFLYRQVRRMT 235

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             L  VG G      ++  L+++D   +    +AP  GL+  SV Y
Sbjct: 236 AVLVAVGLGALRPAQVKVILESRDPLGRHQARVAPAHGLFLKSVLY 281


>gi|225568181|ref|ZP_03777206.1| hypothetical protein CLOHYLEM_04255 [Clostridium hylemonae DSM
           15053]
 gi|225162900|gb|EEG75519.1| hypothetical protein CLOHYLEM_04255 [Clostridium hylemonae DSM
           15053]
          Length = 245

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 128/249 (51%), Gaps = 17/249 (6%)

Query: 6   MIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQV 61
           + IEY+GS Y GW R   +++ +++   I + +  +TGE ++    G RT+ GVHA  QV
Sbjct: 6   LTIEYDGSRYQGWCRLGKEESNNTVSNKIIEVLRKMTGEYIIELNCGCRTEVGVHAYAQV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F    +   + +   LN YL +   I+I N+  V  +FHA+ +A  ++Y+YR+     
Sbjct: 66  ANFKTDSDMDILEIKHYLNRYLPMD--IAITNVEDVPDRFHAQLNATSKTYVYRMTIDDV 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   ++   +   K  D + M+ A+   +G+HDF  F ++  +  + ++ I  F++  +G
Sbjct: 124 PSVFDRKYTYHCFKIPDKKLMQQASLLFIGKHDFKNFSTVK-KNKTTVKEI--FEIEVYG 180

Query: 182 NLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP--PE 237
           +  E++++  A  FLH   R  VG+L  +G G     D+E+           P +P   +
Sbjct: 181 DTEEMQILIHADDFLHNMARLVVGTLLEIGFGTRKKEDIEEIFAGTK----TPSSPCDAK 236

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 237 GLYLQEVSY 245


>gi|296141060|ref|YP_003648303.1| tRNA pseudouridine synthase A [Tsukamurella paurometabola DSM
           20162]
 gi|296029194|gb|ADG79964.1| tRNA pseudouridine synthase A [Tsukamurella paurometabola DSM
           20162]
          Length = 273

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 80/252 (31%), Positives = 123/252 (48%), Gaps = 14/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + I Y+G+ + GW RQ    ++ G +E+AI  V    V +  AGRTD+GVHA  Q
Sbjct: 1   MTRYRLDIAYDGTDFSGWARQPERRTVCGVVEEAIGTVLRTPVQLTVAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D     +P  L + L   L     + +  ++    +F ARFSA+RR Y YR+    
Sbjct: 61  VAHVDTDLA-LPEGLVRRLARMLP--QDVRVTAIAEAPAEFDARFSALRRHYEYRLT--D 115

Query: 121 APLALEKGRA-----WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           AP      RA     W  P  +D E M+ A+  L+G HDF  F     + ++ +R +  F
Sbjct: 116 APYGANPLRARDTAPWRRP--VDVERMQAASDALLGLHDFAAF-CRRREGATTVRELQRF 172

Query: 176 DVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                 + +    V A +F  + +RS VG++  VG+G+ +   +   L  ++R     +A
Sbjct: 173 AWRRDADGVCTAEVSADAFCWSMVRSLVGAVAAVGEGRRSVEWVAGLLDERERSSAINVA 232

Query: 235 PPEGLYFDSVEY 246
              GL    V+Y
Sbjct: 233 AACGLTLVRVDY 244


>gi|149193965|ref|ZP_01871063.1| Pseudouridylate synthase [Caminibacter mediatlanticus TB-2]
 gi|149135918|gb|EDM24396.1| Pseudouridylate synthase [Caminibacter mediatlanticus TB-2]
          Length = 223

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 113/228 (49%), Gaps = 6/228 (2%)

Query: 19  QRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA 78
           Q+Q N  +IQG IE A+  +    +V H AGRTD GVHAL QV  F +   W    L  +
Sbjct: 2   QKQPNKKTIQGEIELALNKLNINSIVQH-AGRTDKGVHALNQVISFTIPNFWDLNKLQTS 60

Query: 79  LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD 138
           LN  +     I  +     D  F+ RF+A +RSY Y I    +P   +    +   K ++
Sbjct: 61  LNKIIHPYIHIKKIKFIKND--FNPRFNAKKRSYRYIISPIFSPHKADYETYY--DKKIN 116

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
            E ++ A +   G +DF  F     + ++ IRTI   D+  + N + ++++   FL  QI
Sbjct: 117 IELLKKAIKKFEGTYDFEYFAKTGSEVNNYIRTIYKTDIIEYKNKVILKIIGNGFLRGQI 176

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           R     L ++ + K T  DL+K L  +D+     LAPP GLY + + Y
Sbjct: 177 RIITNFLLMINENKLTIDDLQKQLN-KDQLFTKHLAPPNGLYLERIWY 223


>gi|326777220|ref|ZP_08236485.1| tRNA pseudouridine synthase A [Streptomyces cf. griseus XylebKG-1]
 gi|326657553|gb|EGE42399.1| tRNA pseudouridine synthase A [Streptomyces cf. griseus XylebKG-1]
          Length = 284

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 121/253 (47%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVAH DL    W      L + L   L +   + I   +     F+ARFSA+ R Y YR+
Sbjct: 70  QVAHVDLPEAVWAEHEEKLLRRLAGRLPLD--VRIWRAAPAPAGFNARFSALWRRYAYRV 127

Query: 117 ITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
             R   +  L +G      + LD + M  AA  +VG HDF  +     + ++ IRT+   
Sbjct: 128 GDRPGGVDPLTRGHVLWHDRPLDLDAMNEAAALMVGEHDFAAY-CKKREGATTIRTLQKL 186

Query: 176 D--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
               +    L+   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +
Sbjct: 187 RWVRDPATGLLTATVQADAFCHNMVRALIGAALFVGDGRRPAAWPAEVLAAKVRDPGVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVAY 259


>gi|126640496|ref|YP_001083480.1| tRNA pseudouridine synthase A [Acinetobacter baumannii ATCC 17978]
          Length = 205

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 63/192 (32%), Positives = 94/192 (48%), Gaps = 12/192 (6%)

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           VAHFD       R W+       + A  ++   ISI  +  +D++FHARF A  R Y Y 
Sbjct: 2   VAHFDTNAIRPERGWI-------MGANSQLPKDISIQWIKQMDEEFHARFKATARRYRYV 54

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +       AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H 
Sbjct: 55  VYNAPHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKHC 114

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  AP
Sbjct: 115 RLFEHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDAMFAAEDRKAAGITAP 174

Query: 236 PEGLYFDSVEYS 247
           P+GLYF    Y 
Sbjct: 175 PDGLYFIQCYYP 186


>gi|295838433|ref|ZP_06825366.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB74]
 gi|197695769|gb|EDY42702.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB74]
          Length = 284

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/254 (31%), Positives = 125/254 (49%), Gaps = 11/254 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G+ + GW RQ  G  ++Q ++E+A+ +VT   E   +  AGRTD+GVHA 
Sbjct: 1   MRLRLDLSYDGTEFHGWARQPAGRRTVQETLEEALRVVTRAPEPYELTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QVAH ++  E W      L K L    ++   + +  ++   + F ARFSAI R Y YR
Sbjct: 61  GQVAHVEMADEVWAEHGEKLLKRLAG--RLPKDVRVWRVAPAPEGFDARFSAIWRRYAYR 118

Query: 116 IITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +  +      L +G      + LD + M  AA+ L+G HDF  +     + ++ IR +  
Sbjct: 119 VADQPGGADPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAY-CKKREGATTIREMQR 177

Query: 175 -FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            F       ++E  V A +F H  +RS VG+L  VGDG    +   K L A  R     +
Sbjct: 178 LFWTRRADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSAVHV 237

Query: 234 APPEGLYFDSVEYS 247
             P GL  + V Y 
Sbjct: 238 VRPVGLTLEEVGYP 251


>gi|302519630|ref|ZP_07271972.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB78]
 gi|318058099|ref|ZP_07976822.1| tRNA pseudouridine synthase A [Streptomyces sp. SA3_actG]
 gi|302428525|gb|EFL00341.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB78]
          Length = 284

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 82/256 (32%), Positives = 126/256 (49%), Gaps = 17/256 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG-----EIVVVHGAGRTDSGV 55
           +R  + + Y+G+ + GW RQ  G  ++Q ++E+A+ +VT      E+ V   AGRTD+GV
Sbjct: 1   MRLRLDLSYDGTDFHGWARQPGGRRTVQETLEEALRVVTRAPAPYELTV---AGRTDAGV 57

Query: 56  HALRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           HA  QVAH  +  E W      L K L    ++   + +  ++   + F ARFSAI R Y
Sbjct: 58  HARGQVAHVGMADEVWAEHGEKLLKRLAG--RLPKDVRVWRVAPAPEGFDARFSAIWRRY 115

Query: 113 LYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
            YR+  +   +  L +G      + LD + M  AA+ L+G HDF  +     + ++ IR 
Sbjct: 116 AYRVADQAGGVDPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAY-CKKREGATTIRE 174

Query: 172 IDH-FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +   F       ++E  V A +F H  +RS VG+L  VGDG    +   K L A  R   
Sbjct: 175 MQQLFWTRRADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSA 234

Query: 231 GPLAPPEGLYFDSVEY 246
             +  P GL  + V Y
Sbjct: 235 VHVVRPVGLTLEEVGY 250


>gi|152993424|ref|YP_001359145.1| tRNA pseudouridine synthase A [Sulfurovum sp. NBC37-1]
 gi|151425285|dbj|BAF72788.1| tRNA pseudouridine synthase A [Sulfurovum sp. NBC37-1]
          Length = 240

 Score =  105 bits (262), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 120/247 (48%), Gaps = 9/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGS-IEKAIFLVTGEIVV-VHGAGRTDSGVHALR 59
           +R   +I Y+GS + G+Q+Q   +    + IE A  L   +I+  + G+GRTD+GVHA  
Sbjct: 1   MRVKAVIAYDGSAFQGFQKQTRTNRTVTTTIENA--LADLQIISPLTGSGRTDAGVHASG 58

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL   W    L +  N+  K   TI   ++S     FHARFSA +R  +YR I +
Sbjct: 59  QVIHFDLPEFWSD--LNRLKNSLNKKLSTIRFKHISAAPDDFHARFSAKKR--IYRYIFK 114

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  L++ + +      S D + ++ A    VG HDF  F        + +R I   +   
Sbjct: 115 ENELSVFERKYVAHYSSFDPDILKRALLMFVGEHDFIYFHKTGSDIHTTVRKIYDANYRQ 174

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G    +   A  FL +Q+R  V S  L    + T   L+K + A+ R     L+PPEGL
Sbjct: 175 EGKYHFLYFTANGFLRSQVRMMVESAMLCAQNELTLEQLQKQINAEKRYHS-RLSPPEGL 233

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 234 YLARILY 240


>gi|269837096|ref|YP_003319324.1| tRNA pseudouridine synthase A [Sphaerobacter thermophilus DSM
           20745]
 gi|269786359|gb|ACZ38502.1| tRNA pseudouridine synthase A [Sphaerobacter thermophilus DSM
           20745]
          Length = 271

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 86/254 (33%), Positives = 114/254 (44%), Gaps = 21/254 (8%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+GS +FG QRQ    ++QG++E A   + GE   V  AGRTD GVHA+ QVA   +   
Sbjct: 16  YDGSAFFGSQRQPGVRTVQGALESAAERLAGEPTRVALAGRTDRGVHAVGQVASLRIRWA 75

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
                L +AL A     D + +     VD++FHARFSA  R Y Y +     P  L +GR
Sbjct: 76  RSADELARALMAL--TPDDLVVYGAREVDERFHARFSARWREYRYFVWEGPVP-TLMRGR 132

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF--------- 180
            W++   L+   M  AA   +GR DF            P   ID     S          
Sbjct: 133 VWVVRTPLNLAAMNAAADAFIGRRDFAA--VAGAGVGVPWSGIDTTRTVSLARWRIVDQP 190

Query: 181 -------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                  G L+E R+ A  FL   +R+ VGSL  VG G       E+ L  +DR+     
Sbjct: 191 FERHDRSGRLLEFRIRADGFLPHMVRNIVGSLVAVGRGDRPIGWTEELLAGRDRRRGEAP 250

Query: 234 APPEGLYFDSVEYS 247
           AP +GL    V Y 
Sbjct: 251 APAQGLVLWRVAYD 264


>gi|157738399|ref|YP_001491083.1| tRNA pseudouridine synthase A [Arcobacter butzleri RM4018]
 gi|157700253|gb|ABV68413.1| tRNA pseudouridine synthase A [Arcobacter butzleri RM4018]
          Length = 240

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 118/242 (48%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
            ++ Y+GS + G Q+Q NG +++  + KA   +  +  +V  +GRTD  VH+  QV +  
Sbjct: 5   FVVAYDGSLFQGSQKQPNGKTVENELLKAFENINIKTQIVL-SGRTDKEVHSSGQVFNCQ 63

Query: 66  LVREWVPVILCKA-LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +   W      K  LN  L  S  I I  +S VD+ FH+RFSA +R Y Y I T++    
Sbjct: 64  IPSYWEDFFKLKEILNKNLPTS--IKIKKISKVDESFHSRFSAKKRVYRYLITTKETTPF 121

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            +K   ++  KS+D + ++ A +  +G HDF  F        +  R I       + ++ 
Sbjct: 122 NDKFITYV--KSVDEKLLKKAIKEFIGIHDFKYFHKTGSDKENTNREIFDTKFYKYKDIY 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             +  A S+L +QIR  VG L  + D K T  DL K L  +      P+  P GLY   +
Sbjct: 180 VFKFTANSYLRSQIRLMVGFLLAINDKKLTIEDLRKQLNCEKIIFKTPIK-PNGLYLAKI 238

Query: 245 EY 246
           +Y
Sbjct: 239 KY 240


>gi|295395151|ref|ZP_06805359.1| tRNA pseudouridine synthase A [Brevibacterium mcbrellneri ATCC
           49030]
 gi|294971913|gb|EFG47780.1| tRNA pseudouridine synthase A [Brevibacterium mcbrellneri ATCC
           49030]
          Length = 303

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 88/271 (32%), Positives = 124/271 (45%), Gaps = 32/271 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + + Y G+ + GW  Q +  ++QG +E A+  +    V V  AGRTD+GVHA RQV 
Sbjct: 18  RFRIDLGYVGTHFHGWALQPHLRTVQGELETALARILSAPVRVTVAGRTDAGVHARRQVV 77

Query: 63  HFDLVREWVPVI----------------LCKALNAYLKISDT--ISILNLSIVDKQFHAR 104
           H D+     P +                L   L   L   D   I I +++ V   F AR
Sbjct: 78  HVDIPHTDFPRLVGQPRARAEQRTPARGLTSRLRGVLARQDASDIVIHDVTAVHADFDAR 137

Query: 105 FSAIRRSYLYRIITRQA---PLALEKGRAWLIP--KSLDCENMRIAAQHLVGRHDFTTFR 159
           FSA+ RSY YR+   QA   PL      A+ +     LD   M  AAQ + G  DF  F 
Sbjct: 138 FSALWRSYTYRLADPQAFTDPLTA----AFTVEHRAELDVAAMSAAAQQVCGLRDFLPFC 193

Query: 160 SIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               + S+ IRT++   V   G+ +IE  + A +F H  +R+ VG L  VG+GKW    L
Sbjct: 194 KPR-EGSTTIRTLEELRVERVGSGVIEFFLRADAFCHHMVRALVGGLVKVGEGKWGPGRL 252

Query: 219 EKALQAQDRKECG-PL--APPEGLYFDSVEY 246
               +   R     P+   P  GL  + V Y
Sbjct: 253 AGMCEEAGRGGSEFPMFVFPAHGLVLEDVGY 283


>gi|307721208|ref|YP_003892348.1| tRNA pseudouridine synthase A [Sulfurimonas autotrophica DSM 16294]
 gi|306979301|gb|ADN09336.1| tRNA pseudouridine synthase A [Sulfurimonas autotrophica DSM 16294]
          Length = 236

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 13/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + YNG+ +FG Q QK  S ++ G +E  +  +  E  V+  +GRTD GVHA  Q
Sbjct: 1   MRVALHLAYNGTHFFGSQTQKETSKTVLGELENVLKKLGIEQKVI-ASGRTDKGVHATMQ 59

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL   W     L + LN  L  +D + +  +  V   FHAR+SA +R+Y Y I T 
Sbjct: 60  VCHIDLPPYWEDTQKLKRVLNEML--NDALHVKRIRPVSDDFHARYSAKKRTYRYIIKTT 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q+    EK     + K ++ EN++      VG+HDF  F     +  S  R I       
Sbjct: 118 QSN-PFEKDFVTFL-KDINFENIQENIALFVGKHDFKQFMKTGSEVKSTTRIIYKAFAYK 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + + + +   A  FL +QIR  VG+L  +      +  +++ L   +  +  P AP  GL
Sbjct: 176 YKDYVVLNFQANGFLRSQIRLMVGALLSLN-----AQQIQEQLNCSNNYKIKP-APANGL 229

Query: 240 YFDSVEY 246
           Y  ++ Y
Sbjct: 230 YLSTITY 236


>gi|254383143|ref|ZP_04998497.1| tRNA pseudouridine synthase A [Streptomyces sp. Mg1]
 gi|194342042|gb|EDX23008.1| tRNA pseudouridine synthase A [Streptomyces sp. Mg1]
          Length = 283

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 79/252 (31%), Positives = 122/252 (48%), Gaps = 10/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q+   ++QG +E A+  V    + V +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQRVLRTVQGELESALTTVMRLPDPVELTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVA FD+  E W      L + L    ++   + +  ++   + F+ARFSAI R Y YR+
Sbjct: 70  QVAQFDVAEEVWAEHHDKLLRRLAG--RLPHDVRVWKVAEAPQGFNARFSAIWRRYAYRV 127

Query: 117 ITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  +  L +G        LD + M  AA  L+G HDF  +     + ++ IRT+   
Sbjct: 128 GDHQGGVDPLRRGHVLWHQWPLDVDAMNRAAAALLGEHDFAAY-CKKREGATTIRTLQQL 186

Query: 176 DVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                G+ ++   V A +F H  +RS VG+L  VGDG        + L A  R     + 
Sbjct: 187 SWERAGDGIVTATVRADAFCHNMVRSLVGALLHVGDGHRPVEWPGQVLAAGVRDSSVHVV 246

Query: 235 PPEGLYFDSVEY 246
            P GL  + V Y
Sbjct: 247 KPHGLTLEEVGY 258


>gi|326332230|ref|ZP_08198510.1| tRNA pseudouridine synthase A [Nocardioidaceae bacterium Broad-1]
 gi|325949936|gb|EGD41996.1| tRNA pseudouridine synthase A [Nocardioidaceae bacterium Broad-1]
          Length = 287

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 135/265 (50%), Gaps = 23/265 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----TGE--IVVVHGAGRTDSG 54
           +R  + + Y+G+ + GW  Q    ++QG ++ A+        TGE   V V  AGRTDSG
Sbjct: 1   MRIRIDLAYDGTMFHGWATQPGLRTVQGELQAALATALRVPSTGERSQVWVTVAGRTDSG 60

Query: 55  VHALRQVAHFDL----------VREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHA 103
           VHA  QVAHFD+            E  P+  L + LN  L     + +       + F+A
Sbjct: 61  VHARGQVAHFDIDADVLESSRGRSEQSPLDSLVRRLNGILPAD--LRVHRAVEAPEGFNA 118

Query: 104 RFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R Y+YRI+   A +  L +G      + LD   M +A+  LVG +DF +F    
Sbjct: 119 RFSALSRRYVYRIVDDPAFVDPLLRGHVLYRTRPLDLSLMNVASADLVGLNDFASFCKPR 178

Query: 163 CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            + ++ IR +     +   + +IE  V+A +F H+ +RS VG L ++G+G+   T  +++
Sbjct: 179 -EGATTIRDLRQLTWDRRPDGIIEATVLADAFCHSMVRSLVGCLMVIGEGRKDVTWAKES 237

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           L A+ R    P+AP  GL  + V Y
Sbjct: 238 LAARSRSSSIPIAPANGLTLEEVAY 262


>gi|241896974|ref|NP_001028662.1| tRNA pseudouridine synthase-like 1 [Mus musculus]
 gi|218525914|sp|A2ADA5|PUSL1_MOUSE RecName: Full=tRNA pseudouridine synthase-like 1; AltName:
           Full=tRNA pseudouridylate synthase-like 1; AltName:
           Full=tRNA-uridine isomerase-like 1
 gi|123295163|emb|CAM18398.1| pseudouridylate synthase-like 1 [Mus musculus]
          Length = 291

 Score =  105 bits (261), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 85/274 (31%), Positives = 128/274 (46%), Gaps = 32/274 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           RY + ++Y G+ + G    +      G +    E A  L + + V    + RTD+GVHAL
Sbjct: 13  RYLVFLQYLGTDFNGVAAVRGNPRAVGVLNFLEEAAKRLNSVDPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P ++ KALN +LK    I +L    V   FHAR +A  R+Y 
Sbjct: 73  SNAAHLDIQRRPGQSPFSPEVVAKALNTHLK-HPAIRVLKAFRVPNDFHARHAATSRTYQ 131

Query: 114 YRIIT-----RQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           YR+ T      Q P+  E+   W L  + LD   M+ AAQHL+G HDF+ F+S     ++
Sbjct: 132 YRLATGCSWPNQLPV-FEQNVCWALQTEYLDMAAMQEAAQHLLGTHDFSAFQSAGSPVTN 190

Query: 168 PIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
            +RT+    V+                    +   ++SFL+ Q+R     L  VG G   
Sbjct: 191 TVRTLRRVSVSPGPASPFVLPEGSRRLQFWTLEFESQSFLYRQVRRMTAVLVAVGLGILA 250

Query: 215 STDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            T ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 251 PTQVKVILESQDPLGKYQARVAPARGLFLKSVLY 284


>gi|332159317|ref|YP_004424596.1| tRNA pseudouridine synthase A [Pyrococcus sp. NA2]
 gi|331034780|gb|AEC52592.1| tRNA pseudouridine synthase A [Pyrococcus sp. NA2]
          Length = 263

 Score =  105 bits (261), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 78/250 (31%), Positives = 123/250 (49%), Gaps = 30/250 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + G+QRQ N  +++G I KA+     E      A RTD GV AL  V
Sbjct: 1   MRVALKIAYDGTKFHGFQRQPNIRTVEGEIIKALNNSGIEYSDFKSASRTDKGVSALGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYL---KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
                  E       KALN  +   ++ D + IL+   V   FH RF A  + Y Y    
Sbjct: 61  VAITTEDE-------KALNPMVLNARLED-VWILSAIEVPPDFHPRFWAKSKVYRY---- 108

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                       +L    LD E ++  +Q  +G HDF+ F  +  + +  IR+ID  +V 
Sbjct: 109 ------------YLPSIGLDVERVKECSQLFLGVHDFSAFSKVDERDT--IRSIDRIEVL 154

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPE 237
             G ++ I + A+SFL   +R  V +L+L G GK ++ D+++ L+ + ++ +  P APPE
Sbjct: 155 VLGPILVIEIEAKSFLWEMVRRIVKALELCGLGKLSAEDVKEMLEGKFNKSKKVPPAPPE 214

Query: 238 GLYFDSVEYS 247
           GL    V+Y 
Sbjct: 215 GLLLVDVKYE 224


>gi|15639816|ref|NP_219266.1| tRNA pseudouridine synthase A [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189026054|ref|YP_001933826.1| tRNA pseudouridine synthase A [Treponema pallidum subsp. pallidum
           SS14]
 gi|6136049|sp|O83802|TRUA_TREPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238689345|sp|B2S468|TRUA_TREPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3323141|gb|AAC65796.1| pseudouridylate synthase (hisT) [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018629|gb|ACD71247.1| pseudouridylate synthase [Treponema pallidum subsp. pallidum SS14]
          Length = 280

 Score =  105 bits (261), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 114/233 (48%), Gaps = 12/233 (5%)

Query: 8   IEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           I Y+G+ + GWQ+Q +GS     S+QG +EK    +  + + V G+GRTDSGVHA+ Q A
Sbjct: 11  ISYDGTRFCGWQKQVSGSRERAPSVQGELEKVAEKIHHQKIAVIGSGRTDSGVHAVGQAA 70

Query: 63  HF-DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HF   +R  +      A N+ L  S  I I +   V  Q HARFSA+ R+Y Y +     
Sbjct: 71  HFCTPMRNILAYRFIPAFNSLLPHS--IRITDAREVSSQLHARFSAVMRTYRYHLHCAPV 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVNS 179
             A E    W I +  D   +   A  L G  D T+F +   +++S  R     HF  N 
Sbjct: 129 AYAHELPYCWHIARMPDIHLLNQYAATLKGELDCTSFAAAGDKSASKSRYFYDTHFSFNH 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              ++   + A +FL   +RS  G+L      + +  +  + L A+DR+  GP
Sbjct: 189 --RVLTFEISANAFLWKMVRSLTGTLLHCEKKRCSVREFVRILHAKDRRLQGP 239


>gi|315636694|ref|ZP_07891924.1| tRNA pseudouridine synthase A [Arcobacter butzleri JV22]
 gi|315479009|gb|EFU69712.1| tRNA pseudouridine synthase A [Arcobacter butzleri JV22]
          Length = 240

 Score =  105 bits (261), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 119/242 (49%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
            ++ Y+GS + G Q+Q NG +++  + KA   +  +  +V  +GRTD  VH+  QV +  
Sbjct: 5   FVVAYDGSLFQGSQKQPNGKTVENELLKAFENINIKTQIVL-SGRTDKEVHSSGQVFNCQ 63

Query: 66  LVREWVPVILCKA-LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +   W      K  LN  L  S  I I  +S V++ FH+RFSA +R Y Y I T++    
Sbjct: 64  IPSYWEDFFKLKEILNKNLPTS--IKIKKISKVEESFHSRFSAKKRVYRYLITTKETTPF 121

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            +K   ++  KS+D + ++ A +  +G HDF  F        +  R I       + ++ 
Sbjct: 122 NDKFITYV--KSVDEKLLKKAIKEFIGVHDFKYFHKTGSDKENTNREIFDTKFYKYKDIY 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             +  A S+L +QIR  VG L  + D K T  DL+K L  +      P+  P GLY   +
Sbjct: 180 VFKFTANSYLRSQIRLMVGFLLAINDKKLTIEDLKKQLNCEKSIFKTPIK-PNGLYLAKI 238

Query: 245 EY 246
           +Y
Sbjct: 239 KY 240


>gi|229821589|ref|YP_002883115.1| tRNA pseudouridine synthase A [Beutenbergia cavernae DSM 12333]
 gi|229567502|gb|ACQ81353.1| tRNA pseudouridine synthase A [Beutenbergia cavernae DSM 12333]
          Length = 286

 Score =  104 bits (260), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 82/261 (31%), Positives = 123/261 (47%), Gaps = 16/261 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           ++R  + + Y+G+ + GW RQ    ++QG +E+A+   L   E   +  AGRTD+GVHA 
Sbjct: 4   VLRVRLDLAYDGAAFAGWARQPGLRTVQGDLEEALGRVLRLPEPPRLTVAGRTDAGVHAR 63

Query: 59  RQVAHFDLVREW---VPVILCKALNAYLK------ISDTISILNLSIVDKQFHARFSAIR 109
            QVAH DL RE     P    +   A L+      +   + + +++     F ARFSAI 
Sbjct: 64  GQVAHVDLPREAYLAAPGRSERDPGAALRTRLAGVLPPDVVVGHVAPAPPGFDARFSAIW 123

Query: 110 RSYLYRIITRQAPLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           R Y YR+    A L     R W +   + LD   M  AA+ L+G HDF  F      A++
Sbjct: 124 RRYAYRVADDGA-LHDPLRRGWTVWHRRPLDVVAMDAAARRLLGEHDFAAFCRPREGATT 182

Query: 168 PIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            IRT+     V     L+   V A +F H+ +R+ VG+   VG+ +         L A  
Sbjct: 183 -IRTLQELTWVRDDAGLLVAHVRADAFCHSMVRALVGACLAVGESRREVGWPRAVLDAAR 241

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R     +AP  GL  + + Y 
Sbjct: 242 RDSAVQVAPAHGLVLEEIGYP 262


>gi|318079697|ref|ZP_07987029.1| tRNA pseudouridine synthase A [Streptomyces sp. SA3_actF]
          Length = 282

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 17/250 (6%)

Query: 8   IEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG-----EIVVVHGAGRTDSGVHALRQV 61
           + Y+G+ + GW RQ  G  ++Q ++E+A+ +VT      E+ V   AGRTD+GVHA  QV
Sbjct: 5   LSYDGTDFHGWARQPGGRRTVQETLEEALRVVTRAPAPYELTV---AGRTDAGVHARGQV 61

Query: 62  AHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           AH  +  E W      L K L    ++   + +  ++   + F ARFSAI R Y YR+  
Sbjct: 62  AHVGMADEVWAEHGEKLLKRLAG--RLPKDVRVWRVAPAPEGFDARFSAIWRRYAYRVAD 119

Query: 119 RQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH-FD 176
           +   +  L +G      + LD + M  AA+ L+G HDF  +     + ++ IR +   F 
Sbjct: 120 QAGGVDPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAY-CKKREGATTIREMQQLFW 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 ++E  V A +F H  +RS VG+L  VGDG    +   K L A  R     +  P
Sbjct: 179 TRRADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSAVHVVRP 238

Query: 237 EGLYFDSVEY 246
            GL  + V Y
Sbjct: 239 VGLTLEEVGY 248


>gi|297159627|gb|ADI09339.1| tRNA pseudouridine synthase A [Streptomyces bingchenggensis BCW-1]
          Length = 292

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 82/256 (32%), Positives = 124/256 (48%), Gaps = 13/256 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSI---QGSIEKAIFLVT--GEIVVVHGAGRTDSGVH 56
           +R  + + Y+G+ + GW +Q+   ++   QG +E A+ +V    + V +  AGRTD+GVH
Sbjct: 10  VRVRLNLSYDGTDFSGWAKQRGRDTVRTVQGELESALKVVMRMQDPVELTVAGRTDAGVH 69

Query: 57  ALRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           A  QVAH DL    W      L + L    ++   I + ++      F+ARFSAI R Y+
Sbjct: 70  ARGQVAHVDLPEPIWAEHHEKLLRRLAG--RLPHDIRVWSVGEAPPGFNARFSAIWRRYV 127

Query: 114 YRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR++     +  L +G        LD + M  AAQ L+G HDF  +      A++ IRT+
Sbjct: 128 YRVVDHPGGVDPLLRGHVLWHDWPLDVDAMNEAAQKLLGEHDFAAYCKKRDGATT-IRTL 186

Query: 173 DHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                    + +I   V A +F H  +RS VG+L  VGDG   +    K L A  R    
Sbjct: 187 QRLSWERGPDGIITATVRADAFCHNMVRSLVGALLFVGDGHRPADWPAKVLAAGVRDSAV 246

Query: 232 PLAPPEGLYFDSVEYS 247
            +  P GL  + V Y 
Sbjct: 247 HVVRPHGLTLEQVGYP 262


>gi|182436598|ref|YP_001824317.1| tRNA pseudouridine synthase A [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|238689026|sp|B1W3X8|TRUA_STRGG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|178465114|dbj|BAG19634.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 284

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/253 (30%), Positives = 121/253 (47%), Gaps = 11/253 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVRE-WV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVAH DL    W      L + L   L +   + I   +     F+ARFSA+ R Y YR+
Sbjct: 70  QVAHVDLPEAVWAEHEEKLLRRLAGRLPLD--VRIWRAAPAPAGFNARFSALWRRYAYRV 127

Query: 117 ITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
             R   +  L +G      + LD + M  AA  +VG HDF  +     + ++ IRT+   
Sbjct: 128 GDRPGGVDPLTRGHVLWHDRPLDLDAMNEAAALMVGEHDFAAY-CKKREGATTIRTLQKL 186

Query: 176 D--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
               +    ++   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +
Sbjct: 187 RWVRDPATGVLTATVQADAFCHNMVRALIGAALFVGDGRRPAAWPAEVLAAKVRDPGVHV 246

Query: 234 APPEGLYFDSVEY 246
             P GL  + V Y
Sbjct: 247 VRPHGLTLEEVAY 259


>gi|331085203|ref|ZP_08334289.1| hypothetical protein HMPREF0987_00592 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330407986|gb|EGG87476.1| hypothetical protein HMPREF0987_00592 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 248

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 116/249 (46%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + +EY+GS Y GWQR   G S   +   I + +  +T E V +    RT+ GVHA
Sbjct: 1   MRNILLTLEYDGSRYQGWQRLGKGESTNTVSNKILEVLKKMTNEDVELFCGARTEVGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV +F    +   + +   +N YL +   I++L++    ++FHA  +A  R YLYR+ 
Sbjct: 61  YGQVVNFKTTTDMTLLEIKHYMNRYLPMD--IAVLSVEEKPERFHASLNAKSRIYLYRVA 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P   ++   +   K  D E M+ AA  L G+HDF  F ++    S+  + I + D+
Sbjct: 119 IAEVPSVFDRKYTYHSFKKPDTELMKQAALLLAGKHDFKKFSTVKKNKSTE-KEILNIDI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I+I + A  FLH   R  + +L  +G G     ++++               P+
Sbjct: 178 YEDLEEIQITLEATDFLHNMPRMILSTLLDIGLGIRRKEEIDEIFSPTSSTVASAPCDPK 237

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 238 GLYLQEVVY 246


>gi|13507935|ref|NP_109884.1| tRNA pseudouridine synthase A [Mycoplasma pneumoniae M129]
 gi|2499079|sp|Q50291|TRUA_MYCPN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1215692|gb|AAC43685.1| hypothetical 28k protein (alkaline endoglucanase); GT9_orf321
           [Mycoplasma pneumoniae]
 gi|1674340|gb|AAB96283.1| pseudouridylate synthase I [Mycoplasma pneumoniae M129]
 gi|301633310|gb|ADK86864.1| tRNA pseudouridine synthase A [Mycoplasma pneumoniae FH]
          Length = 243

 Score =  104 bits (259), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 111/248 (44%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  I+ YNG+ + GW +Q    ++QG IE+ + L+    + ++G+GRTD GVHA+ Q
Sbjct: 1   MPRYLAIVAYNGAPFRGWAKQPGYHTVQGQIEQNLALIYQTPINIYGSGRTDKGVHAINQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             H DL  +     L   LN  L   D I +  L  V  +FHARF+   + Y Y I TR 
Sbjct: 61  TFHVDLPDKLPLKQLIAKLNQ-LNYPD-IFVKALVPVAPRFHARFAVKTKVYEYLINTRA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
              A +    W     LD   +       +GR DF +F +   + +   RTI    V   
Sbjct: 119 FNPA-QYHTVWQYNHPLDLAQLEADTTLFLGRKDFWSFSTASQKDTQ--RTISKIIVQQD 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +++      FL  QIR  V SL  + +       +++      +  C   AP  GL
Sbjct: 176 HTGTVKLTFFGNGFLRNQIRMMVASLVALNNRTLMRETVQQLFDQPQKGGCKVKAPACGL 235

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 236 YLKTVLYE 243


>gi|116490689|ref|YP_810233.1| pseudouridylate synthase [Oenococcus oeni PSU-1]
 gi|290890104|ref|ZP_06553187.1| hypothetical protein AWRIB429_0577 [Oenococcus oeni AWRIB429]
 gi|122277127|sp|Q04G54|TRUA_OENOB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116091414|gb|ABJ56568.1| Pseudouridylate synthase [Oenococcus oeni PSU-1]
 gi|290480295|gb|EFD88936.1| hypothetical protein AWRIB429_0577 [Oenococcus oeni AWRIB429]
          Length = 252

 Score =  104 bits (259), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 122/250 (48%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSS--IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y + I Y+G  + G+Q Q    S  +Q  + K +  +    + V GA RTD+GVHA 
Sbjct: 1   MQNYKVTISYDGHYFEGFQTQNRPGSRTVQDELIKVVSKMAKTKIKVIGASRTDAGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV +F    +     +   +N+ L     I +  +  V   F+AR S+ R+ YLYR+ T
Sbjct: 61  GQVINFIFPFDLNEKAILMGMNSQLPTD--ILVKKVEKVPINFNARHSSHRKRYLYRVST 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +     ++        +LD   ++ A   L+G HDF++F +   Q ++ IRT+   ++ 
Sbjct: 119 SKFIDPFKRFYTGHYFWNLDTNKIQEALPDLIGEHDFSSFAASGNQTATTIRTVTKAELK 178

Query: 179 SF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            F   N +       +FL+ QIR  VG L  +G+G     D+ + ++ +DR++    AP 
Sbjct: 179 IFPKNNELLFTFEGNAFLYNQIRIMVGVLLEIGNGTRPVHDIIRLIKIKDRQQARFTAPA 238

Query: 237 EGLYFDSVEY 246
            GLY D V Y
Sbjct: 239 SGLYLDEVYY 248


>gi|84494739|ref|ZP_00993858.1| tRNA pseudouridine synthase [Janibacter sp. HTCC2649]
 gi|84384232|gb|EAQ00112.1| tRNA pseudouridine synthase [Janibacter sp. HTCC2649]
          Length = 283

 Score =  104 bits (259), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 120/258 (46%), Gaps = 12/258 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           ++R  + + Y+G+ + GW  Q    +++G +  A+   L   E V +  AGRTD+GVHA 
Sbjct: 3   LLRVRIDLAYDGTDFSGWAAQPGRRTVEGELSAALTTLLRAPEPVRLTVAGRTDAGVHAR 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDT---------ISILNLSIVDKQFHARFSAIR 109
            QV H D+       +  ++  +  + + T         + +  +S     F ARF+A+R
Sbjct: 63  GQVVHADVDDTLYAALPGRSSRSPEEAARTRLAGILPSDVVVRAVSRAPDGFDARFAALR 122

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R YLYRI      L  L +G   ++   LD   M  AA  LVG HDF  F      A++ 
Sbjct: 123 RRYLYRICDDPGALDPLRRGDTVVLKDPLDVAAMNEAAGRLVGLHDFAAFCKKRDGATTV 182

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
              +D+  V +    +E  VVA +F H+ +R+ VGS+  VG G+       + L    R 
Sbjct: 183 RTLLDYSWVRAPDGTVEATVVADAFCHSMVRALVGSVVPVGMGRAEVDFPREVLTGGARD 242

Query: 229 ECGPLAPPEGLYFDSVEY 246
               + P  GL  + V Y
Sbjct: 243 PRVKVMPAHGLSLEEVTY 260


>gi|325661070|ref|ZP_08149697.1| hypothetical protein HMPREF0490_00430 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472577|gb|EGC75788.1| hypothetical protein HMPREF0490_00430 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 248

 Score =  104 bits (259), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 116/249 (46%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + +EY+GS Y GWQR   G S   +   I + +  +T E + +    RT+ GVHA
Sbjct: 1   MRNILLTLEYDGSRYQGWQRLGKGESTNTVSNKILEVLKKMTNEDIELFCGARTEVGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV +F    +   + +   +N YL +   I++L++    ++FHA  +A  R YLYR+ 
Sbjct: 61  YGQVVNFKTTTDMTLLEIKHYMNRYLPMD--IAVLSVEEKPERFHASLNAKSRIYLYRVA 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P   ++   +   K  D E M+ AA  L G+HDF  F ++    S+  + I + D+
Sbjct: 119 IAEVPSVFDRKYTYHSFKKPDTELMKQAALLLAGKHDFKKFSTVKKNKSTE-KEILNIDI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I+I + A  FLH   R  + +L  +G G     ++++               P+
Sbjct: 178 YEDLEEIQITLEATDFLHNMPRMILSTLLDIGLGIRRKEEIDEIFSPTSSTVASAPCDPK 237

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 238 GLYLQEVVY 246


>gi|152990852|ref|YP_001356574.1| tRNA pseudouridine synthase A [Nitratiruptor sp. SB155-2]
 gi|151422713|dbj|BAF70217.1| tRNA pseudouridine synthase A [Nitratiruptor sp. SB155-2]
          Length = 241

 Score =  104 bits (259), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 120/251 (47%), Gaps = 16/251 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R   +I Y+GS + G+Q QK+  +++   +  A+  V  E  +V G+GRTD GVHA  Q
Sbjct: 1   MRIKAVISYDGSRFDGFQIQKHTANTVMHHLYNALQRVGIESKIV-GSGRTDKGVHATAQ 59

Query: 61  VAHFDLVREWVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFDL   W  +     +L ++L  Y++I   +       V K+FHAR+SA RR+Y Y 
Sbjct: 60  VIHFDLPPFWSELERLQNLLNESLRPYIQIKRVVK------VPKEFHARYSAKRRAYRY- 112

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++ +  P   E      +  +LD E ++       GRHDF  F        S +R I   
Sbjct: 113 LLKKSEPSVFENAYLHHV-SNLDIEIIKRNISLFEGRHDFRYFMKTGSDTKSSVRRIFKT 171

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +    +L  +      FL  QIR  VG+L  +G G+     +   L  + R     LAP
Sbjct: 172 ALYEKDDLYVLYFEGDGFLRAQIRLIVGALIKLGKGELKPEQIIDQLACKAR-YTSTLAP 230

Query: 236 PEGLYFDSVEY 246
           P GLY   + Y
Sbjct: 231 PNGLYLCKIIY 241


>gi|294814496|ref|ZP_06773139.1| Pseudouridylate synthase [Streptomyces clavuligerus ATCC 27064]
 gi|326442885|ref|ZP_08217619.1| tRNA pseudouridine synthase A [Streptomyces clavuligerus ATCC
           27064]
 gi|294327095|gb|EFG08738.1| Pseudouridylate synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 288

 Score =  103 bits (258), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/256 (33%), Positives = 117/256 (45%), Gaps = 17/256 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG-----EIVVVHGAGRTDSGV 55
           +R  + + Y+G  + GW RQ  G  ++QG IE A+  VT      E+ V   AGRTD+GV
Sbjct: 10  VRVRLDLSYDGRDFSGWARQAGGRRTVQGEIEDALRTVTRSARPYELTV---AGRTDAGV 66

Query: 56  HALRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           HA  QVAH DL  E W      L K L    ++   + I         F+ARFSA+ R Y
Sbjct: 67  HARGQVAHVDLPAEVWAEHREKLLKRLAG--RLDRDVRIWRAEEAPAGFNARFSAVWRRY 124

Query: 113 LYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
            YR+      +  L +G        LD   M  A+Q L+G HDF  +     + ++ IRT
Sbjct: 125 AYRVSDHPGGVDPLLRGHVLWHDWPLDVAAMNAASQPLLGEHDFAAY-CKKREGATTIRT 183

Query: 172 IDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +           +I   V A +F H  +RS VG+L  VGDG        K L A  R   
Sbjct: 184 LQRLSWERDAAGVITATVRADAFCHNMVRSLVGALLFVGDGHRPVDWPGKVLAAGVRDSA 243

Query: 231 GPLAPPEGLYFDSVEY 246
             +  P GL  + V Y
Sbjct: 244 VHVVRPHGLTLEEVGY 259


>gi|301629805|ref|XP_002944022.1| PREDICTED: tRNA pseudouridine synthase A-like [Xenopus (Silurana)
           tropicalis]
          Length = 207

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 88/186 (47%), Gaps = 6/186 (3%)

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P    +  N +L     I++     V   FHAR  A  R Y Y ++  
Sbjct: 2   QVVHFDTPLRRTPFAWVRGSNTFLP--PDIAVQWAQAVPASFHARACATARRYAYVLLQS 59

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               ++E  R   + + LD   MR AAQHL+G HDFT+FR+  CQA +P++T+    +  
Sbjct: 60  PVRPSVESARVGWVFQPLDGAAMRAAAQHLLGEHDFTSFRASACQAKTPVKTLHRIGITR 119

Query: 180 FG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            G              +FLH  +R+ +G L  VG G+  +  + + L A+ R    P   
Sbjct: 120 RGAGPHGYWRFEFEGNAFLHHMVRNIMGCLIAVGQGRKPADWMAEVLAARSRDAAAPTFA 179

Query: 236 PEGLYF 241
           P+GLYF
Sbjct: 180 PDGLYF 185


>gi|256831855|ref|YP_003160582.1| tRNA pseudouridine synthase A [Jonesia denitrificans DSM 20603]
 gi|256685386|gb|ACV08279.1| tRNA pseudouridine synthase A [Jonesia denitrificans DSM 20603]
          Length = 310

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 86/268 (32%), Positives = 121/268 (45%), Gaps = 28/268 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +IR    + Y G+ + GW RQ    S+QG++E A+  + GE + V  AGRTD+GVHA  Q
Sbjct: 24  VIRIRCDVAYRGTDFVGWARQPGLRSVQGTLEDALERLMGERIAVTVAGRTDAGVHARGQ 83

Query: 61  VAHFDLVR---EWVP----VILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRS 111
           V H D+     E +P        +AL A L   +   + +  ++     F ARFSA+ R+
Sbjct: 84  VVHCDVPGDRWERLPGRSDRTPGEALRAKLGGILPSDVVVRRVAPAPPGFDARFSALSRT 143

Query: 112 YLYRIITR-------QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           Y YRI           AP  L     W +   LD E M   A  LVG  DF  F      
Sbjct: 144 YYYRIADDVMMRDPLTAPFVL-----W-VRSPLDVEAMNRGAAPLVGLRDFAAFCKPRPG 197

Query: 165 ASSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           AS+ IR +  F     +      L+   V A +F H  +R+ VG+   VG G      L 
Sbjct: 198 AST-IRELQDFRWERVEQGPDEGLVRATVRADAFCHNMVRALVGASLDVGRGVRGEEWLV 256

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +AL ++ R     +  P GL  + V Y 
Sbjct: 257 QALTSKSRVNSSAVVQPHGLTLEQVAYP 284


>gi|254391364|ref|ZP_05006567.1| tRNA pseudouridine synthase A [Streptomyces clavuligerus ATCC
           27064]
 gi|197705054|gb|EDY50866.1| tRNA pseudouridine synthase A [Streptomyces clavuligerus ATCC
           27064]
          Length = 284

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 86/256 (33%), Positives = 117/256 (45%), Gaps = 17/256 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG-----EIVVVHGAGRTDSGV 55
           +R  + + Y+G  + GW RQ  G  ++QG IE A+  VT      E+ V   AGRTD+GV
Sbjct: 6   VRVRLDLSYDGRDFSGWARQAGGRRTVQGEIEDALRTVTRSARPYELTV---AGRTDAGV 62

Query: 56  HALRQVAHFDLVRE-WVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           HA  QVAH DL  E W      L K L    ++   + I         F+ARFSA+ R Y
Sbjct: 63  HARGQVAHVDLPAEVWAEHREKLLKRLAG--RLDRDVRIWRAEEAPAGFNARFSAVWRRY 120

Query: 113 LYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
            YR+      +  L +G        LD   M  A+Q L+G HDF  +     + ++ IRT
Sbjct: 121 AYRVSDHPGGVDPLLRGHVLWHDWPLDVAAMNAASQPLLGEHDFAAY-CKKREGATTIRT 179

Query: 172 IDHFDVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +           +I   V A +F H  +RS VG+L  VGDG        K L A  R   
Sbjct: 180 LQRLSWERDAAGVITATVRADAFCHNMVRSLVGALLFVGDGHRPVDWPGKVLAAGVRDSA 239

Query: 231 GPLAPPEGLYFDSVEY 246
             +  P GL  + V Y
Sbjct: 240 VHVVRPHGLTLEEVGY 255


>gi|237752928|ref|ZP_04583408.1| tRNA pseudouridine synthase A [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375195|gb|EEO25286.1| tRNA pseudouridine synthase A [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 249

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/252 (31%), Positives = 119/252 (47%), Gaps = 19/252 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            +  M I YNG  +FG+Q Q N  S+   +E  +F   G    +  +GRTD GVH+  QV
Sbjct: 10  FKVAMRIAYNGGAFFGFQSQSNVQSVANVLED-VFKSVGVFSKIAASGRTDKGVHSSAQV 68

Query: 62  AHFDLVREWVPVILCKA-LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              ++   W  +   K  LNA  K++  + I ++  V   FHARFSA RR Y Y +    
Sbjct: 69  ISLEIPYFWKNLENLKVCLNA--KLAPNLFIKHIWEVGDDFHARFSATRRGYCYVLSKHF 126

Query: 121 APLALEKGRAWLIPKSL--DCEN---MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +P        +L P SL  + +N   ++ A + LVG H+F  F+       S +R+I   
Sbjct: 127 SP--------FLTPFSLHYNLKNPNLIKQALKLLVGTHNFGAFKKQGSGEKSSVRSIFRA 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D+  F     +      FL +Q+R  VG L  +  G  T   LE  L  + R    P+A 
Sbjct: 179 DLREFKGFWILSFWGNGFLRSQVRLMVGFLLEIDKGNLTLEALEAQLNGEMRYRI-PIA- 236

Query: 236 PEGLYFDSVEYS 247
           P GLY   V+++
Sbjct: 237 PNGLYLSRVDFN 248


>gi|283768478|ref|ZP_06341390.1| tRNA pseudouridine synthase A [Bulleidia extructa W1219]
 gi|283104870|gb|EFC06242.1| tRNA pseudouridine synthase A [Bulleidia extructa W1219]
          Length = 320

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 117/247 (47%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +  I+ Y G+ Y GWQ QK G+SIQ  IE  +  +  E   V  +GRTD+ V+AL Q
Sbjct: 1   MRYFKAIVAYVGANYCGWQSQKKGNSIQEKIEAVLSQINQEKTTVIASGRTDAKVNALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F   +           +++L     I +  +  VD+ FHARF   +++YLYRI    
Sbjct: 61  CFQFQSEKNIDSYRWLGIFHSFL--PKDIYVKQVEEVDETFHARFLVEQKTYLYRIHLGD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNS 179
             +  +K  ++ + + L+ + MR   +   G H F +F  S   +  + +RTI   ++  
Sbjct: 119 YDV-FQKDDSFQLREDLNLKEMRKCWKLFEGTHSFLSFNTSSLSEYPNQVRTIFRTELRK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +E+ +    +L   +R  VG+   VG GK T  ++++ L    R      AP +GL
Sbjct: 178 ISDHLELEISGNGYLRHMVRILVGTCLEVGRGKLTIEEVQRMLNDPSRHYATKKAPAQGL 237

Query: 240 YFDSVEY 246
               V Y
Sbjct: 238 CLKEVSY 244


>gi|317051440|ref|YP_004112556.1| tRNA pseudouridine synthase A [Desulfurispirillum indicum S5]
 gi|316946524|gb|ADU66000.1| tRNA pseudouridine synthase A [Desulfurispirillum indicum S5]
          Length = 263

 Score =  103 bits (257), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 116/248 (46%), Gaps = 9/248 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + + Y+G+ Y GWQ Q+N + +IQ  +E A   V    + +HG+GRTD+GVHA  Q+
Sbjct: 9   RIALKVAYDGTHYHGWQTQENAANTIQAILEHAAGSVCNHPLYIHGSGRTDTGVHARGQI 68

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H           +   +N+ L     I + N   VD+ FH+++S   + Y Y I+    
Sbjct: 69  CHLTTTSTIPLFKIIMGMNSML--PRDIRVRNAFDVDEDFHSQYSTHSKKYSYAILHGCQ 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SF 180
           P  L++  +W + +++D   ++    H VG HDF   R+      + +RTI    V    
Sbjct: 127 PDPLQRLYSWHVRQTIDPARLQEELNHFVGEHDFKACRAKKATTKTTVRTIYSIGVRVES 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSL--KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            + + I      FL   IR  VG+   + +G        + + L ++DR   G  A P G
Sbjct: 187 PHKLHIHFHGNGFLKHMIRIMVGTAVDRAIG---CLDRSIPEILLSRDRTRGGRTAAPCG 243

Query: 239 LYFDSVEY 246
           L  + V Y
Sbjct: 244 LVMEEVLY 251


>gi|296274435|ref|YP_003657066.1| tRNA pseudouridine synthase A [Arcobacter nitrofigilis DSM 7299]
 gi|296098609|gb|ADG94559.1| tRNA pseudouridine synthase A [Arcobacter nitrofigilis DSM 7299]
          Length = 240

 Score =  103 bits (257), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 115/241 (47%), Gaps = 5/241 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M I Y+G  Y G QRQ N  S++  + +   ++  E  +   +GRTD  VHA  QV +  
Sbjct: 5   MTISYDGFSYQGSQRQTNKKSVEDRLIEVFKILNIEPKIT-LSGRTDKQVHATGQVFNIV 63

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +   W   +  K +  Y K+  +I I  +  V+ +FHARF A +R Y Y I T++    L
Sbjct: 64  IPAYWSNFLKLKQVMNY-KLPSSIRIRKIQKVNDEFHARFHAKKRVYRYVISTKEVSPFL 122

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
                ++  K ++ E ++ A +  +G HDF  F     +  + +R I       + +   
Sbjct: 123 ANYVTFV--KEINEEKIKEAIKLFIGVHDFEYFHKSGSEKDNKVREIFDAKFYKYKDFYI 180

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            R  A S+L +QIR  VG L  + +GK +  DL+  L  +      P A P GLY   V+
Sbjct: 181 FRFEANSYLRSQIRIMVGFLLKISEGKLSKNDLKAQLSREKYIYKTP-ALPNGLYLSQVK 239

Query: 246 Y 246
           Y
Sbjct: 240 Y 240


>gi|311064868|ref|YP_003971594.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum PRL2010]
 gi|310867188|gb|ADP36557.1| TruA tRNA pseudouridine synthase A [Bifidobacterium bifidum
           PRL2010]
          Length = 303

 Score =  103 bits (257), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 84/286 (29%), Positives = 135/286 (47%), Gaps = 44/286 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDS 53
           ++R  + + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+
Sbjct: 3   VMRLRIDLAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDT 62

Query: 54  GVHALRQVAHFDLVREWV----------PVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           GVHA  QV H D+  E +          P +  K     +  +D I+I ++++    F A
Sbjct: 63  GVHASHQVCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPAD-ITIHDVTVAPSGFDA 121

Query: 104 RFSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R+Y+YR+  R + +    +G    +   LD   M  AA   +G HDF +F + +
Sbjct: 122 RFSALERTYVYRVADRASEVDPRLRGFVLHLDADLDVAAMNEAAAMTIGLHDFGSFATPN 181

Query: 163 CQASSPIRTID----------HFDVNSFG----------NLIEIRVVARSFLHTQIRSFV 202
              ++ IR +              V+  G          +L+   +VA +F    +RS V
Sbjct: 182 PGGTT-IREVKTAYWRRIPTRPLVVDGMGERYRTPAAESDLLCFTIVADAFARNMVRSLV 240

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKE--CGPLAPPEGLYFDSVEY 246
           G    VG GK  STD  +   A   +E   GP+A P+GL  + V Y
Sbjct: 241 GGCIQVGMGK-RSTDWFREKMAVPLREGSTGPIA-PQGLTLEHVAY 284


>gi|257069454|ref|YP_003155709.1| pseudouridylate synthase I [Brachybacterium faecium DSM 4810]
 gi|256560272|gb|ACU86119.1| pseudouridylate synthase I [Brachybacterium faecium DSM 4810]
          Length = 346

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 87/271 (32%), Positives = 124/271 (45%), Gaps = 29/271 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ + GW  Q    ++QG +EKA+  +      V  AGRTD+GVHA  QV
Sbjct: 34  TRLRLDLSYDGTDFHGWAAQPGQRTVQGELEKALRRIARIPARVTVAGRTDAGVHARGQV 93

Query: 62  AHFDLVREWV-------PVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSY 112
            H DL  + +       P    +AL + L   + + + +     V   F ARF A  R Y
Sbjct: 94  CHLDLPDDVLATLPGRSPRTPAEALVSRLAGVLPEDVVVHVAREVPDDFDARFGAQWRRY 153

Query: 113 LYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            YRI  R A   PL  +  R     + LD E M  A+  L+G HDF ++      A++ I
Sbjct: 154 RYRISDRPAAHDPLRRDVLRHR---RPLDVEAMARASAPLLGEHDFLSYCRPREGATT-I 209

Query: 170 RTIDHFDVNSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDL- 218
           R +        G       LI   VVA +F H  +RS VG+L  VG+G+    W +  L 
Sbjct: 210 RELRELRWERPGEGRADEGLIVATVVADAFCHHMVRSLVGALLGVGEGRRDESWPAEVLA 269

Query: 219 --EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
              +    +D     PL PP+GL  D V Y 
Sbjct: 270 ARTREAARRDGVGAAPLCPPQGLTLDHVAYP 300


>gi|309802980|ref|ZP_07697081.1| tRNA pseudouridine synthase A [Bifidobacterium dentium JCVIHMP022]
 gi|308220447|gb|EFO76758.1| tRNA pseudouridine synthase A [Bifidobacterium dentium JCVIHMP022]
          Length = 302

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/287 (27%), Positives = 129/287 (44%), Gaps = 46/287 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G G+FGW +Q +  ++QG IE+ +  V        GE + +  AGRTD+G
Sbjct: 1   MRLRIDLAYDGGGFFGWAKQPDRRTVQGEIERILHTVLRVPVDDAGEPLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREW---------VPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+             VP ++         + + I+I  ++   + F ARF
Sbjct: 61  VHASHQVCHLDVSETILARCVGHMDVPPVVALTRRLQRMLPNDITIHGINEAPQGFDARF 120

Query: 106 SAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y+YRI  R + +    +G    +   LD E M  AA   +G HDF +F + +  
Sbjct: 121 SALERTYVYRIADRSSEIDPRMRGFVLHVDDDLDLETMNQAAAMTIGLHDFGSFATPNPG 180

Query: 165 ASS------------PIRTI--------DHFDVNSF-GNLIEIRVVARSFLHTQIRSFVG 203
            ++            P R +        + +   S    L    +VA +F    +RS V 
Sbjct: 181 GTTIREVKTAYWRRIPQRPLIDGEMTMGERYHTPSMESGLACFTIVADAFARNMVRSLVN 240

Query: 204 SLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
               VG GK    W +  +   L+       GP+A P+GL  + +EY
Sbjct: 241 GCVQVGIGKRSLDWFADKMATPLR---EGSTGPIA-PQGLTLEHIEY 283


>gi|219682884|ref|YP_002469267.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis AD011]
 gi|254789603|sp|B8DW40|TRUA_BIFA0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219620534|gb|ACL28691.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis AD011]
 gi|289178185|gb|ADC85431.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis BB-12]
          Length = 298

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 85/286 (29%), Positives = 130/286 (45%), Gaps = 47/286 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-----GEIVVVHGAGRTDSGV 55
           M R  + + YNG+ + GW  Q    ++QG++E+A+  +T     G + +   AGRTD+GV
Sbjct: 1   MTRLRIDLAYNGAAFHGWAAQPGCRTVQGTVEEALRRITRMPDAGSLRLTV-AGRTDAGV 59

Query: 56  HALRQVAHFDLVREW-------VPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFS 106
           HA  QV H D+  +        + +   +AL   L   + D I+I  +S+    F ARFS
Sbjct: 60  HATHQVCHVDVPDQTLGQCVGHMNLTPVQALQTRLSRMMPDDIAIHGISVAPAGFDARFS 119

Query: 107 AIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R+Y+YRI   + P     K  AW   + LD   M  AA   +G HDF +F +I    
Sbjct: 120 ALERTYVYRIADARVPWDPRLKDFAWRTDRELDIAQMNAAAALTLGLHDFGSF-AIANPG 178

Query: 166 SSPIRTID---------------------HFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
            + IR +                      H      G L+   +VA +F    +RS VG+
Sbjct: 179 GTTIREVKTAYWQRVPTRPLLGPGMGERYHTPAVESG-LLCFTIVADAFARNMVRSLVGA 237

Query: 205 LKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
              VG GK    W +  +   L+       GP+A P+GL  + + Y
Sbjct: 238 CVQVGMGKRDVDWFAGKMRVPLR---EGSTGPIA-PQGLTLEHIAY 279


>gi|147865780|emb|CAN81146.1| hypothetical protein VITISV_020811 [Vitis vinifera]
          Length = 403

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/253 (32%), Positives = 120/253 (47%), Gaps = 24/253 (9%)

Query: 17  GWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV 73
           GWQ Q++  +IQ  +EKA+   T    E + + GA RTD+GVHA  QVAHF     +  +
Sbjct: 124 GWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTDTGVHAWGQVAHFLTPFNYDGL 183

Query: 74  -ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWL 132
             +  ALN  L     I +  +S    +FHARFS   + Y Y+I          +   + 
Sbjct: 184 ESIHAALNGLL--PPDIRVREISPAVPEFHARFSXKSKIYHYKIYNDAVMDPFLRHYVYH 241

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFDVNSF---------- 180
               L+   MR AA+H  G+HDF+ F   S + ++ +P++ I  FDVN            
Sbjct: 242 SVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKNIFRFDVNEMMFLELIVNCI 301

Query: 181 ---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL---A 234
              G L+++ V    FL+ Q+R+ V  L  +G        +   L  +DRKE       A
Sbjct: 302 IAQGALLQLEVEGSGFLYRQVRNMVALLLQIGREAIPPNIVPWILATRDRKELAKYALSA 361

Query: 235 PPEGLYFDSVEYS 247
           PP GL   SV+Y+
Sbjct: 362 PPHGLCLMSVKYN 374


>gi|313140894|ref|ZP_07803087.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum NCIMB 41171]
 gi|313133404|gb|EFR51021.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum NCIMB 41171]
          Length = 304

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 84/286 (29%), Positives = 135/286 (47%), Gaps = 44/286 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDS 53
           ++R  + + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+
Sbjct: 4   VMRLRIDLAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDT 63

Query: 54  GVHALRQVAHFDLVREWV----------PVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           GVHA  QV H D+  E +          P +  K     +  +D I+I ++++    F A
Sbjct: 64  GVHASHQVCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPAD-ITIHDVTVAPSGFDA 122

Query: 104 RFSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R+Y+YR+  R + +    +G    +   LD   M  AA   +G HDF +F + +
Sbjct: 123 RFSALERTYVYRVADRASEVDPRLRGFVLHLDADLDVAAMNEAAAMTIGLHDFGSFATPN 182

Query: 163 CQASSPIRTID----------HFDVNSFG----------NLIEIRVVARSFLHTQIRSFV 202
              ++ IR +              V+  G          +L+   +VA +F    +RS V
Sbjct: 183 PGGTT-IREVKTAYWRRIPTRPLVVDGVGERYRTPAAESDLLCFTIVADAFARNMVRSLV 241

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKE--CGPLAPPEGLYFDSVEY 246
           G    VG GK  STD  +   A   +E   GP+A P+GL  + V Y
Sbjct: 242 GGCIQVGMGK-RSTDWFREKMAVPLREGSTGPIA-PQGLTLEHVAY 285


>gi|94968472|ref|YP_590520.1| tRNA pseudouridine synthase A [Candidatus Koribacter versatilis
           Ellin345]
 gi|94550522|gb|ABF40446.1| tRNA pseudouridine synthase A [Candidatus Koribacter versatilis
           Ellin345]
          Length = 257

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 82/255 (32%), Positives = 117/255 (45%), Gaps = 14/255 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + + Y+G  + GWQ Q    +IQG++ + I  +TGE  +  G+GRTD+GVHAL QVA 
Sbjct: 5   FKITLAYDGHEFHGWQIQPGKPTIQGTLAETIERITGEQTLPQGSGRTDAGVHALGQVAS 64

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
             L        L  ALN   K+  +I  L +      FHAR SA  ++Y YRI       
Sbjct: 65  VALQTPIPADGLHIALND--KLPPSIRALTVGEAAPDFHARHSAKGKTYRYRIYRAAICS 122

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF--- 180
                  W  P  LD   M+ A   + G HDFT+F +     +  IR  +  D  S    
Sbjct: 123 PFLAHYVWHYPWRLDESVMQSATAFIQGEHDFTSFAASDPDRAQRIRDAEDEDGPSNVRT 182

Query: 181 ---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                    G+ +   V    FLH  +R+ VG+    G  +  +  + K L+ + R   G
Sbjct: 183 IYDAVWRTEGHELIFEVRGNGFLHHMVRNLVGTFVDFGKWQHPAESMAKILREKSRSAAG 242

Query: 232 PLAPPEGLYFDSVEY 246
           P AP  GLY  +VEY
Sbjct: 243 PAAPASGLYLVNVEY 257


>gi|86157969|ref|YP_464754.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85774480|gb|ABC81317.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 272

 Score =  102 bits (255), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/257 (31%), Positives = 123/257 (47%), Gaps = 20/257 (7%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + + Y+G  + G+QRQ    ++Q ++E+A+  + G    +H A RTD+GVHAL QV  
Sbjct: 6   YALRLAYDGGRFRGFQRQPGLPTVQQALEEALERL-GVRAQLHVAARTDAGVHALAQVVS 64

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P  L + LN  L   + I +L+ + V   FHAR SA  R+Y+Y ++    P 
Sbjct: 65  FSARAALDPAALRRGLNEGLP--EGILVLDAARVGPSFHARGSAASRTYVY-LVGAPPPE 121

Query: 124 ALEKGRAWLIPKS-----------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            L +  AW +P +           LD   MR A    VG HDF  F     Q  + +RT+
Sbjct: 122 GL-RPYAWTLPDARAFPELAEVPPLDAAAMREALGAAVGEHDFVGFARPGEQRGT-VRTL 179

Query: 173 DHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              +V   G   L+ + +  + FL   +R+ VG+   VG G+    D+ + L A   +  
Sbjct: 180 LRAEVVEAGWAPLVAVVLEGKGFLRAMVRNLVGTAVAVGLGR-APPDVIRTLLATRGRYR 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           G  AP  GL   +V Y 
Sbjct: 239 GVRAPGWGLTLAAVRYP 255


>gi|117927545|ref|YP_872096.1| tRNA pseudouridine synthase A [Acidothermus cellulolyticus 11B]
 gi|117648008|gb|ABK52110.1| tRNA pseudouridine synthase A [Acidothermus cellulolyticus 11B]
          Length = 297

 Score =  102 bits (255), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 125/262 (47%), Gaps = 22/262 (8%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + G+ RQ    ++Q  +E+A+ +V    E   V  AGRTD+GVHA  Q
Sbjct: 20  RLRIDLGYDGTDFAGFARQPGLRTVQAEVERALAVVLRLPEPPPVTAAGRTDAGVHARGQ 79

Query: 61  VAHFDLVREWVPVILCKA-------------LNAYLKISDTISILNLSIVDKQFHARFSA 107
           V H D+  + + V+                 LN  L   D I++  + +    F ARFSA
Sbjct: 80  VLHVDVPIDALRVVGAAETGAADAVAQLAARLNGVLP--DDIAVHAVGLAPPGFDARFSA 137

Query: 108 IRRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           + R Y YR+  R+  PL       W  P+ LD   M  A   L+G HDF  F      A+
Sbjct: 138 LARRYSYRVADRRWDPLRRRDTLRW--PRPLDETAMNAAGAALLGEHDFAAFCRRRENAT 195

Query: 167 SPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           + IR +  F+    G+ + + +V A +F H+ +R+ VG++  VG G+       + L A+
Sbjct: 196 T-IRRLLRFEWLRDGDGVLVAQVEADAFCHSMVRALVGAVLAVGAGRRPVGWPAEVLAAR 254

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R     + PP GL  + V Y 
Sbjct: 255 ARDPAVTVVPPHGLTLEEVCYP 276


>gi|256390175|ref|YP_003111739.1| tRNA pseudouridine synthase A [Catenulispora acidiphila DSM 44928]
 gi|256356401|gb|ACU69898.1| tRNA pseudouridine synthase A [Catenulispora acidiphila DSM 44928]
          Length = 284

 Score =  102 bits (255), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 79/258 (30%), Positives = 123/258 (47%), Gaps = 16/258 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW  Q    ++ G +  A+  V  + V +  AGRTD+GVHA  QV
Sbjct: 10  VRVRLDLAYDGTHFSGWAIQPKRRTVCGELTSALSTVLRQDVTLVVAGRTDAGVHASGQV 69

Query: 62  AHFDLVRE-WV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           AH D+  E W      L + L A L     + + +       F ARF+A+ R Y YR+  
Sbjct: 70  AHLDVPLELWAEHEERLLRRLAAVLP--GDVRVWSAVPAPVGFDARFAAMGRRYAYRVTD 127

Query: 119 RQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD- 176
               P  L +      P++LD   M  AA  L+G HDF +F     + ++ IR +   + 
Sbjct: 128 AAYGPHPLRRNDVTWHPRTLDPALMNEAAAALLGEHDFASF-CKKREGATTIRCLTRLEW 186

Query: 177 -------VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                  +   G L+   V A +F H+ +RS VG+L  VG+G+    D  + L  + R  
Sbjct: 187 TREAPTSLTPVGLLV-ADVRADAFCHSMVRSLVGALLAVGEGRRPVGDPGRILAEEVRSP 245

Query: 230 CGPLAPPEGLYFDSVEYS 247
              +APP+GL  + V Y 
Sbjct: 246 EVKVAPPQGLTLEEVVYP 263


>gi|283455394|ref|YP_003359958.1| 50S ribosomal protein L17 [Bifidobacterium dentium Bd1]
 gi|283102028|gb|ADB09134.1| rplQ 50S ribosomal protein L17 [Bifidobacterium dentium Bd1]
          Length = 296

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/281 (28%), Positives = 126/281 (44%), Gaps = 46/281 (16%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSGVHALRQ 60
           + Y+G G+FGW +Q +  ++QG IE+ +  V        GE + +  AGRTD+GVHA  Q
Sbjct: 1   MAYDGGGFFGWAKQPDRRTVQGEIERILHTVLRVPVDDAGEPLRLTVAGRTDTGVHASHQ 60

Query: 61  VAHFDLVREW---------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           V H D+             VP ++         + + I+I  ++   + F ARFSA+ R+
Sbjct: 61  VCHLDISETILARCVGHMNVPPVVALTRRLQRMLPNDITIHGINEAPQGFDARFSALERT 120

Query: 112 YLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS--- 167
           Y+YRI  R + +    +G    +   LD E M  AA   +G HDF +F + +   ++   
Sbjct: 121 YVYRIADRSSEIDPRMRGFVLHVDDDLDLETMNQAAAMTIGLHDFGSFATPNPGGTTIRE 180

Query: 168 ---------PIRTI--------DHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                    P R +        + +   S    L    +VA +F    +RS V     VG
Sbjct: 181 VKTAYWRRIPQRPLVDGEMTMGERYRTPSMESGLACFTIVADAFARNMVRSLVNGCVQVG 240

Query: 210 DGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            GK    W +  +   L+       GP+A P+GL  + +EY
Sbjct: 241 IGKRSLDWFADKMATPLR---EGSTGPIA-PQGLTLEHIEY 277


>gi|220913398|ref|YP_002488707.1| tRNA pseudouridine synthase A [Arthrobacter chlorophenolicus A6]
 gi|219860276|gb|ACL40618.1| tRNA pseudouridine synthase A [Arthrobacter chlorophenolicus A6]
          Length = 297

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 81/263 (30%), Positives = 122/263 (46%), Gaps = 19/263 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW  Q    ++QG++E+A+ L+    + V  AGRTD+GVHA  QV
Sbjct: 17  LRIRLDLSYDGGPFSGWAVQPGRRTVQGTLEEALELLVRRPLRVTVAGRTDAGVHARGQV 76

Query: 62  AHFDLVR-EWVPVI--------------LCKALNAYL-KISDTISILNLSIVDKQFHARF 105
            H DL   EW+ +               L  ALN  L  ++  + +  ++     F ARF
Sbjct: 77  VHLDLAESEWLGMARGHELDPATAMTRRLRGALNRVLGDLTGAVQVRGIAPAPDGFDARF 136

Query: 106 SAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R Y YRI    A    LE+         LD E +   A  L+G  +F +F     +
Sbjct: 137 SALWRRYSYRIADGPALWDPLERAFTLWHKNPLDVELLNQGAARLLGLQNFLSFCKPR-E 195

Query: 165 ASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            ++ IR +  F+   +    I   V A +F H  +R+ +GS   VG+G      L + L 
Sbjct: 196 GATTIRELQRFEFARAEDGAIVATVQADAFCHNMVRALIGSALYVGEGTVEPGWLYERLL 255

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           AQ R     LA P  L F+ V Y
Sbjct: 256 AQKRDAKSVLAAPHPLVFEEVAY 278


>gi|306823540|ref|ZP_07456915.1| tRNA pseudouridine synthase A [Bifidobacterium dentium ATCC 27679]
 gi|304553247|gb|EFM41159.1| tRNA pseudouridine synthase A [Bifidobacterium dentium ATCC 27679]
          Length = 296

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/281 (28%), Positives = 126/281 (44%), Gaps = 46/281 (16%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSGVHALRQ 60
           + Y+G G+FGW +Q +  ++QG IE+ +  V        GE + +  AGRTD+GVHA  Q
Sbjct: 1   MAYDGGGFFGWAKQPDRRTVQGEIERILHTVLRVPVDDAGEPLRLTVAGRTDTGVHASHQ 60

Query: 61  VAHFDLVREW---------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           V H D+             VP ++         + + I+I  ++   + F ARFSA+ R+
Sbjct: 61  VCHLDVSETILARCVGHMDVPPVVALTRRLQRMLPNDITIHGINEAPQGFDARFSALERT 120

Query: 112 YLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS--- 167
           Y+YRI  R + +    +G    +   LD E M  AA   +G HDF +F + +   ++   
Sbjct: 121 YVYRIADRSSEIDPRMRGFVLHVDDDLDLETMNQAAAMTIGLHDFGSFATPNPGGTTIRE 180

Query: 168 ---------PIRTI--------DHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                    P R +        + +   S    L    +VA +F    +RS V     VG
Sbjct: 181 VKTAYWRRIPQRPLIDGEMTMGERYHTPSMESGLACFTIVADAFARNMVRSLVNGCVQVG 240

Query: 210 DGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            GK    W +  +   L+       GP+A P+GL  + +EY
Sbjct: 241 IGKRSLDWFADKMATPLR---EGSTGPIA-PQGLTLEHIEY 277


>gi|78185547|ref|YP_377981.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9902]
 gi|123743513|sp|Q3AW68|TRUA_SYNS9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78169841|gb|ABB26938.1| tRNA pseudouridine synthase [Synechococcus sp. CC9902]
          Length = 300

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 112/244 (45%), Gaps = 14/244 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y GS + GWQRQ N  S+Q  +E AI  L     +    AGRTD+GVHA  QV
Sbjct: 17  RIALSLQYEGSDFCGWQRQNNARSVQAVLETAIAQLDPLRPIQSFAAGRTDAGVHAAAQV 76

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD        +W P     ALN  L  S  I +       + +HA +SA+ R Y Y I
Sbjct: 77  VHFDCSGPIPAAKWAP-----ALNGRLPAS--IRVRESVERPRDWHACYSAVYRRYRYII 129

Query: 117 ITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              + P        W      L+ ENMR+A + ++G HDF  F     +      TI   
Sbjct: 130 HNGRRPNLFLTPWTWHRYHHRLNEENMRVALEGMIGLHDFAAFMRAGSRRPHSRTTIQDV 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G+LI + + A  FL+  +R  +  L  VG+ + +    E+  + + R +    AP
Sbjct: 190 LVEREGDLIRVEIQASGFLYGMVRLLMAQLVAVGEHRLSVKAFEQRWRDRRRDQVREAAP 249

Query: 236 PEGL 239
             GL
Sbjct: 250 ARGL 253


>gi|270014158|gb|EFA10606.1| hypothetical protein TcasGA2_TC012867 [Tribolium castaneum]
          Length = 315

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 94/296 (31%), Positives = 128/296 (43%), Gaps = 51/296 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAI-FLVTGEIVVVHGAGRTDS 53
           RY +   Y G+ + G QRQ  G        S++QG +E A+  L      VV+ + RTDS
Sbjct: 5   RYLLHFSYIGTPFMGAQRQVTGRMPRPDDPSTVQGQLEMALKRLNPTNDPVVYLSSRTDS 64

Query: 54  GVHALRQVAHFDLVR----EWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAI 108
           GVHAL    H DL R    E+ P  +   LN Y   ++  I ++    V   FH R +AI
Sbjct: 65  GVHALNSTCHVDLYRSNELEYEPKTITICLNRYFDKNEVPIRVIKTYWVPPDFHCRHTAI 124

Query: 109 RRSYLYRI------ITRQA------PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            R+YLYRI      +T  A      P+   +   +    S + + M+ AA+   G HDF 
Sbjct: 125 SRTYLYRIAIAKTGVTEHATILNLLPIEEYQRCLFFYCDSFNIDEMKEAAKVFEGLHDFR 184

Query: 157 TF--RSIHCQASSPIRTIDHFDV--------NSFG------------NLIEIRVVARSFL 194
           TF  R  H       R +   DV        +SF                +I V A  FL
Sbjct: 185 TFMGRGSHDPDKITRRVVTRVDVCDGRALTYSSFSWPRFASGSAENYQFYDIYVQATGFL 244

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK---ECGPLAPPEGLYFDSVEYS 247
           + Q+R  V SL  VG GK T  +L+  L+    +   E     P  GLY   VEYS
Sbjct: 245 YRQVRRMVASLIAVGQGKKTRRELKLMLEVPSHRSWDERIKTVPAYGLYLCEVEYS 300


>gi|162456345|ref|YP_001618712.1| tRNA pseudouridine synthase A [Sorangium cellulosum 'So ce 56']
 gi|161166927|emb|CAN98232.1| tRNA pseudouridine synthase A [Sorangium cellulosum 'So ce 56']
          Length = 281

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 117/245 (47%), Gaps = 7/245 (2%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + + Y+G  + G+ RQ++  ++ G +  A+ ++   I  + GA RTD+GVHA  Q   F
Sbjct: 1   MLSVAYDGRPFAGFARQRDQRTVSGELLGALRVIDPGIREIRGASRTDAGVHARDQRVAF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P     A   +L   D I I   ++V   F  RF ++R+ Y Y I+       
Sbjct: 61  DTTAPLPPRGWVLATARHLP--DEIVIRRAAVVRLGFSPRFESLRKRYRYLILRDLVRDP 118

Query: 125 LEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN---S 179
               RAW +    D   E  R  A    G HDF  FR+   + ++ +RT+   +++   +
Sbjct: 119 FLSRRAWRVEGITDEAIERARAEALAAKGTHDFAAFRTSADERTTTVRTLYGVELSLDPA 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              ++ I V   +FLH  +R  VG+L  V  G      + +AL + DR++ G  APP+GL
Sbjct: 179 DPRVVRIDVEGNAFLHNMVRILVGTLMDVARGHLAPGAIARALSSLDRRDAGITAPPDGL 238

Query: 240 YFDSV 244
           Y + +
Sbjct: 239 YLERI 243


>gi|78187037|ref|YP_375080.1| tRNA pseudouridine synthase A [Chlorobium luteolum DSM 273]
 gi|123730052|sp|Q3B3P4|TRUA_PELLD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78166939|gb|ABB24037.1| tRNA pseudouridine synthase [Chlorobium luteolum DSM 273]
          Length = 253

 Score =  102 bits (254), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 108/240 (45%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           +EY+G+ Y GWQRQ  G  ++QG +E  +  +  E V +  AGRTD GVHAL QV +F  
Sbjct: 8   VEYDGTPYAGWQRQPGGIVTVQGELEACLSRILQERVNLAAAGRTDRGVHALGQVVNFQT 67

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                   +  +LN  L   DTI +     VD +FHARFSA  R Y Y ++  + P A+ 
Sbjct: 68  ASSLELQRIAHSLNCLLP--DTIRVDCPQEVDMEFHARFSAAERQYRYFLM--EEPSAVF 123

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
              A    + LD   M   A  L G HDF+ F       +  + ++           +  
Sbjct: 124 GRFAGCSSRPLDLPLMHSLAVTLKGIHDFSAFSREDRDGTGSLCSVRMAGWYRHRGFLVF 183

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL + +R  VG++  +G G+      +  L A         A   GL+   V Y
Sbjct: 184 HIAANRFLRSMVRGLVGAMMDIGAGRLDPCSFKAMLDADAHARRVRPAAASGLFLSRVVY 243


>gi|255281297|ref|ZP_05345852.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
 gi|255268254|gb|EET61459.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
          Length = 280

 Score =  102 bits (254), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 73/274 (26%), Positives = 119/274 (43%), Gaps = 35/274 (12%)

Query: 6   MIIEYNGSGYFGWQRQKN-GSSIQGSIEKAI--------------FLVTGEIVV------ 44
           + + Y+G+ Y GW+ +     +IQG +E  +               +     VV      
Sbjct: 7   LTVTYDGTRYHGWEAKPGIEMTIQGKLEAVLTKMLAFPDDVPVQSLIAPAASVVSCNPGA 66

Query: 45  ------------VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISIL 92
                       V GAGRTD+GVHA    A+  L    +P  +   LN YL   + I + 
Sbjct: 67  ADGMPGCPVPVKVIGAGRTDAGVHAREMTANVHLDTAMLPGDIRDYLNRYL--PEDICVR 124

Query: 93  NLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
            + IV  +FH+R++A  ++Y Y   T       ++   +++ K+ D   M+ AA +L G 
Sbjct: 125 EVCIVSDRFHSRYNATGKTYRYTCFTGPLKPVFDRKYVYVLDKTPDIAAMKKAAGYLCGT 184

Query: 153 HDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           HDF +F        S +RTID  ++    + +        FL   +R   G+L   G G+
Sbjct: 185 HDFASFCGNPKMKKSTVRTIDSIEITQNNSYLYFMYHGNGFLQHMVRILTGTLLETGYGR 244

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +   + + L A+ R   G LAP +GL    V+Y
Sbjct: 245 RSPESMPELLAARKRALAGFLAPAQGLCLMKVDY 278


>gi|194336595|ref|YP_002018389.1| tRNA pseudouridine synthase A [Pelodictyon phaeoclathratiforme
           BU-1]
 gi|259550418|sp|B4SA76|TRUA_PELPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|194309072|gb|ACF43772.1| tRNA pseudouridine synthase A [Pelodictyon phaeoclathratiforme
           BU-1]
          Length = 243

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 112/242 (46%), Gaps = 5/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + +EY+G+ + GWQRQ     ++QG IE A+  +  E + +  AGRTD GVHA  Q A+F
Sbjct: 6   VTVEYDGTSFAGWQRQSGAIVTVQGEIEVALGKILQEKISLAAAGRTDKGVHARAQTANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                  P  +  +LN+ L    TI I N   VD  FHAR SA  R Y Y +I  + P A
Sbjct: 66  FTASSLEPSRIVHSLNSLLP--QTIRISNPEEVDADFHARHSAKERQYRYFLI--EEPSA 121

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           +    A      LD   M+  A  LVG HDF+ F          I ++         + +
Sbjct: 122 IYGRFAGCSFGKLDVAIMQQMAAILVGTHDFSAFSKEDRDNPGRICSVTACKWYPCKHYL 181

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +R+ A  FL + +R  V ++   G G+ +  D  + L+          A P GL+   V
Sbjct: 182 VLRISADRFLRSMVRYLVDAMIRAGKGRLSVGDFCRMLETGVTTSQLNPALPAGLFLWDV 241

Query: 245 EY 246
            Y
Sbjct: 242 LY 243


>gi|91215693|ref|ZP_01252663.1| putative tRNA pseudouridine synthase A [Psychroflexus torquis ATCC
           700755]
 gi|91186159|gb|EAS72532.1| putative tRNA pseudouridine synthase A [Psychroflexus torquis ATCC
           700755]
          Length = 224

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 111/222 (50%), Gaps = 5/222 (2%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV-ILCKALNAYLK 84
           S+Q  +  A+     E V V GAGRTD+GVHA   VAHFD  ++     +L   LN+ L 
Sbjct: 5   SVQSQVNLALKTALQETVDVVGAGRTDTGVHASGYVAHFDSSQKIFDFKMLAFKLNSIL- 63

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
               I++ ++  V   FHARF AI R+Y Y II  + P ++  GR++L+   L+ + M+ 
Sbjct: 64  -PPDIAVQSVVGVKDDFHARFDAISRTYRYSIIQTKDPFSV--GRSYLVKNELNLQVMQN 120

Query: 145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
           A+  L    +F +F  +     +    I+  +    G+ +   + A  FL   +R+ VG+
Sbjct: 121 ASNLLFNHKNFKSFSKVKTDVYTFDCHIEKVEWQKEGHHLFFEITANRFLRNMVRAIVGT 180

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           L  VG  K +  +    + A+DR + G   P   L   +++Y
Sbjct: 181 LIEVGLEKISVEEFNDIILAKDRSKAGKSVPAHALVLTNIKY 222


>gi|254819223|ref|ZP_05224224.1| tRNA pseudouridine synthase A [Mycobacterium intracellulare ATCC
           13950]
          Length = 251

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 118/239 (49%), Gaps = 26/239 (10%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP-------------- 72
           + G +++A+  +    V +  AGRTD+GVHA  QVAH D+    +P              
Sbjct: 1   MAGVLDEALTTIFRTPVRLRAAGRTDAGVHATGQVAHVDVPAAALPNAYSRAPHVGEAEF 60

Query: 73  VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR--- 129
           + L + L  +L     + ++++      F ARFSA+RR Y+YR+ T  AP  ++  +   
Sbjct: 61  LPLLRRLGRFLPTD--VRVVDIVRAPAGFDARFSALRRHYVYRLST--APWGVDPQQVRY 116

Query: 130 --AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
             AW  P+ LD E M  A++ L+G HDF  F   H + ++ IR +   +    G+LI  R
Sbjct: 117 VTAW--PRPLDVEAMATASRDLLGLHDFAAF-CRHRENATTIRDLQRLEWTREGDLITAR 173

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           V A +F  + +RS VG+L  VG+ +   +   + L A  R      AP  GL    V+Y
Sbjct: 174 VSADAFCWSMVRSLVGALLAVGEHRRPVSWCRELLSATARSSDYATAPAHGLTLVGVDY 232


>gi|224283738|ref|ZP_03647060.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum NCIMB 41171]
          Length = 298

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 83/279 (29%), Positives = 131/279 (46%), Gaps = 44/279 (15%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSGVHALRQ 60
           + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+GVHA  Q
Sbjct: 5   LAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDTGVHASHQ 64

Query: 61  VAHFDLVREWV----------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           V H D+  E +          P +  K     +  +D I+I ++++    F ARFSA+ R
Sbjct: 65  VCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPAD-ITIHDVTVAPSGFDARFSALER 123

Query: 111 SYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y+YR+  R + +    +G    +   LD   M  AA   +G HDF +F + +   ++ I
Sbjct: 124 TYVYRVADRASEVDPRLRGFVLHLDADLDVAAMNEAAAMTIGLHDFGSFATPNPGGTT-I 182

Query: 170 RTID----------HFDVNSFG----------NLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           R +              V+  G          +L+   +VA +F    +RS VG    VG
Sbjct: 183 REVKTAYWRRIPTRPLVVDGVGERYRTPAAESDLLCFTIVADAFARNMVRSLVGGCIQVG 242

Query: 210 DGKWTSTDLEKALQAQDRKE--CGPLAPPEGLYFDSVEY 246
            GK  STD  +   A   +E   GP+A P+GL  + V Y
Sbjct: 243 MGK-RSTDWFREKMAVPLREGSTGPIA-PQGLTLEHVAY 279


>gi|257054500|ref|YP_003132332.1| pseudouridylate synthase I [Saccharomonospora viridis DSM 43017]
 gi|256584372|gb|ACU95505.1| pseudouridylate synthase I [Saccharomonospora viridis DSM 43017]
          Length = 300

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 127/278 (45%), Gaps = 51/278 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSGV 55
           +R  + + Y+G+ + GW RQ    ++QG +E A+        + G +VV   AGRTD+GV
Sbjct: 15  VRLRIDLSYDGTDFSGWARQPGRRTVQGVLEDALAKQPPGASIAGPVVV---AGRTDAGV 71

Query: 56  HALRQVAHFDLVR-------------------EWVPVILCKALNAYLKISDTISILNLSI 96
           HA+ QV H D+ R                   +W    L + L A       + +L++  
Sbjct: 72  HAIGQVVHVDVTRLAGETRSRMPISSDGLPDLDWARYRLNRVLPA------DVRVLSIRR 125

Query: 97  VDKQFHARFSAIRRSYLYRIITRQ---APLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
               F ARFSA++R Y Y++       +PL      AW  P+ L  + M  AA  L+G H
Sbjct: 126 APAGFDARFSAVKRHYRYQVSDAPWGVSPLRRRDTLAW--PRPLSVDAMNEAASSLLGLH 183

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE----IRVVARSFLHTQIRSFVGSLKLVG 209
           DF  F    C+      TI       +  + E    + V A +F H+ +RS VG+L  VG
Sbjct: 184 DFAAF----CKRREGATTIRELMELRWCRVDEYELHLSVSADAFCHSMVRSLVGALLWVG 239

Query: 210 DGKWTSTDLEKALQA-QDRKECGPLAPPEGLYFDSVEY 246
           DG+    D+   L+  + R+    +AP  GL    V+Y
Sbjct: 240 DGR---RDVGWPLEVLRSRQRSSVVAPAHGLTLVKVDY 274


>gi|119718091|ref|YP_925056.1| tRNA pseudouridine synthase A [Nocardioides sp. JS614]
 gi|119538752|gb|ABL83369.1| tRNA pseudouridine synthase A [Nocardioides sp. JS614]
          Length = 268

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 83/254 (32%), Positives = 120/254 (47%), Gaps = 16/254 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW  Q    ++QG +  A+  V    E+ VV  AGRTD+GVHA  
Sbjct: 1   MRIRLDLAYDGTDFHGWASQPGLRTVQGELSDALATVLRVPEVAVV-CAGRTDAGVHARG 59

Query: 60  QVAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           QV H DL  +       L + LN  L     + +         F ARF A+ R Y YRI 
Sbjct: 60  QVVHADLDGLEPATVEGLVRRLNGRLPAD--VRVRRAVEAPAGFDARFGALWRRYAYRIA 117

Query: 118 TRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
              A   PL      AW  P++LD + M  A+  LVGRHDF +F     + ++ IRT+  
Sbjct: 118 DTPAVVDPLTRSHVLAW--PRALDLDAMNAASAFLVGRHDFASF-CKQREGATTIRTLLE 174

Query: 175 FD--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                +  G L+   V A +F H+ +RS VG L  VG+ +      E  L+A+ R     
Sbjct: 175 LSWARDPAGVLVGT-VRADAFCHSMVRSLVGCLIAVGEARKPVAWAEDILRAEARDPAVA 233

Query: 233 LAPPEGLYFDSVEY 246
           +    GL  + V Y
Sbjct: 234 VVHAHGLTLEEVAY 247


>gi|310287995|ref|YP_003939254.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum S17]
 gi|309251932|gb|ADO53680.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum S17]
          Length = 298

 Score =  102 bits (253), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 83/279 (29%), Positives = 131/279 (46%), Gaps = 44/279 (15%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSGVHALRQ 60
           + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+GVHA  Q
Sbjct: 5   LAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDTGVHASHQ 64

Query: 61  VAHFDLVREWV----------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           V H D+  E +          P +  K     +  +D I+I ++++    F ARFSA+ R
Sbjct: 65  VCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPAD-ITIHDVTVAPSGFDARFSALER 123

Query: 111 SYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y+YR+  R + +    +G    +   LD   M  AA   +G HDF +F + +   ++ I
Sbjct: 124 TYVYRVADRASEVDPRLRGFVLHLDADLDVVAMNEAAAMTIGLHDFGSFATPNPGGTT-I 182

Query: 170 RTID----------HFDVNSFG----------NLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           R +              V+  G          +L+   +VA +F    +RS VG    VG
Sbjct: 183 REVKTAYWRRIPTRPLVVDGMGERYRTPAAESDLLCFTIVADAFARNMVRSLVGGCIQVG 242

Query: 210 DGKWTSTDLEKALQAQDRKE--CGPLAPPEGLYFDSVEY 246
            GK  STD  +   A   +E   GP+A P+GL  + V Y
Sbjct: 243 MGK-RSTDWFREKMAVPLREGSTGPIA-PQGLTLEHVAY 279


>gi|332669550|ref|YP_004452558.1| tRNA pseudouridine synthase A [Cellulomonas fimi ATCC 484]
 gi|332338588|gb|AEE45171.1| tRNA pseudouridine synthase A [Cellulomonas fimi ATCC 484]
          Length = 316

 Score =  102 bits (253), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 113/234 (48%), Gaps = 26/234 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDS 53
           +R  + + Y+G+ + GW RQ    ++QG +E A+  V       HG        AGRTD+
Sbjct: 17  VRLRLDLAYDGTSFSGWARQPALRTVQGVLEDALATVL--RTAAHGEPAPHVTVAGRTDA 74

Query: 54  GVHALRQVAHFDL-------VREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+       VR         AL A L   +   + +  +++    F AR
Sbjct: 75  GVHARGQVAHMDVAPHVLDAVRGRSDRTPTDALVARLAGVLPADVVVHRVAVAPLGFDAR 134

Query: 105 FSAIRRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+RR Y YRI     A   L +       + LD   M  AA+ LVGRHDF  +     
Sbjct: 135 FSALRRRYAYRICDDSGARDPLSRAHVLWHRRPLDVAAMDAAARTLVGRHDFAAYCKPR- 193

Query: 164 QASSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           + ++ IRT++ F        +   L+  RV A +F H+ +R+ VG+   VG+G+
Sbjct: 194 EGATTIRTLEEFVWERASGGAEAGLVVARVQADAFCHSMVRALVGASVAVGEGR 247


>gi|311896534|dbj|BAJ28942.1| putative tRNA pseudouridine synthase A [Kitasatospora setae
           KM-6054]
          Length = 302

 Score =  102 bits (253), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 81/263 (30%), Positives = 122/263 (46%), Gaps = 24/263 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA--IFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + GW RQ+   ++QG +E A  I L + E   +  AGRTD+GVHA  Q
Sbjct: 21  RIRLDLAYHGAEFSGWARQRERRTVQGELEDALRIVLRSEENFPLTVAGRTDAGVHARGQ 80

Query: 61  VAHFDLVREWVPVILCKALNAYL------KISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAH DL     P  L       L      ++   + +  ++     F ARF+AI R Y Y
Sbjct: 81  VAHVDL-----PDALWAQHGEKLLRRLAGRLPADVRVYRVAEAPHGFDARFAAIWRRYAY 135

Query: 115 RIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI- 172
           R+      +  L +G      + LD E M  AA+ LVG HDF  +     + ++ IRT+ 
Sbjct: 136 RVADHPGGVDPLLRGHVLWHDRPLDLEKMNEAARLLVGEHDFAAY-CKKREGATTIRTLL 194

Query: 173 ----DHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
               +   ++ +    G+L    V A +F H  +R+ VG++ LVGDG        K L  
Sbjct: 195 ELHWERVPIDPYAAQEGSLAVATVRADAFCHNMVRALVGAMLLVGDGHRPVEFPGKVLAG 254

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
             R     +  P GL  + V Y 
Sbjct: 255 GVRDSAVNVIRPHGLTLEEVGYP 277


>gi|116075742|ref|ZP_01473001.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9916]
 gi|116067057|gb|EAU72812.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9916]
          Length = 278

 Score =  102 bits (253), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 114/240 (47%), Gaps = 6/240 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH--GAGRTDSGVHALRQ 60
           R  + ++Y GS + GWQRQ+ G+S+Q ++++AI  +   I  VH   AGRTD+GVHA  Q
Sbjct: 4   RIALSLQYEGSAFCGWQRQRQGNSVQAALDEAISQLD-PIRPVHTVAAGRTDAGVHAAGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN   ++  TI +         +HA +SA  R Y Y I   +
Sbjct: 63  VVHFDCCGPIPAWRWAPALNG--RLPGTIRVREAVERPLDWHACYSATYRRYRYTIYNGR 120

Query: 121 APLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P        W      LD   M  A Q L+G HDF  F     + +    TI    +  
Sbjct: 121 RPNLFLTPWTWHRYQARLDDSLMGEALQGLLGLHDFGAFMRAGSRRAHSRTTIQDVSLER 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ + + A  FL+  +R  +G L  VG+ + +    E+  + + R E    APP+GL
Sbjct: 181 EGDLVTVEIQASGFLYGMVRLLMGQLVAVGEHRLSLEAFERRWRERRRSEVKDAAPPQGL 240


>gi|289427598|ref|ZP_06429310.1| tRNA pseudouridine synthase A [Propionibacterium acnes J165]
 gi|289159089|gb|EFD07281.1| tRNA pseudouridine synthase A [Propionibacterium acnes J165]
 gi|313808787|gb|EFS47241.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL087PA2]
 gi|313824843|gb|EFS62557.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL063PA1]
 gi|314979788|gb|EFT23882.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL072PA2]
 gi|315089972|gb|EFT61948.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL072PA1]
 gi|327325121|gb|EGE66927.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL096PA3]
 gi|327449322|gb|EGE95976.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL013PA2]
 gi|332676207|gb|AEE73023.1| tRNA pseudouridine synthase A [Propionibacterium acnes 266]
          Length = 279

 Score =  102 bits (253), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 74/252 (29%), Positives = 120/252 (47%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I   L   +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L  +  I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVL--TPDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAF-CKHREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|282855153|ref|ZP_06264485.1| tRNA pseudouridine synthase A [Propionibacterium acnes J139]
 gi|295131337|ref|YP_003582000.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK137]
 gi|282581741|gb|EFB87126.1| tRNA pseudouridine synthase A [Propionibacterium acnes J139]
 gi|291375873|gb|ADD99727.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK137]
 gi|313773224|gb|EFS39190.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL074PA1]
 gi|313810419|gb|EFS48133.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL083PA1]
 gi|313812247|gb|EFS49961.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL025PA1]
 gi|313817968|gb|EFS55682.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL046PA2]
 gi|313823371|gb|EFS61085.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL036PA2]
 gi|313830085|gb|EFS67799.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL007PA1]
 gi|313832643|gb|EFS70357.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL056PA1]
 gi|314924129|gb|EFS87960.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL001PA1]
 gi|314925807|gb|EFS89638.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL036PA3]
 gi|314960817|gb|EFT04918.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL002PA2]
 gi|314964970|gb|EFT09069.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL082PA2]
 gi|314973066|gb|EFT17162.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL053PA1]
 gi|314975562|gb|EFT19657.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL045PA1]
 gi|314982235|gb|EFT26328.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA3]
 gi|314984846|gb|EFT28938.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA1]
 gi|314986106|gb|EFT30198.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA2]
 gi|314988720|gb|EFT32811.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA3]
 gi|315079903|gb|EFT51879.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL078PA1]
 gi|315083346|gb|EFT55322.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL027PA2]
 gi|315086881|gb|EFT58857.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL002PA3]
 gi|315090495|gb|EFT62471.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA4]
 gi|315093731|gb|EFT65707.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL060PA1]
 gi|315096707|gb|EFT68683.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL038PA1]
 gi|327325250|gb|EGE67055.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL096PA2]
 gi|327325550|gb|EGE67349.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL103PA1]
 gi|327444051|gb|EGE90705.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL043PA1]
 gi|327449450|gb|EGE96104.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL043PA2]
 gi|328756334|gb|EGF69950.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL020PA1]
 gi|328761333|gb|EGF74860.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL099PA1]
          Length = 279

 Score =  102 bits (253), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 74/252 (29%), Positives = 120/252 (47%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I   L   +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L  +  I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVL--TPDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAF-CKHREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|260220773|emb|CBA28673.1| tRNA pseudouridine synthase A [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 192

 Score =  102 bits (253), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 56/146 (38%), Positives = 78/146 (53%)

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           FH R SAI R Y Y ++      ++E GR      +LD  +MR AA +L+G HDFT+FR+
Sbjct: 30  FHCRASAISRRYAYVLLESPIRPSVETGRVGWTFNNLDEMSMRKAADYLIGEHDFTSFRA 89

Query: 161 IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             CQA SP++ +   D +  G    I   A +FLH  IR+ +G L  +G  K     +E+
Sbjct: 90  AQCQALSPVKNVMRIDFHKRGAYWRIEFEANAFLHHMIRNIMGCLVQIGQRKKPPEWMEE 149

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEY 246
            L A+ RK   P   P+GLYF    Y
Sbjct: 150 VLAARSRKVAAPTFSPDGLYFLGPRY 175


>gi|213622844|ref|ZP_03375627.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
          Length = 188

 Score =  102 bits (253), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 60/160 (37%), Positives = 86/160 (53%), Gaps = 2/160 (1%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQ 147
           I++  +  V   FHARFSA  R Y Y I   R  P  L KG      + LD E M  AAQ
Sbjct: 13  IAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLAKGVTHYY-EPLDAERMHRAAQ 71

Query: 148 HLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
            L+G +DFT+FR++ CQ+ +P R + H +V   G  + + + A +F+H  +R+ VGSL  
Sbjct: 72  CLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLLE 131

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           VG      + + + L A+DR      A  EGLY  +V+Y 
Sbjct: 132 VGAHNQPESWIAELLAARDRTLAAATAKAEGLYLVAVDYP 171


>gi|50843266|ref|YP_056493.1| tRNA pseudouridine synthase A [Propionibacterium acnes KPA171202]
 gi|289424889|ref|ZP_06426668.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK187]
 gi|62901286|sp|Q6A6S8|TRUA_PROAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|50840868|gb|AAT83535.1| tRNA pseudouridine synthase A [Propionibacterium acnes KPA171202]
 gi|289154588|gb|EFD03274.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK187]
 gi|313763186|gb|EFS34550.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL013PA1]
 gi|313793310|gb|EFS41368.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA1]
 gi|313801047|gb|EFS42315.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA2]
 gi|313828418|gb|EFS66132.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL063PA2]
 gi|313838001|gb|EFS75715.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL086PA1]
 gi|314914385|gb|EFS78216.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA4]
 gi|314917708|gb|EFS81539.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL050PA1]
 gi|314919564|gb|EFS83395.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL050PA3]
 gi|314930155|gb|EFS93986.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL067PA1]
 gi|314957174|gb|EFT01278.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL027PA1]
 gi|314957815|gb|EFT01918.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL002PA1]
 gi|314963491|gb|EFT07591.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL082PA1]
 gi|314969927|gb|EFT14025.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL037PA1]
 gi|315077220|gb|EFT49285.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL053PA2]
 gi|315097933|gb|EFT69909.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL059PA2]
 gi|315100698|gb|EFT72674.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL046PA1]
 gi|315106086|gb|EFT78062.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL030PA1]
 gi|315109179|gb|EFT81155.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL030PA2]
 gi|327451475|gb|EGE98129.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL087PA3]
 gi|327451552|gb|EGE98206.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL092PA1]
 gi|327451838|gb|EGE98492.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL083PA2]
 gi|328752053|gb|EGF65669.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL087PA1]
 gi|328755550|gb|EGF69166.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL025PA2]
          Length = 279

 Score =  101 bits (252), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 120/252 (47%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I   L   +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L  +  + + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVL--TPDVVVKSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDRLNTAGTSLLGLRDFAAF-CKHREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 KRLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|327332268|gb|EGE74004.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL097PA1]
          Length = 279

 Score =  101 bits (252), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 120/252 (47%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I   L   +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L  +  + + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVL--TPDVVVKSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDRLNTAGTSLLGLRDFAAF-CKHREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 KRLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|218886490|ref|YP_002435811.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           'Miyazaki F']
 gi|226708648|sp|B8DRQ6|TRUA_DESVM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|218757444|gb|ACL08343.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           'Miyazaki F']
          Length = 277

 Score =  101 bits (252), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 86/286 (30%), Positives = 122/286 (42%), Gaps = 49/286 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + + Y G+   GWQ Q         ++QG +E+    + G  V +HGAGRTDSGV
Sbjct: 1   MARLALTVSYVGTRLAGWQIQARTDRPQPRTVQGELERIAERIVGAPVRLHGAGRTDSGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+      +   +A NA L   D IS+  +  V  +FHARF A  ++Y YR
Sbjct: 61  HAEAQVAHMDVPDHRADLDWQRAFNAGL--PDDISVAAVVRVPDEFHARFDARGKTYTYR 118

Query: 116 -------IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC----- 163
                  +  R AP A   G+       LD + M  AA +L G HDF +F++        
Sbjct: 119 LWPERRWVPPRLAPFAWATGQ-------LDMDAMDAAAAYLHGMHDFASFQNTGTDIVTT 171

Query: 164 -----------QASSPIRTI---------DHFDVNSFGNLIEIRV---VARSFLHTQIRS 200
                      +  +P++                N+    + +      A  FL   +R+
Sbjct: 172 VRTVTRVARRHEGEAPVQPALPGAQPLAGAEETANAMAGGLRVMAWDFEADGFLKQMVRN 231

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +G L  VG GK     +   L A+DRK     AP  GL    V Y
Sbjct: 232 MMGLLVAVGRGKLPPDAVPAILAARDRKTAPATAPAHGLTLTRVHY 277


>gi|239918171|ref|YP_002957729.1| pseudouridylate synthase I [Micrococcus luteus NCTC 2665]
 gi|281415639|ref|ZP_06247381.1| tRNA pseudouridine synthase A [Micrococcus luteus NCTC 2665]
 gi|239839378|gb|ACS31175.1| pseudouridylate synthase I [Micrococcus luteus NCTC 2665]
          Length = 297

 Score =  101 bits (252), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 81/263 (30%), Positives = 122/263 (46%), Gaps = 20/263 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW RQ    S+QG++E  +  +    V    AGRTD+GVHA  QV
Sbjct: 19  VRVRLDLAYDGGAFHGWARQPGLDSVQGALEDGLERILRRPVRTVVAGRTDAGVHARGQV 78

Query: 62  AHFDLVR-EWVPVI-----LCKALNAYLKISDTISILNLSIV-------DKQFHARFSAI 108
            H DL   EW  +      L  A +   ++   +S    ++V          F ARFSA+
Sbjct: 79  VHLDLAETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVVVHGARRAPAGFDARFSAL 138

Query: 109 RRSYLYRIITRQAPLALE---KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
            R Y YRI     P A +   +G       +LD   M + A  ++G HDF +F      A
Sbjct: 139 WREYEYRID--DVPAARDPRTRGFTHWHGAALDDRLMALEADAVLGLHDFLSFCRPRAGA 196

Query: 166 SSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           ++ IR + H +V      ++ +R+ A +F H  +R+ VG+L  VG+G      L   +  
Sbjct: 197 TT-IREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAMVGALLQVGEGVREPGWLAHRVAR 255

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
             R     LAPP GL   +V Y 
Sbjct: 256 PARDSEVRLAPPGGLTLLAVGYP 278


>gi|255533538|ref|YP_003093910.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
 gi|255346522|gb|ACU05848.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
          Length = 269

 Score =  101 bits (252), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 80/252 (31%), Positives = 113/252 (44%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I YNG  Y GWQ+Q    ++QG IE A+  V    V + G GRTD+ VHA +  
Sbjct: 1   MRYFVHIGYNGLKYNGWQKQPGVMNVQGVIENALSKVLKTPVFIIGCGRTDAHVHASQFF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D+ ++W    L   +N  L     I+I  +  +D   HARF A+ RSY Y I T + 
Sbjct: 61  FHMDVEQDW-DFDLVFRMNKLLPAG--IAIFEVIQMDGLQHARFDAVLRSYDYFIHTYKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-------RSIHCQASSPIRTIDH 174
           P        +L+ K LD + M+ AA  L    DF  F           C   S    +D 
Sbjct: 118 PFLNGLSSFYLLDK-LDFDKMKQAAAILPKYKDFRAFCTSPDKYEHTLCNVMSASLAVD- 175

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                 G+ +  ++ +  FL   IR  +G L  +G G  +  + E  L      E    A
Sbjct: 176 ----ENGDKLRFQISSNRFLSKMIRIIMGQLLKIGRGVLSVDEFEHYLIYNQTPELITPA 231

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 232 HPQGLYLSKVTY 243


>gi|291451884|ref|ZP_06591274.1| tRNA pseudouridine synthase A [Streptomyces albus J1074]
 gi|291354833|gb|EFE81735.1| tRNA pseudouridine synthase A [Streptomyces albus J1074]
          Length = 287

 Score =  101 bits (252), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 82/260 (31%), Positives = 118/260 (45%), Gaps = 24/260 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG------EIVVVHGAGRTDSG 54
           +R  + + Y+G  + GW +Q  G  ++QG IE A+  VT       E+ V   AGRTDSG
Sbjct: 11  VRVRLDLSYDGRDFSGWAKQAAGRRTVQGEIEDALRTVTRSGERTYELTV---AGRTDSG 67

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYL------KISDTISILNLSIVDKQFHARFSAI 108
           VHA  QVAH DL     P  + +     L      ++   + I  ++     F ARFSA+
Sbjct: 68  VHARGQVAHVDL-----PAAVWEEHREKLLRRLAGRLPHDVRIWRVAEAPAGFDARFSAV 122

Query: 109 RRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R Y YR+      +  L +G       +LD E M  A+  L+G HDF  +     + ++
Sbjct: 123 WRRYAYRVTDHPGGVDPLLRGHVLWHDWTLDVEAMNAASVALLGEHDFAAY-CKRREGAT 181

Query: 168 PIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            IRT+           ++   V A +F H  +RS VG+L  VGDG        K L A  
Sbjct: 182 TIRTLQELSWERDRDGIVTATVRADAFCHNMVRSLVGALLFVGDGHRPVEWPGKVLAAGV 241

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R     +  P GL  + V Y
Sbjct: 242 RDSAVHVVRPHGLTLEEVGY 261


>gi|239980027|ref|ZP_04702551.1| tRNA pseudouridine synthase A [Streptomyces albus J1074]
          Length = 295

 Score =  101 bits (252), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 82/260 (31%), Positives = 118/260 (45%), Gaps = 24/260 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG------EIVVVHGAGRTDSG 54
           +R  + + Y+G  + GW +Q  G  ++QG IE A+  VT       E+ V   AGRTDSG
Sbjct: 19  VRVRLDLSYDGRDFSGWAKQAAGRRTVQGEIEDALRTVTRSGERTYELTV---AGRTDSG 75

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYL------KISDTISILNLSIVDKQFHARFSAI 108
           VHA  QVAH DL     P  + +     L      ++   + I  ++     F ARFSA+
Sbjct: 76  VHARGQVAHVDL-----PAAVWEEHREKLLRRLAGRLPHDVRIWRVAEAPAGFDARFSAV 130

Query: 109 RRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R Y YR+      +  L +G       +LD E M  A+  L+G HDF  +     + ++
Sbjct: 131 WRRYAYRVTDHPGGVDPLLRGHVLWHDWTLDVEAMNAASVALLGEHDFAAY-CKRREGAT 189

Query: 168 PIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            IRT+           ++   V A +F H  +RS VG+L  VGDG        K L A  
Sbjct: 190 TIRTLQELSWERDRDGIVTATVRADAFCHNMVRSLVGALLFVGDGHRPVEWPGKVLAAGV 249

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R     +  P GL  + V Y
Sbjct: 250 RDSAVHVVRPHGLTLEEVGY 269


>gi|72163015|ref|YP_290672.1| tRNA pseudouridine synthase A [Thermobifida fusca YX]
 gi|71916747|gb|AAZ56649.1| tRNA pseudouridine synthase [Thermobifida fusca YX]
          Length = 296

 Score =  101 bits (252), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 123/264 (46%), Gaps = 31/264 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           + R  + I Y+G+ + GW  Q    ++QG ++ A+  V    T ++ V   AGRTD+GVH
Sbjct: 24  LTRLRLDISYDGTDFSGWAEQPGRRTVQGELQAALARVLRIPTPQLTV---AGRTDAGVH 80

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYL------KISDTISILNLSIVDKQFHARFSAIRR 110
           A  QVAH D     VP  + +A    L       +   + +  ++     F ARFSA+ R
Sbjct: 81  ARGQVAHVD-----VPASVWEAEGERLLRRLAGVLPPDVRVTAVAPAPPGFDARFSALFR 135

Query: 111 SYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHC---Q 164
            Y+YR+    AP  ++  R   +    + LD + M  AA  L+G HDF  +    C   +
Sbjct: 136 RYVYRV--SDAPGGVDPLRRHEVLWHRRPLDVDRMNEAAAALLGEHDFAAY----CRKRE 189

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +S +R +   +       +    V A +F H  +R+ VG+L  VGDG+       + L+
Sbjct: 190 GASTVRELQRLEWRRESEHVYAATVQADAFCHNMVRALVGALLAVGDGRRPPEWPAQVLR 249

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           A  R     + PP GL  + V Y 
Sbjct: 250 AGVRDSAVHVVPPHGLTLEEVRYP 273


>gi|313816522|gb|EFS54236.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL059PA1]
          Length = 279

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 120/252 (47%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I   L   +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L  +  + + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVL--TPDVVVKSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDRLNTAGTSLLGLRDFAAF-CKHREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 KRLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLPLEEVGY 249


>gi|257066904|ref|YP_003153160.1| tRNA pseudouridine synthase A [Anaerococcus prevotii DSM 20548]
 gi|256798784|gb|ACV29439.1| tRNA pseudouridine synthase A [Anaerococcus prevotii DSM 20548]
          Length = 246

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 109/248 (43%), Gaps = 4/248 (1%)

Query: 1   MIRYCMI-IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MIR  ++   Y+G+ + G+Q QK+  S++  +  AI  VTGE   +   GRTDSGVHA  
Sbjct: 1   MIRNVLLETAYDGTNFAGFQYQKDERSVEEELRNAIRKVTGEDNRIVSCGRTDSGVHARS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              +F       P      +  +L   D I  L+   V   FHARFS   + Y Y I   
Sbjct: 61  HFVNFLTASNISPKAFSFHIQPHL--PDDILALSSKEVSLDFHARFSCKSKLYKYVIYRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVN 178
           +    + +     I   LD + +    + L G HDF  F R       + +R ID     
Sbjct: 119 RLMYPVFRNYKEEISYPLDLKRLDQGLKILEGEHDFRLFMREDKKLKINTVRKIDEAYFE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + I     SFLH Q+R  VGSL  +  G+ +  D  K     + K   P    +G
Sbjct: 179 EEGDDLAIYFKGESFLHNQVRIMVGSLIELSRGRLSLDDYRKFFDKDNNKRANPALGAQG 238

Query: 239 LYFDSVEY 246
           LY   VE+
Sbjct: 239 LYLRRVEF 246


>gi|14591061|ref|NP_143136.1| tRNA pseudouridine synthase A [Pyrococcus horikoshii OT3]
 gi|3915167|sp|O58941|TRUA_PYRHO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3257659|dbj|BAA30342.1| 262aa long hypothetical pseudouridylate synthase [Pyrococcus
           horikoshii OT3]
          Length = 262

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 123/249 (49%), Gaps = 28/249 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + I Y+G+ + G+QRQ N  +++G I KA+         +  A RTD GV AL  V
Sbjct: 1   MKVALKIAYDGTKFHGFQRQPNVRTVEGEIIKALNNSGIMFNELKSASRTDKGVSALGNV 60

Query: 62  AHFDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                  E +  P+IL    NA LK    + +L+   V   FH RF A  RS +YR    
Sbjct: 61  VAITTEDERITNPMIL----NAKLK---DVWVLSAVKVPSDFHPRFWA--RSKVYRY--- 108

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                      +L    LD E ++  ++  +G HDF+ F  +  + +  +R+ID  +V  
Sbjct: 109 -----------YLPSFDLDVEKVKECSKLFLGVHDFSAFSRVDGRET--VRSIDRIEVLD 155

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEG 238
            G ++ I V A+SFL   +R  V +L+L G GK +S ++ K L+ + ++    P AP EG
Sbjct: 156 LGPVLAIEVEAKSFLWEMVRRIVKTLELCGLGKLSSEEVRKMLRGKFEKSRKVPPAPAEG 215

Query: 239 LYFDSVEYS 247
           L    V+Y 
Sbjct: 216 LLLVEVKYK 224


>gi|307168411|gb|EFN61571.1| tRNA pseudouridine synthase-like 1 [Camponotus floridanus]
          Length = 305

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 133/293 (45%), Gaps = 55/293 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIFLVTGEIVV---VHGAGRT 51
           M+RY +   Y G+ Y G Q+Q      ++  SIQG++E A+  ++ + ++   +  + RT
Sbjct: 1   MVRYLLKFSYIGTQYRGLQKQIGNDFVRDTDSIQGALETALLTISPKSLIRPFIILSSRT 60

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYL-----KISDTISILNLSIVDKQFHARFS 106
           D+GVHAL    H +L  ++  +     +  Y+     K    I +L    + + FHAR+ 
Sbjct: 61  DAGVHALCNTGHVELENKYGQIYDTSRIKQYVNRYFTKCGHNIRLLECIPITQDFHARYC 120

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIP---------KSLDCENMRIAAQHLVGRHDFTT 157
              R+Y+YR +    P   E+ R  L+           + D +  +   +  +G  DFTT
Sbjct: 121 VKSRTYIYRFMI---PKVDEEHRIPLVEGIHTFHLRTYNFDIDRTKRGTKLFMGIKDFTT 177

Query: 158 F-------------RSIHC---QASSPIRTID----HFDVNSFGNLIEIRVVARSFLHTQ 197
           F             RS+H    + + P+   D    HF   ++ N I     ARSFL+ Q
Sbjct: 178 FSAKDEGKRNIRYVRSLHSFTLEETQPLMPFDPLSKHF---TYWNFI---CSARSFLYNQ 231

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEYS 247
           IR  VG+L  +G GK T  D+   LQ        P    APP GL+  +VEY 
Sbjct: 232 IRRMVGALFALGLGKITEKDIIVMLQVPSHYNWNPHATCAPPHGLHLLNVEYD 284


>gi|313819879|gb|EFS57593.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL036PA1]
          Length = 279

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/252 (29%), Positives = 120/252 (47%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I   L   +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L  +  I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRGL--TPDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAF-CKHREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|242398608|ref|YP_002994032.1| tRNA pseudouridine synthase A [Thermococcus sibiricus MM 739]
 gi|259550478|sp|C6A238|TRUA_THESM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|242265001|gb|ACS89683.1| tRNA pseudouridine synthase A [Thermococcus sibiricus MM 739]
          Length = 266

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 120/250 (48%), Gaps = 27/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHA 57
           +R  + I Y+G+ ++G+QRQ +  +++G + K +     +   +     GA RTD GV A
Sbjct: 1   MRIALKIAYDGTKFYGFQRQPDLRTVEGELIKVLKKLGIIEDVKEANFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L  V  F+  +    +   + LN +L+    I IL  + V + FH RF A  + Y Y   
Sbjct: 61  LGNVIAFNTAKP--ELAEARILNHHLR---DIWILGKAEVPEDFHPRFWAKNKIYRY--- 112

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +L  + +D   ++  A+  +GRHDF+ F  +  +   P+R I+  DV
Sbjct: 113 -------------YLFDEGIDVIKLKACAEAFLGRHDFSNFARLE-EFRKPVREINRIDV 158

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S G +I + +  +SFL    R  + +LKL G G  +  D+E  L+ +  K+  P APPE
Sbjct: 159 FSRGRIIVVEIEGKSFLWEMTRRIITALKLCGLGVLSIGDVELMLKEKVDKKLPP-APPE 217

Query: 238 GLYFDSVEYS 247
            L    V Y 
Sbjct: 218 NLVLWEVGYE 227


>gi|124024021|ref|YP_001018328.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9303]
 gi|166228748|sp|A2CC53|TRUA_PROM3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123964307|gb|ABM79063.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9303]
          Length = 295

 Score =  100 bits (250), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 112/244 (45%), Gaps = 14/244 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + ++Y GS + GWQRQ    S+Q  +E+AI  L     +    AGRTD+GVHA  QV
Sbjct: 17  RIGLSVQYEGSNFCGWQRQPQAVSVQQVLEEAISQLDPQRPIQAVAAGRTDAGVHAAGQV 76

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD         W P     ALN   ++ +TI +         +HA  SA  R Y Y I
Sbjct: 77  VHFDCCGPIPAERWAP-----ALNG--RLPNTIRVREAVARPASWHACHSATYRRYRYTI 129

Query: 117 ITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              + P       +W      LD   M++A + L+G  D + F+    + +    T+   
Sbjct: 130 YNGRRPNLFLTPWSWHRYHVRLDETVMQVALEGLLGLQDLSAFQRTGSRRAHARTTVQDV 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   G+LI I + A  FL+  +R  +G L  +G+ +      E+  + + R+E    AP
Sbjct: 190 KIERQGDLIMIEIQASGFLYGMVRLLMGQLVALGEHRLNLQTFERRWKEKRRQEVKEAAP 249

Query: 236 PEGL 239
            +GL
Sbjct: 250 AQGL 253


>gi|148243240|ref|YP_001228397.1| tRNA pseudouridine synthase A [Synechococcus sp. RCC307]
 gi|147851550|emb|CAK29044.1| tRNA pseudouridine synthase A [Synechococcus sp. RCC307]
          Length = 291

 Score =  100 bits (250), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 117/258 (45%), Gaps = 20/258 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL-------VTGEIVVVHGAGRTDSGV 55
           R  + ++Y+G  + GWQRQ    S+Q S+++AI         +  ++     AGRTD+GV
Sbjct: 5   RIALCLQYDGGPFCGWQRQPQHRSVQQSLDEAIEALDPLPAGIAAKLSRTIAAGRTDTGV 64

Query: 56  HALRQVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           HA  QV HFD         W P     ALN   ++  +I +   + V   +HA FSA  R
Sbjct: 65  HAAAQVVHFDCHGPIPAARWAP-----ALNG--RLPGSIRVRASAAVAANWHACFSATYR 117

Query: 111 SYLYRIITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            Y Y I   + P       +W      L    M+   Q L+G HDF+ F+    Q +   
Sbjct: 118 RYRYCIYNARRPNLFLSPFSWHRYQWRLQDHLMQELLQELLGHHDFSAFQRAGSQRAHAR 177

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            T+    +   G+++ + + A  FL+  +R  VG L   G+G+ +     +  + Q R E
Sbjct: 178 TTVQEVSLQREGDILTLEIQASGFLYGMVRLLVGQLVAAGEGRISPEQFRQRWREQRRDE 237

Query: 230 CGPLAPPEGLYFDSVEYS 247
               APP+GL    V Y 
Sbjct: 238 VKEAAPPQGLCLLRVGYP 255


>gi|300779794|ref|ZP_07089650.1| tRNA-pseudouridine synthase I [Corynebacterium genitalium ATCC
           33030]
 gi|300533904|gb|EFK54963.1| tRNA-pseudouridine synthase I [Corynebacterium genitalium ATCC
           33030]
          Length = 303

 Score =  100 bits (250), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 82/269 (30%), Positives = 126/269 (46%), Gaps = 28/269 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-------SIQGSIEKAIFLVTGEIVVVHGAGRTDS 53
           ++R  + I Y+G+ + GW RQ           ++QG +E A+ L+    V +  AGRTD+
Sbjct: 17  IVRLRLDIAYDGTRFHGWARQAAAPGEETPVRTVQGELEDALSLILRHPVELTVAGRTDA 76

Query: 54  GVHALRQVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           GVHA  QVAH D+ +  +        P  L + L   L+    + +  ++   + F ARF
Sbjct: 77  GVHATGQVAHADVPKHALDQRSIVGEPEKLTRRLARLLEPD--LRVTAVTEAPRDFDARF 134

Query: 106 SAIRRSYLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           SA+ R+Y YR+ T  A   PL      AW   K +D   ++  A  LVG +D+  F    
Sbjct: 135 SALTRTYRYRVTTNTAGPNPLRRTDTAAWT--KKIDLHAVQETATALVGLNDYAAFCKPR 192

Query: 163 CQASSPIRTIDHF---DVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
             A++ IR I  F   DV++     L E  + A +F    +R+ V +   VG G    + 
Sbjct: 193 PHATT-IRDIHSFTWADVSTPEEPELYEATITADAFCWHMVRALVATCLDVGSGARDVSW 251

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +  L A +R     LAP  GL    V+Y
Sbjct: 252 AKTLLAAHERDPLVKLAPANGLTLIRVDY 280


>gi|213964809|ref|ZP_03393008.1| tRNA pseudouridine synthase A [Corynebacterium amycolatum SK46]
 gi|213952345|gb|EEB63728.1| tRNA pseudouridine synthase A [Corynebacterium amycolatum SK46]
          Length = 333

 Score =  100 bits (250), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/265 (29%), Positives = 124/265 (46%), Gaps = 21/265 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSS------IQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           ++R    I Y+G+ + GW  Q++  +      +Q ++E  +  V    V +  AGRTD+G
Sbjct: 45  LVRLRFDIAYDGTDFHGWAAQRDKPTGEPVRTVQATLESTLEKVLRTPVQLTVAGRTDAG 104

Query: 55  VHALRQVAHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           VHA  QVAH D+    +        P  L + +   L     +++   S     F ARFS
Sbjct: 105 VHASGQVAHADVPVSCLDTRSIAGDPGNLVRRVARLLPAD--VTLRGASFAPSGFDARFS 162

Query: 107 AIRRSYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHC 163
           A+RR Y+YR+ +    PL           +S+D + M++AA  L+G +DF  F     H 
Sbjct: 163 ALRRHYVYRVTSCVSGPLPTRARDTAHWRRSVDIDRMQVAADALLGLNDFAAFCRHKPHA 222

Query: 164 QASSPIRTIDHFDVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
             +  ++    FDV++     L E  V A +F  + +RS VG+   VG+G+      E+ 
Sbjct: 223 TTTRDLQRFQWFDVSTRQEPELYEAHVTADAFCWSMVRSLVGACLSVGEGRREVGFTEQL 282

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           L  + R    P+A   GL    V+Y
Sbjct: 283 LSEEKRSPLVPVAEARGLSLVGVDY 307


>gi|297242940|ref|ZP_06926878.1| tRNA pseudouridine synthase [Gardnerella vaginalis AMD]
 gi|296889151|gb|EFH27885.1| tRNA pseudouridine synthase [Gardnerella vaginalis AMD]
          Length = 301

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 83/280 (29%), Positives = 129/280 (46%), Gaps = 36/280 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW +Q    ++QG IE A+ +V         E + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGGFYGWAKQPTLRTVQGDIEAALHMVLRVPENDPTESLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVIL-------CKALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  E +   +         AL   L+  ++  I I  +S+    F ARF
Sbjct: 61  VHASHQVCHLDISDETLQRCIGHTGLDGVSALEYRLRHVLAQDIVIHKVSVAPYGFDARF 120

Query: 106 SAIRRSYLYRIITRQAPLALE---KGRAWLIPKSLDCENMRIAAQHLVGRHDF------- 155
           SA+ R+Y+YRI         +   +G        LD + M  AA+ +VG HDF       
Sbjct: 121 SALERTYVYRIADGYCKAKYDPRMRGFVLRFDSELDIDAMNQAARLMVGLHDFGSFAKPN 180

Query: 156 ---TTFRSI-----HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
              TT R +     H   S   +    F +    +L+E  +VA +F H  +RS V +   
Sbjct: 181 PGGTTIRKVKQARWHRVGSKDAQNSTGFVLPIEQSLLEFTIVADAFAHNMVRSLVQACVQ 240

Query: 208 VGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEY 246
           +G GK +    E+ +    R+   GP+  P GL  + V Y
Sbjct: 241 IGCGKRSVDWFEEKINVPLREGSTGPI-DPHGLTLEYVAY 279


>gi|313836079|gb|EFS73793.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL037PA2]
 gi|314929615|gb|EFS93446.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL044PA1]
 gi|314970609|gb|EFT14707.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL037PA3]
          Length = 279

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/252 (29%), Positives = 123/252 (48%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E+ I   L  G    +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWAVQPDRRTVQGDLERWIPRVLRLGVPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     + + ++  V  +F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDGVDTSSMLRRLSRVLDPD--VVVKSIRSVPDEFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +P+ LD + +  A   L+G  DF  F   + + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVASVPRHLDLDRLNAAGASLLGLRDFAAF-CKYREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+     L++   +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGQRNQGWLDEVAASASRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|183981112|ref|YP_001849403.1| pseudouridine synthase a, TruA [Mycobacterium marinum M]
 gi|183174438|gb|ACC39548.1| pseudouridine synthase a, TruA [Mycobacterium marinum M]
          Length = 237

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 112/219 (51%), Gaps = 22/219 (10%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVP--------------VILCKALNAYLKISDTIS 90
           +  AGRTD+GVHA  QVAH D+  + +P              + L + L  +L     + 
Sbjct: 3   LRAAGRTDAGVHATGQVAHADVPVDALPNAYSRSARAGDPEFLPLVRRLARFLPAD--LR 60

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQ 147
           +L+++     F ARFSA+RR Y+YR+ T  AP  +E  +A  +   P+ LD + M +A++
Sbjct: 61  VLDIARAPTAFDARFSALRRHYVYRLST--APYGVEPQQARYVTVWPRELDIDAMTVASR 118

Query: 148 HLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
            L+G H+F  F     + ++ IR +   D +  G+L+  +V A +F  + +RS VG+L  
Sbjct: 119 ELLGLHNFAAF-CRRREGATTIRDLQRLDWSRNGHLVTAQVSADAFCWSMVRSLVGALLA 177

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           VG+ + T     + L A  R      AP  GL    V+Y
Sbjct: 178 VGEHRRTPDWCRELLTATARSSDFAAAPAHGLVLAKVDY 216


>gi|149278992|ref|ZP_01885126.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
 gi|149230271|gb|EDM35656.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
          Length = 267

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/255 (30%), Positives = 117/255 (45%), Gaps = 22/255 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y+G  Y GWQ+Q    ++QG +EK +  V    V + G GRTD+ VHA +  
Sbjct: 1   MRYFVHIGYHGLHYNGWQKQPGVLNVQGVLEKTLSQVLKRPVEIIGCGRTDAHVHASQFF 60

Query: 62  AHFDLVREW---VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            H D+   W   +   L K+L   + + D I +  L       HARF A++RSY Y + T
Sbjct: 61  FHMDIEEAWDFDLIFRLNKSLPTNIAVFDVIPMPGLQ------HARFDAVQRSYDYFLHT 114

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-------RSIHCQASSPIRT 171
            + P  L+   ++ + K L  + M+ AA  L    DF  F           C   S   T
Sbjct: 115 YKNPF-LQGLSSYYLLKDLKFDEMKAAAAILPKYKDFRPFCTSPDKYEHTICNVMSASLT 173

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +D       G+ +  ++ +  FL   IR  +G L  VG G  +  + E+ L  +   E  
Sbjct: 174 VD-----PNGDRMRFQISSNRFLSKMIRIIMGQLLKVGRGVLSVDEFEQYLIDKRTPELI 228

Query: 232 PLAPPEGLYFDSVEY 246
             A P+GLY   V Y
Sbjct: 229 TPAHPQGLYLSKVTY 243


>gi|148683104|gb|EDL15051.1| mCG23338, isoform CRA_b [Mus musculus]
          Length = 284

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 109/225 (48%), Gaps = 28/225 (12%)

Query: 48  AGRTDSGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFH 102
           + RTD+GVHAL   AH D+ R      + P ++ KALN +LK    I +L    V   FH
Sbjct: 27  SSRTDAGVHALSNAAHLDIQRRPGQSPFSPEVVAKALNTHLK-HPAIRVLKAFRVPNDFH 85

Query: 103 ARFSAIRRSYLYRIIT-----RQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFT 156
           AR +A  R+Y YR+ T      Q P+  E+   W L  + LD   M+ AAQHL+G HDF+
Sbjct: 86  ARHAATSRTYQYRLATGCSWPNQLPV-FEQNVCWALQTEYLDMAAMQEAAQHLLGTHDFS 144

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVG 203
            F+S     ++ +RT+    V+                    +   ++SFL+ Q+R    
Sbjct: 145 AFQSAGSPVTNTVRTLRRVSVSPGPASPFVLPEGSRRLQFWTLEFESQSFLYRQVRRMTA 204

Query: 204 SLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            L  VG G    T ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 205 VLVAVGLGILAPTQVKVILESQDPLGKYQARVAPARGLFLKSVLY 249


>gi|269124177|ref|YP_003306754.1| tRNA pseudouridine synthase A [Streptobacillus moniliformis DSM
           12112]
 gi|268315503|gb|ACZ01877.1| tRNA pseudouridine synthase A [Streptobacillus moniliformis DSM
           12112]
          Length = 244

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 121/238 (50%), Gaps = 5/238 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I +Y+GS ++G QRQK+  ++QG+IE  +     E V +  +GRTD GVHA  QV++F 
Sbjct: 6   IIYQYDGSAFYGSQRQKDKVTVQGTIEDILINSFNEKVNMISSGRTDRGVHAKMQVSNFI 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           + ++    I+   +  Y   +  I IL++  VD ++++RF  + R+Y + +  R+     
Sbjct: 66  INKDIKLDIIKSKIEKYSNYA--IKILSIEKVDIKYNSRFDCMERTYEFILSNRENITPF 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTI-DHFDVNSFGNL 183
            +     I   +D E +    +  +G+H+F+ F     +A+ +PIR I + + +    N 
Sbjct: 124 NRKYITSINYEIDVEKLNDILKQFIGKHNFSNFSKKENKANKNPIREIYECYSIKKDKN- 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           I I +   SFL + +R  +G+   +  GK +   +++A    +      +    GLY 
Sbjct: 183 IHIYIKGNSFLKSMVRIIIGTTLAIYSGKISKHFIKEAFDNPNPNTKKYILDGNGLYL 240


>gi|302851591|ref|XP_002957319.1| tRNA pseudouridine synthase [Volvox carteri f. nagariensis]
 gi|300257414|gb|EFJ41663.1| tRNA pseudouridine synthase [Volvox carteri f. nagariensis]
          Length = 226

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 105/226 (46%), Gaps = 6/226 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHAL 58
           + Y MI+ Y+G+ Y GWQ Q +  ++Q  +E A+  V  E   ++ V  AGRTD+GVHA 
Sbjct: 3   LSYRMIVSYDGTAYCGWQLQPSAPTVQRFLEGALCTVLREERAVLGVRAAGRTDAGVHAR 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F   +E     +   LN+ L     I +L +S     F    SA+ + Y Y I  
Sbjct: 63  GQVVQFSCDKELDVTKMPYKLNSVL--PHDIRVLRMSRTAPDFSVTCSALGKCYRYSITN 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +    L    A  + + LD   MR AA  L G HDF+ F +I  +  SP         N
Sbjct: 121 GETHDPLRHRYALHVRRHLDLAAMRSAAALLTGTHDFSQFSNIGEEGGSPDVQRRRRQRN 180

Query: 179 SFGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
               L  + VV    FL+  +R   G L  VG+GK  +  + + L+
Sbjct: 181 PVKTLRRVDVVEGNGFLYKMVRHISGVLVAVGEGKLQTKAVGRMLE 226


>gi|145356339|ref|XP_001422390.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582632|gb|ABP00707.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 286

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 86/266 (32%), Positives = 124/266 (46%), Gaps = 30/266 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHA 57
           + Y + I Y+G  Y G+Q Q ++  +IQ  +E+A+  +TG   E + +  AGRTD+GVHA
Sbjct: 16  VTYALKISYDGERYNGFQYQGEDVPTIQRELERALAKLTGIDRERLRLGAAGRTDAGVHA 75

Query: 58  LRQVAHF--------DLVREWVPVILC-KALNAYLKISDTISILNLSIVDKQFHARFSAI 108
             QVAHF        DL R       C KA+N  L     I +         FH+RF A 
Sbjct: 76  RGQVAHFYCEKSLGEDLTR-------CQKAMNGML--PKDIRVDAFWEPHPLFHSRFHAS 126

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTF----RSIHC 163
            ++Y Y +  R       +  A  +  +  D E +R AAQ  VG  D+  F    R    
Sbjct: 127 GKTYHYYVDARATSSPFTRKYAHQVGWRPCDVELLRQAAQLFVGTMDYKGFCNTSRDKSN 186

Query: 164 QASSPIRTIDHFDV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +  +  RTI  FDV    +   LI + V    FL+ Q+R+ VG+L +V  GK     L  
Sbjct: 187 EDRNTTRTIRRFDVFEDAADDGLIRLEVEGDGFLYRQVRNMVGALLVVASGKHDLAYLRT 246

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEY 246
            ++ +DR      AP  GL+   V Y
Sbjct: 247 LIETKDRSRAPMGAPARGLFLHEVFY 272


>gi|57640862|ref|YP_183340.1| tRNA pseudouridine synthase A [Thermococcus kodakarensis KOD1]
 gi|62901178|sp|Q5JI92|TRUA_PYRKO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57159186|dbj|BAD85116.1| tRNA pseudouridine synthase A [Thermococcus kodakarensis KOD1]
          Length = 267

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 26/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHA 57
           ++  + + Y+GS ++G+QRQ    +++G I K +     + + E     GA RTD GV A
Sbjct: 1   MKLALRVAYDGSAFYGFQRQPGVRTVEGEIIKVLQKLGIIESPEKNDFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              V  F +  E   +   + LN +L  SD + +L ++ V   FH RF A  ++Y Y   
Sbjct: 61  FFNVVSF-VPSERPDLARPEVLNHHL--SD-VWVLGIAEVPDDFHPRFWAKFKTYRY--- 113

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +L+ +  D   MR  A   VGRHDF+ F  +      PIR ++  +V
Sbjct: 114 -------------YLVNEGFDLSAMRECASLFVGRHDFSAFAKLE-PGRDPIREVERVEV 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + I V  +SFL   +R  V +L+  G G   + ++E+ L  +  K+  P APPE
Sbjct: 160 IERQGYLVIEVQGKSFLWEMVRRIVNALRFCGLGLLEAEEVERMLSGEYGKKIPP-APPE 218

Query: 238 GLYFDSVEYS 247
           GL    +EY 
Sbjct: 219 GLVLWHIEYP 228


>gi|229818212|ref|ZP_04448494.1| hypothetical protein BIFANG_03510 [Bifidobacterium angulatum DSM
           20098]
 gi|229784463|gb|EEP20577.1| hypothetical protein BIFANG_03510 [Bifidobacterium angulatum DSM
           20098]
          Length = 302

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/286 (29%), Positives = 129/286 (45%), Gaps = 43/286 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW  Q +  ++QG IE+A+  +         E + +  AGRTD+G
Sbjct: 1   MRLRIDLAYDGGGFYGWAVQPDIRTVQGEIEQALHRILRVDPNDASEPLRLVVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREW---------VPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  +          VP +          + D I+I  +S     F ARF
Sbjct: 61  VHASHQVCHIDMSPDILERAVGHMKVPAVTALEHRLQRVLPDDITIHRISEAPVGFDARF 120

Query: 106 SAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y+YRI  R + +    +G    I   LD E M +AA   +G HDF +F + +  
Sbjct: 121 SALERTYVYRIADRSSEVDPRLRGCVLHIDGDLDIEAMNLAAAQTIGLHDFGSFATPNPG 180

Query: 165 ASSPIRTIDHFD--------------------VNSF-GNLIEIRVVARSFLHTQIRSFVG 203
            ++ IR +   D                    V +F   L+   +VA +F    +RS V 
Sbjct: 181 GTT-IREVKQADWARVPAQPLIAQPMAGKGYVVPTFESGLVCFTIVADAFARNMVRSLVN 239

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKE--CGPLAPPEGLYFDSVEYS 247
               VG  K    D  K   A  ++E   GP+A P+GL  + V Y 
Sbjct: 240 GCVQVGLDK-RDLDWFKGKMAVPKREGSTGPIA-PQGLTLEHVAYP 283


>gi|163840856|ref|YP_001625261.1| tRNA pseudouridine synthase A [Renibacterium salmoninarum ATCC
           33209]
 gi|162954332|gb|ABY23847.1| tRNA pseudouridine synthase A [Renibacterium salmoninarum ATCC
           33209]
          Length = 297

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/264 (27%), Positives = 125/264 (47%), Gaps = 19/264 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW  Q    ++QG +E ++ ++   +V V  AGRTD+GVHA  QV
Sbjct: 17  LRLRLDLAYDGAPFSGWALQPERLTVQGVLEDSLAMILRRLVRVTVAGRTDAGVHARGQV 76

Query: 62  AHFDL-VREWVPV-----------ILCKALNAYLKI----SDTISILNLSIVDKQFHARF 105
            H +    EW  +           +L +   A  ++    +  + + ++   +  F ARF
Sbjct: 77  VHAEFYPHEWEQIARRSTASPEEAVLRRLRGALSRVLGEQTGAVVVHSVRPAEPGFDARF 136

Query: 106 SAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R Y Y I  R A    +++   W     LD E + +A Q L+G  DF  F      
Sbjct: 137 SALWRRYSYHIADRPAQWDPVQRQMTWWHKTELDVELLNLAVQPLLGLQDFRAFCKPRPG 196

Query: 165 ASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           A++ +R +   + +   +  I++ V A +F H  +R+ +GS   VG G+ +   L + L 
Sbjct: 197 ATT-VRELQRLEFSRQPDGTIKVAVQADAFCHNMVRALIGSAVQVGSGEQSPDWLAERLA 255

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
            + R     LAPP  L  + V Y 
Sbjct: 256 IKVRDAKSGLAPPHPLVLEEVHYP 279


>gi|315104023|gb|EFT75999.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL050PA2]
          Length = 279

 Score = 99.8 bits (247), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 119/252 (47%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I   L   +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L  +  I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVL--TPDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +   LD + +  A   L+G  DF  F   H + ++ IR +     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAF-CKHREGATTIRPLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|297571891|ref|YP_003697665.1| tRNA pseudouridine synthase A [Arcanobacterium haemolyticum DSM
           20595]
 gi|296932238|gb|ADH93046.1| tRNA pseudouridine synthase A [Arcanobacterium haemolyticum DSM
           20595]
          Length = 293

 Score = 99.8 bits (247), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 81/272 (29%), Positives = 126/272 (46%), Gaps = 32/272 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW  Q    ++Q  +EKA+ +V  E VV+  AGRTD+GVHA  QV
Sbjct: 9   LRVRLDLGYDGNHFHGWAAQPGLRTVQDELEKALSVVFREPVVLTVAGRTDAGVHARHQV 68

Query: 62  AHFDLVRE-WVPVI----------LCKALNAYLKIS------------DTISILNLSIVD 98
           AH D+ R  W  +           L   LN+ L  S              + + +   V 
Sbjct: 69  AHCDVSRAAWDALPGRSSRTPGESLVLRLNSLLARSAGGVVAGAPRGYSDVVVHSALEVP 128

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
             F ARFSA+ R+Y YRI    A    ++     +   LD + M  A+  L+G HDF ++
Sbjct: 129 ADFDARFSALWRAYTYRIADSVAEWDPQRHDVLWLSDRLDLDAMNRASVALLGEHDFLSY 188

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG----KWT 214
                + +S IRT+          ++  R  A +F H+Q+R+ +G+L  VG G    +W 
Sbjct: 189 CKPR-EGASTIRTLLDLGFERVEGIVVGRAKADAFCHSQVRTLMGTLIEVGRGAREERWP 247

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
              LE+      R     +APP  L  + + Y
Sbjct: 248 LLRLEEC----SRDGQVVVAPPHPLTLEEIGY 275


>gi|195490008|ref|XP_002092963.1| GE26463, isoform B [Drosophila yakuba]
 gi|194179064|gb|EDW92675.1| GE26463, isoform B [Drosophila yakuba]
          Length = 306

 Score = 99.4 bits (246), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 93/303 (30%), Positives = 130/303 (42%), Gaps = 59/303 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F    EI  V  + R
Sbjct: 1   MNRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALRVFHPINEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL      DL R     +    L   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQGLPIRVLSSKLVSNSFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALE------KGRAWLIP------------KSLDCENMRIAAQ 147
            AI R+YLYR    + P +LE      K     IP             S D   ++ AA+
Sbjct: 120 HAIGRTYLYRFAVAKDP-SLEDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVQAAAR 178

Query: 148 HLVGRHDFTTFRSIHCQASS------PIRTIDHFDVN---------------SFGNLIEI 186
             +G HDF TF S+  Q  S       +R ID  ++                   N  +I
Sbjct: 179 MFIGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDI 238

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDS 243
            + A+SFL+ Q+R  VG+L  +G+G+     L + L    +    P   LAP  GLY   
Sbjct: 239 EIKAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNSWDPRILLAPACGLYLCK 298

Query: 244 VEY 246
           V Y
Sbjct: 299 VHY 301


>gi|254756839|ref|ZP_05208867.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Australia
           94]
          Length = 185

 Score = 99.0 bits (245), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 61/176 (34%), Positives = 88/176 (50%), Gaps = 9/176 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  L  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD    + EW       ALN  L   D I I  +    ++FHAR+   R+ Y YR+
Sbjct: 66  QVIHFDTPLSLEEWQ---WSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRV 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +  +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI
Sbjct: 121 LVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTI 176


>gi|195436012|ref|XP_002065972.1| GK25867, isoform A [Drosophila willistoni]
 gi|194162057|gb|EDW76958.1| GK25867, isoform A [Drosophila willistoni]
          Length = 508

 Score = 99.0 bits (245), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 87/266 (32%), Positives = 121/266 (45%), Gaps = 55/266 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLDQPRLDTNSVQGCLELALRVFRPTNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVR----EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTIHVDLERYDGQPYALTTLTGVLNRTLGKQRLPIRVLSTELVPDTFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPL----ALEKGRAWLIP------------KSLDCENMRIAAQH 148
            AI R+YLYR  + R +P+       +G    IP             S D E +R AA+ 
Sbjct: 120 HAIGRTYLYRFAVARNSPVDDGKLKNRGYEAFIPVEELDRCYFLQAASFDIERVRSAARL 179

Query: 149 LVGRHDFTTFRSIHCQASSP-------IRTIDHFDV--------NSFGNLI-------EI 186
            +G HDF TF S+  Q           +R ID  ++        N+   L        EI
Sbjct: 180 FLGIHDFRTFMSVSRQKGPSRDHPMFTVRKIDEINIRPGHSLALNAHAKLANETYDHWEI 239

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGK 212
            + A+SFL+ Q+R  VG+L  +G GK
Sbjct: 240 EIKAKSFLYKQVRRIVGTLLALGTGK 265


>gi|119356907|ref|YP_911551.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides DSM 266]
 gi|166228693|sp|A1BFF0|TRUA_CHLPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119354256|gb|ABL65127.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides DSM 266]
          Length = 258

 Score = 99.0 bits (245), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 116/245 (47%), Gaps = 11/245 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + IEY+G+GY GWQRQ     ++QG IE+ +  +  E + + GAGRTD GVHA  Q+A F
Sbjct: 14  ITIEYDGTGYAGWQRQAGSFCTVQGEIERILSQILQEDIRLAGAGRTDKGVHARAQIATF 73

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                  P  +  ++NA L   +TI I +  +V + FHAR SA  R Y Y    R+ P A
Sbjct: 74  KSRSSLGPDRMVHSMNALLP--NTIRISDPLVVPEGFHARHSAKEREYRY--FVREEPSA 129

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTID--HFDVNSFG 181
           +    +     SLD  +M   A +++G HDF+ F +    +     R I    F    F 
Sbjct: 130 VLGRFSGCSYGSLDLMSMNRVASYVLGEHDFSVFSKETRDRTGCLCRVISCKWFRQREF- 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
               +R+ A  FL + +R     +   G G  +  +  + +++         A P GL+ 
Sbjct: 189 --FVLRISANRFLRSMVRYLAALMIDSGKGLLSPEEAREMIESGILTRQLVPAAPNGLFL 246

Query: 242 DSVEY 246
             + Y
Sbjct: 247 WKITY 251


>gi|283782782|ref|YP_003373536.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 409-05]
 gi|283442111|gb|ADB14577.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 409-05]
          Length = 305

 Score = 99.0 bits (245), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 83/287 (28%), Positives = 130/287 (45%), Gaps = 46/287 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW +Q    ++QG IE A+  V       + E + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGGFYGWAKQPTLRTVQGEIEGALHTVLRVPEGDSAEPLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVILCK---------ALNAYLK--ISDTISILNLSIVDKQFHA 103
           VHA  QV H D+  E +  + C          AL   LK  +   IS+  +S+    F A
Sbjct: 61  VHASHQVCHLDVCEETL--LRCVGHTGLDGVCALEYRLKHVLPQDISLHKVSVAPIGFDA 118

Query: 104 RFSAIRRSYLYRIITRQAPLALE---KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           RFSA+ R+Y+YRI         +   +G    +   LD + M  AA+ ++G HDF +F  
Sbjct: 119 RFSALERTYVYRICDASDYCDYDPRMRGFVLKLDDVLDVDAMNQAARLMIGLHDFGSFAR 178

Query: 161 IHCQASSPIRTIDHFDVNSFGN--------------------LIEIRVVARSFLHTQIRS 200
            +    + IR +        G                     L+E  +VA +F H  +RS
Sbjct: 179 PN-PGGTTIRDVKSACWERVGTRANDVRVKLKTGCVPPVEQGLLEFTIVADAFAHNMVRS 237

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEY 246
            V +   +G GK T     + +    R+   GP+A P+GL  + V Y
Sbjct: 238 LVQACVQIGCGKRTLDWFVEKINTPLREGSTGPIA-PQGLTLEYVAY 283


>gi|110598437|ref|ZP_01386709.1| tRNA pseudouridine synthase A [Chlorobium ferrooxidans DSM 13031]
 gi|110339971|gb|EAT58474.1| tRNA pseudouridine synthase A [Chlorobium ferrooxidans DSM 13031]
          Length = 244

 Score = 98.6 bits (244), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 118/244 (48%), Gaps = 8/244 (3%)

Query: 6   MIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + +EY+G+ Y GWQRQ  K   ++QG IE A+ ++  E + +  AGRTD GVHA  Q+A+
Sbjct: 6   ITVEYDGTPYSGWQRQNRKGCVTVQGEIESALGMILQEKISLAAAGRTDKGVHAKAQIAN 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F          +  +LNA L   DTI I +   + K+FH+R SA  R Y Y +I    P 
Sbjct: 66  FSTASPMDLSRMVHSLNALLP--DTIRITDPLEMPKEFHSRHSARERHYRYFLIAE--PS 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+    +     + D   M+  A  + G HDF+ F      +   + T+       + + 
Sbjct: 122 AIYGRFSGCSFGTPDLAVMQQVAGSVRGVHDFSAFSREDRDSPGRLCTVTACQWYRYQHF 181

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEGLYFD 242
           + + + A  FL + +R  V  +   G G  ++ + ++ L+      +  P+A P GL+  
Sbjct: 182 LVLSISANRFLRSMVRYLVDGMLRAGKGTLSAEEFKRMLETGVMTTQLNPVA-PSGLFLW 240

Query: 243 SVEY 246
            V Y
Sbjct: 241 RVTY 244


>gi|167583949|ref|ZP_02376337.1| tRNA pseudouridine synthase A [Burkholderia ubonensis Bu]
          Length = 193

 Score = 98.2 bits (243), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 57/168 (33%), Positives = 86/168 (51%), Gaps = 2/168 (1%)

Query: 80  NAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDC 139
           NA+L    T+++     +   FHARFSA  R+Y Y +        +   RA  I   LD 
Sbjct: 2   NAFLP--PTVAVQWAKPMPDAFHARFSAFERTYYYALYVHPVRSPMLDARAGWIHTPLDD 59

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
           + MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G+ +  R  A +FLH  +R
Sbjct: 60  DAMRAAAAHLIGEHDFSAFRSSECQSKTPVKHLYQIDIRRAGHFLHFRFRANAFLHHMVR 119

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + +G L  VG G++ +  +   L  +DR    P    +GLY   V Y 
Sbjct: 120 NLMGCLVAVGRGRYPAEWIADVLAGRDRNRAAPTFMADGLYLAHVGYP 167


>gi|294660547|ref|NP_853358.2| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str.
           R(low)]
 gi|298286877|sp|Q7NAQ9|TRUA_MYCGA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|284812210|gb|AAP56926.2| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str.
           R(low)]
 gi|284930851|gb|ADC30790.1| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str.
           R(high)]
          Length = 263

 Score = 98.2 bits (243), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 112/240 (46%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+  Q +  ++Q  ++ A+  +    + V+ +GRTD GVHA+ Q   F + 
Sbjct: 29  ISYHGTKFHGYAVQNDYETVQSKLQDALAWIYESKIYVNASGRTDKGVHAINQYISFYID 88

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L + LN Y +  +   I  +  VD+ FHARFSA  ++YLY +I   A   L  
Sbjct: 89  DRISLEKLREILNRYGQ--NKWYIKWIKEVDRNFHARFSAKAKTYLY-LIDYCANNPLFY 145

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
             AW++   LD   +  A   L G H+F +F +        +RTI   D+    N + I 
Sbjct: 146 DHAWIVNFQLDFNLIEKAIPILEGTHNFWSFST--ADKDKGLRTIHKIDLKQEDNKVYIY 203

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    FL + +R  VG+L  +G  K+    L+  L    +      AP  GLY   V Y 
Sbjct: 204 ITGDGFLRSMVRMIVGALYNIGIKKYDLNHLKWLLDNPKKGRAITKAPASGLYLYEVYYE 263


>gi|332862130|ref|XP_513709.3| PREDICTED: pseudouridylate synthase-like 1 [Pan troglodytes]
          Length = 261

 Score = 98.2 bits (243), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 66/190 (34%), Positives = 98/190 (51%), Gaps = 15/190 (7%)

Query: 3   RYCMIIEYNGSGYFGW---QRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G    +  +    +Q  +E+A   L + E V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYVGTDFNGVAAVRGTQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR++A  R+YL
Sbjct: 73  SNAAHLDVQRRSGRPPFPPEVLAEALNTHLR-HPAIRVLRAFRVPSDFHARYAATSRTYL 131

Query: 114 YRIIT----RQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T    R      E+   W +P   LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 132 YRLATGCHRRDELPVFERNLCWTLPADCLDVVAMQEAAQHLLGTHDFSAFQSAGSPVPSP 191

Query: 169 IRTIDHFDVN 178
           +RT+    V+
Sbjct: 192 VRTLRRVSVS 201


>gi|328906179|gb|EGG25954.1| tRNA pseudouridine synthase A [Propionibacterium sp. P08]
          Length = 279

 Score = 98.2 bits (243), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 122/252 (48%), Gaps = 9/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E+ I   L       +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWAVQPDRRTVQGDLERWIPRVLRLSVPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     + + ++  V  +F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDGVDTSSMLRRLSRVLDPD--VVVKSIRSVPDEFDARFSALWRRYVYRLWD 118

Query: 119 RQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  + +     +P+ LD + +  A   L+G  DF  F   + + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVASVPRHLDLDRLNAAGASLLGLRDFAAF-CKYREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+     L++   +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGQRNQGWLDEVAASASRASSVLVM 237

Query: 235 PPEGLYFDSVEY 246
           P  GL  + V Y
Sbjct: 238 PACGLTLEEVGY 249


>gi|149916968|ref|ZP_01905469.1| tRNA pseudouridine synthase A [Plesiocystis pacifica SIR-1]
 gi|149822246|gb|EDM81637.1| tRNA pseudouridine synthase A [Plesiocystis pacifica SIR-1]
          Length = 285

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/266 (28%), Positives = 120/266 (45%), Gaps = 32/266 (12%)

Query: 8   IEYNGSGYFGWQRQKNGS----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + Y+G+ + G+ RQ NG     +IQG +E+A+  +  + +   GA RTD+GVHA  Q+  
Sbjct: 7   VAYDGTDFHGFARQDNGGQPLRTIQGCLEQALSTLYKQPIRTRGASRTDAGVHARGQLVA 66

Query: 64  FDLVREWVPVILCKALNAYLKISDTISI---LNLSIVDKQFHARFSAIRRSYLYRI--IT 118
           FD     +P        A    +D I+    L   +  +  + RF    + Y YR+  ++
Sbjct: 67  FDPPFA-IPARGLLLGLAANLPADIIASAAWLAEDVEGEPLNPRFHTRGKLYRYRLRPVS 125

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + PL+      W +P+ +D   M+ AA    G HDF  FR+  CQA S  R +    VN
Sbjct: 126 LRDPLSARY--EWHLPRPIDVAAMQAAAPRFAGTHDFAGFRASDCQAKSTTRRVRSVIVN 183

Query: 179 --SFGNL------------------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
             +   L                  + I V   +FL   +R  VG+L  VG G++ +  +
Sbjct: 184 VETLAELDPLAGQRGRIEGPAAPARVTIDVRGDAFLKNMVRIMVGTLVGVGRGQFGAERI 243

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSV 244
           ++ L + DR   G  AP  GL    V
Sbjct: 244 DEVLASGDRTRAGVTAPACGLTLVEV 269


>gi|254424035|ref|ZP_05037753.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7335]
 gi|196191524|gb|EDX86488.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7335]
          Length = 299

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 118/250 (47%), Gaps = 10/250 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  ++I+Y G+ + GWQRQKN   ++Q  IE  I  V G    + GAGRTD+GVHA  QV
Sbjct: 28  RVALVIQYKGTHFHGWQRQKNAKRTVQAEIESVIASVLGRKPALVGAGRTDAGVHAAAQV 87

Query: 62  AHFDLVREWVPVILCKALNAYL---KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           AHF       P+++     A +   ++ D I +   + V   +HA+FSA  R Y Y   T
Sbjct: 88  AHFA-----APIVIPAERWAIILNDRLGDDIVVRASTRVASDWHAQFSANWRRYRYTFYT 142

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAA-QHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            + P    +   W   +    EN+ +AA Q ++G H+   F       +     +     
Sbjct: 143 SKYPNLFVQPYVWHYYRQRLDENLMLAALQPMMGYHNLLAFHRTGSDRTHSWVELQDVQC 202

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ + I + A+ FL+  +R  +G +  VG+ + +  +     Q + R      APP+
Sbjct: 203 TRSGDFVRIELQAKGFLYGMVRLIMGLIVQVGERRLSPKEFTAIWQKRRRDLVKYSAPPQ 262

Query: 238 GLYFDSVEYS 247
           GL    V YS
Sbjct: 263 GLCLLRVGYS 272


>gi|284931225|gb|ADC31163.1| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str. F]
          Length = 263

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 113/240 (47%), Gaps = 5/240 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+  Q +  ++Q  ++ A+  +    + V+ +GRTD GVHA+ Q   F + 
Sbjct: 29  ISYHGTKFHGYAVQNDYETVQSKLQDALAWIYESKIYVNASGRTDKGVHAINQYISFYID 88

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  L + LN Y +  +   I  +  VD+ FHARFSA  ++YLY +I   A   L  
Sbjct: 89  DRISLEKLREILNRYGQ--NKWYIKWIKEVDRNFHARFSAKAKTYLY-LIDYCANNPLFY 145

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
             AW++   LD   +  A   L G H+F +F +        +RTI+  ++    N + I 
Sbjct: 146 DHAWIVNFQLDFNLIEKAIPILEGTHNFWSFST--ADKDKGLRTINKINLKQEDNKVYIY 203

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    FL + +R  VG+L  +G  K+    L+  L    +      AP  GLY   V Y 
Sbjct: 204 ITGDGFLRSMVRMIVGALYNIGIKKYDLNHLKWLLDNPKKGRAITKAPASGLYLYEVYYE 263


>gi|194746922|ref|XP_001955903.1| GF24924 [Drosophila ananassae]
 gi|190623185|gb|EDV38709.1| GF24924 [Drosophila ananassae]
          Length = 307

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 95/305 (31%), Positives = 129/305 (42%), Gaps = 61/305 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--------SIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N S        +IQG +E A  +F  T +I  V  + R
Sbjct: 1   MHRYLLNISYIGTSFRGIQKTVNKSEQPRLDTNTIQGCLELALRVFRPTNDIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVR----EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K    I IL+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLQRYDGQPYDTGTLTGVLNRTLDKQRLPIRILSSQVVSDSFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALE------KGRAWLIP------------KSLDCENMRIAAQ 147
            A  R+YLYR    +   A+E      KG    IP             S D E +R AA+
Sbjct: 120 HATGRTYLYRFAVSRNTGAVESGNLRNKGYESFIPVEELDRCYFLQSTSFDIERVRNAAR 179

Query: 148 HLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI----------------------- 184
             +G HDF TF S+  Q  SP R    F +    ++                        
Sbjct: 180 MFIGVHDFRTFMSVSRQ-KSPSRDHPRFTLRKIDDISIRPGRALAVAGNAALAANSYDYW 238

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYF 241
           EI + A+SFL+ Q+R  VG+L  +G G+     + + L    +        LAP  GLY 
Sbjct: 239 EIEIRAKSFLYKQVRRIVGTLLALGCGRIDEKSVYQMLTIPSKNSWDHRVLLAPACGLYL 298

Query: 242 DSVEY 246
             V Y
Sbjct: 299 CRVHY 303


>gi|300782641|ref|YP_003762932.1| tRNA pseudouridine synthase A [Amycolatopsis mediterranei U32]
 gi|299792155|gb|ADJ42530.1| tRNA pseudouridine synthase A [Amycolatopsis mediterranei U32]
          Length = 238

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/218 (34%), Positives = 104/218 (47%), Gaps = 26/218 (11%)

Query: 48  AGRTDSGVHALRQVAHFDLV-------------REWVPVILCKALNAYLKISDTISILNL 94
           AGRTD+GVHA  QV H D+V              E +P +   A      +   + +L  
Sbjct: 8   AGRTDAGVHATGQVVHVDVVPLAPGSAGRVPVFAEGIPDLTRMAGRWNRLLPGDVRVLGA 67

Query: 95  SIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR-----AWLIPKSLDCENMRIAAQHL 149
            I  + F ARFSA+RR Y YR+    AP  ++  R     AW  P S D   M  AA  L
Sbjct: 68  RIAPEGFDARFSAVRRHYRYRV--SDAPWGVDPLRRHDTLAWNRPLSTDA--MNAAAAEL 123

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLV 208
           +G HDF  +     +  + IR +   +      +L+E+RV A +F H+ +RS VG L LV
Sbjct: 124 LGLHDFAAY-CKQRETGTTIRELQRLEWTRVDEHLLEVRVSADAFCHSMVRSLVGVLLLV 182

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           GDG+ T     K L++  R     +AP  GL    V+Y
Sbjct: 183 GDGRRTDAWPAKVLESGIRDSA--VAPAHGLTLLGVDY 218


>gi|297625831|ref|YP_003687594.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296921596|emb|CBL56150.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 292

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/251 (29%), Positives = 117/251 (46%), Gaps = 9/251 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALRQ 60
           R+ + + Y+G+ + GW  Q    +++G +   +  + G  + V +  AGRTD+GVHA  Q
Sbjct: 5   RFRLDLSYDGTHFHGWAMQPGQRTVEGELATWLTRIAGTAQPVRLVVAGRTDAGVHARGQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL        L + L     +   I +  L++    F ARF+AI R Y+YR+    
Sbjct: 65  VAHADLPATMDAAELKRRL--LRALPPDIVVRRLTVAPPGFDARFAAIWRRYVYRLWDLS 122

Query: 121 A-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P  L +G        LD E M  A   L+G  DF  F     + ++ IRT+   +   
Sbjct: 123 SHPDPLLRGMVTTKSLDLDPELMTAAGSRLLGLRDFAPF-CRRREGATTIRTLLQCEARR 181

Query: 180 FGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             +    IE+ V A +F H+ +RS  G+L  VG G  +   L++      R     + P 
Sbjct: 182 VADGCGTIELTVRADAFCHSMVRSLTGALVAVGSGTQSMDWLDEVAAGPTRAGSVTVMPA 241

Query: 237 EGLYFDSVEYS 247
            GL  + V Y+
Sbjct: 242 RGLCLEQVAYA 252


>gi|224418450|ref|ZP_03656456.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|253827766|ref|ZP_04870651.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|313141982|ref|ZP_07804175.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|253511172|gb|EES89831.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|313131013|gb|EFR48630.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
          Length = 240

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 89/262 (33%), Positives = 121/262 (46%), Gaps = 38/262 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MI+  M I Y G  +FG+QRQK+  +I G +E+ +F   G   V  G+GRTD GVHA  Q
Sbjct: 1   MIKVAMRIAYYGGEFFGFQRQKDKITICGVLEE-VFRSVGIFDVCMGSGRTDKGVHASAQ 59

Query: 61  VA-------HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           V        H DL R      L + LN  +K+   I I  +  V+ +FH RFS  RR Y 
Sbjct: 60  VISVSIPEFHRDLQR------LKQLLN--VKLYPWIKIKQIWQVENEFHVRFSVKRRGYC 111

Query: 114 YRIITRQAP-LAL-----EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR---SIHCQ 164
           Y +  + +P LAL          +L+ +SLD            G +DF+ F       C+
Sbjct: 112 YVLSQKYSPFLALFSHFYPLKNPFLVQESLDI---------FRGVYDFSAFMKNGGSGCE 162

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            S  +R I H  +   G    I      FL +QIR  VG L  +  G     DL+K L  
Sbjct: 163 GS--VREIFHTKLLKRGEFYLISFWGNGFLRSQIRLMVGFLLEIDRGNLGIEDLKKQLLG 220

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
           +  K     APP GL+   V+Y
Sbjct: 221 E--KIFSIPAPPNGLFLSRVDY 240


>gi|222834648|gb|EEE73111.1| predicted protein [Populus trichocarpa]
          Length = 225

 Score = 97.1 bits (240), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 58/204 (28%), Positives = 95/204 (46%), Gaps = 24/204 (11%)

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +  P    +  N +L     I++     V   FH+R  A  R Y Y ++  
Sbjct: 2   QVVHFDTPLDRAPFSWVRGTNTFLP--PDIAVQWAQPVPDAFHSRACATARRYAYVLLQS 59

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               ++E GR   +  +LD + M+ AAQHL+G HDF++FR+  CQA SP++T+    +  
Sbjct: 60  PVRPSVEAGRVGWVFHALDGDAMQAAAQHLLGEHDFSSFRASGCQAKSPVKTLHRLSITR 119

Query: 180 --FGNLIEIRVVA--------------------RSFLHTQIRSFVGSLKLVGDGKWTSTD 217
              G+  ++   +                     +FLH  +R+ +G L  +G G +    
Sbjct: 120 RMAGDGAQMAAASSMRPGDAAMECCYWRFEFEGSAFLHHMVRNIMGCLIAIGQGAYAPQW 179

Query: 218 LEKALQAQDRKECGPLAPPEGLYF 241
           +++ L A+ R    P   P+GLYF
Sbjct: 180 MQQVLDARSRDAAAPTFSPDGLYF 203


>gi|119025367|ref|YP_909212.1| tRNA pseudouridine synthase A [Bifidobacterium adolescentis ATCC
           15703]
 gi|118764951|dbj|BAF39130.1| tRNA pseudouridine synthase A [Bifidobacterium adolescentis ATCC
           15703]
          Length = 306

 Score = 97.1 bits (240), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/291 (27%), Positives = 133/291 (45%), Gaps = 52/291 (17%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G+G++GW +Q    ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 5   VRLRIDLAYDGTGFYGWAKQPEIRTVQGEIERVLHTILRVPEGDPTEPLRLTVAGRTDTG 64

Query: 55  VHALRQVAHFDLVREW---------VPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  +          VP ++         +   I+I  ++     F ARF
Sbjct: 65  VHASHQVCHLDVNEDVLKRCVGHMDVPPVIALTRRLQRMLPADIAIRGIAPAPDGFDARF 124

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWL--IPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           SA+ R+Y+YRI  R + +   + R ++  I   LD ++M  AA   +G HDF +F + + 
Sbjct: 125 SALERTYVYRIADRSSEVD-PRTRNFVLHIDDELDLKSMNEAAAMTIGLHDFGSFATPNP 183

Query: 164 QASS------------PIRT-IDHFDVNSFGN----------LIEIRVVARSFLHTQIRS 200
             ++            P RT ID  D  + G           L+   +VA +F    +RS
Sbjct: 184 GGTTIREVKTAYWRRVPQRTLID--DGMTMGERYRTPTVESGLVCFVIVADAFARNMVRS 241

Query: 201 FVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            V     VG GK    W +  +   L+       GP+A P+GL  + +EY 
Sbjct: 242 LVNGCVQVGIGKRSLDWFAGKMAAPLR---EGSTGPIA-PQGLTLEHIEYP 288


>gi|260797314|ref|XP_002593648.1| hypothetical protein BRAFLDRAFT_252211 [Branchiostoma floridae]
 gi|229278875|gb|EEN49659.1| hypothetical protein BRAFLDRAFT_252211 [Branchiostoma floridae]
          Length = 259

 Score = 97.1 bits (240), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/248 (31%), Positives = 119/248 (47%), Gaps = 38/248 (15%)

Query: 37  LVTGEIVVVHGAGRTDSGVHALRQVAHFDLV-----REWVPVILCKALN-AYLKISDT-I 89
           L   E   +H + RTDSGVHAL   AH DL+       + P  +  A+N + L +  T I
Sbjct: 8   LKLAEPPNIHVSSRTDSGVHALCNTAHADLIYGDDKEPFDPDSIVHAVNRSILHMGRTDI 67

Query: 90  SILNLSIVDKQFHARFSAIRRSYLYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIA 145
            ++N   V   F +R  A+ R+YLYR+++     + P+  E  R+W I + LD E M+ A
Sbjct: 68  RLMNCRPVSPTFSSRHQALGRTYLYRVVSGCYHSRLPIP-EVNRSWGIKERLDIEAMQEA 126

Query: 146 AQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHFDVNSFG-------------NLIEIRVVA 190
           A+H +G HDFTTFRS   +     P++T+   +V                  ++E+   +
Sbjct: 127 AKHFLGTHDFTTFRSKTPETWTKDPVKTMKVVEVRRASCFLKEHDPFCRDLEVLELIFKS 186

Query: 191 RSFLH--------TQIRSFVGSLKLVGDGKWTSTDLEKALQAQD---RKECGPLAPPEGL 239
           RSFL+         Q+R   G L  +G GK    D+   L  +      +   +AP  GL
Sbjct: 187 RSFLYRQAIVLSLLQVRRMTGLLVAIGRGKLQPEDVCTLLAVRKIAAYPKAAQVAPAHGL 246

Query: 240 YFDSVEYS 247
           Y  +VEY+
Sbjct: 247 YLCNVEYN 254


>gi|170780769|ref|YP_001709101.1| tRNA pseudouridine synthase A [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169155337|emb|CAQ00440.1| putative pseudouridylate synthase [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 323

 Score = 97.1 bits (240), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 110/244 (45%), Gaps = 34/244 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---TGEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G+G+ GW +Q    ++QGS+E A+  +   T     +  AGRTD+GVHA 
Sbjct: 1   MRLRLDVAYDGTGFAGWAKQPGLRTVQGSLEDALAQLLARTPPAPTLVVAGRTDAGVHAT 60

Query: 59  RQVAHFDLVR----------------------EWVPVILCKAL------NAYLKISDTIS 90
            QVAH DL                        + VP     A       N  L     + 
Sbjct: 61  GQVAHLDLTEAQIASLDRPPRGRAAEATAGEGQHVPTAARAASALARRLNGVLGARSDVV 120

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHL 149
           +L  +     F ARFSA  R+Y YR+     P   L++ R   +P +LD   ++ AA  L
Sbjct: 121 VLACAPAPDGFDARFSATWRAYRYRVADADGPRDPLQRHRTVEVPVALDAAVLQEAADAL 180

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
           +G HDF  +     + +S IRT+     + +    +E  V A +F H+ +R+ VG+    
Sbjct: 181 LGLHDFAAYCKPR-EGASTIRTLQELTWIRAADGALEAVVRADAFCHSMVRALVGACVAA 239

Query: 209 GDGK 212
             G+
Sbjct: 240 ASGR 243


>gi|269955466|ref|YP_003325255.1| tRNA pseudouridine synthase A [Xylanimonas cellulosilytica DSM
           15894]
 gi|269304147|gb|ACZ29697.1| tRNA pseudouridine synthase A [Xylanimonas cellulosilytica DSM
           15894]
          Length = 293

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 80/276 (28%), Positives = 118/276 (42%), Gaps = 38/276 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRT 51
           M+R  + + Y+G+ + GW RQ    ++QG +E  +          L    + V   AGRT
Sbjct: 1   MVRVRLDLAYDGTQFAGWARQPALRTVQGVLEDGLEQIVRTAPRGLPAPRLTV---AGRT 57

Query: 52  DSGVHALRQVAHFDL-VREWVPVI----------LCKALNAYLKISDTISILNLSIVDKQ 100
           D+GVHA  QVAH DL V  WV +           L   L   L     + +   ++    
Sbjct: 58  DAGVHARGQVAHVDLPVERWVALPGRSDREPGESLVTRLTGVLPPD--VVVHRAALAPAG 115

Query: 101 FHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
           F ARFSA+ R Y +RI    A    L +       + LD   M  A Q L G  DF  + 
Sbjct: 116 FDARFSALYRRYAFRIADDAAARDPLHRAHVLWHRRPLDVAAMHDAVQPLRGVRDFAAY- 174

Query: 160 SIHCQASSPIRTIDHFDVNSF--------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
              C+      TI      S+          L+  RVVA +F H  +R+ VG+   VG+G
Sbjct: 175 ---CKPRPGATTIRELKELSWTRPADGPDAGLVVARVVADAFCHNMVRALVGASIAVGEG 231

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +   +   + L ++ R+    + PP GL  + V Y 
Sbjct: 232 RKPVSWPAEVLASKQRERAAAVVPPRGLTLEEVVYP 267


>gi|148273765|ref|YP_001223326.1| tRNA pseudouridine synthase A [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147831695|emb|CAN02664.1| putative tRNA pseudouridine synthase [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 334

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 111/243 (45%), Gaps = 34/243 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---TGEIVVVHGAGRTDSGVHALR 59
           R  + I Y+G+G+ GW +Q    ++QG++E A+  +   T     +  AGRTD+GVHA  
Sbjct: 13  RLRLDIAYDGTGFAGWAKQPGLRTVQGALEDALAQLLARTPPAPTLVVAGRTDAGVHATG 72

Query: 60  QVAHFDLVREW----------------------VPVI------LCKALNAYLKISDTISI 91
           QVAH DL  E                       VP +      L + LN  L     + +
Sbjct: 73  QVAHLDLTDEQIASLDRPPRGRAAAADAGEGAHVPSVDRAAAALARRLNGVLGARSDVVV 132

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L  +     F ARFSA  R+Y YRI     P   L++ R   +P +LD   ++ AA  L+
Sbjct: 133 LACAPAPDGFDARFSATWRAYRYRISDVDGPRDPLQRHRTVELPVALDAAVLQEAADALL 192

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           G HDF  +     + +S IRT+       +    +E  V A +F H+ +R+ VG+     
Sbjct: 193 GLHDFAAYCKPR-EGASTIRTLQELTWTRASDGALEATVRADAFCHSMVRALVGACVAAA 251

Query: 210 DGK 212
            G+
Sbjct: 252 SGR 254


>gi|116007752|ref|NP_001036574.1| CG34140 [Drosophila melanogaster]
 gi|113194868|gb|ABI31225.1| CG34140 [Drosophila melanogaster]
 gi|238231868|gb|ACR40402.1| RE01995p [Drosophila melanogaster]
          Length = 306

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 93/302 (30%), Positives = 133/302 (44%), Gaps = 57/302 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N          SIQG +E A  +F  T EI  V  + R
Sbjct: 1   MYRYLLNISYIGTTFRGIQKTVNKLEQSRLDTKSIQGCLELALQVFHPTNEIHTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL      DL R     +   IL   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVQVDLERPNGQPYDTTILTGVLNRTLNKQRLPIRVLSSKLVANSFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALE---KGRAW--LIP------------KSLDCENMRIAAQH 148
            AI R+YLYR    + P   +   + R++   IP             S D + ++ AA+ 
Sbjct: 120 DAIGRTYLYRFAVAKVPTLGDCSLRNRSFETFIPVEEIDRCYFLQSSSFDIKRVQAAARM 179

Query: 149 LVGRHDFTTFRSIHCQASS------PIRTIDHFDV----------NSFG-----NLIEIR 187
            +G HDF TF S+  Q          +R ID  ++          N+       N  +I 
Sbjct: 180 FIGVHDFRTFMSVSRQKVCRDHPMFTVRKIDEINIRPGETRALSSNAIQAAETYNYWDIE 239

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSV 244
           + A+SFL+ Q+R  VG+L  +G+G+     L + L    +        LAP  GLY   V
Sbjct: 240 IRAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNSWDHRVLLAPACGLYLCRV 299

Query: 245 EY 246
            Y
Sbjct: 300 HY 301


>gi|240167785|ref|ZP_04746444.1| tRNA pseudouridine synthase A [Mycobacterium kansasii ATCC 12478]
          Length = 248

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 116/233 (49%), Gaps = 22/233 (9%)

Query: 31  IEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI--------------LC 76
           ++ A+  +    + +  AGRTD+GVHA  QVAH D+  + +P                L 
Sbjct: 2   LDAALTTIFRTPIRLRAAGRTDAGVHASGQVAHADVPVDALPNAYSHSVRAGHPEFRPLV 61

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR---AWLI 133
           + L+ +L  SD + ++++    + F ARFSA+ R Y+YR+ T    +  +  R   AW  
Sbjct: 62  RRLSRFLP-SD-VRVIDIVRAPRDFDARFSALCRHYVYRLSTAPYGVVPQLARYVTAW-- 117

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSF 193
           P+ LD E M IA++ L+G HDF  F   H   ++ IR +   D    G+L+   V A +F
Sbjct: 118 PRDLDVEAMTIASRELLGLHDFAAF-CRHRDGATTIRDLQRLDWARDGDLVTAHVTADAF 176

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             + +RS VG++  VG+ + ++    + L A  R      AP  GL    V+Y
Sbjct: 177 CWSMVRSLVGAVLAVGEHRRSTAWCRELLTATGRSSDFAAAPAHGLTLVQVDY 229


>gi|154486775|ref|ZP_02028182.1| hypothetical protein BIFADO_00600 [Bifidobacterium adolescentis
           L2-32]
 gi|154084638|gb|EDN83683.1| hypothetical protein BIFADO_00600 [Bifidobacterium adolescentis
           L2-32]
          Length = 306

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 81/291 (27%), Positives = 132/291 (45%), Gaps = 52/291 (17%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G+G++GW +Q    ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 5   VRLRIDLAYDGTGFYGWAKQPEIRTVQGEIERVLHTILRVPEGDPTEPLRLTVAGRTDTG 64

Query: 55  VHALRQVAHFDLVREW---------VPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  +          VP ++         +   I+I  ++     F ARF
Sbjct: 65  VHASHQVCHLDVNEDVLKRCVGHMDVPPVIALTRRLQRMLPADIAIRGIAPAPNGFDARF 124

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWL--IPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           SA+ R+Y+YRI  R + +   + R ++  I   LD + M  AA   +G HDF +F + + 
Sbjct: 125 SALERTYVYRIADRSSEVD-PRTRNFVLHIDDELDLKAMNEAAAMTIGLHDFGSFATPNP 183

Query: 164 QASS------------PIRT-IDHFDVNSFGN----------LIEIRVVARSFLHTQIRS 200
             ++            P RT ID  D  + G           L+   +VA +F    +RS
Sbjct: 184 GGTTIREVKTAYWRRVPQRTLID--DGMTMGERYRTPTVESGLVCFVIVADAFARNMVRS 241

Query: 201 FVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            V     VG GK    W +  +   L+       GP+A P+GL  + +EY 
Sbjct: 242 LVNGCVQVGIGKRSLDWFAGKMAAPLR---EGSTGPIA-PQGLTLEHIEYP 288


>gi|212716584|ref|ZP_03324712.1| hypothetical protein BIFCAT_01513 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660288|gb|EEB20863.1| hypothetical protein BIFCAT_01513 [Bifidobacterium catenulatum DSM
           16992]
          Length = 306

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 81/290 (27%), Positives = 134/290 (46%), Gaps = 52/290 (17%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G+ ++GW +Q +  ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 5   VRLRIDLAYDGTDFYGWAKQPDMRTVQGEIERVLHTILRVPEGDDNEPLRLTVAGRTDTG 64

Query: 55  VHALRQVAHFDLVREWV----------PVI-LCKALNAYLKISDTISILNLSIVDKQFHA 103
           VHA  QV H D+  E +          PV+ L + L   L   + I+I ++    + F A
Sbjct: 65  VHASHQVCHLDINEETLARCVGHMQVEPVMALTRRLQRML--PNDIAIHSIKEAPEGFDA 122

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R+Y+YRI  R + +      + L I  +LD   M  AA+  +G HDF +F + +
Sbjct: 123 RFSALERTYVYRIADRSSEIDPRTRNSVLHIDDNLDIAVMNKAAEMTIGLHDFGSFATPN 182

Query: 163 CQASSPIRTIDHF------------DVNSFGN----------LIEIRVVARSFLHTQIRS 200
              ++ IR +               D  + G           L+   +VA +F    +RS
Sbjct: 183 PGGTT-IREVKTAYWRRIPQHPLIDDGTTMGERYRTPALESGLLCFTIVADAFARNMVRS 241

Query: 201 FVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            V     VG GK    W +  +   L+       GP+A P+GL  + +EY
Sbjct: 242 LVNGCVQVGIGKRSLDWFAGKMATPLR---EGSTGPIA-PQGLTLEHIEY 287


>gi|94266218|ref|ZP_01289926.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
 gi|93453191|gb|EAT03652.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
          Length = 319

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 56/155 (36%), Positives = 83/155 (53%), Gaps = 2/155 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I ++G+ + GWQRQ++  +IQ ++E  +  + GE VV+HGAGRTD+GVHA   VA F 
Sbjct: 5   LTIAFDGTAFAGWQRQRHQPTIQATLEDGLARLLGEKVVLHGAGRTDAGVHAAGMVASFQ 64

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             R+         LN+ L  +  I IL    V   FHARFSA  + Y+Y   T       
Sbjct: 65  TARQLPLAAYRHGLNSMLPPA--IRILAAREVAADFHARFSAKGKIYVYGFTTAAIISPR 122

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
            +  +   P S +   ++ A   L+G HDFT+F +
Sbjct: 123 RRLYSAHFPGSFNPGPVQEALPGLLGEHDFTSFEA 157



 Score = 42.0 bits (97), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 29/59 (49%)

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           V    FL   +R+ VG+L  +G GK T   L + L  +DR   GP AP  GL    V Y
Sbjct: 261 VAGDGFLRHMVRNLVGTLLEIGRGKRTPESLPQLLAGRDRCRAGPTAPAHGLTLWRVLY 319


>gi|297564067|ref|YP_003683040.1| tRNA pseudouridine synthase A [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296848516|gb|ADH70534.1| tRNA pseudouridine synthase A [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
          Length = 279

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 79/254 (31%), Positives = 121/254 (47%), Gaps = 15/254 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW  Q    ++QG +E A+  V     V +  AGRTD+GVHA  Q
Sbjct: 6   VRVRLDVAYDGTDFSGWAAQPGRRTVQGELEAALARVLRLPEVSLTCAGRTDAGVHARGQ 65

Query: 61  VAHFDL-VREWVPV---ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           VA  D+  R W      +L +      K    + +    +    F ARFS + R YLYR+
Sbjct: 66  VAQADIPARTWESEGERVLRRLAGVLPK---DVRVRAARLAPPGFDARFSPLFRRYLYRV 122

Query: 117 ITRQAPLALEK--GRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
               AP  ++    R  L  +S LD + M  AA+ LVG HDF  F     + ++ IR + 
Sbjct: 123 S--DAPYGVDPLLRRDVLWHRSPLDVDRMNAAAERLVGEHDFAAF-CKRREGATTIRELL 179

Query: 174 HFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             +      +L+   + A +F H  +R+ VG+L  VGDG+  +    K L A  R     
Sbjct: 180 RLEWTRVDEHLLHGTIQADAFCHNMVRALVGALLAVGDGRRDADWPGKVLGAGTRDSSVH 239

Query: 233 LAPPEGLYFDSVEY 246
           +  P+GL  + V Y
Sbjct: 240 VVGPQGLSLEEVRY 253


>gi|298253049|ref|ZP_06976841.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 5-1]
 gi|297532444|gb|EFH71330.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 5-1]
          Length = 305

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 82/287 (28%), Positives = 129/287 (44%), Gaps = 46/287 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW +Q    ++QG IE A+ +V         E + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGGFYGWAKQPVLRTVQGDIEAALHMVLRVPKNDPTESLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVILCK---------ALNAYLK--ISDTISILNLSIVDKQFHA 103
           VHA  QV H D+  E   ++ C          AL   LK  +   IS+  +S+    F A
Sbjct: 61  VHASHQVCHLDVCEET--LLRCVGHTGLDGVCALEYRLKHVLPQDISLHKVSVAPIGFDA 118

Query: 104 RFSAIRRSYLYRIITRQAPLALE---KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           RFSA+ R+Y+YRI         +   +G    +   LD + M  AA+ ++G HDF +F  
Sbjct: 119 RFSALERTYVYRICDASDYCDYDPRMRGFVLKLDDVLDVDAMNQAARLMIGLHDFGSFAR 178

Query: 161 IHCQASSPIRTIDHFDVNSFGN--------------------LIEIRVVARSFLHTQIRS 200
            +    + IR +        G                     L+E  +VA +F H  +RS
Sbjct: 179 PN-PGGTTIRDVKSVCWERVGTRANDVRVKLKTGCVPPVEQGLLEFTIVADAFAHNMVRS 237

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEY 246
            V +   +G GK +    E+ +    R+   GP+  P GL  + V Y
Sbjct: 238 LVQACVQIGCGKRSFDWFEEKINVPLREGSTGPID-PHGLTLEYVAY 283


>gi|242310521|ref|ZP_04809676.1| tRNA pseudouridine synthase A [Helicobacter pullorum MIT 98-5489]
 gi|239522919|gb|EEQ62785.1| tRNA pseudouridine synthase A [Helicobacter pullorum MIT 98-5489]
          Length = 241

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 81/254 (31%), Positives = 117/254 (46%), Gaps = 22/254 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  M I YNG+ + G+Q+QK+  S+ G +E+ +F   G    + G+GRTD GVHA  Q
Sbjct: 2   MMKVAMKIAYNGANFCGFQKQKDRQSVSGFLEE-VFGSVGIFEKIIGSGRTDKGVHASAQ 60

Query: 61  VA-------HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           V        H DL +      L + LN  LK+   + I  +  VD  FHARF A RR Y 
Sbjct: 61  VISLKIPDFHKDLQK------LQEILN--LKLYPLVKIKKIWRVDDDFHARFDAKRRGYC 112

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTI 172
           Y I    +P        +      +   ++ A +   G H+F  F ++    A   +R I
Sbjct: 113 YVISQEYSPFIAPFAHYYCFQ---NVGIIKEALREFEGLHNFKAFMKNDGSGAKGSVREI 169

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
               +   G           FL +QIR  VG L  +  G    +DL+K L  + R    P
Sbjct: 170 YKARLLKRGKFYIFLFWGNGFLRSQIRLMVGYLLEIDKGNLQISDLKKQLLGE-RIFSIP 228

Query: 233 LAPPEGLYFDSVEY 246
            APP GL+  SV+Y
Sbjct: 229 -APPNGLFLSSVKY 241


>gi|291234813|ref|XP_002737344.1| PREDICTED: MGC80334 protein-like [Saccoglossus kowalevskii]
          Length = 520

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 108/228 (47%), Gaps = 32/228 (14%)

Query: 1   MIRYCMIIEYNGSGYFGW-QRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHAL 58
           M RY + I Y G+ + G  Q      ++Q  IE A+  L   E   ++ + RTD+GVHAL
Sbjct: 1   MCRYLLYISYLGTNFRGVVQTNSTSPTVQRVIEGALHTLKPQEAAKLYFSSRTDAGVHAL 60

Query: 59  RQVAHFDLVRE-----WVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSY 112
              AH D VR      +   +L   LN  L I+   I I ++  V  +FHARF A  R+Y
Sbjct: 61  NNTAHVDFVRRNNQQPFSGEVLKTILNNKLLIAQQDIRINDVKKVPDEFHARFQAKGRTY 120

Query: 113 LYRIITR------QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA- 165
           +YRI +         PL  E  R W++   LD E M+ A +  +G HDF  FRS + +  
Sbjct: 121 VYRIASNWNCALNHIPL-FENHRCWMVSYRLDIEKMKQACEVFIGTHDFAAFRSKNNKNV 179

Query: 166 -SSPIRTIDHFDVNSFGNLI---------------EIRVVARSFLHTQ 197
             S +RTID  ++     ++               EI   A+SFL+ Q
Sbjct: 180 HKSTVRTIDSINIRKSHGILQHLSPCETDARIEYYEIEFKAKSFLYKQ 227


>gi|88603643|ref|YP_503821.1| tRNA pseudouridine synthase ACD [Methanospirillum hungatei JF-1]
 gi|88189105|gb|ABD42102.1| tRNA pseudouridine synthase A [Methanospirillum hungatei JF-1]
          Length = 276

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 116/248 (46%), Gaps = 27/248 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF----LVTGEIVVVHGAGRTDSGVHA 57
           +R    I Y G+ +FG Q Q +  +++G IE A      + + ++  +  +GRTD GVHA
Sbjct: 11  VRLAFRIGYIGTSFFGSQYQPDQRTVEGEIEAACLRAGIITSRQVSRLALSGRTDRGVHA 70

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             Q+          P +  +ALN   ++   I +   +   + F+ R+  I R+Y Y   
Sbjct: 71  KCQILALSTHN---PDLAVRALNG--QLPPDIWVSAWAYAPESFYPRYDVIIRTYRY-YF 124

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           +R              P S D   MR AA   +G HDF  F  I     SP++TID  +V
Sbjct: 125 SR--------------PPS-DINAMRDAAGLFLGTHDFRCFARIE-PGKSPVKTIDRIEV 168

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S  N   + V A+SFL   +R   GSL  V +G+    DL + L+ + + +  P APPE
Sbjct: 169 ISDENGCRLEVTAQSFLWHMVRCMAGSLYQVSEGEMAIRDLTQYLKGECKNKVKP-APPE 227

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 228 GLILWDVQ 235


>gi|94270473|ref|ZP_01291754.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
 gi|93450785|gb|EAT01835.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
          Length = 319

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 56/155 (36%), Positives = 83/155 (53%), Gaps = 2/155 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I ++G+ + GWQRQ++  +IQ ++E  +  + GE VV+HGAGRTD+GVHA   VA F 
Sbjct: 5   LTIAFDGTAFAGWQRQRHQPTIQATLEDGLARLLGEKVVLHGAGRTDAGVHAAGMVASFQ 64

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             R+         LN+ L  +  I IL    V   FHARFSA  + Y+Y   T       
Sbjct: 65  TARQLPLAAYRHGLNSMLPPA--IRILAAREVAADFHARFSARGKIYVYGFTTAAIISPR 122

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
            +  +   P S +   ++ A   L+G HDFT+F +
Sbjct: 123 RRLYSAHFPGSFNPGPVQEALPGLLGEHDFTSFEA 157



 Score = 42.0 bits (97), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 29/59 (49%)

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           V    FL   +R+ VG+L  +G GK T   L + L  +DR   GP AP  GL    V Y
Sbjct: 261 VAGDGFLRHMVRNLVGTLLEIGRGKRTPESLPQLLAGRDRCRAGPTAPAHGLTLWRVLY 319


>gi|212697539|ref|ZP_03305667.1| hypothetical protein ANHYDRO_02112 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675538|gb|EEB35145.1| hypothetical protein ANHYDRO_02112 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 242

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/215 (33%), Positives = 106/215 (49%), Gaps = 7/215 (3%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I+Y+GS + G+Q QK+  ++Q  +E+AI  VTGE   +  +GRTDSGVHA     +F   
Sbjct: 10  IQYDGSLFEGFQIQKDKRTVQKELEEAIRKVTGEKNRIIASGRTDSGVHANEMYVNFLTA 69

Query: 68  REWVPVILCKALNAYLKISDTISILNLS--IVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           ++    I     + +LK      IL LS   VDK FHARFS   ++Y Y I   +    +
Sbjct: 70  KD----IRADKFHFHLKKYLPADILALSSKKVDKNFHARFSVKTKTYKYVISLEKILHPI 125

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFGNLI 184
            +     I   LD + ++   + L G HDF  F  S      + IR ID        N++
Sbjct: 126 YRNYMEQITYKLDFDKLKQGMEILKGEHDFRAFMLSEKNDIINTIRKIDDCYYILDNNIL 185

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            +   A SFLH Q+R   GSL  +  GK +  D +
Sbjct: 186 FLYFKAESFLHNQVRIMAGSLIELSRGKISLDDFK 220


>gi|225351017|ref|ZP_03742040.1| hypothetical protein BIFPSEUDO_02599 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225158473|gb|EEG71715.1| hypothetical protein BIFPSEUDO_02599 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 331

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 81/292 (27%), Positives = 135/292 (46%), Gaps = 54/292 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R  + + Y+G+ ++GW +Q +  ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 30  VRLRIDLAYDGTDFYGWAKQPDIRTVQGEIERVLHTILRVPEGDDNEPLRLTVAGRTDTG 89

Query: 55  VHALRQVAHFDLVREWV----------PVILCKALNAYLK--ISDTISILNLSIVDKQFH 102
           VHA  QV H D+  E +          PV+   AL   L+  + + I+I ++    + F 
Sbjct: 90  VHASHQVCHLDINEETLARCVGHMQVEPVM---ALTRRLQRMLPNDIAIRSIKEAPEGFD 146

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFSA+ R+Y+YRI  R + +      + L I  +LD   M  AA+  +G HDF +F + 
Sbjct: 147 ARFSALERTYVYRIADRSSEIDPRTRNSVLHIDDNLDIGAMNKAAEMTIGLHDFGSFATP 206

Query: 162 HCQASSPIRTIDHF------------DVNSFGN----------LIEIRVVARSFLHTQIR 199
           +   ++ IR +               D  + G           L+   +VA +F    +R
Sbjct: 207 NPGGTT-IREVKTAYWRRIPQHPLIDDGTTMGERYRTPALESGLLCFTIVADAFARNMVR 265

Query: 200 SFVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           S V     VG GK    W +  +   L+       GP+A P+GL  + +EY 
Sbjct: 266 SLVNGCVQVGIGKRSLDWFAGKMATPLR---EGSTGPIA-PQGLTLEHIEYP 313


>gi|195170621|ref|XP_002026110.1| GL16086 [Drosophila persimilis]
 gi|194110990|gb|EDW33033.1| GL16086 [Drosophila persimilis]
          Length = 504

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 83/267 (31%), Positives = 119/267 (44%), Gaps = 57/267 (21%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTINKLEPQSLDTNSVQGCLELALRVFHPTNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLARRDGQPYDTTTLTGVLNRTLDKQRLPIRVLSSQVVPDTFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALEKGRA------------------WLIPKSLDCENMRIAAQ 147
            AI R+YLYR    + PL  + G+                   +L+  + D E +R AA+
Sbjct: 120 HAIGRTYLYRFAVARKPL-FDDGKLRNKGFEAFVPVEEIDRCYFLLAPTFDIERIRNAAR 178

Query: 148 HLVGRHDFTTFRSIHCQASSP-------IRTIDHFDVNSFGNLI---------------E 185
             +G HDF TF S+  Q S         +R ID  ++     L                +
Sbjct: 179 MFIGVHDFRTFMSVSRQKSLSRDHPMFTLRKIDEINIRPGRTLALPSNATLAAETYDYWD 238

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGK 212
           I + A+SFL+ Q+R  VGSL  +G  +
Sbjct: 239 IEIKAKSFLYKQVRRIVGSLLSLGSDR 265


>gi|294494718|ref|YP_003541211.1| tRNA pseudouridine synthase A [Methanohalophilus mahii DSM 5219]
 gi|292665717|gb|ADE35566.1| tRNA pseudouridine synthase A [Methanohalophilus mahii DSM 5219]
          Length = 273

 Score = 95.9 bits (237), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 111/251 (44%), Gaps = 29/251 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV------VHGAGRTDSGV 55
           +R  + I Y GS Y G Q Q   S+I+G I +A  L + EI+          +GRTD+GV
Sbjct: 1   MRVALKIAYIGSSYRGSQVQPGVSTIEGKIFEA--LQSLEIIEDPSSARFVSSGRTDTGV 58

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA+ QV  FD  +    + + + +N+  K+   I   + + VD  FH R  AI R+Y Y 
Sbjct: 59  HAMGQVVAFDTDKP--KLAIPRVINS--KLPGDIWAWSRAEVDSDFHPRRYAINRTYRYI 114

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
             +  A                D   +R A   L G HDF  F        S IR I+  
Sbjct: 115 TPSMDA----------------DISKLRAACSILEGSHDFANF-CFRDTGRSTIRRIEKI 157

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           DV   GNL+ I + A SFL   IR  V  L LVG G      LE  L     +E    A 
Sbjct: 158 DVRLAGNLLRIDITANSFLWKMIRKIVTVLLLVGSGARDLDWLENMLDPASYEEGIKPAK 217

Query: 236 PEGLYFDSVEY 246
           P GL   +V Y
Sbjct: 218 PYGLILTNVNY 228


>gi|14521207|ref|NP_126682.1| tRNA pseudouridine synthase A [Pyrococcus abyssi GE5]
 gi|14548295|sp|Q9UZZ3|TRUA_PYRAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|5458425|emb|CAB49913.1| truA pseudouridylate synthase I [Pyrococcus abyssi GE5]
          Length = 263

 Score = 95.9 bits (237), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 122/250 (48%), Gaps = 30/250 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R    I Y+G+ + G+QRQ N  +++G I KA+            A RTD GV AL  V
Sbjct: 1   MRVAFKIAYDGTRFHGFQRQPNLRTVEGEIIKALNNSGIMYSDFKSASRTDRGVSALGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYL---KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
                  E       KALN  +   ++ D + IL+   V + FH RF A  + Y Y    
Sbjct: 61  VAITTEDE-------KALNPMVLNARLED-VWILSAIEVPQDFHPRFWAKSKVYRY---- 108

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                       +L    L+ E ++  +Q  +G HDF+ F  +  + +  +R+ID  +V 
Sbjct: 109 ------------YLPSIGLEVEKVKECSQLFLGVHDFSAFSRVDGRDT--VRSIDRIEVF 154

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPE 237
           + G ++ I + A+SFL   +R  V +L+L G G+ +  ++++ L+ + ++ +  P APPE
Sbjct: 155 TLGPILIIEIEAKSFLWEMVRRIVKALELCGLGRLSCEEIKEMLEGKFEKSKKVPPAPPE 214

Query: 238 GLYFDSVEYS 247
           GL    ++Y 
Sbjct: 215 GLLLVDIKYE 224


>gi|268679755|ref|YP_003304186.1| tRNA pseudouridine synthase A [Sulfurospirillum deleyianum DSM
           6946]
 gi|268617786|gb|ACZ12151.1| tRNA pseudouridine synthase A [Sulfurospirillum deleyianum DSM
           6946]
          Length = 247

 Score = 95.9 bits (237), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 119/256 (46%), Gaps = 20/256 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           +R  +I+ Y+GS ++G+QRQ N +    ++ G +EK++  +     +V G+GRTD GVHA
Sbjct: 1   MRVKLILSYDGSHFYGFQRQNNENEHFQTVTGILEKSLKALGIHTPIV-GSGRTDRGVHA 59

Query: 58  LRQVAHFDLVREW------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           LRQV H DL   W      +  +L ++L  +L I      L        FHARFSA +R 
Sbjct: 60  LRQVVHLDLPLFWEKEYEKLRSLLNRSLMPHLYIQQIHPTL------PNFHARFSAQKR- 112

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
            LYR                L   +LD + +   AQ   G H+F  F+      +   R 
Sbjct: 113 -LYRYFLYDGVYQPFYAHYALHVNALDVQRLHHVAQSFQGAHNFEFFKKQGGGLTRDERI 171

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +       + +LI I  +  +FL +QIR    +L  V   +    +L   L+ +++K   
Sbjct: 172 LYKVGAYRYKHLIVIYFLGDAFLRSQIRMMCDALLKVCYDEIREEELIAQLR-REKKVST 230

Query: 232 PLAPPEGLYFDSVEYS 247
            L PP GLY   + Y 
Sbjct: 231 TLLPPSGLYLSRIFYE 246


>gi|198462560|ref|XP_001352470.2| GA20054 [Drosophila pseudoobscura pseudoobscura]
 gi|198150878|gb|EAL29967.2| GA20054 [Drosophila pseudoobscura pseudoobscura]
          Length = 504

 Score = 95.5 bits (236), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 83/267 (31%), Positives = 119/267 (44%), Gaps = 57/267 (21%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTINKLEPQSLDTNSVQGCLELALRVFHPTNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLARRDGQPYDTTTLTGVLNRTLDKQRLPIRVLSSQVVPDTFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALEKGRA------------------WLIPKSLDCENMRIAAQ 147
            AI R+YLYR    + PL  + G+                   +L+  + D E +R AA+
Sbjct: 120 HAIGRTYLYRFAVARRPL-FDDGKLRNKGFEAFVPVEEIDRCYFLLAPTFDIERIRNAAR 178

Query: 148 HLVGRHDFTTFRSIHCQASSP-------IRTIDHFDVNSFGNLI---------------E 185
             +G HDF TF S+  Q S         +R ID  ++     L                +
Sbjct: 179 MFIGVHDFRTFMSVSRQKSLSRDHPMFTLRKIDEINIRPGRTLALPSNATLAAETYDYWD 238

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGK 212
           I + A+SFL+ Q+R  VGSL  +G  +
Sbjct: 239 IEIKAKSFLYKQVRRIVGSLLSLGSDR 265


>gi|212223540|ref|YP_002306776.1| tRNA pseudouridine synthase A [Thermococcus onnurineus NA1]
 gi|229470756|sp|B6YTJ2|TRUA_THEON RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|212008497|gb|ACJ15879.1| tRNA pseudouridine synthase A [Thermococcus onnurineus NA1]
          Length = 267

 Score = 95.5 bits (236), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 115/250 (46%), Gaps = 26/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHA 57
           +R  + I Y+G+ ++G+QRQ    +++G I +A+     +   E     GA RTD GV A
Sbjct: 1   MRLALRIAYDGTAFYGFQRQPGLRTVEGEIIRALTKLGIIEDVESSNFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              V  FD+      ++  + LN +LK    + +L  + V + FH RF A  ++Y Y   
Sbjct: 61  FFNVVAFDVASR-PDLVRPEVLNFHLK---DVWVLGTAEVPEDFHPRFWAKSKTYRY--- 113

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +LI    D + MR  A+  +G HDF+ F  +     +P+R +   D+
Sbjct: 114 -------------YLIDAGFDEKAMRECAKLFIGTHDFSAFARLEPH-KNPVRELIRADI 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                   I +  +SFL    R  V +L+  G G  T  ++EK L  +  ++  P A PE
Sbjct: 160 IKRQGYYIIELEGKSFLWEMARRIVNALRFCGLGILTEEEVEKMLNGEYSRKIPP-ARPE 218

Query: 238 GLYFDSVEYS 247
           GL    +EY 
Sbjct: 219 GLVLWGIEYE 228


>gi|227485306|ref|ZP_03915622.1| tRNA-pseudouridine synthase I [Anaerococcus lactolyticus ATCC
           51172]
 gi|227236766|gb|EEI86781.1| tRNA-pseudouridine synthase I [Anaerococcus lactolyticus ATCC
           51172]
          Length = 246

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 112/251 (44%), Gaps = 10/251 (3%)

Query: 1   MIRYCMI-IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MI+  ++ + ++G  + G+Q Q +  S++  + KAI  VTGE   +   GRTD+GVHA  
Sbjct: 1   MIKNVLLKLAFDGRDFKGYQYQIDQRSVEEELRKAIKEVTGEDNRIIACGRTDAGVHARS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              +F    +  P      +  +L   D I  L+   V   FHARFS   ++Y Y I   
Sbjct: 61  FYINFLTACDVNPKGFAYHIQPHL--PDDILALSSKEVGLDFHARFSCKSKTYKYIINQE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----RSIHCQASSPIRTIDHF 175
           + P  + +     I   LD + +    + L G HDF  F    ++I    +   R ID  
Sbjct: 119 KNPHPIYRSYMENITYRLDYDKLDEGLEILKGDHDFRLFMKEDKNIDINTN---RRIDDC 175

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                   +E+   A SFLH Q+R   GSL  +  GK +  D +       +K   P   
Sbjct: 176 YFKRGETRLELYFKAESFLHNQVRIMTGSLIELARGKLSLDDFKAYFDPATKKRANPALS 235

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 236 PVGLYLWEVEY 246


>gi|167948002|ref|ZP_02535076.1| tRNA pseudouridine synthase A [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 201

 Score = 95.1 bits (235), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 55/150 (36%), Positives = 79/150 (52%), Gaps = 2/150 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+GSG+ GWQ+Q +  S+Q  +E A+  V  + V VH AGRTD+GVH   QV
Sbjct: 19  MKIALGVEYDGSGFNGWQKQSHARSVQEDLEAALSRVADQPVRVHCAGRTDTGVHGTGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   E  P      L + + + + +S+     V   FHARFSA  R Y Y I+ R  
Sbjct: 79  VHFETTAERPPRAW--VLGSNVNLPNDVSVSWARQVADDFHARFSATGRHYRYLILNRGT 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
             AL + RA      LD   M+ A   + G
Sbjct: 137 RSALWRNRATWHHHPLDEHRMQPAGTGIGG 166


>gi|195953438|ref|YP_002121728.1| tRNA pseudouridine synthase A [Hydrogenobaculum sp. Y04AAS1]
 gi|229470758|sp|B4U9D9|TRUA_HYDS0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|195933050|gb|ACG57750.1| tRNA pseudouridine synthase A [Hydrogenobaculum sp. Y04AAS1]
          Length = 247

 Score = 95.1 bits (235), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 69/258 (26%), Positives = 115/258 (44%), Gaps = 23/258 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH------GAGRTDSG 54
           M  Y   I + G+ Y GWQ Q N  +IQ  +E+ ++ +  +   +       G  RTD G
Sbjct: 1   MKNYKFTISFVGTNYSGWQYQPNVPTIQNEVEEKLYYIVNKKKPIKQKIRAIGCSRTDKG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA+  V +  +  +     L KALN+ L     I I N+  V  +F++RF A++++Y+Y
Sbjct: 61  VHAIEFVFNVKMEFDKDLNFLRKALNSAL--PKDIKIHNIEEVPLEFNSRFDALKKTYIY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF------RSIHCQASSP 168
           ++   +      + RA L+ K  D   M   +   +G  DF  F       + +C   + 
Sbjct: 119 KLFFDEKNSPFFQDRAMLVYKPTDLGKMMEISHLFLGYKDFRGFTKELEDENGYCSVENI 178

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
              +D+        L+EI + A  FL   +R  VG++     G  +  D+   L+A  ++
Sbjct: 179 TFKVDY-------PLVEISITANRFLRYMVRRMVGTMLSYAQGLISIDDVNDFLKA--KR 229

Query: 229 ECGPLAPPEGLYFDSVEY 246
                A   GLY   V Y
Sbjct: 230 VSNHTAKAHGLYLKKVYY 247


>gi|145596404|ref|YP_001160701.1| tRNA-pseudouridine synthase I [Salinispora tropica CNB-440]
 gi|145305741|gb|ABP56323.1| tRNA-pseudouridine synthase I [Salinispora tropica CNB-440]
          Length = 276

 Score = 95.1 bits (235), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 78/254 (30%), Positives = 116/254 (45%), Gaps = 16/254 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + GW  Q    ++ G++ +A+ LV   G    +  AGRTD+GVHA  Q
Sbjct: 6   RVRLDVSYDGADFSGWAVQPERRTVAGALVQALDLVLGVGAATGLTVAGRTDAGVHATGQ 65

Query: 61  VAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL+ E W              +   + I  ++     F ARFSA  R Y YR+   
Sbjct: 66  VCHVDLLTEVWHRHEHTLLRRLARLLPADVRIRAMTEAPDDFDARFSATFRRYEYRVT-- 123

Query: 120 QAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            AP   E  R     AW  P  LD   + +AA  LVG HDF  +      A++ +R +  
Sbjct: 124 DAPWGAEPLRRHDTLAW--PSRLDLAALNVAADGLVGEHDFAAYCRRKENATT-LREVTR 180

Query: 175 FDVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            +      G L+   V A +F    +RS VG++  VGDG+  +      L  ++R     
Sbjct: 181 LEWRRAPDGTLVAT-VQADAFCQAMVRSLVGAMLAVGDGRRPADWPAGLLTRRERASEVN 239

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GL   +V Y
Sbjct: 240 VAPAHGLTLVAVGY 253


>gi|325964130|ref|YP_004242036.1| pseudouridylate synthase I [Arthrobacter phenanthrenivorans Sphe3]
 gi|323470217|gb|ADX73902.1| pseudouridylate synthase I [Arthrobacter phenanthrenivorans Sphe3]
          Length = 296

 Score = 95.1 bits (235), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 79/268 (29%), Positives = 122/268 (45%), Gaps = 27/268 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW  Q    ++QG +E+A+ L+    V V  AGRTD+GVHA  QV
Sbjct: 17  LRVRLDLSYDGGPFSGWALQPGLRTVQGVLEEALHLLVRRPVRVTVAGRTDAGVHARGQV 76

Query: 62  AHFDLVR-EWV----------PVILCKALNAYLK-----ISDTISILNLSIVDKQFHARF 105
            H DL   EW+           V + + +   L      ++  + +  + +    F ARF
Sbjct: 77  VHLDLTEAEWLGLPRGHELDPAVAMLRRIRGALSRILGDLTGAVEVHRIILAPPGFDARF 136

Query: 106 SAIRRSYLYRIITRQA---PLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRS 160
           SA+ R Y YRI    A   PL    GR   +     LD + +   A  L+G  +F +F  
Sbjct: 137 SALWRRYSYRIADGPALWDPL----GRYSTLWHKNPLDVDLLNEGASKLLGLQNFLSFCK 192

Query: 161 IHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
              + ++ IR +  F+   +   +I   V A +F H  +R+ +GS   VG+G      L 
Sbjct: 193 PR-EGATTIRELQRFEFTRAEDGVIVATVQADAFCHNMVRALIGSALYVGEGVEEPGWLY 251

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + L AQ R     LA P  L  + V Y 
Sbjct: 252 ERLLAQKRDAKSVLAAPHPLVLEEVAYP 279


>gi|262203538|ref|YP_003274746.1| tRNA pseudouridine synthase A [Gordonia bronchialis DSM 43247]
 gi|262086885|gb|ACY22853.1| tRNA pseudouridine synthase A [Gordonia bronchialis DSM 43247]
          Length = 291

 Score = 94.7 bits (234), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 76/257 (29%), Positives = 121/257 (47%), Gaps = 19/257 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y G+ + GW RQ +  ++   +E  +  V    V +  AGRTD+GVHA  QV 
Sbjct: 16  RLRLDVGYEGTDFAGWARQTDQRTVGAVLEDTLATVLRIPVRLTVAGRTDAGVHATGQVC 75

Query: 63  HFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           H D+    +        P +L   L   L   D + +  ++ V   F ARFSA+RR Y Y
Sbjct: 76  HTDIPVSALQTRSIGGDPSLLVGRLAKMLP--DDVRVKEIASVSGDFDARFSALRRHYEY 133

Query: 115 RIITRQ---APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           R+   +    P+       W  P  LD + M  A+  L+G +DF  F     + ++ IR 
Sbjct: 134 RLTDARWGAEPIHARTTATWRRP--LDVDAMNAASASLLGLNDFAAFCRRR-EGATTIRD 190

Query: 172 IDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +  F      G ++  +V A +F  + +RS VG++  VGDG+    D  + L A+ ++  
Sbjct: 191 LQQFSWTRHAGGVLVGQVSADAFCWSMVRSLVGAVASVGDGR-RDIDWCRGLLAETQRSS 249

Query: 231 G-PLAPPEGLYFDSVEY 246
             P+A   GL    V+Y
Sbjct: 250 QVPVADACGLCLVRVDY 266


>gi|330470142|ref|YP_004407885.1| tRNA-pseudouridine synthase i [Verrucosispora maris AB-18-032]
 gi|328813113|gb|AEB47285.1| tRNA-pseudouridine synthase i [Verrucosispora maris AB-18-032]
          Length = 276

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 75/254 (29%), Positives = 116/254 (45%), Gaps = 14/254 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW  Q +  ++ G + + + LV   G    +  AGRTD+GVHA  
Sbjct: 5   VRLRLDVAYDGTDFSGWAAQPDRRTVAGVLVQTLDLVLGAGTATGLTVAGRTDAGVHASG 64

Query: 60  QVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL V  W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHLDLPVEVWREHEGRLLRRLARLLPGDVRVRAMTEVPATFDARFSATFRRYEYRVT- 123

Query: 119 RQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
             AP   E  R     AW  P+ LD + +  A+  LVG HDF  +      A++ +R + 
Sbjct: 124 -DAPWGAEPLRRHEVLAW--PRPLDTDRLAAASAGLVGEHDFAAYCRRKENATT-LREVT 179

Query: 174 HFDVNSFGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             D     + I +  V A +F    +RS VG++ + GDG+         L  ++R     
Sbjct: 180 RLDWRRDPDGILVATVQADAFCQAMVRSLVGAMLVAGDGRRPVEWPAGLLTRRERSSEVT 239

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GL   +V Y
Sbjct: 240 VAPAHGLTLVAVGY 253


>gi|282163988|ref|YP_003356373.1| tRNA pseudouridine synthase A [Methanocella paludicola SANAE]
 gi|282156302|dbj|BAI61390.1| tRNA pseudouridine synthase A [Methanocella paludicola SANAE]
          Length = 279

 Score = 94.4 bits (233), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/251 (29%), Positives = 115/251 (45%), Gaps = 31/251 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALR 59
           ++    + Y G+ + G Q Q    +++G + K +    + GE   V  +GRTD+GVHAL 
Sbjct: 13  LKVAFKLAYVGTDFSGSQSQPGRRTVEGELRKGLVEKGIIGEKTKVEFSGRTDAGVHALG 72

Query: 60  QVAHF----DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           QV  F    D + E  P I+   L A       + +   ++V   F  R  A+ R+Y Y 
Sbjct: 73  QVIAFVPKNDKLTE--PRIINSVLPA------DMWVYAKAVVPDDFDPRRHAVSRTYRYL 124

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +    AP  +E+              +   +Q   G HDFT F S+     +P+RT+   
Sbjct: 125 LY---APDVIER-------------RIVTYSQLFPGTHDFTNFSSVEPN-KNPVRTVKSI 167

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G++  I + A SFL   +R  V  L+LVG  K  +  +E+ L+  + +E  P A 
Sbjct: 168 SVTKRGDMYVIDIEADSFLWNMVRKIVTGLRLVGSNKRPAQWIEQMLKPDEYREGIPPAL 227

Query: 236 PEGLYFDSVEY 246
             GLY   VEY
Sbjct: 228 AAGLYLMKVEY 238


>gi|39938715|ref|NP_950481.1| tRNA pseudouridine synthase A [Onion yellows phytoplasma OY-M]
 gi|42559719|sp|P60351|TRUA_ONYPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|39721824|dbj|BAD04314.1| pseudouridylate synthase [Onion yellows phytoplasma OY-M]
          Length = 243

 Score = 94.4 bits (233), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 109/243 (44%), Gaps = 5/243 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +I+ Y+G+ Y+G+Q+Q    ++Q + EKA+  +T + +    A RTD GVH+  Q  H
Sbjct: 6   YKLILSYDGTCYYGYQKQPQKITVQQTFEKALKKMTHQNIPTFAASRTDKGVHSQGQTLH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P    K LN YL   D I +  ++     FHAR+SA  +S +Y+ +  + PL
Sbjct: 66  FQTTFFLKPTHFQKTLN-YLLPPD-IRVRQMNFATPNFHARYSA--KSKIYQYVFSKKPL 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                   +    L  + +  A + + G H+F  F S   Q  +  +TI    +    + 
Sbjct: 122 NAFNHHFQIFADKLYFDKITKALKFIEGTHNFFAFTS-ETQPKNFSKTIFQAFLKETSHK 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             +      FL   IR  VGSL  +G  K +    +  L     K+   LAP + L    
Sbjct: 181 YILVFHGNGFLKYMIRFLVGSLIEIGKNKLSLEQFQAMLLGNTTKKATLLAPSKALVLKK 240

Query: 244 VEY 246
           + Y
Sbjct: 241 IFY 243


>gi|85057773|ref|YP_456689.1| tRNA pseudouridine synthase A [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|123738898|sp|Q2NIY3|TRUA_AYWBP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|84789878|gb|ABC65610.1| tRNA pseudouridine synthase A [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 243

 Score = 94.4 bits (233), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 107/243 (44%), Gaps = 5/243 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +I+ Y+G+ Y G+Q+Q    ++Q + EKA+  +T + +    A RTD GVH+  Q  H
Sbjct: 6   YKLILSYDGTFYCGYQKQPQKKTVQQTFEKALKKMTHQNIPTFAASRTDKGVHSQGQTLH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P    K LN YL   D I +  +      FHAR+SA  +S +Y+ +  + PL
Sbjct: 66  FQTTFSLKPKHFQKTLN-YLLPPD-IRVRQMHFATPNFHARYSA--KSKIYQYVFSKKPL 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                   +     D   +  A + + G H+F  F S   Q  +  +TI    +    + 
Sbjct: 122 NAFNHHFQIFADKFDFVKITKALKFIEGTHNFFAFTS-ETQPKNFSKTIFQASLKETVHK 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             +      FL   IR  VGSL  +G  K++    +  L     K+   LAP + L    
Sbjct: 181 YILVFHGNGFLKYMIRFLVGSLIEIGKNKFSLEQFQAMLLGNKTKKATLLAPAKALVLKK 240

Query: 244 VEY 246
           + Y
Sbjct: 241 IFY 243


>gi|309812385|ref|ZP_07706140.1| tRNA pseudouridine synthase A [Dermacoccus sp. Ellin185]
 gi|308433690|gb|EFP57567.1| tRNA pseudouridine synthase A [Dermacoccus sp. Ellin185]
          Length = 282

 Score = 94.4 bits (233), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/259 (28%), Positives = 123/259 (47%), Gaps = 17/259 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQ 60
           +R+ +   Y+G+ + GW RQ    +++  +  A+  V   E V +  AGRTD+GVHA   
Sbjct: 1   MRFRIDFAYDGTDFSGWARQPGRRTVEEELTGALTRVLRREDVRLTVAGRTDAGVHARGG 60

Query: 61  VAHFDL-VREWVPV----------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           V H D+    W  +           L   LN  L  +  + +   S     F ARFSA++
Sbjct: 61  VCHGDIDADAWAALPGRSERAPAQALVTRLNGVL--AGDVVVKAASEQPASFDARFSALK 118

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR++   A L  L +    ++ ++LD + M  A+  L+G HDF  +     + ++ 
Sbjct: 119 RRYSYRLLDDAARLDPLRRRDTVVVKRTLDVDAMNAASALLIGLHDFAAYCKPR-EGATT 177

Query: 169 IRT-IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           IRT +D+        ++  R+ A +F H+ +R+ +G +  VG+G+       + L A  R
Sbjct: 178 IRTLLDYAWTREADGVLTARLEADAFCHSMVRALIGGVVPVGEGRRPIDWPAQVLTAGRR 237

Query: 228 KECGPLAPPEGLYFDSVEY 246
                + PP GL  + V Y
Sbjct: 238 DPGVVVMPPHGLCLEEVSY 256


>gi|195135262|ref|XP_002012053.1| GI24889, isoform B [Drosophila mojavensis]
 gi|193918317|gb|EDW17184.1| GI24889, isoform B [Drosophila mojavensis]
          Length = 320

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 89/308 (28%), Positives = 134/308 (43%), Gaps = 63/308 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F    EI  V  + R
Sbjct: 1   MHRYLLNISYIGTRFRGIQKTINKLEESRVDTNSVQGCLELALRVFRPVNEIQTV-LSSR 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +   IL   LN  L K S  I +L+   V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLERNDGKCYDTTILTGVLNRTLDKQSLPIRVLSTQRVADTFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPLALEKGRA---------------------WLIPKSLDCENMR 143
            AI R+YLYR+ +++Q    L   ++                     +L   + D E + 
Sbjct: 120 HAIGRTYLYRVAVSKQKTTVLPDAKSSSLRNRAFEAFLPVEEWDRCYFLQNNNFDIERLI 179

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSP-------IRTIDHFDVNSFGNLI------------ 184
            A++ L+G HD+ TF S+  Q S         +R ID  ++    +L             
Sbjct: 180 AASRMLIGVHDYRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGRSLALGPNATLATENY 239

Query: 185 ---EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG---PLAPPEG 238
              +I + A+SFL+ Q+R  VG+L  + +G+     + + L    +        LAP  G
Sbjct: 240 DYWDIEIKAKSFLYKQVRRIVGTLLALAEGRIDERCIYQMLTIPSKHSWDHRIQLAPACG 299

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 300 LYLCRVHY 307


>gi|322374718|ref|ZP_08049232.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
 gi|321280218|gb|EFX57257.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
          Length = 191

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 58/193 (30%), Positives = 93/193 (48%), Gaps = 6/193 (3%)

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           + QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + I+
Sbjct: 1   MEQVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEF-IV 57

Query: 118 TRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH-- 174
            R  P   + +  A   P  LD E M+ A + L G HDFT F +        +RTI    
Sbjct: 58  DRGRPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFTGFTASGTSVEDKVRTITEAS 117

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V+  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A
Sbjct: 118 LSVDETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTA 177

Query: 235 PPEGLYFDSVEYS 247
            P GLY   + Y 
Sbjct: 178 APNGLYLKEIRYE 190


>gi|312892081|ref|ZP_07751581.1| tRNA-pseudouridine synthase I [Mucilaginibacter paludis DSM 18603]
 gi|311295453|gb|EFQ72622.1| tRNA-pseudouridine synthase I [Mucilaginibacter paludis DSM 18603]
          Length = 268

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 83/257 (32%), Positives = 120/257 (46%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ+     SIQ  +E ++  V      + G GRTD+ VHA +  
Sbjct: 1   MRYFVHLGYHGTQYSGWQKHAGVMSIQQVLENSLSQVLKTPTAIVGCGRTDAKVHASQFF 60

Query: 62  AHFDL--VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            H D+   RE+  +  L K L A + I D I +  L       HARF A +RSY Y I T
Sbjct: 61  FHVDIDNPREFDLLFRLNKILPADIAIFDIIPMAGLP------HARFDATQRSYDYFIHT 114

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR---TIDHF 175
            + P  L    ++   +SLD   M+ A   L   HD+  F    C+  SP R   T+ H 
Sbjct: 115 YKDPF-LNGFSSYYNEQSLDLHEMKKAVALLPLYHDYRAF----CK--SPDRNEHTLCHV 167

Query: 176 DVNSF-----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-QAQDRKE 229
                      + I   + A  FL   IR  VG L  +G G+ +  + E+ L + Q+ + 
Sbjct: 168 TSAELFACKNADRIRFNISANRFLSKMIRVIVGRLISIGTGEMSVDEFEQNLIKPQNAQT 227

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A P+GLY   V Y
Sbjct: 228 ISP-AHPQGLYLSKVTY 243


>gi|116671484|ref|YP_832417.1| tRNA pseudouridine synthase A [Arthrobacter sp. FB24]
 gi|116611593|gb|ABK04317.1| tRNA pseudouridine synthase A [Arthrobacter sp. FB24]
          Length = 280

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/267 (30%), Positives = 120/267 (44%), Gaps = 27/267 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW  Q    ++QG +E A+ L+    V V  AGRTD+GVHA  QV
Sbjct: 1   MRIRLDLAYDGGPFSGWAVQPGLRTVQGVLESALALLIRRKVRVTVAGRTDAGVHARGQV 60

Query: 62  AHFDLV-REW----------VPVILCKALNAYLK-----ISDTISILNLSIVDKQFHARF 105
            H DL   EW            V L + L   L      ++  I + ++++  + F ARF
Sbjct: 61  VHLDLTEEEWQGLNRGVELDPAVALLRRLRGALSRGLGDLTGAIEVHSVTVAPEGFDARF 120

Query: 106 SAIRRSYLYRIITRQA---PLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRS 160
           SA+ R Y YRI    A   PL    GR   +   + LD   +   A  L+G  +F ++  
Sbjct: 121 SALWRRYSYRIADGPALWDPL----GRYSTLWHKEQLDVSLLNEGASKLLGLQNFRSYCK 176

Query: 161 IHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
              + S+ IR +  F+       +I   V A +F H  +R+ VGS   VG G      L 
Sbjct: 177 PR-EGSTTIRELQRFEFARGTDGVIVATVQADAFCHNMVRALVGSALYVGSGAEKPGWLY 235

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEY 246
           + L  Q R     L+ P  L  + V Y
Sbjct: 236 ERLLEQKRDAKSVLSAPHPLVLEEVAY 262


>gi|328955882|ref|YP_004373215.1| tRNA pseudouridine synthase A [Coriobacterium glomerans PW2]
 gi|328456206|gb|AEB07400.1| tRNA pseudouridine synthase A [Coriobacterium glomerans PW2]
          Length = 299

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 116/247 (46%), Gaps = 10/247 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ---VAHF 64
           + Y+G+ Y G+  Q +  ++ G + +A+       + +  AGRTD+GVHA+ Q   VA  
Sbjct: 46  LGYDGTRYSGFAEQPDRCTVAGEVRQAMETFLRRPIELICAGRTDAGVHAIGQHVSVAVL 105

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E       +A++A L     IS+  +    + F ARF A  R+Y YRI       A
Sbjct: 106 PAECEIPRARWLRAMDALLPPD--ISVAGVFRARRGFSARFDARDRTYTYRIAAGSVRPA 163

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVNSF 180
           L +   W     LD   MR AA  LVG HDF +F      A  P    +  +D    +  
Sbjct: 164 LIRPYVWWHRLELDEGAMRDAATCLVGEHDFKSFCRASSAAGRPTSRRVLDVDFAHESEL 223

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G N++   +   +FLH+ +R+ VGSL  VG  +     L  AL A+DR   GP AP  GL
Sbjct: 224 GENVLAFTIRGNAFLHSMVRTIVGSLAEVGTHRRDPAWLADALAARDRAAAGPTAPACGL 283

Query: 240 YFDSVEY 246
            F  V Y
Sbjct: 284 CFMDVSY 290


>gi|197303254|ref|ZP_03168295.1| hypothetical protein RUMLAC_01977 [Ruminococcus lactaris ATCC
           29176]
 gi|197297680|gb|EDY32239.1| hypothetical protein RUMLAC_01977 [Ruminococcus lactaris ATCC
           29176]
          Length = 242

 Score = 93.6 bits (231), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 119/248 (47%), Gaps = 8/248 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  + M ++Y+G+ Y GW + +K+  ++   +E+ +  + G+ V +H A RT+  VHA  
Sbjct: 1   MNNFKMTLQYDGTRYLGWTKNEKSVKTVSYKLEQVLTRLLGQPVTLHAAVRTEPCVHASC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  F+    + P +L K +N YL +   I +L+L  V  +F A       +Y Y + T 
Sbjct: 61  QVCSFEADLPFSPEVLKKQMNQYLPMD--IKVLSLLPVSGRFRADLGIRAYTYEYNVCTA 118

Query: 120 QA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
               +   + +A   P   D   M+ AA  L+G+HDF +F  +  +  +  + + + D  
Sbjct: 119 SVYDVFHSRYQAHFFPAP-DLALMKQAASCLIGKHDFQSFSPVRKKKGTK-KELLYLDFI 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                +  R+ A +FL +  +  VG+L  +G GK +   +    +  +    G   P +G
Sbjct: 177 QNKEQLSFRLTANAFLPSMPQLIVGTLLEIGQGKRSPDCILSIFEGNETP--GNFCPSDG 234

Query: 239 LYFDSVEY 246
           L+   ++Y
Sbjct: 235 LFLTEIQY 242


>gi|153005130|ref|YP_001379455.1| tRNA-pseudouridine synthase I [Anaeromyxobacter sp. Fw109-5]
 gi|152028703|gb|ABS26471.1| tRNA-pseudouridine synthase I [Anaeromyxobacter sp. Fw109-5]
          Length = 265

 Score = 93.6 bits (231), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 83/255 (32%), Positives = 117/255 (45%), Gaps = 18/255 (7%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + + Y G  + G+QRQ    ++Q ++E A+ L  G    +  A RTD+GVHAL QV  
Sbjct: 6   YALRVAYEGGRFRGFQRQPGLPTVQDALEGAL-LAAGVRATLAVAARTDAGVHALDQVVS 64

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P  L  ALNA L   + +++L +  V   FHAR +A  R Y+Y ++    P 
Sbjct: 65  FSARAALDPAALRGALNAALP--EGVAVLEVLRVAPSFHARNTARARRYVY-LVGAPPPE 121

Query: 124 ALEKGRAWLIPKS---------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +L    AW +P           LD   M  A  H VG HDFT F     Q  + +RT+  
Sbjct: 122 SL-AAYAWTLPDPRAFPDGEARLDVAAMSAALAHAVGTHDFTAFARPGEQRGT-VRTVTR 179

Query: 175 FDVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            +V S  +  L  +      FL   IR+  G+   VG G+     + + L A+ R   G 
Sbjct: 180 AEVVSATWAPLHALVFEGHGFLRAMIRNLAGTAVTVGVGRAAPEIVRELLLARGRYR-GV 238

Query: 233 LAPPEGLYFDSVEYS 247
            AP  GL   SV Y 
Sbjct: 239 RAPGWGLTLASVVYP 253


>gi|256825854|ref|YP_003149814.1| pseudouridylate synthase I [Kytococcus sedentarius DSM 20547]
 gi|256689247|gb|ACV07049.1| pseudouridylate synthase I [Kytococcus sedentarius DSM 20547]
          Length = 297

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 120/258 (46%), Gaps = 13/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R  +   Y+G  + GW  Q    ++Q ++E+ +  V   + V +  AGRTD+GVHA  
Sbjct: 20  MPRLRLDFAYDGRDFHGWATQPGLRTVQETLERGLATVLRAQDVSLTVAGRTDAGVHATG 79

Query: 60  QVAHFDLVRE-WVPV------ILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRR 110
            V H D+    W  V         +AL   L   +   + +   + V   F ARFSA+RR
Sbjct: 80  AVCHLDVAHAAWAAVPGRSDRAPAEALVTRLAGVLPADLVVHRATEVPDAFDARFSALRR 139

Query: 111 SYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            Y Y +  R+  L    +G      K LD E M  AAQ LVG  DF  F     + ++ +
Sbjct: 140 HYRYLLCDRRETLDPRRRGMVVAWRKPLDAEAMHAAAQQLVGLGDFAAFCKPR-EGATTV 198

Query: 170 RTIDHFDVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           RT++ F  +      +   V A +F H+ +R+ VG++  VG+G+       +  + ++R 
Sbjct: 199 RTLERFTWHRDEQGWVVGEVSADAFCHSMVRALVGAVVPVGEGRQPVDWPRQVQEGRERL 258

Query: 229 ECGPLAPPEGLYFDSVEY 246
               + P  GL   +V+Y
Sbjct: 259 GAVQVMPAHGLTLVAVDY 276


>gi|251772807|gb|EES53368.1| Pseudouridylate synthase [Leptospirillum ferrodiazotrophum]
          Length = 294

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/254 (29%), Positives = 116/254 (45%), Gaps = 15/254 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +++ Y+G  + GWQ Q N  ++QG++ +A+  +    V V G+GRTD+GV A  QVA
Sbjct: 13  RIALLLAYDGRDFSGWQVQPNRWTVQGTLGEALATLCRAPVGVTGSGRTDAGVSAWGQVA 72

Query: 63  HFDLVREW-VPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           H DL   + +PV  L + LN   ++  ++ +L+   V   FHAR SA  R  +YR + R 
Sbjct: 73  HADLPEGFSIPVDRLPRILNT--RLPGSLRVLDCRSVSSSFHARHSA--RGKIYRYVFRH 128

Query: 121 APLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
            P +L         +  +P +      R A+   +G HDF  F           R ID  
Sbjct: 129 LPASLSHHPLATPFSAPLPPNFFLPRAREASTFFLGTHDFRHFSVASSLPDDSTRRIDGI 188

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECGP 232
                   + + V    FLH  +R   G L   G+G+    ++   L+       +   P
Sbjct: 189 LWEERCAELILWVTGPGFLHKMVRMIGGYLLEAGEGRRPLEEIPALLRKGAPPPFRAVEP 248

Query: 233 LAPPEGLYFDSVEY 246
           L PP+GL    V Y
Sbjct: 249 L-PPDGLALARVLY 261


>gi|159039803|ref|YP_001539056.1| tRNA pseudouridine synthase A [Salinispora arenicola CNS-205]
 gi|157918638|gb|ABW00066.1| tRNA pseudouridine synthase A [Salinispora arenicola CNS-205]
          Length = 276

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 77/254 (30%), Positives = 116/254 (45%), Gaps = 14/254 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
            R  + + Y+G+ + GW  Q +  ++ G + +A  LV G      +  AGRTD+GVHA  
Sbjct: 5   TRVRLDVSYDGTDFSGWAVQPDRRTVAGVLVQAFDLVLGSDAATGLTVAGRTDAGVHATG 64

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL+ E W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHVDLLTEVWRRHEGTLLRRLARLLPGDVRVRAVTGVPGDFDARFSATFRRYEYRVT- 123

Query: 119 RQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
             AP   E  R     AW     LD + +  AA  LVG HDF  +      A++ +R + 
Sbjct: 124 -DAPWGAEPLRRHDTLAW--SSRLDQDALNAAADGLVGEHDFAAYCRRKENATT-LREVT 179

Query: 174 HFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             D   S   ++   V A +F    +RS VG++ +VGDG+  +      L  ++R     
Sbjct: 180 RLDWRRSADGVLVATVQADAFCQAMVRSLVGAMLVVGDGRRPAGWPAGLLARRERANEVN 239

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GL   +V Y
Sbjct: 240 VAPAHGLTLVAVGY 253


>gi|195375299|ref|XP_002046439.1| GJ12898 [Drosophila virilis]
 gi|194153597|gb|EDW68781.1| GJ12898 [Drosophila virilis]
          Length = 513

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 86/300 (28%), Positives = 132/300 (44%), Gaps = 60/300 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F    EI  V  + R
Sbjct: 1   MRRYLLNIAYIGTNFRGIQKTVNKLEEARLDTNSVQGCLELALRVFRPKNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K +  I +L+   V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLERSDNKFYDTTTLTGVLNRTLDKQNLPIRVLSTQRVPDTFHCRY 119

Query: 106 SAIRRSYLYRI-----ITRQAPLA--LEKGRAWLIP------------KSLDCENMRIAA 146
            AI R+YLYR+     +T+   +     KG    +P             + D E ++ AA
Sbjct: 120 HAIGRTYLYRVAVAKNVTQSNTINSLRNKGYESFVPVEEIDRCYFLQNNNFDIERLKNAA 179

Query: 147 QHLVGRHDFTTFRSIHCQASS-------PIRTIDHFDVNSFGNLI--------------- 184
           +  +G HDF +F S+  Q S         +R ID  ++ +  +L                
Sbjct: 180 RMFLGVHDFRSFMSVSRQKSPSRDHPMFTVRKIDEINIRAGQSLALGPNATLASQIYDYW 239

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYF 241
           +I + A+SFL+ Q+R  VG+L  + +G+     + + L    +    P   +AP  GLY 
Sbjct: 240 DIEIKAKSFLYKQVRRIVGTLLALANGRIDERCIYEMLTIPSKHTWEPRILVAPASGLYL 299


>gi|317125837|ref|YP_004099949.1| tRNA pseudouridine synthase A [Intrasporangium calvum DSM 43043]
 gi|315589925|gb|ADU49222.1| tRNA pseudouridine synthase A [Intrasporangium calvum DSM 43043]
          Length = 303

 Score = 92.8 bits (229), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/265 (27%), Positives = 122/265 (46%), Gaps = 26/265 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y G+ + GW  Q    +++G +  A+  V      V +  AGRTD+GVHA  
Sbjct: 20  VRLRLDLAYEGTAFSGWAAQPGLRTVEGELATAVTTVLRAPAPVSLTVAGRTDAGVHARG 79

Query: 60  QVAHFDLVREWVPVILCKA---------LNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           QV H D+    +  +  ++               +   + +  ++   + F ARFSA  R
Sbjct: 80  QVVHVDVEPAALAALPGRSNRTPEEALLRRLGGLLDPDVVVHRVARAPEGFDARFSAQER 139

Query: 111 SYLYRIITRQA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            YLYR+    A   PL       W  P+ LD E M  AA+ LVG  DF  F     + ++
Sbjct: 140 RYLYRLADADALRDPLRRHDTVWW--PRPLDAERMDEAARPLVGLRDFAAF-CKRREGAT 196

Query: 168 PIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKAL 222
            +RT+  +     G+ ++   V A +F H+ +RS VG+   VG+G+    W +   ++  
Sbjct: 197 TVRTLLEYRWVRLGDGVLAATVRADAFCHSMVRSLVGAAVAVGEGRRPTSWPAELQQRTQ 256

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
           +A D +    + P  GL  ++V Y 
Sbjct: 257 RAADVR----VMPAHGLSLEAVTYP 277


>gi|221230534|ref|YP_002503950.1| putative pseudouridylate synthase [Mycobacterium leprae Br4923]
 gi|4539110|emb|CAB39831.1| putative tRNA pseudouridine synthase A [Mycobacterium leprae]
 gi|13093610|emb|CAC30910.1| probable pseudouridylate synthase [Mycobacterium leprae]
 gi|219933641|emb|CAR72052.1| probable pseudouridylate synthase [Mycobacterium leprae Br4923]
          Length = 249

 Score = 92.4 bits (228), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 112/235 (47%), Gaps = 26/235 (11%)

Query: 31  IEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV------------PVILCKA 78
           +++A   V    V +  AGRTD+GVHA  QVAH D+    +            P  L   
Sbjct: 2   LDEAFTTVFRTPVRLRAAGRTDTGVHATGQVAHVDIPGTALSKANPRSPHTGDPEFLPLL 61

Query: 79  LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI---PK 135
                 +   + +L+++     F ARFSA+RR Y YR+ T  AP  ++  +A  +   P+
Sbjct: 62  RRLSRLLPVDVRVLDIACAPVGFDARFSALRRHYRYRLST--APYGVQPNQARYVTAWPR 119

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
            LD ++M  A++ L+G  DF  F   H   ++ IR +   + +  G LI   + A +F  
Sbjct: 120 ELDLDSMSAASRDLLGLRDFAVF-CRHRHGATTIRELQRLEWSREGYLITAHITADAFCW 178

Query: 196 TQIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + +RS +G+L  VGD +    W    L KA ++ D       AP  GL F  V+Y
Sbjct: 179 SMVRSLIGALLAVGDHRRTIGWCGELLTKASRSSDFTT----APAHGLTFIRVDY 229


>gi|116754296|ref|YP_843414.1| tRNA pseudouridine synthase A [Methanosaeta thermophila PT]
 gi|121692939|sp|A0B7V0|TRUA_METTP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116665747|gb|ABK14774.1| tRNA pseudouridine synthase A [Methanosaeta thermophila PT]
          Length = 267

 Score = 92.4 bits (228), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 112/250 (44%), Gaps = 30/250 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----AGRTDSGVHA 57
           ++  + I Y G  Y+G+QRQ    +++  +  A+      I V +G    AGRTD GV A
Sbjct: 1   MKIALKIAYLGDRYYGFQRQPGLRTVESVMRDALL----RIGVANGDFCYAGRTDRGVSA 56

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  F +  +   +   + +N+ L  SD  +    ++    F AR+SA+ R Y Y   
Sbjct: 57  LGQVIDFWIEEDRAYLAFPRVINSLLP-SDVWAWAR-AVAPVGFSARWSALWREYRY--- 111

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +L    +D   +R AA HLVG HDF   R+        +R I   DV
Sbjct: 112 -------------FLFSPDIDLSAVREAAGHLVGTHDF---RNFSMSKVDTVRRIISIDV 155

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N+   ++   V A  F+   +R  VG+L+L+G G+    D    L         P APPE
Sbjct: 156 NAHCGIVVFDVRAEGFIWNMVRRIVGALELIGIGE-KPVDWILELLDPSTPHGAPTAPPE 214

Query: 238 GLYFDSVEYS 247
           GL    V YS
Sbjct: 215 GLMLMDVGYS 224


>gi|194864517|ref|XP_001970978.1| GG25359, isoform B [Drosophila erecta]
 gi|190652761|gb|EDV50004.1| GG25359, isoform B [Drosophila erecta]
          Length = 288

 Score = 92.4 bits (228), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 118/265 (44%), Gaps = 54/265 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALQVFHPTNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL      DL R     +    L   LN  L K    I +L+  +VD  FH R+
Sbjct: 60  TDAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQRLPIRVLSSQLVDNSFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPLA----LEKGRAWLIP------------KSLDCENMRIAAQH 148
            AI R+YLYR  + + + L       K     IP             S D   ++ AA+ 
Sbjct: 120 DAIGRTYLYRFAVAKDSSLGDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVKAAARM 179

Query: 149 LVGRHDFTTFRSIHCQASS------PIRTIDHFDVN---------------SFGNLIEIR 187
            +G HDF TF S+  Q  S       +R ID  ++                   N  +I 
Sbjct: 180 FIGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDIE 239

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGK 212
           + A+SFL+ Q+R  VG+L  +G+G+
Sbjct: 240 IKAKSFLYKQVRRIVGALIALGNGR 264


>gi|238061092|ref|ZP_04605801.1| tRNA-pseudouridine synthase I [Micromonospora sp. ATCC 39149]
 gi|237882903|gb|EEP71731.1| tRNA-pseudouridine synthase I [Micromonospora sp. ATCC 39149]
          Length = 276

 Score = 92.4 bits (228), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 78/255 (30%), Positives = 113/255 (44%), Gaps = 14/255 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW  Q    ++ G +   + LV G  V   +  AGRTD+GVHA  
Sbjct: 5   VRLRLTVAYDGTNFSGWAAQPARRTVAGVLTGTLDLVLGAGVATGLTVAGRTDAGVHATG 64

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL    W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHLDLPAAVWREHEGRLLRRLARLLPTDVRVRAMTEVPADFDARFSATFRRYEYRVT- 123

Query: 119 RQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
             AP   E  R     AW  PK LD   +  AA  LVG HDF  +      A++ +R + 
Sbjct: 124 -DAPFGAEPLRRHEVLAW--PKPLDPALLNAAAAGLVGEHDFAAYCRRKENATT-LREVT 179

Query: 174 HFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             D     G L+   V A +F    +RS VG++ + GDG+         L  ++R     
Sbjct: 180 RLDWRRDPGGLLVATVQADAFCQAMVRSLVGAMLVAGDGRRPVDWPGSLLTRRERSSEVT 239

Query: 233 LAPPEGLYFDSVEYS 247
           +AP  GL   +V Y 
Sbjct: 240 VAPAHGLTLVAVGYP 254


>gi|194864515|ref|XP_001970977.1| GG25359, isoform A [Drosophila erecta]
 gi|190652760|gb|EDV50003.1| GG25359, isoform A [Drosophila erecta]
          Length = 499

 Score = 92.0 bits (227), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 118/265 (44%), Gaps = 54/265 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALQVFHPTNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL      DL R     +    L   LN  L K    I +L+  +VD  FH R+
Sbjct: 60  TDAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQRLPIRVLSSQLVDNSFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPLA----LEKGRAWLIP------------KSLDCENMRIAAQH 148
            AI R+YLYR  + + + L       K     IP             S D   ++ AA+ 
Sbjct: 120 DAIGRTYLYRFAVAKDSSLGDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVKAAARM 179

Query: 149 LVGRHDFTTFRSIHCQASS------PIRTIDHFDVN---------------SFGNLIEIR 187
            +G HDF TF S+  Q  S       +R ID  ++                   N  +I 
Sbjct: 180 FIGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDIE 239

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGK 212
           + A+SFL+ Q+R  VG+L  +G+G+
Sbjct: 240 IKAKSFLYKQVRRIVGALIALGNGR 264


>gi|320094548|ref|ZP_08026315.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178 str.
           F0338]
 gi|319978528|gb|EFW10104.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178 str.
           F0338]
          Length = 218

 Score = 92.0 bits (227), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 66/194 (34%), Positives = 95/194 (48%), Gaps = 11/194 (5%)

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL + A+  L R W      +       +SD + +L+ S V   F ARFSA  RSY+YRI
Sbjct: 7   ALVRRANALLARAWAQREQGRGERPPRGVSDAL-VLSASPVSADFDARFSATGRSYVYRI 65

Query: 117 ITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
             R  PL     R W      + LD   +  AA+ L+G HDF +F     + ++ IR + 
Sbjct: 66  ADRPTPL-----RRWDCVWDDRPLDLAAVNRAAEALLGEHDFLSFCRPR-EGATTIRALT 119

Query: 174 HFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             + V +   L+E  V A +F H+ +RS VG+L LVG G   +      L A+ R    P
Sbjct: 120 RLEAVRAPDGLVEFHVGADAFCHSMVRSLVGALALVGRGARPAPWPRALLDARSRASAAP 179

Query: 233 LAPPEGLYFDSVEY 246
           +AP  GL  + V+Y
Sbjct: 180 IAPARGLTLERVDY 193


>gi|332295380|ref|YP_004437303.1| tRNA pseudouridine synthase A [Thermodesulfobium narugense DSM
           14796]
 gi|332178483|gb|AEE14172.1| tRNA pseudouridine synthase A [Thermodesulfobium narugense DSM
           14796]
          Length = 283

 Score = 91.7 bits (226), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 113/241 (46%), Gaps = 6/241 (2%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           II Y+G+ + G+Q Q    ++Q  IE+ +  +  E V V  AGRTD+GVHA+ QV  F L
Sbjct: 14  IISYDGTNFHGFQMQNQSRTVQLVIEQKLEKIFKERVCVVPAGRTDAGVHAIGQVISFRL 73

Query: 67  VREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
            +    V  L   LN +L   D I I  + ++   F++RFSA  R Y+Y I  ++   A 
Sbjct: 74  AKCPFDVEKLQNILNYHL--PDDIRISEMRLMPADFNSRFSAKSRVYVYAISAKKDICAH 131

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
                W +  SL  E+++     +  R  F +F  +         T+       F + + 
Sbjct: 132 LNRYFWNLDISL--EDLKATLNLIPNRFCFRSFSRVSKDRKLNFGTVTFSKCVVFEDFLY 189

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             + A SFL   +R   G    V  GK T  D ++AL+ + R      APP+GL+   V 
Sbjct: 190 FIIEAPSFLWHTVRFLFGEAVAVAKGKRTLEDYKEALEGKKRLVLYK-APPKGLHLWGVS 248

Query: 246 Y 246
           Y
Sbjct: 249 Y 249


>gi|224438205|ref|ZP_03659140.1| tRNA pseudouridine synthase A [Helicobacter cinaedi CCUG 18818]
 gi|313144651|ref|ZP_07806844.1| tRNA pseudouridine synthase A [Helicobacter cinaedi CCUG 18818]
 gi|313129682|gb|EFR47299.1| tRNA pseudouridine synthase A [Helicobacter cinaedi CCUG 18818]
          Length = 245

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 120/250 (48%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHAL 58
           M RY  +I Y+GS ++G+  QK+  S+ G+++     V   GEI+   G  RTD GVH+ 
Sbjct: 1   MPRYKAVISYDGSAFYGFALQKHKPSVLGALQDGFSRVGIRGEIL---GTSRTDKGVHST 57

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F+         L   LNA  K+   I++  L  V++ FH RF A+ R+Y + +++
Sbjct: 58  GQVISFESRHFEDSHTLQNLLNA--KLYPHIAVRRLERVNEDFHPRFHALWRAYRF-LLS 114

Query: 119 RQAPLALEKGRAWLIPKSLDCENM-RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             AP   +   A++  + +    + + A     G+H+F  F+         IR I     
Sbjct: 115 SHAPSPFQS--AYVSYEKIGNRALFQSALSMFKGKHNFALFKKNGSFTKDSIRDIFRIFS 172

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                L  + +    FL +Q+R  VG+   V  G+ +   L++ +QA+ R    P++ P 
Sbjct: 173 YQHKGLDIVYIKGNGFLRSQVRLMVGAALSVSRGELSLESLQEQIQAKKRHYNFPIS-PN 231

Query: 238 GLYFDSVEYS 247
           GLY   V YS
Sbjct: 232 GLYLCGVGYS 241


>gi|119963259|ref|YP_948625.1| tRNA pseudouridine synthase A [Arthrobacter aurescens TC1]
 gi|119950118|gb|ABM09029.1| tRNA pseudouridine synthase A [Arthrobacter aurescens TC1]
          Length = 296

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 123/265 (46%), Gaps = 23/265 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW  Q    ++QGS+E+A+ L+    V V  AGRTD+GVHA  QV
Sbjct: 17  LRVRLDLSYDGGPFSGWALQPGLRTVQGSLEEALALLLQRPVRVTVAGRTDAGVHARGQV 76

Query: 62  AHFDLVR-EWV----------PVILCKALNAYLK-----ISDTISILNLSIVDKQFHARF 105
            H DL   EW+           V L + L   L      ++ +I + +  +  + F ARF
Sbjct: 77  VHLDLTEAEWLSLPRGHELDPAVALLRRLRGALSRILGDLTGSIEVHDAGLAPEGFDARF 136

Query: 106 SAIRRSYLYRII---TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           SA+ R Y YRI     R  P+   +G        L+ E M   A  L+G  DF ++    
Sbjct: 137 SALWRRYSYRIADGPERWDPVL--RGITLWHKAPLNVELMNEGAFALLGLQDFRSYCKPR 194

Query: 163 CQASSPIRTIDHFDVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            + ++ IR +  F  +    ++I   V A +F H  +RS VGS   VG+G  T   L   
Sbjct: 195 -EGATTIRELQQFSFDRGSDDVIVATVQADAFCHNMVRSLVGSALRVGEGLETPGWLHSR 253

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           L  + R     LA P  L  + V Y
Sbjct: 254 LLERKRDAKSVLAAPHPLVLEEVAY 278


>gi|206895862|ref|YP_002247302.1| tRNA pseudouridine synthase A [Coprothermobacter proteolyticus DSM
           5265]
 gi|238057727|sp|B5Y955|TRUA_COPPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|206738479|gb|ACI17557.1| tRNA pseudouridine synthase A [Coprothermobacter proteolyticus DSM
           5265]
          Length = 259

 Score = 90.9 bits (224), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 117/249 (46%), Gaps = 14/249 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++Y  ++++ G+ Y G+QRQKNG++IQ  +E  +  +     VV  +GRTD+GVHA   
Sbjct: 1   MVKYAGLLQFKGTNYAGFQRQKNGTAIQNVLESTLSQINNRATVVRYSGRTDAGVHAWGM 60

Query: 61  VAHF----DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY-R 115
              F    DL  +    IL + L   +++   IS++  S    +F  + SA+ + YLY  
Sbjct: 61  PFVFWGREDLSADKWMFILNRMLPKDMRV---ISVVRTS---PEFDPQLSAVAKQYLYCA 114

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              R  PL  +   A+L   S++   +  AA+ LVG HDF  F        S  R +   
Sbjct: 115 TQERLGPL-WDDFFAYLPNLSIETSAVISAARKLVGEHDFKGFSKKGSSVKSTRRKLYEV 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V    + +    V   FL+  +R  VG+L  +G GK     +++ L           AP
Sbjct: 174 SVMFTHSRMYFSFVGNGFLYGMVRLMVGTLLQIGWGKQDVNFIDEVLSGNAVANYS--AP 231

Query: 236 PEGLYFDSV 244
            +GL+   V
Sbjct: 232 AQGLHLVKV 240


>gi|73668859|ref|YP_304874.1| tRNA pseudouridine synthase A [Methanosarcina barkeri str. Fusaro]
 gi|121729516|sp|Q46CU8|TRUA_METBF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|72396021|gb|AAZ70294.1| pseudouridylate synthase [Methanosarcina barkeri str. Fusaro]
          Length = 269

 Score = 90.9 bits (224), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 119/250 (47%), Gaps = 25/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHA 57
           +R  + + Y G+ + G Q Q N  +++G + KA+     + + +      AGRTD+GVHA
Sbjct: 1   MRVALKLAYIGTEFHGSQIQPNVETVEGELFKALRNLGIIESPKSANYTCAGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  FD  +  + + + + +N+  +++  I +   + V   F AR  A+ R Y Y   
Sbjct: 61  LEQVVAFDTDK--LNLAIPRVINS--ELTPGIWVWAHAEVPLSFDARRDAVSRHYRYV-- 114

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                         +  K  D   +R A++ L+G HDF  F   + + S+ +RTI+  D 
Sbjct: 115 --------------MSGKEYDISKIREASKFLLGTHDFENFSRTNGEKST-VRTIERIDA 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G LI+I VV  SFL   +R  V +L ++G G   +  L + L  +  +E    AP  
Sbjct: 160 RIDGELIKIDVVGNSFLWNMVRKIVTALSMIGKGVRDTDWLLQMLNPEIYEEGIESAPAY 219

Query: 238 GLYFDSVEYS 247
           GL    V Y+
Sbjct: 220 GLTLLKVNYN 229


>gi|195135260|ref|XP_002012052.1| GI24889, isoform A [Drosophila mojavensis]
 gi|193918316|gb|EDW17183.1| GI24889, isoform A [Drosophila mojavensis]
          Length = 499

 Score = 90.9 bits (224), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/271 (29%), Positives = 122/271 (45%), Gaps = 60/271 (22%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F    EI  V  + R
Sbjct: 1   MHRYLLNISYIGTRFRGIQKTINKLEESRVDTNSVQGCLELALRVFRPVNEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +   IL   LN  L K S  I +L+   V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLERNDGKCYDTTILTGVLNRTLDKQSLPIRVLSTQRVADTFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPLALEKGRA---------------------WLIPKSLDCENMR 143
            AI R+YLYR+ +++Q    L   ++                     +L   + D E + 
Sbjct: 120 HAIGRTYLYRVAVSKQKTTVLPDAKSSSLRNRAFEAFLPVEEWDRCYFLQNNNFDIERLI 179

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSP-------IRTIDHFDVNSFGNLI------------ 184
            A++ L+G HD+ TF S+  Q S         +R ID  ++    +L             
Sbjct: 180 AASRMLIGVHDYRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGRSLALGPNATLATENY 239

Query: 185 ---EIRVVARSFLHTQIRSFVGSLKLVGDGK 212
              +I + A+SFL+ Q+R  VG+L  + +G+
Sbjct: 240 DYWDIEIKAKSFLYKQVRRIVGTLLALAEGR 270


>gi|301117110|ref|XP_002906283.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
 gi|262107632|gb|EEY65684.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
          Length = 316

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/287 (27%), Positives = 133/287 (46%), Gaps = 54/287 (18%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-------SIQGSIEKAIF--LVTGEIVVVHGAGRTDS 53
           RYC+ I Y G+G+ GWQRQ+  +       S+Q  +E A+   L T + V V G  RTD+
Sbjct: 18  RYCLHIAYYGTGFVGWQRQQQETKSSSGHDSVQEVVEAAVTETLGTSKRVNVTGVSRTDA 77

Query: 54  GVHALRQVAHFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           G HAL Q     L  E +P+    L   +N  L I   +++L ++ V     +R  +  +
Sbjct: 78  GTHALYQFGFIRLDSE-LPMTMDELKDRVNTKLDIG-RVAVLGVT-VPTTGPSRIRSRYK 134

Query: 111 SYLYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTF----------- 158
            Y+Y +     P  LE G+ +W + + LD + +R A + L G HDF  F           
Sbjct: 135 KYIYYLQQGHRP-DLELGKYSWFLGRRLDIQRIRDALKFLEGTHDFRPFSQGLQKPKFED 193

Query: 159 ---------------RSIHCQASSPI----RTIDHFDV-----NSFGNLIEIRVVARSFL 194
                          R+++     P+      ID  D+     N+  + + I +VA  FL
Sbjct: 194 MTTLRTVMSAKVVARRNVNFSLDPPVSGSGEIIDAADMYREPGNTPVHFVCIELVANGFL 253

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +R  +G+L+ +G+G   ++ +++ L  +   + GP AP +GL+ 
Sbjct: 254 RHMVRRIIGTLRPIGEGTQPASRMQQVLAGE--VQPGPSAPTKGLWL 298


>gi|195490006|ref|XP_002092962.1| GE26463, isoform A [Drosophila yakuba]
 gi|194179063|gb|EDW92674.1| GE26463, isoform A [Drosophila yakuba]
          Length = 495

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 85/286 (29%), Positives = 122/286 (42%), Gaps = 56/286 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +S+QG +E A  +F    EI  V  + R
Sbjct: 1   MNRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALRVFHPINEIQTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL      DL R     +    L   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQGLPIRVLSSKLVSNSFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALE------KGRAWLIP------------KSLDCENMRIAAQ 147
            AI R+YLYR    + P +LE      K     IP             S D   ++ AA+
Sbjct: 120 HAIGRTYLYRFAVAKDP-SLEDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVQAAAR 178

Query: 148 HLVGRHDFTTFRSIHCQASS------PIRTIDHFDVN---------------SFGNLIEI 186
             +G HDF TF S+  Q  S       +R ID  ++                   N  +I
Sbjct: 179 MFIGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDI 238

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            + A+SFL+ Q+R  VG+L  +G+G+     L + L    +    P
Sbjct: 239 EIKAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNSWDP 284


>gi|13358100|ref|NP_078374.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 3 str.
           ATCC 700970]
 gi|170761947|ref|YP_001752621.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 3 str.
           ATCC 27815]
 gi|183508635|ref|ZP_02958135.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 14 str.
           ATCC 33697]
 gi|26006901|sp|Q9PPV4|TRUA_UREPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030149|sp|B1AJH7|TRUA_UREP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|11269468|pir||B82879 pseudouridylate synthase I UU536 [imported] - Ureaplasma
           urealyticum
 gi|6899540|gb|AAF30949.1|AE002152_8 pseudouridylate synthase I [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|168827524|gb|ACA32786.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 3 str.
           ATCC 27815]
 gi|182676096|gb|EDT88001.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 14 str.
           ATCC 33697]
          Length = 241

 Score = 90.1 bits (222), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/251 (29%), Positives = 120/251 (47%), Gaps = 16/251 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIE---KAIFLVTGEIVVVHGAGRTDSGVHAL 58
           + Y + + Y+GS ++GW RQ    ++QG +E   K+IF +    + + G+GRTD GVHA 
Sbjct: 1   MNYKISLRYDGSLFYGWARQPQKRTVQGDLEEIFKSIFKINN--IRIIGSGRTDKGVHAY 58

Query: 59  RQ---VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            Q   V H  L  ++   I+ +AL +  + S  I IL +  VD  FHA+++A  ++Y Y 
Sbjct: 59  EQTFSVKHSAL--KYDSHIIYQALCS--RTSSDIQILEVQKVDDSFHAQYNATSKTYQYV 114

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I   +  L         + + ++ + +  A +  VG HDF +F +   + +  IR I+  
Sbjct: 115 INDYEFDL-FRNNYELFVNQKINDQKILEALELFVGEHDFKSFST--SELTMTIRRINWV 171

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +    +LI I + A  FL   +R  V S       K +   + + L    +     LAP
Sbjct: 172 KIKRDTHLI-IYINANGFLKNMVRMIVASCLDYAFNKISLAKIHELLIYPKKGASIKLAP 230

Query: 236 PEGLYFDSVEY 246
             GLY   V Y
Sbjct: 231 ACGLYLYKVYY 241


>gi|255609446|ref|XP_002539049.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223509026|gb|EEF23334.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 132

 Score = 90.1 bits (222), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 56/118 (47%), Positives = 72/118 (61%), Gaps = 12/118 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+G+ + GWQ Q N + +Q +IE AI  V GE V +H AGRTDSGVHAL QV
Sbjct: 16  MKIAIGIEYHGAYFQGWQSQPNAAGVQDAIEHAIKQVGGETVRLHAAGRTDSGVHALMQV 75

Query: 62  AHFD--LVR---EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           AHF+  +VR    WV     +  NA+L     + IL  + V   FHARFSA  RSY Y
Sbjct: 76  AHFETSVVRPLSAWV-----RGTNAHLPA--WVRILWATEVAADFHARFSARARSYQY 126


>gi|296187338|ref|ZP_06855733.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
 gi|296047860|gb|EFG87299.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
          Length = 141

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 46/137 (33%), Positives = 72/137 (52%)

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           ++YLY I   +      +  A+ + ++L+   MR AA+ L G HDF +F S+     S +
Sbjct: 5   KTYLYTINNNKFRNVFNRKYAYHVEENLNLSEMRDAAEVLTGTHDFQSFTSLKSNTKSTV 64

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           RTI++  +     +I I V   SFL   +R  VG+L  VG G    +D+EK L  + R E
Sbjct: 65  RTINYISITEEHGMIGIEVNGNSFLLNMVRIIVGTLLDVGKGILKPSDVEKILYEKKRAE 124

Query: 230 CGPLAPPEGLYFDSVEY 246
            GP+A  +GL    ++Y
Sbjct: 125 AGPMAAAKGLCLKDIQY 141


>gi|322792295|gb|EFZ16279.1| hypothetical protein SINV_03177 [Solenopsis invicta]
          Length = 290

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 79/271 (29%), Positives = 124/271 (45%), Gaps = 45/271 (16%)

Query: 17  GWQRQ------KNGSSIQGSIEKAIFLVTGEIV---VVHGAGRTDSGVHALRQVAHFDLV 67
           G QRQ      ++  SIQG+IE A+  V+ + +   V+  + RTD+GVHA    AH +L 
Sbjct: 2   GLQRQSSDNFVRDTDSIQGAIETALLTVSPKSLIRPVLTLSSRTDAGVHAFGNTAHVELE 61

Query: 68  REWVPVI----LCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRI----IT 118
            ++  +     + K +N Y  K    I +L+ + +   FHAR S   R+YLYR     I 
Sbjct: 62  NKYNTIYNSSDVKKYVNRYFAKCGHFIRLLDSTPITNDFHARHSCKSRTYLYRFMIPKIC 121

Query: 119 RQAPLALEKG------RAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIR 170
            +  ++L +       RA+      D +  R   Q  +G  DFTTF  +SI  +    +R
Sbjct: 122 NEQRISLPETIHTHHLRAY----DFDIDKARRGIQLFMGTKDFTTFSAKSITSRKIQYVR 177

Query: 171 TIDHFDVNSFGNLIEIRVVA------------RSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            +  F +     L+    ++            +SFL+ Q+R  +G+L  +G GK T  D+
Sbjct: 178 ALHAFTLEEAQPLMPFDPLSNNFTYWHFTCKGKSFLYNQVRRMIGALIALGLGKITEKDI 237

Query: 219 EKALQAQDRKECGP---LAPPEGLYFDSVEY 246
              LQ        P     PP GL+  +VEY
Sbjct: 238 TVMLQVPSHHNWDPRVTPVPPNGLHLLNVEY 268


>gi|313682232|ref|YP_004059970.1| tRNA pseudouridine synthase a [Sulfuricurvum kujiense DSM 16994]
 gi|313155092|gb|ADR33770.1| tRNA pseudouridine synthase A [Sulfuricurvum kujiense DSM 16994]
          Length = 242

 Score = 89.7 bits (221), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 79/257 (30%), Positives = 112/257 (43%), Gaps = 26/257 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVH---------GAGR 50
           M R  + + YNGS + G Q+Q N  +++ G +          I V+H          +GR
Sbjct: 1   MSRVKITLSYNGSAFMGSQQQPNTDNTVMGHL----------ITVLHRLKITATPKASGR 50

Query: 51  TDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GVHA  QV H DL   W  +  L + LN  +++  ++ I  +  V+  FHAR+SA R
Sbjct: 51  TDRGVHATHQVIHVDLPDFWTDLHRLREMLN--VQLPPSMRIQRIEFVEDDFHARYSAKR 108

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           R Y Y +I        E      +P SL+ E +  A    VG HDF  F+          
Sbjct: 109 RVYRY-VIKEGLSNPFEDNFITFVP-SLNREAICDAIGCFVGTHDFEFFKKSGNDLEHHT 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R I      S+     I      FL +QIR  VG L  +  GK T   L + +    R  
Sbjct: 167 RIIYRAYAYSYKGHFIIVFEGNGFLRSQIRLMVGFLLRISAGKATKEQLIEQINCVKRHT 226

Query: 230 CGPLAPPEGLYFDSVEY 246
              +AP  GLY   ++Y
Sbjct: 227 TD-IAPHNGLYLTHIKY 242


>gi|215737309|dbj|BAG96238.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 223

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 56/167 (33%), Positives = 83/167 (49%), Gaps = 5/167 (2%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           +   I +  +S    +FHAR S   + Y Y+I             A+     L+ + MR 
Sbjct: 27  LPHEIRVREISAAKPEFHARTSTRSKIYHYKIYNGPVMDPFHNHYAYHSAYKLNSQAMRE 86

Query: 145 AAQHLVGRHDFTTF-RSIHC-QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
           AA+H VG HDFT+F  ++H  +  SPI+ I  FDV   G ++++ +    FL+ Q+R+ V
Sbjct: 87  AAKHFVGTHDFTSFANAVHNDRVRSPIKKIMRFDVIEMGAILQLEIEGTGFLYRQVRNMV 146

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEY 246
             L  VG        + K + A+DRKE   +   APP GLY  SV Y
Sbjct: 147 ALLLQVGREALPPDIVAKIIAARDRKELAKVALSAPPHGLYLMSVNY 193


>gi|171920141|ref|ZP_02931545.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 1 str.
           ATCC 27813]
 gi|186701850|ref|ZP_02971512.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 6 str.
           ATCC 27818]
 gi|171902508|gb|EDT48797.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 1 str.
           ATCC 27813]
 gi|186701145|gb|EDU19427.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 6 str.
           ATCC 27818]
          Length = 241

 Score = 89.4 bits (220), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/251 (29%), Positives = 119/251 (47%), Gaps = 16/251 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIE---KAIFLVTGEIVVVHGAGRTDSGVHAL 58
           + Y + + Y+GS ++GW RQ    ++QG +E   K+IF +    + + G+GRTD GVHA 
Sbjct: 1   MNYKISLRYDGSLFYGWARQPQKRTVQGDLEEIFKSIFKINN--IRIIGSGRTDKGVHAY 58

Query: 59  RQ---VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            Q   V H  L  ++   I+ +AL +  + S  I IL +  VD  FHA+++A  ++Y Y 
Sbjct: 59  EQIFSVKHSAL--KYDSHIIYQALCS--RTSSDIQILEVQKVDDSFHAQYNATSKTYQYV 114

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I   +  L         + + ++ + +  A +  VG HDF +F +   + +  IR I+  
Sbjct: 115 INDYEFDL-FRNNYELFVNQKINDQKILEALELFVGEHDFKSFST--SELTMTIRRINWV 171

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +     LI I + A  FL   +R  V S       K +   + + L    +     LAP
Sbjct: 172 KIKRDTRLI-IYINANGFLKNMVRMIVASCLDYAFNKISLAKIHELLIYPKKGASIKLAP 230

Query: 236 PEGLYFDSVEY 246
             GLY   V Y
Sbjct: 231 ACGLYLYKVYY 241


>gi|145219589|ref|YP_001130298.1| tRNA pseudouridine synthase A [Prosthecochloris vibrioformis DSM
           265]
 gi|238685549|sp|A4SE87|TRUA_PROVI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145205753|gb|ABP36796.1| tRNA pseudouridine synthase A [Chlorobium phaeovibrioides DSM 265]
          Length = 243

 Score = 89.4 bits (220), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/206 (31%), Positives = 95/206 (46%), Gaps = 5/206 (2%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           +EY+G+ + GWQRQ NG  ++QG IE  +  +  E + +  AGRTD GVHA  QV +F  
Sbjct: 8   VEYDGTSFAGWQRQPNGIVTVQGEIEAVLSEILQEKINLAAAGRTDRGVHARGQVVNFST 67

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                   +  +LN  L  S  I I +  +V   FHARFSA+ R Y Y  I    P AL 
Sbjct: 68  RSPLEHSRIRHSLNCLLPSS--ICIPSSQLVPDDFHARFSALERQYRYFAIPE--PSALM 123

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
                     +D   M+  +  L G HDF+ F       +  + T+          ++  
Sbjct: 124 GRYTGCSHGDVDFALMQHLSSGLRGTHDFSLFSREDRDGNGSLCTVREAGWYRHKGVMVF 183

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGK 212
            + A  FL + +R  VG +   G G+
Sbjct: 184 HIAANRFLRSMVRGIVGGMLSAGRGE 209


>gi|327401434|ref|YP_004342273.1| tRNA pseudouridine synthase A [Archaeoglobus veneficus SNP6]
 gi|327316942|gb|AEA47558.1| tRNA pseudouridine synthase A [Archaeoglobus veneficus SNP6]
          Length = 290

 Score = 89.4 bits (220), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/249 (27%), Positives = 115/249 (46%), Gaps = 25/249 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---AGRTDSGVHAL 58
           +R  + + Y G+ + G+Q Q +  +++G + KA F   G  V       AGRTD+GVHA 
Sbjct: 25  MRVALKLAYIGTDFAGFQYQPDERTVEGELFKA-FESLGINVKASNYKCAGRTDAGVHAF 83

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV   D+       +L + +NA   + D I +   + V   F+ R+ A  R+Y+Y + +
Sbjct: 84  SQVVALDVSD--AKKVLPRVINA--NLPDDIVVWAWAKVPDDFNPRY-ATSRTYIYVLYS 138

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R+                 D   MR AA+ L+G HDFT F     +  S +RTI + ++ 
Sbjct: 139 RE----------------YDISAMRKAAKLLLGTHDFTNFTKKFGEGQSCVRTIYNVELR 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +   +   +F    +R  + +L+ VG    +    E+ L  +  +E    AP  G
Sbjct: 183 VNGDFLIFEIEGNAFTWNMVRCIIAALEAVGSRHRSVEWFEEMLNPEKHRERIEPAPAYG 242

Query: 239 LYFDSVEYS 247
           L    ++YS
Sbjct: 243 LILKDIKYS 251


>gi|34557089|ref|NP_906904.1| tRNA pseudouridine synthase A [Wolinella succinogenes DSM 1740]
 gi|34482804|emb|CAE09804.1| TRNA PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 267

 Score = 89.4 bits (220), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 113/245 (46%), Gaps = 15/245 (6%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
            +EY+GS +FG Q QK   S+  ++++ +    G    V  +GRTD GVHA RQ   F++
Sbjct: 21  FLEYDGSAFFGSQIQKEEPSVALALQRGL-KSMGIASKVRFSGRTDRGVHATRQAVSFEV 79

Query: 67  VRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             +     +    L K L  YL++        L  + +    RF A  R+Y  R +  + 
Sbjct: 80  PYKKSDWGYFKEELNKKLFPYLRVR------RLYPIREGLDPRFEAKSRAY--RYLLSEE 131

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           PL+    R        D   ++ A + LVG HDF  F+    Q  S +R +    +  + 
Sbjct: 132 PLSAFASRYVTHAHLGDERKIQEAMKLLVGWHDFALFKKSGSQEKSTLREMRRCWLYRYR 191

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +       A  FL  QIR  VG+L  VG G+ +  + ++ L+A+ R  C   APP GLY 
Sbjct: 192 SYWVFYFEANGFLRLQIRLLVGALLKVGRGEMSLEEFKEQLEAKRRFFCEG-APPYGLYL 250

Query: 242 DSVEY 246
             V +
Sbjct: 251 CKVSF 255


>gi|308235466|ref|ZP_07666203.1| tRNA pseudouridine synthase A [Gardnerella vaginalis ATCC 14018]
          Length = 173

 Score = 89.4 bits (220), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 61/177 (34%), Positives = 92/177 (51%), Gaps = 27/177 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG-----------AGR 50
           +R  + + Y+G  ++GW RQ N  ++QG++E A++    +++ VH            AGR
Sbjct: 1   MRLRLDLAYDGGDFYGWARQPNLRTVQGTLEDALY----KVLRVHDGDSCFPLRLTVAGR 56

Query: 51  TDSGVHALRQVAHFDLVREWVP-------VILCKALNAYLK--ISDTISILNLSIVDKQF 101
           TD+GVHA  QV H D+  + +        +   KAL   L+  +   ISI ++SI    F
Sbjct: 57  TDTGVHASYQVCHLDVEDDILQNCVGHTNLTPVKALEYRLRGVLPKDISIHSVSIAPSGF 116

Query: 102 HARFSAIRRSYLYRI---ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            ARFSA+ R+Y+YRI     R+      +G    I   LD  +M  AAQ +VG HDF
Sbjct: 117 DARFSALDRTYVYRISDAANRENLDPRMRGFVLQIDYDLDVNSMNQAAQMIVGLHDF 173


>gi|42559739|sp|Q7M9U3|TRUA_WOLSU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 253

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 113/246 (45%), Gaps = 15/246 (6%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
            +EY+GS +FG Q QK   S+  ++++ +    G    V  +GRTD GVHA RQ   F++
Sbjct: 7   FLEYDGSAFFGSQIQKEEPSVALALQRGL-KSMGIASKVRFSGRTDRGVHATRQAVSFEV 65

Query: 67  VRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             +     +    L K L  YL++        L  + +    RF A  R+Y  R +  + 
Sbjct: 66  PYKKSDWGYFKEELNKKLFPYLRVR------RLYPIREGLDPRFEAKSRAY--RYLLSEE 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           PL+    R        D   ++ A + LVG HDF  F+    Q  S +R +    +  + 
Sbjct: 118 PLSAFASRYVTHAHLGDERKIQEAMKLLVGWHDFALFKKSGSQEKSTLREMRRCWLYRYR 177

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +       A  FL  QIR  VG+L  VG G+ +  + ++ L+A+ R  C   APP GLY 
Sbjct: 178 SYWVFYFEANGFLRLQIRLLVGALLKVGRGEMSLEEFKEQLEAKRRFFCEG-APPYGLYL 236

Query: 242 DSVEYS 247
             V + 
Sbjct: 237 CKVSFE 242


>gi|195336235|ref|XP_002034747.1| GM14299 [Drosophila sechellia]
 gi|194127840|gb|EDW49883.1| GM14299 [Drosophila sechellia]
          Length = 499

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 119/265 (44%), Gaps = 54/265 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +SIQG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLERSRLDTNSIQGCLELALQVFHPTNEIHTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVR----EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL      DL R     +   IL   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVQVDLERTNGQPYDTTILTGVLNRTLNKQRLPIRVLSSKLVANSFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPLA---------------LEKGRAWLI-PKSLDCENMRIAAQH 148
            A  R+YLYR  + +  PL                 E  R + +   S D + ++ A++ 
Sbjct: 120 DATGRTYLYRFAVAKDPPLGDCSLRNRSFETFIPIEEIDRCYFLQSSSFDIKRVQAASRM 179

Query: 149 LVGRHDFTTFRSIHCQASS------PIRTIDHFDVN---------------SFGNLIEIR 187
            +G HDF TF S+  Q  S       +R ID  ++                   N  +I 
Sbjct: 180 FIGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSNAILAAETYNYWDIE 239

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGK 212
           + A+SFL+ Q+R  VG+L  +G+G+
Sbjct: 240 IRAKSFLYKQVRRIVGALIALGNGR 264


>gi|195586672|ref|XP_002083097.1| GD13536 [Drosophila simulans]
 gi|194195106|gb|EDX08682.1| GD13536 [Drosophila simulans]
          Length = 499

 Score = 89.0 bits (219), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 119/265 (44%), Gaps = 54/265 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +SIQG +E A  +F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSIQGCLELALQVFHPTNEIHTVLSS-R 59

Query: 51  TDSGVHALRQVAHFDLVR----EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL      DL R     +   IL   LN  L K    I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTVQVDLERTNGQPYDTTILTGVLNRTLNKQRLPIRVLSSKLVANSFHCRY 119

Query: 106 SAIRRSYLYRI-ITRQAPLA---------------LEKGRAWLI-PKSLDCENMRIAAQH 148
            A  R+YLYR  + +  PL                 E  R + +   S D + ++ A++ 
Sbjct: 120 DATGRTYLYRFAVAKDPPLGDCSLRNRSFETFIPVEEIDRCYFLQSSSFDIKRVQAASRM 179

Query: 149 LVGRHDFTTFRSIHCQASS------PIRTIDHFDVN---------------SFGNLIEIR 187
            +G HDF TF S+  Q  S       +R ID  ++                   N  +I 
Sbjct: 180 FIGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSNAILAAETYNYWDIE 239

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGK 212
           + A+SFL+ Q+R  VG+L  +G+G+
Sbjct: 240 IRAKSFLYKQVRRIVGALIALGNGR 264


>gi|224102643|ref|XP_002312761.1| predicted protein [Populus trichocarpa]
 gi|222852581|gb|EEE90128.1| predicted protein [Populus trichocarpa]
          Length = 232

 Score = 89.0 bits (219), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 62/177 (35%), Positives = 93/177 (52%), Gaps = 8/177 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVH--GAGRTDSGVHAL 58
            ++ ++I Y+G+ Y GWQ Q+   +IQ  +EKA+   T  E   +H  GA RTD GVHA 
Sbjct: 57  FKWRLLISYDGTHYKGWQFQQTPPTIQCILEKALTRATKLERKDLHLVGASRTDGGVHAW 116

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF     +  +  +  ALN  L     I +  +S V  +FHARFSA  ++Y Y+I 
Sbjct: 117 GQVAHFVTPFNYDSLDSIHAALNGLLPPD--IRVREISAVVPEFHARFSAKGKTYHYKIF 174

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTI 172
                   ++  A+ +   L+   MR AA H +G  DF+ F   S +    +P++TI
Sbjct: 175 NDTVMDPFQRLYAYHVTHKLNAAVMREAANHFIGTRDFSAFVNSSRNDGVPNPVKTI 231


>gi|91773587|ref|YP_566279.1| tRNA pseudouridine synthase A [Methanococcoides burtonii DSM 6242]
 gi|121691685|sp|Q12VJ7|TRUA_METBU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91712602|gb|ABE52529.1| tRNA pseudouridine synthase A [Methanococcoides burtonii DSM 6242]
          Length = 275

 Score = 89.0 bits (219), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 112/253 (44%), Gaps = 33/253 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH--------GAGRTDS 53
           +R  + I Y GS + G Q Q N  +++G +    F V  E+ ++          +GRTDS
Sbjct: 1   MRVALKIAYIGSNFHGSQVQLNDPTVEGEL----FKVLKELGIMEDPRTANFISSGRTDS 56

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA+ QV  FD   +   + + + +N+  K+  TI     +IV + F  R  A+ RSY 
Sbjct: 57  GVHAMGQVVAFDT--DAPNLAMPRVINS--KLPGTIWAWAHAIVPENFDPRRHALSRSYR 112

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y +   Q                 D   +R A++ L+G HDF+ F S    +   +R + 
Sbjct: 113 YILYGEQ----------------FDISKIRSASKLLLGSHDFSNF-STSRGSKKTVRIVK 155

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             D+   GNL  I V A SFL   +R  V +L +VG G      L   L  +  +E    
Sbjct: 156 RIDIRVSGNLTRIDVEANSFLWNMVRKIVAALMMVGSGVRDEEWLGHMLDPESYEEGLEP 215

Query: 234 APPEGLYFDSVEY 246
           A   GL    V Y
Sbjct: 216 AHGYGLVLMDVNY 228


>gi|261338249|ref|ZP_05966133.1| tRNA pseudouridine synthase A [Bifidobacterium gallicum DSM 20093]
 gi|270276903|gb|EFA22757.1| tRNA pseudouridine synthase A [Bifidobacterium gallicum DSM 20093]
          Length = 313

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 86/290 (29%), Positives = 128/290 (44%), Gaps = 51/290 (17%)

Query: 1   MIRYCMIIEYNGSGYFGW--QRQKNGSSIQGSIEKAI--FLVTGE----IVVVHGAGRTD 52
           M+R  + + Y+G  + GW  Q Q N  ++QG IE+A+   L  G     +  +  AGRTD
Sbjct: 1   MVRLRIDLAYDGFSFNGWAVQPQSNIRTVQGEIEQALARLLHDGNEPDYVPRLTVAGRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVIL-------CKALNAYLK--ISDTISILNLSIVDKQFHA 103
           +GVHA  QV H D+    +   +        KAL   L   + D I+I  +S   + F A
Sbjct: 61  AGVHASHQVCHLDVTEPMLDACVGHMRVEPVKALETRLSRMMPDDIAIHRVSFAPEGFDA 120

Query: 104 RFSAIRRSYLYRI---ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           RFSA+ R+Y+YRI    T   P  L     W     L+ + M  AA   +G HDF +F +
Sbjct: 121 RFSALERTYVYRISDAATDYDPRQLSY--VWHTDHLLNMDAMNEAAALTLGLHDFGSFAT 178

Query: 161 IHCQASSPIRTID----------HFDVNSFGN----------LIEIRVVARSFLHTQIRS 200
            +   ++ IR +               N  G           L+   +VA +F    +RS
Sbjct: 179 PNPGGTT-IREVKTAYWSRIPTRPLIANPMGERYHTPAIESGLLCFTIVADAFARNMVRS 237

Query: 201 FVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            V +   VG GK    W +  +   L+       GP+A P+GL  + V Y
Sbjct: 238 LVNACVQVGLGKRDVAWFAHKMAVPLR---EGSTGPIA-PQGLTLEHVAY 283


>gi|298674065|ref|YP_003725815.1| tRNA pseudouridine synthase A [Methanohalobium evestigatum Z-7303]
 gi|298287053|gb|ADI73019.1| tRNA pseudouridine synthase A [Methanohalobium evestigatum Z-7303]
          Length = 277

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 115/248 (46%), Gaps = 25/248 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHAL 58
           R  + + Y G+ Y G Q Q    +I+G + K++     +   +      +GRTD+GVH+L
Sbjct: 4   RMALKLAYIGTEYHGSQVQPELPTIEGELFKSLKNLEIIDDPKSANFVSSGRTDTGVHSL 63

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  FD     + V   + +N+  ++ ++I     ++V  +F+ R  A  R YLY    
Sbjct: 64  GQVVTFDTDNPRLAV--PRVINS--QLPESIWAWAYAVVPDEFNPRHGAFSRRYLY---- 115

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 +  G  +      D   +R A+++L+G HDF  F     +  S +RT+   ++ 
Sbjct: 116 ------IMSGEEY------DISRIRTASKYLIGTHDFANF-CTPVKGKSTVRTVQRINIR 162

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G L  I + A SFL   +R  V +L +VG G   +  LE+ L  +  +E    AP  G
Sbjct: 163 VKGTLTLIDIQADSFLWKMVRKIVTALMMVGYGTRDTEWLEQMLNPEYYEEGIEPAPSYG 222

Query: 239 LYFDSVEY 246
           L    V+Y
Sbjct: 223 LILKDVDY 230


>gi|153840131|ref|ZP_01992798.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
 gi|149746249|gb|EDM57337.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
          Length = 142

 Score = 88.6 bits (218), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 44/111 (39%), Positives = 67/111 (60%)

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
            LD + M  A Q+L+G +DF++FR+ HCQ+ SP R + H +V   G+ + I + A +F+H
Sbjct: 11  ELDEKKMHEAGQYLLGENDFSSFRAAHCQSLSPCRNLMHLNVTRHGDYVVIDIKANAFVH 70

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY   V+Y
Sbjct: 71  HMVRNITGSLIKVGRGEEKPEWIKWLLEAKDRKLAGATAKAEGLYLVDVDY 121


>gi|119504507|ref|ZP_01626586.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2080]
 gi|119459529|gb|EAW40625.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2080]
          Length = 226

 Score = 88.6 bits (218), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 42/108 (38%), Positives = 64/108 (59%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
           C  M  A+Q L+G HDF+ FR+  CQA+ P+R I    VN  G+ + + + A +FL+  +
Sbjct: 99  CIAMHNASQILLGEHDFSAFRAAQCQAAHPVRQIFGVSVNRVGDFVILDIEANAFLYHMV 158

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           R+ VGSL++VG G+     +E+ L+ +DR   G  A   GLY  S+ Y
Sbjct: 159 RNLVGSLQMVGSGQRPPEWIEQLLEGKDRTLGGDTASASGLYLQSITY 206


>gi|328702786|ref|XP_003242010.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Acyrthosiphon
           pisum]
          Length = 358

 Score = 88.6 bits (218), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 83/286 (29%), Positives = 125/286 (43%), Gaps = 42/286 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDS 53
           RY +   Y G+ + G QRQ         + SS+QG +E A+  L       +H + RTD 
Sbjct: 5   RYLLYFSYIGTRFRGVQRQLTYDMVHNDDPSSVQGLLEYALKQLQPLNTPKLHLSSRTDQ 64

Query: 54  GVHALRQVAHFDLVREWV--PVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRR 110
           GVH+ +  AH DL   +   P  L   +N +L   +  I +++  IV   F+AR  A  R
Sbjct: 65  GVHSFKSSAHLDLELPYTCHPNKLVFQVNNFLSSCEVPIKLVSAQIVPNDFNARSCAKWR 124

Query: 111 SYLYRIITRQA------------PLAL-EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFT 156
            YLYR+   ++            P+ + E  R + I KS  D E ++      +G  D+ 
Sbjct: 125 KYLYRLAVVKSEFKDLYAERFVFPIPITEDKRCYFIQKSDFDVELVKNVLPLFIGTKDYK 184

Query: 157 TF---RSIHCQASS----------PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVG 203
           TF     ++ + S+          P R+    D++ + N  +IRV ARSFL+ QIR  VG
Sbjct: 185 TFMGKSGLNTELSTIRTWNNIEIVPGRSFYPTDIDKYYNYWDIRVNARSFLYKQIRRTVG 244

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
            L  V     T  D++            P    AP  GLY   + Y
Sbjct: 245 VLIKVAQNIITYDDVKYMFDNPSINSWNPKISTAPSYGLYLYDIGY 290


>gi|269925860|ref|YP_003322483.1| tRNA pseudouridine synthase A [Thermobaculum terrenum ATCC BAA-798]
 gi|269789520|gb|ACZ41661.1| tRNA pseudouridine synthase A [Thermobaculum terrenum ATCC BAA-798]
          Length = 240

 Score = 88.2 bits (217), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 112/249 (44%), Gaps = 15/249 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + ++I Y G  + G Q Q    ++Q  +E A   VTG       AGRTD+GV AL Q
Sbjct: 1   MSTWKLVISYKGEYFSGSQIQPGKRTVQEELENAWEKVTGSRCRAVLAGRTDAGVSALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA         P  L + L  YL  +  I I  +  V   F AR SAI R Y Y + ++ 
Sbjct: 61  VATIKADWPGTPEELLEKLRKYL--TQGIEIRKVERVSDNFDARKSAIWRRYRY-VFSKD 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDV-- 177
                E  R   I      E+MR AA+ LVG  DF  F S         +R I   +V  
Sbjct: 118 -----EIARFGFI----SVESMRQAARALVGEKDFAAFASQSELGPRGTVRRILDINVIW 168

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N + I +VA +FL   +R  V +L  VG GK    +L +A++ + R+     AP +
Sbjct: 169 DKAANNLCIEIVADAFLRQMVRRIVSALIWVGTGKIEVVELLRAVEIKARQLLPGPAPAK 228

Query: 238 GLYFDSVEY 246
            L    V Y
Sbjct: 229 NLTLVEVGY 237


>gi|147919589|ref|YP_686671.1| tRNA pseudouridine synthase A [uncultured methanogenic archaeon
           RC-I]
 gi|121687867|sp|Q0W2P8|TRUA_UNCMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|110622067|emb|CAJ37345.1| tRNA pseudouridine synthase [uncultured methanogenic archaeon RC-I]
          Length = 266

 Score = 88.2 bits (217), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 112/249 (44%), Gaps = 26/249 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---VHGAGRTDSGVHAL 58
           ++  + I Y G+ ++G Q Q    +++  + KA+    G I +   +  AGRTD+GVHAL
Sbjct: 1   MKTALKIAYVGTNFYGSQAQPGLPTVESELRKAL-EEAGAIKLGTKIAMAGRTDAGVHAL 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F+       +   + +N+  K+   +     + V   F  R  A  R Y Y +  
Sbjct: 60  GQVVAFEQADP--KLTAPRIINS--KLPKDLWAYARAEVPDDFDPRRHATSREYRYILY- 114

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
             AP  +E+              ++  +   +G HDFT F S+      P+RT+   D+ 
Sbjct: 115 --APDVIER-------------RLKECSSRFLGTHDFTNFSSVEA-GKYPVRTVTRLDIA 158

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+   I + A SFL   +R  V +L+LVG+ K     +EK    + R E  P A P G
Sbjct: 159 KRGDFYIIDIEADSFLWNMVRKIVTALRLVGENKRPDGWIEKMFDPEYR-EGIPPAAPGG 217

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 218 LYLSRVNYD 226


>gi|50364970|ref|YP_053395.1| tRNA pseudouridine synthase A [Mesoplasma florum L1]
 gi|62901303|sp|Q6F1W2|TRUA_MESFL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|50363526|gb|AAT75511.1| tRNA pseudouridine synthase I [Mesoplasma florum L1]
          Length = 251

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 120/252 (47%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALR 59
           M ++ + +EY+GS + GW  Q   S+IQG + KAI  VT   V    GA +TD+GVHA+ 
Sbjct: 1   MFKFLITLEYDGSDFHGWIEQPKTSTIQGELNKAINRVTKNAVFKTIGASKTDTGVHAID 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q    DL       +  KA+N  L   +TI + ++  V + F+ R   + + Y Y I  +
Sbjct: 61  QKVLLDLGFNPKLDLFKKAINKAL--PETIKVRSIEEVKQDFNIR-DVLYKEYSYTINDK 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-----RSIHCQASSPIRTIDH 174
           +  +   +       + +D + ++      +G H+F  F     + +     + IR I+ 
Sbjct: 118 EYNILSNRFELNWDFEEIDIDKLQNIFNLFIGEHEFKLFSGLNHKELDSNKITTIREIES 177

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGS-LKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            DV    + + I   A+ F+  QIR  V S L    + K ++ ++++ LQ +  K   P 
Sbjct: 178 IDVKRALDKVVITFKAKGFIRYQIRMIVQSALNCYLNKKISADEIKEKLQGKGNK--PPF 235

Query: 234 -APPEGLYFDSV 244
            AP +GL  + +
Sbjct: 236 NAPAKGLKLNKI 247


>gi|119477629|ref|ZP_01617779.1| hypothetical protein GP2143_09210 [marine gamma proteobacterium
           HTCC2143]
 gi|119449132|gb|EAW30372.1| hypothetical protein GP2143_09210 [marine gamma proteobacterium
           HTCC2143]
          Length = 261

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 117/253 (46%), Gaps = 19/253 (7%)

Query: 6   MIIEYNGSGYFGWQRQKNGS------SIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           + I Y G+ YFGWQ Q   +      +I+G+I KA+  ++  +   +  A RTD GVHA 
Sbjct: 6   VTIAYKGTHYFGWQAQSKDTLKEEYPTIEGTILKALKKMSNYQHCTISAASRTDGGVHAQ 65

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
            Q+A   L  +     L   LN+ L +   I IL  +   K F    S++ + Y Y    
Sbjct: 66  GQLAKISLSIDISADHLLLGLNSALPLD--IRILECASSTKNFQPNVSSVSKEYHYYFTA 123

Query: 118 TRQAPLALEKGRAWLIPKS---LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           ++   +A+ +    L       +D   +R A Q  VGRHDF  F       +S +R I +
Sbjct: 124 SKTDNVAISEISLRLSTHDDGPIDMALLRTACQLFVGRHDFYNFSVRDLNNASSVRQISY 183

Query: 175 FDV--NSFGNLIE----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            D+   +F  L++    ++++   FL   IR  +G+L  +G G+ T  D+   LQ Q   
Sbjct: 184 CDILQANFSPLVDEVYYLKIIGDGFLKYMIRYVMGALIELGKGRITLEDIAFYLQHQQDD 243

Query: 229 ECGPLAPPEGLYF 241
           +    A  +GL+ 
Sbjct: 244 KLSAKAKAKGLHL 256


>gi|268324810|emb|CBH38398.1| tRNA pseudouridine synthase A [uncultured archaeon]
          Length = 275

 Score = 87.8 bits (216), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 112/251 (44%), Gaps = 28/251 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVH 56
           R  + I Y G+ Y G+Q Q      +++G + KA+     L   +      AGRTD GVH
Sbjct: 7   RVALKIGYLGTNYHGFQIQPQAELQTVEGELFKALKRLGILEDRKTANYSYAGRTDKGVH 66

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV  FD + + +   +   +     + + I  L ++     F+AR  AIRR Y Y +
Sbjct: 67  ALAQVVSFDTLNQNMTPRMINTM-----LPNDIWALAIAKPHAGFNARKEAIRREYRYFL 121

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHF 175
                           +   LD   MR A++ L+G HDF+ F +    +  S I+ I   
Sbjct: 122 ---------------FLQTELDISRMRDASELLIGAHDFSNFSQRDGLEGKSLIKEIKQV 166

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           ++      I I + A  FL   +R  V +L +VG GK   + ++  L  + +++  P AP
Sbjct: 167 NIVKSDLFIIIDIAASGFLRKMVREIVSALSMVGSGKRAKSWIQDLLDLKIKEQIEP-AP 225

Query: 236 PEGLYFDSVEY 246
             GL    V Y
Sbjct: 226 AFGLVLKDVSY 236


>gi|74191686|dbj|BAE30412.1| unnamed protein product [Mus musculus]
          Length = 280

 Score = 87.8 bits (216), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 110/249 (44%), Gaps = 52/249 (20%)

Query: 48  AGRTDSGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFH 102
           + RTD+GVHAL   AH D+ R      + P ++ KALN +LK    I +L    V   FH
Sbjct: 27  SSRTDAGVHALSNAAHLDIQRRPGQSPFSPEVVAKALNTHLK-HPAIRVLKAFRVPNDFH 85

Query: 103 ARFSAIRRSYLYRIIT-----RQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFT 156
           AR +A  R+Y YR+ T      Q P+  E+   W L  + LD   M+ AAQHL+G HDF+
Sbjct: 86  ARHAATSRTYQYRLATGCSWPNQLPV-FEQNVCWALQTEYLDMAAMQEAAQHLLGTHDFS 144

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFG-------------NLIEIRVVARSFL--------- 194
            F+S     ++ +RT+    V+                    +   ++SFL         
Sbjct: 145 AFQSAGSPVTNTVRTLRRVSVSPGPASPFVLPEGSRRLQFWTLEFESQSFLYRQVGCLNP 204

Query: 195 -------HT--------QIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPE 237
                  HT        Q+R     L  VG G    T ++  L++QD   K    +AP  
Sbjct: 205 HRMGSGRHTCDNLSSLLQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAPAR 264

Query: 238 GLYFDSVEY 246
           GL+  SV Y
Sbjct: 265 GLFLKSVLY 273


>gi|78777192|ref|YP_393507.1| pseudouridylate synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497732|gb|ABB44272.1| Pseudouridylate synthase [Sulfurimonas denitrificans DSM 1251]
          Length = 236

 Score = 87.8 bits (216), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 112/247 (45%), Gaps = 13/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  +II YNG+ + G Q QK   ++I G++E A+  +  E  +V  +GRTD GVHA  Q
Sbjct: 1   MRCALIIAYNGTNFLGSQTQKESKNTILGTLEIALKKINIETKIV-ASGRTDRGVHASGQ 59

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL   W  +  L  +L   L  S  I I  + IVD  FHAR+SA RR Y Y II +
Sbjct: 60  VCHIDLPPYWSDITKLQDSLGRVLPPS--ILIKKIKIVDDTFHARYSAKRRVYRY-IIKK 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 E+     I  + D   ++   +   G  DF  F        S  R I       
Sbjct: 117 AKSNPFEENFVTFIDDT-DFFEIQKNIKLFCGAFDFKFFMKSGGDIKSTTRVIYRAFAYE 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I +   A  FL +QIR  VG+L  + +      ++   L+ +   +  P A   GL
Sbjct: 176 HKGFIVLNFEANGFLRSQIRLMVGALLSLNED-----EILDKLECRVNHKIKP-AKSNGL 229

Query: 240 YFDSVEY 246
           Y   ++Y
Sbjct: 230 YLSKIKY 236


>gi|307110841|gb|EFN59076.1| hypothetical protein CHLNCDRAFT_19189 [Chlorella variabilis]
          Length = 300

 Score = 87.8 bits (216), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 115/239 (48%), Gaps = 20/239 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSG 54
           Y  +++Y+G+ Y+G+Q Q      +   ++Q  +E+A+   TG+    + V  AGRTD+G
Sbjct: 4   YAAVLQYDGTAYWGFQLQPAPQGRRAKPTVQLRVEQALCRATGQGRQALRVQAAGRTDAG 63

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  QV  F   R      L +ALNA +     I  + +  V   ++ R+ A R++Y Y
Sbjct: 64  VHARGQVVQFCCARRQGAAPLLRALNALM--PPDIRAVAVQEVPLDWNVRY-ASRKTYAY 120

Query: 115 RIITRQAPLALEKGRAWLI----PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SP 168
            +     P+A      W      P+ L  + M  AA   VG HDF+ F ++   A+  SP
Sbjct: 121 DLHLD--PVADPFLHRWRCHPRRPERLRLDAMADAAALFVGTHDFSRFANLGPDATRKSP 178

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           ++T+  + +        + V    FL+ Q+R   G+L  VG G   + D+  AL   +R
Sbjct: 179 VKTVLSYRLLPLEGGARLEVTGTGFLYKQVRHMTGALLAVGGGSLGADDIAAALAGGER 237


>gi|240103716|ref|YP_002960025.1| tRNA pseudouridine synthase A [Thermococcus gammatolerans EJ3]
 gi|259550472|sp|C5A7E9|TRUA_THEGJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239911270|gb|ACS34161.1| tRNA-pseudouridine synthase A (truA) [Thermococcus gammatolerans
           EJ3]
          Length = 267

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/256 (26%), Positives = 108/256 (42%), Gaps = 38/256 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVHGAGRTDSGVHA 57
           ++  + I Y+G+ ++G+QRQ    +++G +     K   + + E     GA RTD GV A
Sbjct: 1   MKLALRIAYDGTAFYGFQRQPGIRTVEGELINVLTKLKIIESPEKNDFKGASRTDRGVSA 60

Query: 58  LRQVAHF------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
              V  F      DL R   P +L   L+        + +L ++ V   FH RF AI ++
Sbjct: 61  FFNVVSFVPGERADLAR---PEVLNHNLH-------DLWVLGVAEVPDDFHPRFWAISKT 110

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y Y                +LI +  + E M   A+   GRHDF+ F  +      P+R 
Sbjct: 111 YRY----------------YLIDEGFELEKMVGCAKLFEGRHDFSAFARLE-PGRDPVRE 153

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           I H  +        I +  +SFL   +R  V +L+  G       ++   L     K+  
Sbjct: 154 ITHISITPRHGYYVIEITGKSFLWEMVRRIVNALRFCGLSLLEPEEVGAMLSGVYEKKVP 213

Query: 232 PLAPPEGLYFDSVEYS 247
           P APPE L    +EY 
Sbjct: 214 P-APPENLILWHIEYP 228


>gi|194246764|ref|YP_002004403.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma mali]
 gi|254764860|sp|B3R022|TRUA_PHYMT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|193807121|emb|CAP18559.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma mali]
          Length = 244

 Score = 87.0 bits (214), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 116/244 (47%), Gaps = 6/244 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y +++ Y+G+ Y+G+Q+Q + ++IQ  +E  +  +   + + ++GA RTD GVHA  QV 
Sbjct: 6   YKLVLSYDGTNYYGFQKQLHLNTIQSVLENVLNKITKQKKIKIYGASRTDKGVHASGQVV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF L          K LN  L     I I  + ++ K+FH RF A  +S +Y  +  +  
Sbjct: 66  HFQLPFLIPNDHFQKILNFCL--PSDIQITKIILISKEFHCRFQA--KSKIYHYVFSKKK 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
           L +   R  +   ++D   ++ A   + G+HDF+ F S      +  R I    +     
Sbjct: 122 LNVFNYRFQVYIPNMDFNKIKEAILFIEGKHDFSLFTS-QKSLKNYQRIIFKAFIKETKQ 180

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
              + +   SF+   IR  VG L  +   K T ++ ++ L  +  ++   LAP +GL   
Sbjct: 181 KYFLIIHGNSFIQHMIRFLVGFLIEIAQNKKTLSEFKQMLDLKINQKARLLAPAKGLILK 240

Query: 243 SVEY 246
            + Y
Sbjct: 241 KIFY 244


>gi|86139957|ref|ZP_01058522.1| tRNA pseudouridine synthase [Roseobacter sp. MED193]
 gi|85823375|gb|EAQ43585.1| tRNA pseudouridine synthase [Roseobacter sp. MED193]
          Length = 113

 Score = 87.0 bits (214), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 43/99 (43%), Positives = 63/99 (63%), Gaps = 4/99 (4%)

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI--EIR--V 188
           +P  L    MR  A+HL+G++ FTTFRS  CQA SP++ +D  ++     L   E+R  +
Sbjct: 7   VPPELYVAAMRNGARHLLGKYYFTTFRSRICQAKSPVKALDALEIEEVEGLAGPELRFHL 66

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            ARS L+ Q+RS VG+L+ VG G WT  D++ AL+ +DR
Sbjct: 67  SARSLLYNQVRSIVGTLERVGAGSWTPEDVKTALETRDR 105


>gi|126654438|ref|ZP_01726177.1| pseudouridylate synthase I [Bacillus sp. B14905]
 gi|126589112|gb|EAZ83311.1| pseudouridylate synthase I [Bacillus sp. B14905]
          Length = 214

 Score = 86.3 bits (212), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 62/213 (29%), Positives = 103/213 (48%), Gaps = 8/213 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R  +II Y+G+ + G+Q Q    ++Q  IE+ + ++   E V V  +GRTD+ VHA  
Sbjct: 1   MRRLKVIISYDGTLFSGYQVQPGERTVQAEIERVLAIMHKEEKVKVTASGRTDARVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           KALN  +++   I ++++  V+  FHAR+S   + Y Y  I  
Sbjct: 61  QTLHFDTPLAIPADKYRKALN--VQLPRDIRVMSVEEVEHDFHARYSVTGKRYRY--IWS 116

Query: 120 QAPLALEKGRAWLIPKS---LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             P+     R + +  +    D   M+ AAQ ++G HDF+ F + +      +RT+    
Sbjct: 117 CEPIQNPFRRHYTVETNGVKPDVVAMQKAAQAIIGTHDFSCFCASNTSVQDKVRTVTSLQ 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
               G  + + +    FL+  +R   G+L  VG
Sbjct: 177 FEWHGEELHMVIEGSGFLYNMVRIIAGTLWEVG 209


>gi|197294307|ref|YP_001798848.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma australiense]
 gi|171853634|emb|CAM11505.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma australiense]
          Length = 245

 Score = 86.3 bits (212), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 108/243 (44%), Gaps = 5/243 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +I+ Y+G+ Y G+Q+Q    +IQ ++E A+  +T   +    A RTD GVHA  Q  H
Sbjct: 8   YKLILSYDGTCYCGYQKQPQTKTIQQTLENALKSMTKRQINTFAASRTDKGVHAQEQTIH 67

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              LN  L     I  +  +  D  FHAR+ A  +S +Y  I  + PL
Sbjct: 68  FQTAFAIELKRFKNTLNRILPPDIRIKKIEKATAD--FHARYWA--KSKIYHYIFAKKPL 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                   +   +LD   ++ A   ++G+++F +F +   + +     ++ F   +  N 
Sbjct: 124 NAFNYHFQVFVANLDFAKIKSAMNLIIGKYNFASFTNDKKEKNFNKTVLNAFVKETSQNY 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I I   A  FL   +R  VG L  +G  K +    +  L     ++   LAP +GL+   
Sbjct: 184 ILI-FHADGFLKYMVRFLVGGLIEIGKNKMSLELFKAMLTNTTNQKVSLLAPAKGLFLKK 242

Query: 244 VEY 246
           + Y
Sbjct: 243 IFY 245


>gi|227497212|ref|ZP_03927460.1| pseudouridylate synthase [Actinomyces urogenitalis DSM 15434]
 gi|226833297|gb|EEH65680.1| pseudouridylate synthase [Actinomyces urogenitalis DSM 15434]
          Length = 229

 Score = 85.9 bits (211), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 53/161 (32%), Positives = 85/161 (52%), Gaps = 12/161 (7%)

Query: 97  VDKQFHARFSAIRRSYLYRIIT------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           V   F ARFSA+ R Y+YRI        R+A     +G+   + ++LD E+M ++A+ L+
Sbjct: 41  VPADFDARFSALERRYVYRIDDGAPSQGRRAYDPCRRGQVLWVGQALDVESMALSARGLL 100

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
           G HDF ++     + ++ IRT+   D           L+ + VVA +F H+ +RS VG+ 
Sbjct: 101 GEHDFLSYCKPR-EGATTIRTLRRLDWQRASSGPDAGLVTLTVVADAFCHSMVRSLVGAG 159

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             VG G+   +   + L A+ R +  P+APP GL  + V Y
Sbjct: 160 LAVGQGRQPVSWPARLLAARSRDQAAPVAPPYGLTLEEVVY 200


>gi|24215440|ref|NP_712921.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
 gi|42559814|sp|Q8CXS6|TRUA_LEPIN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|24196565|gb|AAN49939.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
          Length = 207

 Score = 85.9 bits (211), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 56/171 (32%), Positives = 87/171 (50%), Gaps = 12/171 (7%)

Query: 78  ALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
           +LNA   I+D+ +SILN++ VD+ F +RFS   R Y Y I+  + P    K R +     
Sbjct: 20  SLNA---ITDSGLSILNMTEVDENFDSRFSCNSREYEYWILNTKYPRPTWKNRTFWYQHR 76

Query: 137 LDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVN-----SFGNLIEIRVVA 190
           +D   +    + L G HDF +   +   +  S +RTI   DV          L+++++ A
Sbjct: 77  IDVPRLEAELELLKGEHDFRSLAKVASLKGRSTVRTI--LDVKLERSLELEGLLKVKIRA 134

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             FLH  IR   G+L  + +GK   T++ + L ++DR   G   PP GLYF
Sbjct: 135 NGFLHNMIRILTGTLLEISNGKRKDTNVLEILSSKDRTIAGITLPPYGLYF 185


>gi|20089106|ref|NP_615181.1| tRNA pseudouridine synthase A [Methanosarcina acetivorans C2A]
 gi|30913395|sp|Q8TU65|TRUA_METAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|19913971|gb|AAM03661.1| pseudouridylate synthase [Methanosarcina acetivorans C2A]
          Length = 269

 Score = 85.9 bits (211), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 117/249 (46%), Gaps = 25/249 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHA 57
           +R  + + Y G+ + G Q Q N  +++  + KA+     + + +      AGRTD+GVHA
Sbjct: 1   MRVALKLAYIGTEFHGSQIQPNVETVEKELFKALRNLSIIESPKSADYTCAGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  FD   E   + + + +N+  ++   I     + V   F AR SA+ R Y Y   
Sbjct: 61  LGQVVAFDT--EKPNLAIPRVINS--ELPPAIWAWAHAEVPYYFDARRSAVSRHYHYV-- 114

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                         +  +  D   MR A++ L+G HDF  F   + + S+ +RT++  +V
Sbjct: 115 --------------MSGEDYDISKMREASKLLLGTHDFENFSRSNGEKST-VRTLERINV 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G + +I VV  SFL   +R  V +L ++G+G   +  L + L  +  +E    APP 
Sbjct: 160 RVDGEITKIDVVGNSFLWNMVRKIVTALSMIGNGVRDNDWLLQMLNPEIYEEGIEPAPPY 219

Query: 238 GLYFDSVEY 246
           GL    V Y
Sbjct: 220 GLTLMGVNY 228


>gi|47206562|emb|CAF94488.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 181

 Score = 85.9 bits (211), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 59/171 (34%), Positives = 91/171 (53%), Gaps = 20/171 (11%)

Query: 97  VDKQFHARFSAIRRSYLYRI---ITRQAPLAL-EKGRAW-LIPKSLDCENMRIAAQHLVG 151
           V   FHARF A  R+Y+YR+   I R++P+ L E G  W L    LD   M  AA  LVG
Sbjct: 7   VADNFHARFCAQSRTYVYRVALGICRKSPVPLPEHGFCWNLRDTELDVGGMCEAAALLVG 66

Query: 152 RHDFTTFRSIHCQA--SSPIRTIDHFDVN---SFGNL--------IEIRVVARSFLHTQI 198
            HDF++FR+++      +P++ +D   +    SF  +        +E+   +RSFL+ Q+
Sbjct: 67  VHDFSSFRAVNSDLPFKNPVKRLDAATIQTGVSFAQVHYHRVIPFLELIFTSRSFLYKQV 126

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEYS 247
           R   G+L  VG G+ +   L++ L+A+D      G  AP  GL+   V+Y+
Sbjct: 127 RRMTGALVAVGQGRLSVAQLKEVLEARDSLAYPQGLTAPAHGLFLTRVDYT 177


>gi|47097169|ref|ZP_00234734.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 1/2a
           F6854]
 gi|47014428|gb|EAL05396.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 1/2a
           F6854]
          Length = 133

 Score = 85.9 bits (211), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 48/115 (41%), Positives = 63/115 (54%), Gaps = 3/115 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y
Sbjct: 61  QVIHFDSELDITAEKFQKALQVMTPFD--ISFLTVEEVPDDFHARFGTVGKEYRY 113


>gi|195012380|ref|XP_001983614.1| GH25313, isoform B [Drosophila grimshawi]
 gi|193897096|gb|EDV95962.1| GH25313, isoform B [Drosophila grimshawi]
          Length = 317

 Score = 85.9 bits (211), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 126/305 (41%), Gaps = 60/305 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +SIQG +E A  +F    EI  V  + R
Sbjct: 1   MHRYLLNISYIGTNFRGIQKTINKLEEARLDTNSIQGCLELALRVFRPKNEIQTV-LSSR 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K    I IL+   V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLERSDGKPYDTSTLTGVLNRTLDKHKLPIRILSSQRVVDTFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALEKGRA-------------------WLIPKSLDCENMRIAA 146
            A  R+YLYR+   ++     KG +                   +L   + D E +  AA
Sbjct: 120 HATGRTYLYRVAVAKSVSEASKGSSLKNKGYESFVPVEEIDRCYFLHCDNFDVERLHGAA 179

Query: 147 QHLVGRHDFTTFRSIHCQASSP-------IRTIDHFDVNSFGNLI--------------- 184
           +  +G HDF TF S+  Q S         +R ID  ++     L                
Sbjct: 180 RMFLGLHDFRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGQTLALGPNAKLATQTYDYW 239

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYF 241
           +I + A+SFL+ Q+R  VG+L  + + +     + + L    +        +AP  GLY 
Sbjct: 240 DIEIKAKSFLYKQVRRIVGTLLALANSRIDERCIYQMLTIPSKHNWDSRVVVAPACGLYL 299

Query: 242 DSVEY 246
             V Y
Sbjct: 300 CRVHY 304


>gi|315452593|ref|YP_004072863.1| tRNA pseudouridine synthase A [Helicobacter felis ATCC 49179]
 gi|315131645|emb|CBY82273.1| tRNA pseudouridine synthase A [Helicobacter felis ATCC 49179]
          Length = 246

 Score = 85.9 bits (211), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 85/258 (32%), Positives = 117/258 (45%), Gaps = 28/258 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ M++ Y+GS ++G+ +Q N  S++G++E A+ L  G    +  AGRTD GVHAL Q
Sbjct: 1   MGRFQMLLAYDGSAFYGYAKQPNLPSVEGALESAL-LKLGISSPILCAGRTDRGVHALCQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V  F       P+ L + L  +L  K+   I    +  V   FH RF A  R  LYR I 
Sbjct: 60  VISFS-----TPLSL-QTLQRHLPPKLPAPILCKGIQEVPLDFHPRFDATWR--LYRYIC 111

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---RSIHCQASSPIRTIDHF 175
              P +    R          + ++ A    VG HDF  F    + H Q     RTI   
Sbjct: 112 TNIPPSPFLSRFIAHCAYGPLKLIQEALNLFVGTHDFKFFCKRETRHTQ-----RTIHST 166

Query: 176 DV------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            V      N    +I IR  A SFL  Q+R  V +      GK +  DL+  +  + R  
Sbjct: 167 KVYQRVLYNHPCIVIAIR--APSFLRAQVRLMVSAALAHSLGKLSLEDLKAQIATRARHH 224

Query: 230 CGPLAPPEGLYFDSVEYS 247
              LAPP+GLY   V Y 
Sbjct: 225 -HLLAPPQGLYLARVAYP 241


>gi|74227733|dbj|BAE35706.1| unnamed protein product [Mus musculus]
          Length = 219

 Score = 85.9 bits (211), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 63/197 (31%), Positives = 94/197 (47%), Gaps = 26/197 (13%)

Query: 54  GVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           G+HAL   AH D+ R      + P ++ KALN +LK    I +L    V   FHAR +A 
Sbjct: 3   GLHALSNAAHLDIQRRPGQSPFSPEVVAKALNTHLK-HPAIRVLKAFRVPNDFHARHAAT 61

Query: 109 RRSYLYRIIT-----RQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
            R+Y YR+ T      Q P+  E+   W L  + LD   M+ AAQHL+G HDF+ F+S  
Sbjct: 62  SRTYQYRLATGCSWPNQLPV-FEQNVCWALQTEYLDMAAMQEAAQHLLGTHDFSAFQSAG 120

Query: 163 CQASSPIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVG 209
              ++ +RT+    V+                    +   ++SFL+ Q+R     L  VG
Sbjct: 121 SPVTNTVRTLRRVSVSPGPASPFVLPEGSRRLQFWTLEFESQSFLYRQVRRMTAVLVAVG 180

Query: 210 DGKWTSTDLEKALQAQD 226
            G    T ++  L++QD
Sbjct: 181 LGILAPTQVKVILESQD 197


>gi|171920798|ref|ZP_02931982.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 13
           str. ATCC 33698]
 gi|185179091|ref|ZP_02964822.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 5
           str. ATCC 27817]
 gi|188024013|ref|ZP_02996773.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 7
           str. ATCC 27819]
 gi|188518366|ref|ZP_03003873.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 11
           str. ATCC 33695]
 gi|188524280|ref|ZP_03004323.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 12
           str. ATCC 33696]
 gi|195867909|ref|ZP_03079907.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 9
           str. ATCC 33175]
 gi|198273508|ref|ZP_03206044.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 4
           str. ATCC 27816]
 gi|209554225|ref|YP_002284984.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 10
           str. ATCC 33699]
 gi|225550684|ref|ZP_03771633.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 2
           str. ATCC 27814]
 gi|225551354|ref|ZP_03772300.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 8
           str. ATCC 27618]
 gi|238057738|sp|B5ZC44|TRUA_UREU1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171903560|gb|EDT49849.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 13
           str. ATCC 33698]
 gi|184208984|gb|EDU06027.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 5
           str. ATCC 27817]
 gi|188019040|gb|EDU57080.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 7
           str. ATCC 27819]
 gi|188998036|gb|EDU67133.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 11
           str. ATCC 33695]
 gi|195659898|gb|EDX53278.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 12
           str. ATCC 33696]
 gi|195660386|gb|EDX53645.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 9
           str. ATCC 33175]
 gi|198250028|gb|EDY74808.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 4
           str. ATCC 27816]
 gi|209541726|gb|ACI59955.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 10
           str. ATCC 33699]
 gi|225379169|gb|EEH01534.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 8
           str. ATCC 27618]
 gi|225379838|gb|EEH02200.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 2
           str. ATCC 27814]
          Length = 241

 Score = 85.5 bits (210), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 69/251 (27%), Positives = 117/251 (46%), Gaps = 16/251 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIE---KAIFLVTGEIVVVHGAGRTDSGVHAL 58
           + Y + I Y+GS ++GW +Q    ++Q  +E   K IF +    + + G+GRTD GVHA 
Sbjct: 1   MNYKISIRYDGSLFYGWAKQPQKRTVQEHLETVFKTIFKIND--IKIIGSGRTDRGVHAY 58

Query: 59  RQ---VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            Q   V H  L  E  P ++ +AL +  +I   + IL +  V   FHA+  AI ++Y Y 
Sbjct: 59  EQVFSVNHHQLNYE--PQVIYQALCS--QIDPDVQILKVQSVHDTFHAQHDAISKTYQYI 114

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I   +  L  +    + I + ++ + +  A +  VG +DF +F +     ++  R I+  
Sbjct: 115 INDYEFDL-FKHNYEYFIHQKINDQKLLEALELFVGEYDFKSFSTSELPLTT--RKINWV 171

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +      +EI +    FL   +R  + +       K + T ++  L    +     LAP
Sbjct: 172 KITR-NTRLEIYINGNGFLKNMVRMIISACIDYVFNKISLTQIKTLLTNPKKGASVKLAP 230

Query: 236 PEGLYFDSVEY 246
           P GLY   V Y
Sbjct: 231 PCGLYLYKVYY 241


>gi|83409929|emb|CAI64350.1| tRNA pseudouridine synthase A [uncultured archaeon]
          Length = 276

 Score = 85.1 bits (209), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 120/254 (47%), Gaps = 33/254 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH--------GAGRTDS 53
           +R  + I Y G+ Y G+Q Q +  +I    EK +F    E+ ++         G+GRTD+
Sbjct: 1   MRIALKIAYIGTEYHGYQIQPDVPTI----EKELFRTLEELKIITDPKSARYIGSGRTDA 56

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV+AL QV  F+   +   + + + +N+  K+  +I + + + V   F  R  A+ R Y 
Sbjct: 57  GVNALGQVVAFNT--DNPKLAIPRVINS--KLPPSIWVWSRAEVPDDFDPRRHAVSREYK 112

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y                ++  + L+   +R A++ L G HDF  F +     S+ +RT++
Sbjct: 113 Y----------------FVCGECLNISLLRKASKLLRGTHDFANFATPDMDKST-VRTVE 155

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             D+   G LI + + A SF+   +R  V +L++VGD       L++ L   + +E    
Sbjct: 156 RIDIRVEGRLINLDIKADSFVWHMVRKIVTALRMVGDQTREVEWLKRMLHPDEFEEGLEP 215

Query: 234 APPEGLYFDSVEYS 247
           AP  GL   +V Y 
Sbjct: 216 APACGLLLKNVNYD 229


>gi|304314991|ref|YP_003850138.1| tRNA pseudouridine synthase A [Methanothermobacter marburgensis
           str. Marburg]
 gi|302588450|gb|ADL58825.1| tRNA pseudouridine synthase A [Methanothermobacter marburgensis
           str. Marburg]
          Length = 273

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 112/252 (44%), Gaps = 33/252 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG------AGRTDSG 54
           M +  + + Y G+ Y G+QRQ +  +++G +  A  L    ++   G      AGRTD G
Sbjct: 1   MRKIALKVAYIGTNYHGFQRQPDVPTVEGKLLDA--LKEAGVIRSPGDSRFQIAGRTDRG 58

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHAL     F    E    I    +N  L     I +L  + V   F  R+  + R Y Y
Sbjct: 59  VHALGNFVSFFTEEE----IHVNQINDLL--PHDIKVLAWASVMYPFKVRY-PLERHYRY 111

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                     L +G      +S+D + M  AA+H  G HDF+ F     +  +PIR I+ 
Sbjct: 112 ---------ILHRG------ESMDIDAMAKAAEHFRGTHDFSNFS--RRRDRNPIRKIND 154

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V+   N I + V   SFL   +R  V  L LV +G+ +  D+ + L   +R    P A
Sbjct: 155 VRVSEDDNSILVDVYGESFLWQMVRKMVRVLLLVSEGELSPDDVPRLLDTDERVFIDP-A 213

Query: 235 PPEGLYFDSVEY 246
           PPE L    ++Y
Sbjct: 214 PPENLILMDLKY 225


>gi|219129673|ref|XP_002185007.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403502|gb|EEC43454.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 373

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/179 (34%), Positives = 84/179 (46%), Gaps = 32/179 (17%)

Query: 100 QFHARFSAIRRSYLYRII----TRQAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRH 153
           ++ ARFSA +R+YLYRI+         +  E  R+W I  S  LD E M+ AA++L G H
Sbjct: 190 RWDARFSATQRTYLYRILHMCNDTDWAVPFEWNRSWRIRNSIPLDLEAMQRAAKYLTGTH 249

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNS------------------FG--------NLIEIR 187
           DFT+FR+  C   SP+ T++   V S                  FG         L  I 
Sbjct: 250 DFTSFRASGCSRYSPVVTLNQICVQSQPYGIAGLSGTFAKECALFGIPTTIDPLCLTTIS 309

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
               SFL+ Q+R+ VG L  VG G     D    L A+DR +    AP  GL+   V++
Sbjct: 310 FQGNSFLYRQVRNMVGYLVAVGKGWINCEDTVAVLNARDRTKAQSTAPAHGLFLVDVKH 368



 Score = 38.1 bits (87), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 44/96 (45%), Gaps = 17/96 (17%)

Query: 3   RYCMIIEYNGSGYFG--WQRQK------NGSSIQG--SIEKAIFLVTGEIVVVHG----- 47
           RY + ++Y G  + G  WQR +      NG+ ++G  S+E  +     ++V   G     
Sbjct: 9   RYAVSLQYRGPPFLGFSWQRTQEDCILPNGTDLRGRQSVEGRLREALDKLVGRDGYDKIQ 68

Query: 48  -AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAY 82
            + RTD GVHAL+   H D VR   P      L  Y
Sbjct: 69  VSSRTDRGVHALKNTCHID-VRTSFPDESGNVLTPY 103


>gi|288932131|ref|YP_003436191.1| tRNA pseudouridine synthase A [Ferroglobus placidus DSM 10642]
 gi|288894379|gb|ADC65916.1| tRNA pseudouridine synthase A [Ferroglobus placidus DSM 10642]
          Length = 256

 Score = 84.3 bits (207), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 103/240 (42%), Gaps = 29/240 (12%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y G+ + G Q Q    +++G I KA      E   +  AGRTD+GVHA+  V   DL 
Sbjct: 5   IAYIGTNFHGSQYQPELRTVEGEIRKAFEKAGIEYGKIMFAGRTDAGVHAIGNVFATDL- 63

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
            E     + K LN+ L   + +S+    +VD+ F  R  A  R Y Y I+          
Sbjct: 64  -EEFSKKVVKKLNSNL--PEDVSVWGYKVVDENFKPR-KAKWRKYCYVILD--------- 110

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
                  +  + E M+ AA+H VG+HDF  F      + S +R +   DV   GNLI   
Sbjct: 111 -------EGYNLEEMKEAAKHFVGKHDFGIFVR---GSESCVREVYESDVEKRGNLIYFS 160

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + A +F    +R    SL + G        +E+  +    +     APP GL    V Y 
Sbjct: 161 IKANAFAWNMVRRMASSLMIAG-----KEGIEEFFKILKGERAVSAAPPNGLVLVDVHYG 215


>gi|294786442|ref|ZP_06751696.1| tRNA pseudouridine synthase A [Parascardovia denticolens F0305]
 gi|315226006|ref|ZP_07867794.1| tRNA pseudouridine synthase A [Parascardovia denticolens DSM 10105]
 gi|294485275|gb|EFG32909.1| tRNA pseudouridine synthase A [Parascardovia denticolens F0305]
 gi|315120138|gb|EFT83270.1| tRNA pseudouridine synthase A [Parascardovia denticolens DSM 10105]
          Length = 338

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 87/180 (48%), Gaps = 21/180 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--------TGEIVVVHGAGRTDS 53
           +R  +   Y+G+ + GW RQ    ++QG +E  I  V         G  + +  AGRTD+
Sbjct: 1   MRLRIDCSYDGTAFHGWARQPGQRTVQGELEATIAKVLHLWKPDDDGHPITLVVAGRTDA 60

Query: 54  GVHALRQVAHFDLVREWVPVILC----------KALNAYLK--ISDTISILNLSIVDKQF 101
           GVHA  QV H DL  E + V +           +AL   L+  +   IS+ ++      F
Sbjct: 61  GVHASGQVCHLDLEDEVLSVAMGHLDPATYRPWEALAYRLRRILPADISVRSIFPSPAGF 120

Query: 102 HARFSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
            ARFSA  R Y+YR+    +      +G    +P+ LD + M  AAQ LVG HDF +F S
Sbjct: 121 DARFSASDRVYVYRVADESSAYDPRLRGFVLNLPRRLDLDLMNQAAQSLVGLHDFGSFSS 180


>gi|157137669|ref|XP_001657123.1| hypothetical protein AaeL_AAEL003683 [Aedes aegypti]
 gi|108880780|gb|EAT45005.1| conserved hypothetical protein [Aedes aegypti]
          Length = 325

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/301 (26%), Positives = 128/301 (42%), Gaps = 57/301 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAI--FLVTGEIVVVHGAGR 50
           M RY + + Y G+ + G Q+         ++  S++G +E A+  F    E  +   + R
Sbjct: 1   MNRYLINLSYIGTHFRGIQKNLLKDSGYLEDPHSVEGVLEIALKKFAPVNEFKI-KLSSR 59

Query: 51  TDSGVHALRQVAHFDLVR----EWVPVILCKALN-AYLKISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L + LN  +      I IL+  +V    HAR 
Sbjct: 60  TDAGVHALHNTVHVDLERPSGKPYKTYKLTQGLNRTFGSQGLPIRILDTKLVPMSCHARL 119

Query: 106 SAIRRSYLYRI---------------ITRQAPLALEKGRAWLIP-KSLDCENMRIAAQHL 149
            A  R+YLYR+                 R  P+  E  R + I  K  D E ++  A   
Sbjct: 120 CAKSRTYLYRLGVLRPQYCDKVESHPFNRFVPID-EYDRCYFIAHKHFDIERLKRVASTF 178

Query: 150 VGRHDFTTFRSI------HCQASSPIRTIDHFDVN---------------SFGNLIEIRV 188
            G HDF TF S+          S  +RTI+H  ++                + +  +IR+
Sbjct: 179 QGYHDFRTFMSVARGNDRQHDPSFTLRTIEHISIDRGISMASAFNREQAERYYDYWDIRI 238

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK---ECGPLAPPEGLYFDSVE 245
             RSFL+ Q+R  VG+     + + +  D+ + L    ++   +   +AP  GL+   VE
Sbjct: 239 KGRSFLYKQVRRMVGAWIGAAENRLSERDIYRMLTVPSQRSWCDQAVVAPAYGLFLCRVE 298

Query: 246 Y 246
           Y
Sbjct: 299 Y 299


>gi|312136442|ref|YP_004003779.1| tRNA pseudouridine synthase a [Methanothermus fervidus DSM 2088]
 gi|311224161|gb|ADP77017.1| tRNA pseudouridine synthase A [Methanothermus fervidus DSM 2088]
          Length = 277

 Score = 83.6 bits (205), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 115/252 (45%), Gaps = 31/252 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVH 56
           M +  + + Y G+ +FG+QRQ +  +++G + KA+     L    +     AGRTD GVH
Sbjct: 1   MKKIALKVAYIGTHFFGFQRQPDLRTVEGELIKALVETGILDESGVARFRSAGRTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL  V  F    +    ++   +N+ L   D + IL  + V   F  R++  R       
Sbjct: 61  ALGNVVTFFTDED----VIINQINSCL--PDDVYILGKASVPYGFKTRYAYRRHY----- 109

Query: 117 ITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                         +++P   L+ E M+ A++   GRHDFT F S   +  +PIR I+  
Sbjct: 110 -------------RYVLPNDGLNIELMKEASKKFEGRHDFTNF-SRRVEERNPIRYIEKV 155

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           DV   G  I + V+  SFL   +R  V  L  +G  ++    +++ L  +++    P+ P
Sbjct: 156 DVVDKGEYIWVDVIGESFLWQMVRKMVKVLFDIGKEEYEPEKIDEFLDTEEKVYIEPM-P 214

Query: 236 PEGLYFDSVEYS 247
           PE L    V Y 
Sbjct: 215 PENLILMKVMYK 226


>gi|313674169|ref|YP_004052165.1| tRNA pseudouridine synthase a [Marivirga tractuosa DSM 4126]
 gi|312940867|gb|ADR20057.1| tRNA pseudouridine synthase A [Marivirga tractuosa DSM 4126]
          Length = 261

 Score = 83.6 bits (205), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 113/255 (44%), Gaps = 16/255 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GWQ Q    ++QG +EK + FL  GE   + GAGRTD+ V A  + A
Sbjct: 9   YLVEIQYLGFRYHGWQFQHGLKTLQGMLEKTLNFLFQGEKFKILGAGRTDAMVSA--ESA 66

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--ITRQ 120
           +F+L       +   A      +   I++LN+ IVD +F+       ++Y Y    + ++
Sbjct: 67  YFELFTNQALDLESFARELNENLPADINVLNVEIVDSKFNIIQDVRLKTYQYYFASVNKK 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P A        I  SLD   M+ AA+   G +DF  F     +  S +R I    +   
Sbjct: 127 YPFAAPLMNC--IHHSLDISKMKEAARLFEGENDFRHFMVGDAENKSIVREIKESRIEEN 184

Query: 180 -------FGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                  F     + +V  + F+  Q+R  +G+L  +G  + +  DLE ALQ        
Sbjct: 185 TALRASFFPEKSYVFIVKGKGFMRYQVRMMMGALIRIGRNEISLQDLEHALQGNPPNFTK 244

Query: 232 PLAPPEGLYFDSVEY 246
             A   GL    VE+
Sbjct: 245 LNAAASGLMVKEVEF 259


>gi|308233892|ref|ZP_07664629.1| tRNA pseudouridine synthase A [Atopobium vaginae DSM 15829]
 gi|328943600|ref|ZP_08241065.1| tRNA pseudouridine synthase A [Atopobium vaginae DSM 15829]
 gi|327491569|gb|EGF23343.1| tRNA pseudouridine synthase A [Atopobium vaginae DSM 15829]
          Length = 311

 Score = 83.6 bits (205), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/257 (27%), Positives = 110/257 (42%), Gaps = 26/257 (10%)

Query: 10  YNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           Y G+ + G+  Q     S++G + +A+       + +  AGRTD+GVHA  Q   F + +
Sbjct: 50  YVGTHFCGYAAQNESVRSVEGCLTRALSTFLRRNITLTCAGRTDAGVHAHAQYVSFPITQ 109

Query: 69  EWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
             + +   K ++A   +  D ISI  L      F ARFSA  RSY YRI        L  
Sbjct: 110 SELGMSKHKIMSALSGLCPDDISIRTLYRAPLDFSARFSACERSYTYRIALGPLKPILTH 169

Query: 128 GRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----------------I 169
              W +     +  ++M  A ++L G H+F +F    C+ASS                 I
Sbjct: 170 EFVWWVKNIPHVCMDDMNAAGEYLAGEHNFKSF----CKASSAQLLEEQGLSLNRCLTSI 225

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           +    + V     ++ + +   +FLH  +R    SL  VG G      ++  L+ Q R  
Sbjct: 226 KVSRDYIVGE--QILRLDITGNAFLHNMVRIITASLLEVGRGARQPDWIQDVLRQQTRTA 283

Query: 230 CGPLAPPEGLYFDSVEY 246
               AP +GL  + V Y
Sbjct: 284 AAMTAPAQGLTLERVGY 300


>gi|301618506|ref|XP_002938660.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Xenopus
           (Silurana) tropicalis]
          Length = 331

 Score = 83.6 bits (205), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 108/224 (48%), Gaps = 31/224 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG-----AGRTDSGVHA 57
           RY +  +Y G+ Y G        S+ G ++  + +   ++  V       + RTDSGVHA
Sbjct: 7   RYLVFFQYYGTKYSGVMETPVTQSVLG-VQNYLEMAAQKLRPVGTVKFFISSRTDSGVHA 65

Query: 58  LRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +   AH D+ R      +   IL +ALN +L+  + I +L    V   FHAR  A+ R+Y
Sbjct: 66  ICNSAHVDIQRANGKPPFTEDILVQALNHHLQ-PEPIRLLKAVRVCDNFHARHKALSRTY 124

Query: 113 LYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--S 166
           +YR+       + P+  E+   W +P SL+   +  A++ L+G H+F+ FRS + +    
Sbjct: 125 VYRVAAGCSHSELPV-FEENLCWAVPGSLNVAAIHEASEMLLGTHNFSAFRSANSENVFK 183

Query: 167 SPIRTIDHFDVNSFGNLI------------EIRVVARSFLHTQI 198
           SPI+T+   D+     ++            +    ARSFL+ Q+
Sbjct: 184 SPIKTLQQADITPSSGILTHHWQYRNLQFWDFTFRARSFLYKQV 227


>gi|328783921|ref|XP_001121186.2| PREDICTED: tRNA pseudouridine synthase-like 1-like [Apis mellifera]
          Length = 313

 Score = 83.6 bits (205), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 124/289 (42%), Gaps = 47/289 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTGEIV---VVHGAG 49
           M RY +   Y G+ Y G Q+         ++  +IQG++E A   +  + +    +  + 
Sbjct: 1   MTRYLIKFSYLGTQYRGMQKNVIQTENVIRDIDTIQGALETAFTTLIPKCIEWPKITCSS 60

Query: 50  RTDSGVHALRQVAHFDLVREW----VPVILCKALNAYL-KISDTISILNLSIVDKQFHAR 104
           RTD GVH++  +AH D+  ++     P    K +N Y       I +L    V K FH R
Sbjct: 61  RTDIGVHSMCNLAHIDIKNKYDSIYYPNDTLKYVNRYFFDCHHNIRLLEFIPVKKTFHVR 120

Query: 105 FSAIRRSYLYRI-ITRQA-----PLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTT 157
                R+YLYR  +T+       P+  E  R + I   + D E ++ A Q  +G  DF T
Sbjct: 121 KFIHSRTYLYRFSVTKNKDEHRIPIT-EINRCFHIRSDTFDLERIKRATQLFIGTKDFRT 179

Query: 158 F----------------RSIHCQASSPIRTIDHFDVN-SFGNLIEIRVVARSFLHTQIRS 200
           F                 S+  +   P+   D    N  + N+I     +R FL+ Q+R 
Sbjct: 180 FSAKIVGNKPINYVRNLNSLTIEKGYPLMPNDPLSQNFEYWNII---CSSRGFLYKQVRR 236

Query: 201 FVGSLKLVGDGKWTSTDLEKALQ---AQDRKECGPLAPPEGLYFDSVEY 246
            VG+L  +G GK T  D+   LQ     +       AP  GLY  +VEY
Sbjct: 237 IVGALFALGSGKITEKDITVMLQVPGCHNYLSQIETAPAYGLYLMNVEY 285


>gi|32266100|ref|NP_860132.1| tRNA pseudouridine synthase A [Helicobacter hepaticus ATCC 51449]
 gi|42559757|sp|Q7U328|TRUA_HELHP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|32262149|gb|AAP77198.1| tRNA pseudouridine synthase [Helicobacter hepaticus ATCC 51449]
          Length = 248

 Score = 83.2 bits (204), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 77/255 (30%), Positives = 119/255 (46%), Gaps = 17/255 (6%)

Query: 1   MIRYCMIIEYNGSGY--FGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y  +I Y+GS +  F  Q+ K   S+ G++++  F   G    + GAGRTD GVHA 
Sbjct: 1   MPTYKAVIAYDGSVFSGFALQKDKRLKSVLGTLKEG-FARVGIKSDIIGAGRTDKGVHAT 59

Query: 59  RQV-----AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            QV     AHF   +      L   LNA  K+   I + +L IVD  FH RF A+ RSY 
Sbjct: 60  GQVICFQSAHFLDSQVQAIESLRFLLNA--KLYPHIMVRSLHIVDDTFHPRFDALWRSYR 117

Query: 114 YRI-ITRQAPLALEKGRAWLIPKSLDCENM-RIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           + +  T+ +P A      ++  + +  E + + A Q   G+H+F  F+       + IRT
Sbjct: 118 FLLSPTQPSPFAAP----YVSYEKIGDETLFKNALQAFQGQHNFVFFKKNGSYTKNCIRT 173

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           I      ++  L  + V    FL  Q+R  VG+       + +   L++ +  Q +    
Sbjct: 174 IFAIKHYTYKGLDIVYVRGNGFLRAQVRLMVGAALAYSRAELSFHSLQEQINGQKQHYTY 233

Query: 232 PLAPPEGLYFDSVEY 246
           P++ P GLY   V Y
Sbjct: 234 PIS-PNGLYLCEVGY 247


>gi|124486487|ref|YP_001031103.1| tRNA pseudouridine synthase ACD [Methanocorpusculum labreanum Z]
 gi|166228737|sp|A2SU30|TRUA_METLZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|124364028|gb|ABN07836.1| tRNA pseudouridine synthase A [Methanocorpusculum labreanum Z]
          Length = 281

 Score = 83.2 bits (204), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 105/233 (45%), Gaps = 27/233 (11%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           + GS Y   +R   G  + G IE  +F    E      AGRTD GV A RQ+  F +  E
Sbjct: 14  FAGSQYQPHKRTVEGEFVAGGIELGLFSDAKE-AHFRTAGRTDKGVSARRQL--FSITTE 70

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
             P +  +ALN +L   D I  +  + VD++F+ R++A  RSY Y               
Sbjct: 71  -KPELAIEALNFHL--PDDIWCIGAAEVDEEFYPRYAARERSYRY--------------- 112

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI-RV 188
               P   D   M+ AA  L+G H+F+ F  +      P+RT+   +V    +   +  V
Sbjct: 113 --YFPYPADVSRMQDAASRLIGTHNFSGFAKMEA-GRDPVRTVTRAEVFEGKDGCPVFEV 169

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            A+SFL   +R   G+L+ +G G     D+ + L +       P AP EGL F
Sbjct: 170 AAKSFLWNMVRGMAGALQTIGLG-LCEPDVIEELLSSPTARVHP-APAEGLVF 220


>gi|195012378|ref|XP_001983613.1| GH25313, isoform A [Drosophila grimshawi]
 gi|193897095|gb|EDV95961.1| GH25313, isoform A [Drosophila grimshawi]
          Length = 496

 Score = 83.2 bits (204), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 79/268 (29%), Positives = 114/268 (42%), Gaps = 57/268 (21%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKA--IFLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+  N         +SIQG +E A  +F    EI  V  + R
Sbjct: 1   MHRYLLNISYIGTNFRGIQKTINKLEEARLDTNSIQGCLELALRVFRPKNEIQTV-LSSR 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYL-KISDTISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L K    I IL+   V   FH R+
Sbjct: 60  TDAGVHALHSTVHVDLERSDGKPYDTSTLTGVLNRTLDKHKLPIRILSSQRVVDTFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALEKGRA-------------------WLIPKSLDCENMRIAA 146
            A  R+YLYR+   ++     KG +                   +L   + D E +  AA
Sbjct: 120 HATGRTYLYRVAVAKSVSEASKGSSLKNKGYESFVPVEEIDRCYFLHCDNFDVERLHGAA 179

Query: 147 QHLVGRHDFTTFRSIHCQASSP-------IRTIDHFDVNSFGNLI--------------- 184
           +  +G HDF TF S+  Q S         +R ID  ++     L                
Sbjct: 180 RMFLGLHDFRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGQTLALGPNAKLATQTYDYW 239

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +I + A+SFL+ Q+R  VG+L  + + +
Sbjct: 240 DIEIKAKSFLYKQVRRIVGTLLALANSR 267


>gi|217034467|ref|ZP_03439879.1| hypothetical protein HP9810_890g12 [Helicobacter pylori 98-10]
 gi|216943069|gb|EEC22546.1| hypothetical protein HP9810_890g12 [Helicobacter pylori 98-10]
          Length = 242

 Score = 82.8 bits (203), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 109/246 (44%), Gaps = 18/246 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N  S+Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLSVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFCAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W        L  YL       I+   + +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAA----KLFYYLAPKLAPHIVLKKLEEKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGAMTNPKRAIFNAFAYKTFIAGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EGLY 240
           +  +++  +FL + +R  + +      GK T  +    +QAQ       +  P    GLY
Sbjct: 181 VVFKIIGDAFLRSSVRLIIQACVQYSLGKITLAE----IQAQIHNIKAAIRTPIMANGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LHRVYY 242


>gi|261839825|gb|ACX99590.1| pseudo uridylate synthase I [Helicobacter pylori 52]
          Length = 242

 Score = 82.8 bits (203), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 110/248 (44%), Gaps = 22/248 (8%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYHLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE-- 185
             A     SLD  N   A +   G+HDF+ F+      ++P RTI  F+  ++   I   
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRTI--FNAFAYKTFIAGH 178

Query: 186 ----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EG 238
                +++  +FL + +R  V +       K T  +    +QAQ       +  P    G
Sbjct: 179 ECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAE----IQAQIHNAKATIRTPIMANG 234

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 235 LYLHRVYY 242


>gi|58699252|ref|ZP_00374050.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of
          Drosophila ananassae]
 gi|58534228|gb|EAL58429.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of
          Drosophila ananassae]
          Length = 100

 Score = 82.4 bits (202), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/84 (48%), Positives = 59/84 (70%), Gaps = 1/84 (1%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
          +RY + +EYNGS + GWQ+Q++  +SIQ  IE AIF  +GE + ++  GRTD+GVHAL Q
Sbjct: 1  MRYKITVEYNGSSFSGWQKQQHSANSIQEKIENAIFNFSGEKIALYCGGRTDAGVHALGQ 60

Query: 61 VAHFDLVREWVPVILCKALNAYLK 84
          VAHFD+ +E     +  A+N +LK
Sbjct: 61 VAHFDMEKECELYRIRNAINYHLK 84


>gi|255994429|ref|ZP_05427564.1| tRNA pseudouridine synthase A [Eubacterium saphenum ATCC 49989]
 gi|255993142|gb|EEU03231.1| tRNA pseudouridine synthase A [Eubacterium saphenum ATCC 49989]
          Length = 304

 Score = 82.4 bits (202), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 118/281 (41%), Gaps = 48/281 (17%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+GS + G+Q+    +S+QG IE A+  + G+ V +    RTD+GVHA  Q+  F   
Sbjct: 8   ISYDGSAFKGFQKNHGITSVQGEIENALKPIVGD-VEISAVSRTDAGVHAFSQIFSFSYD 66

Query: 68  REWVPVILCKAL-NAY-LKISD-----TISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                  L + L NA+  + SD      I+I   + + +  + R+    + Y+Y      
Sbjct: 67  TNIPHGRLAEVLTNAFSTRKSDYRKQAAIAIEGWAELGRAMNPRYFVKGKRYIYVFKKNA 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-------- 172
                 +    L    L+   M+  A+  VG HDF+ FR+      SPIR +        
Sbjct: 127 GSDIFARNYMLLTNGDLNVGRMKEEAKAFVGEHDFSAFRT--QDGRSPIRKVFSANVISC 184

Query: 173 ----DHFD---VNSFGNLIEI----------------------RVVARSFLHTQIRSFVG 203
               D F     + +G + +I                       V    FL+  +R   G
Sbjct: 185 EELNDGFHEPLTDEYGRISDIIALKKRLLPRLNLSNLQGYVFFAVTGEGFLYNMVRIMAG 244

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +L  VG  K+     +  L++++R+  G  APP+GLY D V
Sbjct: 245 TLLEVGKNKFDKPVCD-VLKSKNRQMAGITAPPQGLYLDEV 284


>gi|94502328|ref|ZP_01308801.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri str. Hc
           (Homalodisca coagulata)]
 gi|94451115|gb|EAT14067.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri str. Hc
           (Homalodisca coagulata)]
          Length = 192

 Score = 82.4 bits (202), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 55/187 (29%), Positives = 90/187 (48%), Gaps = 6/187 (3%)

Query: 62  AHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHF+   + + +        N++L ++  I I+N+  V K+ HARF+AI R Y YRI   
Sbjct: 3   AHFEFYEKKILLYRNFLFKFNSFLPLN--IKIINIFTVKKKIHARFTAISRVYEYRISLG 60

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P +L+    WL  K +    +   A+ L    D+++F    C   + I  I +   + 
Sbjct: 61  KNPFSLDISWQWLSKKKIKLNPLNKGAKILKKYKDYSSFCKKKCNYKTYICNIFNAKWHI 120

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N++   + A  +L   +RS VG+L  +G GK T  D    L A+DR      AP +GL
Sbjct: 121 KNNILYFNIEANRYLRNMVRSIVGTLIELGIGKITIKDFINILYAKDRNIIS--APAKGL 178

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 179 FLTKINY 185


>gi|284161452|ref|YP_003400075.1| tRNA pseudouridine synthase A [Archaeoglobus profundus DSM 5631]
 gi|284011449|gb|ADB57402.1| tRNA pseudouridine synthase A [Archaeoglobus profundus DSM 5631]
          Length = 262

 Score = 82.4 bits (202), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 112/249 (44%), Gaps = 27/249 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALR 59
           +R    + Y G+ + G+Q Q N  ++ G + KA     +  +      AGRTD+GVHA  
Sbjct: 1   MRIAYKLAYVGTNFHGFQYQPNVRTVAGELFKAFRALGIDPKKAKFRCAGRTDAGVHAFG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV   ++ +   P    +  NA+L   + ++    + VD++F+ R  A  R+Y+Y     
Sbjct: 61  QVIAINVEKPIFP----RMFNAHL--PEDVTFWAWTEVDEKFNPR-HAKSRTYVY----- 108

Query: 120 QAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                       ++P +  D   MR A++ L+G HDF+ F     +    IRTI + ++ 
Sbjct: 109 ------------VMPAEGYDISAMRKASKLLLGTHDFSNFTKKFGERRRCIRTIYNVELR 156

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + + +V  +F    +R  V +L+ VG G  +    E  L  +  +E    AP  G
Sbjct: 157 LDDGFVVLEIVGNAFTWNMVRCIVSALREVGSGHRSVEWFEDMLNPERHRERIEPAPAYG 216

Query: 239 LYFDSVEYS 247
           L    VEY 
Sbjct: 217 LILKDVEYE 225


>gi|330507400|ref|YP_004383828.1| tRNA pseudouridine synthase A [Methanosaeta concilii GP-6]
 gi|328928208|gb|AEB68010.1| tRNA pseudouridine synthase A [Methanosaeta concilii GP-6]
          Length = 271

 Score = 82.4 bits (202), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 107/250 (42%), Gaps = 30/250 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----AGRTDSGVHA 57
           ++  + + Y G  Y+G+Q+Q +  ++   + +A+     +I V+HG    AGRTD GV A
Sbjct: 1   MKVALKLAYLGDNYYGFQKQPDRVTVDSQVRRAL----AQIGVIHGDFCYAGRTDRGVSA 56

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  F +  + + +   + +N   ++   I     SI    F AR++A+ R Y Y   
Sbjct: 57  LGQVIDFWIDEDKIDLTRPRCVNG--RLPRDIWTWAWSIAPVGFSARWNALWREYQYL-- 112

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                         L    LD + M  AA  L+G HDF  F S        ++ ++  ++
Sbjct: 113 --------------LWHPGLDRDLMEEAADMLLGEHDFRNFSSAKV---GTVKRVEKLEI 155

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                L    + A  FL   +R  VG+ + VG G+       K L   +     P AP E
Sbjct: 156 RERDGLFIFDIRADGFLWNMVRKIVGATEKVGSGQ-KDMRWFKDLLRPELNHGAPTAPAE 214

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 215 GLILMEVGYD 224


>gi|183601972|ref|ZP_02963341.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|241190461|ref|YP_002967855.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|241195867|ref|YP_002969422.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|183218857|gb|EDT89499.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|240248853|gb|ACS45793.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|240250421|gb|ACS47360.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|295793448|gb|ADG32983.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis V9]
          Length = 258

 Score = 82.0 bits (201), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 103/235 (43%), Gaps = 41/235 (17%)

Query: 48  AGRTDSGVHALRQVAHFDLVREW-------VPVILCKALNAYLK--ISDTISILNLSIVD 98
           AGRTD+GVHA  QV H D+  +        + +   +AL   L   + D I+I  +S+  
Sbjct: 12  AGRTDAGVHATHQVCHVDVPDQTLGQCVGHMNLTPVQALQTRLSRMMPDDIAIHGISVAP 71

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
             F ARFSA+ R+Y+YRI   + P     K  AW   + LD   M  AA   +G HDF +
Sbjct: 72  AGFDARFSALERTYVYRIADARVPWDPRLKDFAWRTDRELDIAQMNAAAALTLGLHDFGS 131

Query: 158 FRSIHCQASSPIRTID---------------------HFDVNSFGNLIEIRVVARSFLHT 196
           F +I     + IR +                      H      G L+   +VA +F   
Sbjct: 132 F-AIANPGGTTIREVKTAYWQRVPTRPLLGPGMGERYHTPAVESG-LLCFTIVADAFARN 189

Query: 197 QIRSFVGSLKLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +RS VG+   VG GK    W +  +   L+       GP+A P+GL  + + Y 
Sbjct: 190 MVRSLVGACVQVGMGKRDVDWFAGKMRVPLR---EGSTGPIA-PQGLTLEHIAYP 240


>gi|170050837|ref|XP_001861491.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167872293|gb|EDS35676.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 476

 Score = 81.6 bits (200), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 75/267 (28%), Positives = 117/267 (43%), Gaps = 47/267 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M RY + + Y G+ +    R ++  S++G++E A+  F    E  +   + RTD+GVHAL
Sbjct: 1   MNRYLINLSYVGTHFRDNGRLEDPQSVEGALEIALKKFRPVNEFKI-KLSSRTDAGVHAL 59

Query: 59  RQVAHFDLVR----EWVPVILCKALN-AYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
               H DL R     + P  L + LN  +      I +L    V   FHAR  A  R+YL
Sbjct: 60  NNAVHVDLERYNGKPYEPDKLTQGLNRTFGSQKIPIRVLRTRHVPLTFHARLCAKSRTYL 119

Query: 114 YRI----------------ITRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFT 156
           YR+                 TR  P+  E  R + I  K+ D + ++ AA    G HDF 
Sbjct: 120 YRVGVLRPEFCDDPEQIHPFTRFIPID-EHDRCYFIANKNFDPDRLKRAAALCEGYHDFR 178

Query: 157 TFRSI------HCQASSPIRTIDHFDVNSFGNLI---------------EIRVVARSFLH 195
           TF +I          +  +R I+   V    ++                +IR+ ARSFL+
Sbjct: 179 TFMAIARGNLWQQMPTYTLRRIERITVERGSSMASAFSRKLADRYYEYWDIRIKARSFLY 238

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKAL 222
            Q+R  VG+     + + T  D+++ L
Sbjct: 239 NQVRRMVGAWIAAAEARITERDVQQML 265


>gi|110004220|emb|CAK98558.1| hypothetical trna pseudouridine synthase a protein [Spiroplasma
           citri]
          Length = 246

 Score = 81.6 bits (200), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 114/253 (45%), Gaps = 14/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+   + IEY+G  Y GW +QKN  +IQG +EKA F +  + +   GA +TD+GVHA  Q
Sbjct: 1   MLYLLLSIEYDGYDYSGWVKQKNAWTIQGELEKAFFGICHQKIWTLGASKTDAGVHASDQ 60

Query: 61  VAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                L  +    V   K ++  L     I+I    +V + F  R + ++  Y+Y I  +
Sbjct: 61  KVLVKLPFQSQHLVFFIKTVSKTL--PPNINIKGYQLVSENFSVRTAKVKE-YVYTINDQ 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVN 178
           +  L         +   L+   +   +Q  VG HDF  F  +   +     RTI+   V 
Sbjct: 118 EYDL-FNHRYELKVNTPLNVRKLHQISQIFVGTHDFGYFAGVKPTENIVTQRTINKIWVK 176

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL----QAQDRKECGPL 233
            +    IEI  + +SF+  QIR    ++     GK + ++L+  L    Q    K C   
Sbjct: 177 RNKAKKIEIHFMGKSFIRYQIRMLTQNILACYAGKVSLSELQAQLKHPPQGATTKYC--- 233

Query: 234 APPEGLYFDSVEY 246
           A P GL    ++Y
Sbjct: 234 AKPYGLCLKKIKY 246


>gi|21227597|ref|NP_633519.1| tRNA pseudouridine synthase A [Methanosarcina mazei Go1]
 gi|34395892|sp|Q8PWT1|TRUA_METMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|20905982|gb|AAM31191.1| tRNA pseudouridine synthase A [Methanosarcina mazei Go1]
          Length = 269

 Score = 81.6 bits (200), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 115/255 (45%), Gaps = 37/255 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDS 53
           +R  + + Y G+ + G Q Q    S++ ++EK +F     + ++          AGRTD+
Sbjct: 1   MRVALKLAYIGTEFHGSQIQ---PSVE-TVEKELFKALRNLRIIESPKSANYICAGRTDA 56

Query: 54  GVHALRQVAHFDLVRE--WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           GVHAL QV  FD  R    +P I+   L        TI +   + V   F AR  A+ R 
Sbjct: 57  GVHALGQVIAFDTDRPNLAIPRIINSGL------PPTIWVWAHAEVPYDFDARRHAVSRH 110

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y Y I           G  +      D   MR A++ L+G HDF  F   + + S+ +RT
Sbjct: 111 YRYVI----------SGEGY------DISKMREASKLLLGTHDFENFSRSNGEKST-VRT 153

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           ++  +V   G++ +I VV  SFL   +R  V +L ++G G   +  L + L     +E  
Sbjct: 154 LERINVRVDGDITKIDVVGNSFLWNMVRKIVTALSMIGKGVRDNDWLIQMLNPDIYEEGI 213

Query: 232 PLAPPEGLYFDSVEY 246
             AP  GL    V Y
Sbjct: 214 EPAPAYGLTLMGVNY 228


>gi|302869940|ref|YP_003838577.1| tRNA-pseudouridine synthase I [Micromonospora aurantiaca ATCC
           27029]
 gi|315501401|ref|YP_004080288.1| tRNA-pseudouridine synthase i [Micromonospora sp. L5]
 gi|302572799|gb|ADL49001.1| tRNA-pseudouridine synthase I [Micromonospora aurantiaca ATCC
           27029]
 gi|315408020|gb|ADU06137.1| tRNA-pseudouridine synthase I [Micromonospora sp. L5]
          Length = 277

 Score = 81.6 bits (200), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 112/255 (43%), Gaps = 14/255 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
            R  + + Y+G+ + GW  Q    ++ G + + + LV   G    +  AGRTD+GVHA  
Sbjct: 5   TRLRLDVSYDGTDFSGWAPQPARRTVAGVLMQTLDLVLGAGTATGLTVAGRTDAGVHATG 64

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL    W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHLDLPTPVWREHEGRLLRRLARLLPPDVRVRAMTEVPADFDARFSATFRRYEYRVT- 123

Query: 119 RQAPLALEKGR-----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
             AP   E  R     AW  PK LD   +  AA  LVG HDF  +      A++ +R + 
Sbjct: 124 -DAPWGAEPLRRGDTLAW--PKPLDLAALNAAAAGLVGEHDFAAYCRRKENATT-LREVT 179

Query: 174 HFDVNSFGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             D     + I +  V A +F    +RS VG++ + GDG+         L  ++R     
Sbjct: 180 RLDWRRDPDGILVATVQADAFCQNMVRSLVGAMLVAGDGRRPVQWPAGLLTRRERSSEVT 239

Query: 233 LAPPEGLYFDSVEYS 247
           +AP  GL   +V Y 
Sbjct: 240 VAPAHGLALVAVGYP 254


>gi|224010986|ref|XP_002294450.1| hypothetical protein THAPSDRAFT_264420 [Thalassiosira pseudonana
           CCMP1335]
 gi|220969945|gb|EED88284.1| hypothetical protein THAPSDRAFT_264420 [Thalassiosira pseudonana
           CCMP1335]
          Length = 264

 Score = 81.6 bits (200), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 77/268 (28%), Positives = 118/268 (44%), Gaps = 34/268 (12%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ + GWQ Q   S++QG IE+ +       + V GAGRTD+GVHA  Q  HFDL 
Sbjct: 2   VAYHGTPFNGWQLQPGRSTVQGEIEEVLTRRFHRRIPVVGAGRTDAGVHARGQAIHFDLF 61

Query: 68  REWVPV-------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII--- 117
            + +P        IL  ++N  + +   +  L L+     +HA   A  + Y YR+    
Sbjct: 62  HDEIPFKPPTPPEILQHSMNRMMPLDIRMFHLQLAPYTP-WHAIQRAQSKWYSYRLTLGP 120

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS---------SP 168
           T   P+     R   +   LD E +    Q  VG HDF  F     Q +         + 
Sbjct: 121 TLWNPME-RFTRTHFV--HLDMERLESILQLYVGTHDFGAFGGQLEQNAKKRNDGKRINT 177

Query: 169 IRTIDHFD---------VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           +RT+   +         +   GN   I  + +  L+  +R+ VG+   V  G+     L 
Sbjct: 178 VRTVFRVELIQQEQLGFIGEEGNY-RIDFLLKGALYKMVRNMVGTAMEVWLGRMKEEQLA 236

Query: 220 KALQAQDRKE-CGPLAPPEGLYFDSVEY 246
           + L+  DRK+     APPEGL  + V Y
Sbjct: 237 ELLKIPDRKDNPSKPAPPEGLTLECVYY 264


>gi|322378343|ref|ZP_08052800.1| tRNA pseudouridine synthase A [Helicobacter suis HS1]
 gi|321149229|gb|EFX43672.1| tRNA pseudouridine synthase A [Helicobacter suis HS1]
          Length = 244

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 77/255 (30%), Positives = 115/255 (45%), Gaps = 20/255 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R+ +++ Y+GS + G+ +Q    +++G + KA+    +  +I+    AGRTD GVHA 
Sbjct: 1   MRRFKLVLAYDGSAFSGFAKQAGLYTVEGRLIKALESLQIPSKIL---AAGRTDRGVHAT 57

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F+    W    L K L    K+   I+  +L  V   FH RF A RR Y Y +  
Sbjct: 58  HQVIAFNTCDIWSSSKLLKHLAP--KLGYFIACKSLEEVPLSFHPRFEATRRRYRYFLSL 115

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHL---VGRHDFTTFRSIHCQASSPIRTIDHF 175
            +    L +   +       C +M I  Q L    G HDF  F        S IR+I   
Sbjct: 116 AKPSPFLSRFVGY-----HPCGDMGILKQALELFKGEHDFKFFSKSGSDPKSTIRSIYKA 170

Query: 176 DVNSFG--NLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
               +   NL  + +V  A SFL +Q+R  +G+       + +  DL K +  Q R    
Sbjct: 171 FCYPYMLYNLPCLVLVFEANSFLRSQVRLMLGAALACSLKQISLEDLYKQITLQRRFLMR 230

Query: 232 PLAPPEGLYFDSVEY 246
            ++ P GLY  SV Y
Sbjct: 231 AVS-PSGLYLSSVFY 244


>gi|189241446|ref|XP_973048.2| PREDICTED: similar to CG34140 CG34140-PA [Tribolium castaneum]
          Length = 258

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/182 (33%), Positives = 86/182 (47%), Gaps = 26/182 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIF-LVTGEIVVVHGAGRTDS 53
           RY +   Y G+ + G QRQ  G        S++QG +E A+  L      VV+ + RTDS
Sbjct: 5   RYLLHFSYIGTPFMGAQRQVTGRMPRPDDPSTVQGQLEMALKRLNPTNDPVVYLSSRTDS 64

Query: 54  GVHALRQVAHFDLVR----EWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAI 108
           GVHAL    H DL R    E+ P  +   LN Y   ++  I ++    V   FH R +AI
Sbjct: 65  GVHALNSTCHVDLYRSNELEYEPKTITICLNRYFDKNEVPIRVIKTYWVPPDFHCRHTAI 124

Query: 109 RRSYLYRI------ITRQA------PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            R+YLYRI      +T  A      P+   +   +    S + + M+ AA+   G HDF 
Sbjct: 125 SRTYLYRIAIAKTGVTEHATILNLLPIEEYQRCLFFYCDSFNIDEMKEAAKVFEGLHDFR 184

Query: 157 TF 158
           TF
Sbjct: 185 TF 186


>gi|270692650|ref|ZP_06222951.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
 gi|270316015|gb|EFA28055.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
          Length = 115

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/106 (36%), Positives = 61/106 (57%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
           M+ A Q L+G HDF++FR+  CQ+ +P R + H +V+  G  I + + A +F+H  +R+ 
Sbjct: 1   MQQAGQCLLGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIGQYIIVDIQANAFVHHMVRNI 60

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           VGSL  VG G      ++  L  ++R+   P A P+GLY   V Y 
Sbjct: 61  VGSLIEVGAGNKPIEWMQWLLDQKNRQLAAPTAKPDGLYLVDVIYP 106


>gi|254756838|ref|ZP_05208866.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Australia
           94]
          Length = 145

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 69/144 (47%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           R+   R+ Y YR++  +      +   +  P  L+  ++R A  + +G HDFT+F S   
Sbjct: 1   RYGVERKEYRYRVLVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKT 60

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                +RTI   ++    + +  R V   FL+  +R  VG+L  VG GK     + + L 
Sbjct: 61  DKKDKVRTIYEIELIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILA 120

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
            Q+R+  G +AP  GLY   V Y+
Sbjct: 121 KQNRQFAGKMAPGHGLYLWQVNYN 144


>gi|270605639|ref|ZP_06221621.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
 gi|270318160|gb|EFA29385.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
          Length = 131

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/106 (36%), Positives = 61/106 (57%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
           M+ A Q L+G HDF++FR+  CQ+ +P R + H +V+  G  I + + A +F+H  +R+ 
Sbjct: 1   MQQAGQCLLGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIGQYIIVDIQANAFVHHMVRNI 60

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           VGSL  VG G      ++  L  ++R+   P A P+GLY   V Y 
Sbjct: 61  VGSLIEVGAGNKPIEWMQWLLDQKNRQLAAPTAKPDGLYLVDVIYP 106


>gi|84489200|ref|YP_447432.1| tRNA pseudouridine synthase A [Methanosphaera stadtmanae DSM 3091]
 gi|121725515|sp|Q2NHB4|TRUA_METST RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|84372519|gb|ABC56789.1| TruA [Methanosphaera stadtmanae DSM 3091]
          Length = 274

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/257 (28%), Positives = 111/257 (43%), Gaps = 34/257 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTD 52
           M R  + I Y GS + G+QRQ N  +++G     +  V  E  ++          AGRTD
Sbjct: 1   MRRVALKIAYIGSNFHGYQRQPNYRTVEGE----LLRVFKETNIIEDTWTAHYSVAGRTD 56

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVH+   V  F    +    I    LN  L   D I I+  + V   F  RF  + R+Y
Sbjct: 57  KGVHSTGNVISFITDED----IHINQLNGLL--PDDIKIIGEARVPYGFKVRF-PLTRTY 109

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y  I   +P            K+LD   M +A +  +G+H+F  F        +P R I
Sbjct: 110 TY--IQPISPFE---------KKNLDITKMHVAMESFIGKHNFRNFSK--RNEKNPNRKI 156

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              ++    +++   +V  SFL   +R  V S+  VG GK    D+ + L+ ++ ++   
Sbjct: 157 IDVNLEVDEDVLIFTIVGESFLWNMVRKMVTSIMEVGYGKLDINDINELLKPKELRQFIR 216

Query: 233 L--APPEGLYFDSVEYS 247
           L  AP  GL    +EY 
Sbjct: 217 LQPAPANGLILSDMEYK 233


>gi|42559721|sp|P60353|TRUA_SPIKU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|34849384|gb|AAP58883.1| tRNA pseudouridine synthase [Spiroplasma kunkelii CR2-3x]
          Length = 260

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/256 (27%), Positives = 115/256 (44%), Gaps = 20/256 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+   + IEY+G  Y GW +QKN  +IQG +EKA F +  + +   GA +TD+GVHA  Q
Sbjct: 1   MLYLLLSIEYDGYDYSGWVKQKNARTIQGELEKAFFGICHQKIWTLGASKTDAGVHACDQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR----RSYLYRI 116
                L  +  P    + L  ++K        N++I   QF A   ++R    + Y+Y I
Sbjct: 61  KVLVKLTFQ--P----RHLAFFIKTVSQTLPPNINIKGYQFVAENFSVRTVKVKEYVYTI 114

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHF 175
             ++  L         +   L+ + +   +Q  VG HDF  F  +   +  + + TI+  
Sbjct: 115 NDQEYDL-FNHRYELKVNAPLNVKKLHQISQIFVGTHDFAYFAGVKPTEDIATVHTINKI 173

Query: 176 DVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR----KEC 230
            V  +    IEI    + F+  QIR    ++     GK + T+L+  L    +    K C
Sbjct: 174 WVKRNKAKKIEIHFRGKIFIRYQIRMLTQNILACYAGKVSLTELQAQLNCPPKGTTTKYC 233

Query: 231 GPLAPPEGLYFDSVEY 246
              A P GL    ++Y
Sbjct: 234 ---AKPYGLCLKKIKY 246


>gi|317180826|dbj|BAJ58612.1| tRNA pseudouridine synthase A [Helicobacter pylori F32]
          Length = 242

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 110/246 (44%), Gaps = 18/246 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFCTP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P RTI + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRTIFNAFAYKTFIAGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EGLY 240
           +  +V+  +FL + +R  + +       K T  +    +QAQ       +  P    GLY
Sbjct: 181 VVFKVIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNIKATIRTPIMANGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LHRVYY 242


>gi|332673893|gb|AEE70710.1| tRNA pseudouridine synthase A [Helicobacter pylori 83]
          Length = 242

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 109/248 (43%), Gaps = 22/248 (8%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHADNQVLSFYAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYHLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE-- 185
             A     SLD  N   A +   G+HDF+ F+      ++P R I  FD  ++   I   
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRAI--FDAFAYKTFIAGH 178

Query: 186 ----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EG 238
                +++  +FL + +R  V +       K T  +    +QAQ       +  P    G
Sbjct: 179 ECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAE----IQAQIHNIKAAIRTPIMANG 234

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 235 LYLHRVYY 242


>gi|217032587|ref|ZP_03438076.1| hypothetical protein HPB128_159g13 [Helicobacter pylori B128]
 gi|298735906|ref|YP_003728431.1| tRNA pseudouridine synthase A [Helicobacter pylori B8]
 gi|216945723|gb|EEC24348.1| hypothetical protein HPB128_159g13 [Helicobacter pylori B128]
 gi|298355095|emb|CBI65967.1| tRNA pseudouridine synthase A [Helicobacter pylori B8]
          Length = 242

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 108/247 (43%), Gaps = 20/247 (8%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+ ++  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNMLGIKSVVV-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYCLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG------ 181
             A     SLD  N   A +   G+HDF+ F+      ++P R I     N+F       
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSLFKKEGGATTNPNRII----FNAFAYKTSIM 176

Query: 182 --NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +  +++  +FL + +R  + +       K T  ++E  +         P+    GL
Sbjct: 177 GHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNLKATIRTPIM-ANGL 235

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 236 YLHRVYY 242


>gi|15644989|ref|NP_207159.1| tRNA pseudouridine synthase A [Helicobacter pylori 26695]
 gi|2499078|sp|P56144|TRUA_HELPY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2313463|gb|AAD07429.1| pseudouridylate synthase I (hisT) [Helicobacter pylori 26695]
          Length = 242

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 110/246 (44%), Gaps = 18/246 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VV+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIEDALNALGIKSVVI-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P RTI + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRTIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EGLY 240
           +  +++  +FL + +R  + +       K T  +    +QAQ       +  P    GLY
Sbjct: 181 VVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNLKATIRTPIMANGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LHRVYY 242


>gi|319955610|ref|YP_004166877.1| tRNA pseudouridine synthase a [Cellulophaga algicola DSM 14237]
 gi|319424270|gb|ADV51379.1| tRNA pseudouridine synthase A [Cellulophaga algicola DSM 14237]
          Length = 264

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/261 (24%), Positives = 122/261 (46%), Gaps = 26/261 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + +++ G  Y GWQ+Q    +I+  + K + F++  +   + GAGRTD+ V AL   A
Sbjct: 8   YLVKLQFLGFRYSGWQKQPGQKTIEAMLVKTLKFILPDQKFKILGAGRTDAKVSALD--A 65

Query: 63  HFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            F+L  +  P+ + +   A     +   I IL+++ VD+ F+   ++  + Y+Y      
Sbjct: 66  AFELYLDDTPIEVLEDFLALFNKNLPPDIRILSMTEVDESFNIIQNSKEKEYIYLFSFG- 124

Query: 121 APLALEKGRAWLIP------KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                EK   +  P       +LD + M+  A++  G H+F ++ +   + +  IRT++ 
Sbjct: 125 -----EKSHPFCAPYLVTFLDNLDLDKMKTVAKYFEGTHNFKSYTARIQENTKVIRTVNS 179

Query: 175 --------FDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                    + N F        V    F+  QIR  +G L  VG G+ +  ++  +L+ +
Sbjct: 180 CGIIENKILEANFFPEKSYAFHVKGEGFMRYQIRMMMGVLVQVGKGELSEEEVLNSLKEE 239

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
           +  +   +AP  GL  + V++
Sbjct: 240 NNMQLPFVAPGSGLILNQVDF 260


>gi|317182345|dbj|BAJ60129.1| tRNA pseudouridine synthase A [Helicobacter pylori F57]
          Length = 242

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 115/255 (45%), Gaps = 36/255 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFYAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y ++T+        
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRY-LLTKNLK----- 116

Query: 128 GRAWLIP-------KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              +L+P        SLD  N   A +   G+HDF+ F+      ++P RTI  F+  ++
Sbjct: 117 -TPFLVPYIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGAITNPKRTI--FNAFAY 171

Query: 181 GNLIE------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              I        +++  +FL + +R  V +       K T  +    +QAQ       + 
Sbjct: 172 KTFITGHECVVFKIIGDAFLRSSVRLIVQACVKYSLEKITLAE----IQAQIHNIKATIR 227

Query: 235 PP---EGLYFDSVEY 246
            P    GLY   V Y
Sbjct: 228 TPIMANGLYLHRVYY 242


>gi|18977290|ref|NP_578647.1| tRNA pseudouridine synthase A [Pyrococcus furiosus DSM 3638]
 gi|24638312|sp|Q8U2C1|TRUA_PYRFU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|18892961|gb|AAL81042.1| putative tRNA pseudouridine synthase a [Pyrococcus furiosus DSM
           3638]
          Length = 266

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 113/249 (45%), Gaps = 28/249 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + G+QRQ N  +I+G I +A+     E      A RTD GV A   V
Sbjct: 1   MRVALKIAYDGTKFHGFQRQPNVRTIEGEILRALKDAGIEFENFKSASRTDRGVSARGNV 60

Query: 62  AHFDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                  + +  P++L        ++SD + I  ++ V + FH RF A  + Y Y     
Sbjct: 61  IALSTEDDRIKNPMVLNS------RMSD-VWIWGIAEVPEDFHPRFWANTKVYRY----- 108

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                      +L    ++ + M+  +   +G HDF+ F  +  + +  IR+ID  ++  
Sbjct: 109 -----------YLPSLGMNIKKMKECSLLFLGTHDFSAFSRVDGRDT--IRSIDRIEIWE 155

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEG 238
             N++ + +  +SFL   +R  V +L L   G      + + L  + ++    P APPEG
Sbjct: 156 KCNVVVVEIEGKSFLWEMVRRIVSALVLCSQGVLAEERIVEMLNGKFEKSRKVPPAPPEG 215

Query: 239 LYFDSVEYS 247
           L    ++Y 
Sbjct: 216 LLLWDIKYE 224


>gi|115376217|ref|ZP_01463459.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
 gi|115366790|gb|EAU65783.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 303

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 103/227 (45%), Gaps = 17/227 (7%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y G G+ G+QRQ  G ++Q ++E A+   TG    V  AGRTD GVHA  QV    L   
Sbjct: 35  YRGGGFHGFQRQPEGPTVQSTLE-AVLRSTGVPATVMPAGRTDRGVHARMQVVSLRLEAG 93

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY------RIITRQAPL 123
             P  L   L A L     + +  +      FHA++SA  ++Y Y      R+     P 
Sbjct: 94  DTPEALAARLPALLPPD--LGVCAVRRPPPSFHAQWSAAGKTYCYRVQLGGRVSETWRPY 151

Query: 124 ALEKG-RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFDVNSF 180
            LE      L  +++  E +    Q  VG+ DF  F +    +SSP   RT++   V+  
Sbjct: 152 VLEAAEEPRLAQRAIAPERLAELLQGAVGQRDFWAFHA----SSSPRKPRTLESATVHEL 207

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            G L EI++   SF   Q+R  VGS  L   G+        AL++ +
Sbjct: 208 EGGLFEIQLRGDSFARYQVRYLVGSALLTAAGQLPEAQWRAALESAE 254


>gi|261838425|gb|ACX98191.1| pseudouridylate synthase I [Helicobacter pylori 51]
          Length = 242

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 110/248 (44%), Gaps = 22/248 (8%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFYAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYHLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE-- 185
             A     SLD  N   A +   G+HDF+ F+      ++P RTI  F+  ++   I   
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRTI--FNAFAYKTFIAGH 178

Query: 186 ----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EG 238
                +++  +FL + +R  + +       K T  +    +QAQ       +  P    G
Sbjct: 179 ECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNIKATIRTPIMANG 234

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 235 LYLHRVYY 242


>gi|2160170|gb|AAB60733.1| F21M12.19 gene product [Arabidopsis thaliana]
          Length = 250

 Score = 80.1 bits (196), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 55/198 (27%), Positives = 91/198 (45%), Gaps = 55/198 (27%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + G Q+Q    ++ G ++                   D+GVHAL  V 
Sbjct: 56  RYLVAIEYIGTRFSGSQQQAKDRTVVGVLQ-------------------DAGVHALSNVC 96

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  R
Sbjct: 97  HVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQER 156

Query: 111 S-----------------------YLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAA 146
           +                       Y YR+++   PL+ LEK R W +P+ L+   M+ A 
Sbjct: 157 TVLGYDLKVYSLQLEIENLFTHCRYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEAC 216

Query: 147 QHLVGRHDFTTFRSIHCQ 164
           + LVG HDF++FR+  CQ
Sbjct: 217 RVLVGSHDFSSFRAAGCQ 234


>gi|315586982|gb|ADU41363.1| tRNA-pseudouridine synthase I [Helicobacter pylori 35A]
          Length = 242

 Score = 79.7 bits (195), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 108/245 (44%), Gaps = 16/245 (6%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G  + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGVYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFYAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  + +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHVVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE-- 185
             A     SLD  N   A +   G+HDF+ F+      ++P RTI  F+  ++   I   
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRTI--FNAFAYKTFIAGH 178

Query: 186 ----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                +V+  +FL + +R  + +       K T  +++  +         P+    GLY 
Sbjct: 179 ECVVFKVIGDAFLRSSVRLIIQACVQYSLEKITLAEIQTQIHNTKAAIRTPIM-ANGLYL 237

Query: 242 DSVEY 246
             V Y
Sbjct: 238 HRVYY 242


>gi|301094360|ref|XP_002896286.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
 gi|262109681|gb|EEY67733.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
          Length = 300

 Score = 79.7 bits (195), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 75/274 (27%), Positives = 118/274 (43%), Gaps = 31/274 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGE--IVVVHGAGRTDSGVH 56
           +R   ++EY+G+ +FG Q Q       ++Q  IE A+F  TGE  +  +  A RTD+GVH
Sbjct: 30  VRRRCVVEYDGAAFFGSQAQDQPGALRTVQEVIEDALFRTTGEKGLPRLRFASRTDTGVH 89

Query: 57  ALRQVAHFDLVREWVPV--ILCKALNAYLKISDTI--SILNLSIVDKQFHARFSAIRRSY 112
           AL QV  F  V + +    +   ALN  L   D +  S+  ++  +  F  R    R+ Y
Sbjct: 90  ALGQVMVF--VSQCIESDRVFRDALNTRLP-DDVLCHSMTTMTEAEADFDPRSDTKRKRY 146

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG---RHDFTTFRSIHC--QASS 167
            Y +I         +   W + K LD   M+ A  HL+      DF+ F       +   
Sbjct: 147 EYELIVGGLRPVAHRRNVWYVHKPLDVAKMQEAIDHLMTPPTTKDFSAFTPQKAVDRERG 206

Query: 168 PIRTIDHFDVNS--------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
            I TI   +++S                  I +      F +  +R  VG+L  +G G+ 
Sbjct: 207 NICTISTIELHSTMMDDRGDAQYREDVATRIRLVFEGNRFRYKMVRILVGTLVDIGLGRL 266

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
              D+   L +Q+R + G  AP +GL    V+Y 
Sbjct: 267 KPDDIPVILASQNRGKAGQGAPSQGLTLIWVKYD 300


>gi|153813978|ref|ZP_01966646.1| hypothetical protein RUMTOR_00185 [Ruminococcus torques ATCC 27756]
 gi|145848374|gb|EDK25292.1| hypothetical protein RUMTOR_00185 [Ruminococcus torques ATCC 27756]
          Length = 221

 Score = 79.3 bits (194), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 99/223 (44%), Gaps = 24/223 (10%)

Query: 6   MIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + ++Y+G+ Y GW R        +I   I   +  +TGE + +    +T  GVHAL Q  
Sbjct: 6   LTLQYDGTRYLGWTRPAADGYAKTISYRISSVLQKMTGEDITLFAGAKTAPGVHALCQTV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F     +        LN YL     I IL+  IV  +F +  +A+ R+YLYRI T  AP
Sbjct: 66  NFHTESPFSDTYFLSKLNEYLP--KDIHILSSEIVSDRFRSDLNAVSRTYLYRICT--AP 121

Query: 123 LALEKGRAWL--IPKSL---DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           +     RA+   IP+ +   +   +R AA  LVG HD   FRS+           + FD+
Sbjct: 122 VQNIFTRAYTANIPEIISESEVAAIRKAADSLVGVHD---FRSLSGVKKKKGTVKEIFDI 178

Query: 178 ---------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                    N   +L+ I++ A  FL+      +  L   G G
Sbjct: 179 SVSHSKETENDSFSLLTIKICANDFLYLMPEHIIEFLNKKGSG 221


>gi|158298879|ref|XP_319023.4| AGAP009903-PA [Anopheles gambiae str. PEST]
 gi|157014098|gb|EAA14028.4| AGAP009903-PA [Anopheles gambiae str. PEST]
          Length = 457

 Score = 79.3 bits (194), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 100/243 (41%), Gaps = 46/243 (18%)

Query: 50  RTDSGVHALRQVAHFDLVRE----WVPVILCKALN-AYLKISDTISILNLSIVDKQFHAR 104
           RTD+GVHAL    H DL R     +    + K LN A+ K   ++ IL+   V   FHAR
Sbjct: 11  RTDTGVHALHNTVHVDLQRPNGKPYDSDRITKTLNRAFEKDGQSLRILSTVRVPASFHAR 70

Query: 105 FSAIRRSYLYRIITRQAPLALEKGR-----AWLIP------------KSLDCENMRIAAQ 147
             A  R+YLYR+   +   A E GR     A  IP               D       A+
Sbjct: 71  LCAKSRTYLYRLAVLKREYARESGRQQHPHARFIPIEEHDRCYFLGHSEFDINAFASVAR 130

Query: 148 HLVGRHDFTTFRSI------HCQASSPIRTIDHFDVNS---------------FGNLIEI 186
              G HDF TF ++        +A   +R ID   V                 + +  ++
Sbjct: 131 MFEGMHDFRTFMAVAKGNPRQQEAMHSLRRIDQITVERGHTMTAAFNRERTEHYYDFWDV 190

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE-CGP--LAPPEGLYFDS 243
           R+  RSFL+ Q+R  VG+     +G+ T  D+ + L    +   C    +AP   LY   
Sbjct: 191 RIRGRSFLYRQVRRMVGAWVAAAEGRITERDIYRMLTVPSQNSWCSNVFVAPAYALYLCH 250

Query: 244 VEY 246
           VEY
Sbjct: 251 VEY 253


>gi|108563457|ref|YP_627773.1| tRNA pseudouridine synthase A [Helicobacter pylori HPAG1]
 gi|122980474|sp|Q1CSH3|TRUA_HELPH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|107837230|gb|ABF85099.1| pseudouridylate synthase I [Helicobacter pylori HPAG1]
          Length = 242

 Score = 79.3 bits (194), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 107/243 (44%), Gaps = 12/243 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIENALNTLGIKSVVV-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W        L  YL       I+   + +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWN----VAKLFYYLAPKLAPHIVLKKLEEKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDLLNS--ALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYTAFIMGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  +++  +FL + +R  + +       K T  ++E  +         P+   +GLY   
Sbjct: 181 VVFKIIGDAFLRSSVRLIIQTCVQYSLEKITLAEIEMQIHNIKATIRTPIM-ADGLYLHR 239

Query: 244 VEY 246
           V Y
Sbjct: 240 VYY 242


>gi|208434988|ref|YP_002266654.1| pseudo uridylate synthase I [Helicobacter pylori G27]
 gi|238057732|sp|B5Z889|TRUA_HELPG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|208432917|gb|ACI27788.1| pseudo uridylate synthase I [Helicobacter pylori G27]
          Length = 242

 Score = 79.0 bits (193), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 107/243 (44%), Gaps = 12/243 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  Q   F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQTLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYCLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSLFKKEGGATTNPKRAIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  +++  +FL + +R  + +       K T  ++E  +         P+    GLY   
Sbjct: 181 VVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNLKATIRTPIM-ANGLYLHR 239

Query: 244 VEY 246
           V Y
Sbjct: 240 VYY 242


>gi|109947020|ref|YP_664248.1| tRNA pseudouridine synthase A [Helicobacter acinonychis str.
           Sheeba]
 gi|122973397|sp|Q17YM7|TRUA_HELAH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|109714241|emb|CAJ99249.1| pseudouridylate synthase I [Helicobacter acinonychis str. Sheeba]
          Length = 242

 Score = 79.0 bits (193), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 60/200 (30%), Positives = 93/200 (46%), Gaps = 19/200 (9%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q +   +Q  IE A+ L+  + VV+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPDKLGVQDKIESALNLLGIKSVVI-AAGRTDKGVHANNQVLSFHAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W        L  YL       I+   + +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWS----ADKLFYYLAPKLAPHIVLKKLEEKNFHARFDAQKRAYRYLLTKSLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG------ 181
             A     SLD  N   A +  +G+HDF+ F+     A++P R I     N+F       
Sbjct: 123 YIACGDYGSLDSLNT--ALKQFIGKHDFSMFKKEGGAATNPKRII----FNAFAYKASIM 176

Query: 182 --NLIEIRVVARSFLHTQIR 199
               +  +++  +FL + +R
Sbjct: 177 GHECVVFKIIGDAFLRSSVR 196


>gi|315304909|ref|ZP_07875014.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
 gi|313626716|gb|EFR95744.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
          Length = 127

 Score = 79.0 bits (193), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 48/120 (40%), Positives = 64/120 (53%), Gaps = 4/120 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALR 59
           M RY  +I Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 8   MTRYKAVISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 67

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           KAL         IS + +      FHARF  + + Y Y II R
Sbjct: 68  QVIHFDSELAISAEKFQKALQVMTPFD--ISFITVEETPADFHARFGTVGKEYRY-IIKR 124


>gi|219363303|ref|NP_001136956.1| hypothetical protein LOC100217116 [Zea mays]
 gi|194697754|gb|ACF82961.1| unknown [Zea mays]
          Length = 201

 Score = 79.0 bits (193), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 52/167 (31%), Positives = 76/167 (45%), Gaps = 5/167 (2%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           +   I +  +S    +FHAR S   + Y Y+I             A+     L+   M+ 
Sbjct: 5   LPPEIRVREISAARPEFHARSSTKSKVYRYKIYNEAIMDPFHNHYAYHSAYKLNPHAMQE 64

Query: 145 AAQHLVGRHDFTTF-RSIHCQASS-PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
           AA + VG HDFT+F  + H      P + I  FDV   G ++++ V    FL+ Q+R+ V
Sbjct: 65  AANYFVGIHDFTSFANAAHNDGERRPTKKITRFDVTEMGAVLQLEVEGTGFLYRQVRNMV 124

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEY 246
             L  VG        +   + A+DRKE   +   APP GLY  SV Y
Sbjct: 125 ALLLQVGKEALPPDIVPAIIAARDRKELAKVALSAPPHGLYLMSVNY 171


>gi|15678860|ref|NP_275977.1| tRNA pseudouridine synthase A [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|3915162|sp|O26928|TRUA_METTH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2621931|gb|AAB85338.1| pseudouridylate synthase I [Methanothermobacter thermautotrophicus
           str. Delta H]
          Length = 275

 Score = 79.0 bits (193), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 109/250 (43%), Gaps = 29/250 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQG----SIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M +  + + Y G+ Y G+QRQ +  +++G    ++E A  +   +      AGRTD GVH
Sbjct: 1   MRKIALKVAYIGTNYHGFQRQPDVPTVEGKLLEALEGAGIIEDPKRARFQIAGRTDRGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL     F    E + V     L     +   I +L  + V   F  R+  + R Y Y I
Sbjct: 61  ALGNFVSF-FTEEDIHVNQINDL-----LPRDIRVLAWASVMYPFKVRY-PLERHYRY-I 112

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           + R+              +S+D  +M  AA H  G HDF+ F         P+R I+   
Sbjct: 113 LHRE--------------ESMDTYSMAEAAAHFRGTHDFSNFS--RRSDRDPVRRINDVR 156

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++  G+ I I V   SFL   +R  V +L +V +G+    D+   L    R    P+ PP
Sbjct: 157 ISEVGDSIIIDVYGESFLWQMVRKMVRALLMVSEGELAPDDMAGLLDTDRRVFLEPM-PP 215

Query: 237 EGLYFDSVEY 246
           E L    ++Y
Sbjct: 216 ENLILMDLKY 225


>gi|308184830|ref|YP_003928963.1| tRNA pseudouridine synthase A [Helicobacter pylori SJM180]
 gi|308060750|gb|ADO02646.1| tRNA pseudouridine synthase A [Helicobacter pylori SJM180]
          Length = 242

 Score = 78.6 bits (192), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 106/248 (42%), Gaps = 20/248 (8%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           I+ Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F  
Sbjct: 7   IVAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFHA 65

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            + W        L  YL       I+   + +K FHARF A +R+Y Y +        L 
Sbjct: 66  PKHWN----ADKLFYYLAPKLAPHIVLKKLEEKNFHARFDAQKRAYRYLLTKSLKTPFLA 121

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG----- 181
              A     SLD  N   A +   G+HDF+ F+      ++P R I     N+F      
Sbjct: 122 PYIACGDYGSLDLLNT--ALKQFTGKHDFSLFKKEGGATTNPNRII----FNAFAYKTSI 175

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                +  +++  +FL + +R  + +       K T  ++E  +         P+    G
Sbjct: 176 MGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNLKATIRTPIM-ANG 234

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 235 LYLHRVYY 242


>gi|219888663|gb|ACL54706.1| unknown [Zea mays]
          Length = 271

 Score = 78.6 bits (192), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 75/163 (46%), Gaps = 5/163 (3%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I +  +S    +FHAR S   + Y Y+I             A+     L+   M+ AA +
Sbjct: 79  IRVREISAARPEFHARSSTKSKVYRYKIYNEAIMDPFHNHYAYHSAYKLNPHAMQEAANY 138

Query: 149 LVGRHDFTTF-RSIHCQASS-PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
            VG HDFT+F  + H      P + I  FDV   G ++++ V    FL+ Q+R+ V  L 
Sbjct: 139 FVGIHDFTSFANAAHNDGERRPTKKITRFDVTEMGAVLQLEVEGTGFLYRQVRNMVALLL 198

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEY 246
            VG        +   + A+DRKE   +   APP GLY  SV Y
Sbjct: 199 QVGKEALPPDIVPAIIAARDRKELAKVALSAPPHGLYLMSVNY 241


>gi|291276765|ref|YP_003516537.1| putative tRNA pseudouridine synthase [Helicobacter mustelae 12198]
 gi|290963959|emb|CBG39798.1| putative tRNA pseudouridine synthase [Helicobacter mustelae 12198]
          Length = 245

 Score = 78.6 bits (192), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 113/246 (45%), Gaps = 15/246 (6%)

Query: 8   IEYNGSGYFGWQRQKNG-SSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           I Y+GS +FG+ +Q +G  S+  ++E A+    +T  I+   GAGRTD GVHA  QV   
Sbjct: 8   IAYDGSKFFGFAKQDDGHKSVVQALEFALKSLGITSNII---GAGRTDRGVHATGQVIRV 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           ++   W    L   LN   K+  +I +  +  V+  FH RFSA +R Y Y        + 
Sbjct: 65  EIPDFWELERLRNLLNQ--KLHPSIFLRRIWRVEASFHPRFSAKKREYRYIFGNYLGNVW 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG--- 181
           +    +W   +  D + +  A    VG+ DF  F        + IR I H  + +     
Sbjct: 123 MASYVSW--ERYGDKKRISEALNLFVGKRDFGYFCKSGSDNKTTIRQIYHTRLYTHQIFK 180

Query: 182 -NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + +   + A  FL+ QIR  +G++      + T  +LE  + A+ R    P A P GLY
Sbjct: 181 HDYLVACIQANGFLYGQIRLMMGAVLAYSRKELTYEELELQVLAKKRFYSIP-ASPNGLY 239

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


>gi|88807910|ref|ZP_01123421.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7805]
 gi|88787949|gb|EAR19105.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7805]
          Length = 251

 Score = 78.6 bits (192), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 101/220 (45%), Gaps = 14/220 (6%)

Query: 27  IQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFD-----LVREWVPVILCKALN 80
           +QG +E+AI  L     V    AGRTD+GVHA  QV HFD         W P     ALN
Sbjct: 1   MQGVLEQAIADLDPHRPVHAVAAGRTDAGVHAAGQVVHFDSSGPIPANRWAP-----ALN 55

Query: 81  AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDC 139
             L  S  I +         +HA +SA  R Y Y +   + P       +W   ++ LD 
Sbjct: 56  GRLPAS--IRVREAVERPLSWHACYSATYRRYRYTLYNGRRPNLFLAPWSWHRYQARLDE 113

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
             M  A   ++G HDF  F+    + +    TI    V   G+LI++ + A  FL+  +R
Sbjct: 114 HAMADALGGMLGSHDFAAFQRAGSRRAHSRTTIQDVSVQRRGDLIDLEIQATGFLYGMVR 173

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +G L  VG+ + T    E+  + + R+E    APP+GL
Sbjct: 174 LLMGQLVAVGEHRLTPEQFERRWRERRREEVKDGAPPQGL 213


>gi|308183197|ref|YP_003927324.1| tRNA pseudouridine synthase A [Helicobacter pylori PeCan4]
 gi|308065382|gb|ADO07274.1| tRNA pseudouridine synthase A [Helicobacter pylori PeCan4]
          Length = 242

 Score = 78.6 bits (192), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 109/246 (44%), Gaps = 18/246 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIEDALNALGIKSVVV-AAGRTDKGVHANNQVLSFYAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKRFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EGLY 240
           +  +V+  +FL + +R  + +       K T  +    +QAQ       +  P    GLY
Sbjct: 181 VVFKVIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNIKATIRTPIMANGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LHRVYY 242


>gi|188527873|ref|YP_001910560.1| tRNA pseudouridine synthase A [Helicobacter pylori Shi470]
 gi|238691941|sp|B2UUJ8|TRUA_HELPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|188144113|gb|ACD48530.1| tRNA pseudouridine synthase A [Helicobacter pylori Shi470]
          Length = 242

 Score = 78.2 bits (191), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 109/246 (44%), Gaps = 18/246 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFYAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  + +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHVVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EGLY 240
           +  +++  +FL + +R  V +       K T  +    +QAQ       +  P    GLY
Sbjct: 181 VVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAE----IQAQIHNIKATIRTPIMANGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LHRVYY 242


>gi|317501503|ref|ZP_07959701.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088022|ref|ZP_08336944.1| hypothetical protein HMPREF1025_00527 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316897132|gb|EFV19205.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330409170|gb|EGG88625.1| hypothetical protein HMPREF1025_00527 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 252

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 95/207 (45%), Gaps = 24/207 (11%)

Query: 6   MIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + ++Y+G+ Y GW R        +I   I   +  +TGE + +    +T  GVHAL Q  
Sbjct: 6   LTLQYDGTRYLGWTRPAADGYAKTISYRISSVLQKMTGEDITLFAGAKTAPGVHALCQTV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F     +        LN YL     I IL+  IV  +F +  +A+ R+YLYRI T  AP
Sbjct: 66  NFHTESPFSDTYFLSKLNEYLP--KDIHILSSEIVSDRFRSDLNAVSRTYLYRICT--AP 121

Query: 123 LALEKGRAWL--IPKSL---DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           +     RA+   IP+ +   +   +R AA  LVG HD   FRS+           + FD+
Sbjct: 122 VQNIFTRAYTANIPEIISESEVAAIRKAADSLVGVHD---FRSLSGVKKKKGTVKEIFDI 178

Query: 178 ---------NSFGNLIEIRVVARSFLH 195
                    N   +L+ I++ A  FL+
Sbjct: 179 SVSHSKETENDSFSLLTIKICANDFLY 205


>gi|317178604|dbj|BAJ56392.1| tRNA pseudouridine synthase A [Helicobacter pylori F30]
          Length = 242

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/196 (31%), Positives = 93/196 (47%), Gaps = 11/196 (5%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFCAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTFIAGHEC 180

Query: 184 IEIRVVARSFLHTQIR 199
           +  +++  +FL + +R
Sbjct: 181 VVFKIIGDAFLRSSVR 196


>gi|317014476|gb|ADU81912.1| tRNA pseudouridine synthase A [Helicobacter pylori Gambia94/24]
          Length = 242

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 110/248 (44%), Gaps = 22/248 (8%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  +  V+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSGVI-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFHYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI--- 184
             A     SLD  N   A +  +G+HDF+ F+     A++P R I  F+  ++   I   
Sbjct: 123 YIACGDYGSLDLLNT--ALKQFIGKHDFSMFKKEGGAATNPNRII--FNALAYKTFIMGH 178

Query: 185 ---EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EG 238
                +++  +FL + +R  + +       K T  +    +QAQ       +  P    G
Sbjct: 179 ECVAFKIIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNLKATIRTPIMANG 234

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 235 LYLHRVYY 242


>gi|317177844|dbj|BAJ55633.1| tRNA pseudouridine synthase A [Helicobacter pylori F16]
          Length = 242

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 114/255 (44%), Gaps = 36/255 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + +VV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSIVV-AAGRTDKGVHANNQVLSFYAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y ++T+        
Sbjct: 67  KHWNAAKLFYHLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRY-LLTKNLK----- 116

Query: 128 GRAWLIP-------KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              +L+P        SLD  N   A +   G+HDF+ F+      ++P R I  F+  ++
Sbjct: 117 -TPFLVPYIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRAI--FNAFAY 171

Query: 181 GNLIE------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              I        +++  +FL + +R  + +       K T  +    +QAQ       + 
Sbjct: 172 KTFIAGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNIKAAIR 227

Query: 235 PP---EGLYFDSVEY 246
            P    GLY   V Y
Sbjct: 228 TPIMANGLYLHRVYY 242


>gi|257461391|ref|ZP_05626487.1| tRNA pseudouridine synthase A [Campylobacter gracilis RM3268]
 gi|257441114|gb|EEV16261.1| tRNA pseudouridine synthase A [Campylobacter gracilis RM3268]
          Length = 203

 Score = 77.8 bits (190), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 90/201 (44%), Gaps = 14/201 (6%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
            + RTD GVHALRQV+  +    W    L + +N +   +  I + ++S V + FH R+ 
Sbjct: 16  SSSRTDKGVHALRQVSCVECTVHWELPRLKELINRH--CAPYIFVQHISPVPRDFHPRYD 73

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           A+ RSY Y ++  + P           P+ +D   +  A  + +G HDF  F        
Sbjct: 74  AVARSYRY-VLNHERPSPFLSDFCVFYPR-VDLAALNAALANFIGEHDFREFMKSGSDIK 131

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVG-SLKLVGDGKWTSTDLEKALQAQ 225
           SP+R +      SF NL  I   A  FL  Q+R  V  +LK V  G+  S    +AL   
Sbjct: 132 SPVRKLYVARAYSFRNLTLINFKANGFLRAQVRLMVANALKSVQSGRKIS--FSRALSRI 189

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
                    PP GLY  SV Y
Sbjct: 190 P-------FPPNGLYLSSVSY 203


>gi|15612084|ref|NP_223736.1| tRNA pseudouridine synthase A [Helicobacter pylori J99]
 gi|8134768|sp|Q9ZKC0|TRUA_HELPJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|4155610|gb|AAD06601.1| PSEUDOURIDYLATE SYNTHASE I [Helicobacter pylori J99]
          Length = 242

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 110/249 (44%), Gaps = 22/249 (8%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           I+ Y+G+ + G+ +Q N   +Q  IE A+  +  +  V+  AGRTD GVHA  Q   F  
Sbjct: 7   IVAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSGVI-AAGRTDKGVHANNQALSFHA 65

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L 
Sbjct: 66  PKHWNAAKLFHYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLA 121

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE- 185
              A     SLD  N  IA +  +G+HDF+ F+      ++P R I  F+  ++   I  
Sbjct: 122 PYIACGDYGSLDALN--IALKQFIGKHDFSMFKKEGGATTNPNRII--FNALAYKTFIMG 177

Query: 186 -----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---E 237
                 +++  +FL + +R  + +       K T  +    +QAQ       +  P    
Sbjct: 178 HECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNLKATIRTPIMAN 233

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 234 GLYLHRVYY 242


>gi|223945645|gb|ACN26906.1| unknown [Zea mays]
          Length = 222

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 43/118 (36%), Positives = 65/118 (55%), Gaps = 2/118 (1%)

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHL 149
           + ++  V   FHAR+ ++ R+Y YR++   ++    EK   W I + LD ++M+ A   L
Sbjct: 2   VTDVCCVAPDFHARYKSLERTYHYRLLAGPESTSVFEKNSVWHISEDLDIQSMKKACSIL 61

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLK 206
           VG HDF++FR+  CQA+SP+RT+D   V   F  +     V RS L     S V S K
Sbjct: 62  VGHHDFSSFRAAGCQANSPVRTLDELSVTEVFPFMFFPSSVERSELELSNVSLVYSRK 119



 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           ARSFL+ Q+R  VG LK VG G  T+ D+E+ L A+       +AP  GLY  +V+Y
Sbjct: 162 ARSFLYHQVRLMVGLLKSVGTGDLTTADVERILDAKTVTAAPSMAPSCGLYLANVKY 218


>gi|297279170|ref|XP_001093509.2| PREDICTED: hypothetical protein LOC705127 [Macaca mulatta]
          Length = 511

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/176 (33%), Positives = 85/176 (48%), Gaps = 20/176 (11%)

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIIT---RQAPLAL-EKGRAW-LIPKSLDCENMRIA 145
           +L    V   FHAR +A  R+YLYR++T   R A L + E+   W L    LD   M+ A
Sbjct: 317 VLRAFRVPSDFHARHAATSRTYLYRLVTGCHRLAELPVFERNLCWTLQADCLDVAAMQEA 376

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS--FGNLI-----------EIRVVARS 192
           AQHL+G HDF+ F+S      SP+RT+    V+      L+            +   ++S
Sbjct: 377 AQHLLGTHDFSAFQSAGSPVPSPVRTLRRVSVSPGQASPLVTPEESRKLQFWSLEFESQS 436

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
           FL+ Q+R     L  VG G      ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 437 FLYRQVRRMTAVLVAVGLGALAPAQVKTILESQDPLGKHQARVAPAHGLFLKSVLY 492


>gi|297380269|gb|ADI35156.1| tRNA pseudouridine synthase A [Helicobacter pylori v225d]
          Length = 242

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/196 (30%), Positives = 93/196 (47%), Gaps = 11/196 (5%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VVV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVV-AAGRTDKGVHANNQVLSFYAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  + +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYHLAP--KLAPHVVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIR 199
           +  +++  +FL + +R
Sbjct: 181 VVFKIIGDAFLRSSVR 196


>gi|254779646|ref|YP_003057752.1| tRNA pseudouridine synthase A [Helicobacter pylori B38]
 gi|254001558|emb|CAX29576.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Helicobacter pylori B38]
          Length = 242

 Score = 77.0 bits (188), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 108/243 (44%), Gaps = 12/243 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VV+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIEGALNALGIKSVVI-AAGRTDKGVHANNQVLSFYAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIARGDYGSLDLLNT--ALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYTAFIMGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  +++  +FL + +R  + +       K T  ++E  +         P+    GLY   
Sbjct: 181 VVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNIKATIRTPIM-ANGLYLHR 239

Query: 244 VEY 246
           V Y
Sbjct: 240 VYY 242


>gi|307637758|gb|ADN80208.1| tRNA pseudo uridine synthase A [Helicobacter pylori 908]
 gi|325996359|gb|ADZ51764.1| tRNA pseudouridine synthase A [Helicobacter pylori 2018]
 gi|325997947|gb|ADZ50155.1| tRNA pseudouridine synthase A [Helicobacter pylori 2017]
          Length = 242

 Score = 77.0 bits (188), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/199 (29%), Positives = 92/199 (46%), Gaps = 15/199 (7%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           I+ Y+G+ + G+ +Q N   +Q  IE A+  +  + VV+  AGRTD GVHA  Q   F  
Sbjct: 7   IVAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVI-AAGRTDKGVHANNQALSFHA 65

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            + W        L  YL       I+   + +K FHARF A +R+Y Y +        L 
Sbjct: 66  PKHWN----ADKLFHYLAPKLAPHIVLKKLEEKNFHARFDAQKRAYRYLLTKNLKTPFLA 121

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE- 185
              A     SLD  N   A +  +G+HDF+ F+      ++P R I  F+  ++   I  
Sbjct: 122 PYIACGDYGSLDLLNT--ALKQFIGKHDFSMFKKEGGATTNPNRII--FNALAYKTFIMG 177

Query: 186 -----IRVVARSFLHTQIR 199
                 +++  +FL + +R
Sbjct: 178 HECVVFKIIGDAFLRSSVR 196


>gi|52548278|gb|AAU82127.1| pseudouridylate synthase [uncultured archaeon GZfos10C7]
          Length = 284

 Score = 77.0 bits (188), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 111/255 (43%), Gaps = 29/255 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVH 56
           R  + I Y G+ Y G+Q Q   +  +I+G + KA+     +   +      AGRTD+GVH
Sbjct: 9   RIALKIGYIGTNYHGFQIQPRSALPTIEGELFKALKKQGIIEDRKTANYSAAGRTDTGVH 68

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV  F    +       + +N+ L    +I +  ++     F+AR  AI R Y Y +
Sbjct: 69  ALAQVVSFVTSNQNTT---PRMINSVLP-DGSIWVSAIAKPYSGFNARRDAISREYRYYL 124

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-----CQASSPIRT 171
              Q  L             LD   MR A++  VG HDF+ F  +          S IR 
Sbjct: 125 FL-QTEL------------DLDITRMREASELFVGTHDFSNFSLLQGNEYEVAGYSTIRD 171

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           I   +V +    + I + A  FL   +R  V +L++VG G      +E  L  + ++   
Sbjct: 172 IKRIEVKTKKPFVIIDIEASGFLRKMVRKIVSALRMVGSGMKDKRWIEDLLDLRIKEGIE 231

Query: 232 PLAPPEGLYFDSVEY 246
           P AP  GL   +V Y
Sbjct: 232 P-APAFGLVLKNVSY 245


>gi|317012865|gb|ADU83473.1| tRNA pseudouridine synthase A [Helicobacter pylori Lithuania75]
          Length = 242

 Score = 76.6 bits (187), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 106/243 (43%), Gaps = 12/243 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE  +  +  +  V+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIEGTLNALGIKSAVI-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFHYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  +++  +FL + +R  V +       K T  ++E  +         P+    GLY   
Sbjct: 181 VVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAEIEMQIHNIKATIRTPIM-ANGLYLHR 239

Query: 244 VEY 246
           V Y
Sbjct: 240 VYY 242


>gi|241745612|ref|XP_002412440.1| pseudouridylate synthase, putative [Ixodes scapularis]
 gi|215505839|gb|EEC15333.1| pseudouridylate synthase, putative [Ixodes scapularis]
          Length = 350

 Score = 76.6 bits (187), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 82/295 (27%), Positives = 127/295 (43%), Gaps = 55/295 (18%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAI--FLVTGEIVVVHGAGRTDSGV 55
           RY +   Y G+ Y G QRQ +       ++QG+IE A+       E V++  A RTD+GV
Sbjct: 4   RYLLKFSYLGTRYRGMQRQSSRPCLENWTVQGAIEGALRNLRPLSEPVLI-LASRTDTGV 62

Query: 56  HALRQVAHFDLVRE-----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
           HA     H DLV       + P+ +   LN +    D  I +  +  V   FHAR+ A  
Sbjct: 63  HASLSAGHVDLVPANTAQCYQPLQIFSVLNRHFARRDHDIVVREVLPVPSWFHARYLAKS 122

Query: 110 RSYLYRIITRQAPLALEKGRAW------LIP----------KSLDCENMRIAAQHLVGRH 153
           RSY+YR+   + P  LE+          L+P            LD   +  A + L G H
Sbjct: 123 RSYVYRVAVLR-PHVLEQSTVLGTTIRHLLPLNEINSCCAVPPLDFSRVHEAMELLSGEH 181

Query: 154 DFTTFRSI-HCQASSPIRTIDHFDVNSFG------------------NLIEIRVVARSFL 194
           DF TF+++   +A   + T+   +V  F                   +L E  + +RSFL
Sbjct: 182 DFRTFKNVGRTKAEDEVNTVR--NVLDFTLRPSQPASAVADPLYDNVDLWEFHIKSRSFL 239

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
           + Q+R  V  +  VG    +   + + L+   +        +AP  GLY  ++EY
Sbjct: 240 YRQVRRMVSVVLHVGMHPESLPLVRRMLENPHKDSWDNKVRIAPACGLYLTNIEY 294


>gi|118474657|ref|YP_891922.1| tRNA pseudouridine synthase A [Campylobacter fetus subsp. fetus
           82-40]
 gi|166228690|sp|A0RNY9|TRUA_CAMFF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|118413883|gb|ABK82303.1| tRNA pseudouridine synthase A [Campylobacter fetus subsp. fetus
           82-40]
          Length = 258

 Score = 76.3 bits (186), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 74/270 (27%), Positives = 116/270 (42%), Gaps = 36/270 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +   YNGS + G Q Q + ++++  +  A+  V G    V  + RTD GVHA+ Q
Sbjct: 1   MMKIALTYSYNGSKFKGSQTQPDKNAVEDCLNFALNRV-GIFKPVVSSSRTDKGVHAISQ 59

Query: 61  VAHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V+  +    W      L   +N + K    I I N+  V  +FH R+ A+ RSY Y I  
Sbjct: 60  VSCVECGEFWNERFERLKNQINKHTK--PYIYIKNIQKVSDEFHPRYDAVARSYRYIIYH 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +  + L     +   K+L+ + + IA +  +G+HDFT F  +     S +R I  F   
Sbjct: 118 DEQNVFLADYVHFY--KTLNIQRLNIALKLFIGKHDFTPFYKVGSGEKSTVREI--FYAK 173

Query: 179 SF------------------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           ++                    L  I   A  FL  Q+R  V +         +  +L K
Sbjct: 174 AYQIYKTKDAKFSAKFKTQKPTLTIINFKANGFLRAQVRLMVAN---ALQACKSDENLYK 230

Query: 221 ALQAQDRKECGPL----APPEGLYFDSVEY 246
            +   + KE  PL    +PP GLY   V Y
Sbjct: 231 FI--SNFKEQKPLTRMPSPPNGLYLKRVFY 258


>gi|303233145|ref|ZP_07319818.1| tRNA pseudouridine synthase A [Atopobium vaginae PB189-T1-4]
 gi|302480730|gb|EFL43817.1| tRNA pseudouridine synthase A [Atopobium vaginae PB189-T1-4]
          Length = 321

 Score = 76.3 bits (186), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 96/221 (43%), Gaps = 25/221 (11%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y G  + G+  Q+   +++G +   +  V    V +  AGRTD+GVHA  Q   F +  E
Sbjct: 62  YEGEQFAGYAFQEGQRTVEGCVRDVLQRVLRRDVTLTCAGRTDAGVHAHAQYVSFPVTHE 121

Query: 70  WVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                   L ++LN  +     I+I  +      F ARF A  RSY YRI T      L 
Sbjct: 122 ECACAKSSLLRSLN--MLCPADIAIRTIYQAAPDFSARFDARSRSYTYRIATAPLKPVLT 179

Query: 127 KGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-------------IRT 171
               W       +  ++M  AAQ L+G H+F +F    C+A+S              I +
Sbjct: 180 APFVWWNRHVHHVCMDDMNAAAQALIGEHNFESF----CKATSADVLKSQGLSLQRCITS 235

Query: 172 ID-HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           I+ H D      LI I +   +FLH  +R   GSL  VG G
Sbjct: 236 INVHRDYVLGEQLICIDIEGNAFLHNMVRIIAGSLLEVGRG 276


>gi|308063876|gb|ADO05763.1| tRNA pseudouridine synthase A [Helicobacter pylori Sat464]
          Length = 242

 Score = 76.3 bits (186), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 108/246 (43%), Gaps = 18/246 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  +  V+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSAVI-AAGRTDKGVHANNQVLSFYAQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  + +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHVVLKKLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EGLY 240
           +  +++  +FL + +R  V +       K T  +    +QAQ       +  P    GLY
Sbjct: 181 VVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAE----IQAQIHNIKATIRTPIMANGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LHRVYY 242


>gi|210135252|ref|YP_002301691.1| tRNA pseudouridine synthase A [Helicobacter pylori P12]
 gi|238057731|sp|B6JMT3|TRUA_HELP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|210133220|gb|ACJ08211.1| pseudouridylate synthase I [Helicobacter pylori P12]
          Length = 242

 Score = 75.9 bits (185), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 105/243 (43%), Gaps = 12/243 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  +  V+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSAVI-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W        L  YL       I+   + +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWS----ADKLFYYLAPKLAPHIVLKKLEEKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDLLNT--ALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYTTFIMGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  +++  +FL + +R  + +       K T  +++  +         P+    GLY   
Sbjct: 181 VVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQMQIHNLKATIRTPIM-ANGLYLHR 239

Query: 244 VEY 246
           V Y
Sbjct: 240 VYY 242


>gi|116072175|ref|ZP_01469443.1| tRNA pseudouridine synthase [Synechococcus sp. BL107]
 gi|116065798|gb|EAU71556.1| tRNA pseudouridine synthase [Synechococcus sp. BL107]
          Length = 253

 Score = 75.9 bits (185), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/199 (31%), Positives = 89/199 (44%), Gaps = 13/199 (6%)

Query: 47  GAGRTDSGVHALRQVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQF 101
            AGRTD+GVHA  QV HFD        +W P     ALN  L  S  I +       + +
Sbjct: 22  AAGRTDAGVHAAAQVVHFDCSGPIPAAKWAP-----ALNGRLPAS--IRVRESVERPQDW 74

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           HA +SA+ R Y Y I   + P        W      L+ ENMR+A + ++G HDF  F  
Sbjct: 75  HACYSAVYRRYRYIIHNGRRPNLFLTPWTWHRYHHRLNEENMRVALEGMIGLHDFAAFMR 134

Query: 161 IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
              +      TI    V   G+LI + + A  FL+  +R  +  L  VG+ + +    E+
Sbjct: 135 AGSRRLHSRTTIQDVLVEREGDLIRVEIQASGFLYGMVRLLMAQLVAVGEHRLSVEAFEQ 194

Query: 221 ALQAQDRKECGPLAPPEGL 239
             + + R +    AP  GL
Sbjct: 195 RWRDRRRDQVKEAAPARGL 213


>gi|308062368|gb|ADO04256.1| tRNA pseudouridine synthase A [Helicobacter pylori Cuz20]
          Length = 242

 Score = 75.5 bits (184), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 108/246 (43%), Gaps = 18/246 (7%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  +  V+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSTVI-AAGRTDKGVHANNQVLSFYTQ 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  + +  L   +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWNAAKLFYHLAP--KLAPHVVLKRLE--EKNFHARFDAQKRAYRYLLTKNLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF---GNL 183
             A     SLD  N   A +   G+HDF+ F+      ++P R I + F   +F      
Sbjct: 123 YIACGDYGSLDALNT--ALKQFTGKHDFSMFKKEGGAITNPKRAIFNAFAYKTFIIGHEC 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP---EGLY 240
           +  +++  +FL + +R  V +       K T  +    +QAQ       +  P    GLY
Sbjct: 181 VVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAE----IQAQIHNIKATIRTPIMANGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LHRVYY 242


>gi|317011288|gb|ADU85035.1| tRNA pseudouridine synthase A [Helicobacter pylori SouthAfrica7]
          Length = 242

 Score = 75.5 bits (184), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/200 (30%), Positives = 92/200 (46%), Gaps = 19/200 (9%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+ L+  +  VV  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFSGYAKQPNKLGVQDKIESALNLLGIKSAVV-AAGRTDKGVHANNQVLSFYAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W        L +YL       I+   + +K FHARF A +R+Y Y +        L  
Sbjct: 67  KHWN----ADRLFSYLAPKLAPHIVLKKLEEKNFHARFDAQKRAYRYLLTKSLKTPFLAP 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG------ 181
             A     SLD  N   A +  +G+HDF+ F+      ++P R I     N+F       
Sbjct: 123 YIACGDFGSLDLLNT--ALKQFIGKHDFSMFKKEGGALTNPKRII----FNAFAYKTSIM 176

Query: 182 --NLIEIRVVARSFLHTQIR 199
               +  +++  +FL + +R
Sbjct: 177 GHECVVFKIIGDAFLRSSVR 196


>gi|149184026|ref|ZP_01862387.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
 gi|148848263|gb|EDL62552.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
          Length = 150

 Score = 75.5 bits (184), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 47/146 (32%), Positives = 74/146 (50%), Gaps = 11/146 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R    + Y+GS + G+Q Q    ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 11  MQRIKCTVAYDGSPFAGYQVQPGKRTVQLEIEKALSAIHKGDQVKITASGRTDAGVHAKG 70

Query: 60  QVAHFD----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           QV HFD    +  E  P +L        K+   I + +   V++ FHARFSA+++ Y Y 
Sbjct: 71  QVFHFDTGLSIPEEKWPTVLNS------KLPPEIVVTSAEEVEEGFHARFSAVKKEYRYS 124

Query: 116 IITRQAPLALEKGRAWLIPKSLDCEN 141
           +   +     ++  A   P  L+ E 
Sbjct: 125 VYQTKTADPFKRDFALHYPFPLNIEE 150


>gi|307595363|ref|YP_003901680.1| tRNA-pseudouridine synthase I [Vulcanisaeta distributa DSM 14429]
 gi|307550564|gb|ADN50629.1| tRNA-pseudouridine synthase I [Vulcanisaeta distributa DSM 14429]
          Length = 272

 Score = 75.5 bits (184), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 114/240 (47%), Gaps = 32/240 (13%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA---HFDL 66
           Y+GS + G+    N  SI+  + +AI     +  +   A RTD GV A+  V    + D 
Sbjct: 10  YDGSLFSGFTGSTN--SIEYYLRRAIRYFIKDFKL-SKASRTDPGVSAIGNVVSINYIDS 66

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
           +R     ++   LN+  ++ + I     + VD+ F AR +A+ R+Y+Y +          
Sbjct: 67  IR-----LVPGMLNS--RLPNGIRAWAWAEVDEGFRAR-AAVSRTYVYVM---------- 108

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
               WL     D + MR AA+  VG HD + F+ +  +       I++ ++  FG+ +  
Sbjct: 109 ---PWLYE---DIDLMRSAAKLFVGVHDLSNFQ-VKEKGVPTTVMINNVNIERFGDYLVF 161

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            V+ R F +  IR  V +L++VG G  T  +L   ++ + RK   P APP GL   +V Y
Sbjct: 162 IVIGRGFRNKMIRKIVNALRMVGSGILTIDELRDLIELRIRKPIPP-APPYGLLLLNVNY 220


>gi|118374735|ref|XP_001020555.1| tRNA pseudouridine synthase family protein [Tetrahymena
           thermophila]
 gi|89302322|gb|EAS00310.1| tRNA pseudouridine synthase family protein [Tetrahymena thermophila
           SB210]
          Length = 309

 Score = 75.1 bits (183), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 122/278 (43%), Gaps = 34/278 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           ++Y     Y G  Y G+Q Q    K   SIQ +++ A+  +T +   +H + RTD GV+A
Sbjct: 15  VKYLATCSYIGMNYSGFQTQILNGKRIPSIQDALQDALKKITKQDTPIHTSSRTDQGVNA 74

Query: 58  LRQVAHFDLVRE-----WVPVILCKALNAYLKISD-TISILNLSIVD-KQFHARFSAIRR 110
           L     F + R        P I+ K++N +LK +   ISI N+  V    F  + +++++
Sbjct: 75  LAHPFVFIINRNQNQKILEPSIIKKSMNMHLKDAKHQISIENIYYVHLTDFDVKANSLKK 134

Query: 111 SYLYRIITRQ----APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
            Y Y I        A    +  +   + + +D E +  A Q  VG H+F  F +I  +  
Sbjct: 135 EYNYFIEANLKDNWANTFQQHKQVTTMTERIDQEKLNQALQQYVGTHNFQNF-TIKAEHI 193

Query: 167 SP----IRTIDHFDVNSF-------GNLIEIRVVARSFLHTQIRSFVGSL------KLVG 209
           S     +RTID   + ++          I+I   A+SFL  QIR  VG        KL  
Sbjct: 194 SHFGCYVRTIDSITIENYSHPFYEEAQCIKIIFKAKSFLAYQIRFMVGEALQYALGKLDF 253

Query: 210 DGKWTSTDLEKALQAQDRKECGPL-APPEGLYFDSVEY 246
           D      D  K L  Q+  E   + A P GL    V+Y
Sbjct: 254 DSFLKLLDPPKELTPQEVHENNRIRAQPRGLMLKRVDY 291


>gi|163784111|ref|ZP_02179057.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880615|gb|EDP74173.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
          Length = 175

 Score = 75.1 bits (183), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 53/172 (30%), Positives = 81/172 (47%), Gaps = 9/172 (5%)

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
           + LNA L     ISI     V   FHARFSA  ++Y+Y++ T+  P   ++G  W I + 
Sbjct: 4   RYLNAVL--PRDISIKECKQVPLSFHARFSAKGKTYIYKVYTQPDPFMYQRG--WYISQK 59

Query: 137 LDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFL 194
           LD EN+  A Q +    +  +   +  + +    IR    F     G L++  + A  FL
Sbjct: 60  LDLENIAEAVQLIKNTENLISMSKKGDYLREDVEIR---EFRFKYDGFLLKFEISASHFL 116

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
              +R  V  +  VG G+ T    ++ L ++D      +APPEGLY   V Y
Sbjct: 117 RYMVRKIVAHVVHVGTGRITIDTFKQILDSKDPARALFIAPPEGLYLKEVYY 168


>gi|184200291|ref|YP_001854498.1| tRNA pseudouridine synthase TruA [Kocuria rhizophila DC2201]
 gi|183580521|dbj|BAG28992.1| tRNA pseudouridine synthase TruA [Kocuria rhizophila DC2201]
          Length = 331

 Score = 75.1 bits (183), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 76/310 (24%), Positives = 121/310 (39%), Gaps = 71/310 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--------------TG------- 40
           +R  + + Y+G+ + GW RQ    S+Q ++E A+ LV              TG       
Sbjct: 8   VRLRIDLAYDGAPFRGWARQPGLPSVQEAVEDALCLVFRVRCPTVVAGRTDTGVHARSQT 67

Query: 41  -----------EIVVVHGAGRTDSGVHALRQVAHFDL------------VREWVPVILCK 77
                       +    G GR    + A    AH                R  V  +L +
Sbjct: 68  VHVDVPREAWERVTRSRGTGRVAGALPASPDPAHASAPAATTGTVAASDARGPVDPVLAR 127

Query: 78  ALNAYLKISDTISILNLSIVDKQ-------------------FHARFSAIRRSYLYRII- 117
            LN  L       +L     D+                    F ARFSA+ R+Y YR+  
Sbjct: 128 RLNGALN-----RVLGKDRADRGWEPVVGAVVVQSVAQAPPGFDARFSALSRAYRYRVAD 182

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R     L +  +W +   LD   M  A + L+G HDF ++      A++ +R +    V
Sbjct: 183 ARTGHDPLTRTFSWWVDPQLDVAAMDGAVRELLGLHDFLSYCKPRAGATT-VRELQRATV 241

Query: 178 N-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +     +I + + A +F H  +RS VG+L  VG+G+   +   + L+A+ R     +AP 
Sbjct: 242 DRDEHGMITVALTADAFCHHMVRSVVGALVRVGEGRHGPSWPGERLRARTRDAAIVMAPA 301

Query: 237 EGLYFDSVEY 246
            GL  D+V Y
Sbjct: 302 HGLVLDAVAY 311


>gi|20094324|ref|NP_614171.1| TruD family pseudouridine synthase [Methanopyrus kandleri AV19]
 gi|30913397|sp|Q8TWZ3|TRUA_METKA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|19887376|gb|AAM02101.1| Pseudouridylate synthase of the TruA family [Methanopyrus kandleri
           AV19]
          Length = 256

 Score = 74.7 bits (182), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 112/249 (44%), Gaps = 30/249 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+GS Y G+Q Q +  +I+G++ KA+  +  E+V    A RTD+G HA  QV
Sbjct: 1   MRVALRVAYDGSRYHGFQYQPDVPTIEGALRKALSELGLELVGY--ASRTDAGAHARYQV 58

Query: 62  AHFDLVREWVPVIL-CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
               +V E  P +     +NA  ++   I ++  + V ++F  R  A+R+ Y Y +    
Sbjct: 59  ----VVVEGDPELAQPDPINA--RLPKDIRVIAKTEVHEEFDPRRDALRKEYRYFLGPLN 112

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNS 179
            P                 E    AA+ L G+HDF+ FR       +PI T++  + V  
Sbjct: 113 RP-----------------EAAARAARKLEGKHDFSAFR--REDGRNPIITVERCELVEI 153

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA-PPEG 238
             N   +RVVA  FL   +R   G +  VG G     D E  L  +      P   P EG
Sbjct: 154 TPNAYVLRVVAPRFLWEMVRRIAGFVWEVGHGLREEGDAEALLSGKFEPSKKPRCLPAEG 213

Query: 239 LYFDSVEYS 247
           L    +EY 
Sbjct: 214 LILWHIEYD 222


>gi|311745752|ref|ZP_07719537.1| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
 gi|311302425|gb|EAZ79545.2| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
          Length = 274

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/254 (26%), Positives = 110/254 (43%), Gaps = 28/254 (11%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVA 62
           Y   I Y G+ Y GW  Q N  ++Q  +E+ +  V G E   + GA RTDSGV  +    
Sbjct: 8   YLFSISYYGARYKGWAPQPNQQTVQRRLERVLRHVLGHEDFSLIGASRTDSGVSCVGGFV 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA- 121
              L  E    +L    N +L     I + ++  V   F+   S  +++Y Y        
Sbjct: 68  QVFLRDEVEMDLLLPQFNEHLP--QDIHLNSVKEVSTTFNLIQSVKKKTYRYYFSNSSDF 125

Query: 122 -PLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHCQASS-------PIRT 171
            P A     A+++  S  L+ E M  A +  +G+HDF +F    C+ S         + +
Sbjct: 126 HPFA----SAFMVNASEELNWEAMNEACKSFIGKHDFKSF----CKPSENKTDYNREVLS 177

Query: 172 IDHFDVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  D N F        +   ++    FLH Q+R  + +L  +G G+   +++E   ++ 
Sbjct: 178 AEICDSNEFMGQYFPHKIYYFQITGTGFLHHQVRMMMSALWQIGKGEMDLSEIEARFESS 237

Query: 226 DRKECGPLAPPEGL 239
           DR E  P AP  GL
Sbjct: 238 DRFEKLPPAPANGL 251


>gi|317009700|gb|ADU80280.1| tRNA pseudouridine synthase A [Helicobacter pylori India7]
          Length = 242

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/252 (26%), Positives = 110/252 (43%), Gaps = 30/252 (11%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  + VV+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSVVI-AAGRTDKGVHANNQVLSFYAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           + W    L   L    K++  I +  L   +K FHARF A +R+Y Y        L  + 
Sbjct: 67  KHWNAAKLFYYLAP--KLAPHIVLKKLE--EKNFHARFDAQKRAYRY--------LLTKN 114

Query: 128 GRAWLIPKSLDCEN------MRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-DHFDVNSF 180
            +   +   + C +      +  A +   G+HDF+ F+      ++P R I + F   +F
Sbjct: 115 LKTPFLAPYIACGDYGSLVALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTF 174

Query: 181 ---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP- 236
                 +  +++  +FL + +R  + +       K T  +    +QAQ       +  P 
Sbjct: 175 IIGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAE----IQAQIHNIKAAIRTPI 230

Query: 237 --EGLYFDSVEY 246
              GLY   V Y
Sbjct: 231 MANGLYLHRVYY 242


>gi|284166628|ref|YP_003404907.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Haloterrigena turkmenica DSM 5511]
 gi|284016283|gb|ADB62234.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Haloterrigena turkmenica DSM 5511]
          Length = 295

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 73/270 (27%), Positives = 112/270 (41%), Gaps = 40/270 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV----------HGAGR 50
           M      I Y+G+GY G+QRQ +      ++E AIF    ++ V+            AGR
Sbjct: 1   MPTRAFRIAYDGTGYHGFQRQPDVP----TVEDAIFDALRDLEVLAADADRPDGYAAAGR 56

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD+GV AL Q    +   +W   +  +ALN  L     I     +    +FHA   A RR
Sbjct: 57  TDAGVSALAQTVALE-APDW---LTPRALNGELPAD--IRAWAAADAPPEFHATHHAERR 110

Query: 111 SYLYRIIT---------RQAPLALEKG-RAWLIPKSLDCENMRIAAQHLVGRHDF--TTF 158
            Y Y +           R AP++   G R     +++D +  R A + L G HDF   T 
Sbjct: 111 EYAYHLYAPPADSRRRDRAAPVSDRAGTRGSPGQRAVDDDRFRAACEALSGSHDFHNLTP 170

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
              + + S  +  I        G+ + + V A  F+   +R  V   + VG G      +
Sbjct: 171 DDRNTERSPTLEAI------RDGDFLVVTVTAGGFVRELVRRLVSLARAVGTGDAPLEKI 224

Query: 219 EKALQAQDRK--ECGPLAPPEGLYFDSVEY 246
           ++A   +     E    APPE L   +V+Y
Sbjct: 225 DRAFDPEPLPGHEGVAPAPPEPLVLTAVDY 254


>gi|42561241|ref|NP_975692.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|62901321|sp|Q6MSQ4|TRUA_MYCMS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|42492739|emb|CAE77334.1| pseudouridylate synthase I [Mycoplasma mycoides subsp. mycoides SC
           str. PG1]
          Length = 251

 Score = 74.3 bits (181), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 112/246 (45%), Gaps = 15/246 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           Y+GS Y GW  Q N  SIQ ++ KAI   + TG+   + GA +TD+ VHAL Q     L+
Sbjct: 11  YDGSNYHGWINQTNAISIQTTLNKAIKKVIKTGQFKTI-GASKTDTNVHALDQKVL--LI 67

Query: 68  REWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             + P++    KA+N  L  SD I IL+   VD  F+ R     + Y Y I   Q  +  
Sbjct: 68  IYFTPILEKFIKAINKALP-SD-IKILDAKFVDPNFNIR-EVEYKIYHYYINDHQFDIFT 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDVNSFGN 182
            +   +   + +D   ++      +G H+F  F  +           RTID   V    N
Sbjct: 125 NRYEYFWKHQKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVLRINN 184

Query: 183 LIEIRVVARSFLHTQIRSFVGS-LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            + I+  A  F+  QIR  + + L    + K ++T L + LQ   +K    +   +GL  
Sbjct: 185 KVVIQFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLQGIGKK-TPFIIDAKGLVL 243

Query: 242 DSVEYS 247
             ++++
Sbjct: 244 QKIQFN 249


>gi|332293112|ref|YP_004431721.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171198|gb|AEE20453.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Krokinobacter diaphorus 4H-3-7-5]
          Length = 259

 Score = 74.3 bits (181), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/255 (26%), Positives = 115/255 (45%), Gaps = 17/255 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GWQ+Q +  +++  +E+   +++  +   +  +GRTD+ V A   VA
Sbjct: 8   YLLKIQYLGFRYHGWQKQPDVLTVERMMERTFSYVLDRKNFKLLASGRTDAKVSA--NVA 65

Query: 63  HFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           + +L     P+      K LN    +   I  L ++ VDK+F+   + I + Y+Y     
Sbjct: 66  YVELFLNDSPLPEEGFLKLLNN--NLPQDIRCLEITQVDKKFNVMDAPIAKEYVYLFSYG 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--------RSIHCQASSPIRT 171
           +            I  SLD E M+ AA+   G HDF ++        ++I   +SS I  
Sbjct: 124 EKNHPFAAPYMINIAGSLDIELMKEAARLFEGEHDFRSYAYKPNPETKTIGNISSSLIEP 183

Query: 172 IDHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            + +  N F       RV  + F   QIR  +G L  +G+GK      +K L A +  + 
Sbjct: 184 NELYTANFFPKESFAFRVSGKGFKRHQIRLMMGMLFDIGEGKVDLDFFKKTLDASNDIKL 243

Query: 231 GPLAPPEGLYFDSVE 245
             +A   GL   +V+
Sbjct: 244 SRIAQASGLLLQNVQ 258


>gi|70952957|ref|XP_745611.1| tRNA pseudouridine synthase [Plasmodium chabaudi chabaudi]
 gi|56525989|emb|CAH74339.1| tRNA pseudouridine synthase, putative [Plasmodium chabaudi
           chabaudi]
          Length = 279

 Score = 74.3 bits (181), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 105/241 (43%), Gaps = 29/241 (12%)

Query: 17  GWQRQKNGSSIQGSIEK--AIFLVTGEIVVVHGAGRTDSG---VHALR---QVAHFDLVR 68
            +Q+  N +     IE+   + L++          RTD G   ++AL    ++ +  L  
Sbjct: 3   AYQKDNNNTVENKLIERLHQLDLISDSNCSFSRVSRTDKGSARMNALTIRLKIKYPHLSI 62

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
             +  I  K LN  LK    I I+++  V   F AR + I+R+YLY  + +         
Sbjct: 63  SIIEKIYLKELNKKLK---NIQIVHIQCVPNNFDARLNCIQRTYLYFFVNKN-------- 111

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLIEIR 187
             + IP+      M  AA+  +G HDF+ F        S IRTI  F++     N    +
Sbjct: 112 --YNIPR------MNEAAKIFLGEHDFSNFCKKRKNTISFIRTIHKFEIKRIDQNFYYFK 163

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG-PLAPPEGLYFDSVEY 246
           +   SFL+ QIR  V SL LVG G+    D++  L+    K     +A   GL   S ++
Sbjct: 164 IKGTSFLYNQIRHMVASLFLVGKGQLDEHDIKSMLENNSVKNKNYKIADECGLLLHSFKF 223

Query: 247 S 247
           S
Sbjct: 224 S 224


>gi|301320977|gb|ADK69620.1| putative tRNA pseudouridine synthase A [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 251

 Score = 74.3 bits (181), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 111/246 (45%), Gaps = 15/246 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           Y+GS Y GW  Q N  SIQ ++ KAI   + TG+   + GA +TD+ VHAL Q     L+
Sbjct: 11  YDGSNYHGWINQTNAISIQTTLNKAIKKVIKTGQFKTI-GASKTDTNVHALDQKVL--LI 67

Query: 68  REWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             + P++    KA+N  L  SD I IL+   VD  F+ R     + Y Y I   Q  +  
Sbjct: 68  IYFTPILEKFIKAINKALP-SD-IKILDAKFVDPNFNIR-EVEYKIYHYYINDHQFDIFT 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDVNSFGN 182
            +   +   + +D   ++      +G H+F  F  +           RTID   V    N
Sbjct: 125 NRYEYFWKHQKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVLRINN 184

Query: 183 LIEIRVVARSFLHTQIRSFVGS-LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            + I   A  F+  QIR  + + L    + K ++T L + LQ   +K    +   +GL  
Sbjct: 185 KVVIEFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLQGIGKK-TPFIIDAKGLVL 243

Query: 242 DSVEYS 247
             ++++
Sbjct: 244 QKIQFN 249


>gi|325287844|ref|YP_004263634.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
 gi|324323298|gb|ADY30763.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
          Length = 270

 Score = 73.9 bits (180), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/267 (24%), Positives = 123/267 (46%), Gaps = 36/267 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + +++ G  + GWQ+Q    +I+G + K + F++      + GAGRTD+ V AL   A
Sbjct: 14  YLIRLQFLGYRFSGWQKQPGYKTIEGMLAKTLKFILPERQYKILGAGRTDAKVSALD--A 71

Query: 63  HFDLVREWVPVILCKALNAYLK-----ISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            F+L  +  P+   + L+ +LK     +   I I+++  V ++F+    +  + Y+Y   
Sbjct: 72  AFELFLDGEPL---QDLDFFLKDFNKNLPSDIRIVSVKHVKEKFNIIQHSKEKEYVYLFS 128

Query: 118 TRQAPLALEKGRAWLIP------KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
                   EK   +  P       +LD + M+ A    VG H+F +F +   +    IR 
Sbjct: 129 FG------EKNHPYTAPFMANIQDNLDLDLMKKATSLFVGTHNFKSFTAKPKENGKFIRK 182

Query: 172 IDHFDVNSFGNLI-----------EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           ++  ++    N I              +    F+  Q+R  +G+L  +G G+ T +D+E+
Sbjct: 183 VNSAEIKE--NTILKANFFPKKSYAFHIKGEGFMRYQVRMLMGALIQLGKGEVTLSDIEE 240

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           AL+     +   +AP  GL   S+++ 
Sbjct: 241 ALKPNSTTKFVFVAPGSGLMLHSLDFK 267


>gi|261885752|ref|ZP_06009791.1| tRNA pseudouridine synthase A [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 257

 Score = 73.9 bits (180), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 73/269 (27%), Positives = 115/269 (42%), Gaps = 36/269 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +   YNGS + G Q Q + ++++  +  A+  V G    V  + RTD GVHA+ QV
Sbjct: 1   MKIALTYSYNGSKFKGSQTQPDKNAVEDCLNFALNRV-GIFKPVVSSSRTDKGVHAISQV 59

Query: 62  AHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  +    W      L   +N + K    I I N+  V  +FH R+ A+ RSY Y I   
Sbjct: 60  SCVECGEFWNERFERLKNQINKHTK--PYIYIKNIQKVSDEFHPRYDAVARSYRYIIYHD 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  + L     +   K+L+ + + IA +  +G+HDFT F  +     S +R I  F   +
Sbjct: 118 EQNVFLADYVHFY--KTLNIQRLNIALKLFIGKHDFTPFYKVGSGEKSTVREI--FYAKA 173

Query: 180 F------------------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           +                    L  I   A  FL  Q+R  V +         +  +L K 
Sbjct: 174 YQIYKTKDAKFSAKFKTQKPTLTIINFKANGFLRAQVRLMVAN---ALQACKSDENLYKF 230

Query: 222 LQAQDRKECGPL----APPEGLYFDSVEY 246
           +   + KE  PL    +PP GLY   V Y
Sbjct: 231 I--SNFKEQKPLTRMPSPPNGLYLKRVFY 257


>gi|261403437|ref|YP_003247661.1| tRNA pseudouridine synthase A [Methanocaldococcus vulcanius M7]
 gi|261370430|gb|ACX73179.1| tRNA pseudouridine synthase A [Methanocaldococcus vulcanius M7]
          Length = 259

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 107/240 (44%), Gaps = 33/240 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           Y + I Y+G   F  Q  +N     +  ++++   L   +I+  +  GRTD GV AL   
Sbjct: 2   YILKIAYDGRYSFQTQPHRNTVCDKVLNTLDEIDLLERRKII--YCGGRTDKGVSALGNF 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              +L +E  P      +NA LK ++ I +L    ++K    R+    R Y Y       
Sbjct: 60  IVVELKKEPSP----SYINAKLK-NEGIWVLGYREIEKIPEVRY----RHYRY------- 103

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
                     ++P    D E ++  A  L G H F    +    +  SPIRTI   DV+ 
Sbjct: 104 ----------ILPNMGYDVEAIKRGASILTGTHSFHNLSKKDRTKDRSPIRTIFKIDVSE 153

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I + +  +SFL   +R  VG+L LVG G+     +EK L+ +D KE  P  PP+GL
Sbjct: 154 NEFYITLDIFGKSFLWNMVRKMVGALDLVGRGERPVNWIEKLLR-EDHKEGVPTFPPDGL 212


>gi|157164133|ref|YP_001466582.1| tRNA pseudouridine synthase A [Campylobacter concisus 13826]
 gi|112800733|gb|EAT98077.1| tRNA pseudouridine synthase A [Campylobacter concisus 13826]
          Length = 243

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 104/247 (42%), Gaps = 17/247 (6%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA--- 62
           +I  Y+GS + G Q Q + + ++  +E+A+  V G    V  + RTD  VHA  Q +   
Sbjct: 5   LIYSYDGSKFQGSQTQPHENGVEDELERALAHV-GIFERVVSSSRTDKSVHANNQSSSVI 63

Query: 63  ---HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              HF  +     +I   A         +I I  +++VD+ F ARF A+ RSY Y +I  
Sbjct: 64  CGDHFTNLERLRDLINHHA-------HPSIHIKRINLVDESFQARFDAVARSYRY-VIDH 115

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                        +PK  D E      ++ +G HDF+ +        SP+R I      +
Sbjct: 116 GKFDVFSSNYKVFLPK-FDIEKANEILRNFIGEHDFSAYMKTGSDTKSPVREIYKAFCYT 174

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           +     I   A  FL  Q+R  V +L      K     ++ +L         P AP EGL
Sbjct: 175 YKEQTIIVFKANGFLRGQVRLMVANLLKALKQKDGGKLIKASLNGHPALTRIP-APAEGL 233

Query: 240 YFDSVEY 246
           Y + V Y
Sbjct: 234 YLNRVFY 240


>gi|194699074|gb|ACF83621.1| unknown [Zea mays]
          Length = 414

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 73/287 (25%), Positives = 121/287 (42%), Gaps = 43/287 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---------IVVVHG----A 48
           + + ++I Y+G  + GWQ+Q   +++QG +EK +     E          + + G    A
Sbjct: 119 VTFKVVISYHGGSFDGWQKQPGLNTVQGLVEKHLGQFVDERKAKQLEARSLPIEGCAIVA 178

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+ V     K A+N      D +  L++S V ++FH  F+A
Sbjct: 179 GRTDKGVTALQQVCSFYTWRKDVKSGDIKGAINE--AAPDKLKPLHVSEVSREFHPNFAA 236

Query: 108 IRRSYLY----------RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR----- 152
             R Y+Y           +   Q+   LE     + P+S D   +    + L G+     
Sbjct: 237 KWRRYMYIFPLDEDADLILGEAQSSKTLENSEHNIKPQSFDVSKVDEILKPLAGKTLSYK 296

Query: 153 ---HDFTTFRSI----HC---QASSPIRTIDHFDVNSFGNLIE--IRVVARSFLHTQIRS 200
               D    RS+     C    + + +  +   + +  G ++   + +VA  FL   +R 
Sbjct: 297 MFARDTQASRSVGPPTECFMFHSRAAVAKLHSANEDHKGGMVVMCVELVANRFLRKMVRV 356

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            V +          +  L   ++A DR+   P APPEGL    V Y 
Sbjct: 357 LVATAIREAAAGAGADALLNLMEATDRRATAPPAPPEGLCLVDVGYE 403


>gi|223558061|gb|ACM91066.1| tRNA pseudouridine synthase A [uncultured bacterium 34R1]
          Length = 189

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/189 (28%), Positives = 86/189 (45%), Gaps = 11/189 (5%)

Query: 62  AHFDLVREWVPVI----LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           AHFD+     P+     LC++LN  L     +++  +  V    HARF A  R+Y Y + 
Sbjct: 3   AHFDVD---APIADTDGLCRSLNGLL--GRDVAVYAIFPVADDAHARFDATSRTYKYFLH 57

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T ++P       +W     LD E M  AA+HL+   DFT+F  +H    +    + +   
Sbjct: 58  TAKSPFLYPL--SWECHFDLDFELMNEAAEHLLHYTDFTSFSKLHTDVKTNNCRVTYAHW 115

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G      + A  FL   +R+ VG+L  VG  + T  +  + ++A+DR E G   P  
Sbjct: 116 ERVGEQWVFTITADRFLRNMVRAVVGTLVEVGRHRITVDEFCRIIEAKDRCEAGNSMPGN 175

Query: 238 GLYFDSVEY 246
            L+   + Y
Sbjct: 176 ALFLWDITY 184


>gi|68072249|ref|XP_678038.1| tRNA pseudouridine synthase [Plasmodium berghei strain ANKA]
 gi|56498378|emb|CAH98757.1| tRNA pseudouridine synthase, putative [Plasmodium berghei]
          Length = 281

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 97/235 (41%), Gaps = 37/235 (15%)

Query: 17  GWQRQKNGSSIQGSIEK--AIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREW---- 70
            +Q+  N +     IEK   + L++          RTD GV A        L  ++    
Sbjct: 3   AYQKDNNNTVENKLIEKLQQLDLISDSNCSFSRVSRTDKGVSARMNALTIRLKNKYPHLS 62

Query: 71  ---VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
              +  I  K LN  LK    I I+++  V   F AR + I+R+Y+Y             
Sbjct: 63  ISIIEKIYLKELNKKLK---NIQIIHIQCVPNNFDARLNCIQRTYVY------------- 106

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLIEI 186
              + I K+ +   M  A +  +G H+F+ F       +S IRTI  F++ +   N    
Sbjct: 107 ---FFINKNYNITKMNEATKIFLGEHNFSNFCKKRKNNTSFIRTIHKFEIKNIDQNFYYF 163

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK--------ECGPL 233
           ++   SFL+ QIR  V +L LVG  +    D++  L+    K        ECG L
Sbjct: 164 KIKGTSFLYNQIRHMVAALFLVGKNQLDGQDIKSMLENNSIKNKNYKIADECGLL 218


>gi|51246208|ref|YP_066092.1| tRNA pseudouridine synthase A [Desulfotalea psychrophila LSv54]
 gi|62901427|sp|Q6AKP0|TRUA2_DESPS RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|50877245|emb|CAG37085.1| related to tRNA pseudouridine synthase A [Desulfotalea psychrophila
           LSv54]
          Length = 261

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 67/255 (26%), Positives = 107/255 (41%), Gaps = 21/255 (8%)

Query: 8   IEYNGSGYFGWQRQ------KNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           I Y G+ YFGWQ Q      +   +++G+I  A+  +T  +   V GA RTD GVHA  Q
Sbjct: 8   IAYKGTHYFGWQAQSIDTLHEEKPTVEGTILNALKKITNYQPCTVSGASRTDGGVHARGQ 67

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A   + ++  P      L     +   I IL      K++ A   ++ + Y Y  I   
Sbjct: 68  IAKITISQKISPE--HLLLGLNSLLPTDIRILECVPSTKEYQASRGSVSKEYHYYFIASP 125

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                    A  +P       D   +R A +  VGRHDF  F S     S   R I + D
Sbjct: 126 VDNVATSDIALHLPIDSIGPDDLALLRSACRLFVGRHDFYNFSSRGSGTS--FREIFYCD 183

Query: 177 VNS------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           ++         ++  ++++   FL   IR  +G+L  +  G+    D+   LQ     + 
Sbjct: 184 IHRANFSPLANDMFYLKIIGDGFLKYMIRYIMGALLELVRGRIVLDDISLYLQQHQEDKL 243

Query: 231 GPLAPPEGLYFDSVE 245
            P A  +GL+   +E
Sbjct: 244 SPRAKAKGLHLIRIE 258


>gi|125556371|gb|EAZ01977.1| hypothetical protein OsI_24011 [Oryza sativa Indica Group]
 gi|125598125|gb|EAZ37905.1| hypothetical protein OsJ_22255 [Oryza sativa Japonica Group]
          Length = 417

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 75/287 (26%), Positives = 121/287 (42%), Gaps = 44/287 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---------IVVVHG----A 48
           + + +++ Y+G  + GWQ+Q   +++QG +EK +     E          + + G    A
Sbjct: 121 VTFKIVLSYHGGSFDGWQKQPGLNTVQGLVEKHLGQFVDEKKAKQLEARSLPLEGCAVVA 180

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+ V     K A+N      D +  L++S V ++FH  F+A
Sbjct: 181 GRTDKGVTALQQVCSFYTWRKDVKSSDIKDAINK--AAPDKLRPLHVSQVSREFHPNFAA 238

Query: 108 IRRSYLY--------RIIT--RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR----- 152
             R YLY        ++I+   Q+   +E     + P+S D   +    + L G+     
Sbjct: 239 KWRRYLYIFPLDEDVKLISGEEQSAKTVEGPECNIKPQSFDVGKVDKIIRQLEGKSLSYK 298

Query: 153 ---HDFTTFRSI---------HCQAS-SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
               D    RS+         H +A+ + + T D          I I +VA  FL   +R
Sbjct: 299 MFARDTQASRSVGPPTECFMFHSRAAVAKLHTADENCEEGTTRAICIELVANRFLRKMVR 358

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             V +             L   ++A  R+   P APP+GL    V Y
Sbjct: 359 VLVATAIREAAAGAEEDALLNLMEATCRRATAPPAPPDGLCLVDVGY 405


>gi|11499319|ref|NP_070558.1| tRNA pseudouridine synthase A [Archaeoglobus fulgidus DSM 4304]
 gi|3915163|sp|O28544|TRUA_ARCFU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2648818|gb|AAB89516.1| pseudouridylate synthase I (truA) # [Archaeoglobus fulgidus DSM
           4304]
          Length = 265

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 101/247 (40%), Gaps = 23/247 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+++   I Y G  + G Q Q +  +++G +  A+  +  E   +  AGRTD+GVHA  Q
Sbjct: 1   MMKFAFKIAYFGDNFHGSQFQPDQRTVEGEVINALRRLGVENPRLRSAGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F    +  P    + LNA  ++ + I+    + V + F  R  A  R Y Y      
Sbjct: 61  VISFYSEDKIFP----RMLNA--ELPEDITAWAWAKVSEDFDPR-RAKSRVYTYV----- 108

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                      +     D   MR A + L+G HDF+ F     +  S +R I   D+ + 
Sbjct: 109 -----------MYGSDYDISAMRKAVKELIGVHDFSNFTKKFGEGESCVREIISADIRAD 157

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I   +   +F    +R  V ++  +G    +       L  +  KE    APP GL 
Sbjct: 158 REFIIFEIEGNAFTWNMVRCIVTAIMEIGKQHRSIEWFRDLLNPEKHKERVEPAPPYGLI 217

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 218 LKDVKYD 224


>gi|325959678|ref|YP_004291144.1| tRNA pseudouridine synthase A [Methanobacterium sp. AL-21]
 gi|325331110|gb|ADZ10172.1| tRNA pseudouridine synthase A [Methanobacterium sp. AL-21]
          Length = 271

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 110/252 (43%), Gaps = 28/252 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-----EIVVVHGAGRTDSGV 55
           M++    + Y G+ Y G+QRQ N  +I+G + +A F  +G     E      AGRTD GV
Sbjct: 1   MLKIAFKVAYIGTDYHGFQRQPNLPTIEGELLRA-FKKSGISDSPEKSDYSIAGRTDRGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            AL  V      ++    +    +N YL     I I+  ++V   F  R++ +R    YR
Sbjct: 60  SALGNVVCLKTDKD----VTINRINYYL--PSNIRIIGSTMVSNGFKPRYAKLRH---YR 110

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
            I  ++          L P +L+ + M+ AA+ + G+H++  F     +A  P R +   
Sbjct: 111 YILDKS----------LCPNTLNLKLMKQAAKQMEGKHNYINFSKRSERA--PERMVYSV 158

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D+    + I   VV  SFL   +R  V  L + G  + T  +LE            P+A 
Sbjct: 159 DLVETPDNIVFDVVGESFLWNMVRKMVKVLVMFGREELTLENLETLFNPDVPAAIKPVA- 217

Query: 236 PEGLYFDSVEYS 247
            +GL    V Y 
Sbjct: 218 SDGLILMDVVYD 229


>gi|52075919|dbj|BAD45865.1| pseudouridylate synthase-like [Oryza sativa Japonica Group]
          Length = 495

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 75/287 (26%), Positives = 121/287 (42%), Gaps = 44/287 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---------IVVVHG----A 48
           + + +++ Y+G  + GWQ+Q   +++QG +EK +     E          + + G    A
Sbjct: 121 VTFKIVLSYHGGSFDGWQKQPGLNTVQGLVEKHLGQFVDEKKAKQLEARSLPLEGCAVVA 180

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+ V     K A+N      D +  L++S V ++FH  F+A
Sbjct: 181 GRTDKGVTALQQVCSFYTWRKDVKSSDIKDAINK--AAPDKLRPLHVSQVSREFHPNFAA 238

Query: 108 IRRSYLY--------RIIT--RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR----- 152
             R YLY        ++I+   Q+   +E     + P+S D   +    + L G+     
Sbjct: 239 KWRRYLYIFPLDEDVKLISGEEQSAKTVEGPECNIKPQSFDVGKVDKIIRQLEGKSLSYK 298

Query: 153 ---HDFTTFRSI---------HCQAS-SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
               D    RS+         H +A+ + + T D          I I +VA  FL   +R
Sbjct: 299 MFARDTQASRSVGPPTECFMFHSRAAVAKLHTADENCEEGTTRAICIELVANRFLRKMVR 358

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             V +             L   ++A  R+   P APP+GL    V Y
Sbjct: 359 VLVATAIREAAAGAEEDALLNLMEATCRRATAPPAPPDGLCLVDVGY 405


>gi|307211854|gb|EFN87801.1| tRNA pseudouridine synthase A [Harpegnathos saltator]
          Length = 270

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 106/243 (43%), Gaps = 44/243 (18%)

Query: 22  KNGSSIQGSIEKAIFLVTGEIVV---VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA 78
           ++G ++QG++E A+  +  +  +   ++ + RTD+GVHAL    H +L  ++  +     
Sbjct: 2   RDGDTVQGALEAALLNILPKTTIRPNIYLSSRTDAGVHALCNAGHVELENKYNVLYKDDN 61

Query: 79  LNAYL-----KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-----LALEKG 128
           + A++     K   TI +L  + V   FHAR S   R+Y+YR +  + P       ++  
Sbjct: 62  IKAFVNRYFNKCGHTIRLLEFTPVTNDFHARGSCKSRTYIYRFMIPKVPGEQRIPLVDAP 121

Query: 129 RAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
             +L+     D + ++   Q  +G  DFTTF S+    S   R I++             
Sbjct: 122 HTYLVKAHDFDVDRVKCGTQLFMGVKDFTTFSSM----SITNRKIEY------------- 164

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSV 244
                     +R  VG+L  +G  K T  D+   LQ        P    AP  GL+  ++
Sbjct: 165 ----------VRRMVGALISLGLRKITEKDINVMLQVPSHHNWNPRASSAPANGLHLVNL 214

Query: 245 EYS 247
           EY 
Sbjct: 215 EYD 217


>gi|110667083|ref|YP_656894.1| tRNA pseudouridine synthase A [Haloquadratum walsbyi DSM 16790]
 gi|109624830|emb|CAJ51238.1| tRNA-pseudouridine synthase [Haloquadratum walsbyi DSM 16790]
          Length = 276

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 101/252 (40%), Gaps = 43/252 (17%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH-----------GAGRTDSGVH 56
           + Y+G  + G+QRQ +      ++E A+F     + V +            AGRTD+GV 
Sbjct: 10  LAYDGRPFSGFQRQPS----VPTVEDALFDALDSLDVFNRDTDSKPSGYAAAGRTDAGVS 65

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           ALRQ   F+      P    +ALN+ L  S  +     + V   FHA   A++R+Y Y  
Sbjct: 66  ALRQTVGFECPSWCTP----RALNSELPTS--VRAWASADVQSGFHATHDALQRTYTY-- 117

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                         +L    LD   +  AA+ L G+HDF  F S     +  +     FD
Sbjct: 118 --------------YLYGPELDMNRLNTAAEILSGKHDFHNFTSDDDGTTRKLSITLEFD 163

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA--QDRKECGPLA 234
                  I  R+ A  F  + IR  + +L+ VG    T   L   L    Q   +  P A
Sbjct: 164 ----DPFITARITADGFPRSLIRRLMSALRGVGSESMTIETLTGLLNTVPQTGPDGIPTA 219

Query: 235 PPEGLYFDSVEY 246
            PE L    V Y
Sbjct: 220 SPEPLILTRVTY 231


>gi|307352726|ref|YP_003893777.1| tRNA pseudouridine synthase A [Methanoplanus petrolearius DSM
           11571]
 gi|307155959|gb|ADN35339.1| tRNA pseudouridine synthase A [Methanoplanus petrolearius DSM
           11571]
          Length = 261

 Score = 72.8 bits (177), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 103/244 (42%), Gaps = 32/244 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHA 57
           +R   ++ Y G+ ++G Q+Q    +++G    A                 +GRTD+GVHA
Sbjct: 1   MRIAFLVSYIGTDFYGSQQQPGIRTVEGEFIGACIDLGLFSDWRDARFQFSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             Q+  FD      P     A+N   K+   I     + V + F+ RF    R Y Y   
Sbjct: 61  RSQICAFDTD---YPERAVSAINR--KLPGDIRCRGWAGVPEGFNPRFEVSERIYRY--- 112

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +    +LD   M +AA++L G HDF+ F  +  +  +P R I   ++
Sbjct: 113 -------------FFPDGNLDWGKMSLAAEYLPGVHDFSRFARV--EGKNPERKIFLAEI 157

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +  G + EIR    SFL   +R    +L LVG G  +   +  AL   D     P AP
Sbjct: 158 IPDKEGIIFEIR--GESFLWNMVRCISHALWLVGSGSESPEVISAALSNTDGPRF-PAAP 214

Query: 236 PEGL 239
           PEGL
Sbjct: 215 PEGL 218


>gi|118395831|ref|XP_001030261.1| tRNA pseudouridine synthase family protein [Tetrahymena
           thermophila]
 gi|89284557|gb|EAR82598.1| tRNA pseudouridine synthase family protein [Tetrahymena thermophila
           SB210]
          Length = 297

 Score = 72.8 bits (177), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/252 (25%), Positives = 111/252 (44%), Gaps = 29/252 (11%)

Query: 19  QRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA 78
           +RQK   +I    ++++     + V +  + RTD GV+A +    F L R+       + 
Sbjct: 21  KRQKESININIKNQQSLNNFAKQEVFIKSSSRTDVGVNARKHPVQFVLQRDS-----KRG 75

Query: 79  LNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR-----QAPLALEKGRAWL 132
           +N YL+ + D I+I  +  V  +F  R   +++ Y++ I ++     + PL   K ++W 
Sbjct: 76  VNFYLRDAGDQIAINEVYQVPMEFDVRNDCLQKEYVFYIDSQVGYNWENPLLFYK-QSWC 134

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTFRS---IHCQASSPIRTIDHFDVNSFGNL------ 183
           IP  +D + ++ A Q  +GRH+F  F S      Q     + ++ F++  + N       
Sbjct: 135 IPDQIDIDRLKQAFQKYLGRHNFYLFTSPEPFQTQFDLFEKELNSFEITHYPNEHFPKIQ 194

Query: 184 -IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-------QAQDRKECGPLAP 235
            I I V  + FL  Q+R  VG   L    K     L   L       Q + R      A 
Sbjct: 195 SIRISVKGKGFLKYQVRYMVGIAVLYAQKKIDENYLNYLLNPTGFIPQDERRNLIRLKAK 254

Query: 236 PEGLYFDSVEYS 247
           PEGL+   V+Y 
Sbjct: 255 PEGLFLYDVQYD 266


>gi|26554422|ref|NP_758356.1| tRNA pseudouridine synthase A [Mycoplasma penetrans HF-2]
 gi|42559813|sp|Q8CXQ1|TRUA_MYCPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|26454432|dbj|BAC44760.1| tRNA pseudouridine synthase [Mycoplasma penetrans HF-2]
          Length = 241

 Score = 72.8 bits (177), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 108/241 (44%), Gaps = 8/241 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           + Y + I Y+GS + G+ +QK+ +  ++Q  +EK + L     +   G+GRTD  VHA+ 
Sbjct: 1   MTYKLKISYDGSFFRGYAKQKDENLITVQSELEKYLSLFFNTKISTFGSGRTDKYVHAID 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q   F    ++ P  +   LN+ L     I + ++  V   FHARFS   ++Y+Y I T 
Sbjct: 61  QTVSFKCDSDYDPKSIQNFLNSKLT---NIYVNSIEKVPNSFHARFSIKSKTYMYVINTG 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  +  ++   +   KS+D +         +G  DF +F +   + ++  RTI    +  
Sbjct: 118 EFDV-FKQRYEYQYNKSIDIKKCEDIINLFIGTKDFLSFSTSKLENTT--RTIRWIRIIK 174

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I +    FL   +R  VG +    + K T  ++    +   +       P  GL
Sbjct: 175 KNKKIYIFINGEGFLRNMVRMIVGIILTYCENKITYQEVLDLFKNPKKGSAVIKVPGCGL 234

Query: 240 Y 240
           Y
Sbjct: 235 Y 235


>gi|290984657|ref|XP_002675043.1| predicted protein [Naegleria gruberi]
 gi|284088637|gb|EFC42299.1| predicted protein [Naegleria gruberi]
          Length = 430

 Score = 72.4 bits (176), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 96/225 (42%), Gaps = 41/225 (18%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH--------GAGRTDSGVHALR 59
           I Y G  Y G  +Q +  +   +IE  +F     + ++           GRTD GV AL 
Sbjct: 74  IAYLGFNYQGLSKQLHTPN---TIEHHLFEALKTLKLIEHEDNCEFTKCGRTDKGVSALG 130

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  F+           + +N+ L   D I +L    V K F ARF  ++R+Y Y     
Sbjct: 131 QVVSFNCRYNPKKNDYVRLINSLL--PDDIRVLAWCPVSKDFDARFGCLQRTYKY----- 183

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                      + I ++L+ E M+ AA H VG HDF  F  I+ + ++  R I   ++  
Sbjct: 184 -----------YFIRQNLNIEKMKQAAAHFVGEHDFRNFCKINEEVTNFRRRILSMEIIK 232

Query: 178 ----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
                     + +  + EI V   SFL  Q+R     L L+G+GK
Sbjct: 233 SDLLHQQHGNDEYFEIYEIVVCGTSFLWHQVRCMTAILFLIGEGK 277


>gi|313125232|ref|YP_004035496.1| pseudouridylate synthase i [Halogeometricum borinquense DSM 11551]
 gi|312291597|gb|ADQ66057.1| pseudouridylate synthase I [Halogeometricum borinquense DSM 11551]
          Length = 272

 Score = 72.4 bits (176), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 65/247 (26%), Positives = 106/247 (42%), Gaps = 34/247 (13%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSGVHALRQV 61
           I Y+G  ++G+QRQ +  +++ SI  A+  +        +      AGRTD+GV AL Q 
Sbjct: 6   IAYDGRPFYGFQRQPSVPTVEDSIFDALRSLGVLDEDARKPTGYAAAGRTDAGVSALAQT 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD   EW      +A+NA  ++ +++     + V ++FHA   A RR+Y+Y +   +A
Sbjct: 66  VAFDCP-EW---CTPRAMNA--ELPESVRAWAAADVGERFHATHDAARRAYVYDLYAPEA 119

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                           D    + AA  L G HD   F ++    +  +R +    V + G
Sbjct: 120 ----------------DESKAQAAADALTGEHD---FHNLTPDDTGTVRDV-TVSVEADG 159

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGL 239
             + + V A  F +  +R     +  V  G     D+E  L  +     E  P AP E L
Sbjct: 160 EFLVLSVAAGGFPYNLVRRLASIVHSVATGDRPLADIETVLGPETVPGPEGVPTAPAEPL 219

Query: 240 YFDSVEY 246
             + V Y
Sbjct: 220 VLERVVY 226


>gi|219853269|ref|YP_002467701.1| tRNA pseudouridine synthase ACD [Methanosphaerula palustris E1-9c]
 gi|254789642|sp|B8GFU5|TRUA_METPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219547528|gb|ACL17978.1| tRNA pseudouridine synthase A [Methanosphaerula palustris E1-9c]
          Length = 280

 Score = 72.4 bits (176), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 103/248 (41%), Gaps = 28/248 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA---IFLVTGEIVVVHG-AGRTDSGVHA 57
           +R    + Y+G+ + G Q Q    +++G +  A   + L           AGRTD GVHA
Sbjct: 1   MRLAFQLSYDGNQFRGSQLQPAYRTVEGELITACQRVQLFDDPCKAGFALAGRTDRGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV  F       P    +ALN   ++S  +     + V   FH RF AI R+Y Y   
Sbjct: 61  RGQVGAFSTP---FPERAVEALNG--QLSPDLWCNGFAEVPPSFHPRFDAISRTYRY--- 112

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +     LD   M  AA  L+G HDF+  R    +  SPIRT+    V
Sbjct: 113 -------------FFADWPLDIRAMDQAAAALIGTHDFS--RLARVREKSPIRTVKSARV 157

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                +    V A ++L   +R    +L L+G  +     +E+ L  + R+   P AP +
Sbjct: 158 FQDRGIPVFEVTAHTYLWHMVRCMAAALLLIGTHEREPELMERLLSGKCRRN-PPAAPAD 216

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 217 GLVLWDVD 224


>gi|2446915|dbj|BAA22474.1| tRNA pseudouridine synthase I [Synechococcus elongatus PCC 6301]
          Length = 81

 Score = 71.6 bits (174), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 41/63 (65%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
          R  ++I+Y G G+ GWQRQ    S+QG +E AI  V G  V V  AGRTD+GVH   QVA
Sbjct: 16 RIALVIQYLGQGFCGWQRQPRQRSVQGELESAIAAVVGHPVSVQSAGRTDTGVHRAAQVA 75

Query: 63 HFD 65
          HF+
Sbjct: 76 HFE 78


>gi|146093784|ref|XP_001467003.1| pseudouridine synthase A-like protein [Leishmania infantum JPCM5]
 gi|134071367|emb|CAM70054.1| putative pseudouridine synthase A-like protein [Leishmania infantum
           JPCM5]
          Length = 499

 Score = 71.2 bits (173), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 95/216 (43%), Gaps = 36/216 (16%)

Query: 49  GRTDSGVHAL--------RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
           GRTD GV AL        R     D   +  P+  C  LN  L    TI I+  ++VD  
Sbjct: 112 GRTDKGVSALGNALSLTARASCTADAEPQLPPLDYCSMLNNVLP--STIRIVGCALVDDT 169

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F ARFS + R+Y Y                +   + L+ E M+ AA   +G H+F  F  
Sbjct: 170 FDARFSCVHRTYRY----------------YFFHRGLNLEAMQEAAAFFLGTHNFRNFCK 213

Query: 161 IHC-QASSPIRTIDHFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +     S+ +RT+    ++    L E+     + A SFL+ QIR  +  L LVG G    
Sbjct: 214 MDVVNVSNFVRTVFSVGLHPSEALPELISYLEIRANSFLYHQIRCIMEVLFLVGRGLEVP 273

Query: 216 TDLEKALQAQDRKECGPLAPPEGLY-----FDSVEY 246
           + ++  L+  DRK   PLA    L      FD+V++
Sbjct: 274 SVVQTLLERGDRKPTYPLADGTPLVLWDCGFDNVQW 309


>gi|322501100|emb|CBZ36178.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 499

 Score = 70.9 bits (172), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 95/216 (43%), Gaps = 36/216 (16%)

Query: 49  GRTDSGVHAL--------RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
           GRTD GV AL        R     D   +  P+  C  LN  L    TI I+  ++VD  
Sbjct: 112 GRTDKGVSALGNALSLTARASCTADAEPQLPPLDYCSMLNNVLP--STIRIVGCALVDDA 169

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F ARFS + R+Y Y                +   + L+ E M+ AA   +G H+F  F  
Sbjct: 170 FDARFSCVHRTYRY----------------YFFHRGLNLEAMQEAAAFFLGTHNFRNFCK 213

Query: 161 IHC-QASSPIRTIDHFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +     S+ +RT+    ++    L E+     + A SFL+ QIR  +  L LVG G    
Sbjct: 214 MDVVNVSNFVRTVFSVGLHPSEALPELISYLEIRANSFLYHQIRCIMEVLFLVGRGLEVP 273

Query: 216 TDLEKALQAQDRKECGPLAPPEGLY-----FDSVEY 246
           + ++  L+  DRK   PLA    L      FD+V++
Sbjct: 274 SVVQTLLERGDRKPTYPLADGTPLVLWDCGFDNVQW 309


>gi|237751255|ref|ZP_04581735.1| tRNA pseudouridine synthase A [Helicobacter bilis ATCC 43879]
 gi|229372621|gb|EEO23012.1| tRNA pseudouridine synthase A [Helicobacter bilis ATCC 43879]
          Length = 253

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 72/252 (28%), Positives = 114/252 (45%), Gaps = 18/252 (7%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---VHGAGRTDSGVHALRQVAH 63
           II Y+GS + G+  QK+   +  S+     L   +I +   + G+GRTD  VHA  QV +
Sbjct: 8   IIAYDGSKFCGFSHQKHTKGVL-SVANFFELTLQKIGIKAKIIGSGRTDKDVHATNQVIN 66

Query: 64  FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F   + ++P+  + K LN   ++   + I  + I D  FHARFSA  R  +YR +  QA 
Sbjct: 67  FH-AKLYMPLDKMKKLLND--RLYPFVLIKRIFIADSSFHARFSAKLR--IYRYVFTQAE 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--DHFDVNSF 180
           L           +  D   ++ A    +G HDF+ F+    +    IRTI   H      
Sbjct: 122 LLPFYSNYIAKVRHGDISLLQTALNEFIGTHDFSLFKKNGSETKDFIRTIVKAHIFPAKI 181

Query: 181 GNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ---DRKEC-GPLA 234
            N+      + A  FL +Q+R  + +      G+ T  +L + +Q     ++  C   LA
Sbjct: 182 HNISCFVAHIGANGFLRSQVRIMLKACFEFSLGRITLQNLVRQIQNDITLEKSLCVRELA 241

Query: 235 PPEGLYFDSVEY 246
           P  GLY   + Y
Sbjct: 242 PACGLYLHRIIY 253


>gi|326774000|ref|ZP_08233282.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
 gi|326636139|gb|EGE37043.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
          Length = 169

 Score = 70.5 bits (171), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/125 (33%), Positives = 64/125 (51%), Gaps = 11/125 (8%)

Query: 131 WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF---------DVNSFG 181
           WL P +LD E M  +A+ L+G HDF ++     + ++ IRT+            D     
Sbjct: 26  WL-PDALDVEAMDASARALLGEHDFLSYCKPR-EGATTIRTLRTLQWRRIEAGPDAGPES 83

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + VVA +F H+ +RS VG+   VG G+   T   + L A+ R+   P+APP GL  
Sbjct: 84  GLVTLSVVADAFCHSMVRSLVGAGLAVGQGRKPVTWPRELLDARTRQSAAPVAPPHGLTL 143

Query: 242 DSVEY 246
           + V Y
Sbjct: 144 EEVTY 148


>gi|331703685|ref|YP_004400372.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802240|emb|CBW54394.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 251

 Score = 70.5 bits (171), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 110/246 (44%), Gaps = 15/246 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           Y+GS Y GW  Q N  SIQ ++ KAI   + T +   + GA +TD+ VHAL Q     L+
Sbjct: 11  YDGSNYHGWINQTNAISIQATLNKAIKKVIKTDQFKTI-GASKTDTNVHALDQKVL--LI 67

Query: 68  REWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             + P++    KA+N  L  SD I IL+   VD  F+ R     + Y Y I   Q  +  
Sbjct: 68  IYFTPILEKFIKAINKALP-SD-IKILDAKFVDSNFNIR-EVEYKIYHYYINDYQFDIFT 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDVNSFGN 182
            +   +   + +D   ++      +G H+F  F  +           RTID   V    N
Sbjct: 125 NRYEYFWKHQKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVLRINN 184

Query: 183 LIEIRVVARSFLHTQIRSFVGS-LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            + I   A  F+  QIR  + + L    + K ++T L + L+   +K    +   +GL  
Sbjct: 185 KVVIEFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLKGIGKK-TPFIIDAKGLVL 243

Query: 242 DSVEYS 247
             ++++
Sbjct: 244 QKIQFN 249


>gi|4220415|gb|AAD12460.1| Homology to pseudouridine synthetase X02743 [Mycoplasma genitalium]
          Length = 102

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 39/104 (37%), Positives = 59/104 (56%), Gaps = 2/104 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  I+ Y+G  + GW  Q N ++IQG +E++  L+ G  + V G+GRTD GVHA+ Q
Sbjct: 1   MARYLGIVSYDGIYFKGWAIQPNLATIQGLLEQSFSLIIGRKIKVIGSGRTDKGVHAINQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
             H D+  E    +L + +N  +K    +    L +V+  FHAR
Sbjct: 61  TFHVDINGEINLNLLIRKINQLIKPHCIVK--TLVLVNDSFHAR 102


>gi|15669871|ref|NP_248685.1| tRNA pseudouridine synthase A [Methanocaldococcus jannaschii DSM
           2661]
 gi|3915177|sp|Q59069|TRUA_METJA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1500579|gb|AAB99697.1| pseudouridylate synthase I (truA) [Methanocaldococcus jannaschii
           DSM 2661]
          Length = 259

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 37/242 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSI----QGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           Y + I Y+G   + +Q+Q +  ++      ++E+  FL   +  V++  GRTD GV AL 
Sbjct: 2   YILKIAYDGR--YSFQQQPHKQTVCDILLDALEETGFLAKKK--VIYSGGRTDKGVSALG 57

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                +L +E  P++    +NA LK    I +L    +D+    ++    R Y Y     
Sbjct: 58  NFVVVELKKE--PIL--SYINAKLK-DKGIWVLGYREIDEIPKVKY----RHYRY----- 103

Query: 120 QAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDV 177
                       ++P    D + ++  A+ ++G H F    +    +  SPIRTI    +
Sbjct: 104 ------------ILPNIGYDVDAIKEGAKKMIGTHSFHNLSKRDRTKEKSPIRTIYDIKI 151

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     + + ++  SFL   +R  VG+L LVG GK     ++K L  ++ +E  P  PPE
Sbjct: 152 SENEFYLTVDIIGESFLWNMVRKIVGALDLVGRGKKPVEWIDKLLD-ENHREGVPTFPPE 210

Query: 238 GL 239
           GL
Sbjct: 211 GL 212


>gi|242062120|ref|XP_002452349.1| hypothetical protein SORBIDRAFT_04g024110 [Sorghum bicolor]
 gi|241932180|gb|EES05325.1| hypothetical protein SORBIDRAFT_04g024110 [Sorghum bicolor]
          Length = 201

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 74/167 (44%), Gaps = 5/167 (2%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           +   I +  +S    +FHAR S   + Y Y+I             A+     L+   M+ 
Sbjct: 5   LPPEIRVREISAARPEFHARTSTKSKVYRYKIYNEAIMDPFHNRYAYHSAYKLNPHAMQE 64

Query: 145 AAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
           AA + VG HDFT+F +   + +     + I  FDV   G ++++ V    FL+ Q+R+ V
Sbjct: 65  AANYFVGTHDFTSFANAAHNDRERRSTKKITRFDVTEMGAVLQLEVEGTGFLYRQVRNMV 124

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEY 246
             L  VG        +   +  +DRKE   +   APP GL   SV Y
Sbjct: 125 ALLLQVGKEALPPDIVPAIIAVRDRKELAKVALSAPPHGLCLMSVNY 171


>gi|154149764|ref|YP_001403382.1| tRNA pseudouridine synthase ACD [Candidatus Methanoregula boonei
           6A8]
 gi|153998316|gb|ABS54739.1| tRNA pseudouridine synthase A [Methanoregula boonei 6A8]
          Length = 276

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 98/242 (40%), Gaps = 28/242 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHA 57
           +R    + Y G+ ++G Q+Q++  +++G   +A                 AGRTD GVHA
Sbjct: 15  VRLACRVSYLGTRFYGSQQQESSRTVEGEFIEACRRLALFSDWRTAGFASAGRTDRGVHA 74

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV  F       P    +ALN+  ++   I     ++V   FH R+ A  R+Y Y   
Sbjct: 75  CGQVIAFSTQ---TPDRARQALNS--QLPPDIWCTATAVVPDHFHPRYDARSRTYRY--- 126

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +      D   M  AA+   G H+FT F  +     +P R I    +
Sbjct: 127 -------------YFGEPPRDPVAMETAAREFSGDHNFTNFARVG--DKNPWRKILEIRI 171

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            + G+   + V A+SFL  Q+R    +    G G+  +  +   L     +   P AP E
Sbjct: 172 GTEGSFTYLEVKAQSFLWHQVRCMAAAALSAGMGEQDADGIRLLLNEAASRPIQP-APAE 230

Query: 238 GL 239
           GL
Sbjct: 231 GL 232


>gi|281201760|gb|EFA75968.1| tRNA pseudouridylate synthase [Polysphondylium pallidum PN500]
          Length = 531

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 74/272 (27%), Positives = 122/272 (44%), Gaps = 42/272 (15%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVH------GAGRTDSGVHALRQ 60
           Y+G+ Y G Q+     +I+  +EKAIF V G   + +  H         RTD GV A+R 
Sbjct: 138 YSGTNYRGMQKNPGFPTIEDELEKAIFKVGGISPDNMYCHRKIDWIRCARTDKGVSAIRN 197

Query: 61  VAHFDLVREWVPVILCK---ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           +    L  E+ P  L +   A+NA L   + I +  +  V+  FHA+    RRSY+Y   
Sbjct: 198 MVSCKL--EYDPPTLDEMKTAINAQL--PNDIRVFAIKRVNNTFHAKNCVDRRSYIYITP 253

Query: 118 TRQAPLALEKGRAWLIP---KSLDCENMRIAA--QHLVGRHDFTTFRS-IHCQASSPIRT 171
           T     A E   A   P   K  + E  R+ +  +  VG   +  + S       S +RT
Sbjct: 254 T----FAFEPIFANNKPAQYKFDELERTRLNSLLKLFVGTRKYHNYTSKKESNDPSAVRT 309

Query: 172 IDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVG-SLKLVGDGKWTSTDLEKALQAQ 225
           ++ F+     +N    L+ I +V +SF+  QIR  +G +++ +  G +  ++ ++A  ++
Sbjct: 310 VNSFECSEPFMNEGVELVAINIVGQSFMLHQIRKMIGVTMQFMRKGFFADSESDEAALSK 369

Query: 226 DRKECG----------PLAPPEGLYFDSVEYS 247
            +K             P+AP  GL  D   Y 
Sbjct: 370 MKKLVEATFAHRQFNLPMAPGAGLLLDRCLYD 401


>gi|256810921|ref|YP_003128290.1| tRNA pseudouridine synthase A [Methanocaldococcus fervens AG86]
 gi|256794121|gb|ACV24790.1| tRNA pseudouridine synthase A [Methanocaldococcus fervens AG86]
          Length = 259

 Score = 69.7 bits (169), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 111/242 (45%), Gaps = 37/242 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSI----QGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           Y + I Y+G   + +Q+Q +  ++      ++E   FL   +I+  +  GRTD GV AL 
Sbjct: 2   YILKIAYDGR--YSFQQQPHKQTVCDILLDTLENTDFLAKKKII--YSGGRTDKGVSALG 57

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                +L +E  P++    +NA LK S  I +L    +D+    ++   R          
Sbjct: 58  NFVVLELKKE--PIL--SYINAKLK-SKGIWVLGYREIDEIPKVKYRYYR---------- 102

Query: 120 QAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDV 177
                      +++P  + + + ++  A+ ++G H F    +    +  SPIRTI    +
Sbjct: 103 -----------YILPNINYNVDAIKEGAKKMIGTHSFHNLSKRDRTKEKSPIRTIYDIKI 151

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     + I ++  SFL   +R  VG+L L+G GK     ++K L  ++ +E  P  PP+
Sbjct: 152 SENEFYLTIDIIGESFLWNMVRKIVGALDLIGRGKKPVEWIDKLLD-ENYREGVPTFPPD 210

Query: 238 GL 239
           GL
Sbjct: 211 GL 212


>gi|126180241|ref|YP_001048206.1| tRNA pseudouridine synthase ACD [Methanoculleus marisnigri JR1]
 gi|166228738|sp|A3CXX4|TRUA_METMJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|125863035|gb|ABN58224.1| tRNA pseudouridine synthase A [Methanoculleus marisnigri JR1]
          Length = 270

 Score = 69.7 bits (169), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 94/242 (38%), Gaps = 29/242 (11%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHALRQVAHFD 65
           Y G  +FG Q Q +  +++G    A  L+             AGRTD GVHA  QV  F 
Sbjct: 9   YFGDRFFGSQMQPDLCTVEGEFIGACRLLRLFDDWREANFATAGRTDRGVHARSQVCSFL 68

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             +   P    +ALN  L     I     +     FH R+SA+ R+Y Y      AP   
Sbjct: 69  TDK---PERAIEALNRVLPAD--IWCTGWAEAPDGFHPRYSAVSRTYRYYF---SAP--- 117

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
                       D   M  AAQ  +GRHDF+ F        +P R I    V   G    
Sbjct: 118 -----------GDAAAMHEAAQEFLGRHDFSAF--ARAGDRNPERRILASRVFIDGEFAV 164

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             V   SFL   +R     L  VG G+  + ++ + L     +     APPEGL    ++
Sbjct: 165 FEVTGESFLWNMVRCMATMLGRVGRGEAEAGEIARLLTGPVERRVA-AAPPEGLILWDID 223

Query: 246 YS 247
           Y 
Sbjct: 224 YG 225


>gi|57167827|ref|ZP_00366967.1| tRNA pseudouridine synthase A [Campylobacter coli RM2228]
 gi|57020949|gb|EAL57613.1| tRNA pseudouridine synthase A [Campylobacter coli RM2228]
          Length = 240

 Score = 68.9 bits (167), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 103/242 (42%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +  S+Q +++ A+  + G    V  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSKFLGSATQPHKKSVQDALQDALSHL-GIFSSVLMASRTDKGVHASYAVACVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  +  L K +N +      I + NL I+   F  R+    R Y Y I        
Sbjct: 64  CGEHFRDLNYLKKQINKF--SHPFIHVKNLKIMPSNFEVRYDVKSREYRY-IFYHGVYNP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    P  +D     +  Q+ VG  DF  F        + IR I      S+ +  
Sbjct: 121 FLASYVHFYP-FIDVLKADLVLQNFVGIKDFKFFCKSGGDNKTTIREIFLAKAYSYKDFT 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R  A  FL  QIR  V S+  V + K +  +L++ ++A+ ++    LAPP GLY   +
Sbjct: 180 IFRFKANGFLRAQIRLMVASVLKVLENKMSIEELKEQIEAK-KQYNHFLAPPCGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 SY 240


>gi|222480083|ref|YP_002566320.1| tRNA pseudouridine synthase [Halorubrum lacusprofundi ATCC 49239]
 gi|222452985|gb|ACM57250.1| tRNA pseudouridine synthase [Halorubrum lacusprofundi ATCC 49239]
          Length = 293

 Score = 68.9 bits (167), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 66/252 (26%), Positives = 112/252 (44%), Gaps = 30/252 (11%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVV------VHGAGRTDSGVHA 57
           + Y+G  Y G+QRQ + ++++G++ +A+     L  G+            AGRTD+GV A
Sbjct: 13  VAYDGREYAGFQRQPHATTVEGTLLRALAKHGILDRGDGPTHATPPGYAAAGRTDAGVSA 72

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           + Q   F+   +W   +  +A N +L  S  + +   + V   FHA   A+RR+Y Y + 
Sbjct: 73  VAQTVAFE-APDW---LTPRAFNGHLPGS--VRVWAAADVPAGFHATHDAVRRTYRYHLY 126

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
              AP  +E+        ++D   +R A   L G  DF    S        + T      
Sbjct: 127 ---APARVEETDH---DHAVDDGRVRDALARLSGEQDFHNLTSDETGTVRDLTTT----A 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD---RKECGPLA 234
              G+++ + V A  F    +R  V +++ VG G    + +++ L ++        GP A
Sbjct: 177 TREGDILVVEVSAGGFPRALVRRLVAAVRAVGRGTADPSLIDRLLASEPISGEFGIGP-A 235

Query: 235 PPEGLYFDSVEY 246
           PPE L    V Y
Sbjct: 236 PPEPLVLWDVSY 247


>gi|71663014|ref|XP_818505.1| pseudouridine synthase A-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70883761|gb|EAN96654.1| pseudouridine synthase A-like protein, putative [Trypanosoma cruzi]
          Length = 409

 Score = 68.9 bits (167), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 104/245 (42%), Gaps = 36/245 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + Y+G  Y G  +Q+  S+     +  +++    +     + +   GRTD GV AL  V 
Sbjct: 26  LAYHGHLYDGLAKQEETSNTVEAYVVAALKHVRLIPQDGPIDLARCGRTDKGVSALGNVF 85

Query: 63  HFDL-VREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
              +    W        P+  C  LN+ L +  TI I+  + VD  F ARFS + R+Y Y
Sbjct: 86  SLTVRASSWPTDSPQKPPLDYCAMLNSALPV--TIRIVGWAYVDDTFDARFSCVGRTYRY 143

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS----PIR 170
                           +   + L+ E M  AA  L G H+F  F        S     +R
Sbjct: 144 ----------------YFCHRGLNVEAMGNAAARLKGVHNFRNFCKTDVVNVSNYERDVR 187

Query: 171 TIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           ++  F   +F  L+  + + A SFL+ QIR  +  L LVG G      + + L+  DRK 
Sbjct: 188 SVGIFASEAFPELVSYLEIHANSFLYHQIRCTMEVLFLVGRGLEDPEVVTQLLERGDRKP 247

Query: 230 CGPLA 234
             PLA
Sbjct: 248 VYPLA 252


>gi|271962666|ref|YP_003336862.1| tRNA-pseudouridine synthase I [Streptosporangium roseum DSM 43021]
 gi|270505841|gb|ACZ84119.1| tRNA-pseudouridine synthase I [Streptosporangium roseum DSM 43021]
          Length = 360

 Score = 68.9 bits (167), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 81/165 (49%), Gaps = 14/165 (8%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIA 145
           + +  +++  + F ARFSA+ R Y YR+    AP  ++  R   +    + LD + +  A
Sbjct: 182 VRVYRVTVAPRGFDARFSAMSRRYAYRV--SDAPGGVDPLRRREVIWYGRPLDVDRLNAA 239

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
           A  L+G HDF  F     + ++ IR +   D     +++   VVA +F H+ +R+ VGSL
Sbjct: 240 AAVLLGEHDFAAF-CKKREGATTIRELQRLDWVRQDDILVATVVADAFCHSMVRALVGSL 298

Query: 206 KLVGDGK----WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             VG+G+    W    L +A+    R     +AP  GL  + V Y
Sbjct: 299 LPVGEGRLAVDWPGRVLTRAV----RDSGVHVAPAHGLCLEEVRY 339



 Score = 59.7 bits (143), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/68 (44%), Positives = 43/68 (63%), Gaps = 2/68 (2%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
          M+R  + + Y+G+ + GW +Q    ++QG IE+A+   L   E  V+  AGRTD+GVHA 
Sbjct: 1  MVRLRLDLAYDGTDFSGWAKQPGRRTVQGEIEEALGKILRLPEPPVLTVAGRTDAGVHAR 60

Query: 59 RQVAHFDL 66
           QVAH DL
Sbjct: 61 GQVAHVDL 68


>gi|289597197|ref|YP_003483893.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Aciduliprofundum boonei T469]
 gi|289534984|gb|ADD09331.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Aciduliprofundum boonei T469]
          Length = 253

 Score = 68.9 bits (167), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 102/243 (41%), Gaps = 45/243 (18%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y+G+ ++G+QRQK+  +++G I KA  L    I  +  A RTD GV AL  V        
Sbjct: 7   YDGTRFYGYQRQKDVPTVEGEILKA--LENMGIKNLKSASRTDRGVSALGNVI------- 57

Query: 70  WVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           W+        L   LNA LK     S  NL I     + R++ IR               
Sbjct: 58  WIKTDIDGKELIGRLNANLKHIYFHSFANLDI-----NPRYARIRWY------------- 99

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
               R  L+    D + ++ AA    G HDF  F  +       I+ I   DVN  G++I
Sbjct: 100 ----RYHLLDMGQDMDRLKEAAMIFQGEHDFRNFTRVRKNTVIEIKKI---DVNKRGSII 152

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I    R++L   IR  V +++    GK    ++        RK  G +APPE L    +
Sbjct: 153 TIDFYGRNYLWNLIRRIVAAMETYSLGKEFGQEIFTI-----RKNFG-IAPPEPLILMDI 206

Query: 245 EYS 247
           +Y 
Sbjct: 207 QYD 209


>gi|302854296|ref|XP_002958657.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
 gi|300255982|gb|EFJ40260.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
          Length = 188

 Score = 68.9 bits (167), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 76/171 (44%), Gaps = 17/171 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +C ++ Y+G  + G+Q Q     ++QG +E+    +      + GA RTD G HA  QV 
Sbjct: 12  WCQVVAYDGCEFAGFQFQAGKVRTVQGELERGAKRLFHGCSRMVGASRTDGGAHAYGQVV 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+       +   AL     +   + +L LS  +  F + FS+  ++YLY+       
Sbjct: 72  HFDVYGT-RDSLESDALYYNSFLPPDVRVLGLSYAEDGFDSHFSSCGKTYLYKFAAGLPD 130

Query: 123 LALEKGRAWLIPK---------------SLDCENMRIAAQHLVGRHDFTTF 158
               K R W+  +                LD   M+ AA  L+GRHDF+ F
Sbjct: 131 PLQSKYRWWVYDRWCERSRGKPGKLSDVELDVGLMQQAADMLLGRHDFSAF 181


>gi|289581033|ref|YP_003479499.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Natrialba magadii ATCC 43099]
 gi|289530586|gb|ADD04937.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Natrialba magadii ATCC 43099]
          Length = 293

 Score = 68.9 bits (167), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 68/262 (25%), Positives = 105/262 (40%), Gaps = 40/262 (15%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSGVHALRQV 61
           + Y+G+GY+G+QRQ +  +++ ++  A+  +        +      AGRTD+GV AL Q 
Sbjct: 6   LAYDGTGYYGFQRQPDVPTVEDAMFDALRALDVLAPDADKPAGYAAAGRTDAGVSALAQT 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI----I 117
             F+   +W   +  +A N  L     I     +    +FHA   A  R Y Y +     
Sbjct: 66  VAFE-APDW---LTPRAFNGELPAD--IRAWAAADAPDEFHATHHAREREYTYYLYAPPA 119

Query: 118 TRQAPLALEKGR----AWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTI 172
              AP A +         +   ++D +  + A   L G HDF       H    SP+   
Sbjct: 120 NDDAPPASDTDEDHAGTPVTAHTVDDDRFQAACDALSGPHDFHNLTPDDHNTERSPV--- 176

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              +    G+   + V A  F    +R  V   + VG G+     +E+AL      E  P
Sbjct: 177 --LESTRDGHFRILTVTAGGFCRELVRRLVSLARDVGTGEANLQTIERAL------ESDP 228

Query: 233 L--------APPEGLYFDSVEY 246
           L        APPE L    VEY
Sbjct: 229 LPGHEGIAPAPPEPLVLTDVEY 250


>gi|153951132|ref|YP_001398256.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. doylei
           269.97]
 gi|166228691|sp|A7H426|TRUA_CAMJD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|152938578|gb|ABS43319.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. doylei
           269.97]
          Length = 241

 Score = 68.9 bits (167), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 104/248 (41%), Gaps = 9/248 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q  + +A+  + G    +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSATQPHKKGVQDVLSEALSHL-GIFSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA  +    +V +  L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +         +  PK  D           VG+ D   F        + +R I      +
Sbjct: 117 SSYSPFMASYVYFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP-LAPPEG 238
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A  +K+C   LAPP G
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEA--KKQCNHFLAPPNG 233

Query: 239 LYFDSVEY 246
           LY   + Y
Sbjct: 234 LYLSRICY 241


>gi|297789719|ref|XP_002862797.1| hypothetical protein ARALYDRAFT_920264 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297308524|gb|EFH39055.1| hypothetical protein ARALYDRAFT_920264 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 244

 Score = 68.6 bits (166), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 78/175 (44%), Gaps = 8/175 (4%)

Query: 78  ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSL 137
           ALN  L     I +  LS    +FHARFSA  + Y Y+I         ++  A+     L
Sbjct: 42  ALNGLL--PKDIRVRELSAAVPEFHARFSAQSKVYRYQIYNDTFMDPFQRYWAYHCAYKL 99

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
           +   MR      VG HD + F +   +     P+++I  F V   G+L+++ V    FL+
Sbjct: 100 NASKMRETVDLFVGMHDVSAFANATREDGVPDPLKSISRFYVIQMGSLLQLEVEGSGFLY 159

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA----PPEGLYFDSVEY 246
            Q+R+ V  L  +G     S  +   L+ +DR+          PP GL   SV+Y
Sbjct: 160 RQVRNMVALLIHIGKESLDSDIVPMILETKDRRVLAKYTTLPVPPHGLCLVSVKY 214


>gi|167967303|ref|ZP_02549580.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Ra]
          Length = 243

 Score = 68.6 bits (166), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 45/137 (32%), Positives = 70/137 (51%), Gaps = 6/137 (4%)

Query: 113 LYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +YR+ T  AP  +E  +A  I   P+ LD + M  A++ L+G HDF  F   H + ++ I
Sbjct: 1   MYRLST--APYGVEPQQARYITAWPRELDLDAMTAASRDLMGLHDFAAF-CRHREGATTI 57

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R +   D +  G L+   V A +F  + +RS VG+L  VG+ +  +T   + L A  R  
Sbjct: 58  RDLQRLDWSRAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRSS 117

Query: 230 CGPLAPPEGLYFDSVEY 246
              +AP  GL    V+Y
Sbjct: 118 DFAVAPAHGLTLIQVDY 134


>gi|119872780|ref|YP_930787.1| tRNA pseudouridine synthase ACD [Pyrobaculum islandicum DSM 4184]
 gi|166228754|sp|A1RU12|TRUA_PYRIL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119674188|gb|ABL88444.1| Pseudouridylate synthase [Pyrobaculum islandicum DSM 4184]
          Length = 255

 Score = 68.2 bits (165), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 109/244 (44%), Gaps = 36/244 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQVA 62
           Y   I Y+G+ ++G+           S+E A+  V GEI+   G G RTD GV A   VA
Sbjct: 3   YLYRIAYDGTLFYGFTGHSR------SLEPALKRVFGEIL---GRGSRTDPGVSA---VA 50

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +  +V + +P+ L  +     K+   +    ++ V + F+ R +  R  YLY      AP
Sbjct: 51  NTVMVSQKLPIALVNS-----KLPRGVWAWAIAEVPQSFNPRRAKFRH-YLY-----VAP 99

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E           D  +M  AA+ L G HDF +F     +  S I T+    V   G+
Sbjct: 100 HWGE-----------DLGSMHEAAEVLAGTHDFASFIQRRGEKISTIATVMEIKVELRGD 148

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI +  V R F +  IR    ++   G G +   D+ + L+ + R    P AP EGL   
Sbjct: 149 LIYMHFVGRGFKNKMIRKLAWAILAAGRGIFNIRDIRELLE-RPRPGVVPSAPAEGLVLL 207

Query: 243 SVEY 246
           ++EY
Sbjct: 208 NIEY 211


>gi|169838040|ref|ZP_02871228.1| tRNA pseudouridine synthase A [candidate division TM7 single-cell
           isolate TM7a]
          Length = 154

 Score = 68.2 bits (165), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 43/154 (27%), Positives = 68/154 (44%), Gaps = 4/154 (2%)

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            ++ F+ARF A  R+YLY +   +     E      + + ++ E  +      +G+HDF+
Sbjct: 1   ANENFNARFDAKNRAYLYIMRAEKDITPFESNYITGLKEKVEAEKFQKIMDSFIGKHDFS 60

Query: 157 TFRSIHCQASSPIRTIDH----FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +F        +P+R I +    +D     N + I +    FL T +R  +GS   V  GK
Sbjct: 61  SFMKKDKAYRNPVREIFYIKCYYDKKFGKNQVNIEICGNGFLKTMVRIMIGSALTVYFGK 120

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                + K L+  D      LAP EGLY   V Y
Sbjct: 121 EKEDYIIKRLKNPDADNKKILAPSEGLYLYKVNY 154


>gi|320165424|gb|EFW42323.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
          Length = 387

 Score = 68.2 bits (165), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 111/243 (45%), Gaps = 38/243 (15%)

Query: 3   RYCMIIEYNGSGYFG----WQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           R+ + +EY+G+ + G         +  S+   +++AI   T +   V  + RTD+GVHAL
Sbjct: 79  RFLLAVEYDGTAFSGVAASPDEPPDRPSVGSVLDRAIAQATRQDARVTFSSRTDAGVHAL 138

Query: 59  RQVAHFDL-----------VREWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARF 105
               H D+            ++W P+ L  A+N +   K+   +S+  +  V +Q HARF
Sbjct: 139 WNTCHVDIEPRTRRGDLMTQQQWTPLALGSAINYFSRGKVPYPMSVRAVCAVPEQVHARF 198

Query: 106 SAIRRSYLYRIITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           +A +R Y+YR++  ++  A +   R  L    +D E++  A          TT R I  Q
Sbjct: 199 NATQRVYIYRVVVGESSAASVFDLRYHLTAAPID-ESLVQAR---------TTTRHI-SQ 247

Query: 165 ASSPI--RTIDHFDVNSFGNLIEIRVVARS-------FLHTQIRSFVGSLKLVGDGKWTS 215
            S  I     D+   NS  + +    VA +       FL+ Q+R  VG +  V  GK T 
Sbjct: 248 FSVQIDKHKTDNPWANSLPDALSKPTVALTFTIRGSGFLYHQVRIMVGHVLSVASGKSTL 307

Query: 216 TDL 218
            DL
Sbjct: 308 ADL 310


>gi|157872401|ref|XP_001684749.1| pseudouridine synthase A-like protein [Leishmania major strain
           Friedlin]
 gi|68127819|emb|CAJ06260.1| putative pseudouridine synthase A-like protein [Leishmania major
           strain Friedlin]
          Length = 498

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 94/216 (43%), Gaps = 36/216 (16%)

Query: 49  GRTDSGVHAL--------RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
           GRTD GV AL        R     D   +  P+  C  LN  L    TI I+  ++VD  
Sbjct: 112 GRTDKGVSALGNAFSLTARASCTGDAEPQLPPLDYCSMLNNVLP--STIRIVGCALVDDA 169

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F ARFS + R+Y Y                +   + L+   M+ AA   +G H+F  F  
Sbjct: 170 FDARFSCVHRTYRY----------------YFFHRGLNLAAMQEAAAFFLGTHNFRNFCK 213

Query: 161 IH-CQASSPIRTIDHFDVNSFGNLIE----IRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +     S+ +RT+    ++    L E    + + A SFL+ QIR  +  L LVG G    
Sbjct: 214 MDVVNVSNFVRTVFSVGLHPSEALPELISYLEIRANSFLYHQIRCIMEVLFLVGRGLEVP 273

Query: 216 TDLEKALQAQDRKECGPLAPPEGLY-----FDSVEY 246
           + ++  L+  DRK   PLA    L      FD+V++
Sbjct: 274 SVVQTLLELGDRKPTYPLADGTPLILWDCGFDNVQW 309


>gi|167377399|ref|XP_001734387.1| tRNA pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165904128|gb|EDR29463.1| tRNA pseudouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 366

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/204 (28%), Positives = 83/204 (40%), Gaps = 33/204 (16%)

Query: 23  NGSSIQGSIEKAIF----LVTGEIVVVHGAGRTDSGVHALRQVAHF----DLVREWV--- 71
           N  +I+  + KA+F    +   +    +  GRTD GV A  QV       +L  E +   
Sbjct: 70  NDGTIEYQLFKALFKTRLIQNTKDCKYNRCGRTDKGVSAFGQVVDLWVRSNLKDETILYT 129

Query: 72  ----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                +  C+ LN  L I   I  L    V   F++RFS   R+Y Y             
Sbjct: 130 KREGELDYCRMLNGLLPID--IRCLGWCGVPDDFNSRFSCQSRTYHY------------- 174

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
              +  P S D   M+ AAQ  +G HDFT F          IR ++ F+V     L    
Sbjct: 175 ---YFDPSSYDVPKMKEAAQLFLGEHDFTNFCKKDPAVPHCIRRVNSFEVEEINGLSRFV 231

Query: 188 VVARSFLHTQIRSFVGSLKLVGDG 211
           V   +F+  Q+R  VG+L  +G G
Sbjct: 232 VCGTAFVWHQVRYMVGALFAIGQG 255


>gi|255322348|ref|ZP_05363494.1| tRNA pseudouridine synthase A [Campylobacter showae RM3277]
 gi|255300721|gb|EET79992.1| tRNA pseudouridine synthase A [Campylobacter showae RM3277]
          Length = 317

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 95/223 (42%), Gaps = 8/223 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G Q Q + + ++ ++  A+  V G    +  + RTD GVHA  QV
Sbjct: 1   MRLKLVFSYDGSKFQGSQTQPHENGVEDALGVALAHV-GIFSKIISSSRTDKGVHANNQV 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A  +    +   +  ++L         I +  +S V   FH R+ A  R+Y Y I   + 
Sbjct: 60  ACVECGEHFKDFVRLRSL-VNRHAHPAIHVKFISRVKDGFHPRYDATARAYRYVINHGEF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L     + IPK  D           VG HDF+ F  +     SP+R +        G
Sbjct: 119 SPFLSPYETF-IPK-FDLNLANELLALFVGEHDFSAFMKLGSDVKSPVRRVSKAFCYERG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGS----LKLVGDGKWTSTDLEK 220
               I   A  FL  Q+R  V S    L+L   GK+  T +++
Sbjct: 177 ERTIIVFKANGFLRAQVRLMVASVLKALELAKSGKFRQTQVQE 219


>gi|313229675|emb|CBY18490.1| unnamed protein product [Oikopleura dioica]
          Length = 402

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 73/261 (27%), Positives = 103/261 (39%), Gaps = 43/261 (16%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH--------GAGRTDSGVHALRQV 61
           Y+G+ Y G QR    +  + +IE  IF       VV           GRTD GVHA+  V
Sbjct: 73  YDGTKYNGLQRSPVPAG-KTTIEDVIFDAILRTKVVDDIGTADYIAGGRTDKGVHAVNNV 131

Query: 62  AHF--------DLVREWVPV---ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
                      D + E V V        +N  L   D I I + + +   F ARFS   R
Sbjct: 132 ISLFVNSRLSEDEINENVTVGERNFVAIINRQL--PDDIWITSWAPISFDFSARFSCKSR 189

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            Y Y                      LD E M+ AA +L+G HDF  F     +  + +R
Sbjct: 190 HYNY----------------IFDSSGLDVELMKEAASYLIGEHDFRNFSQAQLERQNTVR 233

Query: 171 TIDHFDVNSFGNLIEI---RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD- 226
                D+    N+  +    + A  FL+ QIR  +  L LVG+    ST +++ L  +  
Sbjct: 234 VCFAADIKQVPNMSSMCVFSIKASGFLYHQIRLTMAILALVGNKLEKSTIVKELLDVEKY 293

Query: 227 -RKECGPLAPPEGLYFDSVEY 246
            R+     A P+GL     EY
Sbjct: 294 PRRPSYKYANPDGLVLIDCEY 314


>gi|313245560|emb|CBY40253.1| unnamed protein product [Oikopleura dioica]
          Length = 402

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 103/261 (39%), Gaps = 43/261 (16%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH--------GAGRTDSGVHALRQV 61
           Y+G+ Y G QR    +  + +IE  IF       VV           GRTD GVHA+  V
Sbjct: 73  YDGTKYNGLQRSPVPAG-KTTIEDVIFDAMLRTKVVDDIGTADYIAGGRTDKGVHAVNNV 131

Query: 62  AHF--------DLVREWVPV---ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
                      D + E V V        +N  L   D I I + + +   F ARF+   R
Sbjct: 132 ISLFVNSRLSEDEINENVTVGERNFVAIINRQL--PDDIWITSWAQISSDFSARFNCKSR 189

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            Y Y                      LD E M+ AA +L+G HDF  F     +  + +R
Sbjct: 190 HYNY----------------IFDSSGLDVELMKEAASYLIGEHDFRNFSQAQLERQNTVR 233

Query: 171 TIDHFDVNSFGNLIEI---RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD- 226
                D+    N+  +    + A  FL+ QIR  +  L LVG+    ST +++ L  +  
Sbjct: 234 VCFAADIKQVPNMSSMCVFSIKASGFLYHQIRLTMAILALVGNKLEKSTIVKELLDVEKY 293

Query: 227 -RKECGPLAPPEGLYFDSVEY 246
            R+     A P+GL     EY
Sbjct: 294 PRRPSYKYANPDGLVLIDCEY 314


>gi|108760886|ref|YP_632235.1| putative tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
 gi|108464766|gb|ABF89951.1| putative tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
          Length = 281

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 78/258 (30%), Positives = 108/258 (41%), Gaps = 23/258 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           I   + I Y G  + G+QRQ  G ++Q ++E+A+  V G    +  +GRTD GVHA  QV
Sbjct: 9   IPVALWIWYRGGIFRGFQRQPEGPTVQSALEEALRSV-GVPATLMPSGRTDRGVHARMQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ--FHARFSAIRRSYLYR---- 115
               L        L K L   L        L L  V +   FHA++SA  + Y YR    
Sbjct: 68  VSVRLEAGDSAESLEKRLPPRLPPG-----LGLCGVRRPTSFHAQWSACGKEYRYRFQLG 122

Query: 116 --IITRQAPLALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP--IR 170
             ++   AP AL+      L   ++  E +    +   G  DF  F     + SSP   R
Sbjct: 123 GAVMPEWAPYALDVSAEPLLQATAVTPERLAALLRSAEGTRDFIAFH----EKSSPRKPR 178

Query: 171 TIDHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           T++   +++  G L E R+    F   QIR  VGS   V  G         AL+     E
Sbjct: 179 TLESATLHALGGGLYEARLRGDGFARYQIRYLVGSALKVAAGLLPEEAWLAALETGQAME 238

Query: 230 CGPLAPPEGLYFDSVEYS 247
            G  AP  GL    V Y 
Sbjct: 239 -GFKAPAHGLVLWEVRYP 255


>gi|296187337|ref|ZP_06855732.1| tRNA pseudouridine synthase A domain protein [Clostridium
           carboxidivorans P7]
 gi|296047859|gb|EFG87298.1| tRNA pseudouridine synthase A domain protein [Clostridium
           carboxidivorans P7]
          Length = 120

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/107 (38%), Positives = 61/107 (57%), Gaps = 7/107 (6%)

Query: 6   MIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+I+Y+GS Y GWQ+Q +      S+IQ  IE  +  +TGE + V G GRTD+GVHA   
Sbjct: 6   MLIQYDGSRYKGWQKQNHKDNNSVSTIQDKIESVLSKMTGEDIQVVGCGRTDTGVHAENY 65

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           VA+F          + K L  +L   + I + +L    ++FHAR++A
Sbjct: 66  VANFHTDSILTVEDMLKYLYEFL--PEDIVVKSLRDTSERFHARYNA 110


>gi|72390247|ref|XP_845418.1| pseudouridine synthase A-like protein [Trypanosoma brucei TREU927]
 gi|62360588|gb|AAX81000.1| pseudouridine synthase A-like protein, putative [Trypanosoma
           brucei]
 gi|70801953|gb|AAZ11859.1| pseudouridine synthase A-like protein, putative [Trypanosoma brucei
           brucei strain 927/4 GUTat10.1]
          Length = 428

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 100/245 (40%), Gaps = 36/245 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + Y+G  Y G  RQ    +     +  ++E+  F+           GRTD GV AL  V 
Sbjct: 31  LAYHGHIYCGLVRQAETPNTVEAYLVAALERLRFVEPSGPKDFSRCGRTDKGVSALGNVV 90

Query: 63  HF-DLVREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            F      W        P+  C+ LN  L    TI I+  S V+  F ARFS   R+Y Y
Sbjct: 91  SFTSRASSWATDEQQQPPLDYCEKLNNVL--PPTIRIVGWSYVNADFDARFSCTGRTYRY 148

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTID 173
               R                 L+ E MR A  +L G H+F  F ++     ++  R + 
Sbjct: 149 YFCNR----------------GLNLEAMRKAVGYLKGVHNFRNFCKTDVVNVNNYERHVR 192

Query: 174 HFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           H D+     L ++     + A SFL+ QIR  +  L LVG        +++ L   DRK 
Sbjct: 193 HADIVGSDMLPDLVSYFEIEANSFLYNQIRCTMEVLFLVGRCLEEPEVVKQLLDCGDRKP 252

Query: 230 CGPLA 234
             PLA
Sbjct: 253 VYPLA 257


>gi|305432148|ref|ZP_07401314.1| tRNA pseudouridine synthase A [Campylobacter coli JV20]
 gi|304444813|gb|EFM37460.1| tRNA pseudouridine synthase A [Campylobacter coli JV20]
          Length = 240

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 102/242 (42%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +  S+Q +++ A+  + G    V  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSKFLGSATQPHKKSVQDALQDALSHL-GIFSSVLMASRTDKGVHASYAVACVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  +  L K +N +      I + NL I+   F  R+    R Y Y I        
Sbjct: 64  CGEHFRDLNYLKKQINKF--SHPFIHVKNLKIMPSNFEVRYDVKSREYRY-IFYHGVYNP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    P  +D     +  Q+ VG  DF  F        + IR I      S+ +  
Sbjct: 121 FLASYVHFYP-FIDVLKADLVLQNFVGIKDFKFFCKSGGDNKTTIREIFLAKAYSYKDFT 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R  A  FL  QIR  V S+  V + K +  +L++ ++ + ++    LAPP GLY   +
Sbjct: 180 IFRFKANGFLRAQIRLMVASVLKVLENKMSIEELKEQIEVK-KQYNHFLAPPCGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 SY 240


>gi|222823975|ref|YP_002575549.1| tRNA pseudouridine synthase A [Campylobacter lari RM2100]
 gi|222539197|gb|ACM64298.1| tRNA pseudouridine synthase A [Campylobacter lari RM2100]
          Length = 244

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 106/242 (43%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +   Y+GS + G   Q +  S+Q ++E+A+  + G       A RTD GVHA   VA   
Sbjct: 5   LTFSYDGSKFQGSATQPHKLSVQDALEQALSHL-GIYNKTLFASRTDKGVHANNGVACVK 63

Query: 66  LVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +   +  ++  K  +N +      I I ++  V + F  RF   +R+Y Y II+ +    
Sbjct: 64  VGEHFKDLLYLKNKINHF--AHPFIHIKHIQKVHENFQVRFDVKKRAYRY-IISHERYNP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    PK ++ +  +  A    G HDF  F+       +  R I    V ++ N  
Sbjct: 121 FLASYVHFYPK-INIQLAKKIASLFEGEHDFKLFQKEGSDNKTTTRIIYKSKVYTYKNCT 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                A  FL +QIR  + S+  V + K +  +L++ + A+ +     LAP  GLY   +
Sbjct: 180 IFYFEANGFLRSQIRMMIASILKVLEKKISQENLKEQIDAK-KAHIRLLAPASGLYLSKI 238

Query: 245 EY 246
            Y
Sbjct: 239 SY 240


>gi|300709217|ref|XP_002996775.1| hypothetical protein NCER_100100 [Nosema ceranae BRL01]
 gi|239606099|gb|EEQ83104.1| hypothetical protein NCER_100100 [Nosema ceranae BRL01]
          Length = 313

 Score = 67.0 bits (162), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 94/218 (43%), Gaps = 23/218 (10%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF- 64
           ++I Y+G  Y G    K+G SI   I+ A+ L T    +V+ AGRTD GV A+  VA   
Sbjct: 41  LLISYHGEKYRGLAECKDGDSIGNRIKNALLLSTLADHIVY-AGRTDKGVSAIGMVASVK 99

Query: 65  --DLVREWVPVILCKA-----------LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
              L+RE                    LN YL   + I ++  + V+  F ARF+ I+R 
Sbjct: 100 IKSLLRENTSRYFLNDDDNHEFNYQAILNNYL--PEDIRVIGWAPVEDGFSARFTCIKRK 157

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y Y       P    K +  L     D   M    Q ++   +F        +++   RT
Sbjct: 158 YRYYFTN---PFVKIKNQIRL---KYDINKMEEMCQKILTLKNFYNLSKHSDKSARYNRT 211

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           +D   +   G+L  + + A+SFLH  +R     L++ G
Sbjct: 212 VDICQIIKEGDLYYLDIQAKSFLHNMVRKIFWVLEMAG 249


>gi|256384180|gb|ACU78750.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256385012|gb|ACU79581.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455760|gb|ADH21995.1| tRNA pseudouridine synthase A (tRNA-uridine isomeraseI) (tRNA
           pseudouridylate synthase I) [synthetic Mycoplasma
           mycoides JCVI-syn1.0]
          Length = 251

 Score = 67.0 bits (162), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 108/246 (43%), Gaps = 15/246 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           Y+GS Y GW  Q N  SIQ ++ KAI   + T +   + GA +TD+ VHAL Q     L+
Sbjct: 11  YDGSNYHGWINQTNAISIQTTLNKAIKKVIKTDQFKTI-GASKTDTNVHALDQKVL--LI 67

Query: 68  REWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             + P++    KA+N  L  SD I IL+   VD  F+ R     + Y Y I      +  
Sbjct: 68  IYFTPILEKFIKAINKALP-SD-IKILDAKFVDPNFNIR-EVEYKIYHYYINDHHFDIFT 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDVNSFGN 182
            +   +     +D   ++      +G H+F  F  +           RTID   V    N
Sbjct: 125 NRYEYFWKHSKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVLRINN 184

Query: 183 LIEIRVVARSFLHTQIRSFVGS-LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            + I   A  F+  QIR  + + L    + K ++T L + L+   +K    +   +GL  
Sbjct: 185 KVVIEFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLKGIGKK-TPFIIDAKGLVL 243

Query: 242 DSVEYS 247
             ++++
Sbjct: 244 QKIQFN 249


>gi|291550669|emb|CBL26931.1| Pseudouridylate synthase [Ruminococcus torques L2-14]
          Length = 260

 Score = 67.0 bits (162), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 96/231 (41%), Gaps = 32/231 (13%)

Query: 6   MIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + ++Y+G+ Y GW+R +   N  ++   IE  +  VTG  V +    RT+ GVHA     
Sbjct: 6   LTLQYDGTRYLGWKRPEKDHNDRTVSYKIENVLEKVTGTPVTLFSGVRTEPGVHARNLTV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI------ 116
           +F    +  P      LN YL     I++L+     ++F A  +A   +Y Y +      
Sbjct: 66  NFLTESQLTPAEFKTVLNQYL--PQDIAVLDAVSTPERFRADLNAREITYEYAMDLSPIY 123

Query: 117 -------------ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
                        +   +   L   +   +P  L    M  AA  L+G HDF  F SI  
Sbjct: 124 DLFHKNYRGRLTDLLSDSLFDLPPEQTAELPNIL---LMETAAHSLLGTHDFKHFSSIRK 180

Query: 164 QASS--PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +  +   I+TI      S    + IR+ A  FL+      +G+L  +G GK
Sbjct: 181 KKGTEKEIKTITFVTEES---TLYIRMTANDFLYQMAPFILGTLLDIGIGK 228


>gi|316969725|gb|EFV53781.1| tRNA pseudouridine synthase A [Trichinella spiralis]
          Length = 380

 Score = 67.0 bits (162), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 107/261 (40%), Gaps = 64/261 (24%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK---------------AIFLVT--GEIV 43
           M RY     Y GS + G Q Q N  ++QG +E                A+ L++  GE  
Sbjct: 71  MPRYFFNFAYLGSRFSGSQSQPNQLTVQGVLEVSLIKFAYFDCRQNVLAMILLSPLGEEP 130

Query: 44  VVHGAGRTDSGVHALRQVAHFDL--VREWVPVILCKALNAYL-KISDTISILNLSIVDKQ 100
             + + RTD+GVHA    A  DL   R++    L  ALN+ L K+   I I +   V   
Sbjct: 131 RWYFSSRTDAGVHAFMNTATVDLDPERDFDSDYLKSALNSMLTKLDMEIRINSCRRVSGG 190

Query: 101 FHARFSAIRRSYLYRI-------------------ITRQA----PLALEKGRAWLIPKSL 137
           F AR  A+ R YLYR+                    T+ A    PL +E  RAW +  + 
Sbjct: 191 FCARRHALEREYLYRLAILKPEFESDHHKQTNNTSTTQNAHHSLPL-IEHRRAWALSSAF 249

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHC------QASSPIRTIDHFDVN------------- 178
           + E  R AA    G H+F +F +            + ++ I   D++             
Sbjct: 250 NHERFRKAALMFQGSHNFASFMTNSVGNLDRPTGIATVKNISRLDIDFGKALMDSKHEPC 309

Query: 179 -SFGNLIEIRVVARSFLHTQI 198
             F N  ++  V+RSFL+ Q+
Sbjct: 310 SDFFNFFDVSFVSRSFLYNQV 330


>gi|261328820|emb|CBH11798.1| pseudouridine synthase A-like protein, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 458

 Score = 67.0 bits (162), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 100/245 (40%), Gaps = 36/245 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + Y+G  Y G  RQ    +     +  ++E+  F+           GRTD GV AL  V 
Sbjct: 61  LAYHGHIYCGLVRQAETPNTVEAYLVAALERLRFVEPSGPKDFSRCGRTDKGVSALGNVV 120

Query: 63  HF-DLVREWV-------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            F      W        P+  C+ LN  L    TI I+  S V+  F ARFS   R+Y Y
Sbjct: 121 SFTSRASSWATDEHQQPPLDYCEKLNNVL--PPTIRIVGWSYVNADFDARFSCTGRTYRY 178

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTID 173
               R                 L+ E MR A  +L G H+F  F ++     ++  R + 
Sbjct: 179 YFCNR----------------GLNLEAMRKAVGYLKGVHNFRNFCKTDVVNVNNYERHVR 222

Query: 174 HFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           H D+     L ++     + A SFL+ QIR  +  L LVG        +++ L   DRK 
Sbjct: 223 HADIVGSEMLPDLVSYFEIEANSFLYNQIRCTMEVLFLVGRCLEEPEVVKQLLDCGDRKP 282

Query: 230 CGPLA 234
             PLA
Sbjct: 283 VYPLA 287


>gi|323455279|gb|EGB11148.1| hypothetical protein AURANDRAFT_21872 [Aureococcus anophagefferens]
          Length = 264

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 103/264 (39%), Gaps = 34/264 (12%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV----AH 63
           ++Y G  + GWQ Q N  S+      A+            AGRTD GV+A  QV    + 
Sbjct: 9   LQYLGDAFAGWQPQPNERSVHDVFAAALSNAGITDCGAVAAGRTDRGVNAAHQVVSVRSD 68

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            D   E +  +L    +    +   + +L+       FHA  SA  + Y Y +       
Sbjct: 69  ADRGDEDLSAVL---RDVSAALPGDVRVLSCRQAPASFHAITSARSKRYAYYL-----GF 120

Query: 124 ALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDF------------TTFRSIHCQASSPIR 170
           + +  R +W  P  LD   +R  A  LVG  DF            +T RS+       + 
Sbjct: 121 SEDAARYSWQAPPGLDVGRVRRGAALLVGERDFRAFCAPGGRKCGSTVRSLRSVEIDDLE 180

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           T +   V     L+ I      FL  Q R  VG+L  +G G  +   +E AL   D +  
Sbjct: 181 TAELPFVGRVRGLLRIAFDGDGFLKHQCRKIVGALVRLGTGALSEAQVEAAL--ADPRGA 238

Query: 231 GP-------LAPPEGLYFDSVEYS 247
            P        AP  GL+ + V+Y+
Sbjct: 239 HPAVSSRRFAAPARGLWLERVDYA 262


>gi|154341677|ref|XP_001566790.1| pseudouridine synthase A-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134064115|emb|CAM40310.1| putative pseudouridine synthase A-like protein [Leishmania
           braziliensis MHOM/BR/75/M2904]
          Length = 499

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 72/264 (27%), Positives = 114/264 (43%), Gaps = 45/264 (17%)

Query: 8   IEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHG------AGRTDSGVHAL-- 58
           + Y+G  + G  +QK   ++++G +  A+  V   ++   G       GRTD GV AL  
Sbjct: 66  LAYHGHVHDGLAKQKETDNTVEGLVCDALRRV--RLIPEDGPHNFGRCGRTDKGVSALGN 123

Query: 59  ------RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
                 R     D   +  P+  C  LN  L    TI I+  ++VD +F ARFS + R+Y
Sbjct: 124 AFSLTARASCTADADPQLPPLDYCSMLNNVLP--STIRIVGCALVDDRFDARFSCVHRTY 181

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRT 171
            Y                +   + L+   M+ AA   +G H+F  F  +     S+  RT
Sbjct: 182 RY----------------YFCHRGLNLAAMQEAAAFFLGTHNFRNFCQMDVVNVSNFTRT 225

Query: 172 IDHFDVNSFGNLIE----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           +    ++    L E    + + A SFL+ QIR  +  L LVG G    + ++  L+  D 
Sbjct: 226 VLSVGLHPSEELPELISYLEITANSFLYHQIRCTMEVLFLVGRGLEAPSVVQTMLELGDC 285

Query: 228 KECGPLAPPEGL-----YFDSVEY 246
           K   PLA    L      FD+V++
Sbjct: 286 KPTYPLADGTPLILWDCAFDNVQW 309


>gi|30692743|ref|NP_198390.2| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|27311599|gb|AAO00765.1| putative protein [Arabidopsis thaliana]
 gi|30725698|gb|AAP37871.1| At5g35400 [Arabidopsis thaliana]
 gi|332006580|gb|AED93963.1| tRNA pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 420

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 69/127 (54%), Gaps = 16/127 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHG----A 48
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++          L+  +   + G    A
Sbjct: 93  VNFKIVLSYNGASFDGWQKQPDLHTVQGVVEKSLGGFVDERKAQLLKKKCKPLEGRVLVA 152

Query: 49  GRTDSGVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL QV  F   R+ + P+ +  A+N     S  + ++++S V + FH  FSA
Sbjct: 153 GRTDKGVSALNQVCSFYTWRKDIEPIAIEDAINK--DASGKLRVVSISKVSRSFHPNFSA 210

Query: 108 IRRSYLY 114
             R YLY
Sbjct: 211 KWRRYLY 217


>gi|315638468|ref|ZP_07893645.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis JV21]
 gi|315481459|gb|EFU72086.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis JV21]
          Length = 240

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 108/248 (43%), Gaps = 11/248 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G   Q + +S+Q ++  A+  + G    V  A RTD GVHALR V
Sbjct: 1   MRLKLVFSYDGSAFLGSASQPHLNSVQDALAAALAHL-GIFSPVLFASRTDKGVHALRAV 59

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +  + +  ++ L + +N +      I I +L  V + +  RF    R+  YR I   
Sbjct: 60  ACVECGKHFKDLVYLKRQINRF--AHPFIHIKSLERVSENYAVRFDV--RAREYRYIFHH 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                   R     +  D +       H VG  DF  F+     A + +R +      ++
Sbjct: 116 GEFNPFLSRYVCFSERFDIKRANELLSHFVGEKDFKFFQKAGGSAKTSVRIMFFARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP--LAPPEG 238
            +L      A  FL  QIR  V S+  V  G+ +   L++ ++A   K C    LAP  G
Sbjct: 176 KDLSIFCFRANGFLRAQIRLSVASVMAVLRGELSEDKLKEQIEA---KACHYRLLAPANG 232

Query: 239 LYFDSVEY 246
           LY   + Y
Sbjct: 233 LYLSRIIY 240


>gi|154503357|ref|ZP_02040417.1| hypothetical protein RUMGNA_01181 [Ruminococcus gnavus ATCC 29149]
 gi|153796024|gb|EDN78444.1| hypothetical protein RUMGNA_01181 [Ruminococcus gnavus ATCC 29149]
          Length = 252

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 5/159 (3%)

Query: 6   MIIEYNGSGYFGWQ---RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + +EY+G+ Y GW+   +++N  ++ G I  A+  +  E + +  A +TD GVHA  Q+ 
Sbjct: 6   LTVEYDGTRYAGWKAAPKKENLDTVLGRIHTALARLLKEDIQLFCAAKTDPGVHARGQIL 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F      +P  L  +LN  L     I++L+   V ++FHA        +   I T   P
Sbjct: 66  SFQTTSSLLPSALKSSLNQVL--PQDIAVLDARQVSERFHAELLPKHCIWELCIKTGPTP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
               +     +P   D   M+ A   L GRHD   F  +
Sbjct: 124 DVFRQKYTLFLPDLPDPLRMQEAFSFLKGRHDVRCFSPV 162


>gi|67484392|ref|XP_657416.1| pseudouridine synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56474668|gb|EAL52030.1| pseudouridine synthase, putative [Entamoeba histolytica HM-1:IMSS]
          Length = 366

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 83/204 (40%), Gaps = 33/204 (16%)

Query: 23  NGSSIQGSIEKAIF----LVTGEIVVVHGAGRTDSGVHALRQVAHF----DLVREWV--- 71
           N  +I+  + KA+F    +   +    +  GRTD GV A  QV       +L  E +   
Sbjct: 70  NDGTIEYQLFKALFKTRLIQNTKDCKYNRCGRTDKGVSAFGQVVDLWVRSNLKDETILYT 129

Query: 72  ----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                +  C+ LN  L     I  L    V   F++RFS   R+Y Y             
Sbjct: 130 KREGELDYCRMLNGLLPTD--IRCLGWCGVPDDFNSRFSCQSRTYHY------------- 174

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
              +  P S D   M+ AAQ  +G HDFT F       S  +R ++ F+V     L    
Sbjct: 175 ---YFDPSSYDVPKMKEAAQLFLGEHDFTNFCKKDPAVSHCVRRVNSFEVEETDGLSRFV 231

Query: 188 VVARSFLHTQIRSFVGSLKLVGDG 211
           V   +F+  Q+R  VG+L  +G G
Sbjct: 232 VCGTAFVWHQVRYMVGALFAIGQG 255


>gi|297805092|ref|XP_002870430.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297316266|gb|EFH46689.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 420

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 69/127 (54%), Gaps = 16/127 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHG----A 48
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++          L+  +   + G    A
Sbjct: 93  VNFKIVLSYNGTSFDGWQKQPDLHTVQGVVEKSLGGFVDDRKAQLLKKKCKPLEGRVLVA 152

Query: 49  GRTDSGVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL QV  F   R+ + P+ +  A+N     S  + ++++S V + FH  FSA
Sbjct: 153 GRTDKGVSALNQVCSFYTWRKDIEPIAIEDAINK--DASGKLRVVSISKVSRSFHPNFSA 210

Query: 108 IRRSYLY 114
             R YLY
Sbjct: 211 KWRRYLY 217


>gi|283954398|ref|ZP_06371918.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           414]
 gi|283794015|gb|EFC32764.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           414]
          Length = 240

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 101/242 (41%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +  S+Q  + +A+  + G    +  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSAFLGSATQPHKKSVQDVLGEALSHL-GIFSPLLMASRTDKGVHASYAVASVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGEYFTNLEYLKKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHASYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    PK  D +         VG+ D   F        + +R I      ++ +  
Sbjct: 121 FMASYVHFYPK-FDLDKANELLSFFVGKKDLKFFCKSGGDNKTTLREIFLARAYTYKDFS 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R  A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   +
Sbjct: 180 IFRFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNRFLAPPNGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 HY 240


>gi|332006581|gb|AED93964.1| tRNA pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 471

 Score = 66.2 bits (160), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 42/130 (32%), Positives = 71/130 (54%), Gaps = 22/130 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FL--------------VTGEIVVV 45
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++  F+              + G ++V 
Sbjct: 93  VNFKIVLSYNGASFDGWQKQPDLHTVQGVVEKSLGGFVDERKAQLLKKKCKPLEGRVLV- 151

Query: 46  HGAGRTDSGVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
             AGRTD GV AL QV  F   R+ + P+ +  A+N     S  + ++++S V + FH  
Sbjct: 152 --AGRTDKGVSALNQVCSFYTWRKDIEPIAIEDAINK--DASGKLRVVSISKVSRSFHPN 207

Query: 105 FSAIRRSYLY 114
           FSA  R YLY
Sbjct: 208 FSAKWRRYLY 217


>gi|292655987|ref|YP_003535884.1| tRNA pseudouridine synthase A [Haloferax volcanii DS2]
 gi|291370921|gb|ADE03148.1| tRNA pseudouridine synthase A [Haloferax volcanii DS2]
          Length = 283

 Score = 66.2 bits (160), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 65/247 (26%), Positives = 102/247 (41%), Gaps = 31/247 (12%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHALRQVA 62
           + Y+G  Y G+QRQ +  +++ +I  A   +       E      AGRTD+GV AL Q  
Sbjct: 6   VAYDGRPYHGFQRQPDVPTVEDAIFDACRALGVCDDDEEPTDYAAAGRTDAGVSALAQTV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F+      P    +ALN+  ++  T+     +     FHAR    RR Y+Y +    AP
Sbjct: 66  AFECPDWCTP----RALNS--ELPGTVRAWADADAPDDFHARHWPTRREYVYDL---HAP 116

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                       +  D +  + A     G HD   FR++       +R ID   +   G+
Sbjct: 117 T-----------EGFDDDRAKAAFDACRGDHD---FRNLTPDDHGTVRAIDGG-LTRDGD 161

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLY 240
            + +RV A  F    +R  V  ++ VG      + ++ AL     D  E    APP  L 
Sbjct: 162 FLLVRVEAGGFARELVRRLVSLVRAVGSDAAPLSKVDDALGPDHLDGPEGIAPAPPTPLL 221

Query: 241 FDSVEYS 247
             +V+Y 
Sbjct: 222 LTAVDYP 228


>gi|86153529|ref|ZP_01071733.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           HB93-13]
 gi|85843255|gb|EAQ60466.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           HB93-13]
          Length = 241

 Score = 66.2 bits (160), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 65/247 (26%), Positives = 104/247 (42%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA  +    +V +  L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +            PK  D +         VG+ D   F        + +R I      +
Sbjct: 117 SSYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GL
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLSRICY 241


>gi|294790441|ref|ZP_06755599.1| tRNA pseudouridine synthase A [Scardovia inopinata F0304]
 gi|294458338|gb|EFG26691.1| tRNA pseudouridine synthase A [Scardovia inopinata F0304]
          Length = 382

 Score = 66.2 bits (160), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 57/198 (28%), Positives = 88/198 (44%), Gaps = 42/198 (21%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGA------- 48
           +R  +   Y+G+ + GW RQ +  ++QG +E AI  V       G+      A       
Sbjct: 1   MRLKIDCSYDGTDFHGWARQPDLRTVQGELEAAIAKVLHLWQPAGQTADYPSAFAKALAN 60

Query: 49  --------------GRTDSGVHALRQVAHFDLVREWV--------PVIL--CKALNAYLK 84
                         GRTD+GVHA  QV H DL ++ +        P       AL   L+
Sbjct: 61  QSAPVSFWPHLVVAGRTDTGVHARGQVCHLDLDQDLLGRAQGHLDPARFKPWDALTYRLR 120

Query: 85  --ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP--KSLDCE 140
             + D +S+  +S   + F ARFSA  R Y+YR+   Q      + R++++   +S D +
Sbjct: 121 RILPDDLSVSAISPAPEGFDARFSASDRVYVYRVADDQTSYD-PRLRSFVLNLRRSTDIQ 179

Query: 141 NMRIAAQHLVGRHDFTTF 158
            M  A   +VG HDF +F
Sbjct: 180 IMNTALAEIVGLHDFGSF 197


>gi|145590498|ref|YP_001152500.1| pseudouridylate synthase [Pyrobaculum arsenaticum DSM 13514]
 gi|166228752|sp|A4WHI1|TRUA_PYRAR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145282266|gb|ABP49848.1| Pseudouridylate synthase [Pyrobaculum arsenaticum DSM 13514]
          Length = 257

 Score = 66.2 bits (160), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 109/249 (43%), Gaps = 43/249 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQVA 62
           Y   I Y+G+ ++G+    N      S+E  +    GEI+   G G RTD GV A+  V 
Sbjct: 3   YLYRIAYDGTLFYGFTGHPN------SLEPKLRAALGEIL---GRGSRTDPGVSAVANV- 52

Query: 63  HFDLVREWVPVILCKALN-AYL--KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                     V+  + L+  Y+  K+   +    ++ V + F+ R +  RR YLY     
Sbjct: 53  ----------VMTSQRLHLGYVNSKLPRGVWAWGVAEVPEGFNPRRAKARR-YLY----- 96

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVN 178
            AP   E           D E MR AA  LVG HD+++F       ++P + T+   +V 
Sbjct: 97  VAPHWGE-----------DVEAMREAAAVLVGTHDYSSFIKRRGDKATPTVTTVYKIEVE 145

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G LI +  V R F +  IR    ++   G G   ++DL + L  + R    P AP EG
Sbjct: 146 QRGGLIYMMFVGRGFRNKMIRKMAWAILATGRGVLKASDL-RELVERPRPGAVPSAPAEG 204

Query: 239 LYFDSVEYS 247
           L    ++Y 
Sbjct: 205 LVLLDIDYG 213


>gi|71665382|ref|XP_819661.1| pseudouridine synthase A-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70884973|gb|EAN97810.1| pseudouridine synthase A-like protein, putative [Trypanosoma cruzi]
          Length = 429

 Score = 65.9 bits (159), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 104/245 (42%), Gaps = 36/245 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + Y+G  Y G  +Q+  S+     +  +++    +     + +   GRTD GV AL  V 
Sbjct: 46  LAYHGHLYDGLAKQEETSNTVEAYVVAALKHVRLIPQDGPIDLARCGRTDKGVSALGNVF 105

Query: 63  HFDL-VREWV------PVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
              +    W       P +  C  LN+ L +  TI I+  + VD  F ARFS + R+Y Y
Sbjct: 106 SLTVRASSWPTDSPQKPALDYCAMLNSALPV--TIRIVGWAYVDDTFDARFSCVGRTYRY 163

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS----PIR 170
                           +   + L+ E M  AA  L G H+F  F        S     +R
Sbjct: 164 ----------------YFCHRGLNVEAMGNAAARLKGVHNFRNFCKTDVVNVSNYERDVR 207

Query: 171 TIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           ++  F   +F  L+  + + A SFL+ QIR  +  L LVG G      + + L+  DRK 
Sbjct: 208 SVGIFASEAFPELVSYLEIHANSFLYHQIRCTMEVLFLVGRGLEDPEVVTQLLERGDRKP 267

Query: 230 CGPLA 234
             PLA
Sbjct: 268 VYPLA 272


>gi|154148265|ref|YP_001406534.1| tRNA pseudouridine synthase A [Campylobacter hominis ATCC BAA-381]
 gi|153804274|gb|ABS51281.1| tRNA pseudouridine synthase A [Campylobacter hominis ATCC BAA-381]
          Length = 278

 Score = 65.9 bits (159), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 91/208 (43%), Gaps = 7/208 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           I+  +I  ++GS + G Q Q NG +++  +  A+F       V+  A RTD GVHAL QV
Sbjct: 5   IKIRLIYSFDGSKFCGSQTQPNGKAVEDRLNSALFRCGINEKVI-SASRTDKGVHALSQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           +       W    L   +N + K S  I +  +   D+ F  RF A  RSY Y I+    
Sbjct: 64  STTHCAAFWDLQNLRHFINRHAKPS--IYVRKIERADENFQVRFDAKARSYRY-ILNHDE 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                    +  P+ +    + ++    VG+HDF+ F      AS  +R I       + 
Sbjct: 121 FSPFFSNYFYFYPE-ISPFLLNLSLGIFVGKHDFSEFMK-SGSASGSVREIYKAFAYRYK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGS-LKLV 208
           N   I   A  FL  Q+R  V + LK V
Sbjct: 179 NFTIINFKANGFLRAQVRLMVANALKCV 206


>gi|18312431|ref|NP_559098.1| tRNA pseudouridine synthase ACD [Pyrobaculum aerophilum str. IM2]
 gi|24212564|sp|Q8ZXR6|TRUA_PYRAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|18159888|gb|AAL63280.1| tRNA pseudouridine synthase A [Pyrobaculum aerophilum str. IM2]
          Length = 256

 Score = 65.9 bits (159), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 108/247 (43%), Gaps = 41/247 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAG-RTDSGVHALRQVA 62
           Y   I Y+G+ ++G+    N      S+E  + L+ GEI+   G G RTD GV A+  V 
Sbjct: 3   YLYRIAYDGTMFYGFTGHPN------SLEPRLRLIFGEIL---GRGSRTDPGVSAVGNVV 53

Query: 63  HF--DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                +   +V   + K   A+           ++ V + F+ R + +RR YLY      
Sbjct: 54  MTGRKMALGYVNSKMPKGAWAW----------GIAEVPEGFNPRRAKLRR-YLY-----V 97

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNS 179
           AP   E           D + MR AA+ L G HD+++F  +  +  +P + T+   DV  
Sbjct: 98  APHWGE-----------DVDVMREAAKLLTGTHDYSSFIQLRGEKHTPTVTTVYDIDVTL 146

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LI I    R F +  IR    +L   G G  +  DL   L+ + R    P AP EGL
Sbjct: 147 RGDLIFIYFAGRGFRNKMIRKMAWALLAAGRGVLSVDDLADLLK-KPRPGAVPSAPAEGL 205

Query: 240 YFDSVEY 246
               + Y
Sbjct: 206 VLLDIVY 212


>gi|145355737|ref|XP_001422107.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582347|gb|ABP00424.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 308

 Score = 65.9 bits (159), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 71/258 (27%), Positives = 108/258 (41%), Gaps = 25/258 (9%)

Query: 3   RYCMI-IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTD 52
           R C +   Y G+GY G QR     +I+G +E AI    G      G         A RTD
Sbjct: 3   RKCAVTFAYVGAGYAGMQRNPGVRTIEGELEGAIARAGGISDANAGDFAKVQWTRAARTD 62

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV    +V E  P  + + +NA L   +   +  +  V   F+A+    RR Y
Sbjct: 63  KGVSAVGQVVALKMVLE--PSGMVERINAAL--PERFEVFGIDRVTGGFNAKTMCDRRRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAA--QHLVGRHDFTTF----RSIHCQAS 166
            Y I TR     L    A       +    R+    ++  G H+F  +    +    QA 
Sbjct: 119 EYVIPTRAFDPNLGAEGAAEAFAFTEETRSRVDGVLKNYCGTHNFHNYTVKVKPTDAQAK 178

Query: 167 SPIRTID---HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             I + +    F+V      +  +VV +SF+  QIR  +G++  V  G+ T  D + AL 
Sbjct: 179 RYIISFECSAPFEVEG-EQFVRCQVVGQSFMLHQIRKLIGTMLAVVRGELTEDDQKFALL 237

Query: 224 AQDRKECGPLAPPEGLYF 241
             +     P+AP  GL+ 
Sbjct: 238 THEFVPT-PMAPELGLFL 254


>gi|321464475|gb|EFX75483.1| hypothetical protein DAPPUDRAFT_323292 [Daphnia pulex]
          Length = 429

 Score = 65.9 bits (159), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 67/256 (26%), Positives = 112/256 (43%), Gaps = 37/256 (14%)

Query: 8   IEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + Y G  Y G+  Q++      + +  ++EK   L + E    H  GRTD GV +  Q  
Sbjct: 73  VAYVGWDYAGFVVQEHTEKTIEAEVFKALEKTRLLESRETSNYHRCGRTDKGVSSFGQAI 132

Query: 63  HFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR-----FSAIRRSYLY 114
             DL   + E   V +     A  K+ +T+ I  + I++K          ++ I +S   
Sbjct: 133 SIDLRSNLSEGKGVFIPDGHQA--KVGNTVEIDYVGILNKVLPPEIRMIAWAPINQSLSA 190

Query: 115 RIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQ--------- 164
           R   RQ      +   +  PK+ L+ E MR+A+Q L+G HDF     +            
Sbjct: 191 RFDCRQ------RTYHYYFPKANLNIERMRVASQSLIGEHDFRNLCKMDVGNGVIKFDRR 244

Query: 165 -ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                I  ID    NS+ ++I ++++ ++FL  Q+R  V  L L+G GK  +T +++ L 
Sbjct: 245 IMDIQIEAIDDDKANSY-SMIRLKLIGQAFLWHQVRCIVAILFLIGQGKEETTIIQELLN 303

Query: 224 AQDRKECGPLAPPEGL 239
                E  P  P  G+
Sbjct: 304 V----ERNPRKPQYGM 315


>gi|305666822|ref|YP_003863109.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
 gi|88709046|gb|EAR01280.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
          Length = 282

 Score = 65.9 bits (159), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 64/259 (24%), Positives = 109/259 (42%), Gaps = 25/259 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G  + GWQ+Q    +++G I K + F++      +  AGRTDS V AL   A
Sbjct: 30  YVIKLQYLGFRFSGWQKQPGQKTVEGMITKTLKFILPNSEFKILSAGRTDSKVSALD--A 87

Query: 63  HFDL-VREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            F+L + E  P+   +A        +   I ++++  V++ F+       + Y+Y     
Sbjct: 88  AFELFINE--PLTDFEAFIGLFNKNLPSDIRVMSIKEVNEDFNIIQDPKVKEYVYLFSYG 145

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI------- 172
                        +   LD E M+ AA   VG HD + +       +   RTI       
Sbjct: 146 SKNHPYSSPFITNVLDELDLELMKKAASLYVGTHDLSVYTVKAQNNAHKKRTITSCEIIE 205

Query: 173 ------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
                 + F   S+      RV    F+  QIR  +G+L  +G G+    D+E +L   +
Sbjct: 206 NKILQANFFPEKSYA----FRVEGPGFMRYQIRMMMGALIQLGKGELLFADIENSLSNPE 261

Query: 227 RKECGPLAPPEGLYFDSVE 245
             E   +AP  GL  + ++
Sbjct: 262 SIELTYVAPGSGLLLNRLD 280


>gi|213622913|ref|ZP_03375696.1| tRNA pseudouridine synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. E98-2068]
          Length = 91

 Score = 65.5 bits (158), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 41/63 (65%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
          +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11 KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVV 70

Query: 63 HFD 65
          HF+
Sbjct: 71 HFE 73


>gi|86130141|ref|ZP_01048741.1| tRNA pseudouridine synthase A [Dokdonia donghaensis MED134]
 gi|85818816|gb|EAQ39975.1| tRNA pseudouridine synthase A [Dokdonia donghaensis MED134]
          Length = 259

 Score = 65.5 bits (158), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 65/255 (25%), Positives = 110/255 (43%), Gaps = 17/255 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GWQ+Q +  +++  +E+   +++  +   +  +GRTD+ V A   VA
Sbjct: 8   YLLKIQYLGFRYHGWQKQPDVLTVERMMERTFSYVLDRKNFKLLASGRTDAKVSA--NVA 65

Query: 63  HFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           + +L     P+        LN    +   I  L ++ VDK+F+   + I + Y+Y     
Sbjct: 66  YVELFLNDSPLPAEGFLTLLND--NLPQDIRCLQITQVDKKFNVMDAPIAKEYVYLFSYG 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--------RSIHCQASSPIRT 171
           +            I   LD E M+ AA+   G HDF ++        ++I    SS I  
Sbjct: 124 EKNHPFAAPYMINIAGDLDIELMKEAARLFEGEHDFRSYAYKPNPQTQTIGHVLSSTIEI 183

Query: 172 IDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            D +  + F       RV  + F   QIR  +G+L  +G G       +K L A +  + 
Sbjct: 184 NDLYTASFFPEESYAFRVSGKGFKRHQIRLMMGALFDLGQGNIDLEFFKKTLDASNDIKL 243

Query: 231 GPLAPPEGLYFDSVE 245
             +A   GL    V+
Sbjct: 244 TRIAQASGLLLQDVQ 258


>gi|270719040|ref|ZP_06223281.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
 gi|270315483|gb|EFA27724.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
          Length = 96

 Score = 65.1 bits (157), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 41/64 (64%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
          ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1  MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSCIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62 AHFD 65
           HF+
Sbjct: 61 VHFE 64


>gi|195449703|ref|XP_002072187.1| GK22713 [Drosophila willistoni]
 gi|194168272|gb|EDW83173.1| GK22713 [Drosophila willistoni]
          Length = 412

 Score = 65.1 bits (157), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 74/270 (27%), Positives = 113/270 (41%), Gaps = 33/270 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ YFG QR     +I+  + K +              +I     A RTD 
Sbjct: 65  KSAILLSYCGANYFGMQRNPGMQTIEEELFKVMLKHKWITEDSFEQVQIACFQRAARTDK 124

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  +    +  KA N  L   + I +  +  V K F+A+     R+Y 
Sbjct: 125 GVSAARQVCSVKLPDD----LDLKAFNEDL--PEQIRLFGVERVTKGFNAKDQCNARTYT 178

Query: 114 YRIITRQ-APLALEKGRAWLIP--KSLDC------ENMRIAAQHLVGRHDFTTFRSI-HC 163
           Y + T   AP   E  +    P  +S  C      + +R   Q   G  +F  F S  + 
Sbjct: 179 YTLPTVAFAPCQSESDKEAQPPEEQSTYCISPEHLQKVRETLQLYEGTKNFHNFTSKKNF 238

Query: 164 QASSPIRTI------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
              S  R I      D F        + ++V  +SF+  QIR  VG    +  G  T++ 
Sbjct: 239 LDPSAKRFIMLFSCSDPFKSPQGIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTTST 298

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 299 LERAL-TEERLDL-PMAPGLGLVLDTVHYE 326


>gi|194744150|ref|XP_001954558.1| GF18329 [Drosophila ananassae]
 gi|190627595|gb|EDV43119.1| GF18329 [Drosophila ananassae]
          Length = 410

 Score = 65.1 bits (157), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 73/266 (27%), Positives = 113/266 (42%), Gaps = 31/266 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQVQIACFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A NA L   D I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPDE----LDLEAFNADL--PDQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIITRQAPLALEK-----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS----IHCQ 164
           Y + T     + EK         + P+ L  E +R   +   G  +F  F S    +   
Sbjct: 185 YTLPTVAFASSEEKIEDLHDTYRITPELL--EKVRETLKLYEGTKNFHNFTSKKNFLDPS 242

Query: 165 ASSPIRTI---DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           A   I +    D F        + ++V  +SF+  QIR  VG    +  G  T+  LE+A
Sbjct: 243 AKRFIMSFVSSDPFLSPQGIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTTESLERA 302

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
           L  ++R +  P+AP  GL  D+V Y 
Sbjct: 303 L-TEERLDL-PMAPGLGLVLDTVHYE 326


>gi|121613330|ref|YP_001000512.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|166228692|sp|A1VZH1|TRUA_CAMJJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|121504241|gb|EAQ72335.2| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81-176]
          Length = 241

 Score = 65.1 bits (157), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 65/247 (26%), Positives = 103/247 (41%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA       +V +  L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVGCGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +            PK  D +         VG+ D   F        + +R I      +
Sbjct: 117 SSYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GL
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLSRICY 241


>gi|55379749|ref|YP_137599.1| tRNA pseudouridine synthase A [Haloarcula marismortui ATCC 43049]
 gi|62901222|sp|Q5UXW0|TRUA_HALMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|55232474|gb|AAV47893.1| tRNA pseudouridine synthase A [Haloarcula marismortui ATCC 43049]
          Length = 275

 Score = 65.1 bits (157), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 103/249 (41%), Gaps = 27/249 (10%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVV--VHGAGRTDSGVHALRQV 61
           + Y+G  Y G+QRQ +  +++G +  A+  +     GE +      AGRTD+GV A  Q 
Sbjct: 6   VAYDGQPYHGFQRQPDVDTVEGRLRSALVRLGVCERGEGLPDRYAAAGRTDAGVSARTQT 65

Query: 62  AHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             FD      P  L   A N   ++ + + +   + V + FHA   A  R+Y Y +    
Sbjct: 66  VAFD-----APAWLSPAAFNG--ELPNDVRVWASADVPEDFHATHDAAERTYTYYLY--- 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   ++       + +D      A   L G HD   F ++    +   RT+   D    
Sbjct: 116 APADADRPEH----EPVDDGRWADAVDALAGTHD---FHNLTTDETGTERTV-AIDWTRD 167

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEG 238
           G  + +++ A  F    +R  V     V DG    + +++ L  +     +  P APPE 
Sbjct: 168 GQFLVVQLTAGGFCRQLVRRLVSLAAAVADGSAPLSKVDRILSPEPVSGPDGVPPAPPEP 227

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 228 LVLTDVRYP 236


>gi|45360593|ref|NP_988969.1| pseudouridylate synthase 3 [Xenopus (Silurana) tropicalis]
 gi|38174435|gb|AAH61416.1| pseudouridylate synthase 3 [Xenopus (Silurana) tropicalis]
          Length = 505

 Score = 65.1 bits (157), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 97/230 (42%), Gaps = 49/230 (21%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVV------VHGAGRTDSGVHALR 59
           + Y G GY G+  Q+N    + ++E+ +F  L+   +V        H  GRTD GV AL 
Sbjct: 68  LAYLGWGYQGFASQEN---TKNTVEETVFNALIKTRLVESRQTSNYHRCGRTDRGVSALG 124

Query: 60  QVAHFDL--VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV   DL    E  P I     LN  L     I +L+ + V   F ARFS   R+Y Y  
Sbjct: 125 QVISLDLRCSGEGKPEIRYVHILNRVL--PPDIRVLSWAAVPPSFSARFSCRSRTYRY-- 180

Query: 117 ITRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTF-------------RSIH 162
                          L P   LD E M  AA+ L G HDF                R++ 
Sbjct: 181 ---------------LFPCAQLDVEAMDKAARLLEGTHDFRNLCKMDVANGVMNFIRTVL 225

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
                P+  I   D+  F  L  +++   +FL+ Q+R  +G L LVG GK
Sbjct: 226 SARVEPVPEIPG-DMGPF-QLYRLQITGLAFLYHQVRCIMGVLFLVGQGK 273


>gi|289192063|ref|YP_003458004.1| tRNA pseudouridine synthase A [Methanocaldococcus sp. FS406-22]
 gi|288938513|gb|ADC69268.1| tRNA pseudouridine synthase A [Methanocaldococcus sp. FS406-22]
          Length = 262

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 110/245 (44%), Gaps = 35/245 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSI----QGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M+    I++    G + +Q+Q +  ++      ++E+  FL   +I+  +  GRTD GV 
Sbjct: 1   MVITMHILKIAYDGRYSFQQQPHKQTVCDILLDTLEEIDFLAKKKII--YSGGRTDKGVS 58

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL      +L +E  P++    +NA LK    I +L    +D+    ++    R Y Y  
Sbjct: 59  ALGNFVIVELKKE--PIL--SYINAKLK-DKGIWVLGYREIDEIPKVKY----RHYRY-- 107

Query: 117 ITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDH 174
                          ++P  + + + ++  A+ ++G H F    +    +  SPIRTI  
Sbjct: 108 ---------------ILPNINYNIDAIKEGAKKMIGTHSFHNLSKRDKSKEKSPIRTIYD 152

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             ++     + I ++  SFL   +R  VG+L LVG GK    D    L  ++ +E  P  
Sbjct: 153 IKISENEFYLTIDIIGESFLWNMVRKIVGALDLVGRGK-KPVDWIGKLLDENHREGVPTF 211

Query: 235 PPEGL 239
           PP+GL
Sbjct: 212 PPDGL 216


>gi|221054442|ref|XP_002258360.1| tRNA pseudouridine synthase [Plasmodium knowlesi strain H]
 gi|193808429|emb|CAQ39132.1| tRNA pseudouridine synthase, putative [Plasmodium knowlesi strain
           H]
          Length = 306

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/258 (24%), Positives = 111/258 (43%), Gaps = 32/258 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIF---LVTGEIVVVHGAGRTDSGVHA- 57
           ++ +   Y G G+ G   QK N ++++  +   +    L++G         RTD GV A 
Sbjct: 6   KFIIFFSYVGMGFNGSAYQKDNPNTVENRLMDCLHDMNLISGVDQPFSRVSRTDKGVSAR 65

Query: 58  -----LR-QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
                +R ++ H  +  + +  +  K +N  LK    + ++++  V   F AR + I R+
Sbjct: 66  MNALTIRLKIRHPHMTLQDIQRVYVKEINKKLK---NMQVIDIRSVPNFFDARLNCIHRT 122

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           YLY                + I K+ + + ++   +  VG HDF+ F      ++   RT
Sbjct: 123 YLY----------------FFIDKNYNFDRIKQGCKLFVGEHDFSNFCKKRKNSTCFRRT 166

Query: 172 IDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKE 229
           I  F+V     N    ++   SFL+ QIR  V +L  VG G     DL   L      K+
Sbjct: 167 ILKFEVRRMDKNFHYFKIKGTSFLYNQIRHMVAALFQVGTGNLALGDLANMLNNHPSSKK 226

Query: 230 CGPLAPPEGLYFDSVEYS 247
              +A  +GL   S +++
Sbjct: 227 NFQIANEDGLLLYSFKFN 244


>gi|223040118|ref|ZP_03610398.1| tRNA pseudouridine synthase A (tRNA-uridine isomeraseI) (tRNA
           pseudouridylate synthase I) [Campylobacter rectus
           RM3267]
 gi|222878595|gb|EEF13696.1| tRNA pseudouridine synthase A (tRNA-uridine isomeraseI) (tRNA
           pseudouridylate synthase I) [Campylobacter rectus
           RM3267]
          Length = 483

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 97/222 (43%), Gaps = 10/222 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G Q Q + + ++ ++  A+  V G    +  + RTD GVHA  QV
Sbjct: 1   MRLKLVFSYDGSKFQGSQTQPHENGVEDALGAALAHV-GIFSKIISSSRTDKGVHANNQV 59

Query: 62  AHFDLVREWVPVILCKAL-NAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +      K+L N +   +  + +  +S     FH R+ A  R+Y Y I   +
Sbjct: 60  ACVECGEHFRDFTRLKSLINRHAHPA--VHVKFISRARDCFHPRYDATARAYRYVINHGE 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L     +L P+  D           VG HDF+ F  +     SP+R +      + 
Sbjct: 118 FSPFLAPYETFL-PR-FDLNLANELLALFVGEHDFSAFMKLGSDVKSPVRRVSKAFCYAR 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGS----LKLVGDGKWTSTDL 218
           G    I   A  FL  Q+R  V S    L+L  +GK+  TD+
Sbjct: 176 GERSIIVFKANGFLRAQVRLMVASVFKALELAKNGKFKETDV 217


>gi|163788523|ref|ZP_02182969.1| tRNA pseudouridine synthase A [Flavobacteriales bacterium ALC-1]
 gi|159876843|gb|EDP70901.1| tRNA pseudouridine synthase A [Flavobacteriales bacterium ALC-1]
          Length = 261

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/261 (26%), Positives = 113/261 (43%), Gaps = 24/261 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  + GWQ+Q +  +I   I++ +  +  ++     GAGRTD+ V A     
Sbjct: 8   YLIKIQYLGYRFHGWQKQPDVKTIHLMIDRTLKFILKDVRFKTLGAGRTDAMVSANEAAL 67

Query: 63  HFDLVREWVPVILCKALNAYLKISD-----TISILNLSIVDKQFHA-RFSAIRR-SYLYR 115
              +  E  P+       A+LK+ +      I  L++S VDK F+  + S I+   Y++ 
Sbjct: 68  ELFIYNE--PIT---DFEAFLKLFNHNLPQDIRALSISEVDKAFNIIQDSKIKEYHYVFS 122

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              +  P         L P  LD E M+  A+   G H+F T+           RTI+  
Sbjct: 123 EGEKNHPFCAPILTTILEP--LDVELMKKGAKLFEGSHNFKTYCYRATDKGEYFRTIESS 180

Query: 176 DV--NSF--GNLIE-----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           ++  NS    N         +V  + F+  QIR   G L  +G G+ T   +E  L+   
Sbjct: 181 EIIDNSLYTANFFPEQSYVFKVRGKGFMRNQIRLMFGCLIKLGRGEVTLQYIENTLKHDS 240

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
            +    +AP  GL   S+++ 
Sbjct: 241 TEVMDYIAPASGLILHSIDFE 261


>gi|296108989|ref|YP_003615938.1| tRNA pseudouridine synthase A [Methanocaldococcus infernus ME]
 gi|295433803|gb|ADG12974.1| tRNA pseudouridine synthase A [Methanocaldococcus infernus ME]
          Length = 258

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 97/240 (40%), Gaps = 33/240 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           Y + I Y+G   F  Q  K      +  ++EK  FL   E  +++  GRTD GV AL   
Sbjct: 2   YILKIAYDGRYSFQQQPHKETVCDKLLNTLEKLNFL--EERKIIYSGGRTDKGVSALGNF 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               L +E +   +   L  +      I IL    ++                     + 
Sbjct: 60  VILKLKKEPILSYINHELKKF-----GIWILGYKEIE---------------------EI 93

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
           P    +   +++P    + E MR A + L+G H F    +    +  SPIR I    +N 
Sbjct: 94  PKVQYRHYRYIMPNLDYNLELMRKAGEKLIGEHSFHNLSKRDRSKEKSPIRKIYDIKIND 153

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           +G  +E+ VV  SFL   +R  VG L L+G  + +   ++K L    R E     P EGL
Sbjct: 154 YGFFLEVDVVGESFLWQMVRKIVGLLHLIGREEKSLEWVDKILDPNYR-EGVITFPAEGL 212


>gi|322493546|emb|CBZ28834.1| putative pseudouridine synthase A-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 499

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 92/216 (42%), Gaps = 36/216 (16%)

Query: 49  GRTDSGVHAL--------RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
           GRTD GV AL        R     D   +  P+  C  LN  L    TI I+  ++VD  
Sbjct: 112 GRTDKGVSALGNALSLTARASCTADAEPQLPPLDYCSMLNNVLP--STIRIVGCALVDDA 169

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F ARFS + R+Y Y                +   + L+   M+ AA   +G H+F  F  
Sbjct: 170 FDARFSCVHRTYRY----------------YFFHRGLNLAAMQEAAAFFLGTHNFRNFCK 213

Query: 161 IH-CQASSPIRTIDHFDVNSFGNLIE----IRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +     S+ +RT+    +     L E    + + A SFL+ QIR  +  L LVG G    
Sbjct: 214 MDVVNVSNFVRTVFSVGLYPSEELPELISYLEIRANSFLYHQIRCTMEVLFLVGRGLEAP 273

Query: 216 TDLEKALQAQDRKECGPLAPPEGLY-----FDSVEY 246
           + ++  L+  D K   PLA    L      FD+V++
Sbjct: 274 SVVQTLLELGDCKPTYPLADGTPLVLWDCGFDNVQW 309


>gi|154174016|ref|YP_001408137.1| tRNA pseudouridine synthase A [Campylobacter curvus 525.92]
 gi|153793037|gb|EAU00484.2| tRNA pseudouridine synthase A [Campylobacter curvus 525.92]
          Length = 241

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 97/242 (40%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G Q Q + + +Q ++ +A+  V G    +  + RTD GVHA  Q A  +
Sbjct: 5   LIFSYDGSKFQGSQTQPHENGVQDALSRALAHV-GIFDKLALSSRTDKGVHATAQSATVE 63

Query: 66  LVREWVPVILCKAL-NAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  +   K L N +      I I N+  V+  F AR+ A  R  LYR I       
Sbjct: 64  CGEHFKDLDRLKNLINRH--AHPFIHIKNIKRVNDDFQARYDAKAR--LYRYIIDHGRYD 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           +      L     D        +  +G HDF+ F        SPIR I       + N  
Sbjct: 120 VFHAEHCLFAPKFDTARANHILKIFIGEHDFSAFMKTGSGTKSPIREIYKAYCYEYKNKT 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I   A  FL  Q+R  V SL    + K     L  A+  +      P A  +GLY   V
Sbjct: 180 VIVFKANGFLRAQVRLMVASLLKALNLKDGDELLNLAINHKKPLTRIP-AAAQGLYLSRV 238

Query: 245 EY 246
            Y
Sbjct: 239 FY 240


>gi|89266772|emb|CAJ81267.1| pseudouridine synthase 3 [Xenopus (Silurana) tropicalis]
          Length = 505

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 96/229 (41%), Gaps = 47/229 (20%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVV------VHGAGRTDSGVHALR 59
           + Y G GY G+  Q+N    + ++E+ +F  L+   +V        H  GRTD GV AL 
Sbjct: 68  LAYLGWGYQGFASQEN---TKNTVEETVFNALIKTRLVESRQTSNYHRCGRTDRGVSALG 124

Query: 60  QVAHFDL--VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV   DL    E  P I     LN  L     I +L+ + V   F ARFS   R+Y Y  
Sbjct: 125 QVISLDLRCSGEGKPEIRYVHILNRVL--PPDIRVLSWAAVPPSFSARFSCRSRTYRYLF 182

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-------------RSIHC 163
              Q                LD E M  AA+ L G HDF                R++  
Sbjct: 183 SCAQ----------------LDVEAMDKAARLLEGTHDFRNLCKMDVANGVMNFIRTVLS 226

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
               P+  I   D+  F  L  +++   +FL+ Q+R  +G L LVG GK
Sbjct: 227 ARVEPVPEIPG-DMGPF-QLYRLQITGLAFLYHQVRCIMGVLFLVGQGK 273


>gi|324505293|gb|ADY42276.1| tRNA pseudouridine synthase A [Ascaris suum]
          Length = 491

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 72/267 (26%), Positives = 115/267 (43%), Gaps = 28/267 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGEIVV------VHGAGRTDS 53
           RY M+I Y G  Y G Q QK+  +I+G +  A+    L+T E V+         A RTD 
Sbjct: 63  RYAMLIAYQGKNYCGMQVQKDAPTIEGCLLNAMQKYGLITDEEVIKPNLFFFQRAARTDR 122

Query: 54  GVHALRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            V A+RQ+    L   E +P  +   LN  L   + I ++ +    + F+A+     R+Y
Sbjct: 123 AVSAVRQMCSMMLNFDEQLPKTVPDELNKLL--PEDIRVMGIRRATRTFNAQKDCDARTY 180

Query: 113 LYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIR 170
            Y + T   A +      A+ I      E +    Q  VG H+F  + S       S  R
Sbjct: 181 SYTLPTYAFAKVDELTSSAYRITDETINE-INALLQIFVGTHNFFNYTSKREFSDRSCFR 239

Query: 171 TIDHFDVNS---FGN--------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            I  F   +   F N         + I +  +SF+  QIR  +G +  +  G    +D++
Sbjct: 240 YIIDFKCGAKFLFKNELRNEDVEFLTISIKGQSFMLHQIRKMIGMVIAISRGLLYKSDIQ 299

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEY 246
           ++ ++  R +  P AP  GL  + V Y
Sbjct: 300 RSFESA-RMDV-PKAPGLGLLLEKVHY 324


>gi|153792349|ref|NP_001093370.1| pseudouridylate synthase 3 [Xenopus laevis]
 gi|148745611|gb|AAI42593.1| LOC100101318 protein [Xenopus laevis]
          Length = 507

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 95/229 (41%), Gaps = 47/229 (20%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           + Y G GY G+  Q+N    + ++E+ +F    +  +V        H  GRTD GV AL 
Sbjct: 65  LAYLGWGYQGFASQEN---TKNTVEETVFNALLKTRLVESRQTSNYHRCGRTDRGVSALA 121

Query: 60  QVAHFDL--VREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV   DL    E  P I     LN  L     I +L+ + V   F ARFS   R+Y Y  
Sbjct: 122 QVISLDLRCSAEGKPEIRYVHILNRVL--PPDIRVLSWAPVPPSFSARFSCGSRTYRYLF 179

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-------------RSIHC 163
              Q                LD E M  AA+ L G HDF                R++  
Sbjct: 180 PCAQ----------------LDVEAMDKAARLLEGTHDFRNLCKMDVANGVLNFTRTVLS 223

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
               P+  I   D+  F  L  +++   +FL+ Q+R  +G L LVG GK
Sbjct: 224 ARVGPVPEIPG-DMGPF-QLYHLQITGLAFLYHQVRCIMGVLFLVGQGK 270


>gi|300710278|ref|YP_003736092.1| tRNA pseudouridine synthase A [Halalkalicoccus jeotgali B3]
 gi|299123961|gb|ADJ14300.1| tRNA pseudouridine synthase A [Halalkalicoccus jeotgali B3]
          Length = 266

 Score = 64.3 bits (155), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/191 (29%), Positives = 83/191 (43%), Gaps = 29/191 (15%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHG---AGRTDSGVHALRQVAH 63
           I Y+G+ Y+G+QRQ +  +++G +  A+  LVT E     G   AGRTD GV AL Q   
Sbjct: 6   IAYDGAPYYGFQRQPDVETVEGVLFDALDRLVTFEGEKPAGYAAAGRTDRGVSALAQTVA 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F+   EW   +   A N+  ++  T+     +     FHAR+ A  R+Y Y         
Sbjct: 66  FE-APEW---LTPAAFNS--ELPGTVRAWASADAPDDFHARYDARSRTYAY--------- 110

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                  +L     D E +R     L G HD   F ++  +     RTI     N  G  
Sbjct: 111 -------YLHAPGADVEAIRGVLSRLSGTHD---FHNLTPEDGPTTRTITRARANREGPF 160

Query: 184 IEIRVVARSFL 194
           + + + A  FL
Sbjct: 161 VVLTLRADGFL 171


>gi|312892438|ref|ZP_07751932.1| tRNA pseudouridine synthase A [Mucilaginibacter paludis DSM 18603]
 gi|311295072|gb|EFQ72247.1| tRNA pseudouridine synthase A [Mucilaginibacter paludis DSM 18603]
          Length = 358

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/171 (27%), Positives = 77/171 (45%), Gaps = 4/171 (2%)

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK 135
            ++LNA L     I++  +  V    HARF A  RSY Y +   + P       +W +  
Sbjct: 189 TRSLNALLP--HDIAVKRIIPVHADAHARFDATLRSYEYHVHFEKDPFL--NNLSWQLRD 244

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
             D   M  AAQ ++   DF+ F   + Q  +    I   +  S G+ +   + A  FL 
Sbjct: 245 RPDVGLMNQAAQIVMEYTDFSCFSKSNTQVKTNNCKISRAEWVSNGDKLIFHISADRFLR 304

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             +R+ VG+L +VG G     ++ + +++++R   G   P  GLY   V Y
Sbjct: 305 NMVRAIVGTLMMVGKGDIKPEEVRRIIESKNRSNAGVSVPACGLYLTEVRY 355



 Score = 63.9 bits (154), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 44/72 (61%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
          RY + + Y+G+ Y GWQ Q N  S+Q  + KA+  +    V   G GRTD+GVHA +  A
Sbjct: 6  RYFIELAYDGTNYHGWQIQHNAISVQQVLNKALSTLLRMPVETLGCGRTDTGVHAKQLYA 65

Query: 63 HFDLVREWVPVI 74
          HFD+ R+  P++
Sbjct: 66 HFDIGRQEQPIV 77


>gi|86152100|ref|ZP_01070312.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           260.94]
 gi|85840885|gb|EAQ58135.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           260.94]
          Length = 240

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 101/242 (41%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAVASVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +V +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHSSYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    PK  D +         VG+ D   F        + +R I      ++ +  
Sbjct: 121 FMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAYKDFS 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   +
Sbjct: 180 IFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 CY 240


>gi|225011098|ref|ZP_03701561.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
 gi|225004732|gb|EEG42691.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
          Length = 268

 Score = 63.9 bits (154), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 106/226 (46%), Gaps = 28/226 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVHALRQV 61
           Y + + Y G  Y GWQ+Q    +I+  + K I  V GE     + GAGRTD+ V ++   
Sbjct: 8   YLVRVSYLGFRYSGWQKQPGVKTIESMLTKTISFVLGETRSFKILGAGRTDAKVSSIH-- 65

Query: 62  AHFDLVREWVPVILCKALNAY--LKISDTISILNLSIVDKQFHARFSAIRRS--YLYRII 117
             F+L  E  P+    AL     L +   I + +++ V+++F+   SA  ++  YL+   
Sbjct: 66  GAFELFIEHEPLKNLDALMDLFNLNLPADIRVESITAVEEKFNIIHSAKEKTYCYLFSFG 125

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS-PIRTI---- 172
           ++  P        +  P+ L+   M+ AA+   G HDF  F +   + +S  IRTI    
Sbjct: 126 SKAHPFCAPIMANY--PEDLNITLMQEAAKLFEGTHDFKNFTARKDKKNSQTIRTIASCE 183

Query: 173 ---------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                      F  +S+  ++E+R   + FL  QIR  +G+L  +G
Sbjct: 184 LKKNKAISASFFPEDSY--VLEVR--GKGFLRYQIRLMMGALICLG 225


>gi|302023348|ref|ZP_07248559.1| tRNA pseudouridine synthase A [Streptococcus suis 05HAS68]
          Length = 124

 Score = 63.9 bits (154), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/119 (30%), Positives = 54/119 (45%), Gaps = 2/119 (1%)

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDVNSFGNLIEIR 187
           A   P  LD   +  A Q LVG HDFT F +        +RTI     + +     +   
Sbjct: 4   ATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTIKAASMEYDQRRQFLIFT 63

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   GLY   + Y
Sbjct: 64  FSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRSLAGPTAAGNGLYLKEIIY 122


>gi|83320035|ref|YP_424629.1| tRNA pseudouridine synthase A [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|123753714|sp|Q2SRI4|TRUA_MYCCT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83283921|gb|ABC01853.1| tRNA pseudouridine synthase A, putative [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
          Length = 249

 Score = 63.5 bits (153), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 87/201 (43%), Gaps = 11/201 (5%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           Y+GS Y GW  Q N  S Q  + KAI   + T E   + GA +TD+ VHAL Q     L+
Sbjct: 11  YDGSNYHGWINQTNSISTQTVLNKAIKKVIKTSEFKTI-GASKTDANVHALDQKVL--LI 67

Query: 68  REWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
             + P IL K +NA  K + + I ILN   VD  F+ R     + Y Y I   +  +   
Sbjct: 68  IYFTP-ILEKFINAINKALPEDIRILNAKFVDPNFNIR-EVDYKIYNYYINDHKFDIFTN 125

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDVNSFGNL 183
           +   +     +D   ++      +G H+F  F  +           R ID   V    N 
Sbjct: 126 RYEYFWKHSKIDILKLQEIFNLFIGEHEFKLFSGLKENEWDNYQTKRIIDDIKVLRINNK 185

Query: 184 IEIRVVARSFLHTQIRSFVGS 204
           + I+  A  F+  QIR  + +
Sbjct: 186 VVIQFKATGFIRYQIRIIIAN 206


>gi|330902540|gb|EGH33555.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. japonica
          str. M301072PT]
          Length = 231

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

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 AHFDLVRE 69
           HFD   E
Sbjct: 68 VHFDTQAE 75


>gi|242001376|ref|XP_002435331.1| pseudouridylate synthase, putative [Ixodes scapularis]
 gi|215498661|gb|EEC08155.1| pseudouridylate synthase, putative [Ixodes scapularis]
          Length = 442

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 65/269 (24%), Positives = 114/269 (42%), Gaps = 39/269 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGEIVVV------HGAGRTDS 53
           +  + + YNG  Y G QR     +I+  + +A++   L+  E V V        A RTD 
Sbjct: 72  KMALCMSYNGKDYLGMQRNPGTKTIEDDLLQAMYKGDLILKEHVDVPQAMKFQRAARTDK 131

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+RQ+    L        +   +N++L   D I ++++    + F+ + S   R+Y 
Sbjct: 132 GVSAVRQIVSLKLPTNLTVEEMVDKINSHL--VDQIRVIDIKRTTRGFNCKNSCDSRTYT 189

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRS-IH 162
           Y + T           A+  P+S   E+ RI  + +           G H++  F S   
Sbjct: 190 YVLPT----------FAFAPPESPAEESYRITEERIGEVNNVLALYKGCHNYHNFTSGKK 239

Query: 163 CQASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
            +  S +R I   +     V      +++++  +SF+  QIR  VG +  +  G    T 
Sbjct: 240 SEDPSAMRYIISAECAQPFVQGDQEFVQVQIKGQSFMLHQIRKMVGLVIAIMRGCTKETT 299

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + +A   +  K   P+AP  GL  + V Y
Sbjct: 300 IRRAWGPE--KLDLPIAPALGLMLEEVHY 326


>gi|322823466|gb|EFZ29213.1| hypothetical protein TCSYLVIO_4538 [Trypanosoma cruzi]
          Length = 409

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 103/245 (42%), Gaps = 36/245 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + Y+G  Y G  +Q+  S+     +  +++    +     + +   GRTD GV AL  V 
Sbjct: 26  LAYHGHLYDGLAKQEETSNTVEAYVVAALKHVRLIPQDGPIDLARCGRTDKGVSALGNVF 85

Query: 63  HFDL-VREWV------PVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
              +    W       P +  C  LN+ L +  TI I+  + VD  F ARFS + R+Y Y
Sbjct: 86  SLTVRASSWPTDSPQKPALDYCAMLNSALPV--TIRIVGWAYVDDTFDARFSCVGRTYRY 143

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS----PIR 170
                           +   + L+ E M  AA  L G H+F  F        S     +R
Sbjct: 144 ----------------YFCHRGLNVEAMGNAAARLKGVHNFRNFCKTDVVNVSNYERDVR 187

Query: 171 TIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           ++  F   +   L+  + + A SFL+ QIR  +  L LVG G      + + L+  DRK 
Sbjct: 188 SVGIFASEALPELVSYLEIHANSFLYHQIRCTMEVLFLVGRGLEDPEVVTQLLERGDRKP 247

Query: 230 CGPLA 234
             PLA
Sbjct: 248 VYPLA 252


>gi|303288890|ref|XP_003063733.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454801|gb|EEH52106.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 313

 Score = 63.2 bits (152), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/258 (26%), Positives = 103/258 (39%), Gaps = 25/258 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-------LVTGEIVVVH--GAGRTDS 53
           +  + + Y G GY G QR     +I+  +EKAI        L  G+   V    A RTD 
Sbjct: 3   KVAIFLAYVGKGYQGMQRNPGAVTIEDELEKAIVAAGGISDLNAGDFAKVQWMRAARTDK 62

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+ Q     +V +  P  +   +NA L   +         V   F+A+    RR Y 
Sbjct: 63  GVSAVGQCVSLRMVID--PPGVIDRVNAAL--PEGFEFFGYERVTGGFNAKTMCDRRRYE 118

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----VGRHDFTTFR-SIHCQASSP 168
           Y +  +      +       P   D E MR     +    VG H+F  F   +     S 
Sbjct: 119 YVVPVKAFDPRAKNSDDASPPFEFD-ETMRQRVNKILGNYVGTHNFHNFTVRVSPDEPSA 177

Query: 169 IRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R I  FD ++         +   VV +SF+  QIR  +G +  V  G W+  D   AL 
Sbjct: 178 MRYIISFDCSAPFVVDGVAFVRCVVVGQSFMLHQIRKLIGMMLGVIRGAWSEEDQLFALN 237

Query: 224 AQDRKECGPLAPPEGLYF 241
            ++     P+AP  GL+ 
Sbjct: 238 TKESVNV-PMAPELGLFL 254


>gi|195158909|ref|XP_002020326.1| GL13924 [Drosophila persimilis]
 gi|194117095|gb|EDW39138.1| GL13924 [Drosophila persimilis]
          Length = 409

 Score = 63.2 bits (152), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/263 (25%), Positives = 115/263 (43%), Gaps = 27/263 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFDQVQIACFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQ+    L  E    +  +A NA L   + I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQICSVKLPEE----LDLEAFNADL--PEQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIIT---RQAPLALEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFRSIHCQASS- 167
           Y + T          E+    + P+ LD   E +++  +     H+FT+ ++    ++  
Sbjct: 185 YTLPTVAFASCEAESEQDTFRITPELLDRVKETLKLY-EGTKNFHNFTSKKNFLDPSAKR 243

Query: 168 ---PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
                 + + F        + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 244 FIMAFTSSEPFQSPQGVEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAITLERAL-T 302

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           ++R +  P+AP  GL  D+V Y 
Sbjct: 303 EERLDL-PMAPGLGLVLDTVHYE 324


>gi|57242355|ref|ZP_00370294.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis RM3195]
 gi|57017035|gb|EAL53817.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis RM3195]
          Length = 240

 Score = 63.2 bits (152), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/248 (26%), Positives = 107/248 (43%), Gaps = 11/248 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G   Q + +S+Q ++  A+  + G    V  A RTD GVHALR V
Sbjct: 1   MRLKLVFSYDGSAFLGSACQPHLNSVQDALAAALAHL-GIFSPVLFASRTDKGVHALRAV 59

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +  ++ L + +N +      I I +L  V + +  RF    R+  YR I   
Sbjct: 60  ACVECGEHFKDLVYLKRQINRF--THPFIHIKSLERVSENYAVRFDV--RAREYRYIFHH 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                         +  D +       H VG  DF  F+     A + +R +      ++
Sbjct: 116 GEFNPFLSPYVCFSERFDIKKANELLSHFVGEKDFKFFQKAGGSAKTSVRIMFFARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP--LAPPEG 238
            +L      A  FL  QIR  V S+  V  G+ +   L++ ++A   K+C    LAP  G
Sbjct: 176 KDLSIFCFRANGFLRAQIRLSVASVMAVLRGELSEDKLKEQIEA---KKCHYRFLAPANG 232

Query: 239 LYFDSVEY 246
           LY   + Y
Sbjct: 233 LYLSRIIY 240


>gi|167005448|ref|ZP_02271206.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81-176]
          Length = 240

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 100/242 (41%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   VA   
Sbjct: 5   IIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAVASVG 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +V +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHSSYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    PK  D +         VG+ D   F        + +R I      ++ +  
Sbjct: 121 FMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAYKDFS 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   +
Sbjct: 180 IFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 CY 240


>gi|196008069|ref|XP_002113900.1| hypothetical protein TRIADDRAFT_57795 [Trichoplax adhaerens]
 gi|190582919|gb|EDV22990.1| hypothetical protein TRIADDRAFT_57795 [Trichoplax adhaerens]
          Length = 385

 Score = 62.8 bits (151), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 66/259 (25%), Positives = 114/259 (44%), Gaps = 23/259 (8%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
           +  +++ + G+GYFG QR +   +I+  +  A+F             + +    A RTD 
Sbjct: 47  KVALLLGFCGAGYFGMQRNRGTKTIEEDLINALFKAGAIPEAAKEHEQKMAFQRASRTDK 106

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA  QV  F +   +V   +   +N++L     I +     V K F+++ +   R+Y 
Sbjct: 107 GVHAAAQVVSFKM---FVVDDVIAKINSHL--PREIRVFGHFRVTKGFNSKTACDARTYK 161

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTI 172
           Y ++   A    EK   +++      +++R      VG  +F  F S    +  S  R I
Sbjct: 162 Y-VMPTYAFANKEKKNMYILVIEATIKHVRDILAMYVGTRNFHNFTSKKAYEDDSAKRYI 220

Query: 173 DHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             FD     V +    + + V  +SF+  QIR  +G +  +  G  T   +EKA + +DR
Sbjct: 221 MQFDCGLPFVRNNLEFVTLTVKGQSFMLHQIRKMIGLMIGIVRGDATIEAMEKAWE-KDR 279

Query: 228 KECGPLAPPEGLYFDSVEY 246
            +  P AP  GL    + Y
Sbjct: 280 VDI-PRAPGLGLMLYQLHY 297


>gi|19074961|ref|NP_586467.1| tRNA PSEUDOURIDINE SYNTHASE A [Encephalitozoon cuniculi GB-M1]
 gi|19069686|emb|CAD26071.1| tRNA PSEUDOURIDINE SYNTHASE A [Encephalitozoon cuniculi GB-M1]
          Length = 339

 Score = 62.8 bits (151), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 95/225 (42%), Gaps = 41/225 (18%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVAH- 63
           + I Y+G  Y G   Q    +I G +E A+     GE +V   AGRTD+GV A+  +A  
Sbjct: 63  LKISYDGRRYSGVSPQSGRETIGGYLEYALKSTRLGEKLVY--AGRTDAGVSAIGMIASG 120

Query: 64  ----------------FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
                            D  +E+   ++   LN +L     I ++  + V   F ARF+ 
Sbjct: 121 VLTSRIEMPNRSYAVAEDDYKEYKYDVM---LNNHL--PPDIRVVGWAPVPDTFSARFTC 175

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           I+R Y Y                +   K LD + M  AA  + G   F  F     + + 
Sbjct: 176 IQRQYRY----------------YFHKKGLDIDRMSKAASEIKGMSSFYCFSKHSDKNAR 219

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
             RT+D   V   G+L  + + AR+FLH  +R  V ++K  G G+
Sbjct: 220 YERTLDECRVVDDGDLYYLDIRARAFLHNMVRKIVWAIKKSGRGE 264


>gi|159479156|ref|XP_001697664.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158274274|gb|EDP00058.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 382

 Score = 62.8 bits (151), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 76/168 (45%), Gaps = 23/168 (13%)

Query: 10  YNGSGYFGWQRQKNG-SSIQGSIE---KAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           Y+GS + G+Q Q     ++QG +E   K +F+    +V   G+ RTD G HA  QV HFD
Sbjct: 29  YDGSEFAGFQFQPGKVRTVQGELERCAKRLFVGCSRMV---GSSRTDGGAHAYGQVVHFD 85

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  E    +    L     +   + +L LS  ++ F + FSA  ++Y+Y+          
Sbjct: 86  VYGE-RDNLESDTLYYNSFLPPDVRVLELSYAEEGFDSHFSACGKTYIYKFAAGLPDPMQ 144

Query: 126 EKGRAWLIPK---------------SLDCENMRIAAQHLVGRHDFTTF 158
            K R W+  +                LD   M  A Q L+GRHDF+ F
Sbjct: 145 AKYRWWVYDRWCERSRGKPSKLSDIRLDVGAMCEAGQLLLGRHDFSAF 192


>gi|283957185|ref|ZP_06374649.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni 1336]
 gi|283791361|gb|EFC30166.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni 1336]
          Length = 240

 Score = 62.4 bits (150), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 100/242 (41%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSAFLGSATQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAVASVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +V +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHSSYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    PK  D           VG+ D   F        + +R I      ++ +  
Sbjct: 121 FMASYVHFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAYKDFS 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   +
Sbjct: 180 IFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 CY 240


>gi|311264306|ref|XP_003130101.1| PREDICTED: tRNA pseudouridine synthase 3-like [Sus scrofa]
          Length = 479

 Score = 62.4 bits (150), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 97/243 (39%), Gaps = 58/243 (23%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 68  IAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVENRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-----------------ISILNLSIVDKQFH 102
           QV   DL   ++     + +N   +++D                  I +L  + V+  F 
Sbjct: 125 QVISLDLRSHFLKDKDSEDINLKDEVNDATKEIRYTHILNRVLPPDIRVLAWAPVEPSFS 184

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF------- 155
           ARFS + R+Y Y                +     LD   M  AAQ  VG HDF       
Sbjct: 185 ARFSCLERTYRY----------------FFPHADLDIVTMNYAAQKYVGTHDFRNLCKMD 228

Query: 156 -----TTFRS--IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
                T F+   +  Q     ++++         L +  VV ++FL+ Q+R  +  L L+
Sbjct: 229 VANGVTNFQRTILSAQVQLLSQSLEEERWQEAFQLCQFEVVGQAFLYHQVRCMMAVLFLI 288

Query: 209 GDG 211
           G G
Sbjct: 289 GQG 291


>gi|298709054|emb|CBJ31003.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 412

 Score = 62.4 bits (150), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 70/276 (25%), Positives = 126/276 (45%), Gaps = 37/276 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+   + Y+G+ Y G+Q Q +G  ++QG +EKA+       V V  AGRTD+GVH++ Q 
Sbjct: 138 RFVSRVMYDGTNYKGFQLQGHGLPTVQGVLEKALSTRFQTYVPVVAAGRTDTGVHSVGQA 197

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSI--------VDK--QFHARFSAIRR 110
            HFDL      +  L  ++N  +   + + + N+S+        V+K   + +  +A  +
Sbjct: 198 VHFDLPNANEDLSQLAYSMNQMMP--EDVRVWNMSVAPPSSPWQVEKGWPWSSMLNARGK 255

Query: 111 SYLYRIITRQAPLALEK------GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
            Y YR+        L++       +A   P ++D     I    LVG+HDF  F +   +
Sbjct: 256 RYSYRLFVGPVMSPLDRLYRAHASQAAGSPINVDLLYQTIP--KLVGKHDFAGFSNEVTK 313

Query: 165 ASS-----------PIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
            ++            +RT+   + ++  G  I +       L+  +R+ VG+L  V  G+
Sbjct: 314 RATLKKEDGLGEFNTVRTVYSAEIIDEGGGNIRLDFHLDGALYRMVRNMVGALLAVAAGR 373

Query: 213 WTSTDLEK--ALQAQDRKECGPLAPPEGLYFDSVEY 246
                +++  A + +D +     AP  GL  D+V Y
Sbjct: 374 LEPEVIDEIFATRVRDSRLIY-AAPAHGLTLDTVLY 408


>gi|81022386|gb|ABB55198.1| tRNA pseudouridine synthase [Enterococcus faecium]
          Length = 89

 Score = 62.4 bits (150), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 6  MIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
          + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  QVA+F
Sbjct: 6  LTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARGQVANF 65

Query: 65 DLVREWVPVILCKALNAYL 83
              E     +   +N YL
Sbjct: 66 KTNTEIGLAEMIDFMNRYL 84


>gi|219120077|ref|XP_002180785.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407501|gb|EEC47437.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 347

 Score = 62.0 bits (149), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 75/306 (24%), Positives = 127/306 (41%), Gaps = 62/306 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQ---------------------RQKNGSSIQGSIEKAIFLVT 39
           ++RY   + Y+G+ + G+Q                     + K   ++QG +E  +    
Sbjct: 36  VVRYRARVAYDGTSFQGFQIQGSNKVVDDKNCNGITHQNRKDKQQRTVQGELETVLSTRW 95

Query: 40  GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV---ILCKALNAYLKISDTISILNLS- 95
            + V V  AGRTD+GVHA  Q  HFD+     P     L ++L   L    T+  L  + 
Sbjct: 96  NQPVRVVAAGRTDAGVHARGQAIHFDVNVSETPTDHASLERSLARMLPTDVTLWNLQFAP 155

Query: 96  -----IVDKQ-----FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIA 145
                +VD Q     ++  +    + Y YR+ T      L +   W  P ++D   +  A
Sbjct: 156 SARTKLVDGQERVLPWNVMYDNTHKLYSYRLSTAAVMDPLSRQHRWH-PDNVDAYVVGKA 214

Query: 146 A--------QHLVGRHDFTTFRSIHCQ----ASSPI---RTIDHFDVNSFGNLIEIRV-- 188
                    +H  G HDF  F S   Q    +  PI   RT+   +V    N  ++R+  
Sbjct: 215 GLAQLTRLLKHYEGTHDFRAFASAMEQLEKHSDGPIDTVRTVYSVNVVPEANEGDVRIDF 274

Query: 189 VARSFLHTQIRSFVGSLKLVGDGK-WTSTDLEKALQ-------AQDRKECGPLAPPEGLY 240
           V +  L+ Q+R+ VG++     G+    +D+ + LQ       ++      P APP+GL 
Sbjct: 275 VLKGALYKQVRNMVGTVLETCRGEIMKESDMLRLLQDATASGLSRADNPSKP-APPQGLT 333

Query: 241 FDSVEY 246
            ++V +
Sbjct: 334 LENVYF 339


>gi|313231689|emb|CBY08802.1| unnamed protein product [Oikopleura dioica]
          Length = 443

 Score = 62.0 bits (149), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 74/271 (27%), Positives = 103/271 (38%), Gaps = 39/271 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIV-----------VVHGAG 49
           +  ++I Y G  Y G Q       +  +IEK +F  LV  ++V                 
Sbjct: 82  KVAILISYCGKNYHGLQHNPGDDKVD-TIEKRVFQALVAAKVVYSNVINDRKKCAYQSCS 140

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A+  VA        +P  LC+ +NA+L   D I + +   V K F A+     
Sbjct: 141 RTDKGVSAIGNVASLKCK---IPKNLCELVNAHL--PDDIRLTSFEQVTKGFCAKKRCTH 195

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSL-----DCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           R+Y Y   T    +       W  P S        E +R   +  +G   +  F S   Q
Sbjct: 196 RTYSYYCPT----ICFGSKEDWDRPSSFRISTEKLEGVRELLKKYIGTRSYHNFTSGKRQ 251

Query: 165 A-SSPIRTI-------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
              S  R I       D F  N +   +E+RVV +SF+  QIR  VG +           
Sbjct: 252 GDESAKRHILDFRIQGDPFICNEW-EYVELRVVGQSFMIHQIRKMVGLIIARAGNHCQDD 310

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             E+A Q     E  P AP  GL    V Y 
Sbjct: 311 HWERAFQRP--FEDVPKAPGNGLVLRQVHYD 339


>gi|313665546|ref|YP_004047417.1| tRNA pseudouridine synthase A [Mycoplasma leachii PG50]
 gi|312949580|gb|ADR24176.1| putative tRNA pseudouridine synthase A [Mycoplasma leachii PG50]
          Length = 249

 Score = 62.0 bits (149), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 58/202 (28%), Positives = 86/202 (42%), Gaps = 13/202 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           Y+GS Y GW  Q N  SIQ  + KAI   + T E   + GA +TD+ VHAL Q     L+
Sbjct: 11  YDGSNYHGWINQINSISIQTVLNKAIKKVIKTSEFKTI-GASKTDANVHALDQKVL--LI 67

Query: 68  REWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             + P++    KA+N  L     I ILN   V+  F+ R     + Y Y I   +  +  
Sbjct: 68  IYFTPILEKFIKAINKAL--PKDIRILNAKFVNSDFNIR-EVEYKIYNYYINDYKFDIFT 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDVNSFGN 182
            +   +     +D   ++      VG H+F  F  +           R ID   V    N
Sbjct: 125 NRYEYFWKHSKIDILKLQEIFNLFVGEHEFKLFSGLKENEWDNYQTKRIIDDIKVLRINN 184

Query: 183 LIEIRVVARSFLHTQIRSFVGS 204
            + I+  A  F+  QIR  + +
Sbjct: 185 KVVIQFKATGFIRYQIRIIIAN 206


>gi|291383625|ref|XP_002708689.1| PREDICTED: CG3045-like [Oryctolagus cuniculus]
          Length = 480

 Score = 61.6 bits (148), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 98/245 (40%), Gaps = 62/245 (25%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 68  IAYLGWGYQGFASQENTTN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-----------------ISILNLSIVDKQFH 102
           QV   DL  ++      ++ N+  + +D                  I IL  + VD  F 
Sbjct: 125 QVISLDLRSQFPMAKDSESCNSKDEANDVAEEIRYTHILNRVLPPDIRILAWAPVDPGFS 184

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     +
Sbjct: 185 ARFSCLERTYHY-----------------FFPRADLDIVTMNCAAQKYVGTHDFRNLCKM 227

Query: 162 HCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLK 206
              A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L 
Sbjct: 228 DV-ANGVINFQRTILSAKVQLVGQSLGEERWQEHFQLCQFEVTGQAFLYHQVRCMMAILF 286

Query: 207 LVGDG 211
           L+G G
Sbjct: 287 LIGQG 291


>gi|125773069|ref|XP_001357793.1| GA17995 [Drosophila pseudoobscura pseudoobscura]
 gi|54637526|gb|EAL26928.1| GA17995 [Drosophila pseudoobscura pseudoobscura]
          Length = 409

 Score = 61.6 bits (148), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 65/263 (24%), Positives = 115/263 (43%), Gaps = 27/263 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFDQVQIACFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQ+    L  E    +  +A NA L   + I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQICSVKLPEE----LDLEAFNADL--PEQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIIT---RQAPLALEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFRSIHCQASS- 167
           Y + T          E+    + P+ LD   E +++  +     H+FT+ ++    ++  
Sbjct: 185 YTLPTVAFASCEAESEQDTFRITPELLDRVKETLKLY-EGTKNFHNFTSKKNFLDPSAKR 243

Query: 168 ---PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
                 + + F        + ++V  +SF+  QIR  VG    +  G  T+  L++AL  
Sbjct: 244 FIMAFTSSEPFQSPQGVEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAITLDRAL-T 302

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           ++R +  P+AP  GL  D+V Y 
Sbjct: 303 EERLDL-PMAPGLGLVLDTVHYE 324


>gi|302802211|ref|XP_002982861.1| hypothetical protein SELMODRAFT_117099 [Selaginella moellendorffii]
 gi|300149451|gb|EFJ16106.1| hypothetical protein SELMODRAFT_117099 [Selaginella moellendorffii]
          Length = 289

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/257 (23%), Positives = 110/257 (42%), Gaps = 17/257 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-----------FLVTGEI--VVVHGAGR 50
           + +++ Y+G+ + GWQ+Q    ++Q  +EK +               G+I   +V  AGR
Sbjct: 14  FKIVLSYSGTAFAGWQKQPGFLTVQSVLEKQLGRFVDGKRASNLEKQGKIKEALVSVAGR 73

Query: 51  TDSGVHALRQVAHF-DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GVHA  QV  F   +RE     +  A+N+ +     +  ++ S V++ FH  FSA  
Sbjct: 74  TDKGVHACGQVCSFYTWMRECKEEDVKSAVNSAMPT--ILRAVSASEVNRDFHPIFSAKW 131

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           R Y+Y I   ++   ++  +   + + L+  ++  A      +   ++  +  C      
Sbjct: 132 RRYIY-IFPLRSRDEIDVSKVATLLRGLEGHSLSYAIFARDTKIARSSGPATVCTLYHAR 190

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
             +    V +  N++ + +VA  FL   +R  V +             L   ++  DR+ 
Sbjct: 191 AALAKLPVPNEENVMVVELVADRFLRKMVRVLVSTAIKEAFAGANDDALVALMEETDRRA 250

Query: 230 CGPLAPPEGLYFDSVEY 246
             P AP  GL    V Y
Sbjct: 251 SAPPAPAHGLCLAEVGY 267


>gi|196007746|ref|XP_002113739.1| hypothetical protein TRIADDRAFT_26740 [Trichoplax adhaerens]
 gi|190584143|gb|EDV24213.1| hypothetical protein TRIADDRAFT_26740 [Trichoplax adhaerens]
          Length = 279

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 99/237 (41%), Gaps = 47/237 (19%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSG 54
           R    + Y G  Y+G   Q+    I+ +IE  +F    +  ++          +GRTD G
Sbjct: 10  RVAFKLAYIGWDYYGLASQE---GIEKTIEAELFNALTKTCLIENRTNSNYSRSGRTDKG 66

Query: 55  VHALRQVAHFDLVREWV--PVILCKALN--AYLKISDT-----ISILNLSIVDKQFHARF 105
           V AL QV   ++       P ++ + ++  +Y+K+ +      I IL  + VD  F ARF
Sbjct: 67  VSALGQVISLNVRTNLASGPGVIVETVSELSYVKLLNKVLPGDIRILAWAPVDNDFSARF 126

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQ 164
           + + R+Y Y                +    +++ E M  AAQ L G HDF  F  +    
Sbjct: 127 NTVSRTYKY----------------YFPRANMNIEAMNEAAQRLKGEHDFRNFCKMDLAN 170

Query: 165 ASSPIRTIDHFDVNSFGN----------LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
            S+  R I    V S             + EI V  ++FL  Q+R  V  L L+G G
Sbjct: 171 VSNFRREILSIKVQSIETPYVLQNQGFEMCEIIVCGKAFLWHQVRCMVAILFLIGQG 227


>gi|76803149|ref|YP_331244.1| tRNA pseudouridine synthase A [Natronomonas pharaonis DSM 2160]
 gi|121697999|sp|Q3IMP6|TRUA_NATPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76559014|emb|CAI50612.1| tRNA-pseudouridine synthase [Natronomonas pharaonis DSM 2160]
          Length = 267

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/156 (29%), Positives = 67/156 (42%), Gaps = 25/156 (16%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKA-----IFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           I Y+G+G+ G+QRQ +G +++ ++ +A     +    G       AGRTD+GV A  Q  
Sbjct: 6   IAYDGTGFRGFQRQPHGETVENALFEALSSLGVAFEDGRPPGYAAAGRTDAGVSARAQTV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F+    W   +L +ALN  L  S  +     + V   FHA   A  R+Y Y +   +  
Sbjct: 66  AFE-APAW---LLPRALNGELPAS--VRAWAAADVGDAFHATHDATARAYRYFLYAPE-- 117

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
                        S D    R A   L G HDF  F
Sbjct: 118 ------------PSADTTRARAACARLSGSHDFHNF 141


>gi|281362146|ref|NP_001163664.1| CG4159, isoform B [Drosophila melanogaster]
 gi|272477072|gb|ACZ94960.1| CG4159, isoform B [Drosophila melanogaster]
          Length = 442

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 70/281 (24%), Positives = 116/281 (41%), Gaps = 61/281 (21%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 103 KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDK 162

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A NA L     I +  +  V K F+A+     R+Y 
Sbjct: 163 GVSAARQVCSVKLPEE----LDLEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYT 216

Query: 114 YRIIT-----------------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           Y + T                 R +P  L+K +          E +++  +     H+FT
Sbjct: 217 YTLPTVAFAPFEEKVDDVHDTFRISPELLQKVK----------ETLKL-YEGTKNFHNFT 265

Query: 157 TFRS----------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
           + +S          +   +S P R+    +       + ++V  +SF+  QIR  VG   
Sbjct: 266 SKKSFLDPSSKRFIMSFTSSEPFRSPQDIE------FVTLKVKGQSFMLHQIRKMVGLAI 319

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +  G  T+  LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 320 AIVRGNTTAATLERAL-TEERLDL-PMAPGLGLVLDTVHYE 358


>gi|294461715|gb|ADE76416.1| unknown [Picea sitchensis]
          Length = 448

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 74/317 (23%), Positives = 125/317 (39%), Gaps = 76/317 (23%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-------------IVVVHGAGR 50
           + +++ Y+G+ + GWQ+Q   +++QG +EK++     E                V  AGR
Sbjct: 126 FKIVLSYDGNLFDGWQKQPGMNTVQGLVEKSLGKFVDEKKAQELEAKKASVEAAVAVAGR 185

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS--DTISILNLSIVDKQFHARFSAI 108
           TD GV A +QV  F     W      + + + +  +    + ++++S V ++FH  FSA 
Sbjct: 186 TDKGVSAFQQVCSF---YTWRKDTSLEDIESEINAAALGKLKVVSISEVSREFHPNFSAK 242

Query: 109 RRSYLY-----------RIITRQAP-------LALEKGRAWLIPKSLDCENMRIAA---- 146
            R YLY            ++   +P       LA E G        ++ E M I+A    
Sbjct: 243 WRRYLYILPLKDGEGNKTVVDGGSPVTYDSLCLADEGGNQSTDMNVINMEAMNISATGKH 302

Query: 147 QHLVGRHDFT----------------TFR--------------SIHC---QASSPIRTID 173
           Q  V  H+F                 ++R              +  C    A + + T+ 
Sbjct: 303 QASVKPHNFNVDTVNQLLQQLEGQSLSYRIFARDTQASRSRGPATECFMHHARAAVATLP 362

Query: 174 HF--DVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +   D  S G  +  + +VA  FL   +R  V +         T  +L K + A  R+  
Sbjct: 363 YMGQDHTSKGRTVMCVELVANRFLRKMVRVLVATAVREAAAGATPDNLLKLMHATCRRAS 422

Query: 231 GPLAPPEGLYFDSVEYS 247
            P APPEGL    + Y+
Sbjct: 423 APPAPPEGLCLVDIGYT 439


>gi|24648455|ref|NP_650899.1| CG4159, isoform A [Drosophila melanogaster]
 gi|7300636|gb|AAF55785.1| CG4159, isoform A [Drosophila melanogaster]
          Length = 410

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 70/281 (24%), Positives = 116/281 (41%), Gaps = 61/281 (21%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A NA L     I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPEE----LDLEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIIT-----------------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           Y + T                 R +P  L+K +          E +++  +     H+FT
Sbjct: 185 YTLPTVAFAPFEEKVDDVHDTFRISPELLQKVK----------ETLKL-YEGTKNFHNFT 233

Query: 157 TFRS----------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
           + +S          +   +S P R+    +       + ++V  +SF+  QIR  VG   
Sbjct: 234 SKKSFLDPSSKRFIMSFTSSEPFRSPQDIE------FVTLKVKGQSFMLHQIRKMVGLAI 287

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +  G  T+  LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 288 AIVRGNTTAATLERAL-TEERLDL-PMAPGLGLVLDTVHYE 326


>gi|323452423|gb|EGB08297.1| hypothetical protein AURANDRAFT_11850 [Aureococcus anophagefferens]
          Length = 266

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 87/216 (40%), Gaps = 24/216 (11%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSGVHALR 59
           I Y G  Y G+  Q    +   ++E+ +F    +  +V           GRTD GV AL 
Sbjct: 23  ISYEGGAYSGFAEQNIPGAGVDTVERQLFAALKKTCLVESRESCGYSRCGRTDKGVSALG 82

Query: 60  QVAHFDL---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV    +    R   P+     LN  L   D +  L    V  +F ARFS   R+Y Y  
Sbjct: 83  QVVGLRVRSAARAGEPLDYVNMLNRVL--PDDVRALAWRPVVPEFSARFSCASRTYRY-F 139

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF- 175
               +P     G A+ +P          AA  LVG HDF  F  +        R + +  
Sbjct: 140 FPATSP---NTGAAYDVPAMA------AAAARLVGDHDFRNFCKMDVLHVKNFRRVVYAA 190

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           DV   G+     +  ++FL   +RS V  L LVG+G
Sbjct: 191 DVRKTGDGFFFEIHGQAFLWHMVRSLVAVLFLVGEG 226


>gi|195569417|ref|XP_002102706.1| GD20050 [Drosophila simulans]
 gi|194198633|gb|EDX12209.1| GD20050 [Drosophila simulans]
          Length = 411

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 70/281 (24%), Positives = 116/281 (41%), Gaps = 61/281 (21%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A NA L     I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPEE----LDLEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIIT-----------------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           Y + T                 R +P  L+K +          E +++  +     H+FT
Sbjct: 185 YTLPTVAFASFEEKVDDVHDTFRISPELLQKVK----------ETLKL-YEGTKNFHNFT 233

Query: 157 TFRS----------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
           + +S          +   +S P R+    +       + ++V  +SF+  QIR  VG   
Sbjct: 234 SKKSFLDPSSKRFIMSFTSSEPFRSPQDIE------FVTLKVKGQSFMLHQIRKMVGLAI 287

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +  G  T+  LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 288 AIVRGNTTAATLERAL-TEERLDL-PMAPGLGLVLDTVHYE 326


>gi|195353947|ref|XP_002043463.1| GM23177 [Drosophila sechellia]
 gi|194127604|gb|EDW49647.1| GM23177 [Drosophila sechellia]
          Length = 411

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 70/281 (24%), Positives = 116/281 (41%), Gaps = 61/281 (21%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A NA L     I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPEE----LDLEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIIT-----------------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           Y + T                 R +P  L+K +          E +++  +     H+FT
Sbjct: 185 YTLPTVAFASFEEQVEDVHDTFRISPELLQKVK----------ETLKL-YEGTKNFHNFT 233

Query: 157 TFRS----------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
           + +S          +   +S P R+    +       + ++V  +SF+  QIR  VG   
Sbjct: 234 SKKSFLDPSSKRFIMSFTSSEPFRSPQDIE------FVTLKVKGQSFMLHQIRKMVGLAI 287

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +  G  T+  LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 288 AIVRGNTTAATLERAL-TEERLDL-PMAPGLGLVLDTVHYE 326


>gi|270002527|gb|EEZ98974.1| hypothetical protein TcasGA2_TC004829 [Tribolium castaneum]
          Length = 390

 Score = 60.8 bits (146), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 73/265 (27%), Positives = 115/265 (43%), Gaps = 32/265 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           ++ +++ Y+G+ Y+G QR  N  +I+    KA++             + +    A RTD 
Sbjct: 58  KFAVLLGYSGTNYYGMQRNPNTPTIEEEFFKALYKNNYISEENFTQVQTMQFQRAARTDK 117

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L RE + +     +N  L   + I +  +  V K F+++     RSY 
Sbjct: 118 GVSAARQVVSLKL-REDIDI---SKINEQL--PEVIRVFGIRRVTKGFNSKVQCDSRSYT 171

Query: 114 YRI----ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP- 168
           Y +     T    L ++KG   L   +L+  N  +  Q  +G  +F  F S   QA+ P 
Sbjct: 172 YLLPTVSFTPHDQLMVQKG-FRLDDSTLNRINDLL--QKYLGTKNFHNFTS-KKQATDPS 227

Query: 169 ----IRTI--DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
               ++T+  +   V        I++  +SF+  QIR  VG L  V  G +TS D     
Sbjct: 228 AKRYMKTLICEKPFVKDDVEFALIKIRGQSFMLHQIRKMVGLLIAVVKG-YTSEDTLDLA 286

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
              D+    P AP  GL  D V Y 
Sbjct: 287 FGMDKVNI-PKAPGLGLLLDYVHYE 310


>gi|86150269|ref|ZP_01068496.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88597547|ref|ZP_01100781.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|148926529|ref|ZP_01810211.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|218562455|ref|YP_002344234.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           NCTC 11168]
 gi|24212598|sp|Q9PP96|TRUA_CAMJE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|85839385|gb|EAQ56647.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88190139|gb|EAQ94114.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|112360161|emb|CAL34955.1| tRNA pseudouridine synthase [Campylobacter jejuni subsp. jejuni
           NCTC 11168]
 gi|145845223|gb|EDK22317.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni CG8486]
          Length = 241

 Score = 60.8 bits (146), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 101/247 (40%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q ++  A+  + G    +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSATQPHKKGVQDALSGALSHL-GIFSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA  +    +  +  L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVECGDYFTNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +            PK  D           VG+ D   F        + +R I      +
Sbjct: 117 ASYSPFMASYVHFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GL
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLSRICY 241


>gi|195055095|ref|XP_001994456.1| GH16145 [Drosophila grimshawi]
 gi|193892219|gb|EDV91085.1| GH16145 [Drosophila grimshawi]
          Length = 395

 Score = 60.8 bits (146), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 66/272 (24%), Positives = 114/272 (41%), Gaps = 42/272 (15%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 59  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHNWITEDSFKQVQIASFQRAARTDK 118

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E   V   K L       +TI +  +  V K F+A+     R+Y 
Sbjct: 119 GVSAARQVCSIKLPDELDLVAFNKDL------PETIRLFGVERVTKGFNAKEQCNARTYT 172

Query: 114 YRIIT------RQAPLALEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFRS----- 160
           Y + +       +     ++    L P   +  CE +++  +     H+FT+ ++     
Sbjct: 173 YTLPSIAFAGCNEQQNQQDQATFRLTPALHEQICETLKL-YEGTKNFHNFTSKKNFLDPS 231

Query: 161 -----IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
                +   +S+P  +    +       + ++V  +SF+  QIR  VG    +  G  T 
Sbjct: 232 AKRFIMSFTSSAPFHSPQGIE------FVTLQVKGQSFMLHQIRKMVGLAIAIVRGNTTR 285

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 286 ITLERAL-TEERLDL-PMAPGLGLVLDTVHYE 315


>gi|301782183|ref|XP_002926505.1| PREDICTED: tRNA pseudouridine synthase 3-like [Ailuropoda
           melanoleuca]
          Length = 480

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 97/245 (39%), Gaps = 62/245 (25%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 68  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-----------------ISILNLSIVDKQFH 102
           QV   DL   ++     +  +   ++SD                  I +L  + V+  F 
Sbjct: 125 QVISLDLRSHFLKGRASEDFHVKDEVSDAAKEIRYTHILNRVLPPDIRVLAWAPVEPSFS 184

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     +
Sbjct: 185 ARFSCLERTYRY-----------------FFPRADLDIVTMNYAAQKYVGTHDFRNLCKM 227

Query: 162 HCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLK 206
              A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L 
Sbjct: 228 DV-ANGVINFQRTILSAQVQLVGQSLDKETWQEAFQLCQFEVTGQAFLYHQVRCMMAILF 286

Query: 207 LVGDG 211
           L+G G
Sbjct: 287 LIGQG 291


>gi|148693449|gb|EDL25396.1| pseudouridine synthase 3, isoform CRA_b [Mus musculus]
          Length = 322

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/266 (25%), Positives = 102/266 (38%), Gaps = 72/266 (27%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHA 57
           + I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A
Sbjct: 74  LKIAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSA 130

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISD-----------------TISILNLSIVDKQ 100
             QV   DL  ++      +  N   +  D                  I +L  + V+  
Sbjct: 131 FGQVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPS 190

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF- 158
           F ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF    
Sbjct: 191 FSARFSCLERTYRY-----------------FFPRADLDIATMNYAAQKYVGTHDFRNLC 233

Query: 159 ------------RSIHC-------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
                       R+I C       Q+    R  + F       L +  V+ ++FL+ Q+R
Sbjct: 234 KMDVANGVINFQRTILCAQVQLVAQSPGEERRQEPF------QLCQFEVIGQAFLYHQVR 287

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQ 225
             +  L L+G G      +++ L  Q
Sbjct: 288 CMMAILFLIGQGMEKPEIIDELLNIQ 313


>gi|281338704|gb|EFB14288.1| hypothetical protein PANDA_016156 [Ailuropoda melanoleuca]
          Length = 479

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 97/245 (39%), Gaps = 62/245 (25%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 68  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-----------------ISILNLSIVDKQFH 102
           QV   DL   ++     +  +   ++SD                  I +L  + V+  F 
Sbjct: 125 QVISLDLRSHFLKGRASEDFHVKDEVSDAAKEIRYTHILNRVLPPDIRVLAWAPVEPSFS 184

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     +
Sbjct: 185 ARFSCLERTYRY-----------------FFPRADLDIVTMNYAAQKYVGTHDFRNLCKM 227

Query: 162 HCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLK 206
              A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L 
Sbjct: 228 DV-ANGVINFQRTILSAQVQLVGQSLDKETWQEAFQLCQFEVTGQAFLYHQVRCMMAILF 286

Query: 207 LVGDG 211
           L+G G
Sbjct: 287 LIGQG 291


>gi|294949997|ref|XP_002786409.1| tRNA pseudouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
 gi|239900701|gb|EER18205.1| tRNA pseudouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
          Length = 427

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 115/283 (40%), Gaps = 71/283 (25%)

Query: 10  YNGSGYFGWQRQKNG------SSIQGSIEKAIF---LVTGEIVVVHG------AGRTDSG 54
           Y+G G  G Q Q N       S+I+G  +KA+    L T EI+          A RTD G
Sbjct: 81  YSGEGLKGMQIQTNEKGEEIHSTIEGIFQKALLATNLSTEEILADKKKLKFSRAARTDKG 140

Query: 55  VH------------------------ALRQVAHFDLVREWVPVILCKALNAYLKISDTIS 90
           VH                        A R V  FD  +        KALN +L+  + + 
Sbjct: 141 VHAALNILALALPVTLDKTLPQGEGDATRNVWTFDEKKN------VKALNDFLEPLN-MQ 193

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           +  +  V  +F AR    RR Y Y +       AL+ G+A       D   +       V
Sbjct: 194 VFGIQRVSNKFDARKQCERRRYEYLL----PEFALD-GKA-------DAAKLEEVMSQYV 241

Query: 151 GRH-DFTTFRS-IHCQASSPIRTI-------DHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
           G++ +F  F + I  +  S  R I          D N+F   I I++V +SFL  QIR  
Sbjct: 242 GKNKNFFNFTAKIPAEDPSAKRHIISITCQPTEIDANTF---IRIQLVGQSFLLHQIRKM 298

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +G    V  G      +E+ L A++RK    LAP EGL+ D V
Sbjct: 299 IGLAVEVCRGSAPEGAIEECLAAKERKHIH-LAPAEGLFLDRV 340


>gi|260062928|ref|YP_003196008.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
 gi|88784496|gb|EAR15666.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
          Length = 274

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 70/266 (26%), Positives = 104/266 (39%), Gaps = 28/266 (10%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + + I + G  + GWQ Q    ++ G I K   F++    V + GAGRTD+ V A R  A
Sbjct: 9   FLIRIAFLGFRFHGWQEQPGQRTVAGMIRKTFRFVLPDTPVKILGAGRTDARVSA-RDFA 67

Query: 63  HFDLVR--EWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              + R  E  P  +L  ALN  L     I + ++  V   F+       ++Y Y   T 
Sbjct: 68  VQVIARAPELPPFGVLADALNENL--PPDIRVNSIRPVPPGFNPIRDCASKTYRYYFQTG 125

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF------------RSIHCQ--A 165
             P A        +P S D   MR AA    G H+F  F            R   C+   
Sbjct: 126 NHPDAYWTPFVGFLPGSPDITRMREAAPLFEGMHNFRCFTASPSEDKKYVRRVTRCRLGV 185

Query: 166 SSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            SP+  +        D     +++E+R  A  F   Q+R  + +L  VG  +     L K
Sbjct: 186 GSPMDGVVAGKDPEGDTGFTAHMLEVR--APGFGRNQVRLMMAALAAVGRQELQPETLVK 243

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEY 246
            L          + P  GL+   VE+
Sbjct: 244 VLDEGQGWMSDSIVPASGLHLMHVEF 269


>gi|189236260|ref|XP_974416.2| PREDICTED: similar to pseudouridylate synthase [Tribolium
           castaneum]
          Length = 275

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 88/216 (40%), Gaps = 39/216 (18%)

Query: 15  YFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVAHF 64
           Y GW  Q          +IE  +F    +  ++        H  GRTD GV +L   ++ 
Sbjct: 64  YLGWDYQGYVTQEDTVNTIEHHVFNALIKTCLIENRSSANYHRCGRTDKGVISLDLRSNG 123

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D       +  CK LN  L   + I  +    V+  F ARF    R+Y Y          
Sbjct: 124 DDFES--EINYCKILNRVL--PENIQFVAWCPVESAFSARFDCKNRTYKY---------- 169

Query: 125 LEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFDVNSFG 181
                    PKS LD + M+IAA +LVG HDF  F    ++       R I   D++ F 
Sbjct: 170 -------FFPKSNLDIDAMKIAANYLVGTHDFRNFCKMDVNNGVVEFKRNILSVDISLFQ 222

Query: 182 -----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
                ++  + +   +FL  QIR  VG L LVG GK
Sbjct: 223 EDERYSIQVLTIKGNAFLWHQIRCIVGILILVGQGK 258


>gi|12847644|dbj|BAB27651.1| unnamed protein product [Mus musculus]
          Length = 316

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/266 (25%), Positives = 102/266 (38%), Gaps = 72/266 (27%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHA 57
           + I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A
Sbjct: 68  LKIAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSA 124

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISD-----------------TISILNLSIVDKQ 100
             QV   DL  ++      +  N   +  D                  I +L  + V+  
Sbjct: 125 FGQVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPS 184

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF- 158
           F ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF    
Sbjct: 185 FSARFSCLERTYRY-----------------FFPRADLDIATMNYAAQKYVGTHDFRNLC 227

Query: 159 ------------RSIHC-------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
                       R+I C       Q+    R  + F       L +  V+ ++FL+ Q+R
Sbjct: 228 KMDVANGVINFQRTILCAQVQLVAQSPGEERRQEPF------QLCQFEVIGQAFLYHQVR 281

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQ 225
             +  L L+G G      +++ L  Q
Sbjct: 282 CMMAILFLIGQGMEKPEIIDELLNIQ 307


>gi|296005181|ref|XP_001351959.2| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|225631808|emb|CAD51770.2| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 312

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 97/216 (44%), Gaps = 36/216 (16%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGEIVVVHGAGRTDSGVHA------L 58
           +E+NGS Y    ++ N ++++  + + ++   L+      +    RTD GV A      L
Sbjct: 16  MEFNGSAY----QKDNDNTVENKLLENLYKLELIDNYDTPLSRVSRTDKGVSARINGINL 71

Query: 59  RQVAHFDLVREWVPV--ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           R     ++  E VP+  I  K +    K    I I ++  V   F AR + I+R+Y+Y  
Sbjct: 72  R----LNIKYENVPIFEIEKKYVKELKKKLKNIHIHDIKHVSNTFDARLNCIQRTYVY-- 125

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                         + I K+ + E M+ AA+  +G HDF+         +S  RT+  FD
Sbjct: 126 --------------FFINKNYNIEKMKKAAKLFIGEHDFSNCCKKGKNVTSNRRTVLKFD 171

Query: 177 V-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           + N   +    ++   SFL+ QIR  V  L LVG G
Sbjct: 172 IRNIDKHFYYFKIKGISFLYNQIRHMVAILFLVGKG 207


>gi|328873128|gb|EGG21495.1| tRNA pseudouridylate synthase [Dictyostelium fasciculatum]
          Length = 510

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/142 (30%), Positives = 63/142 (44%), Gaps = 24/142 (16%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I +L  + V   F+ARFS + R+Y Y                +  P  LD E M+ A  H
Sbjct: 217 IRVLAWTPVPFHFNARFSTLYRTYKY----------------YFNPAGLDIEAMKEAGNH 260

Query: 149 LVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSF-------GNLIEIRVVARSFLHTQIRS 200
            +G HDF+ F  I  +A  S  R I  FD+          G L E  +   +FL  QIR 
Sbjct: 261 FLGSHDFSNFCKIDLEAVKSFTRVILSFDIAPVPVGQFQSGGLYEATICGYAFLWHQIRC 320

Query: 201 FVGSLKLVGDGKWTSTDLEKAL 222
            +  L L+G  K+ +T ++  L
Sbjct: 321 MMAMLLLIGQKKFPTTIIKDLL 342


>gi|91076290|ref|XP_968649.1| PREDICTED: similar to AGAP002409-PA [Tribolium castaneum]
          Length = 588

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 73/265 (27%), Positives = 115/265 (43%), Gaps = 32/265 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           ++ +++ Y+G+ Y+G QR  N  +I+    KA++             + +    A RTD 
Sbjct: 256 KFAVLLGYSGTNYYGMQRNPNTPTIEEEFFKALYKNNYISEENFTQVQTMQFQRAARTDK 315

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L RE + +     +N  L   + I +  +  V K F+++     RSY 
Sbjct: 316 GVSAARQVVSLKL-REDIDI---SKINEQL--PEVIRVFGIRRVTKGFNSKVQCDSRSYT 369

Query: 114 YRI----ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP- 168
           Y +     T    L ++KG   L   +L+  N  +  Q  +G  +F  F S   QA+ P 
Sbjct: 370 YLLPTVSFTPHDQLMVQKG-FRLDDSTLNRINDLL--QKYLGTKNFHNFTS-KKQATDPS 425

Query: 169 ----IRTI--DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
               ++T+  +   V        I++  +SF+  QIR  VG L  V  G +TS D     
Sbjct: 426 AKRYMKTLICEKPFVKDDVEFALIKIRGQSFMLHQIRKMVGLLIAVVKG-YTSEDTLDLA 484

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
              D+    P AP  GL  D V Y 
Sbjct: 485 FGMDKVNI-PKAPGLGLLLDYVHYE 508


>gi|207093371|ref|ZP_03241158.1| tRNA pseudouridine synthase A [Helicobacter pylori HPKX_438_AG0C1]
          Length = 120

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 38/107 (35%), Positives = 53/107 (49%), Gaps = 5/107 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  +  V+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSAVI-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           + W        L  YL       I+   + +K FHARF A +R Y Y
Sbjct: 67  KHWN----ASKLFYYLAPKLAPHIVLKKLEEKNFHARFDAQKRVYRY 109


>gi|194899730|ref|XP_001979411.1| GG15313 [Drosophila erecta]
 gi|190651114|gb|EDV48369.1| GG15313 [Drosophila erecta]
          Length = 410

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 110/264 (41%), Gaps = 27/264 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  +    +  +A NA L     I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPED----LDLEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV------GRHDFTTFRSIHCQASS 167
           Y + T       EK         +  E ++   + L         H+FT+ +S    +S 
Sbjct: 185 YTLPTMAFAPFEEKVEDLHDTFQISPELLQKVKETLKLYEGTKNFHNFTSKKSFLDPSSK 244

Query: 168 ----PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                  + D F        + ++V  +SF+  QIR  VG    +  G  T+  LE+AL 
Sbjct: 245 RFIMSFTSSDPFRSPQGIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAATLERAL- 303

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
            ++R +  P+AP  GL  D+V Y 
Sbjct: 304 TEERLDL-PMAPGLGLVLDTVHYE 326


>gi|207108295|ref|ZP_03242457.1| tRNA pseudouridine synthase A [Helicobacter pylori HPKX_438_CA4C1]
          Length = 122

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 40/116 (34%), Positives = 58/116 (50%), Gaps = 6/116 (5%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I Y+G+ + G+ +Q N   +Q  IE A+  +  +  V+  AGRTD GVHA  QV  F   
Sbjct: 8   IAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSAVI-AAGRTDKGVHANNQVLSFHAP 66

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           + W        L  YL       I+   + +K FHARF A +R Y Y ++T+   L
Sbjct: 67  KHWN----ASKLFYYLAPKLAPHIVLKKLEEKNFHARFDAQKRVYRY-LLTKNLKL 117


>gi|9652099|gb|AAF91402.1|AF266505_1 pseudouridine synthase 3 [Mus musculus]
          Length = 481

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 101/264 (38%), Gaps = 72/264 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 70  IAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 126

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISD-----------------TISILNLSIVDKQFH 102
           QV   DL  ++      +  N   +  D                  I +L  + V+  F 
Sbjct: 127 QVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSFS 186

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF--- 158
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF      
Sbjct: 187 ARFSCLERTYRY-----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 229

Query: 159 ----------RSIHC-------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
                     R+I C       Q+    R  + F       L +  V+ ++FL+ Q+R  
Sbjct: 230 DVANGVIDFQRTILCAQVQLVAQSPGEERRQEPF------QLCQFEVIGQAFLYHQVRCM 283

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQ 225
           +  L L+G G      +++ L  Q
Sbjct: 284 MAILFLIGQGMEKPEIIDELLNIQ 307


>gi|152964686|ref|YP_001360470.1| tRNA-pseudouridine synthase I [Kineococcus radiotolerans SRS30216]
 gi|151359203|gb|ABS02206.1| tRNA-pseudouridine synthase I [Kineococcus radiotolerans SRS30216]
          Length = 252

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 98/216 (45%), Gaps = 22/216 (10%)

Query: 48  AGRTDSGVHALRQVAHFDLVR---EWVP--------VILCKALNAYLKISDTISILNLSI 96
           AGRTD+GVHA  QVAH DL R   E +P          L + L   L     + +     
Sbjct: 24  AGRTDAGVHASGQVAHADLPRAVWEALPGRSDAPPAAALVRRLAGVLPPD--VRVHGARP 81

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI---PKSLDCENMRIAAQHLVGRH 153
               F ARF A+RR Y YR+     P  +   R + +    + LD   M +AA  LVG  
Sbjct: 82  APPGFDARFGALRRRYAYRVC--DDPAGVPPLRRFDVLHHRRPLDAAAMDLAAGSLVGLR 139

Query: 154 DFTTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +F  F      AS+ +RT+  +        L+   V A +F H+ +R+ VG++  VGDG+
Sbjct: 140 EFAAFCRPREGAST-VRTLLAYSWRRDEDGLLVADVQADAFCHSMVRALVGAVLAVGDGR 198

Query: 213 WTSTDLEKALQ-AQDRKECGPLAPPEGLYFDSVEYS 247
               D  + +Q A  R     +  P+GL  + V Y 
Sbjct: 199 -RDVDWPRVVQDAAVRDPAVAVVGPQGLTLEEVVYP 233


>gi|227499255|ref|NP_075781.3| tRNA pseudouridine synthase 3 [Mus musculus]
 gi|52783242|sp|Q9JI38|PUS3_MOUSE RecName: Full=tRNA pseudouridine synthase 3; AltName: Full=tRNA
           pseudouridylate synthase 3; AltName: Full=tRNA-uridine
           isomerase 3
 gi|22137577|gb|AAH29253.1| Pseudouridine synthase 3 [Mus musculus]
 gi|148693450|gb|EDL25397.1| pseudouridine synthase 3, isoform CRA_c [Mus musculus]
          Length = 481

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 101/264 (38%), Gaps = 72/264 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 70  IAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 126

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISD-----------------TISILNLSIVDKQFH 102
           QV   DL  ++      +  N   +  D                  I +L  + V+  F 
Sbjct: 127 QVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSFS 186

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF--- 158
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF      
Sbjct: 187 ARFSCLERTYRY-----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 229

Query: 159 ----------RSIHC-------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
                     R+I C       Q+    R  + F       L +  V+ ++FL+ Q+R  
Sbjct: 230 DVANGVINFQRTILCAQVQLVAQSPGEERRQEPF------QLCQFEVIGQAFLYHQVRCM 283

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQ 225
           +  L L+G G      +++ L  Q
Sbjct: 284 MAILFLIGQGMEKPEIIDELLNIQ 307


>gi|195391039|ref|XP_002054173.1| GJ24293 [Drosophila virilis]
 gi|194152259|gb|EDW67693.1| GJ24293 [Drosophila virilis]
          Length = 408

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 71/263 (26%), Positives = 111/263 (42%), Gaps = 27/263 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + K +              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKVMLKHKWITEDSFEQVQIASFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A NA L   D I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPEE----LDLQAFNADL--PDQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRI--ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIR 170
           Y +  I   A     +   + IP  L  E +    +   G  +F  F S  +    S  R
Sbjct: 185 YTLPTIAFAAFDEQHEQETYRIPLKLQ-EVVNTTLKLYEGTKNFHNFTSKKNFLDPSAKR 243

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F  ++          + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 244 YIMSFTCSAPFLSPQSIEFVTLQVKGQSFMLHQIRKMVGLAIAIVRGNTTTATLERAL-T 302

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           ++R +  P+AP  GL  D+V Y 
Sbjct: 303 EERLDL-PMAPGLGLVLDTVHYE 324


>gi|26347775|dbj|BAC37536.1| unnamed protein product [Mus musculus]
          Length = 481

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 101/264 (38%), Gaps = 72/264 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 70  IAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 126

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISD-----------------TISILNLSIVDKQFH 102
           QV   DL  ++      +  N   +  D                  I +L  + V+  F 
Sbjct: 127 QVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSFS 186

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF--- 158
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF      
Sbjct: 187 ARFSCLERTYRY-----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 229

Query: 159 ----------RSIHC-------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
                     R+I C       Q+    R  + F       L +  V+ ++FL+ Q+R  
Sbjct: 230 DVANGVINFQRTILCAQVQLVAQSPGEERRQEPF------QLCQFEVIGQAFLYHQVRCM 283

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQ 225
           +  L L+G G      +++ L  Q
Sbjct: 284 MAILFLIGQGMEKPEIIDELLNIQ 307


>gi|310821765|ref|YP_003954123.1| tRNA pseudouridylate synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309394837|gb|ADO72296.1| tRNA pseudouridylate synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 252

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 92/210 (43%), Gaps = 17/210 (8%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS 86
           +Q ++E A+   TG    V  AGRTD GVHA  QV    L     P  L   L A L   
Sbjct: 1   MQSTLE-AVLRSTGVPATVMPAGRTDRGVHARMQVVSLRLEAGDTPEALAARLPALLPPD 59

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLY------RIITRQAPLALEKG-RAWLIPKSLDC 139
             + +  +      FHA++SA  ++Y Y      R+     P  LE      L  +++  
Sbjct: 60  --LGVCAVRRPPPSFHAQWSAAGKTYCYRVQLGGRVSETWRPYVLEAAEEPRLAQRAIAP 117

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFDVNSF-GNLIEIRVVARSFLHT 196
           E +    Q  VG+ DF  F +    +SSP   RT++   V+   G L EI++   SF   
Sbjct: 118 ERLAELLQGAVGQRDFWAFHA----SSSPRKPRTLESATVHELEGGLFEIQLRGDSFARY 173

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           Q+R  VGS  L   G+        AL++ +
Sbjct: 174 QVRYLVGSALLTAAGQLPEAQWRAALESAE 203


>gi|322490513|emb|CBZ25774.1| tRNA pseudouridine synthase A-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 525

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 83/188 (44%), Gaps = 30/188 (15%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKNGSSIQ--------------GS-------IEKAI 35
           M RY + ++Y GS + GW    QR +NG +                GS       +E+A+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNGKNGASAGSTATAAADYGAGSRHFAKVVLEEAL 189

Query: 36  FLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE--WVPVILCKALNAYL-KISDTISI 91
            +      V +  A   ++GV   R   H D+  E    P  + +    +L +    +++
Sbjct: 190 AVALDVPTVSIVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRTTLWLHQRRQPLAV 249

Query: 92  LNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+      Q FHAR + +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + 
Sbjct: 250 LSCHPCRNQDFHARHNGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLME 309

Query: 151 GRHDFTTF 158
           G HD+  F
Sbjct: 310 GTHDYGFF 317



 Score = 42.7 bits (99), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 41/86 (47%), Gaps = 9/86 (10%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--- 225
           IRT+D  +V    + I I  V +SFL  QIR+ V  LK  G G W   +L+ A Q+    
Sbjct: 415 IRTLDKIEVVRQEDEILIWFVGQSFLRHQIRNMVSVLKAGGHGLWDDQELQHAFQSGFEV 474

Query: 226 -----DRKECGPLAPPEGLYFDSVEY 246
                 R+   P AP  GL    VEY
Sbjct: 475 SRKKFKRERLSP-APVHGLTLWDVEY 499


>gi|322368335|ref|ZP_08042904.1| tRNA pseudouridine synthase A [Haladaptatus paucihalophilus DX253]
 gi|320552351|gb|EFW93996.1| tRNA pseudouridine synthase A [Haladaptatus paucihalophilus DX253]
          Length = 263

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 94/244 (38%), Gaps = 31/244 (12%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---AGRTDSGVHALRQVAHF 64
           + Y+G  ++G+QRQ +  +++ S+ +++  +     V  G   AGRTDSGV AL Q   F
Sbjct: 6   VAYDGRPFYGFQRQPDVPTVEDSLFESLRALGVADRVPDGYAAAGRTDSGVSALAQTVAF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +      P      L A +++  +  ++        FHA   A  R Y+Y     +A L 
Sbjct: 66  ECPEWLTPSAFNSELPAEIRVWASADVV------PAFHATHDAYYREYVYHCYAPRANLG 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L K                 A+  L G HDF    S        +R +   DV   G  +
Sbjct: 120 LAKE----------------ASDRLSGEHDFHNLTS---DTEGTVRDL-GIDVVQDGEYL 159

Query: 185 EIRVVARSFLHTQIRSFVGSLKLV--GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
                A  F    +R  V  +  +  GD +    D   A +  D +   P A    LY  
Sbjct: 160 VFTFQAGGFARNLVRRVVSLIHSIATGDAEMAKIDTVLAPEPLDGRAGVPCASAHPLYLA 219

Query: 243 SVEY 246
            V Y
Sbjct: 220 DVGY 223


>gi|303391559|ref|XP_003074009.1| tRNA pseudouridine synthase A [Encephalitozoon intestinalis ATCC
           50506]
 gi|303303158|gb|ADM12649.1| tRNA pseudouridine synthase A [Encephalitozoon intestinalis ATCC
           50506]
          Length = 317

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 103/245 (42%), Gaps = 35/245 (14%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           I Y+G  Y G   Q    ++ G +E A+ F   GE +V   AGRTD+GV A+  V     
Sbjct: 41  ISYDGRRYSGMAPQSGKETVGGHLENALKFTGLGEKLVY--AGRTDAGVSAISMVVSGVF 98

Query: 67  V-REWVP---VILCKA----------LNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           + R  +P    ++ ++          LN++L     I ++  + V   F ARF+ I+R Y
Sbjct: 99  ISRIEMPNRSYVVTESDYKEYKYDMILNSHL--PSDIRVIGWAPVPDTFSARFTCIQRQY 156

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y                +   + LD + MR  A  +    +F  F     + +   R +
Sbjct: 157 RY----------------YFHKEDLDADRMREMASRIKKMENFYYFSKHSDKNARYERKL 200

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           D   +   G++  + + AR+FLH  +R  V +++  G G+    +     +      CG 
Sbjct: 201 DECRIVDEGDVYYLDIRARAFLHNMVRKIVWAIQKAGKGETYDAERVGTSEPDPLVFCGA 260

Query: 233 LAPPE 237
           + P E
Sbjct: 261 IYPHE 265


>gi|15790870|ref|NP_280694.1| tRNA pseudouridine synthase A [Halobacterium sp. NRC-1]
 gi|169236616|ref|YP_001689816.1| tRNA pseudouridine synthase A [Halobacterium salinarum R1]
 gi|24212587|sp|Q9HNP6|TRUA_HALSA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|229470757|sp|B0R6V1|TRUA_HALS3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|10581435|gb|AAG20174.1| pseudouridylate synthase I [Halobacterium sp. NRC-1]
 gi|167727682|emb|CAP14470.1| tRNA-pseudouridine synthase A [Halobacterium salinarum R1]
          Length = 266

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/255 (25%), Positives = 97/255 (38%), Gaps = 35/255 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVH 56
           M R    + Y+G  Y G+QRQ + S++ G +  A+         +      AGRTD+GV 
Sbjct: 1   MPRRAFRVAYDGRPYHGFQRQPDVSTVAGELFGALRRLDVFDGAKPPGYAAAGRTDAGVS 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  Q   FD      P     AL       D I +   +    +FHA   A+ R+Y+Y  
Sbjct: 61  ARAQTVAFDAPAWLTPDAFTGAL------PDPIQVWAHADAPPEFHATHDAVARTYVYY- 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAA-QHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                         W  P S   ++    A   L G HD   F ++    ++ +R +D  
Sbjct: 114 --------------WYAPDSRATDDRAAGALDRLTGTHD---FHNLTPNTTNTVRELDAT 156

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV---GDGKWTSTDLEKALQAQDRKECGP 232
            ++  G    I V A  F    +R  V  ++LV   GD     T L     A    +  P
Sbjct: 157 -LDRDGAFRVITVRAGGFCRELVRRVVSLVQLVTETGDTDRIDTVLGDEPVAG--PDGVP 213

Query: 233 LAPPEGLYFDSVEYS 247
            A P  L   +V Y 
Sbjct: 214 PADPHPLVLHAVAYD 228


>gi|327282044|ref|XP_003225754.1| PREDICTED: tRNA pseudouridine synthase 3-like [Anolis carolinensis]
          Length = 455

 Score = 60.1 bits (144), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 94/235 (40%), Gaps = 56/235 (23%)

Query: 14  GYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVAH 63
            Y GW+ Q   S  +   +IE+ +F   G+  +V        H  GRTD GV A  QV  
Sbjct: 71  AYLGWEYQGFASQENTNNTIEEKLFEALGKTRLVKNRQTSNYHRCGRTDKGVSAFGQVIS 130

Query: 64  FDLVREWVP------VILCKALNAYLKISDT----------ISILNLSIVDKQFHARFSA 107
            DL R  +P          KA  A  +I  T          I +L  + V+  F ARF+ 
Sbjct: 131 LDL-RSNLPENKPGDTATNKATKASEEIHYTHILNQVLPPDIRVLAWAPVEPNFSARFNC 189

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF------------ 155
           ++R+Y Y       P A           +LD   M  AAQ  VG HDF            
Sbjct: 190 LKRTYRYFF-----PCA-----------TLDVALMNRAAQKFVGTHDFRNLCKMDVANGV 233

Query: 156 TTF-RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           T+F R+I      P+      +  +   +    V  ++FL+ Q+R  +  L L+G
Sbjct: 234 TSFHRTILAAEVQPVDGESETEQQNPFRMYYFEVTGQAFLYHQVRCMMAILFLIG 288


>gi|302818580|ref|XP_002990963.1| hypothetical protein SELMODRAFT_132613 [Selaginella moellendorffii]
 gi|300141294|gb|EFJ08007.1| hypothetical protein SELMODRAFT_132613 [Selaginella moellendorffii]
          Length = 289

 Score = 60.1 bits (144), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/257 (22%), Positives = 110/257 (42%), Gaps = 17/257 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-----------FLVTGEI--VVVHGAGR 50
           + +++ Y+G+ + GWQ+Q    ++Q  +EK +               G+I   +V  AGR
Sbjct: 14  FKIVLSYSGTAFAGWQKQPGFLTVQSVLEKQLGRFVDGKRASNLEKQGKIKEALVSVAGR 73

Query: 51  TDSGVHALRQVAHF-DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GVHA  QV  F   +RE     +  A+N+ +     +  ++ S V++ FH  FSA  
Sbjct: 74  TDKGVHACGQVCSFYTWMRECKEEDVKSAVNSAMPT--ILRAVSASEVNRDFHPIFSAKW 131

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           R Y+Y I   ++   ++  +   + ++L+  ++  A      +   ++  +  C      
Sbjct: 132 RRYIY-IFPLRSRDEIDVSKVATLLRALEGHSLSYAIFARDTKIARSSGPATVCTLYHAR 190

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
             +      +  N++ + +VA  FL   +R  V +             L   ++  DR+ 
Sbjct: 191 AALAKLPFPNEENVMVVELVADRFLRKMVRVLVSTAIKEAFAGANDDALVALMEETDRRA 250

Query: 230 CGPLAPPEGLYFDSVEY 246
             P AP  GL    V Y
Sbjct: 251 SAPPAPAHGLCLAEVGY 267


>gi|296216591|ref|XP_002754614.1| PREDICTED: tRNA pseudouridine synthase 3 [Callithrix jacchus]
          Length = 477

 Score = 60.1 bits (144), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 96/242 (39%), Gaps = 59/242 (24%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 68  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT--------------ISILNLSIVDKQFHARF 105
           QV   DL  ++      +  N   + ++               I IL  + V+  F ARF
Sbjct: 125 QVISLDLRSQFPRRRDSEDFNVKEEAAEEIRYTHILNRVLPPDIRILAWAPVEPSFSARF 184

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           S + R+Y Y                   P++ LD   M  AAQ  VG HDF     +   
Sbjct: 185 SCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKMDV- 226

Query: 165 ASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L L+G
Sbjct: 227 ANGVINFQRTILSAQVQPVGQSPDEERWQVPFQLCQFEVTGQAFLYHQVRCMMAILFLIG 286

Query: 210 DG 211
            G
Sbjct: 287 QG 288


>gi|120436099|ref|YP_861785.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
 gi|117578249|emb|CAL66718.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
          Length = 262

 Score = 60.1 bits (144), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/262 (24%), Positives = 121/262 (46%), Gaps = 25/262 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G    GWQ+Q +  +++G + K + +++      + G  RTD+ V A  + +
Sbjct: 8   YFIKVQYLGYRLHGWQKQPDVKTVEGLVTKTLGWVIPDAKYKILGTSRTDAMVSA--EES 65

Query: 63  HFDLVREWVPVILCKALNAYL-----KISDTISILNLSIVDKQFHA-RFSAIRR-SYLYR 115
            F+L  +  P+   + L+ +L      +   I  L++  VD +F+  + S  +  +YL+ 
Sbjct: 66  AFELFLDHEPL---EDLDGFLHLFNKNLPQDIRALSIEEVDDKFNIIQHSKTKEYAYLFS 122

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--- 172
           I  +  P        +   + LD + M+ AA+   G H+F  +     + S+  R +   
Sbjct: 123 IGDKFHPFCAPFMANF--QEDLDVDRMKEAAKLFHGIHNFRNYCIRVSEKSTFEREMLKS 180

Query: 173 -----DHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
                D +  N F     I  + A  FL  Q+R  +GSL LVG G+ +  D+E +L+   
Sbjct: 181 ELVENDIYTANFFPEKSYIFHIHASGFLRHQVRLMMGSLVLVGRGELSLQDIEDSLKPDS 240

Query: 227 RK-ECGPLAPPEGLYFDSVEYS 247
            + +   +AP  GL    +E+ 
Sbjct: 241 PQLQMDYIAPASGLILRKIEFE 262


>gi|57237668|ref|YP_178916.1| tRNA pseudouridine synthase A [Campylobacter jejuni RM1221]
 gi|62901173|sp|Q5HUW9|TRUA_CAMJR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57166472|gb|AAW35251.1| tRNA pseudouridine synthase A [Campylobacter jejuni RM1221]
 gi|315058277|gb|ADT72606.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           S3]
          Length = 240

 Score = 60.1 bits (144), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 99/242 (40%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+G+ + G   Q +   +Q ++  A+  + G    +  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGTAFLGSATQPHKKGVQDALSGALSHL-GIFSPLLMASRTDKGVHASYAVASVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGDYFTNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHSSYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    PK  D +         VG+ D   F        + +R I      ++ +  
Sbjct: 121 FMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAYKDFS 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   +
Sbjct: 180 IFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 CY 240


>gi|77735971|ref|NP_001029684.1| tRNA pseudouridine synthase 3 [Bos taurus]
 gi|119391067|sp|Q3SX07|PUS3_BOVIN RecName: Full=tRNA pseudouridine synthase 3; AltName: Full=tRNA
           pseudouridylate synthase 3; AltName: Full=tRNA-uridine
           isomerase 3
 gi|74356305|gb|AAI04570.1| Pseudouridylate synthase 3 [Bos taurus]
          Length = 481

 Score = 59.7 bits (143), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 98/246 (39%), Gaps = 64/246 (26%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVENRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVPVIL-CKALNAYLKISDT-----------------ISILNLSIVDKQF 101
           QV   DL R  +P     +  N   +++D                  I +L  + V+  F
Sbjct: 126 QVISLDL-RSHIPKGRDSEHFNLKNEVNDVATEIRYTHILNRVLPPDIRVLAWAPVETSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRS 160
            ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     
Sbjct: 185 SARFSCLERTYRY-----------------FFPRANLDIVTMNYAAQKYVGTHDFRNLCK 227

Query: 161 IHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSL 205
           +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L
Sbjct: 228 MDV-ANGVINFQRTILSAQVQRVGQNLGEEGWQEPFQLCQFEVTGQAFLYHQVRCMMAVL 286

Query: 206 KLVGDG 211
            L+G G
Sbjct: 287 FLIGQG 292


>gi|296471772|gb|DAA13887.1| tRNA pseudouridine synthase 3 [Bos taurus]
          Length = 481

 Score = 59.7 bits (143), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 98/246 (39%), Gaps = 64/246 (26%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYLGWGYQGFASQENTSN---TIEEKLFEALTKTRLVENRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVPVIL-CKALNAYLKISDT-----------------ISILNLSIVDKQF 101
           QV   DL R  +P     +  N   +++D                  I +L  + V+  F
Sbjct: 126 QVISLDL-RSHIPKGRDSEHFNLKNEVNDVATEIRYTHILNRVLPPDIRVLAWAPVETSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRS 160
            ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     
Sbjct: 185 SARFSCLERTYRY-----------------FFPRANLDIVTMNYAAQKYVGTHDFRNLCK 227

Query: 161 IHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSL 205
           +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L
Sbjct: 228 MDV-ANGVINFQRTILSAQVQRVGQNLGEEGWQEPFQLCQFEVTGQAFLYHQVRCMMAVL 286

Query: 206 KLVGDG 211
            L+G G
Sbjct: 287 FLIGQG 292


>gi|146084629|ref|XP_001465060.1| tRNA pseudouridine synthase A-like protein [Leishmania infantum
           JPCM5]
 gi|134069156|emb|CAM67303.1| tRNA pseudouridine synthase A-like protein [Leishmania infantum
           JPCM5]
          Length = 525

 Score = 59.7 bits (143), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 82/188 (43%), Gaps = 30/188 (15%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKN-------GSSIQGS--------------IEKAI 35
           M RY + ++Y GS + GW    QR +N       G++   +              +E+A+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNSKDAAPAGNTTTAAADYGTGSRHFAKVVLEEAL 189

Query: 36  FLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE---WVPVILCKALNAYLKISDTISI 91
            +      V V  A   ++GV   R   H D+  E       IL +A     +    +++
Sbjct: 190 AVALDVPTVSVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRATLWLHQRRQPLAV 249

Query: 92  LNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+      Q FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + 
Sbjct: 250 LSCHPCRNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLME 309

Query: 151 GRHDFTTF 158
           G HD+  F
Sbjct: 310 GTHDYGFF 317



 Score = 44.3 bits (103), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 42/86 (48%), Gaps = 9/86 (10%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--- 225
           IRT+D  +V    + + I  V +SFL  QIR+ V +LK  G G W   +L+ A Q+    
Sbjct: 415 IRTLDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVSALKAGGHGLWDDQELQHAFQSGFEV 474

Query: 226 -----DRKECGPLAPPEGLYFDSVEY 246
                 R+   P AP  GL    VEY
Sbjct: 475 SRKKFKRERLSP-APAHGLTLWDVEY 499


>gi|323454991|gb|EGB10860.1| hypothetical protein AURANDRAFT_58785 [Aureococcus anophagefferens]
          Length = 305

 Score = 59.7 bits (143), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 78/175 (44%), Gaps = 20/175 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFL-VTGEIVVVHGAGRTDSGVHALR 59
            RY + + Y+G+ + GWQ Q  G+ ++QG +  A+     G  +   GA RTD+GVHA  
Sbjct: 33  TRYALRVAYDGTRFKGWQVQPGGARTVQGELNAALRTRFGGADIPTLGASRTDAGVHARG 92

Query: 60  QVAHFDLVRE---WVPV-ILCKALNAYLKISDTISILNLSIVDKQFHAR--------FSA 107
           Q AH DL        P+ +L   +N  L     +  L  +   K + AR         +A
Sbjct: 93  QCAHADLPVAPLGGAPLELLEHQINRLLPDDARVHDLRPAPAPKPWQAREGLPWHAIANA 152

Query: 108 IRRSYLYRIITRQA---PLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
             + Y YR+  R+    PL  L +G      + +D   +  A    VG HDF  F
Sbjct: 153 AGKRYAYRLTARRGSADPLGRLYRGHVAY--RDVDFGRLDDALSCFVGEHDFAAF 205


>gi|322498495|emb|CBZ33568.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 525

 Score = 59.7 bits (143), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 79/188 (42%), Gaps = 30/188 (15%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKNGSSIQGS---------------------IEKAI 35
           M RY + ++Y GS + GW    QR +N      +                     +E+A+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNSKDAAPAGNTATAAADYGTGSRHFAKVVLEEAL 189

Query: 36  FLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE---WVPVILCKALNAYLKISDTISI 91
            +      V V  A   ++GV   R   H D+  E       IL +A     +    +++
Sbjct: 190 AVALDVPTVSVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRATLWLHQRRQPLAV 249

Query: 92  LNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+      Q FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + 
Sbjct: 250 LSCHPCRNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLME 309

Query: 151 GRHDFTTF 158
           G HD+  F
Sbjct: 310 GTHDYGFF 317



 Score = 44.3 bits (103), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 42/86 (48%), Gaps = 9/86 (10%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--- 225
           IRT+D  +V    + + I  V +SFL  QIR+ V +LK  G G W   +L+ A Q+    
Sbjct: 415 IRTLDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVSALKAGGHGLWDDQELQHAFQSGFEV 474

Query: 226 -----DRKECGPLAPPEGLYFDSVEY 246
                 R+   P AP  GL    VEY
Sbjct: 475 SRKKFKRERLSP-APAHGLTLWDVEY 499


>gi|242003078|ref|XP_002422603.1| tRNA pseudouridine synthase A, putative [Pediculus humanus
           corporis]
 gi|212505404|gb|EEB09865.1| tRNA pseudouridine synthase A, putative [Pediculus humanus
           corporis]
          Length = 410

 Score = 59.3 bits (142), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 70/262 (26%), Positives = 117/262 (44%), Gaps = 32/262 (12%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGEIV----VVH--GAGRTDSGV 55
            +++ YNGS Y G Q+  +  +I+  +  A+    L+  E +    ++H   A RTD GV
Sbjct: 77  ALLMAYNGSNYHGMQKNLDFKTIEYELLNALVKANLIPSEAIDNLPLIHFQRAARTDKGV 136

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A +QV  F +   +      + +N +L   + I + ++  V K F+ +     R+Y Y 
Sbjct: 137 SAAKQVVSFKIAENFQ----VEKINMFL--PEDIRVFSIKRVTKGFNCKNQCTARTYSYT 190

Query: 116 IIT-RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTI 172
           + T   AP    E  + + I K    +   I +Q+L G H F  F S    +  S  R I
Sbjct: 191 LPTFALAPEFHDEYPKNYRIDKLTIQKTNEILSQYL-GTHPFHNFTSKKDGRDPSAKRYI 249

Query: 173 DHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-- 225
             F+       +    I ++V  +SF+  QIR  VG    V  G  +     +A+Q++  
Sbjct: 250 MSFEAEEPFLENEEEFITLKVKGQSFMLHQIRKMVGYTIAVMKGFAS-----EAIQSKIW 304

Query: 226 -DRKECGPLAPPEGLYFDSVEY 246
            + K   P+AP  GL  + V Y
Sbjct: 305 TNEKVSLPMAPGLGLVLEDVHY 326


>gi|167590068|ref|ZP_02382456.1| tRNA pseudouridine synthase A [Burkholderia ubonensis Bu]
          Length = 77

 Score = 59.3 bits (142), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 26/64 (40%), Positives = 41/64 (64%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
          +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1  MRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFAQTPLHTTVAGRTDTGVHGLGQV 60

Query: 62 AHFD 65
           HFD
Sbjct: 61 VHFD 64


>gi|328777716|ref|XP_393954.4| PREDICTED: tRNA pseudouridine synthase 3-like [Apis mellifera]
          Length = 400

 Score = 59.3 bits (142), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 105/258 (40%), Gaps = 58/258 (22%)

Query: 15  YFGWQRQKNG----SSIQGSIEKAIF--------LVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y GW    NG     SI  +IE+ +F        + + E    H  GRTD GV +  QV 
Sbjct: 63  YLGWDY--NGFVVQESIDNTIEEHLFEALIKSCCIESRETSNYHRCGRTDKGVSSFSQVI 120

Query: 63  HFDLVREWVP---------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
             D+  +  P         +  CK LN  L     I  +    V   F ARF+   R+Y 
Sbjct: 121 SLDIRSKLNPEDQYKLEDELPYCKILNRLL--PSNIRCIAWCPVPNDFSARFNCKFRTYK 178

Query: 114 YRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIR 170
           Y                   P+ +L+ + M  A ++++G HDF     +       + IR
Sbjct: 179 Y-----------------FFPRGNLNIDAMNKAVKYIIGEHDFRNICKMDVANGVINYIR 221

Query: 171 TIDHFDVNSFG---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            + + +V  +          ++ ++ + +++FL  QIR  +G L L+G+GK    + E  
Sbjct: 222 KVINAEVRMYRQDFRNISGYDMYQLIITSQAFLWHQIRCLMGVLFLIGEGK---EEAEIM 278

Query: 222 LQAQDRKECGPLAPPEGL 239
           L+  D + C P  P   L
Sbjct: 279 LELLDIENC-PKKPQYNL 295


>gi|57085889|ref|XP_536533.1| PREDICTED: similar to tRNA pseudouridine synthase 3 (tRNA-uridine
           isomerase 3) (tRNA pseudouridylate synthase 3) [Canis
           familiaris]
          Length = 480

 Score = 58.9 bits (141), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 96/244 (39%), Gaps = 60/244 (24%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 68  IAYLGWGYQGFASQENTNN---TIEEKLFDALTKTRLVESRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-----------------ISILNLSIVDKQFH 102
           QV   DL   +      +  N   +++D                  I +L  + V+  F 
Sbjct: 125 QVISLDLRSHFPEGSTSEDSNLKNEVNDVAKEIRYTHILNRVLPPDIRVLAWAPVEPSFS 184

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF--- 158
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF      
Sbjct: 185 ARFSCLERTYRY-----------------FFPRADLDIITMNYAAQKYVGTHDFRNLCKM 227

Query: 159 ----------RSI-HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                     R++   Q     +++D         L +  VV ++FL+ Q+R  +  L L
Sbjct: 228 DVANGVINFQRTVLFAQVELVGQSLDKEQWQEPFQLCQFEVVGQAFLYHQVRCMMAILFL 287

Query: 208 VGDG 211
           +G G
Sbjct: 288 IGQG 291


>gi|255566350|ref|XP_002524161.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223536579|gb|EEF38224.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 443

 Score = 58.9 bits (141), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 42/127 (33%), Positives = 65/127 (51%), Gaps = 16/127 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---------IVVVHG----A 48
           + + + + Y+G  + GWQ+Q   +++QG +EK++     E            + G    A
Sbjct: 120 VNFKIDLSYHGGSFDGWQKQPGLNTVQGLVEKSLGKFVDEKKAQQLKEACKPLEGCAVVA 179

Query: 49  GRTDSGVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV ALRQV  F   R+ V P  +  A+N+       I ++++S V + FH  FSA
Sbjct: 180 GRTDKGVSALRQVCSFYTWRKDVRPHEIEDAINS--SAPGKIRVISVSEVSRVFHPNFSA 237

Query: 108 IRRSYLY 114
             R YLY
Sbjct: 238 KWRRYLY 244


>gi|157415094|ref|YP_001482350.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81116]
 gi|172047118|sp|A8FLN6|TRUA_CAMJ8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157386058|gb|ABV52373.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|284926072|gb|ADC28424.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           IA3902]
 gi|307747736|gb|ADN91006.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           M1]
 gi|315927713|gb|EFV07042.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           DFVF1099]
 gi|315931164|gb|EFV10137.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           327]
          Length = 240

 Score = 58.9 bits (141), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 98/242 (40%), Gaps = 7/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +   +Q ++  A+  + G    +  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSAFLGSATQPHKKGVQDALSGALSHL-GIFSPLLMASRTDKGVHASYAVASVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGDYFTNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHASYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                    PK  D           VG+ D   F        + +R I      ++ +  
Sbjct: 121 FMASYVHFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAYKDFS 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   +
Sbjct: 180 IFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLYLSRI 238

Query: 245 EY 246
            Y
Sbjct: 239 CY 240


>gi|171741245|ref|ZP_02917052.1| hypothetical protein BIFDEN_00320 [Bifidobacterium dentium ATCC
           27678]
 gi|171276859|gb|EDT44520.1| hypothetical protein BIFDEN_00320 [Bifidobacterium dentium ATCC
           27678]
          Length = 219

 Score = 58.9 bits (141), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 86/202 (42%), Gaps = 30/202 (14%)

Query: 71  VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE-KGR 129
           VP ++         + + I+I  ++   + F ARFSA+ R+Y+YRI  R + +    +G 
Sbjct: 3   VPPVVALTRRLQRMLPNDITIHGINEAPQGFDARFSALERTYVYRIADRSSEIDPRMRGF 62

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS------------PIRTI----- 172
              +   LD E M  AA   +G HDF +F + +   ++            P R +     
Sbjct: 63  VLHVDDDLDLETMNQAAAMTIGLHDFGSFATPNPGGTTIREVKTAYWRRIPQRPLVDGEM 122

Query: 173 ---DHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK----WTSTDLEKALQA 224
              + +   S    L    +VA +F    +RS V     VG GK    W +  +   L+ 
Sbjct: 123 TMGERYRTPSMESGLACFTIVADAFARNMVRSLVNGCVQVGIGKRSLDWFADKMATPLR- 181

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
                 GP+A P+GL  + +EY
Sbjct: 182 --EGSTGPIA-PQGLTLEHIEY 200


>gi|149716663|ref|XP_001505142.1| PREDICTED: pseudouridylate synthase 3 [Equus caballus]
          Length = 479

 Score = 58.9 bits (141), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 102/259 (39%), Gaps = 62/259 (23%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 67  IAYLGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 123

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-----------------ISILNLSIVDKQFH 102
           QV   DL   +      +  N   +++D                  I +L  + V+  F 
Sbjct: 124 QVISLDLRSHFPNGRDSEDFNLKDEVNDAAKEIRYTHILNRVLPPDIRVLAWAPVEPSFS 183

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     +
Sbjct: 184 ARFSCLERTYRY-----------------FFPRADLDIITMNSAAQKYVGTHDFRNLCKM 226

Query: 162 HCQASSPI---RTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLK 206
              A+  I   RTI    V   G             L +  V+ ++FL+ Q+R  +  L 
Sbjct: 227 DV-ANGVINFQRTILSAQVQLVGQSLAEERGQEPFQLCQFEVIGQAFLYHQVRCMMAILF 285

Query: 207 LVGDGKWTSTDLEKALQAQ 225
           L+G G      +++ L  Q
Sbjct: 286 LIGQGMEKPEVIDELLNIQ 304


>gi|157868264|ref|XP_001682685.1| tRNA pseudouridine synthase A-like protein [Leishmania major]
 gi|68126140|emb|CAJ07193.1| tRNA pseudouridine synthase A-like protein [Leishmania major strain
           Friedlin]
          Length = 525

 Score = 58.9 bits (141), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 82/188 (43%), Gaps = 30/188 (15%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKN-------GSSIQGS--------------IEKAI 35
           M RY + ++Y GS + GW    QR +N       G++   +              +E+A+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNNKDAAPVGNTATAAADYGAGSRHFAKVVLEEAL 189

Query: 36  FLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE---WVPVILCKALNAYLKISDTISI 91
            +      V V  A   ++GV   R   H D+  E       IL +A     +    +++
Sbjct: 190 GVALDVPTVSVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRATLWLHQRRQPLAV 249

Query: 92  LNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+      Q FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + 
Sbjct: 250 LSCHPCRNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLME 309

Query: 151 GRHDFTTF 158
           G HD+  F
Sbjct: 310 GTHDYGFF 317



 Score = 42.4 bits (98), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 41/86 (47%), Gaps = 9/86 (10%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--- 225
           IRT+D  +V    + + I  V +SFL  QIR+ V  LK  G G W   +L+ A Q+    
Sbjct: 415 IRTLDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVSVLKAGGHGLWDDQELQHAFQSGFEV 474

Query: 226 -----DRKECGPLAPPEGLYFDSVEY 246
                 R+   P AP  GL    VEY
Sbjct: 475 SRKKFKRERLSP-APVHGLTLWDVEY 499


>gi|298229126|ref|ZP_06962807.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae str.
          Canada MDR_19F]
          Length = 57

 Score = 58.9 bits (141), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/57 (50%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVH 56
          M RY   I Y+G  + G+QRQ +  S+Q  IEK +  L  G+ + VHGAGRTDSGVH
Sbjct: 1  MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVH 57


>gi|195113035|ref|XP_002001075.1| GI22173 [Drosophila mojavensis]
 gi|193917669|gb|EDW16536.1| GI22173 [Drosophila mojavensis]
          Length = 401

 Score = 58.5 bits (140), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 72/271 (26%), Positives = 110/271 (40%), Gaps = 43/271 (15%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDS 53
           +  +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD 
Sbjct: 71  KSAILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQVQIACFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A N  L   + I I  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPEE----LDLEAFNKDL--PEQIRIFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRS-IH 162
           Y + T    +A             D E  RI  + L           G  +F  F S  +
Sbjct: 185 YTLPT----IAFA-----AFDDQHDQETYRIPIERLEKVSATLKLYEGTKNFHNFTSKKN 235

Query: 163 CQASSPIRTIDHFDVNS------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
               S  R I  F  ++          + ++V  +SF+  QIR  VG    +  G  T+ 
Sbjct: 236 FLDPSAKRFIMSFTCSTPFLSPQSVEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTTA 295

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 296 TLERAL-TEERLDL-PMAPGLGLVLDTVHYE 324


>gi|312378112|gb|EFR24771.1| hypothetical protein AND_10418 [Anopheles darlingi]
          Length = 376

 Score = 58.5 bits (140), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 66/255 (25%), Positives = 105/255 (41%), Gaps = 58/255 (22%)

Query: 15  YFGWQRQ---KNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSGVHALRQVAH 63
           Y GW  Q       SI+ +IE  +F    ++ ++           GRTD GV A  QV  
Sbjct: 81  YLGWDYQGFAAQEDSIE-TIEHHLFTALQKVCLIESRETSNYNRCGRTDKGVSAFHQVIS 139

Query: 64  FDLVREWVP-------------VILCKALNAYLKISDTISILN-LSIVDKQFHARFSAIR 109
            D+  +  P             +  C  LN  L   + I  L  + +V+  + ARF    
Sbjct: 140 IDVRSKIAPEDDQLSEDSLATELDYCGMLNRVL--PEEIRCLAWMPMVNPGYSARFDCRS 197

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-- 166
           R+Y Y                   P+ +L  + M+ A +HLVG HDF     +       
Sbjct: 198 RTYRY-----------------FFPRGNLRIDAMQEACRHLVGAHDFRNLCKMDVGNGVV 240

Query: 167 SPIRTID-------HFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           + +R+ID         D +  G  +++ +++  ++FL  Q+R  +  L LVGDGK   T 
Sbjct: 241 NFVRSIDECTIHASQTDSSGMGSYDMMYLQLRGKAFLWHQVRCIMAVLLLVGDGKEDPTI 300

Query: 218 LEKALQAQDRKECGP 232
           +++ L   DR  C P
Sbjct: 301 VKELLDV-DRNPCKP 314


>gi|171184695|ref|YP_001793614.1| tRNA pseudouridine synthase ACD [Thermoproteus neutrophilus V24Sta]
 gi|229470755|sp|B1YAT9|TRUA_THENV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|170933907|gb|ACB39168.1| tRNA-pseudouridine synthase I [Thermoproteus neutrophilus V24Sta]
          Length = 255

 Score = 58.5 bits (140), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 101/244 (41%), Gaps = 34/244 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y   I Y+G+ ++G+       S++  + +A+  V G         RTD GV A+  V  
Sbjct: 3   YLYRIAYDGTLFYGFTGHPR--SLEPHLRRALGDVLGR------GSRTDPGVSAVGNVV- 53

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
                  +     +   A  K+   + +   + V + F+ R  A  R YLY      AP 
Sbjct: 54  -------MTSAKVQPAAANSKLPRGVWVWAAAEVPEGFNPR-RARSRHYLY-----VAPH 100

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
             E           D ++MR AA+ L G HD+ +F     + +S + TI    V + G+L
Sbjct: 101 WGE-----------DLDSMREAAELLAGTHDYASFVQRRGEPASTVTTIFSITVETRGDL 149

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + +  V R F +  IR    ++   G G     D+   L+ + +    P AP EGL    
Sbjct: 150 VFLHFVGRGFRNKMIRKLAWAILAAGRGVLRKRDIADLLE-RPKPGAVPSAPAEGLVLLD 208

Query: 244 VEYS 247
           ++Y 
Sbjct: 209 IDYG 212


>gi|16550495|dbj|BAB70990.1| unnamed protein product [Homo sapiens]
          Length = 481

 Score = 58.5 bits (140), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 96/245 (39%), Gaps = 62/245 (25%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVPVILCKALNAYLK-----------------ISDTISILNLSIVDKQFH 102
           QV   DL  ++      + LN   +                 +   I IL  + V+  F 
Sbjct: 126 QVISLDLRSQFPRGRDSEDLNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSFS 185

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     +
Sbjct: 186 ARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 HCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLK 206
              A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L 
Sbjct: 229 DV-ANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILF 287

Query: 207 LVGDG 211
           L+G G
Sbjct: 288 LIGQG 292


>gi|303275814|ref|XP_003057201.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461553|gb|EEH58846.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 281

 Score = 58.2 bits (139), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 75/271 (27%), Positives = 100/271 (36%), Gaps = 59/271 (21%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGS--IEKAIFLV-----------TGEIVVVHGAGRTDSG 54
           + Y G  Y G+  Q N ++   S  IE A+F             T   V     GRTD+G
Sbjct: 22  VAYAGWDYHGFASQGNDAAEARSPTIEGALFAALKRTRLIADDATWTDVDYTRCGRTDAG 81

Query: 55  VHALRQVAHF-------------------DLVREWVPVILCKALNAYLKISDTISILNLS 95
           V A+ Q+                      D      P IL +AL       D I +    
Sbjct: 82  VSAMGQLVSLRARSRGTRYTPPSPPPPAKDADELDYPSILNRAL------PDDIRVTGWC 135

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            VD+ F ARF    R Y Y          L  G        LD E MR AA+ L G HDF
Sbjct: 136 YVDEAFSARFDCEWRHYKYF-------FTLHDG-------GLDLEKMRDAARRLEGEHDF 181

Query: 156 TTF-----RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
             F     +++H  A   + +       +   L  I V   +FL  Q+R     L LVG 
Sbjct: 182 RNFCKMDVKNVHNHARRILESASSSASGAPPRLCYISVKGTAFLWHQVRCVAAVLFLVGL 241

Query: 211 GKWTSTDLEK--ALQAQDRKECGPLAPPEGL 239
           GK   + ++    L+   RK    +AP E L
Sbjct: 242 GKEPPSVIDDLLDLEKTTRKPQYEMAPEEPL 272


>gi|89890078|ref|ZP_01201589.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BBFL7]
 gi|89518351|gb|EAS21007.1| tRNA  pseudouridine synthase A [Flavobacteria bacterium BBFL7]
          Length = 267

 Score = 58.2 bits (139), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 56/257 (21%), Positives = 104/257 (40%), Gaps = 13/257 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y + ++Y G  + GWQ+Q +  +++  +++ + F++      V  AGRTD+ V     
Sbjct: 9   LYYLIKLQYLGFRFHGWQKQPDVPTVEKMVKRTLRFVLDHHNFKVLAAGRTDARVSVNET 68

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +    L  E + +       N  L +   I  L++   + QF+       + Y+Y     
Sbjct: 69  IIELFLDDEALNLDTFLAEFN--LNLPSDIRALDIEETNAQFNVIQHPKEKEYIYLFSHG 126

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +            +   LD E M+ AA+   G H+F ++       +  + T++  H + 
Sbjct: 127 EKFHPFCASLMVYMKTELDIELMKTAARLFEGTHNFWSYTYKPSDTTDTVSTVNSCHIEE 186

Query: 178 NSF--GNLIE-----IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           N+    N         RV    F   Q+R  +G+L  +G  K T  D +  L    +   
Sbjct: 187 NNLFTANFFPEESFVFRVTGMGFKRHQVRLMMGALFDLGMHKITLEDFKATLDGSKKIHL 246

Query: 231 GPLAPPEGLYFDSVEYS 247
             +AP  GL    +E S
Sbjct: 247 SHIAPASGLMLYRMELS 263


>gi|313223412|emb|CBY40401.1| unnamed protein product [Oikopleura dioica]
          Length = 307

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 89/224 (39%), Gaps = 37/224 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIV-----------VVHGAGRTD 52
           ++I Y G  Y G Q       +  +IEK +F  LV  ++V                 RTD
Sbjct: 85  ILISYCGKNYHGLQHNPGDDKVD-TIEKRVFQALVAAKVVYSNVINDRKKCAYQSCSRTD 143

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+  VA        +P  LC+ +NA+L   D I + +   V K F A+     R+Y
Sbjct: 144 KGVSAIGNVASLKCK---IPKNLCELVNAHL--PDDIRLTSFEQVTKGFCAKKRCTHRTY 198

Query: 113 LYRIITRQAPLALEKGRAWLIPKSL-----DCENMRIAAQHLVGRHDFTTFRSIHCQA-S 166
            Y   T    +       W  P S        E +R   +  +G   +  F S   Q   
Sbjct: 199 SYYCPT----ICFGSKEDWDRPSSFRISAEKLEGVRELLKKYIGTRSYHNFTSGKRQGDE 254

Query: 167 SPIRTI-------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVG 203
           S  R I       D F  N +   +E+RVV +SF+  QIR  VG
Sbjct: 255 SAKRHILDFRIQGDPFICNEW-EYVELRVVGQSFMIHQIRKMVG 297


>gi|325186551|emb|CCA21092.1| tRNA pseudouridine synthase putative [Albugo laibachii Nc14]
          Length = 493

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 77/295 (26%), Positives = 115/295 (38%), Gaps = 77/295 (26%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIF-------LVTG-EIVVVHGAGRTDSGVHALRQV 61
           Y+G  Y G+ RQ +   I+ +IEK +F       L+T  +       GRTD GV A  QV
Sbjct: 86  YSGERYCGFARQDH---IEETIEKYLFDTMQRTKLITSIDDCCYSRCGRTDKGVSAFGQV 142

Query: 62  AHFDLVREWVPV------------------ILCKALNAYLK--------------ISDTI 89
                VR  VP+                  +  K  +  ++              +   I
Sbjct: 143 IGIK-VRSNVPIDAELLDVDSLDQVASGGRVRVKTQDGRIRKITEVDYAASLNRTLPSDI 201

Query: 90  SILNLSIVDKQFHARFSAIR-RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
            + ++      F ARF+  R RSY Y                + + K LD E MR+AA  
Sbjct: 202 RVYSVVNAPNNFSARFNCDRGRSYRY----------------FFMKKDLDIEKMRLAAIG 245

Query: 149 LVGRHDFTTFRSI--HCQA------SSPIRTIDHF-DVNSFGNLIEIRVVARSFLHTQIR 199
             G HDF  F  I  +CQ       S  I++ D   D N +  +    +   +FL  Q+R
Sbjct: 246 FEGLHDFRNFCRIDTNCQTFDRNVRSFKIKSSDEIGDKNPYRQMYYFEIHGNAFLWHQVR 305

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLY-----FDSVEYS 247
             V  L L+G G+   + ++K L  +   RK    +AP   L      FDS+ + 
Sbjct: 306 CMVSILFLIGQGREEPSIVKKMLDIEKYPRKPQYAIAPDHPLVLHDCRFDSINFD 360


>gi|38639411|gb|AAR25833.1| tRNA pseudouridine synthase A [Buchnera aphidicola (Tetraneura
           caerulescens)]
          Length = 107

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 51/92 (55%)

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           F+ FR+ +CQ+ +  R I   D+      + I + A +FL+  +R+ VGSL  VG  +  
Sbjct: 1   FSGFRAKNCQSKTAFRKIIRLDIFRKNFFVIIEIEANAFLYKMVRNIVGSLIEVGLKRKN 60

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + ++  L++++RK  GP A   GLY   V+Y
Sbjct: 61  VSWIDTILKSKNRKLSGPTASANGLYLVYVDY 92


>gi|76156463|gb|ABA40375.1| SJCHGC06804 protein [Schistosoma japonicum]
          Length = 334

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 114/268 (42%), Gaps = 40/268 (14%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTDSGV 55
           +++ Y+G GY+G QR     +I+G + KA+F   G++V V            A +TD  V
Sbjct: 51  ILMMYSGWGYYGMQRGPIYPTIEGELSKALF-TCGQLVNVTSEEHKKVNFQRASKTDKYV 109

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            AL QV    L  +     L   LN  L     I IL++  V + F +  S   R Y Y 
Sbjct: 110 SALGQVCSLKLYDD---ADLLNKLNTAL--PQDIRILDIIRVTRSFSSYNSCTHRVYDYL 164

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV----------GRHDFTTFRSIHCQA 165
           + T     AL  G   L   +  C   R+ A+ +           G H+F  F S     
Sbjct: 165 LPT----FALSSGNLSLSDST--CWTYRVTAEKITKLNNLLERYKGTHNFYNFTSGRLPT 218

Query: 166 SSP----IRTIDHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
                  I++++       G      IR++ +SF+  Q+R  +G +  +  G + + D+ 
Sbjct: 219 DKSCYRHIKSVECIPTFLLGEHEYTVIRIIGQSFMLHQVRKMIGLVLGILRG-YATEDVF 277

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +  ++R +  P AP  GL  + V++S
Sbjct: 278 DIVFCKERVDI-PKAPGLGLMLNQVDFS 304


>gi|322786132|gb|EFZ12740.1| hypothetical protein SINV_14818 [Solenopsis invicta]
          Length = 444

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/253 (24%), Positives = 100/253 (39%), Gaps = 55/253 (21%)

Query: 15  YFGWQ------RQKNGSSIQ----GSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           Y GW       ++ N ++I+     ++ K+  + + E    H  GRTD GV +  QV   
Sbjct: 100 YLGWDYHGFTVQEDNCNTIEHHLFAALLKSCCIESRESANYHRCGRTDKGVSSFSQVISL 159

Query: 65  DLVREWVP---------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           D+  +  P         +  CK LN  L  +  I  +    V   F ARF    R Y Y 
Sbjct: 160 DIRSKLAPEDQGNLSNELPYCKMLNRLLPTN--IRCVAWCPVASNFSARFDCKYRRYKY- 216

Query: 116 IITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDF------------TTFRSIH 162
                             P+ +LD + M  AA+++VG HDF              F+   
Sbjct: 217 ----------------FFPRGNLDIDAMNKAAKYVVGDHDFRNICKMDVANGIINFKRTV 260

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             A          + ++  ++ E+ + +++FL  QIR  +G L LVG  K    + E  L
Sbjct: 261 IDAKVSFVNEQSMEKSTGYDMCELEITSQAFLWHQIRCLMGILLLVGQRK---EEPEVIL 317

Query: 223 QAQDRKECGPLAP 235
           +  D + C P  P
Sbjct: 318 KLLDTETC-PQKP 329


>gi|213406756|ref|XP_002174149.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|212002196|gb|EEB07856.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 426

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 81/192 (42%), Gaps = 22/192 (11%)

Query: 49  GRTDSGVHALRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQ-FHARFS 106
           GRTD GV A+ QV   ++   E  P+  C  LN  L   + I ++  S    + F ARFS
Sbjct: 126 GRTDKGVSAMGQVVSLNVRYSEERPIAYCDVLNRLL--PEDIRVIAYSPNPPEGFDARFS 183

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--Q 164
            +RR Y Y +  +Q P              LD E M  AA   +G HDF  F  I    Q
Sbjct: 184 CVRRHYKY-LFLKQYPGG-----------ELDIERMSQAAALYLGEHDFRNFCKIDASKQ 231

Query: 165 ASSPIRTIDHFD---VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            ++  R I H     V+    L    +   +FL  Q+R  +  L LVG       D+   
Sbjct: 232 ITNYNRGILHSKIICVDPQKQLYAFDLQGTAFLWHQVRCMMAILFLVGQ-HLEPVDIVSE 290

Query: 222 LQAQDRKECGPL 233
           L   ++  C P+
Sbjct: 291 LLNVEKNPCKPV 302


>gi|288560959|ref|YP_003424445.1| tRNA pseudouridine synthase A TruA [Methanobrevibacter ruminantium
           M1]
 gi|288543669|gb|ADC47553.1| tRNA pseudouridine synthase A TruA [Methanobrevibacter ruminantium
           M1]
          Length = 290

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 104/249 (41%), Gaps = 48/249 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +     K  ++   +      AGRTD+GVH
Sbjct: 1   MKRTALKIAYIGTHFHGFQRQPDVRTVEEELIYHLRKLEYIDDLKASRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E    +    +N  L   D I I+  + V   F  RF A RR Y Y  
Sbjct: 61  SLGNVISFQSEKE----VRVNQINNSL--PDDIQIIAWAPVRFGFKPRF-AKRRWYRY-- 111

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---------RSIH-CQAS 166
                          L  + LD + +R  A+   G HDFT F         R+I   + +
Sbjct: 112 --------------ILFEEDLDIDLLRKTAEVFKGTHDFTNFTKRKQKTTVRTIEDIRIT 157

Query: 167 SPIRTIDHFDVN---SFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
            PI  ID  D N    F +L      I + +   SFL   +R  +     V  GK T  D
Sbjct: 158 KPI--IDEEDKNKKSDFAHLNKSYSPIFVDIYGESFLWNMVRKMMRIFLDVNYGKLTLDD 215

Query: 218 LEKALQAQD 226
           +E+ L  ++
Sbjct: 216 VERLLNPEE 224


>gi|312093536|ref|XP_003147717.1| hypothetical protein LOAG_12156 [Loa loa]
 gi|307757118|gb|EFO16352.1| hypothetical protein LOAG_12156 [Loa loa]
          Length = 414

 Score = 57.8 bits (138), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 97/249 (38%), Gaps = 71/249 (28%)

Query: 15  YFGWQ------RQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           YFGW+      +Q+   +I+  + KA+     + + E    +  GRTD GV A +QVA  
Sbjct: 40  YFGWEYNGLVEQQEIAGTIEEEMRKALMKTKLVESWENCGWNRCGRTDKGVSAFKQVASL 99

Query: 65  DLVREWVP----------------------VILCKALNAYLKISDTISILNLSIVDKQFH 102
            +VR   P                      +   K LN+ L  +  I +L  + V + F 
Sbjct: 100 -IVRSNEPEGEGVFWPAIAHTSSETAVKGELQYVKMLNSTLPTN--IRVLAWAPVPENFS 156

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           AR+   +R+Y Y       P A           + D E MR A Q LVG HDF  F  I 
Sbjct: 157 ARYRCTQRTYTYAF-----PRA-----------NFDIEAMRQACQFLVGEHDFRNFCRID 200

Query: 163 CQAS----SPIRTIDHFDVNSFGN----------------LIEIRVVARSFLHTQIRSFV 202
                   + IRTI + D++   N                 +++ V    FL  QIR  +
Sbjct: 201 MNKGRVEMNYIRTISYADISLISNNSLLASKQSDEVTHYEFLQLTVKGSGFLWHQIRCIM 260

Query: 203 GSLKLVGDG 211
             L  +G G
Sbjct: 261 ALLCEIGLG 269


>gi|195498243|ref|XP_002096440.1| GE25055 [Drosophila yakuba]
 gi|194182541|gb|EDW96152.1| GE25055 [Drosophila yakuba]
          Length = 410

 Score = 57.8 bits (138), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 69/270 (25%), Positives = 112/270 (41%), Gaps = 39/270 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---VTGE------IVVVHGAGRTDS 53
           +  +++ Y G+ ++G QR     +I+  + K +     +T E      I     A RTD 
Sbjct: 71  KSAILLSYCGANFYGMQRNPGMQTIEEELFKVMLKHKWITEESFEQIQISCFQRAARTDK 130

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A RQV    L  E    +  +A NA L     I +  +  V K F+A+     R+Y 
Sbjct: 131 GVSAARQVCSVKLPEE----LDLEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYT 184

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL------VGRHDFTTFRS------- 160
           Y + T       EK         +  E ++   + L         H+FT+ +S       
Sbjct: 185 YTLPTVAFASFEEKVEDLHDTFQISPELLQKVKETLKLYEGTKNFHNFTSKKSFLDPSSK 244

Query: 161 ---IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
              +   +S P R+    +       + + V  +SF+  QIR  VG    +  G  T+  
Sbjct: 245 RFIMSFTSSEPFRSPQGIE------FVTLNVKGQSFMLHQIRKMVGLAIAIVRGNTTAAT 298

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           LE+AL  ++R +  P+AP  GL  D+V Y 
Sbjct: 299 LERAL-TEERLDL-PMAPGLGLVLDTVHYE 326


>gi|150403192|ref|YP_001330486.1| tRNA pseudouridine synthase A [Methanococcus maripaludis C7]
 gi|150034222|gb|ABR66335.1| tRNA pseudouridine synthase [Methanococcus maripaludis C7]
          Length = 262

 Score = 57.8 bits (138), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 106/245 (43%), Gaps = 39/245 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGR--LSFQTQPHGETVCDKISNALLDCGYLDDKDRVPLYHGGRTDRGVSALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR-RSYLYRIIT 118
               +++ ++  PV+    + + LK  D I +L    +D      F  I  R Y Y +  
Sbjct: 60  NYIVYEMDKK--PVL--PRVQSNLK-KDGIWVLGCKEIDT-----FPEIEYRHYQYNLPN 109

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDV 177
                           K+ D E M+ A++ L+G H F    +    +   P+RT+    +
Sbjct: 110 ----------------KNHDVELMKKASEKLIGTHYFQNLSKRDKTKVKDPVRTLHDIKI 153

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECGPLA 234
           +S    I I +   SFL   +R  +  L  VG  K+   D EK ++   ++D  +  P +
Sbjct: 154 SSNDYFITIDIFGESFLWNMVRRIIRLLSDVGKHKF--EDPEKFIELILSKDYNKGYPPS 211

Query: 235 PPEGL 239
           P EGL
Sbjct: 212 PAEGL 216


>gi|109109191|ref|XP_001111887.1| PREDICTED: tRNA pseudouridine synthase 3 [Macaca mulatta]
          Length = 480

 Score = 57.8 bits (138), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 96/245 (39%), Gaps = 62/245 (25%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 68  IAYMGWGYQGFASQENTNN---TIEEKLFEALSKTRLVESRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-----------------ISILNLSIVDKQFH 102
           QV   DL  ++      +  N   + + T                 I IL  + V+  F 
Sbjct: 125 QVISLDLRSQFPRGRDSEDFNVKEEANATAEEIRYTHILNRVLPPDIRILAWAPVEPSFS 184

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     +
Sbjct: 185 ARFSCLERTYRY-----------------FFPRADLDIVAMDYAAQKYVGTHDFRNLCKM 227

Query: 162 HCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLK 206
              A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L 
Sbjct: 228 DV-ANGVINFQRTILSAQVRLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILF 286

Query: 207 LVGDG 211
           L+G G
Sbjct: 287 LIGQG 291


>gi|261333810|emb|CBH16805.1| tRNA pseudouridine synthase A-like protein,putative [Trypanosoma
           brucei gambiense DAL972]
          Length = 588

 Score = 57.8 bits (138), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 80/202 (39%), Gaps = 44/202 (21%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDS- 53
           + RY + ++Y G+ + GW     RQ  +    + GSI +      G I    GA R ++ 
Sbjct: 184 LTRYRVDVQYQGNDFDGWWKSTTRQLFRREVGLDGSITRVPVAEPGTIGNAAGASRGETM 243

Query: 54  ---------------------------------GVHALRQVAHFDLVR--EWVPVILCKA 78
                                            GV   R   H D+    E  P  + + 
Sbjct: 244 GSRYHARTVLEEALAVALDVNTVRVVAGVIPEVGVSVRRLCCHVDVPSHIELQPRTVIQR 303

Query: 79  LNAYL-KISDTISILNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
              ++ K    ++IL+      Q FHAR S +RR Y+YRI+ R AP   + G  W + + 
Sbjct: 304 ATMWMEKRQQPLAILSYRRCKNQDFHARHSGLRRVYVYRILNRVAPPLFDAGLQWHVDRH 363

Query: 137 LDCENMRIAAQHLVGRHDFTTF 158
           LD + M+  A+ L G  DF  F
Sbjct: 364 LDVDRMKRFAKALEGTKDFGYF 385



 Score = 53.1 bits (126), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 45/85 (52%), Gaps = 7/85 (8%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA---- 224
           +RT+D  DV    + + I  V RSFL  QIR+ V  LK  G G W   +L++ALQ+    
Sbjct: 478 VRTVDRLDVVRQDDEVLIWFVGRSFLRHQIRNMVSVLKAAGHGLWNDLELQQALQSGFEP 537

Query: 225 ---QDRKECGPLAPPEGLYFDSVEY 246
              + ++E  P AP  GL    VEY
Sbjct: 538 SRHRFKRERFPTAPAYGLTLWDVEY 562


>gi|156537085|ref|XP_001602396.1| PREDICTED: similar to pseudouridylate synthase [Nasonia
           vitripennis]
          Length = 421

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 92/228 (40%), Gaps = 48/228 (21%)

Query: 10  YNGSGYFGWQRQKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           Y G  Y G+  Q++ +S     +  ++ K+  + + E    H  GRTD GV A  QV   
Sbjct: 79  YLGWDYQGFAAQEDTTSTIEYYLFAALTKSCLIESRETSNYHRCGRTDKGVSAFSQVISL 138

Query: 65  DLVREWVP---------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           D+     P         +  CK LN  L     I   + S    +  ARF    RSY Y 
Sbjct: 139 DIRSRLEPEKQDNLSDELHYCKMLNRLL--PKNIRCFSWSPAHPEMSARFDCKFRSYKY- 195

Query: 116 IITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTT-------------FRSI 161
                             P+ +L+ E M  AA+  VG HDF               FR+I
Sbjct: 196 ----------------FFPRGNLNIEAMDKAAKLTVGSHDFRNLCKMDVANGVVNFFRNI 239

Query: 162 HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                + I+  D   ++ + ++ E+ + + +FL  QIR  +G L LVG
Sbjct: 240 VNAQVTCIKREDPEKISGY-DMCELSIKSNAFLWHQIRCIMGILLLVG 286


>gi|332024452|gb|EGI64650.1| tRNA pseudouridine synthase 3 [Acromyrmex echinatior]
          Length = 443

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 94/231 (40%), Gaps = 53/231 (22%)

Query: 15  YFGWQ------RQKNGSSIQ----GSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           Y GW       ++ N  +I+     ++ K+  + + E    H  GRTD GV +  QV   
Sbjct: 82  YLGWDYHGFAVQEDNTDTIEHHLFAALLKSCCIESRESSNYHRCGRTDKGVSSFSQVISL 141

Query: 65  DLVREWVP---------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           D+     P         +  CK LN  L  +  I  +    V   F ARF    RSY Y 
Sbjct: 142 DVRSRLEPENQDNLSDELPYCKILNRLLPAN--IRCIAWCPVSSIFSARFDCKFRSYRY- 198

Query: 116 IITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI---RT 171
                             P+ +LD E M  AA++++G HDF     +   A+  I   RT
Sbjct: 199 ----------------FFPRGNLDIEAMDKAAKYVIGDHDFRNICKMDV-ANGVINFKRT 241

Query: 172 IDHFDVNSFGN----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +    VNS  +          + E+ + +++FL  QIR  +G L L+G  K
Sbjct: 242 VMDARVNSLNDQNVEKSTGYDMCELEITSQAFLWHQIRCLMGILLLIGQRK 292


>gi|297690638|ref|XP_002822721.1| PREDICTED: tRNA pseudouridine synthase 3-like [Pongo abelii]
          Length = 481

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 98/246 (39%), Gaps = 64/246 (26%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVP--------VILCKALNAYLKISDT----------ISILNLSIVDKQF 101
           QV   DL R   P         +  +A  A  +I  T          I IL  + V+  F
Sbjct: 126 QVISLDL-RSQFPRGKDSEDFNVKGEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRS 160
            ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     
Sbjct: 185 SARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCK 227

Query: 161 IHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSL 205
           +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  +  L
Sbjct: 228 MDV-ANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAIL 286

Query: 206 KLVGDG 211
            L+G G
Sbjct: 287 FLIGQG 292


>gi|169839443|ref|ZP_02872631.1| tRNA pseudouridine synthase A [candidate division TM7 single-cell
          isolate TM7a]
          Length = 68

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/61 (44%), Positives = 41/61 (67%), Gaps = 2/61 (3%)

Query: 6  MIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
          +I +Y+GS + G+QRQK  N  ++QG IEK I     + + +  +GRTD GVHA+ QV++
Sbjct: 8  IIYQYDGSKFLGFQRQKDNNVKTVQGEIEKVILKTFSQNINMISSGRTDKGVHAMEQVSN 67

Query: 64 F 64
          F
Sbjct: 68 F 68


>gi|257053070|ref|YP_003130903.1| tRNA pseudouridine synthase A [Halorhabdus utahensis DSM 12940]
 gi|256691833|gb|ACV12170.1| tRNA pseudouridine synthase [Halorhabdus utahensis DSM 12940]
          Length = 275

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 67/252 (26%), Positives = 105/252 (41%), Gaps = 34/252 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVV--HGAGRTDSGVH 56
           R    I Y+G  + G+QRQ + +++  +I  A+     L  G+ V      AGRTD+GV 
Sbjct: 6   RRAFRIAYDGRPFHGFQRQPDVATVSDAILDALRELDVLEDGDNVPPGYAAAGRTDAGVS 65

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL Q   FD   +W   +   ALN+ L     +     + V  +FHA   A+ R Y Y +
Sbjct: 66  ALAQTVAFD-CPDW---LSPAALNSELPAD--VRAWASADVPAEFHATHDAVAREYTYHL 119

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               A ++    RA     +LD          L G HDF  F       +  +R +   +
Sbjct: 120 HAPDASVS----RAG---DALDA---------LAGEHDFHNFTP---DDTGTVRDL-TGE 159

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP- 235
             S G+ + + + A  F    +R  V  +  +  G      +E+ L     +    +AP 
Sbjct: 160 ARSEGDFLVVTLRADGFPRQFVRRAVTVIDALASGVAELDRIEQLLGDDPVEGPAGVAPA 219

Query: 236 -PEGLYFDSVEY 246
            PE L   +VEY
Sbjct: 220 APEALVLTAVEY 231


>gi|226533212|ref|NP_001145731.1| hypothetical protein LOC100279238 [Zea mays]
 gi|219884209|gb|ACL52479.1| unknown [Zea mays]
          Length = 486

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 88/228 (38%), Gaps = 42/228 (18%)

Query: 8   IEYNGSGYFGWQRQKN-----GSSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHALRQV 61
           + Y G  ++G+  + N      S I  ++E+A  +V       +   GRTD GV A  QV
Sbjct: 155 VMYFGQRFYGFSSEGNIEPTVESEIFKALERAKLMVANRKESCYSRCGRTDKGVSATGQV 214

Query: 62  AHF-----------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
                         D++ E   +   K LN  L     I +L    V   FHARF+ + R
Sbjct: 215 ISLYLRSNIKDVGGDMLDERSEIDYVKVLNRIL--PRDIRVLGWCPVPADFHARFTCLSR 272

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            Y Y            KG        LD   M+ AA   +G HDF  F  +     S  R
Sbjct: 273 EYKY---------LFWKG-------DLDILEMQKAASKFIGEHDFRNFCKMDAANVSNYR 316

Query: 171 ------TIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                 TI   D  S  + L  + +   +FL  Q+R  V  L L+G G
Sbjct: 317 RHITEFTISACDRRSNNDELCSMTIKGSAFLWHQVRCMVAVLFLIGQG 364


>gi|126302589|sp|Q9BZE2|PUS3_HUMAN RecName: Full=tRNA pseudouridine synthase 3; AltName: Full=tRNA
           pseudouridylate synthase 3; AltName: Full=tRNA-uridine
           isomerase 3
 gi|12276176|gb|AAG50280.1|AF325689_1 FKSG32 [Homo sapiens]
 gi|189055315|dbj|BAG36917.1| unnamed protein product [Homo sapiens]
          Length = 481

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 95/248 (38%), Gaps = 68/248 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVP--------------------VILCKALNAYLKISDTISILNLSIVDK 99
           QV   DL R   P                    +     LN  L     I IL  + V+ 
Sbjct: 126 QVISLDL-RSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVL--PPDIRILAWAPVEP 182

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            F ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF   
Sbjct: 183 SFSARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNL 225

Query: 159 RSIHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVG 203
             +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  + 
Sbjct: 226 CKMDV-ANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMA 284

Query: 204 SLKLVGDG 211
            L L+G G
Sbjct: 285 ILFLIGQG 292


>gi|119588071|gb|EAW67667.1| pseudouridylate synthase 3 [Homo sapiens]
          Length = 481

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 95/248 (38%), Gaps = 68/248 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVP--------------------VILCKALNAYLKISDTISILNLSIVDK 99
           QV   DL R   P                    +     LN  L     I IL  + V+ 
Sbjct: 126 QVISLDL-RSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVL--PPDIRILAWAPVEP 182

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            F ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF   
Sbjct: 183 SFSARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNL 225

Query: 159 RSIHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVG 203
             +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  + 
Sbjct: 226 CKMDV-ANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMA 284

Query: 204 SLKLVGDG 211
            L L+G G
Sbjct: 285 ILFLIGQG 292


>gi|199559785|ref|NP_112597.3| tRNA pseudouridine synthase 3 [Homo sapiens]
          Length = 481

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 95/248 (38%), Gaps = 68/248 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVP--------------------VILCKALNAYLKISDTISILNLSIVDK 99
           QV   DL R   P                    +     LN  L     I IL  + V+ 
Sbjct: 126 QVISLDL-RSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVL--PPDIRILAWAPVEP 182

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            F ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF   
Sbjct: 183 SFSARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNL 225

Query: 159 RSIHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVG 203
             +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  + 
Sbjct: 226 CKMDV-ANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMA 284

Query: 204 SLKLVGDG 211
            L L+G G
Sbjct: 285 ILFLIGQG 292


>gi|194706182|gb|ACF87175.1| unknown [Zea mays]
 gi|195612012|gb|ACG27836.1| hypothetical protein [Zea mays]
          Length = 457

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 87/228 (38%), Gaps = 42/228 (18%)

Query: 8   IEYNGSGYFGWQRQKN-----GSSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHALRQV 61
           + Y G  ++G+  + N      S I  ++E+A  +V       +   GRTD GV A  QV
Sbjct: 126 VMYFGQRFYGFSSEGNIEPTVESEIFKALERAKLMVANRKESCYSRCGRTDKGVSATGQV 185

Query: 62  AHF-----------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
                         D++ E   +   K LN  L     I +L    V   FHARF+ + R
Sbjct: 186 ISLYLRSNIKDVGGDMLDERSEIDYVKVLNRIL--PRDIRVLGWCPVPADFHARFTCLSR 243

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            Y Y                W     LD   M+ AA   +G HDF  F  +     S  R
Sbjct: 244 EYKYLF--------------W--KGDLDILEMQKAASKFIGEHDFRNFCKMDAANVSNYR 287

Query: 171 ------TIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                 TI   D  S  + L  + +   +FL  Q+R  V  L L+G G
Sbjct: 288 RHITEFTISACDRRSNNDELCSMTIKGSAFLWHQVRCMVAVLFLIGQG 335


>gi|14919399|gb|AAH04822.1| Pseudouridylate synthase 3 [Homo sapiens]
 gi|124000287|gb|ABM87652.1| pseudouridylate synthase 3 [synthetic construct]
 gi|124000289|gb|ABM87653.1| pseudouridylate synthase 3 [synthetic construct]
 gi|157928602|gb|ABW03597.1| pseudouridylate synthase 3 [synthetic construct]
 gi|157929242|gb|ABW03906.1| pseudouridylate synthase 3 [synthetic construct]
          Length = 481

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 95/248 (38%), Gaps = 68/248 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVP--------------------VILCKALNAYLKISDTISILNLSIVDK 99
           QV   DL R   P                    +     LN  L     I IL  + V+ 
Sbjct: 126 QVISLDL-RSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVL--PPDIRILAWAPVEP 182

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            F ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF   
Sbjct: 183 SFSARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNL 225

Query: 159 RSIHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVG 203
             +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  + 
Sbjct: 226 CKMDV-ANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMA 284

Query: 204 SLKLVGDG 211
            L L+G G
Sbjct: 285 ILFLIGQG 292


>gi|291227559|ref|XP_002733751.1| PREDICTED: PseudoUridine Synthase family member (pus-1)-like
           [Saccoglossus kowalevskii]
          Length = 320

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 70/273 (25%), Positives = 115/273 (42%), Gaps = 57/273 (20%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  +++ Y+G GY G QR K   +I+G + KAI +  G +   H             RTD
Sbjct: 57  KVVLLLSYSGKGYMGMQRNKGVETIEGDLIKAI-VTAGAVPQSHADIPQKMQFQRCARTD 115

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISD----TISILNLSIVDKQFHARFSAI 108
            GV A+RQV    ++            NA  +I++    +I ++        F+A+ +  
Sbjct: 116 KGVSAVRQVVSLKMML---------VDNAVEQINNSLPPSIRVITYKRTTGGFNAKNTCS 166

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDC-ENMRIA------AQHLV----GRHDFTT 157
            R+Y Y + T     AL          S +C EN R+       AQ L+    G H+F  
Sbjct: 167 HRTYSYLMPT----FAL----------SSNCNENYRVTDEVHQKAQDLLNCYKGTHNFHN 212

Query: 158 FRSIHC-QASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           F S       S +R +   +V+          + I ++ +SF+  QIR  +G +  +  G
Sbjct: 213 FTSGKAFTEQSAMRFMRELNVSQAFVRCGLEFVVITIIGQSFMIHQIRKMIGLVIAIIRG 272

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
               + L+K  +A   K   P AP  GL  ++V
Sbjct: 273 VAPKSTLDKCWEAG--KMDIPKAPSLGLMLENV 303


>gi|118350997|ref|XP_001008777.1| tRNA pseudouridine synthase A family protein [Tetrahymena
           thermophila]
 gi|89290544|gb|EAR88532.1| tRNA pseudouridine synthase A family protein [Tetrahymena
           thermophila SB210]
          Length = 481

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 90/227 (39%), Gaps = 49/227 (21%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSGV 55
           Y + + Y G  Y G   Q+       ++E+ +F    +  ++          +GRTD GV
Sbjct: 114 YALKMSYVGINYQGLAYQQ---ETDNTVEEQLFKALEKTTLIKNRDNCNFTRSGRTDKGV 170

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKIS--DTISILNLSIVDKQFHARFSAIRRSYL 113
            AL QV         + + L  ++     I   D I IL  S VD  F+ARF   +R Y 
Sbjct: 171 SALGQV---------IGITLRTSIKIGENIDEIDDIRILGCSKVDPAFNARFDCQKRIYK 221

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTI 172
           Y                +     +D + M+ AA   +G HDF  F  I   Q  + +R I
Sbjct: 222 Y----------------YFFENQMDIQRMKEAANLFLGEHDFRNFCKIDVLQTLNYVRII 265

Query: 173 DHFDVN----SFGNLIE------IRVVARSFLHTQIRSFVGSLKLVG 209
              D+     +FG L          +   +FL  QIR+ +  L LVG
Sbjct: 266 YQLDIEEVQANFGTLDPRSKLYVATIQGSAFLWHQIRNMMAILFLVG 312


>gi|302677288|ref|XP_003028327.1| hypothetical protein SCHCODRAFT_42694 [Schizophyllum commune H4-8]
 gi|300102015|gb|EFI93424.1| hypothetical protein SCHCODRAFT_42694 [Schizophyllum commune H4-8]
          Length = 296

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 93/237 (39%), Gaps = 58/237 (24%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVVVHGA---------GR 50
           +++C    Y G  Y G   QK+ + +  ++E  +F  LV   +V   G          GR
Sbjct: 50  LKFC----YGGWDYGGLAIQKDRTPLP-TVEGKLFGALVRARLVDPKGGLEGCGWERCGR 104

Query: 51  TDSGVHALRQVAHFDLVR------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           TD GV A  QV     VR      E +P      +N +L   D I IL  S VD  F +R
Sbjct: 105 TDRGVSAAGQVISL-WVRSALSQEELLPHPFTYMINRHL--PDPIKILAWSPVDLSFSSR 161

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           +S   R Y Y                +  P  LD   MR A  +L G H+F     I   
Sbjct: 162 YSCTWRHYKY----------------FFPPVGLDIPAMRAACAYLPGTHEFRNLCKI--- 202

Query: 165 ASSPIRTID------------HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
              P + +D            H D ++ G +    +   SFL+  +R+ +G L  +G
Sbjct: 203 --DPTKQLDQFRRDILHASISHVDASNPGGMHVFDLKGSSFLYHMVRNIMGVLLSIG 257


>gi|126327379|ref|XP_001371991.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 575

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 101/249 (40%), Gaps = 68/249 (27%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHA 57
           + I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A
Sbjct: 70  LKIAYLGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSA 126

Query: 58  LRQVAHFDLVREWVP--------------------VILCKALNAYLKISDTISILNLSIV 97
             QV   +L R  +P                    +     LN  L     I +L  + V
Sbjct: 127 FGQVISLNL-RSQLPRDKDPEDKNLKDTVNDSVEEICYTHILNRVL--PPDIRVLAWATV 183

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
           +  F ARFS + R+Y Y       P A           +LD E M  AAQ  VG HDF  
Sbjct: 184 ESSFSARFSCLERTYRYFF-----PCA-----------NLDIEAMNDAAQKYVGTHDFRN 227

Query: 158 FRSIHCQASSPI---RTIDHFDVN--SFGN------------LIEIRVVARSFLHTQIRS 200
              +   A+  I   RTI    V   +FG+            L +  V+ ++FL+ Q+R 
Sbjct: 228 LCKMDV-ANGVINFQRTILSAKVQLVAFGSPEEKLQQQESFQLCQFEVIGQAFLYHQVRC 286

Query: 201 FVGSLKLVG 209
            +  L L+G
Sbjct: 287 MMAILFLIG 295


>gi|91217701|ref|ZP_01254658.1| tRNA pseudouridine synthase A [Psychroflexus torquis ATCC 700755]
 gi|91184205|gb|EAS70591.1| tRNA pseudouridine synthase A [Psychroflexus torquis ATCC 700755]
          Length = 261

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 109/262 (41%), Gaps = 33/262 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G  Y GWQ+Q +  +++  + K + F++  +   V  AGRTD+ V A +   
Sbjct: 8   YLIQLQYLGFRYHGWQKQPDVLTVEHMLHKTLNFILENQRFKVLAAGRTDAMVSANQTYI 67

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
              +  + + +    +  N    +   I  L++      F+       + Y Y    ++ 
Sbjct: 68  ELFIYEDELDLETFLEQFNK--NLPQDIRALSIEETTADFNIIQHPKIKEYFYFFCVKEK 125

Query: 121 -----APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT--TFRS----------IHC 163
                AP  +       + + LD E M++ A+   G HDF   TFR             C
Sbjct: 126 MHPFCAPFMVN------LQEDLDIELMKLGAKLFEGEHDFYSFTFRPNPETKTEGNIERC 179

Query: 164 Q-ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           +   + I T + F   SF     ++VV   F   QIR  +G+L  +G  K +  +LEK +
Sbjct: 180 ELTENDIYTANFFPNQSFV----LKVVGEGFKRQQIRLMMGALIDLGRHKISLEELEKTI 235

Query: 223 QAQDRKECGPLAPPEGLYFDSV 244
               + +   +A   GL  + V
Sbjct: 236 DGSHKIKLEHIAQASGLILNKV 257


>gi|154335976|ref|XP_001564224.1| tRNA pseudouridine synthase A-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134061258|emb|CAM38282.1| tRNA pseudouridine synthase A-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 525

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/188 (26%), Positives = 83/188 (44%), Gaps = 30/188 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQR------QKNGSSIQGS-------------------IEKAI 35
           + RY + ++Y GS + GW +      +K  ++  G+                   +E+A+
Sbjct: 130 LTRYRVDVQYQGSDFDGWYKSVQRTNKKRDAAPAGNTTAGVADYGAGSHHFARVVLEEAL 189

Query: 36  FLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE--WVPVILCKALNAYL-KISDTISI 91
            +     +V V  A   ++GV   R   H D+  E    P  + +    +L +    ++I
Sbjct: 190 AVALDVPMVGVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRSTLWLHQRRQPLAI 249

Query: 92  LNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+      Q FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + 
Sbjct: 250 LSCHPCHNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLME 309

Query: 151 GRHDFTTF 158
           G HD+  F
Sbjct: 310 GTHDYGFF 317



 Score = 49.7 bits (117), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 45/85 (52%), Gaps = 7/85 (8%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA---- 224
           +RT+D  +V    + + I  V +SFL  QIR+ VG LK  G G W   +L+ ALQ+    
Sbjct: 415 VRTVDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVGVLKAGGHGLWDDQELQHALQSGFEV 474

Query: 225 ---QDRKECGPLAPPEGLYFDSVEY 246
              + ++E  P AP  GL    VEY
Sbjct: 475 SRKKFKRERLPPAPVHGLTLWDVEY 499


>gi|126459314|ref|YP_001055592.1| tRNA pseudouridine synthase ACD [Pyrobaculum calidifontis JCM
           11548]
 gi|166228753|sp|A3MU09|TRUA_PYRCJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|126249035|gb|ABO08126.1| Pseudouridylate synthase [Pyrobaculum calidifontis JCM 11548]
          Length = 257

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 2/111 (1%)

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHT 196
           D E MR  A+   G HDF++F     +  + P+ T+D   V   G L+ +  V + F + 
Sbjct: 104 DVEAMREVAELFKGTHDFSSFIQFRGERGTPPVTTVDEVGVEVAGRLVYLYFVGKGFRNK 163

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           QIR    ++   G G  +   +E+ L+ + R    P AP EGL    +EY 
Sbjct: 164 QIRKMAWAILAAGRGVVSRRYVEELLE-RPRPGAVPSAPAEGLILLDIEYD 213


>gi|224118612|ref|XP_002331405.1| predicted protein [Populus trichocarpa]
 gi|222873619|gb|EEF10750.1| predicted protein [Populus trichocarpa]
          Length = 428

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/127 (31%), Positives = 64/127 (50%), Gaps = 16/127 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---------IVVVHG----A 48
           + + +++ Y+G  + GWQ+Q   +++QG +EK++     E            + G    A
Sbjct: 105 VTFKIVLSYHGGSFDGWQKQPGLNTVQGLVEKSLGRFVDEKKAQQLKEQCKPLEGCASVA 164

Query: 49  GRTDSGVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+ V P  +  A+N        + + ++S V + FH  FSA
Sbjct: 165 GRTDKGVSALQQVCSFYTWRKDVKPHEIEDAINDV--APGKVRVESISEVSRAFHPNFSA 222

Query: 108 IRRSYLY 114
             R YLY
Sbjct: 223 KWRRYLY 229


>gi|332208632|ref|XP_003253411.1| PREDICTED: tRNA pseudouridine synthase 3 [Nomascus leucogenys]
          Length = 481

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 95/245 (38%), Gaps = 62/245 (25%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVPVILCKALNAYLK-----------------ISDTISILNLSIVDKQFH 102
           QV   DL  ++      +  N   +                 +   I IL  + V+  F 
Sbjct: 126 QVISLDLRSQFPRGRESEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSFS 185

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI 161
           ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF     +
Sbjct: 186 ARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 HCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLK 206
              A+  +   RTI    V   G             L +  V  ++FL+ Q+R  +  L 
Sbjct: 229 DV-ANGVVNFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILF 287

Query: 207 LVGDG 211
           L+G G
Sbjct: 288 LIGQG 292


>gi|321468438|gb|EFX79423.1| hypothetical protein DAPPUDRAFT_319620 [Daphnia pulex]
          Length = 424

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 84/202 (41%), Gaps = 46/202 (22%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG---------SSIQGSIEKAI--FL-----VTGEIVV 44
           M RY +   Y+G+ + G QRQ            +SIQ  +EK I  FL      T     
Sbjct: 1   MQRYLIKFSYSGTRFRGLQRQPGEIYNDEIPYRASIQTILEKGILRFLQHKKSATSFEPG 60

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           V  + RTD GVH+   +AH DL        L K +N            N+  V   FHAR
Sbjct: 61  VQFSSRTDQGVHSFCNLAHVDLE-------LLKNVN------------NVEAVPSTFHAR 101

Query: 105 FSAIRRSYLYRI-ITRQ---APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           +S+  R YLYRI +T Q       +E  + + I K    +      +   G  DF +F  
Sbjct: 102 YSSYSRHYLYRIGVTPQDVKCHPVIEWRKCYFIEKPFCLDKAIEVCKLFEGTKDFASF-- 159

Query: 161 IHCQASSP-----IRTIDHFDV 177
            H  +  P     +RTID F +
Sbjct: 160 CHGISGRPPGYPTVRTIDAFHI 181


>gi|194389944|dbj|BAG60488.1| unnamed protein product [Homo sapiens]
          Length = 142

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/123 (32%), Positives = 57/123 (46%), Gaps = 21/123 (17%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS----------------FGNLIE 185
           M+ AAQHL+G HDF+ F+S      SP+RT+    V+                 F NL  
Sbjct: 4   MQEAAQHLLGTHDFSAFQSAGSPVPSPVRTLRRVSVSPGQASPLVTPEESRKLRFWNL-- 61

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDS 243
               ++SFL+ Q+R     L  VG G      ++  L++QD   K    +AP  GL+  S
Sbjct: 62  -EFESQSFLYRQVRRMTAVLVAVGLGALAPAQVKTILESQDPLGKHQTRVAPAHGLFLKS 120

Query: 244 VEY 246
           V Y
Sbjct: 121 VLY 123


>gi|71416935|ref|XP_810423.1| tRNA pseudouridine synthase A-like protein [Trypanosoma cruzi
           strain CL Brener]
 gi|70874950|gb|EAN88572.1| tRNA pseudouridine synthase A-like protein, putative [Trypanosoma
           cruzi]
          Length = 608

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 37/109 (33%), Positives = 53/109 (48%), Gaps = 4/109 (3%)

Query: 54  GVHALRQVAHFDLVR--EWVPVILCKALNAYL-KISDTISILNLSIVDKQ-FHARFSAIR 109
           GV   R   HFD+    E  P  + +    +L K    +++L+      Q FHAR S +R
Sbjct: 297 GVSVRRLCCHFDVPSHIELQPRTIIQRATMWLEKRQQPLAVLSCQRCKNQDFHARHSGLR 356

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           R Y+YRI+ R AP   + G  W + + LD   M+  A+ L G  DF  F
Sbjct: 357 RVYVYRILNRVAPPLFDAGLQWHVDRHLDVPRMQRFAKALEGTKDFGYF 405



 Score = 50.4 bits (119), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 45/85 (52%), Gaps = 7/85 (8%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA---- 224
           IRTID  +V    + + I  V +SFL  QIR+ V  LK  G G W   +L++ALQ+    
Sbjct: 498 IRTIDRLEVVRQDDEVLIWFVGKSFLRHQIRNMVSLLKAAGHGLWNELELQQALQSGFEP 557

Query: 225 ---QDRKECGPLAPPEGLYFDSVEY 246
              + ++E  P AP  GL    VEY
Sbjct: 558 SRRRFKRERFPPAPVYGLTLWDVEY 582


>gi|114641137|ref|XP_001148378.1| PREDICTED: tRNA pseudouridine synthase 3 [Pan troglodytes]
          Length = 481

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 95/248 (38%), Gaps = 68/248 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N ++   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 69  IAYMGWGYQGFASQENTNN---TIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAFG 125

Query: 60  QVAHFDLVREWVP--------------------VILCKALNAYLKISDTISILNLSIVDK 99
           QV   DL R   P                    +     LN  L     I IL  + V+ 
Sbjct: 126 QVISLDL-RSHFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVL--PPDIRILAWAPVEP 182

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            F ARFS + R+Y Y                   P++ LD   M  AAQ  VG HDF   
Sbjct: 183 SFSARFSCLERTYRY-----------------FFPRADLDIVTMDYAAQKYVGTHDFRNL 225

Query: 159 RSIHCQASSPI---RTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVG 203
             +   A+  I   RTI    V   G             L +  V  ++FL+ Q+R  + 
Sbjct: 226 CKMDV-ANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMA 284

Query: 204 SLKLVGDG 211
            L L+G G
Sbjct: 285 ILFLIGQG 292


>gi|10640247|emb|CAC12061.1| tRNA-pseudouridine synthase I related protein [Thermoplasma
           acidophilum]
          Length = 257

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 86/203 (42%), Gaps = 25/203 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y     Y GS + G+QR     S++ +I   +   +G    +  A RTD  V AL  
Sbjct: 6   MTNYAFKFGYEGSYFTGFQRGNGDHSVEDTIIDTL-KASGFDYAIKAAARTDRYVSALSN 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F L     P  +   +N+ +   D I + + + V   F+ R    + +Y Y      
Sbjct: 65  V--FSLETGRSPEAVAGLINSRI---DHIYVHSYAEVPDDFNPRHCTFK-TYRY------ 112

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                     +++ + LDC ++ I     +G HDF  F  +   + + +RTI +    + 
Sbjct: 113 ----------YILRQDLDCISLDINLGKFIGTHDFRRF--VRADSRNTVRTIINASCKND 160

Query: 181 GNLIEIRVVARSFLHTQIRSFVG 203
             L+ +   ARSFL  QIR+ V 
Sbjct: 161 NGLLYLEFSARSFLWNQIRTMVA 183


>gi|167948001|ref|ZP_02535075.1| tRNA pseudouridine synthase A [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 67

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/64 (42%), Positives = 38/64 (59%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +I I V A +FLH  +R+  G L  +G GK   +  E+ LQ +DR++ G  APP GLY  
Sbjct: 1   MIAIEVHANAFLHHMVRNLAGVLMAIGQGKQEVSWAEEILQLRDRRKGGVTAPPHGLYLT 60

Query: 243 SVEY 246
            V+Y
Sbjct: 61  KVDY 64


>gi|16082568|ref|NP_394390.1| tRNA pseudouridine synthase A [Thermoplasma acidophilum DSM 1728]
 gi|24212586|sp|Q9HJN5|TRUA_THEAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 252

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 86/203 (42%), Gaps = 25/203 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y     Y GS + G+QR     S++ +I   +   +G    +  A RTD  V AL  
Sbjct: 1   MTNYAFKFGYEGSYFTGFQRGNGDHSVEDTIIDTL-KASGFDYAIKAAARTDRYVSALSN 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F L     P  +   +N+ +   D I + + + V   F+ R    + +Y Y      
Sbjct: 60  V--FSLETGRSPEAVAGLINSRI---DHIYVHSYAEVPDDFNPRHCTFK-TYRY------ 107

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                     +++ + LDC ++ I     +G HDF  F  +   + + +RTI +    + 
Sbjct: 108 ----------YILRQDLDCISLDINLGKFIGTHDFRRF--VRADSRNTVRTIINASCKND 155

Query: 181 GNLIEIRVVARSFLHTQIRSFVG 203
             L+ +   ARSFL  QIR+ V 
Sbjct: 156 NGLLYLEFSARSFLWNQIRTMVA 178


>gi|324517253|gb|ADY46767.1| tRNA pseudouridine synthase-like protein 1 [Ascaris suum]
          Length = 315

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/289 (22%), Positives = 116/289 (40%), Gaps = 47/289 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQG---SIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           RY + I Y+GS +    +  +G  +     +I ++ F   GE +    A RTD GVHALR
Sbjct: 6   RYLLWISYDGSRFPEMAKGGSGYGVLDFLTTILRSSFPNVGERLKSSAASRTDRGVHALR 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTIS---------ILNLSIVDKQFHARFSAIRR 110
                 +  E+   IL +  +  L   ++I+         IL+   V   F AR +   R
Sbjct: 66  NAIIIQVPLEY--GILDQRKDTLLAEWNSIAEQCKPKALQILDFHTVSPGFSARRNVSYR 123

Query: 111 SYLYRIIT----------RQAPLAL---EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
            Y YR+            ++ P  +   E+  AW++P   D    + A     G H+  +
Sbjct: 124 CYKYRVCVALTSDAWQRFKEKPSLMHYAERDYAWILPPGFDLYKAQQACSIFKGTHNMAS 183

Query: 158 F-------RSIHCQASSPIRTIDHFDV---------NSFGNLIEIRVVARSFLHTQIRSF 201
           F       R    +  S IR + H  +         ++     +  +++ SFL  Q+R  
Sbjct: 184 FFKHRERDRRKENEYPSAIRHMRHVAITGGEPRCIDDADHAFYDFSIISTSFLREQVRRM 243

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGP----LAPPEGLYFDSVEY 246
           +G +     G+ +   +E  L+             +AP +GL+ ++V Y
Sbjct: 244 IGIIVAHAYGRVSRELIEWLLKNPHPTNFFTRRLLIAPAQGLFLENVVY 292


>gi|224083654|ref|XP_002193509.1| PREDICTED: similar to Pseudouridylate synthase 3 [Taeniopygia
           guttata]
          Length = 462

 Score = 56.2 bits (134), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/261 (25%), Positives = 95/261 (36%), Gaps = 71/261 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N  +   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 72  IAYLGWGYQGFASQENTPN---TIEEKLFEALKKTRLVDDRQTSNYHRCGRTDKGVSAFG 128

Query: 60  QVAHFDLVREWVPVILCKALNAYLK----------------ISDTISILNLSIVDKQFHA 103
           QV   DL R  +P    + LN +                  +   I +L  + V  +F A
Sbjct: 129 QVISLDL-RSSLPE--GQQLNGHGGEGQQEELRYTHILNRVLPPDIRVLAWAPVGPEFSA 185

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----- 158
           RFS + R+Y Y     Q                LD   M  AAQ  VG HDF        
Sbjct: 186 RFSCLSRTYRYFFPCAQ----------------LDVALMDTAAQRYVGTHDFRNLCKMDV 229

Query: 159 --------------RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
                         R          R  D F       L +  V  ++FL+ Q+R  +  
Sbjct: 230 ANGVLNFQRTILRARVTRVSGGGEARPRDPF------QLCQFEVTGQAFLYHQVRCMMAV 283

Query: 205 LKLVGDGKWTSTDLEKALQAQ 225
           L L+G G  +   +++ L  +
Sbjct: 284 LFLIGQGMESPDVIDELLNVE 304


>gi|149580877|ref|XP_001519338.1| PREDICTED: similar to FKSG32 [Ornithorhynchus anatinus]
          Length = 695

 Score = 56.2 bits (134), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 101/245 (41%), Gaps = 64/245 (26%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHA 57
           + I Y G GY G+  Q+N ++   +IE+ +F    +  ++        H  GRTD GV A
Sbjct: 65  LRIAYLGWGYQGFASQENTNN---TIEERLFEALTKTRLIERRQTANYHRCGRTDKGVSA 121

Query: 58  LRQVAHFDLVREWV--------PVILCKALNAYLK--------ISDTISILNLSIVDKQF 101
             QV   DL  + V              A  A ++        +   I +L  + V   F
Sbjct: 122 FGQVISLDLRSQTVRGGQEEEGSKDRMDARTAEIRYTHILNRVLPPDIRVLAWAPVGSGF 181

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDF----- 155
            ARF+ ++R+Y Y                   P++ LD E M  AAQ  VG HDF     
Sbjct: 182 SARFNCLQRTYRY-----------------FFPRADLDLEAMDRAAQKYVGTHDFRNLCK 224

Query: 156 -------TTF-RSIHCQASSPIRTIDH---FDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
                  T+F R+I    S+ +R +D     D      L +  V  ++FL+ Q+R  +  
Sbjct: 225 MDVANGVTSFQRTI---LSAQVRRVDQSEETDRRDPFRLCQFEVTGQAFLYHQVRCMMAI 281

Query: 205 LKLVG 209
           L LVG
Sbjct: 282 LFLVG 286


>gi|157106978|ref|XP_001649570.1| pseudouridylate synthase [Aedes aegypti]
 gi|108879706|gb|EAT43931.1| pseudouridylate synthase [Aedes aegypti]
          Length = 467

 Score = 56.2 bits (134), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 59/251 (23%), Positives = 99/251 (39%), Gaps = 52/251 (20%)

Query: 15  YFGWQRQKNGSSIQG--SIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVAHF 64
           Y GW  Q   S      +IE  +F     + ++        H  GRTD GV A  QV   
Sbjct: 82  YLGWDYQGYASQEDSARTIEHLLFNALTRVCLIENRETSNYHRCGRTDKGVSAFHQVVSL 141

Query: 65  DLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           D+  ++ P            +  C+ LN  L   D   +  + +V+  + ARF    R+Y
Sbjct: 142 DVRSKFAPENQLEPESIANEINYCQLLNRVLP-QDIRCVAWMPMVNPNYSARFDCRSRTY 200

Query: 113 LYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPI 169
            Y                   P+ SL+ + M+ A   LVG HDF     +       +  
Sbjct: 201 RY-----------------FFPRGSLNIDAMKEACTFLVGAHDFRNLCKMDVGNGVVTFT 243

Query: 170 RTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           R I +  +         S  +++ + +  ++FL  Q+R  +  L LVG+GK   + +++ 
Sbjct: 244 RRISYVSIEDSQSDAKESPYDMLYLELRGKAFLWHQVRCIMAVLFLVGEGKEEPSVVKEL 303

Query: 222 LQAQDRKECGP 232
           L   ++  C P
Sbjct: 304 LDV-NKNPCKP 313


>gi|255087382|ref|XP_002505614.1| predicted protein [Micromonas sp. RCC299]
 gi|226520884|gb|ACO66872.1| predicted protein [Micromonas sp. RCC299]
          Length = 294

 Score = 56.2 bits (134), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 108/262 (41%), Gaps = 30/262 (11%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVHA 57
            + Y G GY G+QR     +I+  +E+AI    G      G         A RTD GV A
Sbjct: 10  FLAYVGKGYQGFQRNPGARTIEDELERAIVAAGGISADNAGDFTKVQWTRAARTDKGVSA 69

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           + Q     +V +  P  + + +NA L   +   I     V   F+A+    RR Y Y I 
Sbjct: 70  VGQCIALRMVLD--PPGVLERINAAL--PEGFKIFGYKRVTGGFNAKTMCDRRRYEYVIP 125

Query: 118 T------RQAPLALE--KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSP 168
           T      R  P   +  + +A++  + L     +I   +  G H+F  +   +    ++ 
Sbjct: 126 TCAFDPRRCLPRREDDKEAKAFVFDEELRARVNKILGNY-CGTHNFHNYTVRVDPNDAAA 184

Query: 169 IRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R I  F+     V      +   VV +SF+  QIR  +G++  V  G     D   AL+
Sbjct: 185 MRYIISFECGEPFVIDGVEFVRTTVVGQSFMLHQIRKLIGTMLCVVRGYLAEEDQIFALK 244

Query: 224 AQDRKECGPLAPPEGLYFDSVE 245
            ++     PLA  E  Y D VE
Sbjct: 245 TKESCSHEPLALDE--YADDVE 264


>gi|46205610|ref|ZP_00209946.1| COG0101: Pseudouridylate synthase [Magnetospirillum magnetotacticum
           MS-1]
          Length = 193

 Score = 56.2 bits (134), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/158 (30%), Positives = 73/158 (46%), Gaps = 17/158 (10%)

Query: 101 FHARFSAIRRSYLYRIITRQA---PLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDF 155
           F ARFSA+ R+Y YR+    A   PL  E    W++   + LD   M  A + L+G  DF
Sbjct: 11  FDARFSALHRAYTYRVADDPAQRDPLRRE----WVLWNRRPLDVAAMDAAVRPLLGVRDF 66

Query: 156 TTFRSIHCQASSPIRTIDHFDVNSFGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGD 210
            +F      A++ IR + H   +   +     L+   V A +F H  +R+ VG+   VG+
Sbjct: 67  ASFCKPRPGATT-IRELQHLSWSRPADGPDAGLVVAHVRADAFCHNMVRALVGASLAVGE 125

Query: 211 GKWTSTDLEKALQAQDRKECGP-LAPPEGLYFDSVEYS 247
           G+         L A  R++ G  + P  GL  + V Y 
Sbjct: 126 GR-RDVGWPAELLASRRRDAGAGVVPAHGLVLEEVTYP 162


>gi|312374395|gb|EFR21957.1| hypothetical protein AND_15974 [Anopheles darlingi]
          Length = 163

 Score = 56.2 bits (134), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 67/135 (49%), Gaps = 14/135 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIF-LVTGEIVVVHGAGRT 51
           M RY + + Y G+ + G QR+        K+  ++QG IE+A+  L       +  + RT
Sbjct: 1   MNRYLINLSYIGTRFRGIQRKIDKAAGQFKDPHTVQGVIEEALLRLRPVNEPTLKLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALN-AYLKISDTISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    + + +N A  +    + I++   V   FHAR S
Sbjct: 61  DTGVHALHNTVHVDLQRPNGKPYDEDRITQTINRACERDGHALRIISTIRVPDTFHARLS 120

Query: 107 AIRRSYLYRIITRQA 121
           A  R+YLYR+   +A
Sbjct: 121 AKSRTYLYRLAVLKA 135


>gi|302676700|ref|XP_003028033.1| hypothetical protein SCHCODRAFT_60363 [Schizophyllum commune H4-8]
 gi|300101721|gb|EFI93130.1| hypothetical protein SCHCODRAFT_60363 [Schizophyllum commune H4-8]
          Length = 455

 Score = 56.2 bits (134), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 93/242 (38%), Gaps = 61/242 (25%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVVVHGA---------GR 50
           +++C    Y G  + G   QK+ + +  ++E  +F  LV   +V   G          GR
Sbjct: 83  LKFC----YGGWDFGGLAIQKDRTPLP-TVEGKLFGALVRARLVDPKGGLEGCGWERCGR 137

Query: 51  TDSGVHALRQVAHFDLVR------EWVPVILCKALNAYL-----KISDTISILNLSIVDK 99
           TD GV A  QV     VR      E  P       + ++      + DTI IL  S VD 
Sbjct: 138 TDRGVSAAGQVISL-WVRSALSQEELTPTATPTEEHPFIYMINRHLPDTIKILAWSPVDP 196

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F +R+S   R Y Y                +  P  LD   MR A  +L G HDF    
Sbjct: 197 SFSSRYSCTWRHYKY----------------FFSPVGLDVAAMRAACAYLPGTHDFRNLC 240

Query: 160 SIHCQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
            I      P + +D F            D ++ G +    +   SFL+  +R+ +G L  
Sbjct: 241 KI-----DPTKQLDQFRRDILHASISPVDASNPGGMHVFDLKGSSFLYHMVRNIMGVLLS 295

Query: 208 VG 209
           +G
Sbjct: 296 IG 297


>gi|242040775|ref|XP_002467782.1| hypothetical protein SORBIDRAFT_01g033960 [Sorghum bicolor]
 gi|241921636|gb|EER94780.1| hypothetical protein SORBIDRAFT_01g033960 [Sorghum bicolor]
          Length = 459

 Score = 56.2 bits (134), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 87/228 (38%), Gaps = 42/228 (18%)

Query: 8   IEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHALRQV 61
           + Y G  ++G+  + N      S I  ++E+A  +V       +   GRTD GV A  QV
Sbjct: 128 VMYFGQRFYGFSSEGNTEPTVESEIFKALERAKLMVGSRKESCYSRCGRTDKGVSATGQV 187

Query: 62  AHF-----------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
                         D++ E   +   K LN  L     I +L    V   FHARF+ + R
Sbjct: 188 ISLYLRSNIKDVGGDMLDERSEIDYVKVLNRIL--PRDIRVLGWCPVPADFHARFTCLSR 245

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            Y Y                W     LD   M+ AA   +G HDF  F  +     S  R
Sbjct: 246 EYKYLF--------------W--KGDLDILEMQKAASKFIGEHDFRNFCKMDAANVSNYR 289

Query: 171 ------TIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                 TI   D  S  + L  + +   +FL  Q+R  V  L L+G G
Sbjct: 290 RRITEFTISACDRRSNNDELCSMMIKGSAFLWHQVRCMVAVLFLIGQG 337


>gi|157822367|ref|NP_001101604.1| tRNA pseudouridine synthase 3 [Rattus norvegicus]
 gi|149027806|gb|EDL83266.1| pseudouridylate synthase 3 (predicted) [Rattus norvegicus]
 gi|165971639|gb|AAI58694.1| Pseudouridylate synthase 3 [Rattus norvegicus]
          Length = 479

 Score = 55.8 bits (133), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 94/246 (38%), Gaps = 64/246 (26%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVV------VHGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F  L+   +V        H  GRTD GV A  
Sbjct: 68  IAYLGWGYQGFASQENTSN---TIEEKLFEALIKTRLVESRQTSNYHRCGRTDKGVSAFG 124

Query: 60  QVAHFDLVREWVP--------------------VILCKALNAYLKISDTISILNLSIVDK 99
           QV   DL R   P                    +     LN  L     I +L  +  + 
Sbjct: 125 QVISLDL-RSQFPRSRDSEDSNLKDGADDIAKEIRYAHILNRVLPAD--IRVLAWAPAEP 181

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS + R+Y Y       P A            LD   M  AAQ  VG HDF    
Sbjct: 182 SFSARFSCLERTYRYFF-----PCA-----------DLDIATMNYAAQKYVGTHDFRNLC 225

Query: 160 SIHCQ--ASSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSL 205
            +      ++  RTI    V +               L +  V+ ++FL+ Q+R  +  L
Sbjct: 226 KMDVANGVTNFQRTILSAQVQTVAQSPGEEGRQGPFQLCQFEVIGQAFLYHQVRCMMAIL 285

Query: 206 KLVGDG 211
            L+G G
Sbjct: 286 FLIGQG 291


>gi|325190406|emb|CCA24877.1| tRNA pseudouridine synthase putative [Albugo laibachii Nc14]
          Length = 463

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 77/298 (25%), Positives = 120/298 (40%), Gaps = 60/298 (20%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           RY   + Y G  Y G Q  +  ++I+  +E+A+F   G     +G         A RTD 
Sbjct: 73  RYGFWVAYCGEKYSGMQLNEGVATIEAELERALFQAGGISDANYGFLQKIGWSRAARTDK 132

Query: 54  GVHALRQV----------AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           GVHA  Q+          +  D   E +   + K +NA L  SD I ++++  V K F+A
Sbjct: 133 GVHAAGQLVTAKLSFDSKSSEDRNGEQIKGFIEK-INASLP-SD-IRVMDMVTVTKNFNA 189

Query: 104 RFSAIRRSYLYRIIT----------RQAPLALEKGRAWLIPKSLDC-------ENMRIAA 146
           + S   R+Y Y I T           + P+ + +    ++PK+ D        +  R++ 
Sbjct: 190 KLSCDYRTYEYLIPTFVFAGRQRKDHKDPVKVTQAEE-IVPKTTDLHLDVNHQQAYRMST 248

Query: 147 QH----------LVGRHDFTTFRSIHCQASSPI-RTIDHFDV-------NSFGNLIEIRV 188
           +             G H F  F S     S    R I  F         NS    I +RV
Sbjct: 249 EQYDDLNRILAKFEGSHTFHNFTSKLLPTSPKCQRYIVSFKADQPFVPSNSAFEWIRLRV 308

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             +SFL  QIR  +G+   +  G   S  +E+ +   D+ +  P AP  GLY     +
Sbjct: 309 KGQSFLLHQIRKMIGTAVDLCAGAAESNVIERVM-LLDKMDL-PKAPSVGLYLSEAHF 364


>gi|313223491|emb|CBY41917.1| unnamed protein product [Oikopleura dioica]
          Length = 281

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 78/168 (46%), Gaps = 13/168 (7%)

Query: 85  ISDTISI-LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
           +++ IS+ +N  + + + +   +   R+++  II RQ P        W I   LD E M+
Sbjct: 33  VNNVISLFVNSRLSEDEINENVTVGERNFV-AIINRQLP-----DDIW-ITSGLDVELMK 85

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI---RVVARSFLHTQIRS 200
            AA +L+G HDF  F     +  + +R     D+    N+  +    + A  FL+ QIR 
Sbjct: 86  EAASYLIGEHDFRNFSQAQLERQNTVRVCFAADIKQVPNMSSMCVFSIKASGFLYHQIRL 145

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEY 246
            +  L LVG+    ST +++ L  +   R+     A P+GL     EY
Sbjct: 146 TMAILALVGNKLEKSTIVKELLDVEKYPRRPSYKYANPDGLVLIDCEY 193


>gi|301091109|ref|XP_002895746.1| tRNA pseudouridine synthase [Phytophthora infestans T30-4]
 gi|262096658|gb|EEY54710.1| tRNA pseudouridine synthase [Phytophthora infestans T30-4]
          Length = 470

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 71/296 (23%), Positives = 119/296 (40%), Gaps = 64/296 (21%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           RY + + + G  Y G Q  +   +I+  +E+A+F   G     +G         A RTD 
Sbjct: 72  RYGLWVAFCGKNYCGMQMNEGVKTIEAELERALFEAGGIAESNYGYLQKIGWSRAARTDK 131

Query: 54  GVHALRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GVHA  Q+    L V + +   + K   A   + + I ++++  V K F+A+ +  +R+Y
Sbjct: 132 GVHAAGQLLTAKLHVGDDIAGFMAKVDAA---LPEDIRVMHMVTVTKNFNAKMTCDQRTY 188

Query: 113 LYRIIT----------------RQAP------------------------LALEKGRAWL 132
            Y   T                +QA                           LE  +A+ 
Sbjct: 189 EYLAPTFIFGKRMRSSASKNEEKQAEGTNQWPSNLRDSEEGFDSNVVIDNTTLEAHKAFR 248

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI--RTIDHFD-----VNSFGNLIE 185
           +   +  E +    +  VG H+F  F S   + ++P   R I  F+     V +    + 
Sbjct: 249 LSDEI-LEQLNATLKQYVGTHNFHNFTS-KMEPTNPQANRFIISFEAERPFVQNDMEWVR 306

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +RVV +SFL   IR  +G+   V  G    + +E+A++    K   P AP  GLY 
Sbjct: 307 LRVVGQSFLLHHIRKMIGTAVEVVSGVSDPSTIERAMELT--KMDLPKAPSVGLYL 360


>gi|158298322|ref|XP_318500.4| AGAP010807-PA [Anopheles gambiae str. PEST]
 gi|157014345|gb|EAA13705.4| AGAP010807-PA [Anopheles gambiae str. PEST]
          Length = 485

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 60/255 (23%), Positives = 104/255 (40%), Gaps = 58/255 (22%)

Query: 15  YFGWQRQ---KNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSGVHALRQVAH 63
           Y GW  Q       SI+ +IE  +F    ++ ++           GRTD GV A  QV  
Sbjct: 82  YLGWDYQGFAAQEDSIE-TIEHHMFAALKKVCLIESRETSNYNRCGRTDKGVSAFHQVIS 140

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILN------------LSIVDKQFHARFSAIRRS 111
            D+  ++ P +   A N   ++ D  ++LN            + +V+  + ARF    R+
Sbjct: 141 LDVRSKFAPELQLDANNLTNEL-DYCAMLNRVLPEEIRCLAWMPMVNPAYSARFDCRSRT 199

Query: 112 YLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF------------ 158
           Y Y                   P+  L+   M  +A++LVG HDF               
Sbjct: 200 YRY-----------------FFPRGDLNITAMEESARYLVGAHDFRNLCKMDVGNGVVSF 242

Query: 159 -RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
            RSI   +  P +     D +S+ +++ + +  ++FL  Q+R  +  L LVG G+   + 
Sbjct: 243 VRSIDAISIKPSQRDSERDGSSY-DMMYLELQGKAFLWHQVRCIMAVLLLVGQGREKPSV 301

Query: 218 LEKALQAQDRKECGP 232
           ++  L  + +  C P
Sbjct: 302 VKDLLDVE-QNPCKP 315


>gi|88802196|ref|ZP_01117723.1| pseudouridylate synthase I [Polaribacter irgensii 23-P]
 gi|88781054|gb|EAR12232.1| pseudouridylate synthase I [Polaribacter irgensii 23-P]
          Length = 260

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 67/263 (25%), Positives = 110/263 (41%), Gaps = 33/263 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + +E+ G  + GWQ+Q N  ++   ++K++ F+         G GRTD+ V A     
Sbjct: 7   YLIRLEFLGFRFSGWQKQLNAKTVHDIVDKSLSFVFEDSAYKTIGVGRTDAKVSA--NAY 64

Query: 63  HFDLVR--EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII--T 118
           +F L R  E   V    +LN+          + +  V   ++   ++ R+ Y Y      
Sbjct: 65  YFQLFRDSEIKEVSFLASLNS--NFPPDFRAITVQEVGTDYNVIQASKRKEYHYYFSFGA 122

Query: 119 RQAPLALEKGRAWL--IPKSLDCENMRIAAQHLVGRHDF----------TTFRSI--HCQ 164
           +  P A      +L  +   LD + M  AA+   G H F          T F+ +   C+
Sbjct: 123 KNHPFA----APFLVNVAADLDLKKMMDAARLFEGEHYFHKYCTKPSAQTVFKRVIDVCE 178

Query: 165 -ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
              + I T   F   S+     +RV  + FL  QIR  + +L  VG G   +T +  +L+
Sbjct: 179 IVENTILTASFFPEKSY----MLRVQGKGFLRYQIRLMMATLFEVGKGTLDATFIIASLK 234

Query: 224 A-QDRKECGPLAPPEGLYFDSVE 245
              DRK    +AP  GL    +E
Sbjct: 235 EDNDRKFMRNIAPSSGLQLYDIE 257


>gi|163783824|ref|ZP_02178806.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880914|gb|EDP74436.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
          Length = 64

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/60 (45%), Positives = 38/60 (63%)

Query: 4  YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
          Y + I Y G+ Y GWQRQ    +IQ  IE  + ++    V ++ +GRTD+GVHAL QVA+
Sbjct: 5  YKLTISYLGTNYHGWQRQPKHITIQQVIEDNLKVLVKHPVKLYASGRTDAGVHALGQVAN 64


>gi|295133853|ref|YP_003584529.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
 gi|294981868|gb|ADF52333.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
          Length = 262

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 115/262 (43%), Gaps = 25/262 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G    GWQ+Q N  +++G I K +  V  E    V G  RTD+ V +    +
Sbjct: 8   YLIKVQYLGYRLHGWQKQPNFKTVEGLITKTLRYVMPETRYKVLGCSRTDAMVSS--NGS 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVD-KQFHARFSAIRRS------YLYR 115
            F+L  +  P+   + L  +L + +     ++ + D ++  A F+ I+ S      YL+ 
Sbjct: 66  AFELFVDEQPL---ENLEDFLALFNLNLPQDIRVTDIEEVGANFNIIQHSKIKEYAYLFS 122

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI--- 172
             ++  P        +     LD + M+  AQ   G H+F  +     + S+  R I   
Sbjct: 123 FGSKNHPFCAPFMANFQF--DLDIDKMKKGAQLFNGTHNFRNYCVRVSEKSTFEREILKA 180

Query: 173 -----DHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-QAQ 225
                  +  N F     I  V  + FL  Q+R  +G++  +G G+++  D+E++L +  
Sbjct: 181 EIVENKLYTANFFPKKSYIFHVHGKGFLRHQVRLMMGAMIQLGRGEFSLGDIEQSLKEGN 240

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +  +    AP  GL  + + + 
Sbjct: 241 EHLQMDYSAPASGLILNDIHFD 262


>gi|307177137|gb|EFN66370.1| tRNA pseudouridine synthase 3 [Camponotus floridanus]
          Length = 345

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 89/230 (38%), Gaps = 52/230 (22%)

Query: 15  YFGWQ------RQKNGSSIQ----GSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           Y GW       ++ N  +I+     ++ K+  + + E    H  GRTD GV +  QV   
Sbjct: 25  YLGWDYHGFTVQEDNNDTIEHHLFTALLKSCCIESRESANYHRCGRTDKGVSSFSQVISL 84

Query: 65  DLVREWVP---------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           D+     P         +  CK LN  L  +  I  +    V   F ARF    R+Y Y 
Sbjct: 85  DIRSRLEPENQHNLSEELPYCKILNRLLPTN--IRCIAWCPVSPNFSARFDCKYRTYKY- 141

Query: 116 IITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDF------------TTFRSIH 162
                             PKS LD + M  + ++ +G HDF              F+   
Sbjct: 142 ----------------FFPKSNLDIDAMDKSVKYAIGDHDFRNICKMDVANGVINFKRTV 185

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
             A   +   +   +  + N+ E+ + +++FL  QIR  +G L LVG  K
Sbjct: 186 IDAKVSMSNQNVEKITGY-NMCELEITSQAFLWHQIRCLMGILLLVGQRK 234


>gi|71749392|ref|XP_828035.1| tRNA pseudouridine synthase A-like protein [Trypanosoma brucei
           TREU927]
 gi|70833419|gb|EAN78923.1| tRNA pseudouridine synthase A-like protein [Trypanosoma brucei]
          Length = 579

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 79/202 (39%), Gaps = 44/202 (21%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDS- 53
           + RY + ++Y G+ + GW     RQ  +    + GSI +      G I    G  R ++ 
Sbjct: 175 LTRYRVDVQYQGNDFDGWWKSTTRQLFRREVGLDGSITRVPVAEPGTIGNAAGVSRGETM 234

Query: 54  ---------------------------------GVHALRQVAHFDLVR--EWVPVILCKA 78
                                            GV   R   H D+    E  P  + + 
Sbjct: 235 GSRYHARTVLEEALAVALDVNTVRVVAGVIPEVGVSVRRLCCHVDVPSHIELQPRTVIQR 294

Query: 79  LNAYL-KISDTISILNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
              ++ K    ++IL+      Q FHAR S +RR Y+YRI+ R AP   + G  W + + 
Sbjct: 295 ATMWMEKRQQPLAILSYRRCKNQDFHARHSGLRRVYVYRILNRVAPPLFDAGLQWHVDRH 354

Query: 137 LDCENMRIAAQHLVGRHDFTTF 158
           LD + M+  A+ L G  DF  F
Sbjct: 355 LDVDRMKRFAKTLEGTKDFGYF 376



 Score = 53.1 bits (126), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 45/85 (52%), Gaps = 7/85 (8%)

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA---- 224
           +RT+D  DV    + + I  V RSFL  QIR+ V  LK  G G W   +L++ALQ+    
Sbjct: 469 VRTVDRLDVVRQDDEVLIWFVGRSFLRHQIRNMVSVLKAAGHGLWNDLELQQALQSGFEP 528

Query: 225 ---QDRKECGPLAPPEGLYFDSVEY 246
              + ++E  P AP  GL    VEY
Sbjct: 529 SRHRFKRERFPTAPAYGLTLWDVEY 553


>gi|294901661|ref|XP_002777462.1| tRNA pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239885099|gb|EER09278.1| tRNA pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 387

 Score = 55.8 bits (133), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 53/168 (31%), Positives = 76/168 (45%), Gaps = 24/168 (14%)

Query: 49  GRTDSGVHALRQVA--HFDLVREWVPVILCKALNAYLKISDTISILNL-SIVDKQFHARF 105
           GRTD GVHA    A     L  +       + +N  L   D I +L + S+    F ARF
Sbjct: 108 GRTDKGVHARGNYATLRLRLKPDGTEFPYIQMINRVL--PDDIRVLRICSVPSDDFDARF 165

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           S   R+Y Y                +     LD E M  AAQ LVG+HD+  F  +  + 
Sbjct: 166 SCKSRTYKY----------------FFPSTGLDLEVMAEAAQRLVGQHDYRNFCRMDVEQ 209

Query: 166 SSPI-RTIDHFDVNSFGNLIEIRVVARS-FLHTQIRSFVGSLKLVGDG 211
           ++   RTI  F++ + G++I   V+  S FL  Q+R  +  L L+G G
Sbjct: 210 TTNFERTIYSFEICN-GDVISHAVITGSAFLWHQVRCMMEVLMLIGKG 256


>gi|193706844|ref|XP_001945291.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like
           [Acyrthosiphon pisum]
          Length = 441

 Score = 55.8 bits (133), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 66/257 (25%), Positives = 113/257 (43%), Gaps = 25/257 (9%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIE---KAIFLVTGE------IVVVHGAGRTDSGVH 56
           +++ Y+G GY G QR K   +++  +    K+  L+T E       +    A RTD GV 
Sbjct: 70  ILLAYSGLGYLGLQRNKGVKTVEEELLLALKSKNLITDEGFEQIQTMQFQRAARTDKGVS 129

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           ALRQ+    L  +    ++  AL       + I +L++  V K F+++ S   R+Y Y  
Sbjct: 130 ALRQIISLLLPEDVDKQVINTAL------PEQIRVLDIRRVTKGFNSKNSCDGRTYSYTC 183

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTID 173
            T   AP       ++ I  ++  + +    +  +G H++  + S       S+    + 
Sbjct: 184 PTFAFAPAETTIDFSYRIDATV-IDRINEVVKSFLGCHNYHNYTSKKKPGDPSAQRYMVS 242

Query: 174 HFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            +    F      LI + V  +SF+  QIR  VG +  +  G      +E+A Q  DR +
Sbjct: 243 FYCDKPFEKDGVELISLYVRGQSFMLHQIRKMVGVIIAICRGVAKHDVIERAWQP-DRLD 301

Query: 230 CGPLAPPEGLYFDSVEY 246
             P+AP  GL  + V Y
Sbjct: 302 L-PIAPGLGLVLEEVHY 317


>gi|242096622|ref|XP_002438801.1| hypothetical protein SORBIDRAFT_10g026490 [Sorghum bicolor]
 gi|241917024|gb|EER90168.1| hypothetical protein SORBIDRAFT_10g026490 [Sorghum bicolor]
          Length = 318

 Score = 55.8 bits (133), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 93/227 (40%), Gaps = 30/227 (13%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFS 106
           AGRTD GV AL+QV  F   R+ V     K A+N      D +  L++S V ++FH  FS
Sbjct: 82  AGRTDKGVTALQQVCSFYTWRKDVKSGDIKDAINE--AAPDKLKPLHVSEVPREFHPNFS 139

Query: 107 AIRRSYLY--------RIITRQAPLA--LEKGRAWLIPKSLDCENMRIAAQHLVGR---- 152
           A  R Y+Y         +I  +A  +  LE     + P+S D   +    + L G+    
Sbjct: 140 AKWRRYMYIFPLDEDANLILGEAHSSKILENSEHNIKPQSFDVAKVDKILKTLAGKTLSY 199

Query: 153 ----HDFTTFRSI---------HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
                D    RS+         H +A+       + D      ++ + +VA  FL   +R
Sbjct: 200 KMFARDTQASRSVGPPTECFMFHSRAAVAKLHYANEDYKEGMMVMCVELVANRFLRKMVR 259

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             V +             L   ++A DR+   P APPEGL    V Y
Sbjct: 260 VLVATAIREAAAGAGDDALLNLMEATDRRATAPPAPPEGLCLIDVGY 306


>gi|145527104|ref|XP_001449352.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124416940|emb|CAK81955.1| unnamed protein product [Paramecium tetraurelia]
          Length = 414

 Score = 55.5 bits (132), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 66/276 (23%), Positives = 107/276 (38%), Gaps = 56/276 (20%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSG 54
           R    + Y G  Y G ++Q N    Q +IE  +F     + ++          AGRTD G
Sbjct: 50  RVAFKLAYVGINYHGLEQQINQ---QNTIENHLFKALQRVRMIDNRDDCNYTRAGRTDKG 106

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKI-----SDTISILNLSIVDKQFHARFSAIR 109
           V A+  V   ++ +      + K+   Y +I      + I IL+  IVD++F+AR+  I+
Sbjct: 107 VSAIGNVVALNVRK------IGKSDKLYAQILNRVLPEDIQILDECIVDEKFNARYDCIK 160

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP- 168
           R Y Y                +      + E M  A    +G HDF  F  +   A+   
Sbjct: 161 RVYKY----------------YFYKMDYNIELMTEAMLLFIGEHDFRNFCKLDVIANQNF 204

Query: 169 IRTIDHFDVNS------------FGNLIEIR-----VVARSFLHTQIRSFVGSLKLVGDG 211
           +RTI +  +              F +   +R     +   +FL  QIR  +  L L+G G
Sbjct: 205 VRTIMNITIEEVFPENAPRCSTLFKDDDRLRLYCVTIEGNAFLWHQIRYMMAVLFLIGKG 264

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
              S+ +       D K    +AP   L   + E+ 
Sbjct: 265 IEKSSVITDLFTKFDGKPNYQMAPDYPLVLHNCEFK 300


>gi|159905071|ref|YP_001548733.1| tRNA pseudouridine synthase A [Methanococcus maripaludis C6]
 gi|238686937|sp|A9A828|TRUA_METM6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|159886564|gb|ABX01501.1| tRNA pseudouridine synthase [Methanococcus maripaludis C6]
          Length = 262

 Score = 55.5 bits (132), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 108/246 (43%), Gaps = 41/246 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGR--LSFQTQPHGETVCDKISNALLDCGYLDNKDRVPLYHGGRTDRGVSALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR-RSYLYRIIT 118
               +++ ++  PV+    + + LK  D + +L    +D      F  I  R Y Y +  
Sbjct: 60  NYIVYEMDKK--PVL--PRVQSKLKW-DGVWVLGCKEIDT-----FPEIEYRHYQYNLPN 109

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDV 177
                           K+ D E M+ A++ L+G H F    +    +   P+RT+ +  +
Sbjct: 110 ----------------KNHDVELMKKASEKLIGTHYFQNLSKRDKSKVKDPVRTLYNIKI 153

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD-GKWTSTDLEKALQ---AQDRKECGPL 233
           +S    I I +   SFL   +R  +   +L+ D GK    D EK ++   ++D  +  P 
Sbjct: 154 SSNDYFITIDIFGESFLWNMVRRII---RLLSDIGKHKIKDPEKFIELILSEDYSKGYPP 210

Query: 234 APPEGL 239
           +P EGL
Sbjct: 211 SPAEGL 216


>gi|156097182|ref|XP_001614624.1| tRNA pseudouridine synthase [Plasmodium vivax SaI-1]
 gi|148803498|gb|EDL44897.1| tRNA pseudouridine synthase, putative [Plasmodium vivax]
          Length = 241

 Score = 55.5 bits (132), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 79/185 (42%), Gaps = 26/185 (14%)

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           DL R +V     K +N  LK    + ++++  V   F AR + I R+YLY          
Sbjct: 19  DLQRVYV-----KEINKKLK---HMQVIDMRSVPNFFDARLNCIHRTYLY---------- 60

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                 + + K+ + E M+   +  +G HDF+ F      ++   RTI  F+V       
Sbjct: 61  ------FFMDKNYNFERMKEGCKLFLGEHDFSNFCKKRKNSTCFRRTILKFEVRRMDKKF 114

Query: 185 E-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD-RKECGPLAPPEGLYFD 242
              ++   SFL+ QIR  V +L  +G G     DL   L     R +   +A  +GL   
Sbjct: 115 HYFKIKGTSFLYNQIRHMVAALFQLGTGNLEVEDLANMLNNHPCRDKNFKIADEDGLLLY 174

Query: 243 SVEYS 247
           S ++S
Sbjct: 175 SFKFS 179


>gi|219123859|ref|XP_002182234.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406195|gb|EEC46135.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 308

 Score = 55.5 bits (132), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 78/312 (25%), Positives = 120/312 (38%), Gaps = 69/312 (22%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-------------------------SIQGSIEKAI 35
           M  Y +I+ Y+G+ + G+QRQ   +                         ++Q  +E+A+
Sbjct: 1   MPLYKLIVAYDGTRFNGFQRQSTTTDMSKKIALKRPHWDSATGKRKGIALTVQECLEQAL 60

Query: 36  FLVTGEIVVVHG-----AGRTDSGVHALRQVAHFDLVREWVPVILC---KALNAYLKISD 87
              TG    V       AGRTD GVHA  QV    L     P  L    KALN+ L +  
Sbjct: 61  MDWTGNETNVEAFRFRFAGRTDKGVHARGQVVAVQLPIVVEPTELWRVHKALNSRLPVDI 120

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIITRQ-------------------APLALEKG 128
           ++  + L      F  R     + Y Y I  R+                   A  A++  
Sbjct: 121 SVERVELCENQLDFDPRHDVQSKQYSYTIKFRRKAYNEEGQLLPICTSGPQSARSAMDSP 180

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR----TIDHFDVNSF---- 180
             WL P  LD   +    Q L G+H F +F  +H +A   +R    T+D   V +     
Sbjct: 181 CLWLCPWVLDDSKLYELCQRLQGQHSFRSF--VH-RADRNLRDHILTLDRVWVEALSCTR 237

Query: 181 --GNLIEIRV--VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAP 235
               ++ +R+   A+ F  + +R+ VG    V  G +   D +   +  D   +    AP
Sbjct: 238 EDAPVVTVRLWFQAKGFRRSMVRNLVGFCVDVCRGMY-QPDWDALWEGSDEIAQKVHSAP 296

Query: 236 PEGLYFDSVEYS 247
             GL  +SV YS
Sbjct: 297 ACGLCLESVAYS 308


>gi|170097145|ref|XP_001879792.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164645195|gb|EDR09443.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 446

 Score = 55.5 bits (132), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 70/176 (39%), Gaps = 34/176 (19%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKI-----SDTISILNLSIVDKQFHA 103
           GRTD GV A  QV     V  W         + YL I      DTI +L  S V  +F A
Sbjct: 107 GRTDRGVSAAGQV-----VSLWATTSKPTFEHDYLSILNRLLPDTIRVLAWSPVAPKFSA 161

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           RFS + R Y Y                +  P  LD   M+ AA  LVG HDF     +  
Sbjct: 162 RFSCLYRHYKY----------------FFSPLGLDIPRMQQAALRLVGDHDFRNLCKLDP 205

Query: 164 QASSPI-------RTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDG 211
           Q    I         I+   +   G  + +  +V  +FL+ Q+R  +  L LVG G
Sbjct: 206 QKQITIFRRKVITAEIEPLSLAENGEGVYVFNLVGTAFLYHQVRHIMAILFLVGTG 261


>gi|195122857|ref|XP_002005927.1| GI20747 [Drosophila mojavensis]
 gi|193910995|gb|EDW09862.1| GI20747 [Drosophila mojavensis]
          Length = 500

 Score = 55.1 bits (131), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 63/259 (24%), Positives = 98/259 (37%), Gaps = 56/259 (21%)

Query: 15  YFGWQRQ------KNGSSIQG----SIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           YFGW  Q       +  +I+G    ++E+   + +      H  GRTD  V A  QV   
Sbjct: 109 YFGWDYQGFACQEDSADTIEGYLFRALERTCLIESRATSNYHRCGRTDKEVSAFCQVISI 168

Query: 65  DLVREWVPVILCKALNAYLKISDTISILN------------LSIVDKQFHARFSAIRRSY 112
           +L  +  P    K  +   +I D  S+LN            + + +  + ARF  I R+Y
Sbjct: 169 NLRSKHSPDTQMKPESLNTEI-DYCSLLNRVLPKNIQCVSWMPLRNPDYSARFDCISRTY 227

Query: 113 LYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPI 169
            Y                   PK  LD ++M+ A Q LV   DF  F    +H   ++ +
Sbjct: 228 RY-----------------YFPKGDLDIDSMQQACQLLVCHGDFRNFCKMDVHNGVTNYM 270

Query: 170 RTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           R + H ++    N            +  + + A +FL  QIR  +  L LVG      + 
Sbjct: 271 RNLQHAEIRPCDNTERQLEQNSGYIMYYLEIKANAFLWHQIRCIMAVLLLVGQKNEQPSI 330

Query: 218 LEKALQAQDRKECGPLAPP 236
           + K L       C P   P
Sbjct: 331 ITKLLDV-GSNPCKPQYTP 348


>gi|198429149|ref|XP_002129315.1| PREDICTED: similar to Pseudouridylate synthase 3 [Ciona
           intestinalis]
          Length = 510

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 74/289 (25%), Positives = 108/289 (37%), Gaps = 86/289 (29%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG------SSIQGSIEKAIF-------LVTG--EIVVVHG 47
           R  + + Y G  Y G+   K+        SI   +E+ +        L+TG   ++    
Sbjct: 102 RIALKVLYLGWDYVGYAFTKSSLAFSKPESISNVVERVLLEALLRQQLITGVGSVLNFDR 161

Query: 48  AGRTDSGVHALRQVAHFDLVRE-------WVPVIL-------CKALNAYLK----ISDT- 88
           AGRTD  V  L QV   ++          W P +         K    Y +    +SDT 
Sbjct: 162 AGRTDRQVSGLSQVVSVNVRSNLNKGHGVWYPKVEGSDNVGNTKPETEYFEDGFPVSDTT 221

Query: 89  -------------------ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
                              I IL  S V K F  R+    R+Y Y         A  +G 
Sbjct: 222 LDDGELPYVSLLNQALPPDIRILAWSPVKKTFSPRYQCRSRTYRY---------AFVRG- 271

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP------IRTIDHFDVNSFG-- 181
                 S+D E M  AAQ  VGRHD   F    C+ SS       +RTI+   V  F   
Sbjct: 272 ------SMDIELMNEAAQKFVGRHDMRNF----CKVSSENAYRTYVRTINSIKVEEFNQT 321

Query: 182 NLIEIRVV-----ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           NL E  +      A S+++ QIR  +  L  +G G+   + +++ L  +
Sbjct: 322 NLPECDICVATISAESYVYKQIRRMMSILGRIGSGEIPPSTIDEMLDVE 370


>gi|301122837|ref|XP_002909145.1| tRNA pseudouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262099907|gb|EEY57959.1| tRNA pseudouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 510

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 67/261 (25%), Positives = 97/261 (37%), Gaps = 67/261 (25%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVV------VHGAGRTDSGVHALRQV 61
           Y G  Y G+ RQ +   +  ++E+ +   LV  +++           GRTD GV A  QV
Sbjct: 81  YLGEKYAGFARQDH---MPETVERYLLEALVRSKLIENIDDAGYSRCGRTDRGVSAFGQV 137

Query: 62  ------------------AHFDLVR--EWVPVILCKALNAYLKISDTISILNLSI----- 96
                             A  D VR  E   V L       L   D  S +N ++     
Sbjct: 138 VALRVRSNLPATAELLSAASIDDVRPGEKFQVRLATGEEKTLTEVDYASHINRALPADIR 197

Query: 97  ------VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
                    +F ARF    R Y Y                + + + LD E MR AAQ+LV
Sbjct: 198 VYAVASCRPEFSARFDCKARMYRY----------------FFVRRDLDIEKMRTAAQYLV 241

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDV---------NSFGNLIEIRVVARSFLHTQIRSF 201
           G+HDF  F  I        R +  F++         +    +    V  R+FL  Q+R  
Sbjct: 242 GKHDFRNFCRIDPNCHVFERNVRSFEIVECPGQRADDPSQQMYRCEVFGRAFLWHQVRCM 301

Query: 202 VGSLKLVGDGKWTSTDLEKAL 222
           V  L L+G G+   + + K L
Sbjct: 302 VEVLFLIGSGREEPSIIPKLL 322


>gi|257387360|ref|YP_003177133.1| tRNA pseudouridine synthase A [Halomicrobium mukohataei DSM 12286]
 gi|257169667|gb|ACV47426.1| tRNA pseudouridine synthase [Halomicrobium mukohataei DSM 12286]
          Length = 263

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 102/245 (41%), Gaps = 32/245 (13%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA-GRTDSGVHALRQVAH 63
           I Y+G  Y G+QRQ +  +++G +   +    +  G++   + A GRTD+GV AL Q   
Sbjct: 6   IAYDGQPYHGFQRQPDVETVEGELLATLDRLGVTAGDVPAGYAAAGRTDAGVSALAQTVA 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F+   EW   +   A N+ L  S  + +   + V   FHA   A  R Y+Y         
Sbjct: 66  FE-APEW---LSPAAFNSELPAS--VRVWASADVPDDFHATHDAREREYVY--------- 110

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                  +L       +  R AA  L G HD   F ++    S  +R +   D+   G  
Sbjct: 111 -------YLYAPERHDDRARRAADALSGEHD---FHNLTPDDSGTVRAL-SIDLTREGEF 159

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP--PEGLYF 241
           +  R+ A  F    +R  VG +  +  G    + +++ L ++       + P  P  L  
Sbjct: 160 LVCRLRAGGFCRQLVRRVVGLVDEIRRGDAPLSKVDRVLGSKPIDGAAGVGPASPTPLVL 219

Query: 242 DSVEY 246
            +V+Y
Sbjct: 220 VAVDY 224


>gi|50294374|ref|XP_449598.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49528912|emb|CAG62574.1| unnamed protein product [Candida glabrata]
          Length = 317

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 75/276 (27%), Positives = 104/276 (37%), Gaps = 54/276 (19%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTDSGV 55
            +++ Y G+GY G Q      +I   + KA+                     A RTD GV
Sbjct: 2   ALVLGYLGTGYQGIQYNPPAHTIDNELFKALVATNCISQSNSDDFSKSSFSRATRTDKGV 61

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HAL  +    + R  VP  +   LN  L   D I I ++  V K+F+AR  A  R Y Y 
Sbjct: 62  HALTNLVALKMQRYEVPQQVKAELNEILP--DDIRIWDVVPVKKKFNARVMAGTRHYRYV 119

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAA-----QHLVGRHDFTTF--RSIHCQASSP 168
           I T      L+ G     P S D    ++A         +G H++  F  R     A SP
Sbjct: 120 IPT----FLLQCG-----PHS-DLSTSQLARFKNIWNMFLGTHNYYNFTPRRKDTNADSP 169

Query: 169 --------IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFV--------------GSLK 206
                   I+  D F +      + I +  +SFL  QIR  V               S++
Sbjct: 170 QNMRHMYSIQVSDPFTIAGSTQWLSIAIHGQSFLLHQIRKMVHYALSEYHRSSSDTKSME 229

Query: 207 LVGDGKWTSTDLEKALQAQDRKECG-PLAPPEGLYF 241
           L+   +    DL  A       E   PLAP  GLY 
Sbjct: 230 LL---ETVDPDLTSATALDTPTEQYIPLAPAAGLYL 262


>gi|193666867|ref|XP_001946781.1| PREDICTED: tRNA pseudouridine synthase 3-like isoform 1
           [Acyrthosiphon pisum]
 gi|328702018|ref|XP_003241780.1| PREDICTED: tRNA pseudouridine synthase 3-like isoform 2
           [Acyrthosiphon pisum]
          Length = 402

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 80/225 (35%), Gaps = 52/225 (23%)

Query: 15  YFGWQRQKNGSSIQGSIEKAI------------FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y GW     G + Q   EK I             + + +    H  GRTD GV +  QV 
Sbjct: 65  YLGWDYH--GFATQDVSEKTIEYELFRALTICCLIESRQTSNYHRCGRTDKGVSSFSQVI 122

Query: 63  HFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              +       E +P   CK LN  L     I ++    V   F ARF    R+Y Y   
Sbjct: 123 SLTVRSNGDDSEELP--YCKMLNRLL--PKDIRVVAWGPVKDDFSARFDCGSRTYKY--- 175

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT-------------FRSIHCQ 164
                        W     LD + M  A Q +VG HDF               +R I   
Sbjct: 176 -------------WFPRGDLDVDLMNQAIQQVVGTHDFRNLCKMDVANGVVQFYRRITSA 222

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                   + F  N   ++ E+ +V ++FL  QIR  V  L LVG
Sbjct: 223 DIKICSENNQFSKNRDYDMCELTIVGKAFLWHQIRCIVSVLILVG 267


>gi|270006513|gb|EFA02961.1| hypothetical protein TcasGA2_TC030541 [Tribolium castaneum]
          Length = 365

 Score = 54.3 bits (129), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 87/218 (39%), Gaps = 48/218 (22%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           Y GW  Q  G   Q     +IE  +F    +  ++        H  GRTD  + +     
Sbjct: 46  YLGWDYQ--GYVTQEDTVNTIEHHVFNALIKTCLIENRSSANYHRCGRTDKDLRSNGD-- 101

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
             D   E   +  CK LN  L   + I  +    V+  F ARF    R+Y Y        
Sbjct: 102 --DFESE---INYCKILNRVL--PENIQFVAWCPVESAFSARFDCKNRTYKY-------- 146

Query: 123 LALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFDVNS 179
                      PKS LD + M+IAA +LVG HDF  F    ++       R I   D++ 
Sbjct: 147 ---------FFPKSNLDIDAMKIAANYLVGTHDFRNFCKMDVNNGVVEFKRNILSVDISL 197

Query: 180 FG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           F      ++  + +   +FL  QIR  VG L LVG GK
Sbjct: 198 FQEDERYSIQVLTIKGNAFLWHQIRCIVGILILVGQGK 235


>gi|297742024|emb|CBI33811.3| unnamed protein product [Vitis vinifera]
          Length = 402

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 66/292 (22%), Positives = 115/292 (39%), Gaps = 53/292 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----------------FLVTGEIVVV 45
           + + +++ Y+G+ + GWQ+Q   +++QG +E ++                  V G + V 
Sbjct: 108 LTFKIVLSYHGASFDGWQKQPGLNTVQGLVEASLGRFVDERKAQQLKEKNLPVEGMVTV- 166

Query: 46  HGAGRTDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHAR 104
             AGRTD GV AL+QV  F   ++ V V  +  A+N        + ++++S V + FH  
Sbjct: 167 --AGRTDKGVTALQQVCSFYTWKKDVKVQDIEDAING--AAPGKLRVISVSEVSRIFHPN 222

Query: 105 FSAIRRSYLYRII------------------------TRQAPLALEKGRAWLIPKSLDCE 140
           FSA  R Y Y                            R+ P      R   + + L+ +
Sbjct: 223 FSAKWRHYFYIFPLNDGDDGEQISENEMDIQKISFNENRKKPSTFSISRVDQLLRQLEGK 282

Query: 141 --NMRIAAQHLVGRHDF---TTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
             + +I A+      +    T     H +A+     +   D      ++ I +VA  FL 
Sbjct: 283 LLSYKIFARDTKASRNIGPPTECFVFHARATEA--RLQFSDDGEGTKVMCIELVANRFLR 340

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +R  V +             L K + A  R+   P APP+GL    V ++
Sbjct: 341 KMVRVLVATSIREAAAGAEQDALLKLMDATCRRATAPPAPPDGLCLIDVGFT 392


>gi|225427081|ref|XP_002275354.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 448

 Score = 53.5 bits (127), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/130 (29%), Positives = 65/130 (50%), Gaps = 22/130 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----------------FLVTGEIVVV 45
           + + +++ Y+G+ + GWQ+Q   +++QG +E ++                  V G + V 
Sbjct: 123 LTFKIVLSYHGASFDGWQKQPGLNTVQGLVEASLGRFVDERKAQQLKEKNLPVEGMVTV- 181

Query: 46  HGAGRTDSGVHALRQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHAR 104
             AGRTD GV AL+QV  F   ++ V V  +  A+N        + ++++S V + FH  
Sbjct: 182 --AGRTDKGVTALQQVCSFYTWKKDVKVQDIEDAING--AAPGKLRVISVSEVSRIFHPN 237

Query: 105 FSAIRRSYLY 114
           FSA  R Y Y
Sbjct: 238 FSAKWRHYFY 247


>gi|326773999|ref|ZP_08233281.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
 gi|326636138|gb|EGE37042.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
          Length = 113

 Score = 53.5 bits (127), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 40/69 (57%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
          M R  + + Y+G+ + GW  Q    +++G +  A+  V  E V +  AGRTD+GVHA  Q
Sbjct: 7  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTSALATVLREPVRLTVAGRTDAGVHAAAQ 66

Query: 61 VAHFDLVRE 69
          VAH D+  E
Sbjct: 67 VAHLDVSPE 75


>gi|224370989|ref|YP_002605153.1| TruA2 [Desulfobacterium autotrophicum HRM2]
 gi|223693706|gb|ACN16989.1| TruA2 [Desulfobacterium autotrophicum HRM2]
          Length = 257

 Score = 53.5 bits (127), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/265 (24%), Positives = 112/265 (42%), Gaps = 36/265 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GW +Q    +++  +EK +  + G     + G+ RTD+ V A     
Sbjct: 6   YLIHIQYLGFRYHGWLKQPGLKTVEAMVEKTVAFILGHSDFKILGSSRTDAMVSANHSA- 64

Query: 63  HFDL-VREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            F+L V E + V  L K  N    + + I ++    VD+ F    +   ++Y+Y     +
Sbjct: 65  -FELFVHEPLNVEQLVKDFNQ--NLPNDIRVIKAQGVDRNFSIINAPRTKAYIYLFAFGE 121

Query: 121 ------APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF----------TTFRS---I 161
                 APL +     WL     D + M+  A    GRH+F          TTF+    +
Sbjct: 122 KCHPFCAPL-ISSFCHWL-----DIDLMKQGALLFQGRHNFRSYCTKPGTRTTFKREVLV 175

Query: 162 HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
                + I   + F   S+   I     ++ F+  Q+R  +G L  +G G+    D++ +
Sbjct: 176 SKIEENRIFKANFFPAESYAYHIH----SKGFMRYQVRLIMGQLLSLGRGEIGLEDIKVS 231

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           L+         +AP  GL  + +E+
Sbjct: 232 LKGMSHLPLRHIAPSSGLMLNKIEF 256


>gi|328876653|gb|EGG25016.1| tRNA pseudouridylate synthase [Dictyostelium fasciculatum]
          Length = 542

 Score = 53.5 bits (127), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 96/224 (42%), Gaps = 30/224 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRT 51
           I +C  + Y+G+ Y G Q+    S+I+  +EKA F  TG I   +             RT
Sbjct: 118 IAFC--VGYSGTNYCGMQKNWGYSTIEEELEKACFK-TGSISPNNFYSQRKIDWIRCART 174

Query: 52  DSGVHALRQVAHFDLVREWVPVILCK---ALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           D GV A+R +    L  E+ P  L +   A+N++L   + I +  +  V+  FHA+    
Sbjct: 175 DKGVSAVRNMVSCKL--EYDPPTLEELKNAINSHL--PEDIKVFGIKRVNNSFHAKNCVD 230

Query: 109 RRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQ--HLVGRHDFTTFRSIHCQA 165
            RSYLY   T    P+    GR     K  + E  R+ +     +G H F  + S     
Sbjct: 231 GRSYLYITPTFAFEPVHATSGRPETY-KFDETERSRVNSMLAMFLGTHKFHNYTSRKDSG 289

Query: 166 S-SPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVG 203
             S  RT+  F      V      + I ++  SF+  QIR  +G
Sbjct: 290 DPSAKRTMSLFQCSEPFVMEGIEFVSINIIGGSFMLHQIRKMIG 333


>gi|320094550|ref|ZP_08026316.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178
          str. F0338]
 gi|319978465|gb|EFW10042.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178
          str. F0338]
          Length = 94

 Score = 53.5 bits (127), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 38/65 (58%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
          +R  + + Y+G+ + GW  Q    ++QG +E  +  +  + V    AGRTD+GVHA  QV
Sbjct: 16 VRVRIDLAYDGTRFHGWAAQPGLRTVQGELEAVLSTLVRQPVATTVAGRTDAGVHARHQV 75

Query: 62 AHFDL 66
          AH DL
Sbjct: 76 AHVDL 80


>gi|316970789|gb|EFV54664.1| tRNA pseudouridine synthase A [Trichinella spiralis]
          Length = 390

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 78/266 (29%), Positives = 114/266 (42%), Gaps = 46/266 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA---IFLVTGEIVV------VHGAGRTDS 53
           +Y M + Y G  Y G Q   N  +++  I +A   + L+T + VV         A RTD 
Sbjct: 53  KYAMFLAYRGKNYHGMQVNPNVPTVEKYIMEALQKLNLITVDQVVQPSLFKFQRAARTDK 112

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILN-LSIVDKQFHARFSAIRRSY 112
           GV A +Q+    L     P I  K        +DT+++LN L    K F ++     RSY
Sbjct: 113 GVSATKQICSLLL-----PTIEGKE-------NDTVNLLNGLQRATKSFDSKKWCDYRSY 160

Query: 113 LYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHCQAS 166
            Y + +     Q+ L  +K R  L  K ++ E  RI  Q+ VG H+F  F S  +H   S
Sbjct: 161 SYTLPSYCFRHQSDLERDKFR--LDNKDIE-EINRILMQY-VGTHNFYNFTSGKLHKDES 216

Query: 167 SPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
                I       F  N+   L  + +  +SFL  QIR  +G    +  G     DL+  
Sbjct: 217 CKRFIIRCECGKRFLYNNIEYLT-VDIKGQSFLIHQIRKMIGFCISLIRG-----DLDPC 270

Query: 222 LQA---QDRKECGPLAPPEGLYFDSV 244
           LQ    Q+ +   P AP  GL  + V
Sbjct: 271 LQQKVWQNERIKVPKAPSLGLVLEEV 296


>gi|84996449|ref|XP_952946.1| tRNA-pseudouridine synthase I [Theileria annulata strain Ankara]
 gi|65303943|emb|CAI76322.1| tRNA-pseudouridine synthase I, putative [Theileria annulata]
          Length = 480

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 96/242 (39%), Gaps = 49/242 (20%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDK------- 99
           + RTD GVH++  V+  +LV E      C+ L+   K + D++     S+  +       
Sbjct: 217 SSRTDRGVHSMGTVSLINLVSEIYLFQACQYLSFDKKFNFDSLEEFQDSLNKRLPSDIRV 276

Query: 100 ---------QFHARFSAIRRSYLYRIITRQAPLALEKGRAW-----------LIPKSLDC 139
                    +F+ R   I +SY Y++     P   E+   W           L+ K  D 
Sbjct: 277 TSVITPPHDEFNVRHHNIGKSYSYKVDLSPNPSLFERNHYWQIMSDTHFVNTLLRKYRDV 336

Query: 140 ------ENMRIAAQHLVGRHDFTTFRSIHCQAS------SPIRTIDHFDVNSFGNL---- 183
                 E ++ AA+   G+H+F  FR  +C+ +       PI TI   +   F N+    
Sbjct: 337 KAPFSFEKLKEAARVFHGKHNFEAFRK-NCRGNERDKIIDPICTIHSIE---FVNIPQDK 392

Query: 184 -IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +EI V    FL+  +R  V  L L G        +++AL         P AP  GLY  
Sbjct: 393 KVEIIVNGDRFLYKMVRCIVSHLILAGFNVIKPDQIKRALDNATEIPNIPYAPAHGLYLK 452

Query: 243 SV 244
            V
Sbjct: 453 KV 454


>gi|300175988|emb|CBK22205.2| unnamed protein product [Blastocystis hominis]
          Length = 399

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 72/283 (25%), Positives = 104/283 (36%), Gaps = 81/283 (28%)

Query: 20  RQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSGVHALRQV---------- 61
           +Q +G +   S+E AIF     + ++           GRTD+GV A  QV          
Sbjct: 11  QQIDGVADDNSVESAIFSALKRVHLIDDISKCHYQRCGRTDAGVSAFNQVISLYLRSNLR 70

Query: 62  AHFDLVREWVPVILCKALNAYLK-----------------------ISDTISILNLSIVD 98
           +  + V E+ P I   A N   +                       +  TI I     VD
Sbjct: 71  SGVEFVDEFDPSIPYNAPNTSNQPQSAPSSSTPVTEFDYASVLNKVLPPTIRITGWCPVD 130

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           + F AR+S     +   +       A    R + + ++ D E MR A +   G HDF  F
Sbjct: 131 RSFSARYSCCGEDWAANLS------AGRVYRYYFLRRNYDVELMRSAVKLFEGEHDFRNF 184

Query: 159 RSIHCQASSPIRTIDHFDVNSF------GNLIEIR-------------VVARSFLHTQIR 199
               C+       ID  +V  F      G+++EIR             +V R+FL  QIR
Sbjct: 185 ----CR-------IDAVNVCDFTRTVFRGDVVEIRKGETPQHDVLAVEIVGRAFLWHQIR 233

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGL 239
             +  L LV   K   T +   L    +  C P   LA PE L
Sbjct: 234 CMMSILFLVASKKEKQTIISDLLDVS-KSPCKPQYHLADPEPL 275


>gi|13541901|ref|NP_111589.1| tRNA pseudouridine synthase A [Thermoplasma volcanium GSS1]
 gi|24212574|sp|Q979R4|TRUA_THEVO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|14325334|dbj|BAB60238.1| pseudouridylate synthase I [Thermoplasma volcanium GSS1]
          Length = 246

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 56/245 (22%), Positives = 104/245 (42%), Gaps = 39/245 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y     Y G  + G+QR     S++ +I KA+ L +  ++    A RTD GV AL  V +
Sbjct: 5   YFFKFGYIGYMFTGYQRGNGVKSVEDTIIKALNLNSPSLI--KTAARTDRGVSALSNVFY 62

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            +  R   P  +   +N+    ++ + + + + V+   + R+   + +Y+Y         
Sbjct: 63  IETERR--PQDIAGIINSK---NEYVFVHSFAEVEHGRNPRYCDTK-TYMY--------- 107

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--SFG 181
                   ++P   +C+++ + A   +G HDF+ F     +  +P R+ID    +  SFG
Sbjct: 108 --------MLPGETECDSLMVTASGFLGFHDFSKFSKKDTR--NPWRSIDEVKCHRESFG 157

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++E    A+SFL  Q+R  +  +      K     +              +APPE L  
Sbjct: 158 VVLEFS--AKSFLWNQVRRMLAFILEFRGNKIDPFSVSNIYSH--------IAPPENLIL 207

Query: 242 DSVEY 246
             + Y
Sbjct: 208 KDIVY 212


>gi|134046431|ref|YP_001097916.1| tRNA pseudouridine synthase A [Methanococcus maripaludis C5]
 gi|132664056|gb|ABO35702.1| tRNA pseudouridine synthase [Methanococcus maripaludis C5]
          Length = 262

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 106/245 (43%), Gaps = 39/245 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGK--LSFQTQPHGETVCDKISNALLDCGYLDNKDKVPLYHGGRTDRGVAALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
               +++ ++  PV+    + + LK  D I +L      K+         R Y Y +   
Sbjct: 60  NYVVYEMDKK--PVL--PRVQSKLKW-DGIWVLGC----KEIEIFPEIEHRHYQYTLPN- 109

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVN 178
                          K+ D E M+ A++ L+G H F    +    +   P+RT+    ++
Sbjct: 110 ---------------KNHDVELMKKASEKLIGTHYFQNLSKRDKTKVKDPVRTLYDIKIS 154

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD-GKWTSTDLEKALQ---AQDRKECGPLA 234
           S    I I +   SFL   +R  +   +L+ D GK    D EK ++   +++ K+  P +
Sbjct: 155 SNDYFITIDIFGESFLWNMVRRII---RLLSDIGKHKIEDPEKFIELILSEEYKKGYPPS 211

Query: 235 PPEGL 239
           P EGL
Sbjct: 212 PAEGL 216


>gi|45357831|ref|NP_987388.1| tRNA pseudouridine synthase A [Methanococcus maripaludis S2]
 gi|62901319|sp|Q6M0K2|TRUA_METMP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|45047391|emb|CAF29824.1| tRNA pseudouridine synthase Related [Methanococcus maripaludis S2]
          Length = 262

 Score = 53.1 bits (126), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 105/243 (43%), Gaps = 35/243 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGK--LSFQTQPHGETVCDKISNALLDCGYLDNKDRVPLYHGGRTDRGVAALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR-RSYLYRIIT 118
               +++ ++  PV+    + + LK  D I +L    ++      F  I  R Y Y +  
Sbjct: 60  NYVVYEMDKK--PVL--PRVQSKLKW-DGIWVLGCKKIE-----IFPEIEHRHYQYTLPN 109

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDV 177
                           K+ D E M+ A++ L+G H F    +    +   P+RT+    +
Sbjct: 110 ----------------KNHDVELMKKASEKLIGTHYFQNLSKRDKTKVKDPVRTLYDIKI 153

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD-LEKALQAQDRKECGPLAPP 236
           +S    I I +   SFL   +R  +  L  +G  K  + +   + + ++D K+  P +P 
Sbjct: 154 SSNDYFITIDIFGESFLWNMVRRIIRLLSDIGKHKIENPEKFIELILSEDYKKGYPPSPA 213

Query: 237 EGL 239
           EGL
Sbjct: 214 EGL 216


>gi|327311135|ref|YP_004338032.1| Pseudouridylate synthase [Thermoproteus uzoniensis 768-20]
 gi|326947614|gb|AEA12720.1| Pseudouridylate synthase [Thermoproteus uzoniensis 768-20]
          Length = 250

 Score = 53.1 bits (126), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 104/247 (42%), Gaps = 39/247 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MI Y  ++ Y+GS ++G+   +   S++ ++ +A+  + G         RTD GV AL  
Sbjct: 1   MIAY--LVAYDGSLFYGFTGHER--SVEPALARALGPLLGR------GSRTDPGVSALGN 50

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V    + R   P+     +NA  ++   + +   + V + F+ R  A  R+Y+Y    R 
Sbjct: 51  VV---VARSLKPL---GQINA--ELPRGVWVWGYAEVPEGFNPR-RARARTYVYFAPYRG 101

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             L L                +R AA   VG HD+  F          + TI   +V   
Sbjct: 102 EDLGL----------------VREAASLFVGTHDYRNFAK---GVRDAVTTIYSIEVEDR 142

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  IEI    + F +  +R  V +L  VG G     D+ + L++       P AP EGL 
Sbjct: 143 GAYIEIAFRGKGFRNKMLRKIVWALLAVGRGVLGIDDVRRLLESGGGGPV-PSAPAEGLV 201

Query: 241 FDSVEYS 247
             S++Y 
Sbjct: 202 LLSIDYG 208


>gi|195382396|ref|XP_002049916.1| GJ20484 [Drosophila virilis]
 gi|194144713|gb|EDW61109.1| GJ20484 [Drosophila virilis]
          Length = 509

 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 93/236 (39%), Gaps = 63/236 (26%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 106 YFGWDYQ--GFACQEDSMDTIEAYLFRALIRTCLIESRATSNYHRCGRTDKEVSAFCQVI 163

Query: 63  HFDLVREWVPVILCK--ALNAYLKISDTISILN------------LSIVDKQFHARFSAI 108
             DL  +  P +  +  AL++ +   D  S+LN            + + +  + ARF  I
Sbjct: 164 SIDLRSKHAPDVQMEPEALSSEI---DYCSLLNRVLPKNIQCVSWMPLRNPAYSARFDCI 220

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQA 165
            R+Y Y                   PK  LD E MRIA Q LV   DF  F    +H   
Sbjct: 221 SRTYRY-----------------YFPKGDLDIEAMRIACQSLVCHGDFRNFCKMDVHNGV 263

Query: 166 SSPIRTI--------DHFDVNSFGN----LIEIRVVARSFLHTQIRSFVGSLKLVG 209
           ++ +R +        D+ D+    N    +  + +   +FL  QIR  +  L LVG
Sbjct: 264 TNYMRNLQGAAIKPCDNTDIQMHSNSGYAMYYLEIQGNAFLWHQIRCIMAVLLLVG 319


>gi|209882282|ref|XP_002142578.1| tRNA pseudouridine synthase A family protein [Cryptosporidium muris
           RN66]
 gi|209558184|gb|EEA08229.1| tRNA pseudouridine synthase A family protein [Cryptosporidium muris
           RN66]
          Length = 332

 Score = 52.8 bits (125), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 65/261 (24%), Positives = 96/261 (36%), Gaps = 35/261 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AGRTDSG 54
           R+   I Y G+ Y+G   Q   +    +IE+  +     + ++           GRTD G
Sbjct: 26  RFLFRISYIGTNYYGMAYQ---NETIPTIEREFYNACLRLKLIKNREDCDLIRCGRTDKG 82

Query: 55  VHALRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           VH+       +L  R+  P    + +N  L     I IL    V+  F ARF    R Y 
Sbjct: 83  VHSTGNYISINLRTRDTSPYNYQEMINGVLPWD--IRILGFCQVNNNFSARFDCDSRVYK 140

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIR 170
           Y     Q           L    +D   M  + +  +G HDF  F  +  +     + +R
Sbjct: 141 YIFPIDQIQNFEHNYFPKLNINHID--QMNKSCKQFIGTHDFRVFCKMDIKNRPNQTYVR 198

Query: 171 TIDHFDVNSFGN----------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           TI  F V  F N                L  I ++  +FL  Q+R  VG L  +  GK  
Sbjct: 199 TIYDFRVEVFNNNKISSSSFDNSINDTKLGVITIIGSAFLWHQVRLMVGILFEISLGKIR 258

Query: 215 STDLEKALQAQDRKECGPLAP 235
           S  + K L     K+  P  P
Sbjct: 259 SECITKLLDNYFDKDEIPFFP 279


>gi|170068141|ref|XP_001868750.1| pseudouridylate synthase [Culex quinquefasciatus]
 gi|167864259|gb|EDS27642.1| pseudouridylate synthase [Culex quinquefasciatus]
          Length = 470

 Score = 52.8 bits (125), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 66/266 (24%), Positives = 102/266 (38%), Gaps = 65/266 (24%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           Y GW  Q  G + Q     +IE  +F     + ++        H  GRTD GV A  QV 
Sbjct: 82  YLGWDFQ--GYATQEDSANTIEHHLFNALTRVCLIESRESSNYHRCGRTDKGVSAFHQVV 139

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             D+  ++ P            +  C+ LN  L  ++   +  +   +  + ARF    R
Sbjct: 140 SLDVRSKFPPESQLAPESLQNELNYCQLLNRVLP-AEIRCVAWMPTANPNYSARFDCRSR 198

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDF------------TT 157
           +Y Y                   P+ SLD + MR   + LVG HDF             T
Sbjct: 199 TYRY-----------------FFPRGSLDVDAMRKGCEFLVGSHDFRNLCKMDVGNGVVT 241

Query: 158 F-RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           F R++H    + IR       +S  +++   +  ++FL  Q+R  +  L LVG G+   T
Sbjct: 242 FQRNVH---YAVIRDSLKDGGDSSYDMLYFELRGKAFLWHQVRCIMAILILVGQGREDPT 298

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFD 242
            + + L      E  P  P   L  D
Sbjct: 299 VIRELLDV----EKNPRKPQYSLAND 320


>gi|268529206|ref|XP_002629729.1| C. briggsae CBR-TAG-124 protein [Caenorhabditis briggsae]
 gi|187038647|emb|CAP22290.1| CBR-TAG-124 protein [Caenorhabditis briggsae AF16]
          Length = 401

 Score = 52.8 bits (125), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 90/247 (36%), Gaps = 72/247 (29%)

Query: 15  YFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGA--------GRTDSGVHALRQVAHF 64
           Y GW+        + Q ++E  +     +  ++  +        GRTD GV A +Q A F
Sbjct: 38  YLGWEHDGLVQQPNTQNTVEHHLMEALIKTHIIEDSIKCDFSRCGRTDKGVSAFKQTAAF 97

Query: 65  DLVREWVP-------------------------VILCKALNAYLKISDTISILNLSIVDK 99
            L R   P                         +   K LN  L    TI +   + V  
Sbjct: 98  -LARSTCPDHPNVFWSDSTAEDVKNSYKSKDEELPYIKMLNGVL--PKTIRVFAWAPVAP 154

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            F+ARF   RR+Y Y                   PK+ LD E MR AA+ L+G HD++ F
Sbjct: 155 TFNARFDCNRRTYKYSF-----------------PKAGLDLEKMREAAKLLIGEHDYSNF 197

Query: 159 RSIHCQA----SSPIRTIDHFDV----------NSFGNLIEIRVVARSFLHTQIRSFVGS 204
             I         S  R I  +DV          N   +++E+ V    FL   IR  V  
Sbjct: 198 CQIDMNKMRLEQSYTRKI--YDVTVEQVSTHSENDIYSMVELTVSGSGFLWHMIRYIVTV 255

Query: 205 LKLVGDG 211
           L+ V  G
Sbjct: 256 LQEVARG 262


>gi|307184937|gb|EFN71202.1| tRNA pseudouridine synthase A [Camponotus floridanus]
          Length = 330

 Score = 52.8 bits (125), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 69/276 (25%), Positives = 114/276 (41%), Gaps = 49/276 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGE------IVVVHGAGRTDSG 54
           + +++ Y G  Y+G QR     +I+  +  A+    L+T E       +    A RTD G
Sbjct: 48  HAILLGYLGKDYYGMQRNPGMKTIEEDLVTALLKADLITTEHFKNIRSISFQRAARTDKG 107

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A+RQ+    L  +    ++ K L       D I I  +  V K F+++     R+Y Y
Sbjct: 108 VSAIRQIVSLKLPEKPDKTVINKFL------PDVIKIFGIKRVTKGFNSKNQCDARTYRY 161

Query: 115 RIIT---------------------RQAPLALEKGRAW----LIPKSLDCENMRIAAQHL 149
            I T                     R   L+   G+++    L P+SL+  N  +  + +
Sbjct: 162 IIPTFAFAPEDLTLLKIGEEINEEERIKQLSTIDGKSYVDYRLSPESLNRLNSIL--KLM 219

Query: 150 VGRHDFTTFRS-IHCQASSPIRTIDHFD-VNSF-GNLIE---IRVVARSFLHTQIRSFVG 203
            G H+F  F S +        R I  F  V +F  N +E   + +  +SF+  QIR  V 
Sbjct: 220 EGTHNFHNFTSKVKPLDPRAQRYIIKFHCVETFISNGMEFAILEIKGQSFMLHQIRKMVA 279

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +  +     +   + +A +  DR E  P+AP  GL
Sbjct: 280 VVVGIARNIISEEIINEAFKTMDRLEI-PIAPSLGL 314


>gi|325182027|emb|CCA16480.1| tRNA pseudouridine synthase A putative [Albugo laibachii Nc14]
          Length = 209

 Score = 52.4 bits (124), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 93/204 (45%), Gaps = 45/204 (22%)

Query: 84  KISDTISILNLSIVDKQFHARFSAIR---RSYLYRIITRQAP-LALEKGRAWLIPKSLDC 139
           ++  TI +  L+ ++ +F   F+ IR   + Y+Y I     P L L K  +W + K ++ 
Sbjct: 4   RLPSTIRVHCLAPLE-EFVDDFTRIRPRYKRYVYYIQQGARPDLELSK-YSWFLRKRIEP 61

Query: 140 ENMRIAAQHLVGRHDFTTF--------------RSIHCQASSPIRTIDHFDVN------- 178
             ++ A   L+G HDF  F              R+++ QAS  ++   +F ++       
Sbjct: 62  TRLQQALNFLLGTHDFEPFSQGLGMVLEGKSTTRTLY-QASVTLKRNVNFCLDPAVCGSG 120

Query: 179 ---------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                          +  + I I +VA  FL   +R  VGSL+L+G+G     ++ + L+
Sbjct: 121 DTVNNQAKLCDMEGKTLTHFICIELVANGFLRHMVRRIVGSLRLIGEGSQHPQEMHRILK 180

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           +Q   E GP AP +GL+   + ++
Sbjct: 181 SQ--VEAGPSAPAKGLWLQQIWFT 202


>gi|332520423|ref|ZP_08396885.1| Pseudouridine synthase I, TruA, alpha/beta domain [Lacinutrix
           algicola 5H-3-7-4]
 gi|332043776|gb|EGI79971.1| Pseudouridine synthase I, TruA, alpha/beta domain [Lacinutrix
           algicola 5H-3-7-4]
          Length = 227

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 97/230 (42%), Gaps = 28/230 (12%)

Query: 36  FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDT-----IS 90
           F++ G+      +GRTD+ V A        L   + P+   +   A+LK+ +T     I 
Sbjct: 8   FILEGKRFKSLASGRTDAMVSAEETAIELFL---YEPI---EDQKAFLKLFNTNLPQDIR 61

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
            L ++ VD +F+   +   + Y+Y                  I   LD E M+I A+   
Sbjct: 62  ALEITEVDAKFNIINNPKVKEYIYLFAFGDKFHPFCAPILTTILDDLDVEIMKIGAKLFE 121

Query: 151 GRHDFTTF------------RSIHCQ-ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           G H   T+              + C+   + I T + F   S+     +RV  + F+  Q
Sbjct: 122 GEHYLKTYCYKPSNNGIYTREILTCEIVENTIYTANFFPKKSYL----LRVRGKGFMRNQ 177

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           IR  +G+L  +G GK T  D++ +L+  +  +   +AP  GL   S+++ 
Sbjct: 178 IRLMMGTLIDLGKGKLTLEDIKASLEPDNTIKMEYIAPASGLILKSLKFD 227


>gi|19115377|ref|NP_594465.1| tRNA-pseudouridine synthase (predicted) [Schizosaccharomyces pombe
           972h-]
 gi|74698445|sp|Q9UTB3|YL85_SCHPO RecName: Full=Putative tRNA pseudouridine synthase C25B8.05
 gi|6469292|emb|CAB61771.1| tRNA-pseudouridine synthase (predicted) [Schizosaccharomyces pombe]
          Length = 450

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 52/167 (31%), Positives = 71/167 (42%), Gaps = 20/167 (11%)

Query: 49  GRTDSGVHALRQVAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV A+ QV   ++   E  P+I C  LN  L     I I   +   + F ARFS 
Sbjct: 146 GRTDKGVSAMGQVISLNVRHSERRPIIYCDVLNRLLPAD--IRITGYAFPPEGFDARFSC 203

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QA 165
            +R Y Y + T+  P             SLD + M  AA   +G HDF  F  I    Q 
Sbjct: 204 KQRHYKY-LFTKDYPGG-----------SLDIDRMNEAAALYLGEHDFRNFCKIDASKQI 251

Query: 166 SSPIRTIDHFDV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           ++  R I    V   +    L    +   +FL  Q+R  +  L L+G
Sbjct: 252 TNYHRRILSSKVICIDPSTGLYAFDLQGTAFLWHQVRCMMAILFLIG 298


>gi|326933214|ref|XP_003212702.1| PREDICTED: tRNA pseudouridine synthase 3-like [Meleagris gallopavo]
          Length = 710

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 93/245 (37%), Gaps = 65/245 (26%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 70  IAYLGWGYQGFASQENTSN---TIEEKLFEALKKTRLVDSRQTSNYHRCGRTDKGVSAFG 126

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISD----------------------TISILNLSIV 97
           QV   DL          K LN     S+                       I +L  + V
Sbjct: 127 QVISLDLRSNLSKE---KKLNGCTGDSEGKSSKSEEELRYTHILNRVLPPDIRVLAWAPV 183

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
           +  F ARFS ++R+Y Y       P A            LD   M+ AAQ  VG HDF  
Sbjct: 184 EPDFSARFSCLKRTYRYFF-----PCA-----------DLDVALMQAAAQRYVGTHDFRN 227

Query: 158 FRS-------IHCQASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQIRSFVGS 204
                     I+ Q +     +   D  + G       L +  V  ++FL+ Q+R  +  
Sbjct: 228 LCKMDVANGVINFQRTILSAQVTWVDGGAEGGLRDPFRLCQFEVTGQAFLYHQVRCMMAI 287

Query: 205 LKLVG 209
           L L+G
Sbjct: 288 LFLIG 292


>gi|298208691|ref|YP_003716870.1| tRNA pseudouridine synthase A [Croceibacter atlanticus HTCC2559]
 gi|83848614|gb|EAP86483.1| tRNA pseudouridine synthase A [Croceibacter atlanticus HTCC2559]
          Length = 266

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 62/262 (23%), Positives = 108/262 (41%), Gaps = 27/262 (10%)

Query: 2   IRYCMIIE--YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           +RY  II+  Y G  + GWQ+Q + ++++  +E+ +  V G +   +  +GRTD+ V   
Sbjct: 10  LRYYYIIQLQYLGFRFHGWQKQPDVNTVERMVERTLAYVLGHKKFKLLASGRTDAKVSVN 69

Query: 59  RQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
                  +  + + V    K  N  + +   I  L++   D  F+       + Y+Y   
Sbjct: 70  NTFVELFIDDKPLEVDSFFKDFN--VNLPQDIKALSIKETDANFNIIQHPKLKEYIYLFT 127

Query: 118 TRQAPLALEKGRAWLIP------KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
                   EK   +  P      K L+ E M+ AA    G HDF  +     + +  I  
Sbjct: 128 YG------EKMHPFCAPYMVCYNKPLNIELMQEAAALFQGEHDFKNYTYKPTEDTQTIGV 181

Query: 172 IDH--------FDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           ID         +  N F      ++VV + F   QIR  +G+L  +G G++     +K L
Sbjct: 182 IDACELSENTVYTANFFPEKSYMLKVVGQGFKRHQIRLMMGALFDLGSGEFDMQFFKKTL 241

Query: 223 QAQDRKECGPLAPPEGLYFDSV 244
            + +  +   +A   GL   SV
Sbjct: 242 TSTEFIKLTHIAQASGLILQSV 263


>gi|332029057|gb|EGI69071.1| tRNA pseudouridine synthase A [Acromyrmex echinatior]
          Length = 398

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 68/285 (23%), Positives = 115/285 (40%), Gaps = 51/285 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGE------IVVVHGAGRTDSG 54
           + M++ Y G  Y+G QR     +I+  +  A+    L+T E       +    A RTD G
Sbjct: 45  HAMLLGYVGKDYYGMQRNPGMKTIEEDLIIALLKADLITKEQFENTRAINFQRAARTDKG 104

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A+RQ+    L       ++    N +L   D I +  +  V K F+++     R+Y Y
Sbjct: 105 VSAIRQIVSLKLPENSNKTVI----NQFL--PDAIRVFGIKRVTKGFNSKNQCDARTYRY 158

Query: 115 RIIT---------------------RQAPLALEKGRAW----LIPKSLDCENMRIAAQHL 149
            I +                     R   L++  G+ +    L P+SLD  N  +     
Sbjct: 159 VIPSYAFALEDQSLLKLGEEVDEDERIKQLSIIDGKPYTDYRLSPESLDRLNSILKL--F 216

Query: 150 VGRHDFTTFRS----IHCQASSPIRTI---DHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
            G H+F  F S    +  +A   I +    + F +N    L  + +  +SF+  QIR  V
Sbjct: 217 EGSHNFHNFTSKVKPLDPRARRYIISFCCTETFVLNDI-ELAVLEIKGQSFMLHQIRKMV 275

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +  +     +   +++A +  D+ +  PLAP  GL    V Y 
Sbjct: 276 AIVIAIARNMISKETIDEAFKTMDKMDL-PLAPSLGLCLCHVHYD 319


>gi|325068064|ref|ZP_08126737.1| tRNA pseudouridine synthase A [Actinomyces oris K20]
          Length = 89

 Score = 52.0 bits (123), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 40/69 (57%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
          M R  + + Y+G+ + GW  Q    +++G +  A+ +V  E V +  AGRTD+GVHA  Q
Sbjct: 7  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTSALAIVLREPVRLTVAGRTDAGVHAAAQ 66

Query: 61 VAHFDLVRE 69
          V H D+  E
Sbjct: 67 VVHLDVSPE 75


>gi|148683103|gb|EDL15050.1| mCG23338, isoform CRA_a [Mus musculus]
          Length = 130

 Score = 52.0 bits (123), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 56/120 (46%), Gaps = 15/120 (12%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-------------NLIEIRV 188
           M+ AAQHL+G HDF+ F+S     ++ +RT+    V+                    +  
Sbjct: 4   MQEAAQHLLGTHDFSAFQSAGSPVTNTVRTLRRVSVSPGPASPFVLPEGSRRLQFWTLEF 63

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            ++SFL+ Q+R     L  VG G    T ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 64  ESQSFLYRQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAPARGLFLKSVLY 123


>gi|118101846|ref|XP_417852.2| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 390

 Score = 51.6 bits (122), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 96/246 (39%), Gaps = 67/246 (27%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALR 59
           I Y G GY G+  Q+N S+   +IE+ +F    +  +V        H  GRTD GV A  
Sbjct: 72  IAYLGWGYQGFASQENTSN---TIEEKLFEALKKTRLVDDRQTSNYHRCGRTDKGVSAFG 128

Query: 60  QVAHFDL---VREWVPVILCKA------------------LNAYLKISDTISILNLSIVD 98
           QV   DL   + E   +  C                    LN  L     I +L  + V+
Sbjct: 129 QVISLDLRSNLSEEKKLNGCTGDSEGKSSKSEEELRYTHILNRVLPPD--IRVLAWAPVE 186

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
             F ARFS ++R+Y Y       P A            LD   M  AAQ  VG HDF   
Sbjct: 187 PDFSARFSCLKRTYRYFF-----PCA-----------DLDVALMHTAAQRYVGTHDFRNL 230

Query: 159 RSIHCQASSPI---RTIDHFDV------------NSFGNLIEIRVVARSFLHTQIRSFVG 203
             +   A+  I   RTI    V            + F  L +  V  ++FL+ Q+R  + 
Sbjct: 231 CKMDV-ANGVINFQRTILSAQVTWADGGAESGLRDPF-RLCQFEVTGQAFLYHQVRCMMA 288

Query: 204 SLKLVG 209
            L L+G
Sbjct: 289 ILFLIG 294


>gi|320591696|gb|EFX04135.1| pseudouridylate synthase 3 [Grosmannia clavigera kw1407]
          Length = 522

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 74/260 (28%), Positives = 99/260 (38%), Gaps = 60/260 (23%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS--SIQGSIEKA------IFLVTG----EIVVVH----GA 48
            + + Y G  Y G++ Q +G+  +I+  + KA      +F   G    E+ +V       
Sbjct: 61  ALKLAYLGKRYGGFEYQPSGALPTIEEELWKALTKACLVFPAPGASADEVDLVRCEYSKC 120

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           GRTD GV A  QV     VR     +  K LN  L   D   +   +     F ARFS  
Sbjct: 121 GRTDRGVSAFGQVVAL-RVRSNKRAVYAKVLNRLLP-PDIRVLAWCATPPADFSARFSCR 178

Query: 109 RRSYLYRII---------TRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            R Y Y            +R  P +   G A   P   LD + MR AA   VG HDF  F
Sbjct: 179 ERQYRYFFTQPAYFTEDGSRPGPTS-SAGSASQPPDGWLDIDAMRDAATRFVGLHDFRNF 237

Query: 159 RSIHCQASSPIRTIDHF-------------DVNS-------------FGNLIEIRVVARS 192
               C+   P + I +F             DV+S             F  +    V   +
Sbjct: 238 ----CKV-DPSKQITNFERRIFAAGITEVADVHSSLRCLSSSASSVSFPRVYSFDVRGSA 292

Query: 193 FLHTQIRSFVGSLKLVGDGK 212
           FL  QIR  V  L LVG G+
Sbjct: 293 FLWHQIRHMVAVLFLVGQGR 312


>gi|260781560|ref|XP_002585875.1| hypothetical protein BRAFLDRAFT_110975 [Branchiostoma floridae]
 gi|229270936|gb|EEN41886.1| hypothetical protein BRAFLDRAFT_110975 [Branchiostoma floridae]
          Length = 312

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 71/183 (38%), Gaps = 49/183 (26%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGVH 56
            + + Y G  Y G+Q Q+   +   +IE  +F    +  ++        H  GRTD GV 
Sbjct: 71  ALKVAYLGWSYDGFQSQE---TTDNTIEARLFEALTKTRLIEKRQSSNYHRCGRTDKGVS 127

Query: 57  ALRQVAHFDLV-------------------REWVPVILCKALNAYLKI-SDTISILNLSI 96
           A  QV   DL                    RE       K +    K+    I +L  + 
Sbjct: 128 AFGQVISLDLRTNLTDGAGVIPRPEGTANHREGDKTTEIKYVYILNKVLPPDIRVLAWAP 187

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDF 155
           VD  F ARFS  +R+Y Y                   PK +LD ++M +A Q LVG HDF
Sbjct: 188 VDPDFSARFSCQQRTYKY-----------------FFPKGNLDIQSMHLAGQKLVGEHDF 230

Query: 156 TTF 158
             F
Sbjct: 231 RNF 233


>gi|330793042|ref|XP_003284595.1| hypothetical protein DICPUDRAFT_45589 [Dictyostelium purpureum]
 gi|325085509|gb|EGC38915.1| hypothetical protein DICPUDRAFT_45589 [Dictyostelium purpureum]
          Length = 473

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 87/223 (39%), Gaps = 24/223 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG----EIVVVHG-----AGRTDS 53
           +  +++ Y G  Y G Q+     +I+  +E AIF   G     +   H        RTD 
Sbjct: 69  KVAVLLGYLGKNYAGMQKNPGLRTIEEELEMAIFKAGGILPDNLYFQHKIDWVRCARTDK 128

Query: 54  GVHALRQVAHFDLVREWVPVIL---CKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           GV ALR V    +  E  P  L    KALN  L   + I +  +  V+  FHA+     R
Sbjct: 129 GVSALRNVVSLKM--EVGPPELDEMVKALNKLL--PEDIHVFKIMRVNNSFHAKNGVDAR 184

Query: 111 SYLYRIITR--QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASS 167
           SY+Y   T   +   A  K            E +     + +G H F  + S       S
Sbjct: 185 SYVYVCPTSAFEPKFATNKLVEPFKFTEETRETLNRVLSYYLGNHRFHNYTSRKESNDVS 244

Query: 168 PIRTIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSL 205
             R I  F+ +         ++ I V+  SF+  QIR  +G L
Sbjct: 245 VFRKIIKFECSVPFILEGVEMVSINVIGESFMLHQIRKMIGCL 287


>gi|225718836|gb|ACO15264.1| tRNA pseudouridine synthase 3 [Caligus clemensi]
          Length = 423

 Score = 51.2 bits (121), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 63/267 (23%), Positives = 100/267 (37%), Gaps = 62/267 (23%)

Query: 15  YFGWQ------RQKNGSSIQG----SIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           YFGW       ++ +  +I+G    ++ +   + + E    H  GRTD GV A RQV   
Sbjct: 68  YFGWSYHGFAVQEDSPMTIEGHLFNALSRTCLIRSRETSNYHRCGRTDKGVSAFRQVVSI 127

Query: 65  DLVREWVP-----------------------VILCKALNAYLKISDTISILNLSIVDKQF 101
           +L    +                        +  CK LN+ L   D   I    + ++ F
Sbjct: 128 ELRSNLLEGPGVFDYPECRAHSRPNPTTNEEIDYCKILNSNLP-PDIQVIAWAPLTNRDF 186

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARF    R Y Y       PL   +          D   ++ A   L+G HDF  F  +
Sbjct: 187 SARFDCKIREYKYIF-----PLGAAR----------DLSRIQEAGAKLLGSHDFRNFCKM 231

Query: 162 HCQAS--SPIRTIDHFDVNSFGN-------LIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
                  + IR +    V+   +       L+E+++V  +FL  QIR  V  L  +G G 
Sbjct: 232 DVSNGVLTYIRRMLEVSVSPLESSSTDSYSLVELKIVGNAFLWHQIRCIVTVLFHIGQGL 291

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGL 239
              + +++ L  +      P  P  GL
Sbjct: 292 EEPSLIDELLDVEKH----PRRPQYGL 314


>gi|328770686|gb|EGF80727.1| hypothetical protein BATDEDRAFT_3084 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 289

 Score = 51.2 bits (121), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 89/231 (38%), Gaps = 46/231 (19%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHALRQ 60
           I Y G  Y+G+    N S  +++  I KA+ +       G        GRTD GV A  Q
Sbjct: 30  ISYIGDKYYGFASASNDSVPTVESYIFKALEVARLIPSDGGACAWSRCGRTDKGVSAFDQ 89

Query: 61  VAHFDLVR----------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           V     VR          +W  +     LN  L   D I +L  S VD  F ARF+   R
Sbjct: 90  VVSV-WVRTARPGDRDTLDWDQLPYLNILNRLL--PDDIRVLAWSPVDPIFDARFTCSHR 146

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-- 168
            Y Y                +     LD   MR AA   VG HD      I    ++   
Sbjct: 147 KYNY----------------FFDGAGLDLIAMRDAASRFVGTHDCRHICKIDPTKAAREG 190

Query: 169 --IRTIDHFD-----VNSFGNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDG 211
             +RTI   D     V+   +   + VV  R+FL  Q+R+ +  L L+G G
Sbjct: 191 FFVRTIMECDIVPVPVDGAPDRFHVLVVKGRAFLWHQVRNMMALLFLIGRG 241


>gi|167524395|ref|XP_001746533.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163774803|gb|EDQ88429.1| predicted protein [Monosiga brevicollis MX1]
          Length = 415

 Score = 51.2 bits (121), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 66/262 (25%), Positives = 106/262 (40%), Gaps = 32/262 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI----------VVVHGAGRTD 52
           +Y +++ + G+ Y G QR     +I+ ++ +A+ LVTG I          +      RTD
Sbjct: 32  KYALLMGFQGTSYAGMQRNIGFETIESTLLRAL-LVTGCIDKNNYETPQSMHFQRCARTD 90

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA RQV    ++     V     LNA  K+ D I I       K F+ + +   R Y
Sbjct: 91  KGVHAARQVVAMRMILTENTV---DELNA--KLPDDIRIFGAFRTTKGFNPKNACTGRRY 145

Query: 113 LYRIITRQAPLALEKGRAWLIPK-SLDCENM---RIAAQHLVGRHDFTTFRSIHCQASSP 168
            Y + T     AL       +P+  +D   +   R   +  +G H F  F +    +   
Sbjct: 146 EYLLPT----YALMPKEKVPVPEYRVDEPKLTWFRETLKRYIGTHKFHNFTAGKSASDDS 201

Query: 169 IRT-IDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
            R  I  F V+          + I+V  +SF+  QIR  +G    +  G      +++  
Sbjct: 202 CRRYITDFTVSEPFEREGIEWVRIQVKGQSFILHQIRKMIGLAVAIVRGHVKDDYMDRCF 261

Query: 223 QAQDRKECGPLAPPEGLYFDSV 244
              D +   P  P  GL+ D V
Sbjct: 262 --SDERVDVPKIPGLGLFLDCV 281


>gi|297723909|ref|NP_001174318.1| Os05g0279300 [Oryza sativa Japonica Group]
 gi|255676206|dbj|BAH93046.1| Os05g0279300 [Oryza sativa Japonica Group]
          Length = 133

 Score = 51.2 bits (121), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 41/65 (63%), Gaps = 5/65 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           ++ M+I Y+G+ + GWQ Q +  +IQ SIE A+  +T     E+ +V GAGRTD+GVHA 
Sbjct: 62  KWRMVIAYDGTKFKGWQYQPSPPTIQCSIENALTRITKLDRKELCLV-GAGRTDTGVHAW 120

Query: 59  RQVAH 63
               H
Sbjct: 121 GGAFH 125


>gi|48477852|ref|YP_023558.1| tRNA pseudouridine synthase A [Picrophilus torridus DSM 9790]
 gi|62901313|sp|Q6L0Y7|TRUA_PICTO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|48430500|gb|AAT43365.1| tRNA pseudouridine synthase A [Picrophilus torridus DSM 9790]
          Length = 251

 Score = 50.8 bits (120), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 50/197 (25%), Positives = 85/197 (43%), Gaps = 33/197 (16%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---VHGAGRTDSGVHALRQVAHFDL 66
           Y+G+ + G+ R    S+ + S+E  I  V  E  +   +  A RTD  V A   V  F +
Sbjct: 15  YDGTKFEGFDR----SNSKNSVESVIINVLSEYNITKNIESAARTDKNVSAAGNV--FYI 68

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
             E  P                + ILN +I +  FH+ +  +  SY   I  R   + + 
Sbjct: 69  KTEERP-------------EKILGILNGNIKNMFFHSYY--LSNSY---INPRYNSMKIY 110

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           K   ++IP  +D   ++      +G HDFT F        +P+RTI+  +   + +   +
Sbjct: 111 K---YIIPYRIDSR-LKNNIARFLGTHDFTNFSK--NDYRNPVRTINKIEFEEYNDFTVV 164

Query: 187 RVVARSFLHTQIRSFVG 203
               +SF+  Q+RS +G
Sbjct: 165 NFYGKSFVWHQLRSIIG 181


>gi|71985046|ref|NP_496062.3| Temporarily Assigned Gene name family member (tag-124)
           [Caenorhabditis elegans]
 gi|1353139|sp|Q09524|TG124_CAEEL RecName: Full=Probable tRNA pseudouridine synthase tag-124;
           AltName: Full=tRNA pseudouridylate synthase; AltName:
           Full=tRNA-uridine isomerase
 gi|3875428|emb|CAA87378.1| C. elegans protein E02H1.3, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 402

 Score = 50.8 bits (120), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 56/198 (28%), Positives = 75/198 (37%), Gaps = 56/198 (28%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVP-------------------------VILCKALNAYL 83
           GRTD GV A +Q A   +VR   P                         +   K LN  L
Sbjct: 82  GRTDKGVSAFKQTAAM-VVRSLCPGDSGVFWSDSTQEHQKVDYKASGEELPYVKMLNGVL 140

Query: 84  KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
               TI +   + V + F+ARF   RR+Y Y     +A L LEK              MR
Sbjct: 141 --PKTIRVFAWAPVAQTFNARFDCNRRTYKYSFA--KADLNLEK--------------MR 182

Query: 144 IAAQHLVGRHDFTTFRSIHCQAS----SPIRTIDHFDV--------NSFGNLIEIRVVAR 191
             A+ LVG HDF+ F  I         S +R +    V        N   +++E+ V   
Sbjct: 183 QGAELLVGEHDFSNFCQIDMNEKRLLQSYVRKVYEVKVEQVSTHPENDMYSMVELTVSGS 242

Query: 192 SFLHTQIRSFVGSLKLVG 209
            FL   IR  V  L+ +G
Sbjct: 243 GFLWHMIRYIVTILQEIG 260


>gi|118782859|ref|XP_312543.3| AGAP002409-PA [Anopheles gambiae str. PEST]
 gi|116129767|gb|EAA08062.3| AGAP002409-PA [Anopheles gambiae str. PEST]
          Length = 451

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 70/268 (26%), Positives = 106/268 (39%), Gaps = 44/268 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDSGVH 56
           +++ Y+G  YFG QR     +I+  + +A+              + +    A RTD GV 
Sbjct: 115 ILLGYSGVNYFGMQRNPGTKTIEEDLLRAMQKREWINDEGFRQPQQIQFQRAARTDKGVS 174

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QV    L       +  +ALN+ L   + I +  +  V K F+++ +   R+Y Y +
Sbjct: 175 AAMQVVSIKLPDN----LDIEALNSEL--PEDIRVYAVKRVTKGFNSKTNCDARTYTYTL 228

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRS-IHCQA 165
            T       EK         +D +  R+ A+ L          VG  +F  F S      
Sbjct: 229 PTIAFAPNEEK---------VDIQTYRLPAERLARVNEVLALYVGTKNFHNFTSRKEFLD 279

Query: 166 SSPIRTIDHFDVN-------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            S  R I  F+ +       S      I++  +SF+  QIR  VG    V  G   S  +
Sbjct: 280 PSVKRFIMSFECDPPFLPEGSTAEFATIKIKGQSFMLHQIRKMVGLTIAVVRGLAESDII 339

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
           EKA   QDR    P AP  GL    + Y
Sbjct: 340 EKAF-GQDRYGI-PTAPGLGLVLSRIHY 365


>gi|297846396|ref|XP_002891079.1| hypothetical protein ARALYDRAFT_473569 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297336921|gb|EFH67338.1| hypothetical protein ARALYDRAFT_473569 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 443

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 95/242 (39%), Gaps = 59/242 (24%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVH 56
           + I Y G  ++G+  +   + ++ SIE  +F       ++ G          GRTD GV 
Sbjct: 94  LKIMYFGKRFYGFSAE---AQMEPSIESEVFKALERTRLLVGDKKDSCYSRCGRTDKGVS 150

Query: 57  ALRQV-AHFDLVREWVPVILCKA-LNA---------YLKI-----SDTISILNLSIVDKQ 100
           +  QV A F   R   P    KA +N          Y+++      D I ++  S     
Sbjct: 151 STGQVIALFLRSRLKSPPGDSKAQVNGKTGERPEYDYVRVLNRALPDDIRVIGWSPAPVD 210

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-- 158
           FHARFS   R Y Y                +   ++L+   M IA +  +G HDF  F  
Sbjct: 211 FHARFSCYAREYKY----------------FFWRQNLNLSAMDIAGKKFIGEHDFRNFCK 254

Query: 159 ---RSIHCQASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVG 209
               ++HC      R +  F+V+   N      L    +   +FL  QIR  V  L ++G
Sbjct: 255 MDVANVHCYT----RRVTFFEVSPCQNSHEGDQLCTFTMRGSAFLWHQIRCMVAVLFMIG 310

Query: 210 DG 211
            G
Sbjct: 311 QG 312


>gi|307212020|gb|EFN87913.1| tRNA pseudouridine synthase 3 [Harpegnathos saltator]
          Length = 368

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 92/230 (40%), Gaps = 47/230 (20%)

Query: 10  YNGSGYFGWQRQKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           Y G  Y G+  Q++ ++     +  ++ K+  + + E    H  GRTD GV +  QV   
Sbjct: 25  YLGWNYDGFTVQEDSNATIEHHLFAALTKSCCIESRETSNYHRCGRTDKGVSSFCQVISL 84

Query: 65  DLVREWVP---------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           D+  +  P         +  CK LN  L  +  I  +    +   F ARF    R Y Y 
Sbjct: 85  DIRSKLEPEQQSNLSKELPYCKILNKLLPTN--IRCIAWCPISSDFSARFDCKYRKYKY- 141

Query: 116 IITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDF------------TTFRSIH 162
                             P+ +LD + M  A ++++G  DF            T F+   
Sbjct: 142 ----------------FFPRGNLDIDAMDKAVKYVIGEFDFRNICKMDVANGVTNFKRKV 185

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
             A   +      D ++  ++ E+ + +++FL  QIR  +G L LVG  +
Sbjct: 186 IDAKISMNN-QAVDKSTGYDICELEITSQAFLWHQIRCLMGILLLVGKKR 234


>gi|125811944|ref|XP_001362058.1| GA15853 [Drosophila pseudoobscura pseudoobscura]
 gi|54637235|gb|EAL26638.1| GA15853 [Drosophila pseudoobscura pseudoobscura]
          Length = 497

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 85/230 (36%), Gaps = 55/230 (23%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 110 YFGWDYQ--GFACQEDSNDTIESHLFRALTRTCLIESRATSNYHRCGRTDKEVSAFCQVI 167

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  +  P            +  C  LN  L   +   +  + +    + ARF    R
Sbjct: 168 SIDLRSKHTPDTQLEPASLSSEIDYCGLLNRVLP-KNIQCVAWMPLRSPVYSARFDCTSR 226

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           SY Y                   PK  LD E MR A + LVG  DF  F    +H   + 
Sbjct: 227 SYRY-----------------YFPKGDLDIEAMREACKLLVGHSDFRNFCKMDVHNGVTK 269

Query: 168 PIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
            IR +    V        NS  ++  + + A +FL  QIR  +  L LVG
Sbjct: 270 FIRNLQAARVEPCVEMLNNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVG 319


>gi|157822927|ref|NP_001102169.1| tRNA pseudouridine synthase-like 1 [Rattus norvegicus]
 gi|149024843|gb|EDL81340.1| similar to pseudouridylate synthase-like 1, isoform CRA_a [Rattus
           norvegicus]
          Length = 127

 Score = 50.4 bits (119), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 54/120 (45%), Gaps = 15/120 (12%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-------------NLIEIRV 188
           M+ AAQHL+G HDF+ F+S        +RT+    V+                    +  
Sbjct: 1   MQEAAQHLLGTHDFSAFQSAGSPVPHAVRTLRRVSVSPGPASLFVLPQESRRLQFWTLEF 60

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            ++SFL+ Q+R     L  VG G    T ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 61  ESQSFLYRQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAPAHGLFLKSVLY 120


>gi|50309181|ref|XP_454596.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49643731|emb|CAG99683.1| KLLA0E14345p [Kluyveromyces lactis]
          Length = 444

 Score = 50.4 bits (119), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 87/229 (37%), Gaps = 50/229 (21%)

Query: 14  GYFGWQRQKNGSSIQG------SIEKAIFLVTGEIVVVHG----------AGRTDSGVHA 57
            Y GW    NG +IQ       ++E  I     +  +V             GRTD GV A
Sbjct: 103 AYLGWNY--NGLAIQKDATPLPTVEGTILETMNKCKLVPSMVPQEYKFSRCGRTDRGVSA 160

Query: 58  LRQV------------AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           + QV               D   +   +     LN  L     +S + L    K F ARF
Sbjct: 161 MNQVISLRVRSNLTAEEQLDPSYDDKEIQYVNILNQILPEDIRVSAVCLR-PPKGFDARF 219

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-- 163
           S   R Y Y   +                + LD E M++AA+H  G HDF  F  +    
Sbjct: 220 SCKSRHYKYLFSS----------------EGLDLERMQLAAKHYEGEHDFRNFCKLDGSK 263

Query: 164 QASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           Q ++  RTI   ++     ++    +V  +FL  Q+R  V +L LVG G
Sbjct: 264 QITNYKRTIKSSNIMHVSEDMYCFDLVGSAFLWHQVRCMVANLFLVGQG 312


>gi|149024844|gb|EDL81341.1| similar to pseudouridylate synthase-like 1, isoform CRA_b [Rattus
           norvegicus]
          Length = 127

 Score = 50.4 bits (119), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 55/120 (45%), Gaps = 15/120 (12%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI-------------EIRV 188
           M+ AAQHL+G HDF+ F+S        +RT+    V+     +              +  
Sbjct: 1   MQEAAQHLLGTHDFSAFQSAGSPVPHAVRTLRRVSVSPGPASLFVLPQESRRLQFWTLEF 60

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            ++SFL+ Q+R     L  VG G    T ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 61  ESQSFLYRQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAPAHGLFLKSVLY 120


>gi|195171697|ref|XP_002026640.1| GL11833 [Drosophila persimilis]
 gi|194111566|gb|EDW33609.1| GL11833 [Drosophila persimilis]
          Length = 421

 Score = 50.4 bits (119), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 85/230 (36%), Gaps = 55/230 (23%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 110 YFGWDYQ--GFACQEDSNDTIESHLFRALTRTCLIESRATSNYHRCGRTDKEVSAFCQVI 167

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  +  P            +  C  LN  L   +   +  + +    + ARF    R
Sbjct: 168 SIDLRSKHTPDTQLEPASLSSEIDYCGLLNRVLP-KNIQCVAWMPLRSPVYSARFDCTSR 226

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           SY Y                   PK  LD E MR A + LVG  DF  F    +H   + 
Sbjct: 227 SYRY-----------------YFPKGDLDIEAMREACKLLVGHSDFRNFCKMDVHNGVTK 269

Query: 168 PIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
            IR +    V        NS  ++  + + A +FL  QIR  +  L LVG
Sbjct: 270 FIRNLQAARVEPCVEMLNNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVG 319


>gi|170583043|ref|XP_001896407.1| tRNA pseudouridine synthase family protein [Brugia malayi]
 gi|158596407|gb|EDP34752.1| tRNA pseudouridine synthase family protein [Brugia malayi]
          Length = 234

 Score = 50.4 bits (119), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/198 (26%), Positives = 84/198 (42%), Gaps = 53/198 (26%)

Query: 15  YFGWQ------RQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           YFGW+      +++   +++  + KA+     +   E    + +GRTD GV A +QVA  
Sbjct: 38  YFGWEYNGLVEQREIARTVEEEMRKALIKTKLVENWENCSWNRSGRTDKGVSAFKQVASV 97

Query: 65  DLVRE---------WVPVILCKALNA------YLKISDT-----ISILNLSIVDKQFHAR 104
            +VR          W  V    +  A      Y+K+ ++     I +L  + V + F AR
Sbjct: 98  -IVRSNEPEGEGVFWPNVAHASSETAMKGELQYVKMLNSTLPTNIRVLAWAPVPRNFSAR 156

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHC 163
           ++  +R+Y Y                   P++  + E MR A Q LVG HDF  F  I  
Sbjct: 157 YNCTQRTYTY-----------------AFPRTNFNIEAMRQACQFLVGEHDFRNFCRIDM 199

Query: 164 QAS----SPIRTIDHFDV 177
                  + IRTI + D+
Sbjct: 200 NKKRVEMNYIRTITYADI 217


>gi|219120809|ref|XP_002185636.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582485|gb|ACI65106.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 293

 Score = 50.4 bits (119), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 68/289 (23%), Positives = 113/289 (39%), Gaps = 52/289 (17%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA---------GRTDSGVHA 57
           ++ Y G+ Y G+Q      + Q   E A+      +    G+         GRTD GVHA
Sbjct: 2   LLAYVGTNYGGFQINDGQRTPQAEFELAMLRTRLLLPCNFGSPHKYSWSTSGRTDKGVHA 61

Query: 58  LRQV--AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY- 114
             QV  A  +L+ +     +   +N  L   D + +L++    + F A+    R  Y Y 
Sbjct: 62  CAQVVSAKVELLPDQTMAEVRDEMNTVL--PDDVRVLDVVRTTRNFCAKTQRDRVRYQYM 119

Query: 115 ------------RIITRQAPLALEKGRA---WLIPKSLDC-----ENMRIAAQHLV---- 150
                       R++ +       +G++    L+P+ L       ++ R    H+     
Sbjct: 120 IPSFVFADADTLRVLFKDVVGHSNRGQSKAELLLPEELKSIQSALKDFRANPMHIAKLQE 179

Query: 151 ------GRHDFTTF-RSIHCQASSPIRTIDHFDVNS---FGNLIE---IRVVARSFLHTQ 197
                 G H F  F R +    +   R I+ F V     F N +E    +V+ +SFL  Q
Sbjct: 180 ALQVYEGTHAFHNFSRGVKANEARAARYIERFHVEEPIVFPNGVEWIPTQVLGQSFLLNQ 239

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           IR  V     V  G    T++ +AL+ Q       +AP +GL+ +   Y
Sbjct: 240 IRKMVCMAMDVARGVVPLTNVSRALERQSDVRIN-VAPAQGLFLEMSYY 287


>gi|66812718|ref|XP_640538.1| tRNA pseudouridine synthase [Dictyostelium discoideum AX4]
 gi|60468568|gb|EAL66571.1| tRNA pseudouridine synthase [Dictyostelium discoideum AX4]
          Length = 504

 Score = 50.1 bits (118), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 76/319 (23%), Positives = 119/319 (37%), Gaps = 95/319 (29%)

Query: 5   CMIIEYNGSGYF--GWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVH--GAGRTDS 53
            M+  Y+G+GY+  G+Q      SI+  IEK +F          GE+  +    + RTD 
Sbjct: 92  AMVFGYDGTGYYGLGYQVDIKYPSIENLIEKVLFRCGHILPSNVGELKRLKWSHSSRTDK 151

Query: 54  GVHALRQVAHFDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GVH+L  V    LV      +  +       +N YL  S  I + +   V + F AR   
Sbjct: 152 GVHSLATVISCFLVVDDNTFKNDINQTFIDTINNYLPSS--IRLFSACKVSRSFQARKKG 209

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG---RHDFTTFRSIHC- 163
           I RSY Y + +            +L   ++  + M    Q+ +G    H+FT+ R+ +  
Sbjct: 210 IERSYNYMVPS-----------EYL--NNIKIDEMNKILQNFIGINSYHNFTSKRNTYLS 256

Query: 164 ------------------------------------------------QASSPIRTIDHF 175
                                                             S+ IR I  F
Sbjct: 257 NNNNKNHEKDEKDEEDGDEEEEEDDEVEVENSNNNNSNYRLNEKLLFRNNSTNIRNIKSF 316

Query: 176 DVNSFGNLIEIR--------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            V +   +IEI+        ++  SF+  QIR  VG    +  G  T   LE +L++   
Sbjct: 317 YVEN--EIIEIKGKGWYKFVIIGESFILYQIRRMVGFFLSIVKGYSTVEALELSLKSP-F 373

Query: 228 KECGPLAPPEGLYFDSVEY 246
             C P APP  LY  +V++
Sbjct: 374 SICVPTAPPFPLYLFNVKF 392


>gi|66361768|ref|XP_627406.1| Deg1p-like type II pseudouridylate synthase TruA [Cryptosporidium
           parvum Iowa II]
 gi|46228868|gb|EAK89738.1| Deg1p-like type II pseudouridylate synthase TruA [Cryptosporidium
           parvum Iowa II]
          Length = 283

 Score = 50.1 bits (118), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 96/239 (40%), Gaps = 34/239 (14%)

Query: 17  GWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSGVHALRQVAHFDL--- 66
            +Q+     +I+G I KA+  +       + ++V     GRTD GVH+       +L   
Sbjct: 8   AFQKDDKIPTIEGEIYKALLQLRLIKDIDSCDLV---RCGRTDRGVHSAGNYISVNLRTR 64

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            +   P    + LN  L     I ++    V   F ARF    R Y Y       PL  E
Sbjct: 65  AKNLEPYNYMEMLNGVLPWD--IRVIGYCEVRPDFSARFDCEYRLYKYFF-----PLNHE 117

Query: 127 KGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHC---QASSPIRTIDHFDVNSFG 181
           + +    PK        M +AA+  +G HD+  F  +     +  + IRTI  FD+N   
Sbjct: 118 RTKISKFPKIPPEQVPLMNVAAKQFLGTHDYRRFCKMDLKNRKNQTYIRTIYEFDINFVD 177

Query: 182 NLIEIRVVA------RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              E R  A       +FL  Q+R  +G L  +G  K+    + + L   ++K    L+
Sbjct: 178 ---ENRTFAVATIKGSAFLWHQVRLMMGILFEIGQQKFNPEVITQMLTDVEQKNIAELS 233


>gi|241713555|ref|XP_002412103.1| pseudouridylate synthase, putative [Ixodes scapularis]
 gi|215505180|gb|EEC14674.1| pseudouridylate synthase, putative [Ixodes scapularis]
          Length = 398

 Score = 50.1 bits (118), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 65/270 (24%), Positives = 102/270 (37%), Gaps = 67/270 (24%)

Query: 15  YFGWQ------RQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           Y GW       ++   ++++ ++ +A+     L   E    H  GRTD GV A  QV   
Sbjct: 10  YLGWNYDGYVVQEDTANTVEAALFQALQRTRLLDLRETSNYHRCGRTDKGVSAFSQVISI 69

Query: 65  DL-----------------VREWVPVILCKALNAYLKISD-----TISILNLSIVDKQFH 102
           DL                 +   + V     L+ Y+KI +      I +L  +  +  F 
Sbjct: 70  DLRSNLTEGPEGTAPSARSIHSVISVARSTELD-YVKILNGVLPPDIRVLAWAPAEPSFS 128

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSI 161
           ARF    R+Y Y                  +PK +L  + MR AA+ LVG HDF     +
Sbjct: 129 ARFDCQARTYRY-----------------FLPKGNLVVQRMREAAKLLVGEHDFRNLCKM 171

Query: 162 HCQASSP-----IRTIDHFDVNSFGN-------LIEIRVVARSFLHTQIRSFVGSLKLVG 209
                       I + + +D    G+       ++ + +V ++FL  Q+R  V  L LVG
Sbjct: 172 DVGNGVTRYVRRILSTELYDGEPEGDGGSSGYQMLCLEIVGQAFLWHQVRCIVAILLLVG 231

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G      + K L      E  P  P  G+
Sbjct: 232 QGLEEPEVVSKLLDV----EAHPCKPQYGM 257


>gi|303245000|ref|ZP_07331323.1| tRNA pseudouridine synthase A [Methanothermococcus okinawensis IH1]
 gi|302484652|gb|EFL47593.1| tRNA pseudouridine synthase A [Methanothermococcus okinawensis IH1]
          Length = 263

 Score = 50.1 bits (118), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 103/244 (42%), Gaps = 36/244 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y + + YN   Y G+Q Q +  ++   I  A+    +L   +I+     GRTD GV A+ 
Sbjct: 2   YILKVAYNKHHY-GFQTQPHKETVCDKIMDALKECNYLANDKIIFC--GGRTDKGVSAIG 58

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
                +L +E  P++     + Y K+ +  I I     +D     ++        YR I 
Sbjct: 59  NFIVVELSQE--PILS----HIYSKLKNKGIWIFGYKKIDTIPEVKYRH------YRYIL 106

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDV 177
              P   E     +I           A++ L+G H F    +    +  SPIRTI  +D+
Sbjct: 107 PIIPHIDEYNIDLMIE----------ASKKLIGEHSFHNLSKKDRTKEKSPIRTI--YDI 154

Query: 178 NSFGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
               NL  I I V+ +SFL   +R  + +L  VG        +++ L  ++ K   P AP
Sbjct: 155 KIEKNLYYITIDVIGKSFLWNMVRKIITALSEVGKENKPVGWIDELL-CENHKGGVPPAP 213

Query: 236 PEGL 239
            EGL
Sbjct: 214 AEGL 217


>gi|73994983|ref|XP_852307.1| PREDICTED: similar to tRNA pseudouridine synthase A (tRNA-uridine
           isomerase I) (tRNA pseudouridylate synthase I) [Canis
           familiaris]
          Length = 409

 Score = 50.1 bits (118), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 73/273 (26%), Positives = 112/273 (41%), Gaps = 46/273 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 62  KIVLLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVQSGCIPENHGEDMRKMSFQRCA 120

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     
Sbjct: 121 RTDKGVSAAGQVVSLKV---WLIDDILEKINSHL--PPHIRILGLKRVTGGFNSKNKCDA 175

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A            +  E+ R++A+ L           G H+F  F 
Sbjct: 176 RTYFYMLPT----FAFAHKD-----HDVQDESYRLSAETLQRVNGLLACYKGTHNFHNFT 226

Query: 160 SIHC--QASSPIRTIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S     +AS+    +D F    F         I+V  +SF+  QIR  VG L  +  G  
Sbjct: 227 SQKGPQEASARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLLVAIVKGYA 286

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             + LE++    D K   P AP  GL  + V +
Sbjct: 287 PESVLERSW--GDAKVDVPKAPGLGLVLERVHF 317


>gi|134114618|ref|XP_774017.1| hypothetical protein CNBH0640 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50256647|gb|EAL19370.1| hypothetical protein CNBH0640 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 514

 Score = 50.1 bits (118), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 61/145 (42%), Gaps = 28/145 (19%)

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
           K LN+ L  S  I IL  S +   F +RFS   R Y Y   TR  P + E          
Sbjct: 214 KLLNSVLPPS--IRILAWSPIPASFDSRFSCTYRHYRYAFHTRPTPTSPE---------- 261

Query: 137 LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF-----------DVNSFGN-LI 184
           LD E MR  AQ L+G HD+  F    C+     +  +H            +    G+ ++
Sbjct: 262 LDLELMRQGAQLLLGEHDYRNF----CKLDGSKQIENHTRGVLKAWFEGGESQGVGDGMM 317

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVG 209
              ++  +FL  Q+R  +  L LVG
Sbjct: 318 VFNLIGTAFLWHQVRHIIAVLFLVG 342


>gi|221113814|ref|XP_002153998.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 267

 Score = 49.7 bits (117), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 49/184 (26%), Positives = 71/184 (38%), Gaps = 41/184 (22%)

Query: 15  YFGWQRQ--KNGSSIQGSIEKAIF-------LVTGEIVVVHG-AGRTDSGVHALRQVAHF 64
           Y GW  Q   N  +   +IE AIF       L+   ++  +   GRTD GV A  QV   
Sbjct: 87  YLGWDYQGLANQETTNNTIEDAIFNAMIKAKLIEDRVLCKYSRCGRTDKGVSAFGQVIAL 146

Query: 65  DL-----------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           ++            RE +  +  + LN  L     I +L  + V + F ARF    R Y 
Sbjct: 147 NVRSNTLVSEEEDTREEISYV--RLLNKIL--PPEIRMLAFARVPQDFDARFDCDTRMYK 202

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y                +   K +D + M  AAQ  VG  DF  F        S ++++D
Sbjct: 203 Y----------------FFPAKRMDIKLMDAAAQKFVGEKDFRNFCKFIILTQSWLKSVD 246

Query: 174 HFDV 177
            F +
Sbjct: 247 LFKI 250


>gi|149237835|ref|XP_001524794.1| tRNA pseudouridine synthase 3 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146451391|gb|EDK45647.1| tRNA pseudouridine synthase 3 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 491

 Score = 49.7 bits (117), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 63/250 (25%), Positives = 96/250 (38%), Gaps = 47/250 (18%)

Query: 14  GYFGWQRQ----KNGSSIQGSIEKAIFLVTGEIVVVH---------GAGRTDSGVHALRQ 60
            Y GW       +N  +   ++E+ I     ++ ++            GRTD GV A+ Q
Sbjct: 136 AYLGWNYNGLAFQNDPTPLPTVEEIILKALAKVKLIREPIEEVEYSKCGRTDKGVSAMNQ 195

Query: 61  VAHFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           V    L     P            V     +NA L     +  + L   +  F ARFS  
Sbjct: 196 VISIKLRSNLTPQEQQDPAFDAKEVDYFTVINANLPADIKVHAICLRPPE-NFDARFSCK 254

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
            R Y Y  + R+               +LD + M  AA++  G HDF  F  +    Q +
Sbjct: 255 ERHYRY--LFRKT-------------STLDIDLMAQAAEYYEGLHDFRNFCKLDGSKQLT 299

Query: 167 SPIRTIDH---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           S +R I       ++S GNL    ++  +FL  Q+R  V  L LVG  K  S ++ K L 
Sbjct: 300 SFVRDIRRSKIIPLDSDGNLYCFDLIGNAFLWHQVRCMVAILFLVGQ-KLESPEIVKDLM 358

Query: 224 AQDRKECGPL 233
              +    P+
Sbjct: 359 DVTKFPTKPM 368


>gi|213513998|ref|NP_001134221.1| tRNA pseudouridine synthase A [Salmo salar]
 gi|209731596|gb|ACI66667.1| tRNA pseudouridine synthase A [Salmo salar]
          Length = 392

 Score = 49.7 bits (117), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 70/271 (25%), Positives = 111/271 (40%), Gaps = 41/271 (15%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY+G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 51  KVVLLLAYSGKGYYGMQRNA-GSSQFKTIEDELVTALIKSGCIPDNHGDDMKKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    L   W+   + + +N+ L     I +L L  V   F+++ S   
Sbjct: 110 RTDKGVSAAGQVVSLKL---WMIEDVMEKINSNL--PPQIRVLGLKRVTGGFNSKNSCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAW--------LIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
           R+Y Y + T    +A      +        L P++L   N    +    G H+F  F S 
Sbjct: 165 RTYSYMLPT----VAFSPKDYYTKNYAAFRLEPETLQRVNQLFGS--YKGTHNFHNFTSQ 218

Query: 162 HCQ-ASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
                 S  R I         V       EI V  +SF+  QIR  +G +  V  G ++ 
Sbjct: 219 KAAWDPSARRYITEMSCGEPFVRGGAEFAEITVRGQSFMMHQIRKMIGLVIAVVKG-YSG 277

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            ++ K    +++ +  P AP  GL  + V +
Sbjct: 278 DEVLKRSWGEEKVDV-PKAPGLGLVLEKVHF 307


>gi|156088547|ref|XP_001611680.1| tRNA pseudouridine synthase A family protein [Babesia bovis]
 gi|154798934|gb|EDO08112.1| tRNA pseudouridine synthase A family protein [Babesia bovis]
          Length = 248

 Score = 49.7 bits (117), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 95/230 (41%), Gaps = 40/230 (17%)

Query: 6   MIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGA----GRTDSGVHALRQ 60
           M   Y G+GY G   Q +  ++++G + +A+ L      V++      GRTD  VHAL  
Sbjct: 15  MDFSYIGTGYHGLAYQSDEPNTVEGHLFRALSLANVASDVLNNGYERCGRTDRDVHALHN 74

Query: 61  VAHF--DLVREWVP----------VILCKALNAYLK-----ISDTISILNLSIVDKQFHA 103
            A F  D      P          V  C  +N + K     +   I +  +  V   F +
Sbjct: 75  YASFFPDPCPPNSPCSTVSPDERGVGPCYRINTFTKAINKHLPRGIRVNWVKHVPDDFSS 134

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIH 162
           R +   R Y Y                +    S+D   ++ A +H +G+H+F  F ++ +
Sbjct: 135 RRNCTFRVYKY----------------FFQLGSMDLSLIQDACRHFLGQHNFNQFCKTDN 178

Query: 163 CQASSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDG 211
                   TI  F+V  +  L+ +  +  R+FL  Q+R  +G L  VG+G
Sbjct: 179 RNPKDSHGTIYSFEVERYNELLCVATICGRAFLWHQVRCMMGVLFKVGEG 228


>gi|281200681|gb|EFA74899.1| tRNA pseudouridylate synthase [Polysphondylium pallidum PN500]
          Length = 1052

 Score = 49.7 bits (117), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 42/156 (26%), Positives = 65/156 (41%), Gaps = 28/156 (17%)

Query: 89   ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
            I +L  S +   F+ARFS + R+Y Y                +  P +LD   M+ A + 
Sbjct: 891  IRVLGWSPIPFHFNARFSTLYRTYKY----------------FFDPSNLDLNLMKEAGKS 934

Query: 149  LVGRHDFTTFRSIHCQA-SSPIRTIDHFDVN-------SFGNLIEIRVVARSFLHTQIRS 200
             +G HDF+ F  I  ++  S  R I  FD+        S   +    +   +FL  QIR 
Sbjct: 935  YIGEHDFSNFCKIDLESVKSFTRVILSFDIQPVESGDFSTSGMYVATICGYAFLWHQIRC 994

Query: 201  FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             +  L L+G  K+ +T +   L        G + PP
Sbjct: 995  MMAMLFLIGQKKFPTTIIADLLDLSK----GIVKPP 1026


>gi|195026984|ref|XP_001986382.1| GH21331 [Drosophila grimshawi]
 gi|193902382|gb|EDW01249.1| GH21331 [Drosophila grimshawi]
          Length = 503

 Score = 49.7 bits (117), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 61/236 (25%), Positives = 91/236 (38%), Gaps = 61/236 (25%)

Query: 15  YFGWQRQKNGSSIQG----SIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 105 YFGWDYQ--GFACQEDSNETIEAFLFRALIRTCLIESRATSNYHRCGRTDKEVSAFCQVI 162

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILN------------LSIVDKQFHARFSAIRR 110
             DL  +  P +  ++ +   +I D  S+LN            + + +  + ARF  I R
Sbjct: 163 SIDLRSKHAPDVQLESDSLATEI-DYCSLLNRVLPKNIQCVSWMPLRNHVYSARFDCISR 221

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           +Y Y                   PK  LD E MR+A   +V   DF  F    +H   ++
Sbjct: 222 TYRY-----------------YFPKGDLDIEAMRMACDLIVCHGDFRNFCKMDVHNGVTN 264

Query: 168 PIRTID--------------HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
            +R +                 D+NS   +  + + A +FL  QIR  +  L LVG
Sbjct: 265 YMRNLQAARIQACEGTAVEVENDLNSGYTMYYLEIQANAFLWHQIRCIMAVLLLVG 320


>gi|134056983|emb|CAK44330.1| unnamed protein product [Aspergillus niger]
          Length = 517

 Score = 49.7 bits (117), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 56/182 (30%), Positives = 72/182 (39%), Gaps = 25/182 (13%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ-FHARFS 106
           AGRTD GV A  QV     VR  +P +    LN  L   + I +L       + F ARFS
Sbjct: 165 AGRTDRGVSAFGQVIGI-RVRNELPYV--SMLNKVL--PEDIRVLAWCPRPPEGFDARFS 219

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKS------------LDCENMRIAAQHLVGRHD 154
              R Y Y     Q   +   G +  +P+             LD E MR AA++  G HD
Sbjct: 220 CGERHYKYFFT--QPAFSPTPGASGFVPRDGTGKPPKLREGWLDIEAMRKAAKYFEGTHD 277

Query: 155 FTTFRSIHC--QASSPIRTIDHFDVNSFGNLIEIRVV---ARSFLHTQIRSFVGSLKLVG 209
           F  F  +    Q  S  R I            ++ V      +FL  Q+R  V  L LVG
Sbjct: 278 FRNFCKLDVTKQIESFYRDIFQSSAAPLPTAAQVYVFHLEGSAFLWHQVRHMVNVLFLVG 337

Query: 210 DG 211
            G
Sbjct: 338 QG 339


>gi|66805521|ref|XP_636482.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
 gi|60464862|gb|EAL62978.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
          Length = 491

 Score = 49.3 bits (116), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 44/146 (30%), Positives = 62/146 (42%), Gaps = 22/146 (15%)

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
           E +P I  K LN  L     I IL  + V   F+ARFS + R+Y Y              
Sbjct: 207 EELPYI--KMLNGVL--PPEIRILAWAPVPFHFNARFSTLSRTYKY-------------- 248

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN--LIEI 186
             +  P  LD   M+ A++  +G H++  F  I     S +R I  FD+    N  L   
Sbjct: 249 --FFNPNGLDLNLMKEASKLYLGEHNYINFCKIDVNVKSFMRVILQFDIEKVENSELYVA 306

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGK 212
            +   +FL  QIR  +  L L+G  K
Sbjct: 307 TIKGFAFLWHQIRCMMAVLFLIGQKK 332


>gi|150400022|ref|YP_001323789.1| tRNA pseudouridine synthase A [Methanococcus vannielii SB]
 gi|150012725|gb|ABR55177.1| tRNA pseudouridine synthase [Methanococcus vannielii SB]
          Length = 265

 Score = 49.3 bits (116), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 99/242 (40%), Gaps = 34/242 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           Y   I Y+G   F  Q  +N     I  ++ +  +L  GEI + +G GRTD GV AL   
Sbjct: 2   YIFKIAYDGRYSFQSQPHRNTVCDKITDTLLECGYLKEGEIPISYG-GRTDLGVSALGNY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             +++  + V   +   L+ +      I IL  + +                     ++ 
Sbjct: 61  IVYNITEKPVLSRIYSKLHKH-----GIWILGFNEL---------------------KEL 94

Query: 122 PLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
           P    +   +++P +  D E M+ A++ L+G H F    +    +  SPIRTI +  +  
Sbjct: 95  PDVKYRHYRYILPNTGQDIELMKKASEKLIGTHSFHNLSKRDKTKNRSPIRTIYNIKIAK 154

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD--LEKALQAQDRKECGPLAPPE 237
               I I +  +SFL   +R  V  L  VG  K+   +  ++  L    R    P A  E
Sbjct: 155 NEYFITIEIFGKSFLWNMVRKIVRLLSNVGLSKYKEFEKFIDDLLDRDVRMGVQP-ASAE 213

Query: 238 GL 239
           GL
Sbjct: 214 GL 215


>gi|281340805|gb|EFB16389.1| hypothetical protein PANDA_012338 [Ailuropoda melanoleuca]
          Length = 359

 Score = 49.3 bits (116), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 71/266 (26%), Positives = 113/266 (42%), Gaps = 30/266 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 29  KIVLLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVQSGCIPENHGEDMRKMSFQRCA 87

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     
Sbjct: 88  RTDKGVSAAGQVVSLKV---WLIDDILEKINSHL--PPHIRILGLKRVTGGFNSKNKCDA 142

Query: 110 RSYLYRIIT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR-HDFTTFRSIHCQA 165
           R+Y Y + T         ++  R  L  ++L   N  +A        H+FT+ +  H +A
Sbjct: 143 RTYFYMLPTFAFAHKDHDVQDERYRLSAETLRRVNGLLACYRGTHNFHNFTSQKGPH-EA 201

Query: 166 SSPIRTIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           S+    +D F    F         I+V  +SF+  QIR  VG +  V  G    + LE++
Sbjct: 202 SARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAVVKGYAPESVLERS 261

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
               + K   P AP  GL  + V + 
Sbjct: 262 W--GEAKVDVPKAPGLGLVLERVHFE 285


>gi|320163253|gb|EFW40152.1| tRNA-pseudouridine synthase [Capsaspora owczarzaki ATCC 30864]
          Length = 548

 Score = 49.3 bits (116), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 67/253 (26%), Positives = 98/253 (38%), Gaps = 74/253 (29%)

Query: 14  GYFGWQRQKNGSSIQGSIE----------KAIFLVTGEIVVVHG-AGRTDSGVHALRQVA 62
            Y GW+   NG +IQ  +E          K   L+       +   GRTD+GV A  QV 
Sbjct: 147 AYLGWK--YNGLAIQPDVETVEGHLISALKTCMLIPDLSWANYSRCGRTDAGVSAFGQVV 204

Query: 63  HFDL---VREWVPVIL------------CKALNAYL--------KISDTISILNLSIVDK 99
             D+   + E V VI              +A +A L        ++   I ++  + V  
Sbjct: 205 SLDVRTNLTEGVGVIQQESAIPFQKGRKTEATHAELEYVFKLNRQLPADIRVVAWTPVPL 264

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTF 158
            F ARFS + R Y Y                   PK+ ++ E M+ AAQ+ VG HD+  F
Sbjct: 265 AFDARFSCLYRKYKY-----------------FFPKNNMNIEAMQRAAQYFVGTHDYRNF 307

Query: 159 --RSIHCQASSPIRTIDHFDV--------NS----------FGNLIEIRVVARSFLHTQI 198
              +      S +R I  FDV        NS             + E+ V+  +FL+ Q+
Sbjct: 308 CKTNFDNGVKSFVRRILAFDVVKSTCLPINSATDATDLEGQAAEMYELNVLGFAFLYHQV 367

Query: 199 RSFVGSLKLVGDG 211
           R     L +VG G
Sbjct: 368 RCMTSILFMVGQG 380


>gi|156538138|ref|XP_001608257.1| PREDICTED: similar to pseudouridylate synthase [Nasonia
           vitripennis]
          Length = 437

 Score = 49.3 bits (116), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 70/285 (24%), Positives = 115/285 (40%), Gaps = 50/285 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGEI------VVVHGAGRTDSG 54
           Y M++ Y G  Y+G QR    ++I+  + KA+    L+T E       +    A RTD G
Sbjct: 74  YAMMLGYCGKNYYGMQRNPGFNTIEEELIKAMLKADLITSEAFETIQNINFQRAARTDKG 133

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A+RQV    L  +     + + L       + I +  +  V K F+++     R+Y Y
Sbjct: 134 VSAVRQVVSLKLPEDPSKDSINETL------PEDIRVFAIKRVTKGFNSKSQCDARTYSY 187

Query: 115 RIIT-RQAPLALE---------------------KGRA---WLIPKSLDCENMRIAAQHL 149
            + T   AP  LE                      G+    + +P+    E +    + L
Sbjct: 188 TMPTFALAPENLELFQEMSEYNDVEKRMEQLSTIDGKPFHEYRLPQERK-EKLTELLKVL 246

Query: 150 VGRHDFTTFRS----IHCQASSPIRTI---DHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
            G H+F  F S    +  +A   I +    + F VN+    I ++V  +SF+  QIR  V
Sbjct: 247 EGTHNFHNFTSKVLPLDPRAKRYIMSFIAEEPFLVNNM-EFITLKVKGQSFMLHQIRKMV 305

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +  V        + EK +  Q + +   +AP  GL  + V Y 
Sbjct: 306 AMVIGVIRNIVPREEFEKTVFEQAKYDIT-IAPSLGLMLNIVHYD 349


>gi|261350284|ref|ZP_05975701.1| tRNA pseudouridine synthase A [Methanobrevibacter smithii DSM 2374]
 gi|288861068|gb|EFC93366.1| tRNA pseudouridine synthase A [Methanobrevibacter smithii DSM 2374]
          Length = 288

 Score = 49.3 bits (116), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 63/254 (24%), Positives = 101/254 (39%), Gaps = 48/254 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +     K  ++   +      AGRTD+GVH
Sbjct: 1   MKRTALKIGYIGTNFHGFQRQPDLRTVEEELIYHLRKLGYIDDLKKSRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E    +    +N  L   D I IL  + V   F  R++ +R+   YR 
Sbjct: 61  SLGNVISFQSEKE----VRVNEINNSL--PDDIQILAKAPVRFGFKPRYAEMRQ---YRY 111

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +              L    LD   +   A+   G H+FT F     + ++  RTID   
Sbjct: 112 V--------------LFRSDLDLYKLNEVAEIFKGTHNFTNFTKRFQKTTT--RTIDDIK 155

Query: 177 V----------NSFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +            F NL      + + +   SFL   +R  +     V  GK +   LEK
Sbjct: 156 ITKANLNDYHKKEFPNLHDTLSPVFVDIYGESFLWNMVRKMMRVFVDVAIGKLS---LEK 212

Query: 221 ALQAQDRKECGPLA 234
             +  +  E  P A
Sbjct: 213 VEELLNPAENDPRA 226


>gi|18399149|ref|NP_564438.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|13430550|gb|AAK25897.1|AF360187_1 unknown protein [Arabidopsis thaliana]
 gi|14532756|gb|AAK64079.1| unknown protein [Arabidopsis thaliana]
 gi|332193556|gb|AEE31677.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 446

 Score = 49.3 bits (116), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 94/242 (38%), Gaps = 59/242 (24%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVH 56
           + I Y G  ++G+  +   + ++ SIE  +F       ++ G          GRTD GV 
Sbjct: 94  LKIMYFGKRFYGFSAE---AQMEPSIESEVFKALERTRLLVGDKKDSCYSRCGRTDKGVS 150

Query: 57  ALRQV-AHFDLVREWVPVILCKA-LNA---------YLKI-----SDTISILNLSIVDKQ 100
           +  QV A F   R   P    KA +N          Y+++      D I ++  S     
Sbjct: 151 STGQVIALFLRSRLKSPPGDSKAQVNGRTGERPEYDYVRVLNRALPDDIRVIGWSPAPID 210

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-- 158
           FHARFS   R Y Y                +   ++L+   M  A +  +G HDF  F  
Sbjct: 211 FHARFSCYAREYKY----------------FFWRQNLNLSAMDFAGKKFIGEHDFRNFCK 254

Query: 159 ---RSIHCQASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVG 209
               ++HC      R +  F+V+   N      L    +   +FL  QIR  V  L ++G
Sbjct: 255 MDVANVHCYT----RRVTFFEVSPCQNSHEGDQLCTFTMRGSAFLWHQIRCMVAVLFMIG 310

Query: 210 DG 211
            G
Sbjct: 311 QG 312


>gi|256371245|ref|YP_003109069.1| tRNA pseudouridine synthase [Acidimicrobium ferrooxidans DSM 10331]
 gi|256007829|gb|ACU53396.1| tRNA pseudouridine synthase [Acidimicrobium ferrooxidans DSM 10331]
          Length = 294

 Score = 49.3 bits (116), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 60/258 (23%), Positives = 97/258 (37%), Gaps = 21/258 (8%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++ Y+G  + G   Q    ++ G++  A+ LV      +  AGRTD+GVHA  Q+    
Sbjct: 9   LVVGYDGREFAGAAPQPGVRTVVGALRSALELVLQRPTSLAIAGRTDAGVHARAQLVSVP 68

Query: 66  L-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           L      R      LC  L         + + +  ++     AR  A  R YLYR+    
Sbjct: 69  LQPGERARLGDVERLCGRLGRL--AGRGLWVRSAGVLPGSVDARRVARWRHYLYRLDLGH 126

Query: 121 APLALEKGRAWLIPKSLDCENMRI-----AAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 +GR  L P +  C  + +     A   L G  D T             R +   
Sbjct: 127 GD---RRGRVILEPTAWACGPLELDVLAGALATLRGDLDATGLCRAGAAGGYRRRVLSTR 183

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +++ V+  SF H  +R  VG+   V  G+       + +   +R     +AP
Sbjct: 184 VWARARDRVDVSVIGVSFCHEFVRRAVGNAVAVAQGRLDGERWREGVDRGERALLATVAP 243

Query: 236 PEGLYF------DSVEYS 247
           P GL        D  E+S
Sbjct: 244 PWGLSLWRVGLEDGWEWS 261


>gi|123483294|ref|XP_001323995.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
 gi|121906870|gb|EAY11772.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
          Length = 346

 Score = 48.9 bits (115), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 64/269 (23%), Positives = 110/269 (40%), Gaps = 44/269 (16%)

Query: 5   CMII--EYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEI-----VVVHGAGRTDS 53
           C++I   Y G+GY G Q  +   +I   +    EK+  L  G       +  + A RTD+
Sbjct: 32  CVVIYFRYIGTGYHGLQYNEKVRTIDSDLFEGLEKSGILPEGSYKRRGKIAWNEASRTDA 91

Query: 54  GVHALRQVAHF------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GVHA  Q+  F      D+    +P ++ K L +      TI I++    +  F  +  A
Sbjct: 92  GVHACGQLICFKSYEICDMECSQIPELINKNLPS----DSTIKIMSCLCTNSPFPVKDFA 147

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-S 166
             R Y Y +     PL +        P  LD    +I     +G+H+F  + +   +   
Sbjct: 148 THRKYNYLL-----PLHVFSSTD---PDHLDYLRQKICPL-FIGQHNFHNYTNGTPKTYK 198

Query: 167 SPIRTIDHFDVNSFGNLIEIR--------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
              R I  F   +FG++  I         +   SF+  QIR  +  +      + T  ++
Sbjct: 199 GAQRFITDF---TFGDVFTINGEEYVLFYIRGISFMLNQIRKMISMVTAASFNQVTPEEV 255

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            ++L  +  +    L P +GL+ D +EY 
Sbjct: 256 SRSLTEETCR--IQLLPGDGLFLDQIEYE 282


>gi|301775629|ref|XP_002923235.1| PREDICTED: tRNA pseudouridine synthase A-like [Ailuropoda
           melanoleuca]
          Length = 426

 Score = 48.9 bits (115), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 71/265 (26%), Positives = 113/265 (42%), Gaps = 30/265 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 90  KIVLLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVQSGCIPENHGEDMRKMSFQRCA 148

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     
Sbjct: 149 RTDKGVSAAGQVVSLKV---WLIDDILEKINSHL--PPHIRILGLKRVTGGFNSKNKCDA 203

Query: 110 RSYLYRIIT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR-HDFTTFRSIHCQA 165
           R+Y Y + T         ++  R  L  ++L   N  +A        H+FT+ +  H +A
Sbjct: 204 RTYFYMLPTFAFAHKDHDVQDERYRLSAETLRRVNGLLACYRGTHNFHNFTSQKGPH-EA 262

Query: 166 SSPIRTIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           S+    +D F    F         I+V  +SF+  QIR  VG +  V  G    + LE++
Sbjct: 263 SARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAVVKGYAPESVLERS 322

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
               + K   P AP  GL  + V +
Sbjct: 323 W--GEAKVDVPKAPGLGLVLERVHF 345


>gi|290562699|gb|ADD38745.1| tRNA pseudouridine synthase 3 [Lepeophtheirus salmonis]
          Length = 420

 Score = 48.9 bits (115), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 69/271 (25%), Positives = 110/271 (40%), Gaps = 60/271 (22%)

Query: 8   IEYNGSGYFGWQRQKNGS-SIQGSIEKAIF----LVTGEIVVVHGAGRTDSGVHALRQVA 62
           I Y G  Y G+  Q++   +I+  + KA+     + + E    H  GRTD GV A RQV 
Sbjct: 64  ITYFGWNYHGFTTQEDSCMTIEAHLFKALLTTCLIQSRETSNYHRCGRTDKGVSAFRQVI 123

Query: 63  HFDL---VREWVPVI---LCKALN--------AYLKISDTISILNLSIV------DKQFH 102
             D+   ++E + V     CKA +         Y+KI ++    ++ ++      +++  
Sbjct: 124 SIDVRTNLKEGIGVFDYPDCKADSRPDMPHEIDYIKIINSNLPPDIQLIAWTPAQNRELS 183

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           ARF   +R+Y Y       PL   K  +           M  A   LVG HDF  F  + 
Sbjct: 184 ARFDCKKRTYKYFF-----PLGSIKSLS----------KMNEAGAKLVGSHDFRNFCKM- 227

Query: 163 CQASSPIRTIDHFDVNSFGNLIE--------------IRVVARSFLHTQIRSFVGSLKLV 208
              S+ + T     VN   +++E              ++V   +FL  QIR  V  L  +
Sbjct: 228 -DVSNGVLTYIRRMVNVSTSVLEPSKEKESSPYDLCVLKVEGNAFLWHQIRCIVTVLFHI 286

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G G+     +++ L      E  P  P  GL
Sbjct: 287 GQGREEPELIDELLDI----EKNPCRPQYGL 313


>gi|148642915|ref|YP_001273428.1| tRNA pseudouridine synthase A [Methanobrevibacter smithii ATCC
           35061]
 gi|226708656|sp|A5ULI2|TRUA_METS3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148551932|gb|ABQ87060.1| tRNA pseudouridine synthase A, TruA [Methanobrevibacter smithii
           ATCC 35061]
          Length = 290

 Score = 48.9 bits (115), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 63/254 (24%), Positives = 101/254 (39%), Gaps = 48/254 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +     K  ++   +      AGRTD+GVH
Sbjct: 1   MKRTALKIGYIGTNFHGFQRQPDLRTVEEELIYHLRKLGYIDDLKKSRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E    +    +N  L   D I IL  + V   F  R++ +R+   YR 
Sbjct: 61  SLGNVISFQSEKE----VRVNEINNSL--PDDIQILAKAPVRFGFKPRYAEMRQ---YRY 111

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +              L    LD   +   A+   G H+FT F     + ++  RTID   
Sbjct: 112 V--------------LFRSDLDLYKLNEVAEIFKGTHNFTNFTKRFQKTTT--RTIDDIK 155

Query: 177 V----------NSFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +            F NL      + + +   SFL   +R  +     V  GK +   LEK
Sbjct: 156 ITKANLNDYHKKEFPNLHDTLSPVFVDIYGESFLWNMVRKMMRVFVDVAIGKLS---LEK 212

Query: 221 ALQAQDRKECGPLA 234
             +  +  E  P A
Sbjct: 213 VEELLNPAENDPRA 226


>gi|156844606|ref|XP_001645365.1| hypothetical protein Kpol_1058p44 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156116026|gb|EDO17507.1| hypothetical protein Kpol_1058p44 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 446

 Score = 48.9 bits (115), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 88/229 (38%), Gaps = 50/229 (21%)

Query: 14  GYFGWQRQKNGSSIQG------SIEKAIFLVTGEIVVVHG----------AGRTDSGVHA 57
            Y GW    NG +IQ       ++E  I     +  +V             GRTD GV A
Sbjct: 102 AYLGWNY--NGLAIQKEPTPLPTVEGVILEAMNKCRLVPSMNPQDYKFSRCGRTDKGVSA 159

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD------------KQFHARF 105
           + QV    +     P     + N   +I   + ILN  + D            K F ARF
Sbjct: 160 MSQVISLKVRSNLTPEEQANSDNDSKEIQ-YVDILNQLLPDDIRVSAVCLRPPKDFDARF 218

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-- 163
           S   R Y Y +  ++                LD E M  AA++  G +DF  F  +    
Sbjct: 219 SCKHRHYKY-LFNKEG---------------LDLEKMEQAAKYYEGENDFRNFCKLDGSK 262

Query: 164 QASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           Q ++  RTI    + +  G+     ++  +FL  Q+R  + +L LVG G
Sbjct: 263 QITNYKRTIISASIMHVSGDFYCFDLIGSAFLWHQVRCMMANLFLVGQG 311


>gi|239735631|gb|ACS12725.1| MIP10620p [Drosophila melanogaster]
          Length = 341

 Score = 48.9 bits (115), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 54/219 (24%), Positives = 84/219 (38%), Gaps = 39/219 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDSGVH 56
           +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV 
Sbjct: 131 ILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDKGVS 190

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A RQV    L  E    +  +A NA L     I +  +  V K F+A+     R+Y Y +
Sbjct: 191 AARQVCSVKLPEE----LDLEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYTL 244

Query: 117 IT-----------------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            T                 R +P  L+K     + ++L     R  +     R  F   R
Sbjct: 245 PTVAFAPFEEKVDDVHDTFRISPELLQK-----VKETLKLYEGRRTSTTSPARKAFWILR 299

Query: 160 SIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
                +S P+R   H  V    NL  +R+  R+   T+ 
Sbjct: 300 P--SASSCPLRAASHSGVPRTSNLSHLRLRVRALCCTRF 336


>gi|58271292|ref|XP_572802.1| pseudouridylate synthase [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57229061|gb|AAW45495.1| pseudouridylate synthase, putative [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 514

 Score = 48.9 bits (115), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 60/145 (41%), Gaps = 28/145 (19%)

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
           K LN+ L  S  I IL  S +   F +RFS   R Y Y   TR  P + E          
Sbjct: 214 KLLNSVLPPS--IRILAWSPIPASFDSRFSCTYRHYRYAFHTRPTPTSPE---------- 261

Query: 137 LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF-----------DVNSFGN-LI 184
           LD E MR  AQ L+G HD+  F    C+     +  +H                 G+ ++
Sbjct: 262 LDLELMRQGAQLLLGEHDYRNF----CKLDGSKQIENHTRGVLKAWFEGGKSQGVGDGMM 317

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVG 209
              ++  +FL  Q+R  +  L LVG
Sbjct: 318 VFNLIGTAFLWHQVRHIIAVLFLVG 342


>gi|164659606|ref|XP_001730927.1| hypothetical protein MGL_1926 [Malassezia globosa CBS 7966]
 gi|159104825|gb|EDP43713.1| hypothetical protein MGL_1926 [Malassezia globosa CBS 7966]
          Length = 604

 Score = 48.9 bits (115), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 102/272 (37%), Gaps = 80/272 (29%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVVVHGA---------GR 50
           +R+C    Y+G  Y G   Q    +   ++E+ I+  L T  +V    +         GR
Sbjct: 84  LRFC----YDGGSYSGLAAQMGQMTPLPTVEETIWEALCTARLVDATKSMDDVDWSRCGR 139

Query: 51  TDSGVHALRQVAHF------------------------DLVREWVPVILCKALNAYLKIS 86
           TD+GV A  QV                           D   E +P +    LN  L   
Sbjct: 140 TDAGVSAAGQVVALWIRSRCVDERPLRYKTGEAAIPLTDTSDEELPYV--ATLNRLLP-- 195

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-------LDC 139
            TI I   S V   F ARF  + R Y Y   T  AP  L     W  P+S       LD 
Sbjct: 196 PTIRIQAWSPVRPTFSARFDCVYRHYKY-FFTLGAPSTL----VWQ-PESLSQFSGRLDL 249

Query: 140 ENMRIAAQHLVGRHDF------------TTFR------SIH--CQASS--PIRTIDHFDV 177
           + MR AA  LVG HDF            T FR      SI   C+  S  PI   D    
Sbjct: 250 DRMRDAAARLVGEHDFRNMCKVDASKQITNFRRRIDGASIDPVCRGWSDRPIPAPDPHST 309

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           +    ++ +R  A  FL+ Q+R  +  L +VG
Sbjct: 310 DEPMYVLNLRGSA--FLYHQVRHIMAVLFMVG 339


>gi|126323933|ref|XP_001378494.1| PREDICTED: similar to Pseudouridine synthase 1 [Monodelphis
           domestica]
          Length = 435

 Score = 48.9 bits (115), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 68/277 (24%), Positives = 113/277 (40%), Gaps = 52/277 (18%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGA----------GR 50
           +  +++ Y+G GY G QR    S  +   +  +F +  +G I   HG            R
Sbjct: 101 KIVLLMAYSGKGYHGMQRNLGSSQFKTIEDDLVFALVQSGCIPENHGEDMRKMAFQRCAR 160

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GV A  Q+    +   W+   + + +N++L     I IL L  V   F+++     R
Sbjct: 161 TDKGVSAAGQIVSLKV---WLIDNILEKINSHL--PSHIRILGLKRVTGSFNSKNRCDAR 215

Query: 111 SYLYRIIT-----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS----- 160
           +Y Y + T     +   +  E  R  L  ++L+  N  +A+    G H F  F S     
Sbjct: 216 TYFYMLPTFAFAHKDHDVQDETYR--LSSETLEKVNQLLAS--YKGTHSFHNFTSQKGPK 271

Query: 161 ----------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
                     +HC+A   +R    F V        I+V  +SF+  QIR  VG +  +  
Sbjct: 272 EPSARRYIMEMHCEAPF-VREGMEFAV--------IKVKGQSFMMHQIRKMVGLVIAIMK 322

Query: 211 GKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G    + +E++    + K   P AP  GL  + V + 
Sbjct: 323 GYVPESVMERSW--GEEKVDIPKAPGLGLVLERVHFE 357


>gi|195346649|ref|XP_002039870.1| GM15659 [Drosophila sechellia]
 gi|194135219|gb|EDW56735.1| GM15659 [Drosophila sechellia]
          Length = 498

 Score = 48.9 bits (115), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 91/257 (35%), Gaps = 56/257 (21%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 107 YFGWDYQ--GFACQEDSNDTIESNLFRALTRTCLIESRATSNYHRCGRTDKEVSAFCQVI 164

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  +  P            +  C  LN  L   +   +  + +    + ARF  + R
Sbjct: 165 SIDLRSKHPPESQLDPTSLSSEIDYCGLLNRVLP-KNIQCVAWMPLRSSVYSARFDCVSR 223

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           SY Y                   PK  LD   MR A   LV   DF  F    +H   ++
Sbjct: 224 SYRY-----------------FFPKGDLDIAAMRKACDLLVRHADFRNFCKMDVHNGVTN 266

Query: 168 PIRTI--------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            +R +        D    NS  ++  + + A +FL  QIR  +  L LVG  K     + 
Sbjct: 267 YMRNLQSARVEACDENHTNSGYDMYYLEIRANAFLWHQIRCIMAVLILVGQKKEKPAIIS 326

Query: 220 KALQAQDRKECGPLAPP 236
             L  +    C P   P
Sbjct: 327 DLLNVESNP-CKPQYTP 342


>gi|302789057|ref|XP_002976297.1| hypothetical protein SELMODRAFT_105100 [Selaginella moellendorffii]
 gi|300155927|gb|EFJ22557.1| hypothetical protein SELMODRAFT_105100 [Selaginella moellendorffii]
          Length = 175

 Score = 48.5 bits (114), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 65/163 (39%), Gaps = 20/163 (12%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I +L    V   FHARFS + R Y Y                + I   L+ + M+ A+Q 
Sbjct: 16  IRVLGWCPVPPGFHARFSCLYREYKY----------------FFIDDGLNIDAMKQASQR 59

Query: 149 LVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLK 206
           L+G HDF  F  +      +  R I  FD+      + +  V   +FL  Q+R     L 
Sbjct: 60  LLGEHDFRNFCKMDADNIHNYTRQILAFDILPIEECLWVMHVRGNAFLWHQVRCMAAVLF 119

Query: 207 LVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           ++G G  T T ++  L      RK    +AP   L   S  + 
Sbjct: 120 MIGRGHETLTIIDDLLDVDKTMRKPQYVMAPELPLVLQSCAFQ 162


>gi|195429481|ref|XP_002062787.1| GK19511 [Drosophila willistoni]
 gi|194158872|gb|EDW73773.1| GK19511 [Drosophila willistoni]
          Length = 495

 Score = 48.5 bits (114), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 65/260 (25%), Positives = 92/260 (35%), Gaps = 60/260 (23%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 115 YFGWDYQ--GFACQEDSNDTIESNLFRALTRTCLIESRANSNYHRCGRTDKEVSAFCQVI 172

Query: 63  HFDLVREW------------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  ++              +  C  LN  L   +   +  + +    + ARF  I R
Sbjct: 173 SIDLRSKYPAESQLDPTSLATEIDYCGLLNRVLP-KNIQCVAWMPLRSPVYSARFDCIAR 231

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF----------- 158
           SY Y                   PK  LD E M+ A Q LV   DF  F           
Sbjct: 232 SYRY-----------------YFPKGDLDIEAMQEACQLLVNHADFRNFCKMDVHNGVTS 274

Query: 159 --RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             R++      P     +  V+ +  +  + + A +FL  QIR  +  L LVG  K  S+
Sbjct: 275 FMRNLQAARVQPCEQTRNEKVSGYA-MFYLEIKANAFLWHQIRCIMAILLLVGQRKEKSS 333

Query: 217 DLEKALQAQDRKECGPLAPP 236
            +   L   +   C P   P
Sbjct: 334 IISDLLDV-NVNPCKPQYTP 352


>gi|242062118|ref|XP_002452348.1| hypothetical protein SORBIDRAFT_04g024105 [Sorghum bicolor]
 gi|241932179|gb|EES05324.1| hypothetical protein SORBIDRAFT_04g024105 [Sorghum bicolor]
          Length = 90

 Score = 48.5 bits (114), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 40/62 (64%), Gaps = 3/62 (4%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
          ++ M+I Y+G+ + GWQ Q +  +IQ  +E A+  +T    + + + GAGRTD+GVHA  
Sbjct: 29 KWRMVIAYDGTKFKGWQYQPSIPTIQYFLEDALICITKLDRKKLCLVGAGRTDTGVHAWG 88

Query: 60 QV 61
          QV
Sbjct: 89 QV 90


>gi|237844499|ref|XP_002371547.1| hypothetical protein TGME49_020220 [Toxoplasma gondii ME49]
 gi|211969211|gb|EEB04407.1| hypothetical protein TGME49_020220 [Toxoplasma gondii ME49]
          Length = 370

 Score = 48.5 bits (114), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 43/136 (31%), Positives = 58/136 (42%), Gaps = 21/136 (15%)

Query: 79  LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD 138
           LNA L     I I+  + V   F ARF    R Y Y                +   + LD
Sbjct: 22  LNAVL--PGDIRIVASAPVSPTFDARFDCTGRVYKY----------------FFHSEGLD 63

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGNLI--EIRVVARSFLH 195
            + M  AAQ  VG H+F  F  +   Q  +P RT+  F V S G+ +     +  RSFL 
Sbjct: 64  LQRMHQAAQRFVGEHNFRYFCKLDPRQYRNPRRTLTSFAVESAGDGVCAVATIAGRSFLW 123

Query: 196 TQIRSFVGSLKLVGDG 211
            Q+R  + +L  VG G
Sbjct: 124 HQVRFMMAALLKVGRG 139


>gi|224007503|ref|XP_002292711.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971573|gb|EED89907.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 162

 Score = 48.5 bits (114), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 58/129 (44%), Gaps = 20/129 (15%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           +  +I IL    V  +F ARFS  +R+Y Y    R                +LD   M  
Sbjct: 6   LPPSIRILGWCPVSPEFSARFSCGQRTYRYFFPRR----------------NLDLSAMAQ 49

Query: 145 AAQHLVGRHDFTTFRSIHCQASS---P-IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
             Q+++GRHDF     ++C+ +    P I+  +    +S  ++  + +V ++FL  QIR 
Sbjct: 50  GLQYMMGRHDFRNLCKMNCEQNEGEHPVIQPTEQSKPSSSRDMCHVEIVGQAFLWHQIRC 109

Query: 201 FVGSLKLVG 209
            +  L  VG
Sbjct: 110 IMSILFYVG 118


>gi|195552156|ref|XP_002076382.1| GD15210 [Drosophila simulans]
 gi|194202031|gb|EDX15607.1| GD15210 [Drosophila simulans]
          Length = 498

 Score = 48.5 bits (114), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 91/257 (35%), Gaps = 56/257 (21%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 107 YFGWDYQ--GFACQEDSNDTIESNLFRALTRTCLIESRATSNYHRCGRTDKEVSAFCQVI 164

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  +  P            +  C  LN  L   +   +  + +    + ARF  + R
Sbjct: 165 SIDLRSKHPPESQLDPTSLSSEIDYCGLLNRVLP-KNIQCVAWMPLRSPVYSARFDCVSR 223

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           SY Y                   PK  LD   MR A   LV   DF  F    +H   ++
Sbjct: 224 SYRY-----------------YFPKGDLDIAAMRKACDLLVRHADFRNFCKMDVHNGVTN 266

Query: 168 PIRTI--------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            +R +        D    NS  ++  + + A +FL  QIR  +  L LVG  K     + 
Sbjct: 267 YMRNLQSARVEACDENHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKEKPAVIS 326

Query: 220 KALQAQDRKECGPLAPP 236
             L  +    C P   P
Sbjct: 327 DLLDVESNP-CKPQYTP 342


>gi|86134196|ref|ZP_01052778.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
 gi|85821059|gb|EAQ42206.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
          Length = 260

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/259 (22%), Positives = 108/259 (41%), Gaps = 37/259 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALR--- 59
           Y + + + G  + GWQ+Q N  ++   ++K++  V  ++     GAGRTD+ V A R   
Sbjct: 7   YLISLGFLGFRFSGWQKQTNAKTLHDIVDKSLSFVLKDVDYKTIGAGRTDAKVSANRYLF 66

Query: 60  -----QVAHFDLVREWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARFS--AIRR 110
                +V   D+    +   L     AY   +++   +I+N   + K++H  FS  A+  
Sbjct: 67  QLFTNEVLQQDVFLNELNSNLPADFKAYTVSEVATKFNIINAPKI-KEYHYYFSFGAVNH 125

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            +        AP  + +         L+ + M+  A    G H F  + +     +   R
Sbjct: 126 PF-------AAPFIVNE------ESELNIKLMKKGASLFEGEHYFHKYCTKPSAKTEFKR 172

Query: 171 TIDHFDVNSFGNLIE---------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           TI+   +     L           ++V  + FL  QIR  + +L  +G G  +   +E +
Sbjct: 173 TIESCSIIENSILTASFFPQKSYVLKVRGKGFLRYQIRLMMATLFELGKGNLSLQYIEDS 232

Query: 222 LQA-QDRKECGPLAPPEGL 239
           L+   DR+    +AP  GL
Sbjct: 233 LKEDNDRQFLRTIAPGSGL 251


>gi|145350766|ref|XP_001419769.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580001|gb|ABO98062.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 257

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 100/260 (38%), Gaps = 59/260 (22%)

Query: 15  YFGWQRQKNGSSIQG--------SIEKAIFLVTGEIVVVHGA------------GRTDSG 54
           Y GW    +G + QG        ++E+A+F    +  +V  A            GRTD G
Sbjct: 19  YLGWD--YHGFASQGAANAAAPRTVEQALFDALAKTKLVESARDVFKVADYARCGRTDRG 76

Query: 55  VHALRQVAHF----------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           V  L Q+             D   ++V  +L +AL       + +  L  + VD + +AR
Sbjct: 77  VSGLGQIVTLRARSNGAEGVDEELDYV-ALLNRAL------PNDVRALGWAPVDDELNAR 129

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           F    R Y Y           EK         LD   MR AA+   G HDF  F  +  +
Sbjct: 130 FDCEWRQYKY---------FFEK------TNGLDLGAMREAARAFEGVHDFRNFCRMDAE 174

Query: 165 -ASSPIRTIDHFDVNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
              S  R +    +     G L+ I V   +FL  Q+R     L +VG G  + T + + 
Sbjct: 175 NVKSFTRNVLECTIEESHDGKLMYINVRGTAFLWHQVRCMASVLFMVGLGHESPTVVTEL 234

Query: 222 LQAQ--DRKECGPLAPPEGL 239
           L  +   RK   P+AP   L
Sbjct: 235 LDLERTPRKPQYPMAPEHAL 254


>gi|254168636|ref|ZP_04875479.1| tRNA pseudouridine synthase family [Aciduliprofundum boonei T469]
 gi|197622470|gb|EDY35042.1| tRNA pseudouridine synthase family [Aciduliprofundum boonei T469]
          Length = 225

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/208 (28%), Positives = 84/208 (40%), Gaps = 43/208 (20%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDK 99
           +  A RTD GV AL  V        W+        L   LNA LK     S  NL I   
Sbjct: 12  LKSASRTDRGVSALGNVI-------WIKTDIDGKELIGRLNANLKHIYFHSFANLDI--- 61

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
             + R++ IR  Y Y +        L+ G+        D + ++ AA    G HDF  F 
Sbjct: 62  --NPRYARIR-WYRYHL--------LDMGQ--------DMDRLKEAAMIFQGEHDFRNFT 102

Query: 160 SIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            +       I+ ID   VN  G++I I    R++L   IR  V +++    GK    ++ 
Sbjct: 103 RVRKNTVIEIKKID---VNKRGSIITIDFYGRNYLWNLIRRIVAAMEAYSLGKEFGQEIF 159

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
                  RK  G +APPE L    ++Y 
Sbjct: 160 TI-----RKNFG-IAPPEPLILMDIQYD 181


>gi|296775668|gb|ADH42945.1| hypothetical protein [uncultured SAR11 cluster alpha
           proteobacterium H17925_23J24]
          Length = 52

 Score = 48.1 bits (113), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/40 (50%), Positives = 26/40 (65%)

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           VGSLK +G+GKW  +D +KA  ++ R  C P AP  GL F
Sbjct: 2   VGSLKYLGEGKWKLSDFKKAFSSKKRTMCAPPAPAYGLLF 41


>gi|195488597|ref|XP_002092382.1| GE11697 [Drosophila yakuba]
 gi|194178483|gb|EDW92094.1| GE11697 [Drosophila yakuba]
          Length = 497

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 91/257 (35%), Gaps = 56/257 (21%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 106 YFGWDYQ--GFACQEDSNDTIEANLFRALTRTCLIESRATSNYHRCGRTDKEVSAFCQVI 163

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  +  P            +  C  LN  L   +   +  + +    + ARF  + R
Sbjct: 164 SIDLRSKHPPESQLDPTAISTEIDYCGLLNRVLP-KNIQCVAWMPLRSPVYSARFDCVSR 222

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           SY Y                   PK  LD   M  A   LV   DF  F    +H   ++
Sbjct: 223 SYRY-----------------YFPKGDLDIAAMSKACDLLVRHADFRNFCKMDVHNGVTN 265

Query: 168 PIRTI--------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            +R +        D    NS  ++  + + A +FL  QIR  +  L LVG  K     + 
Sbjct: 266 YMRNLQSARVEACDENHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKENPAVIS 325

Query: 220 KALQAQDRKECGPLAPP 236
           K L  +    C P   P
Sbjct: 326 KLLDVESNP-CKPQYTP 341


>gi|222445148|ref|ZP_03607663.1| hypothetical protein METSMIALI_00769 [Methanobrevibacter smithii
           DSM 2375]
 gi|222434713|gb|EEE41878.1| hypothetical protein METSMIALI_00769 [Methanobrevibacter smithii
           DSM 2375]
          Length = 288

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 63/269 (23%), Positives = 106/269 (39%), Gaps = 47/269 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +     K  ++   +      AGRTD+GVH
Sbjct: 1   MKRTALKIGYIGTNFHGFQRQPDLRTVEEELIYHLRKLGYIDDLKKSRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E    +    +N  L   D I IL  + V   F  R++ +R+   YR 
Sbjct: 61  SLGNVISFQSEKE----VRVNEINNSL--PDDIQILAKAPVRFGFKPRYAEMRQ---YRY 111

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +              L    LD   +   A+   G H+FT F     + ++  RTID   
Sbjct: 112 V--------------LFRSDLDLYKLNEVAEIFKGTHNFTNFTKRFQKTTT--RTIDDIK 155

Query: 177 V----------NSFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +            F NL      + + +   SFL   +R  +     V  GK +   +E+
Sbjct: 156 ITKANLNDYHKKEFPNLHDTLSPVFVDIYGESFLWNMVRKMMRVFVDVAIGKLSLEKVEE 215

Query: 221 ALQA--QDRKECGPLAPPEGLYFDSVEYS 247
            L     D +    +  P+ L    ++Y 
Sbjct: 216 LLNPAENDLRANIKVLDPDYLILMDIKYD 244


>gi|308807767|ref|XP_003081194.1| Exopolyphosphatases and related proteins (ISS) [Ostreococcus tauri]
 gi|116059656|emb|CAL55363.1| Exopolyphosphatases and related proteins (ISS) [Ostreococcus tauri]
          Length = 813

 Score = 47.8 bits (112), Expect = 0.001,   Method: Composition-based stats.
 Identities = 61/203 (30%), Positives = 86/203 (42%), Gaps = 31/203 (15%)

Query: 49  GRTDSGVHALRQVAHFDL-------VREWVPVILCKALNAYLKISDTISILNLSIVDKQF 101
           GRTD GV  L Q+    +        RE +  +    LN  L  SD +  L  + VD++ 
Sbjct: 512 GRTDRGVSGLGQIVTLQVRSNGASDPREELDYV--GLLNRALP-SD-VRALGWAPVDEEL 567

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
           +ARF    R Y Y           EK  A      LD E M  AA+   G HDF  F  +
Sbjct: 568 NARFDCKWRQYKY---------FFEKTTA------LDLEAMGEAARAFEGVHDFRNFCRM 612

Query: 162 HCQ-ASSPIRTIDHFDVNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
             +   S  R +    +   G+  L+ I V   +FL  Q+R+    L +VG G    + +
Sbjct: 613 DAENVKSFTRRVLECTIEEAGDGKLMYINVRGTAFLWHQVRNMASVLFMVGLGHEPPSVV 672

Query: 219 EKALQAQ--DRKECGPLAPPEGL 239
           E+ L  +   RK   P+AP E L
Sbjct: 673 ERLLDLERTPRKPQYPMAPEESL 695


>gi|66803188|ref|XP_635437.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
 gi|60463746|gb|EAL61924.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
          Length = 596

 Score = 47.8 bits (112), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 67/295 (22%), Positives = 110/295 (37%), Gaps = 69/295 (23%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
           +  +I+ Y+G+ Y G Q+     +++  +E A+F   G         + V      RTD 
Sbjct: 141 KVAIILGYSGTNYAGMQKNPGLKTVEEELEHALFRTGGISPDNMYYQQKVDWIRCARTDK 200

Query: 54  GVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           GV A+R V    +       E + + L K L         I++ ++  V+  FHA+ +  
Sbjct: 201 GVSAIRNVVSLKMEMGPPDFEGMKIALNKEL------PKDITVFHIMRVNNSFHAKNAVD 254

Query: 109 RRSYLYRIITRQAPLALEKGRAWLI-------------PKSLDCENMRIAAQHL---VGR 152
            RSY+Y   T        K    ++             P     + + I  + L   +G 
Sbjct: 255 ARSYIYVTPTHVFEPKFSKKNKSIVEEAANGGENNTQPPWKFTSDTLSILNKVLSFYLGN 314

Query: 153 H------------DFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
           H            D + FR IH    S    ++  +      ++ I VV  SF+  QIR 
Sbjct: 315 HRFHNYTSRKESNDVSVFRKIHSFVCSEPFVLEGVE------MVSINVVGESFMLHQIRK 368

Query: 201 FVGSL-KLVGDGKWTSTDLEKALQAQDRKECG------------PLAPPEGLYFD 242
            +G L   +  G +   D E   QA D+ +              P+AP  GL  D
Sbjct: 369 MIGCLISFIRKGMF--EDCETRDQAFDQIKAYINSTFEHTPLNLPMAPGAGLLLD 421


>gi|301605366|ref|XP_002932295.1| PREDICTED: tRNA pseudouridine synthase A-like [Xenopus (Silurana)
           tropicalis]
          Length = 394

 Score = 47.8 bits (112), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 65/269 (24%), Positives = 114/269 (42%), Gaps = 37/269 (13%)

Query: 3   RYCMIIEYNGSGYFGWQ---RQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGR 50
           ++ +++ Y G GY+G Q    + N  +I+ ++  A+         F +  + +      R
Sbjct: 70  KFAIMLAYCGRGYYGMQMDLTRPNFPTIESALISALIQARCIPEMFYMQMKQLKFQRCAR 129

Query: 51  TDSGVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GV AL Q+    L+     PV   + +N++L     I I+++  V K F  +    +
Sbjct: 130 TDKGVSALSQLVSVRLLPSCSNPV---EKINSHL--PPEILIIDMKRVTKGFCPKKMCDK 184

Query: 110 RSYLYRIITRQ----APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-Q 164
           RSY Y + T      AP   +    + +P+  D  N+        G H+F  F S    +
Sbjct: 185 RSYSYMVPTFALSCCAPSVPDSN--FRMPRE-DFHNINNLLSFYKGTHNFHNFTSRKAFE 241

Query: 165 ASSPIRTIDHFDVNSFGNLI-------EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
             S  R +   DV+     +       +I +  +SF+  QIR  VG +  +  G   +  
Sbjct: 242 DPSSFRHM--LDVSCSEPFVFHGTEFAQIHITGQSFMLYQIRKMVGLIIAIAQGIVPADF 299

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           L + +Q +  K   P AP  GL  + V +
Sbjct: 300 LPQCMQRE--KINIPPAPGLGLVLERVHF 326


>gi|224011898|ref|XP_002294602.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220969622|gb|EED87962.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 394

 Score = 47.8 bits (112), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 55/202 (27%), Positives = 89/202 (44%), Gaps = 44/202 (21%)

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIIT------RQAPLALEKGRAWLIPKSLDCEN 141
           +IS  +++ V   F AR+SA  + Y+Y I +         P    +  AWLI +SLD E 
Sbjct: 190 SISAFSVTPVPLTFDARYSAKWKRYIYYICSGINNGETVQPFVWSR-YAWLIRESLDYEG 248

Query: 142 MRIAAQHLVG-RHDF------------TTFRSIHCQASS-PIR-----TIDHFDVNSFGN 182
           M  AA+ L G  H++             T R++H    + P++     T+  + +    N
Sbjct: 249 MVDAAKMLSGEEHNYEWMCVIQEGELRNTRRTVHLNIETVPVKVNGNDTMVPYFLQQNEN 308

Query: 183 LIEIRVVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-------QAQDRKECGPL 233
            +  +VVA S  FL+  +R  VG L  +G  +   T L++ +        A D +E   +
Sbjct: 309 SVVYKVVATSDFFLYKMVRRIVGLLVAIGKKQADLTTLKRCIGVYDKYGAASDDREGERM 368

Query: 234 ---------APPEGLYFDSVEY 246
                    AP +GL  D +EY
Sbjct: 369 KIPVKLLETAPAKGLCLDHIEY 390



 Score = 42.7 bits (99), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + ++G+ Y G+Q Q   ++IQ  IE  +  L+  + V V G GRTD+GVHA   V
Sbjct: 39  RFAIRLSFDGTTYSGFQSQPYQNTIQDQIEHRLRNLLKRDTVRVIGWGRTDAGVHAKGAV 98

Query: 62  AHFDL 66
              DL
Sbjct: 99  VTVDL 103


>gi|256087148|ref|XP_002579738.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665217|emb|CAZ35977.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 413

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 70/267 (26%), Positives = 108/267 (40%), Gaps = 38/267 (14%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-------LVTGEIVVVH--GAGRTDSGVH 56
           +++ Y+G GY+G QR     +I+G + KA+F       L + E   VH   A +TD  V 
Sbjct: 42  ILLMYSGWGYYGMQRCPVFPTIEGELSKALFTCGQLDNLTSEEHKRVHFQRASKTDKSVS 101

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV    L  +     L   LN  L   + I +L++  V + F +  S   R Y Y +
Sbjct: 102 ALGQVCSMQLKED---TDLLSKLNNSLP--ENIRVLDIIRVTRGFSSYSSCTHRIYDYLL 156

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV----------GRHDFTTFRS----IH 162
            T     AL    + L   +  C   R+  + +           G H+F  F S      
Sbjct: 157 PT----FALSPATSSLNDST--CWTYRLTVEQITQVNRLLEKYKGTHNFYNFTSGRLVTD 210

Query: 163 CQASSPIRTIDHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
              S  I + +       G      IR+  +SF+  QIR  +G    V  G  T    + 
Sbjct: 211 RSCSRYIISAECMPTFLLGEHQYTIIRIAGQSFMLHQIRKMIGLALAVLRGYATEAVFDI 270

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
              ++ R +  P AP  GL  + V++S
Sbjct: 271 VF-SKARIDI-PKAPGLGLMLNQVDFS 295


>gi|256087146|ref|XP_002579737.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665216|emb|CAZ35976.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 428

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 70/267 (26%), Positives = 108/267 (40%), Gaps = 38/267 (14%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-------LVTGEIVVVH--GAGRTDSGVH 56
           +++ Y+G GY+G QR     +I+G + KA+F       L + E   VH   A +TD  V 
Sbjct: 57  ILLMYSGWGYYGMQRCPVFPTIEGELSKALFTCGQLDNLTSEEHKRVHFQRASKTDKSVS 116

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV    L  +     L   LN  L   + I +L++  V + F +  S   R Y Y +
Sbjct: 117 ALGQVCSMQLKED---TDLLSKLNNSLP--ENIRVLDIIRVTRGFSSYSSCTHRIYDYLL 171

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV----------GRHDFTTFRS----IH 162
            T     AL    + L   +  C   R+  + +           G H+F  F S      
Sbjct: 172 PT----FALSPATSSLNDST--CWTYRLTVEQITQVNRLLEKYKGTHNFYNFTSGRLVTD 225

Query: 163 CQASSPIRTIDHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
              S  I + +       G      IR+  +SF+  QIR  +G    V  G  T    + 
Sbjct: 226 RSCSRYIISAECMPTFLLGEHQYTIIRIAGQSFMLHQIRKMIGLALAVLRGYATEAVFDI 285

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
              ++ R +  P AP  GL  + V++S
Sbjct: 286 VF-SKARIDI-PKAPGLGLMLNQVDFS 310


>gi|224011902|ref|XP_002294604.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220969624|gb|EED87964.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 394

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 88/202 (43%), Gaps = 44/202 (21%)

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIIT------RQAPLALEKGRAWLIPKSLDCEN 141
           +IS  +++ V   F AR+SA  + Y+Y I +         P    +  AWLI +SLD E 
Sbjct: 190 SISAFSVTPVPLTFDARYSAKWKRYIYYICSGINNGETVQPFVWSR-YAWLIRESLDYEG 248

Query: 142 MRIAAQHLVG-RHDF------------TTFRSIHCQASS-PIR-----TIDHFDVNSFGN 182
           M  AA+ L G  H++             T R++H    + P++     T+  + +    N
Sbjct: 249 MVDAAKMLSGEEHNYEWMCVIQEGELRNTRRTVHLNIETVPVKVNGNDTMVPYFLQQNEN 308

Query: 183 LIEIRVVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG--------- 231
            +  +VVA S  FL+  +R  VG L  +G  +   T L++ +   D+             
Sbjct: 309 SVVYKVVATSDFFLYKMVRRIVGLLVAIGKKQADLTTLKRCIGVYDKYGAASDDRDGERM 368

Query: 232 --PL-----APPEGLYFDSVEY 246
             P+     AP +GL  D +EY
Sbjct: 369 KIPVKLLETAPAKGLCLDHIEY 390



 Score = 42.7 bits (99), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + ++G+ Y G+Q Q   ++IQ  IE  +  L+  + V V G GRTD+GVHA   V
Sbjct: 39  RFAIRLSFDGTTYSGFQSQPYQNTIQDQIEHRLRNLLKRDTVRVIGWGRTDAGVHAKGAV 98

Query: 62  AHFDL 66
              DL
Sbjct: 99  VTVDL 103


>gi|325115883|emb|CBZ51437.1| hypothetical protein NCLIV_012350 [Neospora caninum Liverpool]
          Length = 475

 Score = 47.0 bits (110), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 82/211 (38%), Gaps = 32/211 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + + Y+GS Y G   Q   S+++ ++E A+F    +  ++              +  +
Sbjct: 89  FLLKLAYDGSAYSGIAYQGENSAVR-TVEGALFDALEKTCLIRDRNAWQPAKRLFPE-EN 146

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           +D             LNA L     I I+  + V   F ARF    R Y Y         
Sbjct: 147 YDYA---------AVLNAVL--PGDIRIVASAPVPPGFDARFDCTGRVYKY--------- 186

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGN 182
                  +   + LD   M  AAQ  VG H+F  F  +   Q  +P RT+  F +   G+
Sbjct: 187 -------FFHSEGLDLPRMHRAAQRFVGEHNFRYFCKLDPRQYRNPRRTLTSFAIEPVGD 239

Query: 183 --LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                  +  RSFL  Q+R  + +L  VG G
Sbjct: 240 SACAVATIAGRSFLWHQVRFMMAALLKVGRG 270


>gi|3047089|gb|AAC13601.1| contains similarity to pseudouridylate synthases [Arabidopsis
           thaliana]
 gi|10178103|dbj|BAB11490.1| unnamed protein product [Arabidopsis thaliana]
          Length = 364

 Score = 47.0 bits (110), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 27/88 (30%), Positives = 48/88 (54%), Gaps = 22/88 (25%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FL--------------VTGEIVVV 45
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++  F+              + G ++V 
Sbjct: 93  VNFKIVLSYNGASFDGWQKQPDLHTVQGVVEKSLGGFVDERKAQLLKKKCKPLEGRVLV- 151

Query: 46  HGAGRTDSGVHALRQVA---HFDLVREW 70
             AGRTD GV AL QV+   H +   +W
Sbjct: 152 --AGRTDKGVSALNQVSRSFHPNFSAKW 177


>gi|219116871|ref|XP_002179230.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409121|gb|EEC49053.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 63

 Score = 47.0 bits (110), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/57 (45%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 8  IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
          + Y GS + GWQRQ      S+Q  +E A+    G  V V  AGRTD+GVHAL Q+ 
Sbjct: 3  LAYFGSDFCGWQRQAQSKKPSVQKIVEDAMQDALGYAVNVRVAGRTDAGVHALGQIG 59


>gi|317498141|ref|ZP_07956443.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894618|gb|EFV16798.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 50

 Score = 47.0 bits (110), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/49 (44%), Positives = 30/49 (61%)

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +R   G+L  VG GK    D+ KAL++  R + G  APP+GL+  SVEY
Sbjct: 2   VRILTGTLVEVGYGKIKPEDITKALESTKRSDAGITAPPQGLFLVSVEY 50


>gi|302808177|ref|XP_002985783.1| hypothetical protein SELMODRAFT_181988 [Selaginella moellendorffii]
 gi|300146290|gb|EFJ12960.1| hypothetical protein SELMODRAFT_181988 [Selaginella moellendorffii]
          Length = 372

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 44/162 (27%), Positives = 65/162 (40%), Gaps = 20/162 (12%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I +L    V   FHARFS + R Y Y                + I   L+ + M+ A+Q 
Sbjct: 194 IRVLGWCPVPPGFHARFSCLYREYKY----------------FFIDDGLNIDAMKQASQR 237

Query: 149 LVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLK 206
           L+G HDF  F  +      +  R I  FD+      + +  V   +FL  Q+R     L 
Sbjct: 238 LLGEHDFRNFCKMDADNIHNYTRQILAFDILPIEECLWVMHVRGNAFLWHQVRCMAAVLF 297

Query: 207 LVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEY 246
           ++G G  T T ++  L      RK    +AP   L   S  +
Sbjct: 298 MIGRGHETLTIIDDLLDVDKTMRKPQYVMAPELPLVLQSCAF 339


>gi|321261750|ref|XP_003195594.1| pseudouridylate synthase [Cryptococcus gattii WM276]
 gi|317462068|gb|ADV23807.1| pseudouridylate synthase, putative [Cryptococcus gattii WM276]
          Length = 511

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 50/196 (25%), Positives = 74/196 (37%), Gaps = 39/196 (19%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKI 85
           + +  +EK +  V  E     G  +    V   RQ + F            K LN+ L  
Sbjct: 171 AAEPEVEKPV--VVQEDGEAKGQEKKSKIVQPTRQPSEFPY---------PKLLNSVLPP 219

Query: 86  SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIA 145
           S  I +L  S +   F +RFS   R Y Y   TR  P + E          LD E M   
Sbjct: 220 S--IRVLAWSPIPSSFDSRFSCTYRHYRYAFHTRPTPTSPE----------LDLELMSQG 267

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHF-----------DVNSFGN-LIEIRVVARSF 193
           AQ L+G HD+  F    C+     +  +H            +    G  ++   ++  +F
Sbjct: 268 AQLLLGEHDYRNF----CKLDGSKQIENHTRGVLKAWFEGGESQGVGEGMMVFNLIGTAF 323

Query: 194 LHTQIRSFVGSLKLVG 209
           L  Q+R  V  L L+G
Sbjct: 324 LWHQVRHIVAVLFLIG 339


>gi|149634330|ref|XP_001510884.1| PREDICTED: similar to Pseudouridine synthase 1 [Ornithorhynchus
           anatinus]
          Length = 469

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 114/269 (42%), Gaps = 36/269 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY+G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 101 KIVLLMAYSGKGYYGMQRHV-GSSQFKTIEDDLVSALVQSGCIPENHGDDMKKMSFQRCA 159

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  Q+    +   W+   + + +N++L     I IL L  V   F+++ +   
Sbjct: 160 RTDKGVSAAGQIVSLKV---WLIDNILEKINSHL--PSQIRILGLKRVTGGFNSKNNCTA 214

Query: 110 RSYLYRIIT-----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-C 163
           R+Y Y + T     +      E  R  L P+ L+  N  +A     G H F  F S    
Sbjct: 215 RTYFYMLPTLAFAHKDHDPQDETYR--LSPEVLERVNRLLAC--YKGTHHFHNFTSQKGP 270

Query: 164 QASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
           + +S +R I     +   V        I+V  +SF+  QIR  +G +  +  G    + +
Sbjct: 271 KDASGMRYIMEMYCEEPFVREGMEFAVIKVKGQSFMMHQIRKMIGLVIAIVKGYADQSVM 330

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           E++   +  K   P AP  GL  + V + 
Sbjct: 331 ERSWGEE--KVDIPKAPGLGLVLERVHFE 357


>gi|157115880|ref|XP_001658327.1| pseudouridylate synthase [Aedes aegypti]
 gi|108876737|gb|EAT40962.1| pseudouridylate synthase [Aedes aegypti]
          Length = 455

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 64/268 (23%), Positives = 109/268 (40%), Gaps = 35/268 (13%)

Query: 3   RYCMIIE-YNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
           R C+I+  Y+G  Y G QR     +I+  +  A+              + +    A RTD
Sbjct: 116 RKCVIVMGYSGVNYLGMQRNPGTKTIEEELLVAMLKHNWISEEAFNQPQQIQFQRAARTD 175

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    L       +   ALN  L   + I +  +  V K F+++ +   R+Y
Sbjct: 176 KGVSAATQVVSIKLPDN----VDIDALNKDL--PEQIRVFAVKRVTKGFNSKSNCDARTY 229

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV------GRHDFTTFRSIHCQAS 166
            Y + T     AL + +  +    +  E +++  + L         H+FT+ +     +S
Sbjct: 230 TYTLPT--MAFALHEDKVDMESYRVPEERLKVVEETLKLFEGTKNFHNFTSRKEFIDPSS 287

Query: 167 SPIRTIDHFDVNS----FGNLIE---IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
              R I  F+  +     G+ +E   +++  +SF+  QIR  VG    V  G      + 
Sbjct: 288 K--RFIMSFECEAPFVPEGSTVEFATLKIKGQSFMLHQIRKMVGLTLAVVRGLTPQETIV 345

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           KA + Q  +   P AP  GL  + + Y 
Sbjct: 346 KAFEEQ--RYGVPTAPGLGLVLNRIHYE 371


>gi|294621110|ref|ZP_06700301.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|291599346|gb|EFF30372.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
          Length = 73

 Score = 46.6 bits (109), Expect = 0.003,   Method: Composition-based stats.
 Identities = 21/54 (38%), Positives = 30/54 (55%)

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PEGLY   V+Y
Sbjct: 19  FLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAHPEGLYLYEVKY 72


>gi|17565126|ref|NP_507242.1| PseudoUridine Synthase family member (pus-1) [Caenorhabditis
           elegans]
 gi|3880517|emb|CAA16518.1| C. elegans protein W06H3.2a, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 415

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 63/270 (23%), Positives = 105/270 (38%), Gaps = 33/270 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQG----SIEKAIFLVTGEI-----VVVHGAGRTDS 53
           +Y M++ Y G  Y+G Q QK+  +I+     ++E A ++ T +           A RTD 
Sbjct: 34  KYAMLLGYQGKKYYGMQLQKDLPTIESKLLEAMETAGWITTAQKEKPFDFFFQRAARTDR 93

Query: 54  GVHALRQVAHFDLVREWVPVILCKA--LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
            V A RQ+    L R+        A  LN  L     I +  +      FH +     R+
Sbjct: 94  AVSAARQMCGMQLPRDDAKYQAEGAGILNNILPAD--IRVFGMRRTTNFFHPQKQCDHRT 151

Query: 112 YLYRI--ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--------- 160
           Y Y         P  L      L P++L   N  ++    +G H+F  + +         
Sbjct: 152 YSYTCPSFVFAKPTELTNSSFRLSPETLAEVNSILSI--YLGTHNFFNYTAKRAYDDMSS 209

Query: 161 ----IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
               I  +   P    D F        ++I +  +SF+  QIR  VG +  V       +
Sbjct: 210 NRYIISFECKEPFLFRDDFRKEDV-EFVQIVIKGQSFVLHQIRKMVGMVITVIRELHLKS 268

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            ++++ + Q R +  P+AP  GL  +   Y
Sbjct: 269 SIQRSFEGQ-RMDI-PMAPGLGLLLERTHY 296


>gi|194882124|ref|XP_001975163.1| GG20714 [Drosophila erecta]
 gi|190658350|gb|EDV55563.1| GG20714 [Drosophila erecta]
          Length = 497

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 64/257 (24%), Positives = 92/257 (35%), Gaps = 56/257 (21%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 106 YFGWDYQ--GFACQEDSNDTIESNLFRALSRTCLIDSRANSNYHRCGRTDKEVSAFCQVI 163

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  +  P            +  C  LN  L   +   +  + +    + ARF  + R
Sbjct: 164 SIDLRSKHSPEFQLDPTALSTEIDYCGLLNRVLP-KNIQCVAWMPLRSPVYSARFDCVSR 222

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           SY Y                   PK  LD   M  A   L    DF  F    +H   ++
Sbjct: 223 SYRY-----------------YFPKGDLDIGAMSQACDLLERHADFRNFCKMDVHNGVTN 265

Query: 168 PIRTI--------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            +R +        D    NS  ++  + + A +FL  QIR  +  L LVG  K + T + 
Sbjct: 266 YMRNLQSARVVACDENHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKESPTVIS 325

Query: 220 KALQAQDRKECGPLAPP 236
           + L  +    C P   P
Sbjct: 326 ELLDVESNP-CKPQYSP 341


>gi|302810046|ref|XP_002986715.1| hypothetical protein SELMODRAFT_124462 [Selaginella moellendorffii]
 gi|300145603|gb|EFJ12278.1| hypothetical protein SELMODRAFT_124462 [Selaginella moellendorffii]
          Length = 318

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 70/264 (26%), Positives = 102/264 (38%), Gaps = 29/264 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGR 50
           M +  + + Y G+GY G QR    ++I+G +E+A  LV    +  +G          A R
Sbjct: 1   MEKAALFVVYCGAGYKGMQRNPGAATIEGVLEEA--LVRAGAIGSNGCSRNWLDWKRAAR 58

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD  V AL QV      R ++   L    N +L    +I +L    V   F A+     R
Sbjct: 59  TDKEVSALGQVVS---ARLYLTPDLVHRTNEFL--PGSIRLLGFKRVPDDFSAKKMCASR 113

Query: 111 SYLYRI-ITRQAPLALEKGRAWLIPKSLDCENM-RIAAQHLVGRHDFTTFR-SIHCQASS 167
            Y Y + I    P   +      +    D E   +I  + L   H F  F   +      
Sbjct: 114 RYEYVLPIFAFDPRTGDDLEEEFL---FDFERFNQILGRFLGTDHSFHNFSWRVRPGDRE 170

Query: 168 PIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             RT+  F             + I V+ARSF+  QIR  VG    V       T + +AL
Sbjct: 171 ARRTVVEFRAADKIWIGGSEFVRIIVLARSFMAYQIRKMVGLAVAVMRDIAPVTTINRAL 230

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
           +++      P AP  GL  D   Y
Sbjct: 231 RSE-VDVIVPTAPEVGLLLDESFY 253


>gi|255938179|ref|XP_002559860.1| Pc13g14530 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211584480|emb|CAP92522.1| Pc13g14530 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 548

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 58/180 (32%), Positives = 70/180 (38%), Gaps = 21/180 (11%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILN-LSIVDKQFHARFS 106
           AGRTD GV A  QV    +  + +  I    LN  L   + I +L         F ARFS
Sbjct: 192 AGRTDKGVSAFGQVIGLRVRTDEMNYI--NVLNRVL--PEDIRVLAWCPNPPPGFDARFS 247

Query: 107 AIRRSYLYRIITRQA--PLALEKG-----------RAWLIPKSLDCENMRIAAQHLVGRH 153
              R Y Y   T  A  P     G           RA      LD E MR AA+H  G H
Sbjct: 248 CRERRYKY-FFTNPAFSPTPGSIGFQNRAQNGNGPRAEFREGWLDIEAMREAAKHFEGSH 306

Query: 154 DFTTFRSIHC--QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           DF  F  +    Q  +  R I H    S   +    +   +FL  Q+R  V  L LVG G
Sbjct: 307 DFRNFCKLDTNKQIDNFERIIHHSISQSIPQVYSFNLHGSAFLWHQVRHMVAILFLVGQG 366


>gi|256087150|ref|XP_002579739.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665218|emb|CAZ35978.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 369

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 69/263 (26%), Positives = 107/263 (40%), Gaps = 38/263 (14%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIF-------LVTGEIVVVH--GAGRTDSGVHALRQ 60
           Y+G GY+G QR     +I+G + KA+F       L + E   VH   A +TD  V AL Q
Sbjct: 2   YSGWGYYGMQRCPVFPTIEGELSKALFTCGQLDNLTSEEHKRVHFQRASKTDKSVSALGQ 61

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V    L  +    +L K  N+   + + I +L++  V + F +  S   R Y Y + T  
Sbjct: 62  VCSMQLKED--TDLLSKLNNS---LPENIRVLDIIRVTRGFSSYSSCTHRIYDYLLPT-- 114

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLV----------GRHDFTTFRS----IHCQAS 166
              AL    + L   +  C   R+  + +           G H+F  F S         S
Sbjct: 115 --FALSPATSSLNDST--CWTYRLTVEQITQVNRLLEKYKGTHNFYNFTSGRLVTDRSCS 170

Query: 167 SPIRTIDHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
             I + +       G      IR+  +SF+  QIR  +G    V  G  T    +    +
Sbjct: 171 RYIISAECMPTFLLGEHQYTIIRIAGQSFMLHQIRKMIGLALAVLRGYATEAVFDIVF-S 229

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           + R +  P AP  GL  + V++S
Sbjct: 230 KARIDI-PKAPGLGLMLNQVDFS 251


>gi|260655352|ref|ZP_05860840.1| tRNA pseudouridine synthase A [Jonquetella anthropi E3_33 E1]
 gi|260629800|gb|EEX47994.1| tRNA pseudouridine synthase A [Jonquetella anthropi E3_33 E1]
          Length = 113

 Score = 46.6 bits (109), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 42/98 (42%)

Query: 149 LVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
           L GRHDF+ F        +P R +        G L+ + V   +FL   +R  +G+L  V
Sbjct: 11  LEGRHDFSAFCRQSEVPENPWRRLYSVRFRRRGPLVVVAVCGDAFLTNMVRIMMGNLDDV 70

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             GK +   L   L+   R      APP GL F  V Y
Sbjct: 71  SRGKRSLDWLAGLLEGGRRSSSAMTAPPSGLTFWRVGY 108


>gi|225463117|ref|XP_002264487.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 1520

 Score = 46.2 bits (108), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 45/172 (26%), Positives = 68/172 (39%), Gaps = 27/172 (15%)

Query: 85   ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
            +   I ++    V   FHARFS + R Y Y                +    +L+   M  
Sbjct: 1279 LPKDIRVMGWCPVPIGFHARFSCLSREYKY----------------FFWRGNLNILAMES 1322

Query: 145  AAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQ 197
            A +  VG HDF  F  +      +  R I  F++    N      L  I++   +FL  Q
Sbjct: 1323 AGKKFVGEHDFRNFCKMDAVNVHNYRRHIISFEIAPTNNRYDGNQLWAIKIKGSAFLWHQ 1382

Query: 198  IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
            +R  V  L ++G G   S D+  AL   +R    P   +AP   L  +S E+
Sbjct: 1383 VRCMVAVLFMIGQGL-ESPDVVDALLDTERTSRKPQYAMAPEIPLVLESCEF 1433


>gi|41615123|ref|NP_963621.1| hypothetical protein NEQ333 [Nanoarchaeum equitans Kin4-M]
 gi|42559722|sp|P60354|TRUA_NANEQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|40068847|gb|AAR39182.1| NEQ333 [Nanoarchaeum equitans Kin4-M]
          Length = 209

 Score = 46.2 bits (108), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 37/115 (32%), Positives = 61/115 (53%), Gaps = 13/115 (11%)

Query: 99  KQFHARFSAIRR-SYLYR---IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHD 154
           K F  +  AI + SYL++   II R+  + + KG    +P +LD   M+ AA+H +G+ D
Sbjct: 67  KYFLPKDKAIEQISYLHKVGNIIVRKTKIKV-KG----LP-NLDL--MKEAAKHFIGKKD 118

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           FT F +I  +A +P+ TI  FD+    +     +V   FL+  +R  +  +  VG
Sbjct: 119 FTNF-TIEREAKNPLCTIIKFDIEERKDYYVFSIVGDRFLYHMVRKIISFIVSVG 172


>gi|255572341|ref|XP_002527109.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223533532|gb|EEF35272.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 438

 Score = 45.8 bits (107), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 65/275 (23%), Positives = 105/275 (38%), Gaps = 55/275 (20%)

Query: 8   IEYNGSGYFGWQRQKN-----GSSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHALRQV 61
           + Y G  ++G+  +        S I  ++E+   L+  +  + +   GRTD GV A+ QV
Sbjct: 108 VMYFGQRFYGFSSEGQMDPTVESEIFKALERTRLLIGDKKEIQYSRCGRTDKGVSAVGQV 167

Query: 62  AHFDLVREWVPVI---------------------LCKALNAYLKISDTISILNLSIVDKQ 100
               L+R  V  I                       + LN  L   + I I+    V   
Sbjct: 168 IAL-LLRSKVKDIDEIGKVFGETASQKHSEGEIDYVRVLNRVL--PNDIRIIGWCPVPND 224

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F ARFS + R Y Y                +    +L+   M  A +  +G HDF  F  
Sbjct: 225 FSARFSCLSREYKY----------------FFRGDNLNLLAMESAGKKFIGEHDFRNFCK 268

Query: 161 IHC-QASSPIRTIDHFDVNSF-----GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           +      +  R I  F+++       GN L  I++   +FL  Q+R  V  L ++G G  
Sbjct: 269 MDAMNVHNYRRNITSFEISPCHERYEGNQLFAIKIRGSAFLWHQVRCMVAVLFMIGQGLE 328

Query: 214 TSTDLEKALQA--QDRKECGPLAPPEGLYFDSVEY 246
           +   ++  L      RK   P+AP   L   S ++
Sbjct: 329 SPDVIDVLLDTVRTPRKPQYPMAPEIPLVLHSCDF 363


>gi|324501041|gb|ADY40469.1| tRNA pseudouridine synthase tag-124 [Ascaris suum]
 gi|324504466|gb|ADY41930.1| tRNA pseudouridine synthase tag-124 [Ascaris suum]
          Length = 388

 Score = 45.8 bits (107), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 69/291 (23%), Positives = 106/291 (36%), Gaps = 80/291 (27%)

Query: 15  YFGW------QRQKNGSSIQGSIEKAIF----LVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           Y+GW      Q+Q   ++++  I+ A+     + +        +GRTD GV A RQ+A  
Sbjct: 4   YYGWEYEGLVQQQDTVNTVEEVIKDALLRTRLIESWNKCEWIRSGRTDKGVSAFRQIASL 63

Query: 65  DLVREWVP-----------------------VILCKALNAYLKISDTISILNLSIVDKQF 101
            +VR   P                       ++  K LN  L     I +L  + V   F
Sbjct: 64  -IVRSSDPEGEHVFWPENADPHSRITPPHSELMYLKMLNGVL--PKNIRVLAWAPVALDF 120

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
           +ARFS  +R Y Y         A  +G         D E +R A   L+G HDF     I
Sbjct: 121 NARFSCTKRVYKY---------AFPRG-------DFDLEAIRKACSLLIGEHDFRNICRI 164

Query: 162 HCQAS----SPIRTIDHFDVN--------------------SFGNLIEIRVVARSFLHTQ 197
               +    S +R +  FD +                    S  +L+E  +++  FL  Q
Sbjct: 165 DLNKARVEMSYVRMV--FDASISVVLESGERVEVSSEPEPHSPYSLVEFTMISSGFLWHQ 222

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEY 246
           IR  +  +  +G G      + + L  +   RK    LAP   L      Y
Sbjct: 223 IRCVMALMYEIGKGNEKPEVISELLDIEKTPRKPAYGLAPSSPLCLFDCSY 273


>gi|76638649|ref|XP_593895.2| PREDICTED: pseudouridylate synthase 1 isoform 1 [Bos taurus]
 gi|297484682|ref|XP_002694500.1| PREDICTED: pseudouridylate synthase 1 [Bos taurus]
 gi|296478661|gb|DAA20776.1| pseudouridylate synthase 1 [Bos taurus]
          Length = 433

 Score = 45.8 bits (107), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 74/272 (27%), Positives = 114/272 (41%), Gaps = 50/272 (18%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 94  LLMAYSGKGYHGMQRNV-GSSKFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 152

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 153 KGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDARTY 207

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR--------------HDFTTF 158
           +Y + T     A     A     S D E  R++A+ L GR              H+FT+ 
Sbjct: 208 VYMLPT----FAF----AHKDHDSQD-ETYRLSAETL-GRVNRLLACYKGTHNFHNFTSQ 257

Query: 159 RSIHCQASSPIRTIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           +  H + S+    +D F    F         I+V  +SF+  QIR  VG +  +  G   
Sbjct: 258 KGPH-EPSARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAIVKGYAP 316

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + LE+     + K   P AP  GL  + V +
Sbjct: 317 ESVLERCW--GEAKVDVPKAPGLGLVLERVHF 346


>gi|114647862|ref|XP_001139560.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial [Pan
           troglodytes]
          Length = 427

 Score = 45.8 bits (107), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 72/270 (26%), Positives = 109/270 (40%), Gaps = 46/270 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 88  LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 146

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 147 KGVSAAGQVVSLKV---WLIEDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTY 201

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 202 CYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQK 252

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    +
Sbjct: 253 GPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPES 312

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            LE++   +  K   P AP  GL  + V +
Sbjct: 313 VLERSWGTE--KVDVPKAPGLGLVLERVHF 340


>gi|242008043|ref|XP_002424822.1| tRNA pseudouridine synthase, putative [Pediculus humanus corporis]
 gi|212508372|gb|EEB12084.1| tRNA pseudouridine synthase, putative [Pediculus humanus corporis]
          Length = 430

 Score = 45.8 bits (107), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 98/260 (37%), Gaps = 56/260 (21%)

Query: 15  YFGWQR-----QKNGSS-----IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           YFGW       Q+N S+     +  +++K   +   E       GRTD GV A  QV   
Sbjct: 70  YFGWDTSGFVIQENTSNTIEQFMFDALKKCCLIENIETSNYQKCGRTDKGVSAFSQVISL 129

Query: 65  DLVREWVP----------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           D VR  +           +  C  LN  L     I   + + V     +R     R+Y Y
Sbjct: 130 D-VRSKLENPNHENAEQEIEYCSMLNRLL--PPFIKCYSWAHVGSDVGSRHDCSERTYKY 186

Query: 115 RIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSPIRT 171
                              PK +LD   MR AA+ L+G HDF     +      ++  R 
Sbjct: 187 -----------------YFPKGNLDINLMREAAKSLLGSHDFRNLCKMDVANGITNFNRN 229

Query: 172 IDHFDVNSFGNLIE---------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           I + D+     L+E           + ++ FL+ QIRS +  L LVG  K  S D+   L
Sbjct: 230 IIYADIKPCSFLLEKQSGYQFYIFEIKSKCFLYHQIRSIMSVLLLVGQKK-ESPDIINDL 288

Query: 223 QAQDRKECGP---LAPPEGL 239
              ++    P   LA P  L
Sbjct: 289 LDINKNPAKPQYDLALPMPL 308


>gi|194043580|ref|XP_001928625.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial isoform 2
           [Sus scrofa]
 gi|311270525|ref|XP_003132902.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial [Sus
           scrofa]
          Length = 400

 Score = 45.8 bits (107), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 71/269 (26%), Positives = 110/269 (40%), Gaps = 36/269 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 58  KIVLLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 116

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     
Sbjct: 117 RTDKGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 171

Query: 110 RSYLYRIIT-----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           R+Y Y + T     +   +  E  R  L  ++L   N  +A     G H+F  F S    
Sbjct: 172 RTYFYMLPTFAFAHKDHDVQDETYR--LSTETLQRVNRLLAC--YKGTHNFHNFTSQKGP 227

Query: 165 ASSPIR--TIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
                R   +D F    F         I+V  +SF+  QIR  VG +  +  G    + L
Sbjct: 228 REPSARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAIIKGYAPESVL 287

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           E++    + K   P AP  GL  + V + 
Sbjct: 288 ERSW--GEAKVDVPKAPGLGLVLERVHFE 314


>gi|4455035|gb|AAD21042.1| pseudouridine synthase 1 [Homo sapiens]
          Length = 365

 Score = 45.8 bits (107), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 72/271 (26%), Positives = 109/271 (40%), Gaps = 46/271 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 26  LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 84

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 85  KGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTY 139

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 140 CYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQK 190

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    +
Sbjct: 191 GPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPES 250

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            LE++   +  K   P AP  GL  + V + 
Sbjct: 251 VLERSWGTE--KVDVPKAPGLGLVLERVHFE 279


>gi|70166645|ref|NP_079491.2| tRNA pseudouridine synthase A, mitochondrial isoform 1 [Homo
           sapiens]
 gi|114152895|sp|Q9Y606|TRUA_HUMAN RecName: Full=tRNA pseudouridine synthase A, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase I; AltName:
           Full=tRNA-uridine isomerase I; Flags: Precursor
 gi|18027830|gb|AAL55876.1|AF318369_1 unknown [Homo sapiens]
 gi|94466373|gb|AAH09505.2| Pseudouridylate synthase 1 [Homo sapiens]
 gi|94466377|gb|AAH19320.2| Pseudouridylate synthase 1 [Homo sapiens]
 gi|193786660|dbj|BAG51983.1| unnamed protein product [Homo sapiens]
 gi|261860288|dbj|BAI46666.1| pseudouridylate synthase 1 [synthetic construct]
 gi|311347138|gb|ADP90494.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347141|gb|ADP90496.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347144|gb|ADP90498.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347147|gb|ADP90500.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347150|gb|ADP90502.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347153|gb|ADP90504.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347156|gb|ADP90506.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347159|gb|ADP90508.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347162|gb|ADP90510.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347165|gb|ADP90512.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347168|gb|ADP90514.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347171|gb|ADP90516.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347174|gb|ADP90518.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347177|gb|ADP90520.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347180|gb|ADP90522.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347183|gb|ADP90524.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347186|gb|ADP90526.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347189|gb|ADP90528.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347192|gb|ADP90530.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347195|gb|ADP90532.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347198|gb|ADP90534.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347201|gb|ADP90536.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347204|gb|ADP90538.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347207|gb|ADP90540.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347210|gb|ADP90542.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347213|gb|ADP90544.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347216|gb|ADP90546.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347219|gb|ADP90548.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347222|gb|ADP90550.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347225|gb|ADP90552.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347228|gb|ADP90554.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347231|gb|ADP90556.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347234|gb|ADP90558.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347237|gb|ADP90560.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347240|gb|ADP90562.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347243|gb|ADP90564.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347246|gb|ADP90566.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347249|gb|ADP90568.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347252|gb|ADP90570.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347255|gb|ADP90572.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
          Length = 427

 Score = 45.8 bits (107), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 72/270 (26%), Positives = 109/270 (40%), Gaps = 46/270 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 88  LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 146

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 147 KGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTY 201

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 202 CYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQK 252

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    +
Sbjct: 253 GPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPES 312

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            LE++   +  K   P AP  GL  + V +
Sbjct: 313 VLERSWGTE--KVDVPKAPGLGLVLERVHF 340


>gi|315304866|ref|ZP_07875006.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
 gi|313626765|gb|EFR95758.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
          Length = 83

 Score = 45.4 bits (106), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 6/85 (7%)

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVA---RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           S +RT+   D     N  E  V+A     FL+  +R   G+L   G G+ +  D+ KAL 
Sbjct: 1   SKVRTLYSIDFYEEDN--ETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALL 58

Query: 224 AQDRKEC-GPLAPPEGLYFDSVEYS 247
           A+DR++     APP+GLY   V+Y 
Sbjct: 59  ARDRQKLISKTAPPQGLYLWRVDYE 83


>gi|19922728|ref|NP_611646.1| CG3045 [Drosophila melanogaster]
 gi|7291383|gb|AAF46811.1| CG3045 [Drosophila melanogaster]
 gi|16182987|gb|AAL13605.1| GH14326p [Drosophila melanogaster]
 gi|220945178|gb|ACL85132.1| CG3045-PA [synthetic construct]
 gi|220955082|gb|ACL90084.1| CG3045-PA [synthetic construct]
          Length = 499

 Score = 45.4 bits (106), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 64/258 (24%), Positives = 91/258 (35%), Gaps = 57/258 (22%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 107 YFGWDYQ--GFACQEDSNDTIESNLFRALARTCLIESRATSNYHRCGRTDKEVSAFCQVI 164

Query: 63  HFDLVREWVP------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
             DL  +  P            +  C  LN  L   +   +  + +    + ARF  + R
Sbjct: 165 SIDLRSKHPPESQLDPTALSSEIDYCGLLNRVLP-KNIQCVAWMPLRSPVYSARFDCVSR 223

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQASS 167
           +Y Y                   PK  LD   MR A   LV   DF  F    +H   ++
Sbjct: 224 TYRY-----------------YFPKGDLDIAAMRKACDLLVRHADFRNFCKMDVHNGVTN 266

Query: 168 PIRTIDHFDV---------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            +R +    V         NS  ++  + + A +FL  QIR  +  L LVG  K     +
Sbjct: 267 YMRNLQSARVEACDQTNHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKENPGVI 326

Query: 219 EKALQAQDRKECGPLAPP 236
              L  +    C P   P
Sbjct: 327 SDLLDVESNP-CKPQYTP 343


>gi|163755611|ref|ZP_02162730.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
 gi|161324524|gb|EDP95854.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
          Length = 262

 Score = 45.4 bits (106), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 56/259 (21%), Positives = 110/259 (42%), Gaps = 21/259 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G  Y GWQ+Q + +++Q   E+ +  V G +   +  +GRTD+ V A  ++A
Sbjct: 8   YLITLQYLGFRYHGWQKQPDVNTVQRMTERTLAYVFGHKNFKLLASGRTDAKVSA-NEIA 66

Query: 63  HFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             +L  +   + + + L  + K +   I  L ++  +++F+       + Y+Y     + 
Sbjct: 67  -IELFLDNETLNIPEFLPLFNKNLPQDIRALAITETNEKFNIIQHPKVKEYIYLFAFGEK 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---RSIH---------CQ-ASSP 168
                      +   LD E M+  A+   G H   T+    + H         C+   + 
Sbjct: 126 YHPFAAPYMTNVLGDLDVELMKKGAKLFEGNHYLKTYCYKPTEHTILEGEIELCEITEND 185

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           + T   F   S+     +RV    F   QIR  +G+L L+G  +     ++++L      
Sbjct: 186 LYTASFFPEKSYV----LRVQGAGFKRHQIRMMMGTLILLGRHELDLDFIKRSLLPNSTL 241

Query: 229 ECGPLAPPEGLYFDSVEYS 247
           E   +AP  GL  + + + 
Sbjct: 242 EVNYIAPASGLMLNKMTFK 260


>gi|268568248|ref|XP_002647980.1| C. briggsae CBR-PUS-1 protein [Caenorhabditis briggsae]
 gi|187040672|emb|CAP20635.1| CBR-PUS-1 protein [Caenorhabditis briggsae AF16]
          Length = 437

 Score = 45.4 bits (106), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 65/278 (23%), Positives = 104/278 (37%), Gaps = 49/278 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQG----SIEKAIFLVTGE-----IVVVHGAGRTDS 53
           +Y M++ Y G  Y+G Q QK+  +I+     ++EKA ++   +           A RTD 
Sbjct: 34  KYAMLLGYQGKKYYGMQLQKDLPTIESKLLEAMEKAGWITAAQREKPFDFFFQRAARTDR 93

Query: 54  GVHALRQVAHFDLVR--EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
            V A RQ+    L R  E   V     LN  L   + I +  +      FH +     R+
Sbjct: 94  AVSAARQMCGMQLPRDDEKYKVDGPGILNNLL--PNDIRVFGMKRTINFFHPQKQCDYRT 151

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV----------GRHDFTTFRS- 160
           Y Y   T            +  P  L     RI+ + L           G H+F  + + 
Sbjct: 152 YSYTCPT----------FVFAKPTELTNAAFRISKETLAEVNDILSIYKGTHNFFNYTAK 201

Query: 161 ------------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
                       +  +   P    D F        I+I V  +SF+  QIR  VG +  V
Sbjct: 202 RAYDDMSSNRYIVSFECKEPFLFRDEFRKEDV-EFIQIVVKGQSFVLHQIRKMVGMVITV 260

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                  + ++++ + Q R +  P+AP  GL  +   Y
Sbjct: 261 VRELHLKSAIQRSFEGQ-RMDI-PMAPGLGLLLERTHY 296


>gi|70166599|ref|NP_001002019.1| tRNA pseudouridine synthase A, mitochondrial isoform 2 [Homo
           sapiens]
 gi|70166634|ref|NP_001002020.1| tRNA pseudouridine synthase A, mitochondrial isoform 2 [Homo
           sapiens]
 gi|12804097|gb|AAH02901.1| Pseudouridylate synthase 1 [Homo sapiens]
 gi|123989720|gb|ABM83888.1| pseudouridylate synthase 1 [synthetic construct]
 gi|123999259|gb|ABM87208.1| pseudouridylate synthase 1 [synthetic construct]
 gi|158257916|dbj|BAF84931.1| unnamed protein product [Homo sapiens]
 gi|311347139|gb|ADP90495.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347142|gb|ADP90497.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347145|gb|ADP90499.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347148|gb|ADP90501.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347151|gb|ADP90503.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347154|gb|ADP90505.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347157|gb|ADP90507.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347160|gb|ADP90509.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347163|gb|ADP90511.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347166|gb|ADP90513.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347169|gb|ADP90515.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347172|gb|ADP90517.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347175|gb|ADP90519.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347178|gb|ADP90521.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347181|gb|ADP90523.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347184|gb|ADP90525.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347187|gb|ADP90527.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347190|gb|ADP90529.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347193|gb|ADP90531.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347196|gb|ADP90533.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347199|gb|ADP90535.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347202|gb|ADP90537.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347205|gb|ADP90539.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347208|gb|ADP90541.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347211|gb|ADP90543.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347214|gb|ADP90545.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347217|gb|ADP90547.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347220|gb|ADP90549.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347223|gb|ADP90551.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347226|gb|ADP90553.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347229|gb|ADP90555.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347232|gb|ADP90557.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347235|gb|ADP90559.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347238|gb|ADP90561.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347241|gb|ADP90563.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347244|gb|ADP90565.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347247|gb|ADP90567.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347250|gb|ADP90569.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347253|gb|ADP90571.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347256|gb|ADP90573.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
          Length = 399

 Score = 45.4 bits (106), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 72/270 (26%), Positives = 109/270 (40%), Gaps = 46/270 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 60  LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 118

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 119 KGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTY 173

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 174 CYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQK 224

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    +
Sbjct: 225 GPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPES 284

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            LE++   +  K   P AP  GL  + V +
Sbjct: 285 VLERSWGTE--KVDVPKAPGLGLVLERVHF 312


>gi|257076635|ref|ZP_05570996.1| tRNA pseudouridine synthase A [Ferroplasma acidarmanus fer1]
          Length = 250

 Score = 45.4 bits (106), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 97/245 (39%), Gaps = 41/245 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +   Y+G+ + G+QR    +S++ SI K I    G    +  A RTD  V A   V  
Sbjct: 3   YLIKYGYDGTSFTGFQRGNGENSVEDSIIK-ILKKYGIGNNIESAARTDRYVSARGNVML 61

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            D                   I + + ILN  I    F++ +SA+ R     +  R   +
Sbjct: 62  VD---------------TDTNIGNVMGILNARIPGMFFYS-YSALDRY----LNPRHNSM 101

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS--PIRTIDHFDVNSFG 181
              K  +++I +++D   +       VG+HDF  F    C+  S   +RTI   + ++  
Sbjct: 102 ---KQYSYIITENIDISRVMETLGEFVGQHDFVNF----CKLDSRNTVRTIKSINYSTRN 154

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
               I +  RSF+  QIRS +    +   GK     LE             LA PE L  
Sbjct: 155 GFYIINIQGRSFVWHQIRSMMAFALM---GKKHPFSLENKFTY--------LASPEPLVL 203

Query: 242 DSVEY 246
             + Y
Sbjct: 204 MDISY 208


>gi|213584576|ref|ZP_03366402.1| tRNA pseudouridine synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. E98-0664]
          Length = 57

 Score = 45.4 bits (106), Expect = 0.007,   Method: Composition-based stats.
 Identities = 21/42 (50%), Positives = 27/42 (64%)

Query: 8  IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAG 49
          IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AG
Sbjct: 16 IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAG 57


>gi|290979041|ref|XP_002672243.1| predicted protein [Naegleria gruberi]
 gi|284085818|gb|EFC39499.1| predicted protein [Naegleria gruberi]
          Length = 483

 Score = 45.4 bits (106), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 98/249 (39%), Gaps = 58/249 (23%)

Query: 48  AGRTDSGVHALRQV-----------AHFDLVREWVPVILCKALN---------AYLKISD 87
           A RTD GV A+R              H D  + +    LCK LN           L + D
Sbjct: 172 ACRTDRGVSAVRNAFACVMTLPNTQNHKDTFK-FNNEELCKTLNDRINNHVRIKNLNLMD 230

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAA 146
            I I N+  V  +F        R YLY +     PL AL+     +I K  +  N+    
Sbjct: 231 QIKIFNIQRVPSRFVLHHWCQFRRYLYVL-----PLSALDLSSRNIITKCNNIFNLETNE 285

Query: 147 Q----------HLVGRHDFTTFRSIHCQASSP-----IRTIDHFDVNSFGNL--IEIRVV 189
           Q          H  G H F  F ++  +  S      ++T+   + N  G+L  + I + 
Sbjct: 286 QKCQKLNELLGHFEGIHLFHNF-TVDAKPGSDSSRRHVKTLKIIEQNLEGDLPHVVIEIS 344

Query: 190 ARSFLHTQIRSFVGSL------------KLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            RSF+  QIR  +G++              V D    +   E   +AQ  +   P+AP E
Sbjct: 345 GRSFMLHQIRMMIGTVIALMRGMAPNMNTTVQDNTIVNDFFENLFKAQ-TEVLLPMAPSE 403

Query: 238 GLYFDSVEY 246
           GL+ D++++
Sbjct: 404 GLFLDNLDF 412


>gi|308507857|ref|XP_003116112.1| CRE-PUS-1 protein [Caenorhabditis remanei]
 gi|308251056|gb|EFO95008.1| CRE-PUS-1 protein [Caenorhabditis remanei]
          Length = 438

 Score = 45.4 bits (106), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 64/273 (23%), Positives = 107/273 (39%), Gaps = 37/273 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQG----SIEKAIFLVTGE-----IVVVHGAGRTDS 53
           +Y M++ Y G  Y+G Q QK+  +I+     ++EKA ++   +           A RTD 
Sbjct: 34  KYAMLLGYQGKKYYGMQLQKDLPTIESKLLEAMEKAGWITAAQRDKPFDFFFQRAARTDR 93

Query: 54  GVHALRQVAHFDLVREWVPVILCKA--LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
            V A RQ+    L R+        A  LN  L   D I +  +      FH +     R+
Sbjct: 94  AVSAARQMCGMQLPRDDDKYQTDGAGVLNNLL--PDDIRVFGMRRTINFFHPQKQCDYRT 151

Query: 112 YLYR----IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS------- 160
           Y Y     +  +   L      A+ +PK    E   I + +  G H+F  + +       
Sbjct: 152 YSYTCPSFVFAKPTELT---NSAFRLPKETLAEVNDILSIY-KGTHNFFNYTAKRAYNDM 207

Query: 161 ------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
                 +  +   P    D F        ++I V  +SF+  QIR  VG +  V      
Sbjct: 208 SSNRYIVSFECKEPFLFRDEFRKEDV-EFVQIVVKGQSFVLHQIRKMVGMVITVVRELHL 266

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + ++++ + Q R +  P+AP  GL  +   Y 
Sbjct: 267 KSAIQRSFEGQ-RMDI-PMAPGLGLLLERTHYD 297


>gi|119618938|gb|EAW98532.1| pseudouridylate synthase 1, isoform CRA_c [Homo sapiens]
          Length = 432

 Score = 45.4 bits (106), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 72/270 (26%), Positives = 109/270 (40%), Gaps = 46/270 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 93  LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 151

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 152 KGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTY 206

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 207 CYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQK 257

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    +
Sbjct: 258 GPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPES 317

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            LE++   +  K   P AP  GL  + V +
Sbjct: 318 VLERSWGTE--KVDVPKAPGLGLVLERVHF 345


>gi|316973638|gb|EFV57202.1| putative tRNA pseudouridine synthase tag-124 [Trichinella spiralis]
          Length = 471

 Score = 45.4 bits (106), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 69/277 (24%), Positives = 104/277 (37%), Gaps = 74/277 (26%)

Query: 3   RYC-----MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG--------AG 49
           RYC     +++ Y G    G+  Q N    Q ++E  IF    E  ++           G
Sbjct: 33  RYCRRHIALMVAYLGWDLDGFCAQNNS---QNTVESKIFKALIETKLIQSLETANYSRCG 89

Query: 50  RTDSGVHALRQVAHFDL------------------------VREWVP----VILCKALNA 81
           RTD  V A  QV   D+                         R+  P    +   K LN+
Sbjct: 90  RTDKTVSAFSQVLSLDVRSNQTTGVGVFEPDGYCPNEPKPTSRKTTPKSEELDYAKILNS 149

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWL--------- 132
            L     I +L  + V++ F+AR++   R Y Y        L +     +L         
Sbjct: 150 VL--PQEIRVLAWAPVERTFNARYNCTSRQYKYFFPKGALNLKVSTVVDFLHFSAIVALF 207

Query: 133 --IPKSLDC---ENMRIAAQHLVGRHDFTTFRSIHC---QASSPIRTIDHFDV-----NS 179
               +   C   + M  A++ L+G HDF  F  I     +  S +RT+  FDV     N+
Sbjct: 208 SNFRRGTICVYFQLMEQASKRLIGEHDFRNFCKIDMSKNEIQSCVRTV--FDVQFTKVNA 265

Query: 180 FG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
            G     L    +VA +FL  QIR  +  L  +G+GK
Sbjct: 266 GGLNSRTLCCFTIVANAFLWHQIRCIMSVLFAIGEGK 302


>gi|330804770|ref|XP_003290364.1| hypothetical protein DICPUDRAFT_154861 [Dictyostelium purpureum]
 gi|325079531|gb|EGC33127.1| hypothetical protein DICPUDRAFT_154861 [Dictyostelium purpureum]
          Length = 449

 Score = 45.1 bits (105), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 72/173 (41%), Gaps = 28/173 (16%)

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           +E  P +  K LN  L     I +L  + +   F++RFS + R+Y Y             
Sbjct: 182 KEEFPYV--KMLNGVL--PPEIRVLGWAPIPFHFNSRFSTLFRTYKY------------- 224

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFD---VNSFGNL 183
              +    ++D   M+ A  H +G HDF+ F  +  +   S  R I  F    VN+  +L
Sbjct: 225 ---FFTLNNMDLNLMKEAGNHYLGEHDFSNFCKMDIENVKSFKRVILEFSIEPVNNHNDL 281

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               +   +FL  QIR  +  L L+G  K+  + + + L   +    G   PP
Sbjct: 282 YVATIKGYAFLWHQIRCMMAMLFLIGQKKFPVSIIPELLDTSN----GITKPP 330


>gi|302806719|ref|XP_002985091.1| hypothetical protein SELMODRAFT_44317 [Selaginella moellendorffii]
 gi|300147301|gb|EFJ13966.1| hypothetical protein SELMODRAFT_44317 [Selaginella moellendorffii]
          Length = 363

 Score = 45.1 bits (105), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 51/118 (43%), Gaps = 13/118 (11%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVH 56
           + + Y+G GY G QR K   +I+G +E+A+F          G         A RTD GV 
Sbjct: 5   IFVSYSGYGYQGMQRNKGCKTIEGDLEEALFKAGAIAESTFGDPRKIDWARAARTDKGVS 64

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           A  QV       +  P    + +N++L     I +L  + V   F A+    RR Y Y
Sbjct: 65  AAGQVVSGRFFVD--PPGFVERVNSHL--PKQIRVLGFTRVTGTFSAKNLCDRRRYEY 118


>gi|251823909|ref|NP_001156523.1| tRNA pseudouridine synthase A [Ovis aries]
 gi|238815029|gb|ACR56711.1| pseudouridylate synthase 1 [Ovis aries]
          Length = 400

 Score = 45.1 bits (105), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 72/268 (26%), Positives = 108/268 (40%), Gaps = 36/268 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 58  KIVLLMAYSGKGYHGMQRNV-GSSKFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 116

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     
Sbjct: 117 RTDKGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 171

Query: 110 RSYLYRIIT-----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           R+Y Y + T     +   L  E  R  L  ++L   N  +A     G H+F  F S    
Sbjct: 172 RTYFYMLPTFAFAHKDHDLQDETYR--LSAETLGRVNRLLAC--YKGTHNFHNFTSQKGP 227

Query: 165 ASSPIR--TIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
                R   +D F    F         I+V  +SF+  QIR  VG +  +  G      L
Sbjct: 228 HEPSARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAIIKGYAPEGVL 287

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEY 246
           E+     + K   P AP  GL  + V +
Sbjct: 288 ERCW--GEAKVDVPKAPGLGLVLERVHF 313


>gi|302809155|ref|XP_002986271.1| hypothetical protein SELMODRAFT_44320 [Selaginella moellendorffii]
 gi|300146130|gb|EFJ12802.1| hypothetical protein SELMODRAFT_44320 [Selaginella moellendorffii]
          Length = 363

 Score = 45.1 bits (105), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 51/118 (43%), Gaps = 13/118 (11%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVH 56
           + + Y+G GY G QR K   +I+G +E+A+F          G         A RTD GV 
Sbjct: 5   IFVSYSGYGYQGMQRNKGCKTIEGDLEEALFKAGAIAESTFGDPRKIDWARAARTDKGVS 64

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           A  QV       +  P    + +N++L     I +L  + V   F A+    RR Y Y
Sbjct: 65  AAGQVVSGRFFVD--PPGFVERVNSHL--PKQIRVLGFTRVTGTFSAKNLCDRRRYEY 118


>gi|170586438|ref|XP_001897986.1| tRNA pseudouridine synthase family protein [Brugia malayi]
 gi|158594381|gb|EDP32965.1| tRNA pseudouridine synthase family protein [Brugia malayi]
          Length = 225

 Score = 45.1 bits (105), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 35/127 (27%), Positives = 57/127 (44%), Gaps = 14/127 (11%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEI-----VVVHGAGRTDSG 54
           Y +++ Y G  Y G Q QK+  +I+G + KA+    ++   ++          A RTD  
Sbjct: 29  YALLLAYQGKKYNGMQVQKDFPTIEGELFKAMAKCGYICENDVFSPVRFAFQRAARTDRS 88

Query: 55  VHALRQVAHFDLVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           V A RQ+    L  E     L  A   LN +L   + I +L +    + F A  +  +R+
Sbjct: 89  VSAARQMCSMRLAPENHEYFLKTATDKLNTHL--PEEIRVLGVRRATRSFKAHKNCDKRT 146

Query: 112 YLYRIIT 118
           Y Y + T
Sbjct: 147 YSYTLPT 153


>gi|50293511|ref|XP_449167.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49528480|emb|CAG62137.1| unnamed protein product [Candida glabrata]
          Length = 438

 Score = 45.1 bits (105), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 95/237 (40%), Gaps = 41/237 (17%)

Query: 10  YNGSGYFGWQRQKNGS---SIQGSIEKA------IFLVTGEIVVVHGAGRTDSGVHALRQ 60
           Y G  Y G   QK+ +   +I+G+I +A      +  +T +       GRTD GV A+ Q
Sbjct: 94  YLGWNYNGLAIQKDPTPLPTIEGTIIEALNKCKLVPSITPQEFEFSRCGRTDKGVSAMNQ 153

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD------------KQFHARFSAI 108
           V    +             N + +I   ++ILN  + D              F ARFS  
Sbjct: 154 VISLRVRSNLTDEEQKDPRNDHKEIQ-YVAILNQLLPDDIRISAVCLRPPNSFDARFSCE 212

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
            R Y Y        L  + G        LD + M+ AA+   G HDF  F  +    Q +
Sbjct: 213 YRHYKY--------LFHKDG--------LDLDRMQKAAKLYEGEHDFRNFCKLDGSKQIT 256

Query: 167 SPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           +  RT+   ++   + +     ++  +FL  Q+R     L LVG G    T +EK L
Sbjct: 257 NYNRTMISANIKHVYNDFYCFDLIGSAFLWHQVRCMTAILFLVGQGLEEPTLIEKML 313


>gi|291415803|ref|XP_002724139.1| PREDICTED: pseudouridylate synthase 1-like, partial [Oryctolagus
           cuniculus]
          Length = 391

 Score = 45.1 bits (105), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 70/274 (25%), Positives = 105/274 (38%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            
Sbjct: 58  KIVLLLAYSGKGYHGMQRNV-GSSQFRTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 116

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     
Sbjct: 117 RTDKGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 171

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          +    E  R++A+ L           G H F  F 
Sbjct: 172 RTYFYMLPT----FAFAHKD-----RDPQDETYRLSAETLQRVNRLLACYQGTHSFHNFT 222

Query: 160 SIHCQASSPIRT------IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R        +   V        IRV  +SF+  QIR  VG +  +  G  
Sbjct: 223 SQKGPREPSARRYILQMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYA 282

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    D K   P AP  GL  + V + 
Sbjct: 283 PESVLERSW--GDEKVDVPKAPGLGLVLERVHFE 314


>gi|321464083|gb|EFX75094.1| hypothetical protein DAPPUDRAFT_12957 [Daphnia pulex]
          Length = 319

 Score = 45.1 bits (105), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 63/262 (24%), Positives = 107/262 (40%), Gaps = 27/262 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           ++ +++ Y+G  Y G Q      +++G + +A   +         + + V    A RTD 
Sbjct: 4   KFAILLSYSGQNYLGMQFNHGFKTVEGELFQAFMKLEIMDDESFKSPQTVHFQRAARTDK 63

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+RQV    +        L   LN+ L   + I +  +  V   F+++ +   RSY 
Sbjct: 64  GVSAVRQVISLKI--RTPDEDLVNQLNSLL--PNCIKVFAMRKVTGGFNSKIACDSRSYS 119

Query: 114 YRIIT---RQAPLALEKGRAWLIPKSLDCENMRIAA-QHLVGRHDFTTFRSIHCQASSPI 169
           Y + T       +A   G   +  K LD  N  ++  +     H+FT+ R    Q  S  
Sbjct: 120 YVMPTFAFTSKEVAPTHGYR-VTSKILDEVNSLLSVFKGTRNYHNFTSGRP--AQDPSCK 176

Query: 170 RTIDHFDV-NSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           R I  F   + F       ++I +  +SF+  QIR  +G    V  G      L+KA + 
Sbjct: 177 RYITQFSCGDPFMIKEVEFVKITIKGQSFMLHQIRKMIGLTISVMRGFVPREILDKAFKM 236

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
           +  +   P AP   L  +   Y
Sbjct: 237 E--RVNVPTAPSLNLLLEEPHY 256


>gi|222625021|gb|EEE59153.1| hypothetical protein OsJ_11064 [Oryza sativa Japonica Group]
          Length = 403

 Score = 45.1 bits (105), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 89/223 (39%), Gaps = 51/223 (22%)

Query: 8   IEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHALRQV 61
           I Y G  ++G+  + +      S I  ++E+A  LV       +   GRTD GV A  QV
Sbjct: 98  IMYFGQRFYGFASEAHTEPTVESEIFKALERAKLLVGSRKESCYSRCGRTDKGVSATGQV 157

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ---FHARFSAIRRSYLYRIIT 118
                            ++ +L+    I    L ++D +   F ARFS + R Y Y    
Sbjct: 158 -----------------ISLFLR--SNIKDAKLDVLDNKSGDFLARFSCLGREYKY---- 194

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDV 177
                   KG        L+   M+ AA   +G HD+  F  +     S+  R I  F++
Sbjct: 195 -----LFWKG-------DLNISEMQKAALKFIGEHDYRNFCKMDAANVSNYRRHITDFNI 242

Query: 178 NSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           +++        L  I +   +FL  Q+R  V  L L+G G  T
Sbjct: 243 SAYDQRSNYDELWAITIKGSAFLWHQVRCMVAVLFLIGQGLET 285


>gi|218135247|ref|ZP_03464051.1| hypothetical protein BACPEC_03152 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990632|gb|EEC56643.1| hypothetical protein BACPEC_03152 [Bacteroides pectinophilus ATCC
           43243]
          Length = 83

 Score = 45.1 bits (105), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           + FD++  G  I IRV    FL+  +R   G+L   G  + T   +++AL   +R+  GP
Sbjct: 6   EKFDLDR-GREIVIRVSGNGFLYNMVRIIAGTLIDAGCKRRTPLSVKEALDGCNRELAGP 64

Query: 233 LAPPEGLYFDSVEY 246
            APP+GL    +++
Sbjct: 65  TAPPQGLTLIEIKH 78


>gi|125544113|gb|EAY90252.1| hypothetical protein OsI_11824 [Oryza sativa Indica Group]
          Length = 403

 Score = 45.1 bits (105), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 56/220 (25%), Positives = 88/220 (40%), Gaps = 51/220 (23%)

Query: 8   IEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHALRQV 61
           I Y G  ++G+  + +      S I  ++E+A  LV       +   GRTD GV A  QV
Sbjct: 98  IMYFGQRFYGFASEAHTEPTVESEIFKALERAKLLVGSRKESCYSRCGRTDKGVSATGQV 157

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ---FHARFSAIRRSYLYRIIT 118
                            ++ +L+    I    L ++D +   F ARFS + R Y Y    
Sbjct: 158 -----------------ISLFLR--SNIKDAKLDVLDNKSGDFLARFSCLGREYKY---- 194

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDV 177
                   KG        L+   M+ AA   +G HD+  F  +     S+  R I  F++
Sbjct: 195 -----LFWKG-------DLNISEMQKAALKFIGEHDYRNFCKMDAANVSNYRRHITDFNI 242

Query: 178 NSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           +++        L  I +   +FL  Q+R  V  L L+G G
Sbjct: 243 SAYDQRSNYDELWAITIKGSAFLWHQVRCMVAVLFLIGQG 282


>gi|168049023|ref|XP_001776964.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162671665|gb|EDQ58213.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 680

 Score = 45.1 bits (105), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 67/150 (44%), Gaps = 14/150 (9%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN--M 142
           + + I +L    V   F+ARFS + R Y Y  I     + +     W +  + + +   M
Sbjct: 387 LPEDIRVLGWCPVPPGFNARFSCMYREYKYFFIDDGLNIDV-----WTLIYAFNRQYNVM 441

Query: 143 RIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDV----NSFG--NLIEIRVVARSFLH 195
           + A +   G HDFT F  +      + +RTI HFD+      +G  ++  + V   +FL 
Sbjct: 442 KFACKQFEGEHDFTNFCKMDAANVHNYMRTITHFDIIPSNEKWGGKSVWIMNVKGTAFLW 501

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            Q+R     L +VG G    T +E+ L  +
Sbjct: 502 HQVRCMAAVLFMVGAGHEKPTIVEELLDVK 531


>gi|40882706|gb|AAR96247.1| putative pseudouridine synthase [Oryza sativa Japonica Group]
 gi|108708473|gb|ABF96268.1| tRNA pseudouridine synthase A family protein [Oryza sativa Japonica
           Group]
          Length = 411

 Score = 45.1 bits (105), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 92/231 (39%), Gaps = 51/231 (22%)

Query: 8   IEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGVHALRQV 61
           I Y G  ++G+  + +      S I  ++E+A  LV       +   GRTD GV A  QV
Sbjct: 98  IMYFGQRFYGFASEAHTEPTVESEIFKALERAKLLVGSRKESCYSRCGRTDKGVSATGQV 157

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ---FHARFSAIRRSYLYRIIT 118
                            ++ +L+    I    L ++D +   F ARFS + R Y Y    
Sbjct: 158 -----------------ISLFLR--SNIKDAKLDVLDNKSGDFLARFSCLGREYKY---- 194

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDV 177
                   KG        L+   M+ AA   +G HD+  F  +     S+  R I  F++
Sbjct: 195 -----LFWKG-------DLNISEMQKAALKFIGEHDYRNFCKMDAANVSNYRRHITDFNI 242

Query: 178 NSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           +++        L  I +   +FL  Q+R  V  L L+G G  T   ++  L
Sbjct: 243 SAYDQRSNYDELWAITIKGSAFLWHQVRCMVAVLFLIGQGLETPCIVDSLL 293


>gi|194755854|ref|XP_001960194.1| GF13245 [Drosophila ananassae]
 gi|190621492|gb|EDV37016.1| GF13245 [Drosophila ananassae]
          Length = 492

 Score = 44.7 bits (104), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 86/234 (36%), Gaps = 55/234 (23%)

Query: 14  GYFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQV 61
            YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV
Sbjct: 105 SYFGWDYQ--GLACQEDSNDTIESHLFRALTRTCLIESRATSNYHRCGRTDKEVSAFCQV 162

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILN------------LSIVDKQFHARFSAIR 109
              DL  +  P     A +   +I D   +LN            + +    + ARF  + 
Sbjct: 163 ISIDLRSKHPPESQLDATSISSEI-DYCGLLNRVLPKNIQCVAWMPLRSPVYSARFDCVA 221

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTF--RSIHCQAS 166
           R+Y Y                   PK  LD   M+ A  HLV   DF  F    +H   +
Sbjct: 222 RTYRY-----------------YFPKGDLDIPAMQEACNHLVRHADFRNFCKMDVHNGVT 264

Query: 167 SPIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +  R +    V        +S  ++  + + A +FL  QIR  +  L LVG  K
Sbjct: 265 NYTRNLQSARVEACEETLTDSGYDMYYLEIQANAFLWHQIRCIMAVLILVGQKK 318


>gi|323449394|gb|EGB05282.1| hypothetical protein AURANDRAFT_12283 [Aureococcus anophagefferens]
          Length = 239

 Score = 44.7 bits (104), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 60/131 (45%), Gaps = 19/131 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG-------------AG 49
           +  +++ Y G+ Y+G Q+Q   S +  +IE A+         VH              A 
Sbjct: 7   KLALLLGYRGANYYGLQKQSKESDLP-TIELALQEALNRAGAVHEGNQGDLSKIGWSRAA 65

Query: 50  RTDSGVHALRQV--AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           RTD  V A RQV  A  ++  + VP +L + LN   ++ D I + +   V K F+ + S 
Sbjct: 66  RTDKRVSAARQVVSAKLEVENDDVPALLER-LNG--ELPDDIKVFDAVRVIKGFNCKQSC 122

Query: 108 IRRSYLYRIIT 118
            RR Y Y + T
Sbjct: 123 DRRHYTYLLPT 133


>gi|115756434|ref|XP_001202324.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115938206|ref|XP_796203.2| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 494

 Score = 44.7 bits (104), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 67/264 (25%), Positives = 109/264 (41%), Gaps = 32/264 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  +++ Y G+ Y G QR     +I+  +  A+ + +G I    G            RTD
Sbjct: 72  KVAILLSYAGANYVGMQRNPGVQTIEEDLVNAL-VKSGAIPEDCGRNMNKMSFQRCARTD 130

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    ++   +   L + +N +L     I ++ ++     F+ + +   R+Y
Sbjct: 131 KGVSAAGQVVSLKVL---MLDNLMERINEHL--PPVIRVMGVTRTTGGFNCKNNCEFRTY 185

Query: 113 LYRIITRQ-APL---ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
           +Y I T    PL    LEK R          E +    +  +G H+F  F S       S
Sbjct: 186 MYLIPTFAFTPLEDFTLEKYRV----SDEKIEEVGEQLKKYIGTHNFHNFTSGKAFTDPS 241

Query: 168 PIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             R I  F      V+       I+V  +SF+  QIR  +G +  V  G    + +E+A 
Sbjct: 242 ANRYIKEFTCEKGFVDDGMEFAVIKVKGQSFMLHQIRKMLGLVLAVVRGLTPPSTVERAF 301

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
             Q+ K   P AP  GL  ++V Y
Sbjct: 302 --QEPKLDIPRAPGLGLVLEAVHY 323


>gi|332254114|ref|XP_003276176.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial [Nomascus
           leucogenys]
          Length = 421

 Score = 44.7 bits (104), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 70/273 (25%), Positives = 110/273 (40%), Gaps = 45/273 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY G Q +  GS    +IE  +    + +G I   HG            
Sbjct: 78  KIVLLMAYSGKGYHGMQWRNLGSLQAQTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 137

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     
Sbjct: 138 RTDKGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 192

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E  R++A+ L           G H+F  F 
Sbjct: 193 RTYCYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFT 243

Query: 160 SIHC-QASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S    Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G  
Sbjct: 244 SQKGPQEPSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYA 303

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             + LE++  ++  K   P AP  GL  + V +
Sbjct: 304 PESVLERSWGSE--KVDVPKAPGLGLVLERVHF 334


>gi|323337610|gb|EGA78855.1| Pus2p [Saccharomyces cerevisiae Vin13]
          Length = 406

 Score = 44.7 bits (104), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 16/121 (13%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTDSGV 55
           M++ Y GSGY+G Q      +I+G I   +F V G I   +           A RTD GV
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDV-GAISEENSLAPKKNSFMAAARTDKGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y 
Sbjct: 60  HAMLNLLSLKITLREDTV---AKLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYL 114

Query: 116 I 116
           I
Sbjct: 115 I 115


>gi|328350038|emb|CCA36438.1| pseudouridylate synthase [Pichia pastoris CBS 7435]
          Length = 422

 Score = 44.3 bits (103), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 51/194 (26%), Positives = 74/194 (38%), Gaps = 34/194 (17%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD---------- 98
           GRTD GV A+ QV   ++     P  L    N  +K  D I+ILN  +            
Sbjct: 104 GRTDKGVSAMNQVIGLNVRSRLTPEELESPEND-IKELDYINILNQLLPSDIRIHGVCLR 162

Query: 99  --KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
             K F ARFS   R Y Y        +  ++G        LD E+M+ AA    G HDF 
Sbjct: 163 PPKGFDARFSCRGRHYKY--------VFQDEG--------LDLESMKKAAPMFEGVHDFR 206

Query: 157 TFRSIH-----CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
            F  +         +  +R+     +          +   +FL  Q+R  V  L ++G G
Sbjct: 207 NFCKVDGAKQMTNYTRAVRSSQILPLEGHPGYYVFDLKGTAFLWHQVRCMVAILLMIGQG 266

Query: 212 KWTSTDLEKALQAQ 225
             +   + K L  Q
Sbjct: 267 FESPDIVSKLLDIQ 280


>gi|296213295|ref|XP_002753209.1| PREDICTED: tRNA pseudouridine synthase A [Callithrix jacchus]
          Length = 428

 Score = 44.3 bits (103), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 72/270 (26%), Positives = 108/270 (40%), Gaps = 46/270 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 89  LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 147

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N +L     I IL L  V   F+++     R+Y
Sbjct: 148 KGVSAAGQVVSLKV---WLIDGILEKINRHL--PSHIRILGLKRVTGGFNSKNKCDARTY 202

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 203 CYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYEGTHNFHNFTSQK 253

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    +
Sbjct: 254 GPQEPSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPES 313

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            LE++   +  K   P AP  GL  + V +
Sbjct: 314 LLERSWGTE--KVDVPKAPGLGLVLERVHF 341


>gi|148693448|gb|EDL25395.1| pseudouridine synthase 3, isoform CRA_a [Mus musculus]
          Length = 361

 Score = 44.3 bits (103), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 62/158 (39%), Gaps = 44/158 (27%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQ 147
           I +L  + V+  F ARFS + R+Y Y                   P++ LD   M  AAQ
Sbjct: 53  IRVLAWAPVEPSFSARFSCLERTYRY-----------------FFPRADLDIATMNYAAQ 95

Query: 148 HLVGRHDFTTF-------------RSIHC-------QASSPIRTIDHFDVNSFGNLIEIR 187
             VG HDF                R+I C       Q+    R  + F       L +  
Sbjct: 96  KYVGTHDFRNLCKMDVANGVINFQRTILCAQVQLVAQSPGEERRQEPF------QLCQFE 149

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           V+ ++FL+ Q+R  +  L L+G G      +++ L  Q
Sbjct: 150 VIGQAFLYHQVRCMMAILFLIGQGMEKPEIIDELLNIQ 187


>gi|328771895|gb|EGF81934.1| hypothetical protein BATDEDRAFT_87010 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 491

 Score = 44.3 bits (103), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 35/116 (30%), Positives = 59/116 (50%), Gaps = 6/116 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  +++ Y G+GY G Q   +  SI+  + KA+   +G I  +  A RTD GVHA  QV 
Sbjct: 100 KVVLLMSYCGTGYQGMQINPDVPSIELDLHKAL-AASGAIAFMRCA-RTDKGVHAGGQVV 157

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
              ++ +   +I  + +NA  ++   I +   + V +QFHA+     R Y Y + T
Sbjct: 158 SLKMIIQDSDII--ERINA--RLPPQIRVWGYARVQQQFHAKHHCDSRIYEYILPT 209


>gi|151943741|gb|EDN62051.1| pseudouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190407023|gb|EDV10290.1| pseudouridine synthase [Saccharomyces cerevisiae RM11-1a]
 gi|256269708|gb|EEU04978.1| Pus2p [Saccharomyces cerevisiae JAY291]
 gi|259146442|emb|CAY79699.1| Pus2p [Saccharomyces cerevisiae EC1118]
 gi|323333685|gb|EGA75078.1| Pus2p [Saccharomyces cerevisiae AWRI796]
 gi|323348667|gb|EGA82910.1| Pus2p [Saccharomyces cerevisiae Lalvin QA23]
 gi|323354937|gb|EGA86768.1| Pus2p [Saccharomyces cerevisiae VL3]
          Length = 370

 Score = 44.3 bits (103), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 16/121 (13%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTDSGV 55
           M++ Y GSGY+G Q      +I+G I   +F V G I   +           A RTD GV
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDV-GAISEENSLAPKKNSFMAAARTDKGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y 
Sbjct: 60  HAMLNLLSLKITLREDTV---AKLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYL 114

Query: 116 I 116
           I
Sbjct: 115 I 115


>gi|297693488|ref|XP_002824050.1| PREDICTED: tRNA pseudouridine synthase A-like [Pongo abelii]
          Length = 424

 Score = 44.3 bits (103), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 72/270 (26%), Positives = 108/270 (40%), Gaps = 46/270 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE  +    + +G I   HG            RTD
Sbjct: 85  LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 143

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 144 KGVSAAGQVVSLKV---WLIDNILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTY 198

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 199 CYLLPT----FAFAHKD-----RDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQK 249

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G     
Sbjct: 250 GPQEPSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPEC 309

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            LE++   +  K   P AP  GL  + V +
Sbjct: 310 VLERSWGTE--KVDVPKAPGLGLVLERVHF 337


>gi|326429850|gb|EGD75420.1| hypothetical protein PTSG_06496 [Salpingoeca sp. ATCC 50818]
          Length = 460

 Score = 44.3 bits (103), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 44/154 (28%), Positives = 63/154 (40%), Gaps = 41/154 (26%)

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
           K LN  L     I +++   VD  F ARFS   R Y Y                +    +
Sbjct: 164 KILNGLL--PPEIRVVDWGAVDTDFSARFSCNARHYKY----------------FFHRAN 205

Query: 137 LDCENMRIAAQHLVGRHDFTTFRSIHCQA------SSPIRTIDHFDV-----------NS 179
           +D   M+ A  HLVG HDF  F    C+A      ++ +RTI    V           +S
Sbjct: 206 MDTAAMQAACDHLVGEHDFRNF----CKADVAGGVTNFVRTIKEARVCPAEIGDASVHSS 261

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
            G  +L E  ++  +FL  Q+R  +  L +VG G
Sbjct: 262 DGDFDLWEFNIIGHAFLWHQVRCMMAVLFMVGRG 295


>gi|10086461|gb|AAG12521.1|AC015446_2 Putative pseudouridine synthase [Arabidopsis thaliana]
          Length = 442

 Score = 44.3 bits (103), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 36/138 (26%), Positives = 54/138 (39%), Gaps = 31/138 (22%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           + D I ++  S     FHARFS   R Y Y                +   ++L+   M  
Sbjct: 220 LPDDIRVIGWSPAPIDFHARFSCYAREYKY----------------FFWRQNLNLSAMDF 263

Query: 145 AAQHLVGRHDFTTF-----RSIHCQASSPIRTIDHFDVNSFGN------LIEIRVVARSF 193
           A +  +G HDF  F      ++HC      R +  F+V+   N      L    +   +F
Sbjct: 264 AGKKFIGEHDFRNFCKMDVANVHCYT----RRVTFFEVSPCQNSHEGDQLCTFTMRGSAF 319

Query: 194 LHTQIRSFVGSLKLVGDG 211
           L  QIR  V  L ++G G
Sbjct: 320 LWHQIRCMVAVLFMIGQG 337


>gi|109099290|ref|XP_001113470.1| PREDICTED: tRNA pseudouridine synthase A-like [Macaca mulatta]
          Length = 483

 Score = 44.3 bits (103), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 72/270 (26%), Positives = 109/270 (40%), Gaps = 46/270 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEK---AIFLVTGEIVVVHG----------AGRTD 52
           +++ Y+G GY G QR   GSS   +IE    +  + +G I   HG            RTD
Sbjct: 144 LLMAYSGKGYHGMQRNV-GSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTD 202

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV    +   W+   + + +N++L     I IL L  V   F+++     R+Y
Sbjct: 203 KGVSAAGQVVSLKV---WLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTY 257

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFRSIH 162
            Y + T     A          + +  E  R++A+ L           G H+F  F S  
Sbjct: 258 CYLLPT----FAFAH-----KDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQK 308

Query: 163 -CQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
             Q  S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    +
Sbjct: 309 GPQEPSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPES 368

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            LE++   +  K   P AP  GL  + V +
Sbjct: 369 VLERSWGTE--KVDVPKAPGLGLVLERVHF 396


>gi|330443553|ref|NP_011452.2| Pus2p [Saccharomyces cerevisiae S288c]
 gi|1403093|emb|CAA56699.1| pseudouridine synthase 2 [Saccharomyces cerevisiae]
 gi|329138894|tpg|DAA08039.2| TPA: Pus2p [Saccharomyces cerevisiae S288c]
          Length = 370

 Score = 44.3 bits (103), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 16/121 (13%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTDSGV 55
           M++ Y GSGY+G Q      +I+G I   +F V G I   +           A RTD GV
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDV-GAISEENSLAPKKNSFMAAARTDKGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y 
Sbjct: 60  HAMLNLLSLKITLREDTV---AKLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYL 114

Query: 116 I 116
           I
Sbjct: 115 I 115


>gi|19113277|ref|NP_596485.1| tRNA pseudouridine synthase Pus2 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74676179|sp|O94295|PUS2_SCHPO RecName: Full=tRNA pseudouridine synthase 2; AltName: Full=tRNA
           pseudouridylate synthase 2; AltName: Full=tRNA-uridine
           isomerase 2
 gi|3850107|emb|CAA21896.1| tRNA pseudouridine synthase Pus2 (predicted) [Schizosaccharomyces
           pombe]
          Length = 451

 Score = 44.3 bits (103), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 39/125 (31%), Positives = 59/125 (47%), Gaps = 12/125 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSI----EKAIFLVTGEIVVVH----GAGRTDS 53
           +R  +++ Y+G GY G Q      +I+G +    +K  +L T  I   H     A RTD 
Sbjct: 39  VRIIILLGYSGYGYHGIQINNPLKTIEGDVVAVLKKLGYLKTNNIDAEHLCIARAARTDK 98

Query: 54  GVHALRQVAHFDL-VREWVPVILCKA-LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           GVH LR +   +L V + + + L K  LN  L     I + ++    K F+ R S   R+
Sbjct: 99  GVHTLRNLISLNLFVDKPLDISLLKTELNEAL--CSQIRVWSVFPAPKYFNPRISCESRT 156

Query: 112 YLYRI 116
           Y Y I
Sbjct: 157 YEYLI 161


>gi|226468594|emb|CAX69974.1| putative tRNA pseudouridine synthase 3 [Schistosoma japonicum]
          Length = 388

 Score = 44.3 bits (103), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 43/142 (30%), Positives = 58/142 (40%), Gaps = 24/142 (16%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I +L  S V  +F+ARF   RRSY Y                +     LD E+M  A   
Sbjct: 181 IRVLAWSPVSPEFNARFDCRRRSYEY----------------YFPESGLDIESMIDAGNR 224

Query: 149 LVGRHDFTTF--RSIHCQASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQIRS 200
           LVG HDF  F    I     S +R I    +N   +      L  + V A  FL+ QIR 
Sbjct: 225 LVGVHDFRNFCASRIEKDTVSFVREIFEVVINVVDSSDHHTKLYCLCVSASGFLYHQIRY 284

Query: 201 FVGSLKLVGDGKWTSTDLEKAL 222
               L +VG G  + + ++  L
Sbjct: 285 IASILFMVGRGYESPSVIDDML 306


>gi|207345339|gb|EDZ72195.1| YGL063Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 330

 Score = 44.3 bits (103), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 56/122 (45%), Gaps = 18/122 (14%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTDSGV 55
           M++ Y GSGY+G Q      +I+G I   +F V G I   +           A RTD GV
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDV-GAISEENSLAPKKNSFMAAARTDKGV 59

Query: 56  HALRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           HA+  +    + +RE         LNA L     I +  +  V+K+F+AR +   R Y Y
Sbjct: 60  HAMLNLLSLKITLRE----DTVAKLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQY 113

Query: 115 RI 116
            I
Sbjct: 114 LI 115


>gi|302656723|ref|XP_003020113.1| hypothetical protein TRV_05887 [Trichophyton verrucosum HKI 0517]
 gi|291183894|gb|EFE39489.1| hypothetical protein TRV_05887 [Trichophyton verrucosum HKI 0517]
          Length = 614

 Score = 44.3 bits (103), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 84/231 (36%), Gaps = 60/231 (25%)

Query: 37  LVTGEIVVVHGAG--RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNL 94
           ++  ++    G G   T SGV    +   +D + + +P I  + LN  L   + I +L  
Sbjct: 205 VMDSDVATESGMGDRNTQSGVSDTGEAKGWDDIADELPYI--QILNGAL--PEDIRVLAW 260

Query: 95  SI-VDKQFHARFSAIRRSYLY-------------RIITRQAPLALEKGRAWLIPKSLDCE 140
              +   F ARFS  +R Y Y             R I R + L  +   A L    LD E
Sbjct: 261 CPHLPPDFDARFSCRQRRYRYFFTQPAFCPTPGARGIVRSSELKDDLSLARLREGWLDIE 320

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQAS----------------SPIRTIDHF--------- 175
            MR AAQ+ VG HDF  F  +                      P RT   F         
Sbjct: 321 AMREAAQYFVGSHDFRNFCKVDTSKQITNFVRRILRADIELVDPQRTPLGFVQMPGFEPF 380

Query: 176 --------------DVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                         D+N + G +    V   +FL  QIR  VG L LVG G
Sbjct: 381 ENGPRNTGVPESIDDINPAAGKVYSFTVHGTAFLWHQIRHMVGILFLVGQG 431


>gi|83305357|sp|P53167|PUS2_YEAST RecName: Full=tRNA pseudouridine synthase 2; AltName: Full=tRNA
           pseudouridylate synthase 2; AltName: Full=tRNA-uridine
           isomerase 2
 gi|1322568|emb|CAA96766.1| PUS2 [Saccharomyces cerevisiae]
          Length = 370

 Score = 44.3 bits (103), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 16/121 (13%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTDSGV 55
           M++ Y GSGY+G Q      +I+G I   +F V G I   +           A RTD GV
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDV-GAISEENSLAPKKNSFMAAARTDKGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y 
Sbjct: 60  HAMLNLLSLKITLREDTV---AKLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYL 114

Query: 116 I 116
           I
Sbjct: 115 I 115


>gi|302781376|ref|XP_002972462.1| hypothetical protein SELMODRAFT_97541 [Selaginella moellendorffii]
 gi|300159929|gb|EFJ26548.1| hypothetical protein SELMODRAFT_97541 [Selaginella moellendorffii]
          Length = 428

 Score = 44.3 bits (103), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 40/126 (31%), Positives = 58/126 (46%), Gaps = 21/126 (16%)

Query: 8   IEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
           + Y G+ Y G Q Q+  +   S++  +E+AI+   G         + V    + RTD GV
Sbjct: 8   VGYVGTDYKGLQIQRGVAGIHSVENELEEAIYKAGGISEENYRHLDKVRWKRSSRTDKGV 67

Query: 56  HALRQVAHFDL---VREWVP----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           H+L  V    L   V  W+     + +  A NAYL  +  ISI  +  V K F AR S  
Sbjct: 68  HSLCTVVTMKLEVAVNSWLNDVDGIKIADAFNAYLPAN--ISIFGVVPVTKSFDARRSCY 125

Query: 109 RRSYLY 114
            R+Y Y
Sbjct: 126 SRTYDY 131


>gi|254565011|ref|XP_002489616.1| Non-essential tRNA:pseudouridine synthase [Pichia pastoris GS115]
 gi|238029412|emb|CAY67335.1| Non-essential tRNA:pseudouridine synthase [Pichia pastoris GS115]
          Length = 438

 Score = 44.3 bits (103), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 50/194 (25%), Positives = 71/194 (36%), Gaps = 34/194 (17%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD---------- 98
           GRTD GV A+ QV   ++     P  L    N  +K  D I+ILN  +            
Sbjct: 120 GRTDKGVSAMNQVIGLNVRSRLTPEELESPEND-IKELDYINILNQLLPSDIRIHGVCLR 178

Query: 99  --KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
             K F ARFS   R Y Y                    + LD E+M+ AA    G HDF 
Sbjct: 179 PPKGFDARFSCRGRHYKYVFQD----------------EGLDLESMKKAAPMFEGVHDFR 222

Query: 157 TFRSIH-----CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
            F  +         +  +R+     +          +   +FL  Q+R  V  L ++G G
Sbjct: 223 NFCKVDGAKQMTNYTRAVRSSQILPLEGHPGYYVFDLKGTAFLWHQVRCMVAILLMIGQG 282

Query: 212 KWTSTDLEKALQAQ 225
             +   + K L  Q
Sbjct: 283 FESPDIVSKLLDIQ 296


>gi|323305032|gb|EGA58786.1| Pus2p [Saccharomyces cerevisiae FostersB]
          Length = 370

 Score = 44.3 bits (103), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 16/121 (13%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTDSGV 55
           M++ Y GSGY+G Q      +I+G I   +F V G I   +           A RTD GV
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDV-GAISEENSLAPKKNSFMAAARTDKGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y 
Sbjct: 60  HAMLNLLSLKITLREDTV---AKLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYL 114

Query: 116 I 116
           I
Sbjct: 115 I 115


>gi|320582058|gb|EFW96276.1| Non-essential tRNA:pseudouridine synthase [Pichia angusta DL-1]
          Length = 404

 Score = 44.3 bits (103), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 91/238 (38%), Gaps = 53/238 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           R  +   Y G  Y G   Q + S+I  ++E  I     +  ++             GRTD
Sbjct: 59  RIALKFSYLGWNYHGLAYQNDTSNI-PTVELFILKALEKTKLIRNLDPTDCDFSRCGRTD 117

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD------------KQ 100
            GV A+ QV    +        +   LN  +K  D + ILN  + +            + 
Sbjct: 118 KGVSAMNQVISLVVRSNLTQDEMANPLND-VKELDYVKILNKVLPEDIRIHSICLRPPEG 176

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F ARFS + R Y Y     QA L +EK              M+ AA + VG  DF  F  
Sbjct: 177 FDARFSCLSRHYKY--FFEQANLNIEK--------------MQQAASYFVGEQDFRNF-- 218

Query: 161 IHCQASSPIRTIDH--------FDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVG 209
             C+     + +++         +   FG+   +  +   +FL  Q+RS +  L LVG
Sbjct: 219 --CKVDGSKQIVNYKRKIISSSIERTKFGHKTYVFSLRGSAFLWHQVRSMMSILFLVG 274


>gi|47187449|emb|CAG13480.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 97

 Score = 43.9 bits (102), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 33/92 (35%), Positives = 46/92 (50%), Gaps = 10/92 (10%)

Query: 3  RYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHA 57
          RY +  +Y G+ Y G  +    Q    S+Q  +E A+  L     V +  + RTD+GVHA
Sbjct: 1  RYLIFFQYIGTKYSGVVKVPPHQLFKKSVQDHLEDALRKLRPLNPVSLSVSSRTDAGVHA 60

Query: 58 LRQVAHFDLVRE-----WVPVILCKALNAYLK 84
          L   AHFDL R      +   IL  ALN +L+
Sbjct: 61 LCNSAHFDLQRRNDKPPFTADILVDALNYHLR 92


>gi|47208274|emb|CAF91572.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 375

 Score = 43.9 bits (102), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 93/225 (41%), Gaps = 32/225 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK---AIFLVTGEIVVVHG----------AG 49
           +  +++ Y+G GY+G QR   GSS   +IE    A  + +G I   H             
Sbjct: 76  KVALLLAYSGKGYYGMQRNP-GSSEFRTIEDDLVAALVKSGCIPENHAEDMKKMSFQRCA 134

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    L   W+   L + +N +L     I +L +  V + F+++ +   
Sbjct: 135 RTDKGVSAAGQVVSLKL---WLIDDLAEKINQHL--PPQIRVLGVKRVTQGFNSKNNCDA 189

Query: 110 RSYLYRIIT-----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC- 163
           R+Y Y + T     + +  A +     L P++L   N   A     G H+F  F S    
Sbjct: 190 RTYAYMLPTVAFAPKDSDAASDAASFRLQPETLQRVNRLFALYK--GTHNFHNFTSQKAP 247

Query: 164 QASSPIRTIDHFDVNS--FGNLIEIRVV---ARSFLHTQIRSFVG 203
              S  R + H        G   E  V+    +SF+  QIR  +G
Sbjct: 248 NDPSARRYVTHVCCGEPFMGGDTEFAVITVRGQSFMLHQIRKMIG 292


>gi|331234741|ref|XP_003330029.1| pseudouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309309019|gb|EFP85610.1| pseudouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 252

 Score = 43.9 bits (102), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 42/163 (25%), Positives = 61/163 (37%), Gaps = 30/163 (18%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           + +++ +L    V   F  RFS   R Y Y     ++P A            LD E M+ 
Sbjct: 116 LHNSVRVLAWLPVHHDFDTRFSCQARHYKYFFSLYKSPQA----------PGLDIEAMKW 165

Query: 145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
           AA  L+G HDF  F  I      P + + HF               R  L  +I+  +  
Sbjct: 166 AAHRLIGEHDFHNFFKI-----DPSKQLTHF--------------RRKILSAEIKPVLNP 206

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKEC-GPLAPPEGLYFDSVEY 246
             L+      S+  EK LQ Q   +   P    EG   D ++Y
Sbjct: 207 HHLLQQQPSGSSGSEKDLQPQIYPDALSPETLSEGTPSDKLDY 249


>gi|302309334|ref|NP_986663.2| AGL003Wp [Ashbya gossypii ATCC 10895]
 gi|299788309|gb|AAS54487.2| AGL003Wp [Ashbya gossypii ATCC 10895]
          Length = 432

 Score = 43.9 bits (102), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 86/234 (36%), Gaps = 60/234 (25%)

Query: 14  GYFGWQRQKNGSSIQG------SIEKAIFLVTGEIVVVHG----------AGRTDSGVHA 57
            Y GW    NG +IQ       ++E  I     +  +V             GRTD GV A
Sbjct: 89  AYLGWNY--NGLAIQKDPTPLPTVEGTILEAMNKCRMVPSMVPQDYKFSRCGRTDKGVSA 146

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD------------KQFHARF 105
           + QV    +     P       N   +I   I ILN  + D            K F ARF
Sbjct: 147 MNQVISLRVRSNLTPQEQEDPANDAREIP-YIHILNQLLPDDIRISAICLRPPKGFDARF 205

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHC- 163
           S   R Y Y                 L  KS LD   M  AA+   G HDF  F  +   
Sbjct: 206 SCKYRHYKY-----------------LFNKSGLDLSKMEEAARLYEGEHDFRNFCKLDGS 248

Query: 164 -QASSPIRT-----IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
            Q ++  RT     I H D    G++    ++  +FL  Q+R  + +L +VG G
Sbjct: 249 KQITNFKRTILSAKILHVD----GDMYCFDLLGSAFLWHQVRCMMANLFIVGQG 298


>gi|168058399|ref|XP_001781196.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667349|gb|EDQ53981.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 499

 Score = 43.9 bits (102), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 13/123 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +I+ Y G+ Y G QR     +I+G +E+A+F          G         A RTD 
Sbjct: 58  KVALILAYCGAAYQGMQRNPGAITIEGELEQALFRADAIAECNFGDMRKVDWMRAARTDK 117

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+ Q+    LV +  P  L + +N +L     I +   + V   F+A+    +R Y 
Sbjct: 118 GVSAIGQIVSARLVID--PPGLVERVNQHL--PKDIRVFGYTRVTSNFNAKQMCDKRRYE 173

Query: 114 YRI 116
           Y +
Sbjct: 174 YLV 176


>gi|297739353|emb|CBI29343.3| unnamed protein product [Vitis vinifera]
          Length = 466

 Score = 43.5 bits (101), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 67/168 (39%), Gaps = 27/168 (16%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I ++    V   FHARFS + R Y Y                +    +L+   M  A + 
Sbjct: 229 IRVMGWCPVPIGFHARFSCLSREYKY----------------FFWRGNLNILAMESAGKK 272

Query: 149 LVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQIRSF 201
            VG HDF  F  +      +  R I  F++    N      L  I++   +FL  Q+R  
Sbjct: 273 FVGEHDFRNFCKMDAVNVHNYRRHIISFEIAPTNNRYDGNQLWAIKIKGSAFLWHQVRCM 332

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
           V  L ++G G   S D+  AL   +R    P   +AP   L  +S E+
Sbjct: 333 VAVLFMIGQG-LESPDVVDALLDTERTSRKPQYAMAPEIPLVLESCEF 379


>gi|242215757|ref|XP_002473691.1| predicted protein [Postia placenta Mad-698-R]
 gi|220727176|gb|EED81103.1| predicted protein [Postia placenta Mad-698-R]
          Length = 495

 Score = 43.5 bits (101), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 63/277 (22%), Positives = 94/277 (33%), Gaps = 93/277 (33%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA-----------GRT 51
           +  +   YNG+ Y G + QK  +++  ++E  +F       ++  A           GRT
Sbjct: 49  KIALKFTYNGADYSGLEFQKTPTTLP-TVEAVLFDALVHTRLIDPATGFEGCGWEKCGRT 107

Query: 52  DSGVHALRQV--------------------------------AHFDLVREWVPVILCKAL 79
           D GV A  QV                                    L+ EW       A 
Sbjct: 108 DRGVSAAGQVISLWVRSALGQARVRTSLEDANVMDVHPTGLEGDLALMGEWDETPTNAAR 167

Query: 80  NAYLKISD--------------TISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
            A  + ++              TI ++  S V   F ARFS   R Y Y           
Sbjct: 168 PATPQATNELRYITLLNNVLPPTIRVIAWSPVGPDFSARFSCRYRHYKY----------- 216

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDF------------TTF-RSIHCQASSPIRTI 172
                +  P+ LD   M+ AA  LVG HDF            TTF R I     +P +  
Sbjct: 217 -----FFSPEGLDLAAMQDAADRLVGEHDFRNLCKLDPSKQLTTFARKILSARLNPAQ-- 269

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                +    L  + ++  +FL+ Q+R  +  L LVG
Sbjct: 270 ----ADGASTLYVLDLIGTAFLYNQVRHIMAVLFLVG 302


>gi|83317781|ref|XP_731310.1| tRNA-pseudouridine synthase I [Plasmodium yoelii yoelii str. 17XNL]
 gi|23491305|gb|EAA22875.1| tRNA-pseudouridine synthase I [Plasmodium yoelii yoelii]
          Length = 497

 Score = 43.5 bits (101), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 51/109 (46%), Gaps = 8/109 (7%)

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF------DVNSF-GNLIEIRVVA 190
           D + ++  ++  +G H+F  FR I  + +   RTI+ F      D+     NL +  +  
Sbjct: 368 DIDKIKECSKLFIGYHNFECFRGI-LKGTEKQRTINTFCNIHFLDIYKLKDNLYQFIIQG 426

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             FL+  IR  VG+L  VG G     D++ AL      +    APP+GL
Sbjct: 427 DRFLYHMIRIIVGTLIQVGVGILNFQDVKDALYNSKPLKVKLCAPPQGL 475


>gi|260817697|ref|XP_002603722.1| hypothetical protein BRAFLDRAFT_93048 [Branchiostoma floridae]
 gi|229289044|gb|EEN59733.1| hypothetical protein BRAFLDRAFT_93048 [Branchiostoma floridae]
          Length = 352

 Score = 43.5 bits (101), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 65/263 (24%), Positives = 108/263 (41%), Gaps = 36/263 (13%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTDSGVH 56
           ++ Y+G GY G QR +   +I+  +  A F   G I   H             RTD GV 
Sbjct: 47  LLAYSGVGYMGMQRNQGFKTIEEDL-LAAFYKAGAIPKDHMDCMQKMHFQRCARTDKGVS 105

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISD----TISILNLSIVDKQFHARFSAIRRSY 112
           A  Q+         V + +    +A  KI+D    +I ++ +      F ++ +   R+Y
Sbjct: 106 AAGQI---------VSLKMYMIEDAVQKINDCLAESIRLIGIKRTTNGFDSKNACDARTY 156

Query: 113 LYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHCQASSPI 169
           +Y + T   AP   E  + +     +  E +        G H+F  F S       S+  
Sbjct: 157 MYVLPTYSFAPTKEETEQDFRATDDV-MEKVNDVLSAYKGTHNFHNFTSGKKFKDPSAKR 215

Query: 170 RTIDHFDVNSF-GNLIE---IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
             I+   +++F  + IE   I +  +SF+  QIR  +G +  +  G    + LE+A Q  
Sbjct: 216 YIIESKCLDTFVRDDIEWTVISIKGQSFMIHQIRKMIGMMLAIVRGLAPRSMLERAWQ-- 273

Query: 226 DRKECG-PLAPPEGLYFDSVEYS 247
              +C  P AP  GL  D V + 
Sbjct: 274 -EGKCDIPKAPGLGLVLDKVHFD 295


>gi|327307008|ref|XP_003238195.1| tRNA pseudouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326458451|gb|EGD83904.1| tRNA pseudouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 614

 Score = 43.1 bits (100), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 61/219 (27%), Positives = 77/219 (35%), Gaps = 58/219 (26%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSI-VDKQFHARF 105
           G   T SGV    +   +D + + +P I  + LN  L   + I +L     +   F ARF
Sbjct: 217 GDKNTQSGVSDTGEAKGWDDIADELPYI--QILNGAL--PEDIRVLAWCPHLPPDFDARF 272

Query: 106 SAIRRSYLY-------------RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
           S  +R Y Y             R I R   L  +   A      LD E MR AAQ+ VG 
Sbjct: 273 SCRQRRYRYFFTQPAFCPTPGTRGIVRSPELKDDLSLARPREGWLDIEAMRKAAQYFVGS 332

Query: 153 HDFTTFRSIHCQAS----------------SPIRTIDHF--------------------- 175
           HDF  F  +                      P RT   F                     
Sbjct: 333 HDFRNFCKVDTSKQITNFVRRILRADIELVDPQRTPLGFVQMPGFEPFENGPRNTGVPGS 392

Query: 176 --DVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
             D+NS  G +    V   +FL  QIR  VG L LVG G
Sbjct: 393 INDINSAAGKVYSFTVHGTAFLWHQIRHMVGILFLVGQG 431


>gi|115442996|ref|XP_001218305.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
 gi|114188174|gb|EAU29874.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
          Length = 1199

 Score = 43.1 bits (100), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 38/126 (30%), Positives = 58/126 (46%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 80  KVAVLLGYSGTGYKGMQLSDTEKTIEGELFTA-FVAAGAISKANAADPKKSSLVRCARTD 138

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E  P I+ K +N   K+S  I + ++ + +K F A      R Y
Sbjct: 139 KGVHAAGNVVSLKLIVE-DPDIVQK-INE--KLSPQIRVWDILVANKSFSAYQMCDSRIY 194

Query: 113 LYRIIT 118
            Y I T
Sbjct: 195 EYLIPT 200


>gi|330835922|ref|XP_003292011.1| hypothetical protein DICPUDRAFT_156689 [Dictyostelium purpureum]
 gi|325077781|gb|EGC31472.1| hypothetical protein DICPUDRAFT_156689 [Dictyostelium purpureum]
          Length = 539

 Score = 43.1 bits (100), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 35/132 (26%), Positives = 66/132 (50%), Gaps = 22/132 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVH----------GAGRT 51
           + +   Y+G+G++G    K+    +I+ +IEKA+F + G I   +           + RT
Sbjct: 129 FALCFGYDGTGFYGLSYNKDLKYKAIENAIEKALF-INGHIAPSNVGDLSRIKWSRSSRT 187

Query: 52  DSGVHALRQ-VAHFDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           D GVH+L   ++ F LV      RE +     +++N +L   +++ +L+ + + K F AR
Sbjct: 188 DKGVHSLSTLISCFILVDEKTNQREGLSKETIESINKHL--PESVRLLSGTRISKSFRAR 245

Query: 105 FSAIRRSYLYRI 116
                R+Y Y +
Sbjct: 246 RGVCERTYHYMV 257


>gi|268536920|ref|XP_002633595.1| Hypothetical protein CBG05472 [Caenorhabditis briggsae]
 gi|187035020|emb|CAP25947.1| hypothetical protein CBG_05472 [Caenorhabditis briggsae AF16]
          Length = 322

 Score = 43.1 bits (100), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 66/298 (22%), Positives = 112/298 (37%), Gaps = 54/298 (18%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQG----SIEKAIFLVTGE-------IVVVHGAGRT 51
           RY   I Y+GS +    +   G  +      ++ ++IF    E        +    + RT
Sbjct: 6   RYLFWIRYDGSKFPEMAKGGTGFGVMDLLNQTVSQSIFGPRREQHPEQKDKLKFSPSSRT 65

Query: 52  DSGVHALRQVAHFDLVREWVPVILC-----KALNAYLKISDTISILNLSIVDKQ-----F 101
           D+ VHA+R      +  E+  +  C     + +  +  I D  +  +L I+D       F
Sbjct: 66  DAKVHAIRSSVICQVPLEFADLDKCPETKIQYMRTWKSIIDAANPGSLEILDAHSVSAGF 125

Query: 102 HARFSAIRRSYLYRIIT----------RQAPLAL---EKGRAWLIPKSLDCENMRIAAQH 148
             R S   R Y YR+            RQ P      E+  AW +P     E +  A + 
Sbjct: 126 CIRRSVSYRKYTYRLAVCRSWDLWDTIRQEPSIACFSERDYAWRLPPGFSPERLLRAGKI 185

Query: 149 LVGRHDFTTF-----RSIHCQASSP----------IRTIDHFDV-NSFGNLIEIRVVARS 192
             G     +F     R    +  SP          +   + + V N   +   + +VA+S
Sbjct: 186 FEGEQVMGSFFKHTNREKRTEPISPSALKYIFYVGLSNGEAYSVENDIYDYYNVTIVAKS 245

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECG-PLAPPEGLYFDSVEY 246
           F+  QIR  +  L      +   + +   L+   + +  + G P+APP+GLY   V Y
Sbjct: 246 FVREQIRRMISCLVNYSYDRIPLSTVNWLLKNPISSNFYDMGIPVAPPQGLYLTDVVY 303


>gi|312091557|ref|XP_003147023.1| hypothetical protein LOAG_11456 [Loa loa]
 gi|307757811|gb|EFO17045.1| hypothetical protein LOAG_11456 [Loa loa]
          Length = 236

 Score = 42.7 bits (99), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 33/125 (26%), Positives = 58/125 (46%), Gaps = 14/125 (11%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIV-----VVHGAGRTDSG 54
           Y +++ Y G  Y G Q QK+  +++G + KA+    ++   +I+         A RTD  
Sbjct: 104 YALLLAYQGKKYNGMQVQKDFPTVEGELFKAMAKCGYISEDDILSPVRFAFQRAARTDRS 163

Query: 55  VHALRQVAHFDLVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           V A RQ+    L  E     L  A   LNA  ++ + I ++ +    + F A  +  +R+
Sbjct: 164 VSAARQMCSMRLAPENHEYFLKTASDKLNA--QLPEEIRVMGVRRATRSFKAHKNCDKRT 221

Query: 112 YLYRI 116
           Y Y +
Sbjct: 222 YSYTL 226


>gi|299469782|emb|CBN76636.1| tRNA Pseudouridine Synthase [Ectocarpus siliculosus]
          Length = 677

 Score = 42.7 bits (99), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 56/132 (42%), Gaps = 24/132 (18%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI----------VVVHGAGRTD 52
           +  ++I Y G+ Y G Q  K   +I+  +E A++L  G I          V    AGRTD
Sbjct: 192 KVALLISYWGNNYQGLQINKGARTIEAELELALYLA-GTISKDNFGNPRKVSWSRAGRTD 250

Query: 53  SGVHALRQVAHFDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
            GVHA  QV    L       RE V  I     N YL   D I  +++    K F +R  
Sbjct: 251 KGVHAAAQVISVKLTYLNDGERETVEKI-----NKYL--PDDIRAVDIRRAPKSFDSRTR 303

Query: 107 AIRRSYLYRIIT 118
              R Y Y + T
Sbjct: 304 CSGRRYEYIMPT 315


>gi|169854752|ref|XP_001834048.1| pseudouridine synthase [Coprinopsis cinerea okayama7#130]
 gi|116504845|gb|EAU87740.1| pseudouridine synthase [Coprinopsis cinerea okayama7#130]
          Length = 511

 Score = 42.7 bits (99), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 38/135 (28%), Positives = 52/135 (38%), Gaps = 29/135 (21%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           + +TI +   S V   F ARFS   R Y Y                +  PK LD   M+ 
Sbjct: 208 LPETIRVSAWSPVPSTFSARFSCNFRHYKY----------------FFTPKGLDIVRMQE 251

Query: 145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE--------IRVVARSFLHT 196
           AA  L+G HDF       C+   P + I  F        IE          +   +FL+ 
Sbjct: 252 AAGRLIGEHDFRNL----CKL-DPAKQITSFKRKVMSAHIERLNDNLHVFNLTGSAFLYH 306

Query: 197 QIRSFVGSLKLVGDG 211
           Q+R  +  L L+G G
Sbjct: 307 QVRHIMAILFLIGMG 321


>gi|307214388|gb|EFN89459.1| tRNA pseudouridine synthase A [Harpegnathos saltator]
          Length = 364

 Score = 42.7 bits (99), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 66/282 (23%), Positives = 108/282 (38%), Gaps = 58/282 (20%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGE------IVVVHGAGRTDSGVHALRQ 60
           Y G  Y+G QR     +I+  +  A+    L+T E       +    A RTD GV A+RQ
Sbjct: 4   YLGKNYYGMQRNPGMKTIEEDLVNALLKANLITTEQFENLRTINFQRAARTDKGVSAVRQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +    L       I    +N +L   D I +  +  V K F+++     R+Y Y  I   
Sbjct: 64  IVSLKLPENPDKTI----INQFL--PDVIRVFGIKRVTKGFNSKNQCDARTYRY--IIPS 115

Query: 121 APLALEKGRAWLIPKSLDCE---------------NMRIAAQHL----------VGRHDF 155
              A+E      + + +D                 + R++ + L           G H+F
Sbjct: 116 FTFAMEDQSLLKMGEEVDINERIKQISTIDGEPYIDYRLSIESLNRLNSILKLFEGTHNF 175

Query: 156 TTFRSIHCQASSPI-----RTIDHFD-VNSFGN----LIEIRVVARSFLHTQIRSFVGSL 205
             F S     + P+     R I +F  V++F +     + + V  +SF+  QIR  V ++
Sbjct: 176 HNFTS----KTKPLDPRARRYIINFHCVDTFVSKGIEFVVLEVKGQSFMLHQIRKMVATV 231

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             V         + +A +    K   P+AP  GL    V Y 
Sbjct: 232 IAVARNIIPEETINEAFKTV--KMEIPIAPSLGLCLCHVHYD 271


>gi|56693277|ref|NP_001008603.1| tRNA pseudouridine synthase A [Danio rerio]
 gi|56269412|gb|AAH86827.1| Pseudouridine synthase 1 [Danio rerio]
          Length = 376

 Score = 42.7 bits (99), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 61/275 (22%), Positives = 106/275 (38%), Gaps = 48/275 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG------------AGR 50
           +  +++ Y+G GY+G QR    S  +   ++ +  + G   +  G            + R
Sbjct: 41  KVALLMAYSGKGYYGMQRNARNSQFKTIEDELVTALVGARCIPEGHAEEMKKMSFQRSAR 100

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GV A+ +V    +   W+   + + +NA+L     I +L    V   F+++ +   R
Sbjct: 101 TDKGVSAVGRVVSLKV---WMIENILEKINAHL--PPRIRVLGCKRVTGGFNSKNNCYAR 155

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCEN--MRIAAQHL----------VGRHDFTTF 158
           +Y Y + T               PK  + E+   R+ +  L           G H+F  F
Sbjct: 156 TYSYMLPT-----------VAFSPKDYNQEDTSFRLTSDTLQTVNRLFCLYKGTHNFHNF 204

Query: 159 RSIHC-QASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
            S    +  S +R I H       +        I V  +SF+  QIR  +G +  V  G 
Sbjct: 205 TSQKGHRDPSAMRYITHMSCGEPFIRKDVEFAVITVRGQSFMMHQIRKMIGLVIAVVKGY 264

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
                +EK+   +  K     AP  GL  + V + 
Sbjct: 265 VDEGVMEKSWGEE--KVGVSKAPGLGLVLERVHFD 297


>gi|302495964|ref|XP_003009994.1| hypothetical protein ARB_03805 [Arthroderma benhamiae CBS 112371]
 gi|291173519|gb|EFE29349.1| hypothetical protein ARB_03805 [Arthroderma benhamiae CBS 112371]
          Length = 409

 Score = 42.7 bits (99), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 81/220 (36%), Gaps = 68/220 (30%)

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSI-VDKQFHARFSAIR 109
           T SGV    +   +D + + +P I  + LN  L   + I +L     +   F ARFS  +
Sbjct: 16  TQSGVSDTGEAKGWDDIADELPYI--QILNGAL--PEDIRVLAWCPHLPPDFDARFSCRQ 71

Query: 110 RSYLY-------------RIITRQAPL----ALEKGR-AWLIPKSLDCENMRIAAQHLVG 151
           R Y Y             R I R + L    +LE+ R  WL     D E MR AAQ+ VG
Sbjct: 72  RRYRYFFTQPAFCPTPGARGIVRSSELKDDLSLERPREGWL-----DIEAMREAAQYFVG 126

Query: 152 RHDFTTFRSIHCQAS----------------SPIRTIDHF-------------------- 175
            HDF  F  +                      P RT   F                    
Sbjct: 127 SHDFRNFCKVDTSKQITNFVRRILRADIELVDPQRTPLGFVQMPGFEPFENGSRNTGVPE 186

Query: 176 ---DVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
              D+N + G +    V   +FL  QIR  VG L LVG G
Sbjct: 187 NINDINPAAGKVYSFTVHGTAFLWHQIRHMVGILFLVGQG 226


>gi|148688059|gb|EDL20006.1| pseudouridine synthase 1, isoform CRA_d [Mus musculus]
          Length = 402

 Score = 42.7 bits (99), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 108/274 (39%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 60  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 118

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 119 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 173

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 174 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFT 224

Query: 160 SIHCQASSPIR--TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R   ++ +    F         I+V  +SF+  QIR  VG +  +  G  
Sbjct: 225 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 284

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 285 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 316


>gi|112180395|gb|AAH21446.2| Pseudouridine synthase 1 [Mus musculus]
          Length = 423

 Score = 42.7 bits (99), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 108/274 (39%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 81  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 140 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 194

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 195 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFT 245

Query: 160 SIHCQASSPIR--TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R   ++ +    F         I+V  +SF+  QIR  VG +  +  G  
Sbjct: 246 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 305

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 306 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 337


>gi|256087925|ref|XP_002580112.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665620|emb|CAZ36351.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 1304

 Score = 42.7 bits (99), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 58/200 (29%), Positives = 71/200 (35%), Gaps = 60/200 (30%)

Query: 48   AGRTDSGVHALRQVAHF---DLVREWVPVI-------------------LCKALNAYLKI 85
             GRTD GV  + QV       L+   V VI                      ALN  L  
Sbjct: 971  CGRTDRGVSGMCQVISLVSRSLIARGVGVIEDSGPCISERQDVPDEEMDYVSALNRNL-- 1028

Query: 86   SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRI 144
               I +L  S V   F ARF   +RSY Y                   P+S LD ++M  
Sbjct: 1029 PRDIRVLAWSPVSPDFSARFMCCKRSYEY-----------------YFPESGLDIKSMID 1071

Query: 145  AAQHLVGRHDFTTF-------------RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVAR 191
            A   LVG HDF  F             R I     S + + DH        L  I + A 
Sbjct: 1072 AGNRLVGVHDFRNFCASRIEKDTVTFIREIFEVVVSDVDSCDH-----HSKLCRISISAS 1126

Query: 192  SFLHTQIRSFVGSLKLVGDG 211
             FL+ QIR  +  L +VG G
Sbjct: 1127 GFLYHQIRFVMSILFMVGRG 1146


>gi|219122763|ref|XP_002181709.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406985|gb|EEC46923.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 421

 Score = 42.7 bits (99), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 84/345 (24%), Positives = 125/345 (36%), Gaps = 115/345 (33%)

Query: 8   IEYNGSGYFGW-------QRQKNGS-----------------------SIQGSIEKAIFL 37
           + Y+G  ++GW        R+ N +                       S+QG I+  +  
Sbjct: 75  VSYDGRQFYGWSSGNDPKDRESNAARPRYSTRSRRRRRNRGNYDGTVRSVQGEIQYCLSK 134

Query: 38  VTGEI----VVVHGAGRTDSGVHALRQVAHF-----------DLVREW------------ 70
           V G I    VVV G  RTD GVHA   +A             D V +W            
Sbjct: 135 VYGNIDPQRVVVEGCSRTDKGVHARGMMAQIYCLHETTSPNDDPVVDWSIPGKRQPHPRN 194

Query: 71  ---------VPVILCK-ALNAYLKISDTISIL-------------NLSIVDKQFHARFSA 107
                    +P+ L K A      +   ISI+             N +I    FH   S 
Sbjct: 195 ATDTSYFTQLPMNLTKLAFTLNRMLPHDISIMGIAPTPHPHVTGCNPAISALPFHPTLSC 254

Query: 108 IRRSYLY--RIITRQAPLALEKGRAWLIPKSLDC---ENMRIAAQHLVGRHDFTTFRSIH 162
             ++Y Y   + TR  P   ++   W + +++     +    A Q L G H+F  F+   
Sbjct: 255 RHKTYRYVVSVGTRADPT--KRLYVWHLDRAISTFSLDQAEQACQILQGSHNFAAFQGAP 312

Query: 163 CQASSPIRTIDHFDV-NSFGNLIEIRVVARS----------------FLHTQIRSFVGSL 205
             + + I+    F + N+   LI IR+  +S                FL+  IR  VG++
Sbjct: 313 RGSDNKIK----FTMRNTTCQLISIRIQHQSTWLDTETYVVSVTGDRFLYKMIRFLVGTV 368

Query: 206 KLVGDGKWTSTDLEKALQAQDRK----ECGPLAPPEGLYFDSVEY 246
             VG GK T  ++   L  Q R     EC   APP  L  + VEY
Sbjct: 369 VGVGTGKLTLDNVAAMLLTQSRNNLQVEC---APPHALVLEHVEY 410


>gi|194696534|gb|ACF82351.1| unknown [Zea mays]
          Length = 257

 Score = 42.7 bits (99), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 51/130 (39%), Gaps = 23/130 (17%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I +L    V   FHARF+ + R Y Y            KG        LD   M+ AA  
Sbjct: 22  IRVLGWCPVPADFHARFTCLSREYKY---------LFWKG-------DLDILEMQKAASK 65

Query: 149 LVGRHDFTTFRSIHCQASSPIR------TIDHFDVNSFGN-LIEIRVVARSFLHTQIRSF 201
            +G HDF  F  +     S  R      TI   D  S  + L  + +   +FL  Q+R  
Sbjct: 66  FIGEHDFRNFCKMDAANVSNYRRHITEFTISACDRRSNNDELCSMTIKGSAFLWHQVRCM 125

Query: 202 VGSLKLVGDG 211
           V  L L+G G
Sbjct: 126 VAVLFLIGQG 135


>gi|260942163|ref|XP_002615380.1| hypothetical protein CLUG_04262 [Clavispora lusitaniae ATCC 42720]
 gi|238850670|gb|EEQ40134.1| hypothetical protein CLUG_04262 [Clavispora lusitaniae ATCC 42720]
          Length = 447

 Score = 42.4 bits (98), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 88/233 (37%), Gaps = 62/233 (26%)

Query: 14  GYFGWQRQKNGSSIQG------SIEKAIFLVTGEIVVVHGA----------GRTDSGVHA 57
            Y GW    NG + Q       ++E+ I     +  +V  A          GRTD GV A
Sbjct: 91  AYMGWNY--NGLNFQNEPTPLPTVEEEILQAMTKAKLVPEADPASCNFSRCGRTDKGVSA 148

Query: 58  LRQV------------AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           L QV             H D  ++   +     LNA L     I+ + L      F+ARF
Sbjct: 149 LNQVISLDVRSALSKEEHADKEKDVKELPYLTILNALLPPDIRITAVCLR-PPPNFNARF 207

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI--- 161
           S   R Y Y                 L  K+ LD + M+ AA    G HDF  F  I   
Sbjct: 208 SCKYRHYKY-----------------LFKKTDLDVDLMQEAALKYEGPHDFRNFCKIDGS 250

Query: 162 -----HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                HC+     R I+HF  + +  + +++  A  FL  Q+R  V  L  VG
Sbjct: 251 KQITNHCREVYSAR-IEHFKDDFY--VFDLKGTA--FLWHQVRCMVAVLFSVG 298


>gi|149063709|gb|EDM14032.1| pseudouridine synthase 1, isoform CRA_c [Rattus norvegicus]
          Length = 402

 Score = 42.4 bits (98), Expect = 0.054,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 108/274 (39%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 60  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 118

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 119 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 173

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 174 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLGCYKGTHNFHNFT 224

Query: 160 SIHCQASSPIR--TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R   ++ +    F         I+V  +SF+  QIR  VG +  +  G  
Sbjct: 225 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 284

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 285 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 316


>gi|209876690|ref|XP_002139787.1| tRNA pseudouridine synthase family protein [Cryptosporidium muris
          RN66]
 gi|209555393|gb|EEA05438.1| tRNA pseudouridine synthase family protein [Cryptosporidium muris
          RN66]
          Length = 497

 Score = 42.4 bits (98), Expect = 0.056,   Method: Compositional matrix adjust.
 Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 32/91 (35%)

Query: 4  YCMIIEYNGSGYFGWQRQKNGS------SIQGSIEKAIFLVTGEIVVVHGA--------- 48
          YCM I YNG+ Y+G Q Q N +      +I+  +E+A  L+   ++V+  +         
Sbjct: 10 YCMAIGYNGTNYYGMQIQSNTNNCKYIETIESKLEEA--LIKSSMLVIRKSKNEYVNLKE 67

Query: 49 ---------------GRTDSGVHALRQVAHF 64
                         GRTD GVH++ Q+  F
Sbjct: 68 FNSSSFLTSINWTRVGRTDKGVHSVCQIVSF 98


>gi|70906470|ref|NP_062674.2| tRNA pseudouridine synthase A, mitochondrial isoform 2 [Mus
           musculus]
 gi|114152896|sp|Q9WU56|TRUA_MOUSE RecName: Full=tRNA pseudouridine synthase A, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase I; AltName:
           Full=tRNA-uridine isomerase I; Flags: Precursor
 gi|112180429|gb|AAH34359.2| Pseudouridine synthase 1 [Mus musculus]
 gi|148688056|gb|EDL20003.1| pseudouridine synthase 1, isoform CRA_a [Mus musculus]
          Length = 423

 Score = 42.4 bits (98), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 106/274 (38%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 81  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 140 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 194

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 195 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFT 245

Query: 160 SIHCQASSPIRT------IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R        +   V        I+V  +SF+  QIR  VG +  +  G  
Sbjct: 246 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 305

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 306 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 337


>gi|156369650|ref|XP_001628088.1| predicted protein [Nematostella vectensis]
 gi|156215055|gb|EDO36025.1| predicted protein [Nematostella vectensis]
          Length = 464

 Score = 42.4 bits (98), Expect = 0.060,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 85/252 (33%), Gaps = 74/252 (29%)

Query: 14  GYFGWQRQKNGS--SIQGSIE--------KAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
            Y GW      S   I  ++E        KA  + + E       GRTD GV A  QV  
Sbjct: 87  SYLGWDMHGFASQEKIDNTVEAHLFDALIKACLVKSRESCSYSRCGRTDKGVSAFGQVIS 146

Query: 64  FDLV-----------------------REWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
            ++                        +    ++    LN  L     I +L  + V+  
Sbjct: 147 LNVRTNLDKGPGVILRQESSVGRDTKGKTMKEILYVDILNKVL--PKEIRVLAWAPVELD 204

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFR 159
           F ARFS   R Y Y                 L P + LD + M +A++ L G HDF  F 
Sbjct: 205 FDARFSCSYRKYKY-----------------LFPSANLDIDLMNLASKKLEGEHDFRNFC 247

Query: 160 SIHCQASSPI---RTIDHFDVNSFGN-----------------LIEIRVVARSFLHTQIR 199
            +   A+  I   R I  F V    N                 + E  +   +FL  Q+R
Sbjct: 248 KMDV-ANGVIQFTRNITSFKVQKVSNATYSAPGENKAKQRGYEMCEAVICGSAFLWHQVR 306

Query: 200 SFVGSLKLVGDG 211
             +  L +VG G
Sbjct: 307 CMMSILLMVGQG 318


>gi|26354378|dbj|BAC40817.1| unnamed protein product [Mus musculus]
          Length = 393

 Score = 42.4 bits (98), Expect = 0.060,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 108/274 (39%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 51  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 165 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFT 215

Query: 160 SIHCQASSPIR--TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R   ++ +    F         I+V  +SF+  QIR  VG +  +  G  
Sbjct: 216 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 275

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 276 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|70906472|ref|NP_001020733.1| tRNA pseudouridine synthase A, mitochondrial isoform 3 [Mus
           musculus]
 gi|4455033|gb|AAD21041.1| pseudouridine synthase 1 [Mus musculus]
 gi|11464734|gb|AAG35308.1| pseudouridine synthase 1 [Mus musculus]
 gi|148688058|gb|EDL20005.1| pseudouridine synthase 1, isoform CRA_c [Mus musculus]
          Length = 393

 Score = 42.4 bits (98), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 108/274 (39%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 51  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 165 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFT 215

Query: 160 SIHCQASSPIR--TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R   ++ +    F         I+V  +SF+  QIR  VG +  +  G  
Sbjct: 216 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 275

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 276 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|70906466|ref|NP_001020734.1| tRNA pseudouridine synthase A, mitochondrial [Rattus norvegicus]
 gi|182676393|sp|Q4KM92|TRUA_RAT RecName: Full=tRNA pseudouridine synthase A, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase I; AltName:
           Full=tRNA-uridine isomerase I; Flags: Precursor
 gi|149063708|gb|EDM14031.1| pseudouridine synthase 1, isoform CRA_b [Rattus norvegicus]
 gi|171847186|gb|AAI61821.1| Pseudouridylate synthase 1 [Rattus norvegicus]
          Length = 423

 Score = 42.4 bits (98), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 106/274 (38%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 81  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 140 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 194

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 195 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLGCYKGTHNFHNFT 245

Query: 160 SIHCQASSPIRT------IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R        +   V        I+V  +SF+  QIR  VG +  +  G  
Sbjct: 246 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 305

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 306 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 337


>gi|123976924|ref|XP_001330657.1| tRNA pseudouridine synthase A family protein [Trichomonas vaginalis
           G3]
 gi|121897278|gb|EAY02404.1| tRNA pseudouridine synthase A family protein [Trichomonas vaginalis
           G3]
          Length = 353

 Score = 42.4 bits (98), Expect = 0.062,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 86/226 (38%), Gaps = 52/226 (23%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVIL-----------------CKALNAYLKISDTISI 91
           GRTD+GV  +  V     VR   P  L                  + LN  L  S  I +
Sbjct: 72  GRTDAGVSGVGNVISV-RVRSVCPTGLGSIPREGAKVQKEEMNYAQILNGILPPS--IRV 128

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
             ++ V   F+ARF    R Y Y                    K++D   M+ AA+HL+G
Sbjct: 129 TGVAYVKPDFNARFDCATRGYRYFFHK--------------FDKNIDL--MKEAAEHLLG 172

Query: 152 RHDFTTF------RSIHCQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGS 204
            HD+  F       + HC     +R I   +  ++ G +    +V   F+  QIR     
Sbjct: 173 EHDYRAFCKFSPDSTKHC-----VRKIYKCEFGDAGGGVWYFEIVGSGFIWHQIRCIASI 227

Query: 205 LKLVGDGKWTSTDLEKALQAQDR---KECGPLAPPEGLYFDSVEYS 247
           L  VG+G +    + K L    +   +   P+A PE L F +  Y 
Sbjct: 228 LFAVGNG-FEKPSITKELLNTAKYPGRPNYPIADPEPLVFWNAGYE 272


>gi|331231235|ref|XP_003328281.1| pseudouridine synthase 3 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309307271|gb|EFP83862.1| pseudouridine synthase 3 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 650

 Score = 42.4 bits (98), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 39/91 (42%), Gaps = 15/91 (16%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           + +++ +L  S V   F ARFS   R Y Y     ++P A            LD E M  
Sbjct: 312 LPNSVRVLAWSPVHHDFDARFSCQARHYKYFFSLYESPQA----------PGLDIEAMNR 361

Query: 145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           AA  L+G HDF  F  I      P + + HF
Sbjct: 362 AADRLIGEHDFRNFCKI-----DPSKQLAHF 387


>gi|74149634|dbj|BAE36440.1| unnamed protein product [Mus musculus]
          Length = 393

 Score = 42.4 bits (98), Expect = 0.065,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 108/274 (39%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 51  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 165 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFT 215

Query: 160 SIHCQASSPIR--TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R   ++ +    F         I+V  +SF+  QIR  VG +  +  G  
Sbjct: 216 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 275

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 276 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|297619849|ref|YP_003707954.1| Pseudouridine synthase I, TruA, alpha/beta domain-containing
           protein [Methanococcus voltae A3]
 gi|297378826|gb|ADI36981.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Methanococcus voltae A3]
          Length = 271

 Score = 42.4 bits (98), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 83/204 (40%), Gaps = 34/204 (16%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVIL-----CKALNAYLKISDTISILNLSIVDK 99
           ++  GRTD GV AL     +DL +E  P++      CK           I +L    +++
Sbjct: 44  LYYGGRTDLGVSALGNFVIYDLDKE--PILTHIYSKCKGFG--------IWVLGYQKINE 93

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF- 158
             +  +    R Y Y          L K  A+      D + ++  ++ L+G H F    
Sbjct: 94  FPNVEY----RHYRY---------ILPKVDAY--GNFHDMDKIKKVSECLIGTHSFHNLS 138

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
           +    +   P+RTI    V      I + +  +SFL   +R  +G +  VG  + T+ ++
Sbjct: 139 KRDKTKNRDPVRTIYDITVEDNEYFITLNIYGKSFLWNMVRKIIGLISNVGISEMTNEEI 198

Query: 219 EKALQA---QDRKECGPLAPPEGL 239
           E+ +        K   P++  EGL
Sbjct: 199 EEYMDKVFNPSIKVGSPISSAEGL 222


>gi|149063707|gb|EDM14030.1| pseudouridine synthase 1, isoform CRA_a [Rattus norvegicus]
          Length = 393

 Score = 42.0 bits (97), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 108/274 (39%), Gaps = 46/274 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +  G I   HG            
Sbjct: 51  KIVLLMAYSGKGYHGMQRNL-GSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSLKV---WLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          + +  E+ R++A+ L           G H+F  F 
Sbjct: 165 RTYCYMLPT----FAFAHKD-----RDVQDESYRLSAETLQQVNRLLGCYKGTHNFHNFT 215

Query: 160 SIHCQASSPIR--TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S         R   ++ +    F         I+V  +SF+  QIR  VG +  +  G  
Sbjct: 216 SQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYA 275

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + LE++    + K   P AP  GL  + V + 
Sbjct: 276 PESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|159487841|ref|XP_001701931.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158281150|gb|EDP06906.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 287

 Score = 42.0 bits (97), Expect = 0.075,   Method: Compositional matrix adjust.
 Identities = 69/290 (23%), Positives = 100/290 (34%), Gaps = 90/290 (31%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA-------------GRTDSGVH 56
           Y G  + G+ RQ N    + +IE  +F    +  ++  A             GRTD GV 
Sbjct: 19  YVGWAFQGFARQDN---TENTIEGVLFSALRKTKLIPEAAAKPISELAYSRCGRTDRGVS 75

Query: 57  ALRQVAHFDL---------------------VRE------WV------PVILCKALNAYL 83
           AL QV    L                      RE      W       P ++ KAL    
Sbjct: 76  ALGQVVALQLRSCARPGGGGLGYHDPSMCGPARESLQCPSWCVQEFDYPRLINKAL---- 131

Query: 84  KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
                + IL  + V   F+AR       ++Y+                    SLD + MR
Sbjct: 132 --PPEVRILGWTPVPADFNARCGGRAGEWVYQQ------------------HSLDIQAMR 171

Query: 144 IAAQHLVGRHDFTTF------------RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVAR 191
            AA H +G HDF  F            R I      P+ T      ++   +  + V   
Sbjct: 172 TAAAHFIGEHDFRNFCKPDVATVRSFRRRILSFTVEPVTTS---AADAAHQVYALTVRGT 228

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGL 239
           +FL  Q+R     L +VG G+     + + L  +A  RK    +AP E L
Sbjct: 229 AFLWHQVRCMAAILLMVGRGQEAPDVVARLLDVEACPRKPQYSMAPEEPL 278


>gi|295660198|ref|XP_002790656.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb01]
 gi|226281531|gb|EEH37097.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb01]
          Length = 600

 Score = 42.0 bits (97), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 56/126 (44%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 107 KVAVLLGYSGSGYHGMQLSQTEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 165

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   V+  + +N +L  S  I +  + + +K F +      R Y
Sbjct: 166 KGVHAAGNVVSLKLIVEDSNVV--QKINNHL--SPQIRVWGIEVTNKSFSSYQLCDSRVY 221

Query: 113 LYRIIT 118
            Y I T
Sbjct: 222 EYLIPT 227


>gi|328871318|gb|EGG19689.1| hypothetical protein DFA_00267 [Dictyostelium fasciculatum]
          Length = 568

 Score = 42.0 bits (97), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 29/127 (22%), Positives = 61/127 (48%), Gaps = 19/127 (14%)

Query: 6   MIIEYNGSGYFGWQ---RQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTD 52
           M+  Y G+GY G +     ++  +++  +E+A+FL +G I+  +           + RTD
Sbjct: 134 MLFAYVGTGYHGLEFHMTDQDYPTLENCLERALFL-SGMILPTNFGDPSRLNWRRSSRTD 192

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYL-----KISDTISILNLSIVDKQFHARFSA 107
            GVH++  +   +L  +   ++  + +  Y+      + D + I+++ +  K F  R   
Sbjct: 193 KGVHSMSTIIKANLEIDRSRMLTPEKIADYVALINSNLPDALRIISMEMTKKSFDPRRQG 252

Query: 108 IRRSYLY 114
           I R+Y Y
Sbjct: 253 IARTYHY 259


>gi|255023069|ref|ZP_05295055.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-208]
          Length = 33

 Score = 42.0 bits (97), Expect = 0.087,   Method: Composition-based stats.
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK 33
          M RY  II Y+GSG++G+Q Q N  ++Q  IEK
Sbjct: 1  MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEK 33


>gi|255088059|ref|XP_002505952.1| predicted protein [Micromonas sp. RCC299]
 gi|226521223|gb|ACO67210.1| predicted protein [Micromonas sp. RCC299]
          Length = 290

 Score = 41.6 bits (96), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 84/245 (34%), Gaps = 60/245 (24%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG-----------AGRTDSGVH 56
           + Y G  Y G+  Q        ++E+A+F     + ++              GRTD+GV 
Sbjct: 19  VMYAGWDYRGFASQGAERDGVRTVEEALFRALKRVRLIAPDATWKTCDYTRCGRTDAGVS 78

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLK--------------------ISDTISILNLSI 96
           AL QV    L R  VP       +  L                     +   I IL  + 
Sbjct: 79  ALGQVVSARL-RCRVPRRDDDDDDDDLSETGRLHEGDEIDYPAVLNRALPRDIRILGWTY 137

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           V   F ARF    R Y Y                W     LD   M  AA   VG HDF 
Sbjct: 138 VPPAFSARFDCDYRHYKYFFTD------------W---NGLDVRAMNEAASAFVGEHDFR 182

Query: 157 TF-----RSIHCQASSPIRTIDHFDV----NSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
            F     R++H    +  R ID   V         +  I VV  +FL  Q+R     L L
Sbjct: 183 NFCKMDARNVH----NYRRRIDSCRVVLAAGEPPGVAHIEVVGTAFLWHQVRCIASVLFL 238

Query: 208 VGDGK 212
           VG G+
Sbjct: 239 VGLGR 243


>gi|42572123|ref|NP_974152.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|332197678|gb|AEE35799.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 356

 Score = 41.6 bits (96), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 52/121 (42%), Gaps = 13/121 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +I  + G GY G Q+     +I+G +E+A+F        + G         + RTD 
Sbjct: 23  KVAIIFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPESIRGKPKLYDFARSARTDK 82

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+ QV     + +  P+     LN+ L   + I I     V   F ++    RR Y+
Sbjct: 83  GVSAVGQVVSGRFIVD--PLGFVNRLNSNL--PNQIRIFGYKHVTPSFSSKKFCDRRRYV 138

Query: 114 Y 114
           Y
Sbjct: 139 Y 139


>gi|240282351|gb|EER45854.1| tRNA pseudouridine synthase [Ajellomyces capsulatus H143]
          Length = 612

 Score = 41.2 bits (95), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 180

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   V+  + +N +L  S  I +  + I +K F +      R Y
Sbjct: 181 KGVHAAGNVVSLKLIVEDPNVV--QKINGHL--SPQIRVWGIEITNKSFSSYHLCDSRIY 236

Query: 113 LYRI 116
            Y I
Sbjct: 237 EYLI 240


>gi|325088485|gb|EGC41795.1| tRNA pseudouridine synthase [Ajellomyces capsulatus H88]
          Length = 612

 Score = 41.2 bits (95), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 180

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   V+  + +N +L  S  I +  + I +K F +      R Y
Sbjct: 181 KGVHAAGNVVSLKLIVEDPNVV--QKINGHL--SPQIRVWGIEITNKSFSSYHLCDSRIY 236

Query: 113 LYRI 116
            Y I
Sbjct: 237 EYLI 240


>gi|218192790|gb|EEC75217.1| hypothetical protein OsI_11484 [Oryza sativa Indica Group]
          Length = 722

 Score = 41.2 bits (95), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 17/129 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHG---------AGR 50
           R  + + Y G+ Y G Q+Q+     S+I+  +E AIF   G +   +G         + R
Sbjct: 73  RVVLRVGYVGTEYRGLQKQRELSADSTIESVLETAIFKAGGILESNYGKLQKVGWERSSR 132

Query: 51  TDSGVHALRQVAHFDLV---REWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +    R W       AL+ ++   + D + + ++    + F  R 
Sbjct: 133 TDKGVHSLATMISLKMEIPDRAWENDPDGIALSNFINSNLPDNVRVFSVLPAQRSFDVRR 192

Query: 106 SAIRRSYLY 114
             + R YLY
Sbjct: 193 ECLYREYLY 201


>gi|225559412|gb|EEH07695.1| tRNA pseudouridine synthase [Ajellomyces capsulatus G186AR]
          Length = 612

 Score = 41.2 bits (95), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 180

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   V+  + +N +L  S  I +  + I +K F +      R Y
Sbjct: 181 KGVHAAGNVVSLKLIVEDPNVV--QKINGHL--SPQIRVWGIEITNKSFSSYHLCDSRIY 236

Query: 113 LYRI 116
            Y I
Sbjct: 237 EYLI 240


>gi|325182026|emb|CCA16479.1| tRNA pseudouridine synthase A putative [Albugo laibachii Nc14]
          Length = 97

 Score = 41.2 bits (95), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 4  YCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVH 56
          Y M I Y G+ + GWQRQ   S     S+Q  IE ++   L   E V V+   RTD+G H
Sbjct: 24 YGMSIAYYGTDFIGWQRQPAASKPGFFSVQQIIEDSLSRALSKSERVNVNAVSRTDAGTH 83

Query: 57 AL 58
          A+
Sbjct: 84 AV 85


>gi|224126927|ref|XP_002319961.1| predicted protein [Populus trichocarpa]
 gi|222858337|gb|EEE95884.1| predicted protein [Populus trichocarpa]
          Length = 445

 Score = 41.2 bits (95), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 59/131 (45%), Gaps = 21/131 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIFLVTGEIVVVHG---------AGR 50
           +  + + Y G+ Y G Q+Q +  S   I+G +E+AI+   G     +G         + R
Sbjct: 33  KVALRVGYVGTDYRGLQKQHDQHSLLTIEGELERAIYEAGGIRESNYGNLNKISWARSSR 92

Query: 51  TDSGVHAL-------RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           TD GVH+L        ++       +   ++L K +N+YL   D+I +L++    K F  
Sbjct: 93  TDKGVHSLATTITMKMEIPENAWKDDLYGMVLAKHVNSYL--PDSIRVLSILPAQKSFDP 150

Query: 104 RFSAIRRSYLY 114
           R     R Y Y
Sbjct: 151 RRECDIRKYSY 161


>gi|328780691|ref|XP_624092.3| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like [Apis
           mellifera]
          Length = 389

 Score = 41.2 bits (95), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 67/287 (23%), Positives = 112/287 (39%), Gaps = 54/287 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGS----IEKAIFLVTGEI-----VVVHGAGRTDSG 54
           + M++ Y G  Y G Q  +   +I+GS    + KA F+   E      +    A RTD G
Sbjct: 49  FVMVLGYLGKNYSGMQINRGIKTIEGSLLSALLKADFITKNEFEDLKEIKFQRAARTDKG 108

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A+RQ+    L       +  + +N +L     I + ++  V + F+++     R+Y Y
Sbjct: 109 VSAVRQIVSLQLPNH----VNKEDINKHL--PKDIKVFDIKRVTRNFNSKNKCDARTYRY 162

Query: 115 RIIT-----------------------RQAPLALEKGRAW----LIPKSLDCENMRIAAQ 147
            + T                       R   L++  G+ +    L    LD  N  +   
Sbjct: 163 VLPTFALASEDPSFLQMDKEEEIDEEKRLEKLSMIDGKPYNEFRLNSDMLDKLNEILKL- 221

Query: 148 HLVGRHDFTTF----RSIHCQASSPI---RTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
              G H+F  F    R +  +A   I   R I+ F  N+    + + V  +SF+  QIR 
Sbjct: 222 -FEGTHNFHNFTSKIRPMDPRAKRYIVYFRCIETFIANNM-EFVVLEVQGQSFMLHQIRK 279

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            V  +  +     T   ++ A   +  K   P+AP  GL    V Y+
Sbjct: 280 MVSLIIGICRNIITIDFVKDAFSLE--KVDIPIAPGLGLSLHFVHYT 324


>gi|18411027|ref|NP_565126.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|6573728|gb|AAF17648.1|AC009978_24 T23E18.5 [Arabidopsis thaliana]
 gi|21592498|gb|AAM64448.1| unknown [Arabidopsis thaliana]
 gi|21703099|gb|AAM74492.1| At1g76120/T23E18_5 [Arabidopsis thaliana]
 gi|23308411|gb|AAN18175.1| At1g76120/T23E18_5 [Arabidopsis thaliana]
 gi|332197677|gb|AEE35798.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 463

 Score = 41.2 bits (95), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 52/121 (42%), Gaps = 13/121 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +I  + G GY G Q+     +I+G +E+A+F        + G         + RTD 
Sbjct: 23  KVAIIFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPESIRGKPKLYDFARSARTDK 82

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+ QV     + +  P+     LN+ L   + I I     V   F ++    RR Y+
Sbjct: 83  GVSAVGQVVSGRFIVD--PLGFVNRLNSNL--PNQIRIFGYKHVTPSFSSKKFCDRRRYV 138

Query: 114 Y 114
           Y
Sbjct: 139 Y 139


>gi|315928911|gb|EFV08168.1| tRNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 186

 Score = 41.2 bits (95), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 66/167 (39%), Gaps = 10/167 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAVASVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +V +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHSSYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
                    PK  D +         VG+ D   F    C++    +T
Sbjct: 121 FMASYVHFYPK-FDLDKANELLGFFVGKKDLKFF----CKSGGDNKT 162


>gi|315124345|ref|YP_004066349.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|315018067|gb|ADT66160.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
          Length = 178

 Score = 41.2 bits (95), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 66/167 (39%), Gaps = 10/167 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   VA  +
Sbjct: 5   IIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAVASVE 63

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +V +  L K LN +      I I  +  V   F  RF    R Y Y I +  +   
Sbjct: 64  CGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHSSYSP 120

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
                    PK  D +         VG+ D   F    C++    +T
Sbjct: 121 FMASYVHFYPK-FDLDKANELLGFFVGKKDLKFF----CKSGGDNKT 162


>gi|301604562|ref|XP_002931922.1| PREDICTED: tRNA pseudouridine synthase A [Xenopus (Silurana)
           tropicalis]
          Length = 399

 Score = 40.8 bits (94), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 109/283 (38%), Gaps = 64/283 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGA----------G 49
           +  +++ Y+G GY G QR   GSS   +IE  +    +++G I   H             
Sbjct: 56  KVVLLMAYSGKGYHGMQRNV-GSSQFKTIEDELVQALVLSGCIPDNHAEDMKKMSFQRCA 114

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    +   W+   + + +N  L     I IL L  V  +F+++ S   
Sbjct: 115 RTDKGVSAAGQVVSLKI---WLIDNVVEKINENL--PSHIRILGLKRVTGRFNSKNSCDA 169

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A          K    EN R++ + L           G  +F  F 
Sbjct: 170 RTYSYTLPT----FAFSHK-----DKEAQDENFRLSQETLNRVNELLALYKGTRNFHNFT 220

Query: 160 S---------------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
           S               +HC+          F       L  I+V  +SF+  QIR  +G 
Sbjct: 221 SQKGPRDPSAKRYIMEMHCEPP--------FQQGGL-ELAVIKVKGQSFMMHQIRKMIGL 271

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  V  G   ++ +E++    + K   P AP  GL  + V + 
Sbjct: 272 VIAVVKGFAPTSIIERSW--GEEKVDIPKAPGLGLVLERVHFE 312


>gi|242776451|ref|XP_002478840.1| tRNA pseudouridine synthase, putative [Talaromyces stipitatus ATCC
           10500]
 gi|218722459|gb|EED21877.1| tRNA pseudouridine synthase, putative [Talaromyces stipitatus ATCC
           10500]
          Length = 580

 Score = 40.8 bits (94), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 38/126 (30%), Positives = 53/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  ++I Y+G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 75  KVAVMIGYSGTGYHGMQLSPTEKTIEGDL-FAAFVAAGAISKANAADPKKSSLVRCARTD 133

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  K +N  L  S  I +    IV K F        R Y
Sbjct: 134 RGVHAAGNVVSLKLIVEDPDIV--KKINDNL--SPQIRVWGYEIVTKGFSCYQLCDSRMY 189

Query: 113 LYRIIT 118
            Y I T
Sbjct: 190 EYLIPT 195


>gi|225459791|ref|XP_002284797.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 558

 Score = 40.8 bits (94), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 35/116 (30%), Positives = 49/116 (42%), Gaps = 13/116 (11%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVHALRQ 60
           Y G GY G Q+     +I+G +E+A+F          G         + RTD GV A+ Q
Sbjct: 47  YCGVGYQGMQKNPGAKTIEGDLEEALFFSGAVPEQDRGHPKRFDWARSARTDKGVSAVGQ 106

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           V       +  P  L + LN+ L     I I     V   F+A+    RR Y+Y I
Sbjct: 107 VVSGRFYID--PPGLVERLNSNL--PPQIRIFGFKRVTASFNAKKFCDRRRYVYLI 158



 Score = 38.1 bits (87), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 48/106 (45%), Gaps = 7/106 (6%)

Query: 148 HLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFGNL-----IEIRVVARSFLHTQIRSF 201
           H VG H+F  F + I  +  S  R I  FD N+   +     ++  VV +SF+  QIR  
Sbjct: 374 HYVGTHNFHNFTTRIKAEDPSAQRFIVSFDGNTIVTVEGIEFVKCEVVGQSFMLHQIRKM 433

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +G    +       + LE AL  +D     P AP  GLY D   +S
Sbjct: 434 IGLAVAIMRNVAPESLLETAL-LKDVNINVPTAPEVGLYLDECFFS 478


>gi|125586190|gb|EAZ26854.1| hypothetical protein OsJ_10771 [Oryza sativa Japonica Group]
          Length = 516

 Score = 40.8 bits (94), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 17/129 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHG---------AGR 50
           R  + + Y G+ Y G Q+Q+     S+I+  +E AIF   G +   +G         + R
Sbjct: 73  RVVLRVGYVGTEYRGLQKQRELSADSTIESVLETAIFKAGGILESNYGKLQKVGWERSSR 132

Query: 51  TDSGVHALRQVAHFDLV---REWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +    R W       AL+ ++   + D + + ++    + F  R 
Sbjct: 133 TDKGVHSLATMISLKMEIPDRAWENDPDGIALSNFINSNLPDNVRVFSVLPAQRSFDVRR 192

Query: 106 SAIRRSYLY 114
             + R YLY
Sbjct: 193 ECLYREYLY 201


>gi|115452911|ref|NP_001050056.1| Os03g0338600 [Oryza sativa Japonica Group]
 gi|108708043|gb|ABF95838.1| tRNA pseudouridine synthase family protein, expressed [Oryza sativa
           Japonica Group]
 gi|113548527|dbj|BAF11970.1| Os03g0338600 [Oryza sativa Japonica Group]
          Length = 516

 Score = 40.8 bits (94), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 17/129 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHG---------AGR 50
           R  + + Y G+ Y G Q+Q+     S+I+  +E AIF   G +   +G         + R
Sbjct: 73  RVVLRVGYVGTEYRGLQKQRELSADSTIESVLETAIFKAGGILESNYGKLQKVGWERSSR 132

Query: 51  TDSGVHALRQVAHFDLV---REWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +    R W       AL+ ++   + D + + ++    + F  R 
Sbjct: 133 TDKGVHSLATMISLKMEIPDRAWENDPDGIALSNFINSNLPDNVRVFSVLPAQRSFDVRR 192

Query: 106 SAIRRSYLY 114
             + R YLY
Sbjct: 193 ECLYREYLY 201


>gi|67624003|ref|XP_668284.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54659475|gb|EAL38050.1| hypothetical protein Chro.80602 [Cryptosporidium hominis]
          Length = 210

 Score = 40.8 bits (94), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 43/157 (27%), Positives = 64/157 (40%), Gaps = 19/157 (12%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK--SLDCENMRIAA 146
           I ++    V   F ARF    R Y Y       PL  E+ +    PK        M IAA
Sbjct: 12  IRVIGYCEVRPDFSARFDCEYRLYKYFF-----PLNHERTKISKFPKIPPEQVPLMDIAA 66

Query: 147 QHLVGRHDFTTFRSIHC---QASSPIRTIDHFDVNSFGNLIEIRVVA------RSFLHTQ 197
           +  +G HD+  F  +     +  + IRTI  FD+N      E R  A       +FL  Q
Sbjct: 67  KQFLGTHDYRRFCKMDLKNRKNQTYIRTIYEFDINFVD---ENRTFAVATIKGSAFLWHQ 123

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +R  +G L  +G  K+    + + L   ++K    L+
Sbjct: 124 VRLMMGILFEIGQQKFNPEVITQMLTDVEQKNIAELS 160


>gi|320583409|gb|EFW97622.1| tRNA pseudouridine synthase [Pichia angusta DL-1]
          Length = 491

 Score = 40.8 bits (94), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 37/121 (30%), Positives = 50/121 (41%), Gaps = 15/121 (12%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTDSGVHA 57
           + Y G+GY G Q      +I+G +  A F+  G I   +           A RTD GVHA
Sbjct: 85  LSYCGTGYHGMQMNPPAKTIEGDLFDA-FVKAGAISKNNSNDLKKSSFMRAARTDKGVHA 143

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              V    L+ E     L + +N+YL   D I       V+K F  R     R Y Y + 
Sbjct: 144 AGNVISLKLIIE--DPDLVEKINSYL--PDQIRFWGYERVNKSFDCRKVCSSRIYEYLMP 199

Query: 118 T 118
           T
Sbjct: 200 T 200


>gi|327283197|ref|XP_003226328.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like
           [Anolis carolinensis]
          Length = 406

 Score = 40.8 bits (94), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 64/273 (23%), Positives = 108/273 (39%), Gaps = 50/273 (18%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---TGEIVVVHGA----------GRTD 52
           +++ Y+G GY G QR    S  + +IE  + L    +G I   HG            RTD
Sbjct: 65  LLVAYSGKGYHGMQRNVGNSQFK-TIEDDLVLALIQSGCIPENHGEDMKKMSFQRCARTD 123

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  Q+    +   W+   + + +N +L     I IL L  V   F+++     R+Y
Sbjct: 124 KGVSAAGQIVSLKV---WLIEDILQKINNHL--PPHIRILGLKRVTGGFNSKNKCDARTY 178

Query: 113 LYRIIT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--------- 160
            Y + T          +     L  ++L   N  +A     G H+F  F S         
Sbjct: 179 SYMLPTFAFAHKDCDFQDHTFHLNTETLATVNRLLAG--YKGTHNFHNFTSQKGPKDPSA 236

Query: 161 ------IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
                 ++C+    +R    F V        ++V  +SF+  QIR  +G +  +  G  +
Sbjct: 237 KRYIMEMYCEEPF-VRQGMEFAV--------MKVKGQSFMMHQIRKMIGLVIAIVKGYAS 287

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + +E++   +  K   P AP  GL  + V + 
Sbjct: 288 ESIMEQSWGEE--KVDVPKAPGLGLVLERVHFE 318


>gi|323454992|gb|EGB10861.1| hypothetical protein AURANDRAFT_62396 [Aureococcus anophagefferens]
          Length = 321

 Score = 40.8 bits (94), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 43/152 (28%), Positives = 64/152 (42%), Gaps = 23/152 (15%)

Query: 26  SIQGSIEKAIFL-VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV------ILCKA 78
           ++QG +  A+     G  +   GA RTD+GVHA  Q AH DL     P+      +L   
Sbjct: 74  TVQGELNAALRTRFGGADIPTLGASRTDAGVHARGQCAHADL--PVAPLGGAPLELLEHQ 131

Query: 79  LNAYLKISDTISILNLSIVDKQFHAR--------FSAIRRSYLYRIITRQA---PLA-LE 126
           +N  L     +  L  +   K + AR         +A  + Y YR+  R+    PL  L 
Sbjct: 132 INRLLPDDARVHDLRPAPAPKPWQAREGLPWHAIANAAGKRYAYRLTARRGSADPLGRLY 191

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           +G      +++D   +  A    VG HDF  F
Sbjct: 192 RGHVAY--RAVDFGRLDDALACFVGEHDFAAF 221


>gi|328861209|gb|EGG10313.1| hypothetical protein MELLADRAFT_76951 [Melampsora larici-populina
           98AG31]
          Length = 568

 Score = 40.8 bits (94), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 43/88 (48%), Gaps = 14/88 (15%)

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           +E +P I    LN+ L   ++I ++  S V  +F ARFS   R Y Y     ++ L    
Sbjct: 236 QEELPYI--SILNSLL--PESIKVIAWSPVSTEFDARFSCKGRHYKYFFTKFESDLN--- 288

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDF 155
                  +SLD E MR  A+ L+G HDF
Sbjct: 289 -------QSLDIEMMREGAKKLIGEHDF 309


>gi|299470490|emb|CBN78481.1| pseudouridylate synthase, putative [Ectocarpus siliculosus]
          Length = 743

 Score = 40.8 bits (94), Expect = 0.18,   Method: Composition-based stats.
 Identities = 43/188 (22%), Positives = 73/188 (38%), Gaps = 35/188 (18%)

Query: 3   RYCMIIEYNGSGYFGWQRQ---KNGSSIQGSIEKAIFLVTGEIVVVHG---------AGR 50
           +  +++ Y G+ + GWQ+    +N  +++G +E A++         +G           R
Sbjct: 30  KVAIVVGYVGTAFHGWQQSTDAQNVRTVEGELETALWKAGAIADSNYGDLNKIGWGRTSR 89

Query: 51  TDSGVHALRQVAHFDLVREWVP--VILCKALNAY------LKISDTISILNLSIVDKQFH 102
           TD GVHA + VA   L+   +P        ++ Y       K+ D I   ++S V K F 
Sbjct: 90  TDKGVHASKTVAAAKLL---LPQETFTATGMSQYGKDKLNEKLPDDIRCFSVSKVPKSFR 146

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
            R     R Y Y  + R+           L+P        R   +  VG H F  + S  
Sbjct: 147 GREECTLREYTY-YLPRE-----------LLPDDEALGKFRELLKLFVGTHSFHNYASTK 194

Query: 163 CQASSPIR 170
            +    +R
Sbjct: 195 GRQLKEVR 202


>gi|218191324|gb|EEC73751.1| hypothetical protein OsI_08404 [Oryza sativa Indica Group]
          Length = 581

 Score = 40.8 bits (94), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 52/122 (42%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD 
Sbjct: 50  KVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYRAGAVPEADRAAPRRYDWARAARTDK 109

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A  QV      R +V P +    LNA L  +  I       V   F+A+    RR Y
Sbjct: 110 GVSAAAQVVSG---RFYVDPPVFTDRLNAQL--APQIRAFGYVRVTNSFNAKKFCDRRRY 164

Query: 113 LY 114
           +Y
Sbjct: 165 VY 166


>gi|226293711|gb|EEH49131.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 597

 Score = 40.8 bits (94), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 30/116 (25%), Positives = 54/116 (46%), Gaps = 15/116 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 135 KVAVLLGYSGSGYHGMQLSQTEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 193

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            GVHA   V    L+ E   V+  + +N +L  S  I +  + + +K ++ R + +
Sbjct: 194 KGVHAAGNVVSLKLIVEDSDVV--QKINNHL--SPQIRVWGIEVTNKSYNQRQAEV 245


>gi|147780612|emb|CAN69118.1| hypothetical protein VITISV_031845 [Vitis vinifera]
          Length = 559

 Score = 40.8 bits (94), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 35/123 (28%), Positives = 51/123 (41%), Gaps = 13/123 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +   Y G GY G Q+     +I+G +E+A+F          G         + RTD 
Sbjct: 28  KIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFFSGAVPEQDRGHPKRFDWARSARTDK 87

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+ QV       +  P  L + LN+ L     I I     V   F+A+    RR Y+
Sbjct: 88  GVSAVGQVVSGRFYID--PPGLVERLNSNL--PPQIRIFGFKRVTASFNAKKFCDRRRYV 143

Query: 114 YRI 116
           Y I
Sbjct: 144 YLI 146



 Score = 38.5 bits (88), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 48/106 (45%), Gaps = 7/106 (6%)

Query: 148 HLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFGNL-----IEIRVVARSFLHTQIRSF 201
           H VG H+F  F + I  +  S  R I  FD N+   +     ++  VV +SF+  QIR  
Sbjct: 375 HYVGTHNFHNFTTRIKAEDPSAQRFIVSFDGNTIVTVEGIEFVKCEVVGQSFMLHQIRKM 434

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +G    +       + LE AL  +D     P AP  GLY D   +S
Sbjct: 435 IGLAVAIMRNVAPESLLETAL-LKDVNINVPTAPEVGLYLDECFFS 479


>gi|167383737|ref|XP_001736651.1| tRNA pseudouridine synthase A [Entamoeba dispar SAW760]
 gi|165900832|gb|EDR27064.1| tRNA pseudouridine synthase A, putative [Entamoeba dispar SAW760]
          Length = 403

 Score = 40.8 bits (94), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 59/272 (21%), Positives = 109/272 (40%), Gaps = 40/272 (14%)

Query: 5   CMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSG 54
            +I  Y G GYFG      N  +I+G IE A++             + V      RTD G
Sbjct: 46  AVIFSYVGRGYFGLMYLNNNPKTIEGEIENAMYKAKCISEDNKHDLKKVGWSRCARTDKG 105

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A   +    +  +   +   + +N++L   +TI I ++  V   F+A+     R+Y Y
Sbjct: 106 VSAANNLISLKMGLDGNYI---ERINSFL--PETIRIQDVVKVSHSFNAKTRVDSRTYEY 160

Query: 115 --------RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT--TFRSIHCQ 164
                   +I +    + +E       P+  D +       + V  H+F   TF +   +
Sbjct: 161 IFPSYAIQKIDSEHPEINVEYN-----PQQEDVDYFNSVISNYVKTHNFQNYTFNTKETK 215

Query: 165 ASSP-----IRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
           A S      I ++    V   G N+I + +  +SF+  QIR  +G   ++ + +     +
Sbjct: 216 ADSKSNNRYIISMSAQLVQRNGLNVIAVSIHGQSFMLWQIRRMIGFAIVLTNFRLPIEQM 275

Query: 219 EKALQAQ----DRKECGPLAPPEGLYFDSVEY 246
            + ++      + +   P AP  GL+ D   +
Sbjct: 276 NEIMKTSFTLINWRSVIPTAPAHGLFLDQCHF 307


>gi|115447813|ref|NP_001047686.1| Os02g0668400 [Oryza sativa Japonica Group]
 gi|50251324|dbj|BAD28300.1| putative pseudouridine synthase 1 [Oryza sativa Japonica Group]
 gi|50252138|dbj|BAD28134.1| putative pseudouridine synthase 1 [Oryza sativa Japonica Group]
 gi|113537217|dbj|BAF09600.1| Os02g0668400 [Oryza sativa Japonica Group]
          Length = 581

 Score = 40.8 bits (94), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 52/122 (42%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD 
Sbjct: 50  KVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYRAGAVPEADRAAPRRYDWARAARTDK 109

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A  QV      R +V P +    LNA L  +  I       V   F+A+    RR Y
Sbjct: 110 GVSAAAQVVSG---RFYVDPPVFTDRLNAQL--APQIRAFGYVRVTNSFNAKKFCDRRRY 164

Query: 113 LY 114
           +Y
Sbjct: 165 VY 166


>gi|50287019|ref|XP_445939.1| hypothetical protein [Candida glabrata CBS 138]
 gi|74637780|sp|Q6FV05|PUS1_CANGA RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|49525245|emb|CAG58858.1| unnamed protein product [Candida glabrata]
          Length = 549

 Score = 40.4 bits (93), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 40/128 (31%), Positives = 57/128 (44%), Gaps = 21/128 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGR 50
           MI YC      G+GY G Q      +I+ ++ KA F+  G I   +           A R
Sbjct: 92  MIGYC------GTGYHGMQYNPPNPTIEAALFKA-FVDAGAISKANSNDLKKNNFMRAAR 144

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GVHA   +    ++ E  P I+ K +NA L   + I I ++  V+K F  R     R
Sbjct: 145 TDKGVHAGGNLISLKMIIE-DPEIMDK-INANL--PEGIRIWDIERVNKAFDCRKMCSSR 200

Query: 111 SYLYRIIT 118
            Y Y + T
Sbjct: 201 WYEYLLPT 208


>gi|159118829|ref|XP_001709633.1| Pseudouridylate synthase, putative [Giardia lamblia ATCC 50803]
 gi|157437750|gb|EDO81959.1| Pseudouridylate synthase, putative [Giardia lamblia ATCC 50803]
          Length = 531

 Score = 40.4 bits (93), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 76/189 (40%), Gaps = 45/189 (23%)

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM 142
           +++ +TI +L  + VD+ F AR S   R Y+Y        +  E G       SL+   M
Sbjct: 236 MRLPETIRVLGWAPVDENFSARHSTSSRRYVY--------MFGEVG-------SLNIRRM 280

Query: 143 RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR--------------- 187
             A   LVG HD   FR+I C+ S  + +I  F+   F   +EI                
Sbjct: 281 AEACTKLVGFHD---FRNI-CKPS--LDSIKTFERVIFSCFLEIDGQPYDCENDRMAMKE 334

Query: 188 -------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEG 238
                  V   +FL+ QIR     L  +G      + +   L  +    K   P+AP E 
Sbjct: 335 NSTLSLVVCGSAFLYHQIRCIASLLLHIGAELEPPSLISDLLNVEQFPGKPDYPIAPGEL 394

Query: 239 LYFDSVEYS 247
           L F+  EY+
Sbjct: 395 LLFERAEYT 403


>gi|320532726|ref|ZP_08033515.1| hypothetical protein HMPREF9057_01391 [Actinomyces sp. oral taxon
          171 str. F0337]
 gi|320135064|gb|EFW27223.1| hypothetical protein HMPREF9057_01391 [Actinomyces sp. oral taxon
          171 str. F0337]
          Length = 57

 Score = 40.4 bits (93), Expect = 0.22,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
          M R  + + Y+G+ + GW  Q    +++G +  A+  V  E V +  AGRTD+GVHA
Sbjct: 1  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTCALATVVREPVRLTVAGRTDAGVHA 57


>gi|194697948|gb|ACF83058.1| unknown [Zea mays]
          Length = 516

 Score = 40.4 bits (93), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 56/129 (43%), Gaps = 17/129 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHG---------AGR 50
           R  + I Y G+ Y G Q+Q+     S+I+  +E AIF   G +   +G         + R
Sbjct: 78  RVVLRIGYVGTDYRGLQKQQELGVDSTIESVLESAIFKSGGILESNYGKLQKIGWERSSR 137

Query: 51  TDSGVHALRQVAHFDLV---REWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +    R W       AL +++   + D + + ++    + F  R 
Sbjct: 138 TDKGVHSLATMISLKMEIPDRAWEDDPDGIALASFINSNLPDNVRVFSILPAQRSFDVRR 197

Query: 106 SAIRRSYLY 114
             + R Y Y
Sbjct: 198 ECLYREYFY 206


>gi|296423394|ref|XP_002841239.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295637475|emb|CAZ85430.1| unnamed protein product [Tuber melanosporum]
          Length = 483

 Score = 40.4 bits (93), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 63/267 (23%), Positives = 93/267 (34%), Gaps = 71/267 (26%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVVVHG------------------ 47
           I Y G  Y G++   N  +   +IE+ IF  L+   +V  +G                  
Sbjct: 30  IAYLGGNYTGFEYHANSPNTTNTIEEHIFKALLKARLVPCNGIEGEEETVLGWPGDEVAE 89

Query: 48  ---AGRTDSGVHALRQV------------------------------AHFDLVREWVPVI 74
               GRTD+GV A  QV                                FD  ++ +P  
Sbjct: 90  YSKCGRTDTGVSAFGQVIGVRVRSNRPLPKKPTDDVAEEGGEEGKEKTEFDDEKDELP-- 147

Query: 75  LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
             + LN  L   D   +         F ARF+  +R Y Y   T  A +           
Sbjct: 148 YPQILNRLLP-KDIRVLAWCPHPPPTFSARFNCQQRHYRY-FFTNPAIVPSPNSTV---- 201

Query: 135 KSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDV--------NSFGNLI 184
            +LD + MR AA+  VG HDF  F  +    Q +   R I H D+        N+   + 
Sbjct: 202 GNLDIDKMREAAKLYVGDHDFRNFCKLDASKQITRFDRVIHHADIVELPQSSPNNNPKVY 261

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDG 211
              +   +FL  Q+R  +  L L+  G
Sbjct: 262 YFELHGSAFLWHQVRHMIAILFLIAQG 288


>gi|150400596|ref|YP_001324362.1| tRNA pseudouridine synthase A [Methanococcus aeolicus Nankai-3]
 gi|150013299|gb|ABR55750.1| tRNA pseudouridine synthase A [Methanococcus aeolicus Nankai-3]
          Length = 310

 Score = 40.4 bits (93), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 58/249 (23%), Positives = 100/249 (40%), Gaps = 35/249 (14%)

Query: 4   YCMIIEYNGS--GYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           Y + I Y+G+  G+     +KN     I  ++ K  ++   E   +   GRTD+GV AL 
Sbjct: 39  YILKIAYDGNNDGFQSHPHKKNNVCDIIINALLKCGYMDKEETKPLLRGGRTDNGVLALG 98

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
                +L +E  P++     + Y K+  T + +L  S + +    ++    R Y Y    
Sbjct: 99  NFIIVNLNQE--PILS----HVYAKLKYTGVWVLGYSKISELPEIKY----RHYKY---- 144

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRI-AAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFD 176
                        ++P      N+ I  A  L+G H F    +  + +  +P+RTI    
Sbjct: 145 -------------ILPNEGQNINLMIEGANKLIGTHSFHNLSKRDNTKNKNPLRTIYDIK 191

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +      I I +  ++FL   +R  V +L  VG        ++K L     +   P AP 
Sbjct: 192 IKENDFFITIDIFGKNFLWNMVRRIVTALSEVGKENKPLNWIDKLLDINHTEGVAP-APA 250

Query: 237 EGLYFDSVE 245
            GL    V+
Sbjct: 251 NGLILVDVK 259


>gi|67481869|ref|XP_656284.1| tRNA pseudouridine synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56473473|gb|EAL50898.1| tRNA pseudouridine synthase, putative [Entamoeba histolytica
           HM-1:IMSS]
          Length = 401

 Score = 40.4 bits (93), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 59/272 (21%), Positives = 109/272 (40%), Gaps = 40/272 (14%)

Query: 5   CMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSG 54
            +I  Y G GYFG      N  +I+G IE A++             + V      RTD G
Sbjct: 44  AVIFSYVGRGYFGLMYLNNNPKTIEGEIENAMYKAKCISEDNKHDLKKVGWSRCARTDKG 103

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A   +    +  +   +   + +N++L   +TI I ++  V   F+A+     R+Y Y
Sbjct: 104 VSAANNLISLKMGLDGNYI---ERINSFL--PETIRIQDVVKVSHSFNAKTRVDSRTYEY 158

Query: 115 --------RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT--TFRSIHCQ 164
                   +I +    + +E       P+  D +       + V  H+F   TF +   +
Sbjct: 159 IFPSYAIQKIDSEHPEINVEYN-----PQQEDIDYFNSVISNYVKTHNFQNYTFNTKETK 213

Query: 165 ASSP-----IRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
           A S      I ++    V   G N+I + +  +SF+  QIR  +G   ++ + +     +
Sbjct: 214 ADSKSNNRYIISMSAQLVQRNGLNVIAVSIHGQSFMLWQIRRMIGFAIVLTNFRLPIEQM 273

Query: 219 EKALQAQ----DRKECGPLAPPEGLYFDSVEY 246
            + ++      + +   P AP  GL+ D   +
Sbjct: 274 NEIMKTSFTLINWRSVIPTAPAHGLFLDQCHF 305


>gi|50303379|ref|XP_451631.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|74637053|sp|Q6CWQ8|PUS1_KLULA RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|49640763|emb|CAH02024.1| KLLA0B02244p [Kluyveromyces lactis]
          Length = 553

 Score = 40.4 bits (93), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 55/128 (42%), Gaps = 21/128 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGR 50
           MI YC      G+GY G Q      +I+  + +A F+  G I   +           A R
Sbjct: 104 MIGYC------GTGYHGMQYNPPNDTIEKELFEA-FVRAGAISKANSTDLKKNGFQRAAR 156

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GVHA   V    L+ E  P +  K  N   ++ D I + ++S V+K F  R     R
Sbjct: 157 TDKGVHAGGNVISLKLIIE-DPEVKEKINN---ELPDQIRVWDISRVNKAFDCRKMCSSR 212

Query: 111 SYLYRIIT 118
            Y Y + T
Sbjct: 213 WYEYLLPT 220


>gi|328772887|gb|EGF82924.1| hypothetical protein BATDEDRAFT_33866 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 580

 Score = 40.4 bits (93), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 32/124 (25%), Positives = 58/124 (46%), Gaps = 10/124 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-----GEIVVVHGAGRTDSGVH 56
           +R  ++  YNG+G+   +R K   +I+G++   +  +           +  A  T++G H
Sbjct: 23  VRLAILYGYNGTGFDALERTKGEVTIEGTLLAVLASLLSADGKATFTNISRASTTEAGEH 82

Query: 57  ALRQVAHFDLVREWVPVIL--CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           A +QV  F+      P+IL   +A+N  L  S  + +  +  V   F AR +   R+Y +
Sbjct: 83  ASKQVVSFE-THAPTPIILPAVEAVNKLLPSS--MRVFRIIPVASDFSARRTCEARTYEF 139

Query: 115 RIIT 118
            I T
Sbjct: 140 LIPT 143


>gi|255710543|ref|XP_002551555.1| KLTH0A02222p [Lachancea thermotolerans]
 gi|238932932|emb|CAR21113.1| KLTH0A02222p [Lachancea thermotolerans]
          Length = 443

 Score = 40.4 bits (93), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 89/240 (37%), Gaps = 50/240 (20%)

Query: 14  GYFGWQRQKNGSSIQG------SIEKAIFLVTGEIVVVHG----------AGRTDSGVHA 57
            Y GW    NG +IQ       ++E  I        +V             GRTD GV A
Sbjct: 94  AYLGWNY--NGLAIQKEPTPLPTVEGTILEAMNACKLVPSMVPQDYNFSRCGRTDKGVSA 151

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDK------------QFHARF 105
           + QV    +             N   +I D I ILN  + D              F ARF
Sbjct: 152 MNQVISLHVRSNLTREEQQDEENDGREI-DYIHILNQLLPDDIRISAVCLRPPTNFDARF 210

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-- 163
           S   R Y Y        L  + G        LD + M  AA+   G HDF  F  +    
Sbjct: 211 SCQYRHYRY--------LFHKDG--------LDIKKMEEAARMYEGEHDFRNFCKLDGSK 254

Query: 164 QASSPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           Q ++  R I+   + S    I  + ++  +FL  Q+R  + +L L+G G   +T L+  +
Sbjct: 255 QINNYKRNIERSRIISLSEDIYCLDLIGSAFLWHQVRCMMANLFLIGQGLEDTTLLKDLM 314


>gi|154418432|ref|XP_001582234.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
 gi|121916468|gb|EAY21248.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
          Length = 345

 Score = 40.4 bits (93), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 60/266 (22%), Positives = 112/266 (42%), Gaps = 44/266 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVH-----GAGRTDSGVH 56
           ++  Y G+ Y G Q+  +  +++  + +A+    FL       ++      A RTD+GVH
Sbjct: 31  LLYRYIGTQYHGLQQNIDTHTVEKELFQALISAGFLSDQANCNLNRIKWSEASRTDAGVH 90

Query: 57  ALRQVAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           A  QV  F    ++      +   +N  L  +  I I+    + +QF+A+  A  R+Y +
Sbjct: 91  ACAQVLSFKASGLKGICIADIPDLINKQLPRTSDIEIITCITLRRQFYAQKFAESRNYNF 150

Query: 115 RIITR----QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            + T      +   L   R  ++P  +   N           H+FT+ +S    AS+P  
Sbjct: 151 LLPTNAFSSNSIEHLNYLRTSILPLFIGWLNY----------HNFTSNKS----ASNP-S 195

Query: 171 TIDHFDVNSFGNLIEIRVV--------ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           ++   DV +F +  E+  V          SF+  QIR  + ++         + ++++ L
Sbjct: 196 SMRKIDVFTFTDPFEVEGVEFVLFTIHGESFMLNQIRKMIATVISASHNYIGAEEVKRCL 255

Query: 223 QAQ--DRKECGPLAPPEGLYFDSVEY 246
             +    K C    P +GL  D V+Y
Sbjct: 256 SEEGWSIKMC----PGDGLMLDHVDY 277


>gi|255719542|ref|XP_002556051.1| KLTH0H03894p [Lachancea thermotolerans]
 gi|238942017|emb|CAR30189.1| KLTH0H03894p [Lachancea thermotolerans]
          Length = 546

 Score = 40.0 bits (92), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 58/126 (46%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  ++I Y G+GY G Q      +I+  + +A F+  G I   +           A RTD
Sbjct: 76  KVAVMIGYCGTGYHGMQYNPPTPTIEAELFRA-FVEAGAISQANSKDLKKSGFMRAARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E  P I+ K +N+  K+ + I + ++  V+K F  R     R Y
Sbjct: 135 KGVHAGGNVVSLKLIIE-DPDIIAK-INS--KLPEGIRVWDIERVNKAFDCRKLCGSRWY 190

Query: 113 LYRIIT 118
            Y + T
Sbjct: 191 EYLLPT 196


>gi|289742875|gb|ADD20185.1| pseudouridylate synthase [Glossina morsitans morsitans]
          Length = 444

 Score = 40.0 bits (92), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 67/262 (25%), Positives = 100/262 (38%), Gaps = 64/262 (24%)

Query: 15  YFGWQRQKNGSSIQ----GSIEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVA 62
           YFGW  Q  G + Q     +IE  +F       ++        H  GRTD  V A  QV 
Sbjct: 63  YFGWDYQ--GFACQEDSNNTIEFHLFKALTRTCLIESRSSANYHRCGRTDKKVSAFCQVI 120

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILN------------LSIVDKQFHARFSAIRR 110
             DL R   P       +   K  D   I+N            + I +  F ARF  I R
Sbjct: 121 SIDL-RSKFPEKQQFEESCLEKEIDYCGIMNRVLPKNIRCISWMPIRNHLFSARFDCITR 179

Query: 111 SYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRS-----IHCQ 164
           +Y Y                   PK +L+   M+ A + L+ RH  T FR+     +H  
Sbjct: 180 TYRY-----------------FFPKGNLNITAMQDACK-LLQRH--TDFRNLCKMDVHNG 219

Query: 165 ASSPIRTIDHFDV------NSFGN----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
            ++ +R I+  +V      N   N    +  + + A +FL  QIR  +  L L+G  K  
Sbjct: 220 VTNYVRHIEAANVRLCPHQNESKNKGYAMHYLEIKANAFLWHQIRCIMTVLLLIGQEKEE 279

Query: 215 STDLEKALQAQDRKECGPLAPP 236
            + + + L   ++  C P   P
Sbjct: 280 PSVINELLNV-EKNPCKPQYTP 300


>gi|164661239|ref|XP_001731742.1| hypothetical protein MGL_1010 [Malassezia globosa CBS 7966]
 gi|159105643|gb|EDP44528.1| hypothetical protein MGL_1010 [Malassezia globosa CBS 7966]
          Length = 226

 Score = 40.0 bits (92), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 13/128 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI----------VVVHGAGRTD 52
           +  +   Y G+ Y G Q      +I+G I +A F   G +          V +  A RTD
Sbjct: 78  KVALFFGYCGTDYSGLQVNPGVKTIEGDIFEA-FCRAGAVSKENAVNPNKVQLQRAARTD 136

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRR 110
            GVHA   +    L+ +   +   + L  Y+   + D I I  +  V   F+AR S   R
Sbjct: 137 RGVHAAGNLLTLKLILDPPNLPPNQTLTTYVNSLLPDQIRIWGMRRVQSAFNARTSCDSR 196

Query: 111 SYLYRIIT 118
            Y Y + T
Sbjct: 197 LYEYLLPT 204


>gi|327353057|gb|EGE81914.1| tRNA pseudouridine synthase [Ajellomyces dermatitidis ATCC 18188]
          Length = 610

 Score = 40.0 bits (92), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 54/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q      +I+G +  A F+  G I   +             RTD
Sbjct: 122 KVAVMLGYSGSGYKGMQLSPTEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 180

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +N  L  S  I +  + I +K F +      R Y
Sbjct: 181 KGVHAAGNVVSLKLIVEDSDIV--QKINEQL--SPQIRVWGIEITNKSFSSYHLCDSRIY 236

Query: 113 LYRIIT 118
            Y I T
Sbjct: 237 EYLIPT 242


>gi|239606367|gb|EEQ83354.1| tRNA pseudouridine synthase [Ajellomyces dermatitidis ER-3]
          Length = 596

 Score = 40.0 bits (92), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 54/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q      +I+G +  A F+  G I   +             RTD
Sbjct: 122 KVAVMLGYSGSGYKGMQLSPTEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 180

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +N  L  S  I +  + I +K F +      R Y
Sbjct: 181 KGVHAAGNVVSLKLIVEDSDIV--QKINEQL--SPQIRVWGIEITNKSFSSYHLCDSRIY 236

Query: 113 LYRIIT 118
            Y I T
Sbjct: 237 EYLIPT 242


>gi|308477475|ref|XP_003100951.1| hypothetical protein CRE_16900 [Caenorhabditis remanei]
 gi|308264295|gb|EFP08248.1| hypothetical protein CRE_16900 [Caenorhabditis remanei]
          Length = 322

 Score = 40.0 bits (92), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 54/249 (21%), Positives = 91/249 (36%), Gaps = 43/249 (17%)

Query: 41  EIVVVHGAGRTDSGVHALRQVAHFDLVREW-----VPVILCKALNAYLKISD-----TIS 90
           E +    + RTD+ VHA+R      +  E+      P I    +  +    D     ++ 
Sbjct: 55  ECLKFSPSSRTDAKVHAIRNSVICQIPLEYSELDKTPEIKADYMKKWKSTIDAANPGSLV 114

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIIT----------RQAPLAL---EKGRAWLIPKSL 137
           I ++  V   F  R S   R Y YR+            RQ P      E+  AW +P   
Sbjct: 115 IRDVHSVSAGFCIRRSVSYRKYTYRLAVCRSWELWESIRQEPSIACFSERDYAWRLPPGF 174

Query: 138 DCENMRIAAQHLVGRHDFTTF-------RSIHCQASSPIRTIDHFDV---------NSFG 181
             E +  A +   G     +F       +       S ++ I H  +         N   
Sbjct: 175 SPERLLTAGRRFEGEQVMGSFFKHTNREKRFEPITPSALKYILHVGLSNGEAYSINNDIY 234

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECG-PLAPPE 237
           +   + +VA+SF+  QIR  +  L      +     ++  L    + +  + G P+APP+
Sbjct: 235 DYYNVTIVAKSFVREQIRRMMSCLVNYSYDRIPLATVDWLLNNPISSNFFDMGIPIAPPQ 294

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 295 GLFLTDVVY 303


>gi|14318522|ref|NP_116655.1| Deg1p [Saccharomyces cerevisiae S288c]
 gi|399356|sp|P31115|PUS3_YEAST RecName: Full=tRNA pseudouridine synthase 3; AltName:
           Full=Depressed growth-rate protein DEG1; AltName:
           Full=tRNA pseudouridylate synthase 3; AltName:
           Full=tRNA-uridine isomerase 3
 gi|836755|dbj|BAA09239.1| depressed growth-rate protein [Saccharomyces cerevisiae]
 gi|51013845|gb|AAT93216.1| YFL001W [Saccharomyces cerevisiae]
 gi|285811895|tpg|DAA12440.1| TPA: Deg1p [Saccharomyces cerevisiae S288c]
          Length = 442

 Score = 40.0 bits (92), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 93/244 (38%), Gaps = 47/244 (19%)

Query: 10  YNGSGYFGWQRQKNGS---SIQGSIEKAIF---LVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y G  Y G   QK  +   +++G+I +A+    LV   ++  +     GRTD GV A+ Q
Sbjct: 100 YLGWNYNGLAVQKEYTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKGVSAMNQ 159

Query: 61  VAHF------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           V               D   +   +     LN  L     IS + L      F ARFS +
Sbjct: 160 VISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR-PPPNFDARFSCV 218

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
            R Y Y          +  G      K+L+ E M  AA + VG  DF  F  +    Q +
Sbjct: 219 HRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDFRNFCKLDGSKQIT 262

Query: 167 SPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTS------TDLE 219
           +  RTI    +           +V  +FL  Q+R  +  L LVG            TD+E
Sbjct: 263 NFKRTIISSKILPLSETFYCFDLVGSAFLWHQVRCMMAILFLVGQSLEVPEIVLRLTDIE 322

Query: 220 KALQ 223
           K  Q
Sbjct: 323 KTPQ 326


>gi|308161029|gb|EFO63491.1| Pseudouridylate synthase, putative [Giardia lamblia P15]
          Length = 515

 Score = 40.0 bits (92), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 50/189 (26%), Positives = 76/189 (40%), Gaps = 45/189 (23%)

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM 142
           +++ +TI +L  + VD+ F AR S   R Y+Y             G+      SL+   M
Sbjct: 220 MRLPETIRVLGWAPVDENFSARHSTSSRHYIYTF-----------GQIG----SLNIRRM 264

Query: 143 RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR--------------- 187
             A   LVG HD   FR+I C+ S  + +I  F+   F   +EI                
Sbjct: 265 AEACTKLVGFHD---FRNI-CKPS--LDSIKTFERVIFSCYLEIDGQPYECENDRMVIKE 318

Query: 188 -------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEG 238
                  V   +FL+ QIR     L  +G      + +   L  ++   K   P+AP E 
Sbjct: 319 NSSLSLVVCGSAFLYHQIRCIASLLLHIGAELEPPSLISDLLNIENFPGKPDYPIAPGEL 378

Query: 239 LYFDSVEYS 247
           L F+  EY+
Sbjct: 379 LLFEKAEYT 387


>gi|302141694|emb|CBI18897.3| unnamed protein product [Vitis vinifera]
          Length = 419

 Score = 39.7 bits (91), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 48/106 (45%), Gaps = 7/106 (6%)

Query: 148 HLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFGNL-----IEIRVVARSFLHTQIRSF 201
           H VG H+F  F + I  +  S  R I  FD N+   +     ++  VV +SF+  QIR  
Sbjct: 235 HYVGTHNFHNFTTRIKAEDPSAQRFIVSFDGNTIVTVEGIEFVKCEVVGQSFMLHQIRKM 294

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +G    +       + LE AL  +D     P AP  GLY D   +S
Sbjct: 295 IGLAVAIMRNVAPESLLETAL-LKDVNINVPTAPEVGLYLDECFFS 339


>gi|242040995|ref|XP_002467892.1| hypothetical protein SORBIDRAFT_01g035980 [Sorghum bicolor]
 gi|241921746|gb|EER94890.1| hypothetical protein SORBIDRAFT_01g035980 [Sorghum bicolor]
          Length = 520

 Score = 39.7 bits (91), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 56/129 (43%), Gaps = 17/129 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHG---------AGR 50
           R  + I Y G+ Y G Q+Q+     S+I+  +E AIF   G +   +G         + R
Sbjct: 78  RVVLRIGYIGTEYRGLQKQRELGVDSTIESVLESAIFKSGGILESNYGKLQKVGWERSSR 137

Query: 51  TDSGVHALRQVAHFDLV---REWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +    R W       AL +++   + D + + ++    + F  R 
Sbjct: 138 TDKGVHSLATMISLKMEIPDRAWEDDPDGIALASFINSNLPDNVRVFSILPAQRSFDVRR 197

Query: 106 SAIRRSYLY 114
             + R Y Y
Sbjct: 198 ECLYREYFY 206


>gi|326527051|dbj|BAK04467.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 572

 Score = 39.7 bits (91), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 51/122 (41%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +I+ Y G+GY G Q+     +I+G +E+A++                    A RTD 
Sbjct: 49  KVAIILAYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRAAPARYEWARAARTDK 108

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A  QV      R +V P      LNA  K++  I       V   F A+    RR Y
Sbjct: 109 GVSAAAQVVSG---RFYVDPPGFIDRLNA--KLAPQIRAFGYVRVTNSFSAKKFCDRRRY 163

Query: 113 LY 114
           +Y
Sbjct: 164 VY 165


>gi|307136307|gb|ADN34131.1| tRNA pseudouridine synthase family protein [Cucumis melo subsp.
           melo]
          Length = 519

 Score = 39.7 bits (91), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 50/216 (23%), Positives = 83/216 (38%), Gaps = 24/216 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +   Y G GY G Q+     +I+  +E+A++L         G         + RTD 
Sbjct: 56  KVAIFFAYCGVGYQGMQKNPGAKTIEADLEEALYLAGAVPEQDRGLSKRYDWARSARTDK 115

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+ QV       +  P      LN+ L  S  I I     V   F+A+    RR Y+
Sbjct: 116 GVSAVGQVVSGRFYID--PPGFVDRLNSNL--SPQIRIFGYKRVTASFNAKKFCDRRRYV 171

Query: 114 YRIIT---------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           Y I            +  +    G    + K L+C       + L+G+ +F    +I   
Sbjct: 172 YLIPVFALDPNCHRDRESVKASLGSDNELVKCLECSERGRKVEGLMGKRNFEVKTAITES 231

Query: 165 --ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
             +S+ +  I+  DV + G L +    + S   T +
Sbjct: 232 DISSNIVNAIEVSDVQANGVLEDSATTSDSNKQTSV 267



 Score = 39.3 bits (90), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 48/103 (46%), Gaps = 9/103 (8%)

Query: 147 QHLVGRHDFTTFRSIHCQASSPI--RTIDHFDVNSFG-----NLIEIRVVARSFLHTQIR 199
           +H VG H+F  F +   +A  P   R I  FD ++         ++  VV +SF+  QIR
Sbjct: 332 KHYVGTHNFHNF-TTRTKAEDPAARRFIVSFDASTTVVVEGIEFVKCEVVGQSFMLHQIR 390

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
             +G    +       + +EKALQ +D     P AP  GLY D
Sbjct: 391 KMMGLAVAIMRNCAPESLIEKALQ-KDVNINVPTAPEVGLYLD 432


>gi|296824052|ref|XP_002850540.1| pseudouridylate synthase 3 [Arthroderma otae CBS 113480]
 gi|238838094|gb|EEQ27756.1| pseudouridylate synthase 3 [Arthroderma otae CBS 113480]
          Length = 614

 Score = 39.7 bits (91), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 37/95 (38%), Gaps = 25/95 (26%)

Query: 89  ISILNLSIVD------------KQFHARFSAIRRSYLY-------------RIITRQAPL 123
           I ILN ++ D              F ARFS  +R Y Y             R I R   L
Sbjct: 244 IQILNGALPDDIRVLAWCPHPPPDFDARFSCRQRRYRYFFTQPAFCPAPGARGIVRAPEL 303

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
             +     L    LD E MR AAQH VG HDF  F
Sbjct: 304 KQDLSLPKLREGWLDIEAMREAAQHFVGSHDFRNF 338


>gi|224085970|ref|XP_002307759.1| predicted protein [Populus trichocarpa]
 gi|222857208|gb|EEE94755.1| predicted protein [Populus trichocarpa]
          Length = 426

 Score = 39.7 bits (91), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 54/125 (43%), Gaps = 17/125 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAG-----------RT 51
           +  + + Y G GY G Q+     +I+G +E+A+F      V  H  G           RT
Sbjct: 2   KIAIFLTYCGVGYQGMQKNPGAKTIEGDLEEALFHAGA--VPEHDRGIPKRYDWARSART 59

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D GV A+ QV       +  P  L + L++ L  S  I I     V   F+A+    RR 
Sbjct: 60  DKGVSAVGQVVSGRFYID--PPGLVERLHSNL--SPQIRIFGYKRVTGSFNAKKFCDRRR 115

Query: 112 YLYRI 116
           Y+Y I
Sbjct: 116 YVYLI 120


>gi|119480651|ref|XP_001260354.1| tRNA pseudouridine synthase, putative [Neosartorya fischeri NRRL
           181]
 gi|119408508|gb|EAW18457.1| tRNA pseudouridine synthase, putative [Neosartorya fischeri NRRL
           181]
          Length = 577

 Score = 39.7 bits (91), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 53/124 (42%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  ++I Y G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 80  KVAVLIGYAGTGYHGMQLSDKEKTIEGDLFTA-FVAAGAISKANAADPKKSSLVRCARTD 138

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   +I  K +N   K+   I + ++ + +K F        R Y
Sbjct: 139 KGVHAAGNVVSLKLIVEDPDLI--KKINE--KLCPQIRVWDIQVTNKGFSCYQMCDSRVY 194

Query: 113 LYRI 116
            Y I
Sbjct: 195 EYLI 198


>gi|156095520|ref|XP_001613795.1| tRNA pseudouridine synthase [Plasmodium vivax SaI-1]
 gi|148802669|gb|EDL44068.1| tRNA pseudouridine synthase, putative [Plasmodium vivax]
          Length = 545

 Score = 39.7 bits (91), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 38/141 (26%), Positives = 59/141 (41%), Gaps = 16/141 (11%)

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           S+  RII R        G +  IP   D E ++   +  +GRH F  FR    + +   +
Sbjct: 397 SHCVRIINRTG------GSSSAIP--CDVEKIKECCKLFLGRHSFELFRGT-LKGTEKQK 447

Query: 171 TIDHFDVNSFGNLIEIR-------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            ++ F   SF  L ++R       +    FL+  IR  VG+L  VG G  +  D+  AL 
Sbjct: 448 QVNPFCNISFLELHQLRSNIYQFVIQGDRFLYHMIRIIVGTLVQVGVGLLSYEDVRDALH 507

Query: 224 AQDRKECGPLAPPEGLYFDSV 244
                +    AP +GL    +
Sbjct: 508 FSKPLKVKLCAPAQGLCLTKI 528


>gi|297850452|ref|XP_002893107.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297338949|gb|EFH69366.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 571

 Score = 39.7 bits (91), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 33/102 (32%), Positives = 50/102 (49%), Gaps = 9/102 (8%)

Query: 148 HLVGRHDFTTFRSIHCQASSPI--RTIDHFDVNSFGNL-----IEIRVVARSFLHTQIRS 200
           + VG H+F  F +   +A+ P   R I  F+ N+  NL     I+  VV +SF+  QIR 
Sbjct: 339 YYVGSHNFHNF-TTRTKAADPAANRYILSFNANTVINLDGKDFIKCEVVGQSFMLHQIRK 397

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +G    V       + +E A + +D +   P+AP  GLY D
Sbjct: 398 MIGLAVAVMRNYAPESLIETAFK-KDVRINVPMAPEVGLYLD 438



 Score = 37.7 bits (86), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 33/121 (27%), Positives = 52/121 (42%), Gaps = 15/121 (12%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVH 56
           ++  + G GY G Q+     +I+G +E+A+F                    + RTD GV 
Sbjct: 62  IVFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPEADRNKPRNYEWARSARTDKGVS 121

Query: 57  ALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           A+ QV      R +V P    + LN+  K+ D I +     V   F ++    RR Y+Y 
Sbjct: 122 AVGQVVSG---RFYVDPPGFVERLNS--KLPDQIRVFGYKRVAPSFSSKKLCDRRRYVYL 176

Query: 116 I 116
           I
Sbjct: 177 I 177


>gi|124506245|ref|XP_001351720.1| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|23504649|emb|CAD51527.1| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 681

 Score = 39.7 bits (91), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 71/173 (41%), Gaps = 30/173 (17%)

Query: 86  SDTISILN--LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
           +D IS  N   S   K   + ++ I  S   +II +      EK    +IP   D   ++
Sbjct: 508 NDNISPSNDPPSFYHKNMKSSYNDISHSM--KIINK------EKEIRSVIP--CDINKIK 557

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-------GNLIEIRVVARSFLHT 196
             A+  +G H+F  FR    + +  +R I+ F    F        NL +  +    FL+ 
Sbjct: 558 ECAKLFIGHHNFECFRGT-LKGTEKLRKINTFCTIHFLDVYELKNNLYQFVIQGDRFLYH 616

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL-----APPEGLYFDSV 244
            IR  VG+L  VG G     D+  AL       C PL     AP +GL  + +
Sbjct: 617 MIRIIVGTLVQVGVGLLNVEDVRDALHL-----CKPLKVKLCAPSQGLCLNKI 664


>gi|17544142|ref|NP_500962.1| hypothetical protein Y73B6BL.29 [Caenorhabditis elegans]
 gi|15375270|gb|AAK95894.1|AC084197_22 Hypothetical protein Y73B6BL.29 [Caenorhabditis elegans]
          Length = 322

 Score = 39.7 bits (91), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 56/243 (23%), Positives = 93/243 (38%), Gaps = 45/243 (18%)

Query: 48  AGRTDSGVHALR---------QVAHFDLVREWVPVILCKALNAYLKISD--TISILNLSI 96
           + RTD+ VHA+R         + A  D   E     +    N  + +++  ++ I ++  
Sbjct: 62  SSRTDAKVHAIRNSVICQVPLEYAELDKTPETKKAFMTSWKNT-IDVANPGSLEIHDVHS 120

Query: 97  VDKQFHARFSAIRRSYLYRIIT----------RQAP---LALEKGRAWLIPKSLDCENMR 143
           V   F  R S   R Y YR+            RQ P      E+  AW +P       + 
Sbjct: 121 VSAGFCIRRSVSYRKYTYRMAVCRSWELWESIRQEPSISCFSERDYAWRLPPGFSAHKVL 180

Query: 144 IAAQHLVGRHDFTTF-----RSIHCQASSP--IRTIDHFDV---------NSFGNLIEIR 187
            A +   G     +F     R    +  SP  ++ I H  +         N   +   + 
Sbjct: 181 QAGKLFEGEQVMGSFFKHTAREKRYEPISPTALKYIFHVGLSKGEAYSMENDIYDYYNVT 240

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECG-PLAPPEGLYFDS 243
           +VA+SF+  QIR  +  L      +   T +E  L    + +  + G P+APP+GL+   
Sbjct: 241 IVAKSFVREQIRRMMSCLVNYSYDRIPLTTIEWLLSNPISSNFFDLGIPVAPPQGLFLTD 300

Query: 244 VEY 246
           V Y
Sbjct: 301 VVY 303


>gi|238493757|ref|XP_002378115.1| tRNA pseudouridine synthase, putative [Aspergillus flavus NRRL3357]
 gi|317157361|ref|XP_003190833.1| tRNA pseudouridine synthase [Aspergillus oryzae RIB40]
 gi|220696609|gb|EED52951.1| tRNA pseudouridine synthase, putative [Aspergillus flavus NRRL3357]
          Length = 601

 Score = 39.3 bits (90), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 33/122 (27%), Positives = 54/122 (44%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 118 KVAVLLGYSGTGYKGMQLSATEKTIEGDL-FAAFVAAGAISKANAADPKKSSLVRCARTD 176

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +NA+L  S  I +  + +  K F +      R Y
Sbjct: 177 KGVHAAGNVVSLKLIVEDEDIV--QKINAHL--SPQIRVWGILVASKSFSSYQMCDSRIY 232

Query: 113 LY 114
            Y
Sbjct: 233 EY 234


>gi|297850446|ref|XP_002893104.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297338946|gb|EFH69363.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 557

 Score = 39.3 bits (90), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 32/102 (31%), Positives = 50/102 (49%), Gaps = 9/102 (8%)

Query: 148 HLVGRHDFTTFRSIHCQASSPI--RTIDHFDVNSFGNL-----IEIRVVARSFLHTQIRS 200
           + VG H+F  F +   +A+ P   R I  F+ N+  NL     ++  VV +SF+  QIR 
Sbjct: 325 YYVGSHNFHNF-TTRTKAADPAANRYILSFNANTVINLDGKDFVKCEVVGQSFMLHQIRK 383

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +G    V       + +E A + +D +   P+AP  GLY D
Sbjct: 384 MIGLAVAVMRNYAPESLIETAFK-KDVRINVPMAPEVGLYLD 424



 Score = 38.1 bits (87), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 33/124 (26%), Positives = 53/124 (42%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  ++  + G GY G Q+     +I+G +E+A+F                    + RTD 
Sbjct: 59  KVAIVFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPDADRNKPRNYEWARSARTDK 118

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A+ QV      R +V P    + LN+  K+ D I +     V   F ++    RR Y
Sbjct: 119 GVSAVGQVVSG---RFYVDPPGFVERLNS--KLPDQIRVFGYKRVAPSFSSKKLCDRRRY 173

Query: 113 LYRI 116
           +Y I
Sbjct: 174 VYLI 177


>gi|156040419|ref|XP_001587196.1| hypothetical protein SS1G_12226 [Sclerotinia sclerotiorum 1980]
 gi|154696282|gb|EDN96020.1| hypothetical protein SS1G_12226 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 592

 Score = 39.3 bits (90), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 78/180 (43%), Gaps = 33/180 (18%)

Query: 45  VHGAGRTDSGVHAL-----RQVAHFDLVREWVPV--ILCKALNAYLKISDTISILNLSIV 97
           + G   TDSG   L     ++   F+ + + +P   +L + L   ++I   ++      V
Sbjct: 193 IPGPRGTDSGAFVLSDPHIQESLDFNHITDEIPYPQVLNRLLPPDIRI---LAWCPSPPV 249

Query: 98  DKQFHARFSAIRRSYLYRIITRQA----PLALEKGRAWLIPKS--LDCENMRIAAQHLVG 151
           D  F ARFS   R Y Y   T+ A    P  LE G +    K   LD E MR AA+   G
Sbjct: 250 D--FSARFSCRERRYRY-FFTQPAFSPIPSQLEHGASASKMKDGWLDIEAMREAAKLYEG 306

Query: 152 RHDFTTFRSIHCQASSPIRTIDHFDVNSF-GNLIEIR--------VVARSFLHTQIRSFV 202
            HDF  F    C+   P + I +F+   F  N+ E++        V   SFL   IRS +
Sbjct: 307 LHDFRNF----CKV-DPGKQITNFERRIFYANIEEVKDYTSSLAYVNGDSFLDDSIRSKI 361


>gi|169783932|ref|XP_001826428.1| tRNA pseudouridine synthase [Aspergillus oryzae RIB40]
 gi|83775172|dbj|BAE65295.1| unnamed protein product [Aspergillus oryzae]
          Length = 563

 Score = 39.3 bits (90), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 33/122 (27%), Positives = 54/122 (44%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 80  KVAVLLGYSGTGYKGMQLSATEKTIEGDL-FAAFVAAGAISKANAADPKKSSLVRCARTD 138

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +NA+L  S  I +  + +  K F +      R Y
Sbjct: 139 KGVHAAGNVVSLKLIVEDEDIV--QKINAHL--SPQIRVWGILVASKSFSSYQMCDSRIY 194

Query: 113 LY 114
            Y
Sbjct: 195 EY 196


>gi|259146190|emb|CAY79449.1| Deg1p [Saccharomyces cerevisiae EC1118]
          Length = 442

 Score = 39.3 bits (90), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 93/244 (38%), Gaps = 47/244 (19%)

Query: 10  YNGSGYFGWQRQKNGS---SIQGSIEKAIF---LVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y G  Y G   QK  +   +++G+I +A+    LV   ++  +     GRTD GV A+ Q
Sbjct: 100 YLGWNYNGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQNYKFSRCGRTDKGVSAMNQ 159

Query: 61  VAHF------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           V               D   +   +     LN  L     IS + L      F ARFS +
Sbjct: 160 VISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR-PPPNFDARFSCV 218

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
            R Y Y          +  G      K+L+ E M  AA + VG  DF  F  +    Q +
Sbjct: 219 HRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDFRNFCKLDGSKQIT 262

Query: 167 SPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTS------TDLE 219
           +  RTI    +           ++  +FL  Q+R  +  L LVG            TD+E
Sbjct: 263 NFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLRLTDIE 322

Query: 220 KALQ 223
           K  Q
Sbjct: 323 KTPQ 326


>gi|151940762|gb|EDN59149.1| tRNA-pseudouridine synthase [Saccharomyces cerevisiae YJM789]
          Length = 442

 Score = 39.3 bits (90), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 93/244 (38%), Gaps = 47/244 (19%)

Query: 10  YNGSGYFGWQRQKNGS---SIQGSIEKAIF---LVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y G  Y G   QK  +   +++G+I +A+    LV   ++  +     GRTD GV A+ Q
Sbjct: 100 YLGWNYNGLAVQKEYTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKGVSAMNQ 159

Query: 61  VAHF------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           V               D   +   +     LN  L     IS + L      F ARFS +
Sbjct: 160 VISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR-PPPNFDARFSCV 218

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
            R Y Y          +  G      K+L+ E M  AA + VG  DF  F  +    Q +
Sbjct: 219 HRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDFRNFCKLDGSKQIT 262

Query: 167 SPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTS------TDLE 219
           +  RTI    +           ++  +FL  Q+R  +  L LVG            TD+E
Sbjct: 263 NFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLRLTDIE 322

Query: 220 KALQ 223
           K  Q
Sbjct: 323 KTPQ 326


>gi|323305104|gb|EGA58854.1| Deg1p [Saccharomyces cerevisiae FostersB]
          Length = 431

 Score = 39.3 bits (90), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 87/247 (35%), Gaps = 56/247 (22%)

Query: 14  GYFGWQRQKNGSSIQG------SIEKAIFLVTGEIVVVHG----------AGRTDSGVHA 57
            Y GW    NG ++Q       ++E  I     +  +V             GRTD GV A
Sbjct: 88  AYLGWNY--NGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKGVSA 145

Query: 58  LRQVAHF------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           + QV               D   +   +     LN  L     IS + L      F ARF
Sbjct: 146 MNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR-PPPNFDARF 204

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-- 163
           S + R Y Y          +  G      K+L+ E M  AA + VG  DF  F  +    
Sbjct: 205 SCVHRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDFRNFCKLDGSK 248

Query: 164 QASSPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTS------T 216
           Q ++  RTI    +           ++  +FL  Q+R  +  L LVG            T
Sbjct: 249 QITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLRLT 308

Query: 217 DLEKALQ 223
           D+EK  Q
Sbjct: 309 DIEKTPQ 315


>gi|123438137|ref|XP_001309856.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
 gi|121891601|gb|EAX96926.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
          Length = 365

 Score = 39.3 bits (90), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 59/211 (27%), Positives = 87/211 (41%), Gaps = 30/211 (14%)

Query: 48  AGRTDSGVHALRQVAHFDLV-REWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARF 105
           + RTD+GVHA +QVA F LV  E V V  L + +   L  +  I +         F+A+ 
Sbjct: 91  SSRTDTGVHAAKQVATFRLVLPEGVKVKDLPRLIQKQLSKNSPIRVWAAVKPGIIFNAQQ 150

Query: 106 SAIRRSYLYRI----ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RS 160
           SA  R Y Y +     + +    L   RA + P               VGRH +  + R 
Sbjct: 151 SASSRRYHYLLPVNTFSSENIDHLNYLRAKICPI-------------FVGRHQYANYTRH 197

Query: 161 IHCQ-ASSPIRTI------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           I  +   + I+TI      D FDVN     +   +   SF+  QIR  + ++  V     
Sbjct: 198 ITDELLHTSIKTISEFTFTDPFDVNG-TKYVLFTISGNSFMLNQIRKMIAAVLAVSHHLM 256

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           T  DL+  L   + +   P     GL+ D V
Sbjct: 257 TEDDLKDTL--TETRWLLPRLIGTGLFLDQV 285


>gi|19075416|ref|NP_587916.1| tRNA pseudouridine synthase (predicted) [Schizosaccharomyces pombe
           972h-]
 gi|74676082|sp|O74451|YCG6_SCHPO RecName: Full=Putative tRNA pseudouridine synthase C16C4.06c
 gi|6855456|emb|CAA20745.2| tRNA pseudouridine synthase (predicted) [Schizosaccharomyces pombe]
          Length = 413

 Score = 39.3 bits (90), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 12/68 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTDS 53
           YC ++ Y G+G+ G Q   N  +IQ ++ +A F   G +V V+           A RTD 
Sbjct: 40  YC-VVSYRGTGFAGLQYNANVKTIQDTLFQA-FARVGAVVQVNADSPKKIRMCSAARTDK 97

Query: 54  GVHALRQV 61
           GVHA+  V
Sbjct: 98  GVHAIVNV 105


>gi|323337774|gb|EGA79017.1| Deg1p [Saccharomyces cerevisiae Vin13]
          Length = 442

 Score = 39.3 bits (90), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 93/244 (38%), Gaps = 47/244 (19%)

Query: 10  YNGSGYFGWQRQKNGS---SIQGSIEKAIF---LVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y G  Y G   QK  +   +++G+I +A+    LV   ++  +     GRTD GV A+ Q
Sbjct: 100 YLGWNYNGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQBYKFSRCGRTDKGVSAMNQ 159

Query: 61  VAHF------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           V               D   +   +     LN  L     IS + L      F ARFS +
Sbjct: 160 VISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR-PPPNFDARFSCV 218

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
            R Y Y          +  G      K+L+ E M  AA + VG  DF  F  +    Q +
Sbjct: 219 HRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDFRNFCKLDGSKQIT 262

Query: 167 SPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTS------TDLE 219
           +  RTI    +           ++  +FL  Q+R  +  L LVG            TD+E
Sbjct: 263 NFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLRLTDIE 322

Query: 220 KALQ 223
           K  Q
Sbjct: 323 KTPQ 326


>gi|190406572|gb|EDV09839.1| tRNA pseudouridine synthase 3 [Saccharomyces cerevisiae RM11-1a]
 gi|256268860|gb|EEU04212.1| Deg1p [Saccharomyces cerevisiae JAY291]
 gi|323309245|gb|EGA62466.1| Deg1p [Saccharomyces cerevisiae FostersO]
          Length = 442

 Score = 39.3 bits (90), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 93/244 (38%), Gaps = 47/244 (19%)

Query: 10  YNGSGYFGWQRQKNGS---SIQGSIEKAIF---LVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y G  Y G   QK  +   +++G+I +A+    LV   ++  +     GRTD GV A+ Q
Sbjct: 100 YLGWNYNGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKGVSAMNQ 159

Query: 61  VAHF------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           V               D   +   +     LN  L     IS + L      F ARFS +
Sbjct: 160 VISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR-PPPNFDARFSCV 218

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
            R Y Y          +  G      K+L+ E M  AA + VG  DF  F  +    Q +
Sbjct: 219 HRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDFRNFCKLDGSKQIT 262

Query: 167 SPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTS------TDLE 219
           +  RTI    +           ++  +FL  Q+R  +  L LVG            TD+E
Sbjct: 263 NFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLRLTDIE 322

Query: 220 KALQ 223
           K  Q
Sbjct: 323 KTPQ 326


>gi|168042339|ref|XP_001773646.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162675034|gb|EDQ61534.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 445

 Score = 39.3 bits (90), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 39/129 (30%), Positives = 57/129 (44%), Gaps = 17/129 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHG---------AGR 50
           +  M + Y G+ Y G Q Q+   +  +I+  +E AIF   G I    G         + R
Sbjct: 3   KVAMWLGYVGTRYKGLQIQRGPGSAQTIEEELELAIFKAGGMIESNFGNLSKISWTRSSR 62

Query: 51  TDSGVHALRQVAHFDL-VRE--WVPVILCKAL--NAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  V    + V E  WV  +   AL  N    +S  I +  ++ V + F AR 
Sbjct: 63  TDKGVHSLCTVISMKMEVPEAAWVNDMDGFALADNINFHLSPFIRVFGITPVTRSFRARH 122

Query: 106 SAIRRSYLY 114
               R+Y Y
Sbjct: 123 DCCTRTYDY 131


>gi|71000998|ref|XP_755180.1| tRNA pseudouridine synthase [Aspergillus fumigatus Af293]
 gi|66852818|gb|EAL93142.1| tRNA pseudouridine synthase, putative [Aspergillus fumigatus Af293]
 gi|159129271|gb|EDP54385.1| tRNA pseudouridine synthase, putative [Aspergillus fumigatus A1163]
          Length = 577

 Score = 39.3 bits (90), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 53/124 (42%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  ++I Y G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 80  KVAVLIGYAGTGYHGMQLSDKEKTIEGDLFTA-FVAAGAISKANAADPKKSSLVRCARTD 138

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   +I  K +N   K+   I + ++ + +K F        R Y
Sbjct: 139 KGVHAAGNVVSLKLIIEDPDLI--KKINE--KLCPQIRVWDIQVTNKGFSCYQMCDSRVY 194

Query: 113 LYRI 116
            Y I
Sbjct: 195 EYLI 198


>gi|50548607|ref|XP_501773.1| YALI0C12749p [Yarrowia lipolytica]
 gi|74635069|sp|Q6CC39|PUS1_YARLI RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|49647640|emb|CAG82083.1| YALI0C12749p [Yarrowia lipolytica]
          Length = 528

 Score = 39.3 bits (90), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 16/124 (12%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTDSG 54
           CMI  Y G+GY G Q      +I+G I +A F+  G I   +           A RTD G
Sbjct: 89  CMI-GYCGTGYHGMQLNPPQKTIEGDIFQA-FVKAGAISQNNADDPKKSAFMRAARTDKG 146

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA   V    ++ E   ++  + +N++L   + + +  +S  +K F  R     R Y Y
Sbjct: 147 VHAAGNVISLKMIIEDENIV--EKINSHL--PEQLRVWGVSRTNKAFECRKLCSSRVYEY 202

Query: 115 RIIT 118
            + T
Sbjct: 203 LMPT 206


>gi|150865014|ref|XP_001384060.2| hypothetical protein PICST_58964 [Scheffersomyces stipitis CBS
           6054]
 gi|149386270|gb|ABN66031.2| predicted protein [Scheffersomyces stipitis CBS 6054]
          Length = 476

 Score = 38.9 bits (89), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 40/128 (31%), Positives = 56/128 (43%), Gaps = 17/128 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHG----------AGR 50
           +  ++I Y G+GY G Q Q +    +I+  + +A F   G +   +           A R
Sbjct: 81  KVAVMIGYCGTGYNGMQLQNDPKIPTIERDLYEA-FAAAGAVSPENAMDIKKSGFMRAAR 139

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GVHA   V    L+ E  P IL K +N   K+ D I I  +  V K F  R     R
Sbjct: 140 TDKGVHAAGNVISLKLIIE-DPEILAK-INE--KLPDQIRIWGIQRVTKSFDCRKMCSSR 195

Query: 111 SYLYRIIT 118
            Y Y + T
Sbjct: 196 VYEYLLPT 203


>gi|67608685|ref|XP_666896.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54657966|gb|EAL36665.1| hypothetical protein Chro.80065 [Cryptosporidium hominis]
          Length = 501

 Score = 38.9 bits (89), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 37/86 (43%), Gaps = 22/86 (25%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGS-------SIQGSIEK-----AIFLVTGEIVVVHGA 48
          M  YCM   Y+GS Y G Q Q   +       +I+G +E       +F V+ E     G 
Sbjct: 7  MRTYCMSFGYDGSDYHGMQIQMRNNKKVEELRTIEGEMEDCLEKLGMFFVSNEQNDDQGG 66

Query: 49 ----------GRTDSGVHALRQVAHF 64
                    GRTD GVH++ QV  F
Sbjct: 67 LLKKIKWSRVGRTDKGVHSVCQVVSF 92


>gi|328873726|gb|EGG22093.1| hypothetical protein DFA_01983 [Dictyostelium fasciculatum]
          Length = 604

 Score = 38.9 bits (89), Expect = 0.64,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 61/129 (47%), Gaps = 22/129 (17%)

Query: 5   CMIIEYNGSGYFG--WQRQKNGSSIQGSIEKAIFLVTGEIVVVH----------GAGRTD 52
            M+  Y G+G+FG  +  ++   +++  +EKA+FL +G I+  +           + RTD
Sbjct: 157 AMLFSYVGTGHFGLEYTYEEKYPALENYLEKALFL-SGMILPTNFGDVTRIKWSRSSRTD 215

Query: 53  SGVHALRQV--AHFDLVREWVPV-----ILCKALNAYLKISDTISILNLSIVDKQFHARF 105
            GVH+L  +  A   + RE +            +N+YL    T+ I++++   + F  R 
Sbjct: 216 KGVHSLSTIIGASILINREKIQTKEGVRAYIDQINSYL--PPTLHIVSMATTSRSFMPRR 273

Query: 106 SAIRRSYLY 114
               R+Y Y
Sbjct: 274 QTSSRTYHY 282


>gi|67539990|ref|XP_663769.1| hypothetical protein AN6165.2 [Aspergillus nidulans FGSC A4]
 gi|40738761|gb|EAA57951.1| hypothetical protein AN6165.2 [Aspergillus nidulans FGSC A4]
 gi|259479643|tpe|CBF70055.1| TPA: tRNA pseudouridine synthase, putative (AFU_orthologue;
           AFUA_2G08460) [Aspergillus nidulans FGSC A4]
          Length = 574

 Score = 38.9 bits (89), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  ++I Y+G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 80  KVAVLIGYSGTGYKGMQLSTTEKTIEGELFTA-FVAAGAISKANAADPKKSSLVRCARTD 138

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    L+ E  P I+ K +N +L  S  I +  + + +K F +      R Y
Sbjct: 139 KGVHAAGNIVSLKLIVE-DPDIVQK-INDHL--SPQIRVWGILVANKSFSSYQMCDSRIY 194

Query: 113 LYRI 116
            Y I
Sbjct: 195 EYLI 198


>gi|323348774|gb|EGA83014.1| Deg1p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 315

 Score = 38.9 bits (89), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 53/197 (26%), Positives = 72/197 (36%), Gaps = 38/197 (19%)

Query: 48  AGRTDSGVHALRQVAHF------------DLVREWVPVILCKALNAYLKISDTISILNLS 95
            GRTD GV A+ QV               D   +   +     LN  L     IS + L 
Sbjct: 20  CGRTDKGVSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR 79

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
                F ARFS + R Y Y          +  G      K+L+ E M  AA + VG  DF
Sbjct: 80  -PPPNFDARFSCVHRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDF 122

Query: 156 TTFRSIHC--QASSPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGK 212
             F  +    Q ++  RTI    +           ++  +FL  Q+R  +  L LVG   
Sbjct: 123 RNFCKLDGSKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSL 182

Query: 213 WTS------TDLEKALQ 223
                    TD+EK  Q
Sbjct: 183 EVPEIVLRLTDIEKTPQ 199


>gi|207345658|gb|EDZ72410.1| YFL001Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 315

 Score = 38.9 bits (89), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 53/197 (26%), Positives = 72/197 (36%), Gaps = 38/197 (19%)

Query: 48  AGRTDSGVHALRQVAHF------------DLVREWVPVILCKALNAYLKISDTISILNLS 95
            GRTD GV A+ QV               D   +   +     LN  L     IS + L 
Sbjct: 20  CGRTDKGVSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLR 79

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
                F ARFS + R Y Y          +  G      K+L+ E M  AA + VG  DF
Sbjct: 80  -PPPNFDARFSCVHRHYKY----------IFNG------KNLNIEKMSKAASYFVGERDF 122

Query: 156 TTFRSIHC--QASSPIRTIDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGK 212
             F  +    Q ++  RTI    +           ++  +FL  Q+R  +  L LVG   
Sbjct: 123 RNFCKLDGSKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSL 182

Query: 213 WTS------TDLEKALQ 223
                    TD+EK  Q
Sbjct: 183 EVPEIVLRLTDIEKTPQ 199


>gi|302851624|ref|XP_002957335.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
 gi|300257294|gb|EFJ41544.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
          Length = 642

 Score = 38.9 bits (89), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 68/256 (26%), Positives = 100/256 (39%), Gaps = 56/256 (21%)

Query: 10  YNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD--- 65
           Y G  Y G+ RQ N  ++I+ S  K  +   G +V ++           LR VA  D   
Sbjct: 117 YVGWSYQGFARQDNTENTIEASSVKRGW---GGVVALN-----------LRSVARVDEPE 162

Query: 66  --LVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
             L  E+  P ++ KAL         + +L  + V + F++R       Y+Y       P
Sbjct: 163 APLELEYDYPRLVNKAL------PPDVRVLGWTAVPENFNSR-------YVYH------P 203

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR------TIDHFD 176
              E  R      SLD + MR AA   VG HDF  F           R      T+D   
Sbjct: 204 DPPESCR-----YSLDIDAMRAAAARFVGEHDFRNFCKPDVATVRSFRRRILSFTLDPVP 258

Query: 177 VNSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECG 231
            +S      +  I V   +FL  Q+R     L +VG G+     + + L  +A  RK   
Sbjct: 259 TSSSDGAHRVFAITVRGTAFLWHQVRCMAAVLLMVGRGQERPEVVSELLDVEAHPRKPQY 318

Query: 232 PLAPPEGLYFDSVEYS 247
            +AP E L   +  +S
Sbjct: 319 SMAPEEPLLLYACGFS 334


>gi|223998991|ref|XP_002289168.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
 gi|220974376|gb|EED92705.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
          Length = 469

 Score = 38.5 bits (88), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 37/108 (34%), Positives = 46/108 (42%), Gaps = 14/108 (12%)

Query: 26  SIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAY 82
           ++Q  +E A+   TG     + V GAGRTD GVHA  QV  FD     VP+ L K     
Sbjct: 110 TVQQQLETALHQWTGLSIATLRVRGAGRTDKGVHASGQVVGFD-----VPLSLLKGEGGG 164

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRA 130
                T S   LS      HA F  +R +Y      R  P   + G A
Sbjct: 165 GSDETTDSCDRLS-----EHA-FPLLRGAYQSLTQHRDQPTNSDTGNA 206


>gi|18394855|ref|NP_564112.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|9558589|gb|AAF88152.1|AC026234_3 Contains similarity to a pseudouridine synthase 1 from Homo sapiens
           gi|4455035 and contains tRNA pseudoridine synthase
           PF|01416 domain. ESTs gb|T76494, gb|W43440 come from
           this gene [Arabidopsis thaliana]
 gi|14334544|gb|AAK59680.1| unknown protein [Arabidopsis thaliana]
 gi|16323470|gb|AAL15229.1| unknown protein [Arabidopsis thaliana]
 gi|332191845|gb|AEE29966.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 549

 Score = 38.5 bits (88), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 32/102 (31%), Positives = 50/102 (49%), Gaps = 9/102 (8%)

Query: 148 HLVGRHDFTTFRSIHCQASSPI--RTIDHFDVNSFGNL-----IEIRVVARSFLHTQIRS 200
           + VG H+F  F +   +A+ P   R I  F+ N+  NL     ++  VV +SF+  QIR 
Sbjct: 327 YYVGSHNFHNF-TTRTKAADPAANRYILSFNANTVINLDGKDFVKCEVVGQSFMLHQIRK 385

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +G L +     +    L +A   +D +   P+AP  GLY D
Sbjct: 386 MIG-LAVAIMRNYAPESLIEASFKKDVRINVPMAPEVGLYLD 426



 Score = 38.1 bits (87), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 33/124 (26%), Positives = 53/124 (42%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  ++  + G GY G Q+     +I+G +E+A+F                    + RTD 
Sbjct: 59  KVAIVFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPDADRNKPRNYEWARSARTDK 118

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A+ QV      R +V P    + LN+  K+ D I +     V   F ++    RR Y
Sbjct: 119 GVSAVGQVVSG---RFYVDPPGFVERLNS--KLPDQIRVFGYKRVAPSFSSKKFCDRRRY 173

Query: 113 LYRI 116
           +Y I
Sbjct: 174 VYLI 177


>gi|321265516|ref|XP_003197474.1| pseudouridylate synthase [Cryptococcus gattii WM276]
 gi|317463954|gb|ADV25687.1| Pseudouridylate synthase, putative [Cryptococcus gattii WM276]
          Length = 560

 Score = 38.5 bits (88), Expect = 0.78,   Method: Compositional matrix adjust.
 Identities = 37/124 (29%), Positives = 54/124 (43%), Gaps = 12/124 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
           R  ++I Y G+GY G Q Q +   +I+G I  A+           V    V +  A RTD
Sbjct: 124 RCAVLIGYCGTGYQGMQIQDHTDRTIEGEIFAALVKAGAVSADNAVDARKVDIARAARTD 183

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRR 110
           +GVHA   V    ++ E       K +  Y+   + D I +       K F+AR +A  R
Sbjct: 184 AGVHAAGNVISIKMITEPPLPEGFKNVAEYVNTFLPDQIRMWGWVRTVKSFNARTAADSR 243

Query: 111 SYLY 114
            Y Y
Sbjct: 244 IYEY 247


>gi|212526856|ref|XP_002143585.1| pseudouridylate synthase 3 [Penicillium marneffei ATCC 18224]
 gi|210072983|gb|EEA27070.1| pseudouridylate synthase 3 [Penicillium marneffei ATCC 18224]
          Length = 630

 Score = 38.5 bits (88), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 42/125 (33%), Positives = 53/125 (42%), Gaps = 23/125 (18%)

Query: 52  DSGVHALRQVAH---FDLVREWVPVILCKALNAYLKISDTISILN-LSIVDKQFHARFSA 107
           D  V  L ++     +D +R+ +P I  + LN  L     I IL         F ARFS 
Sbjct: 242 DVEVQPLDEIEEDDGWDDIRDELPYI--QVLNGVL--PQDIRILAWCPNPGPDFDARFSC 297

Query: 108 IRRSYLYRIITRQA--PLALEKG------------RAWLIPKSLDCENMRIAAQHLVGRH 153
             R Y Y   T+ A  P+A E G            +  L    LD E MR A +H VGRH
Sbjct: 298 RERQYRY-FFTQPAFNPIAGELGFLRSAAHHRGIAKKELRDGWLDIEAMREACKHYVGRH 356

Query: 154 DFTTF 158
           DF  F
Sbjct: 357 DFRNF 361


>gi|121698285|ref|XP_001267772.1| tRNA pseudouridine synthase, putative [Aspergillus clavatus NRRL 1]
 gi|119395914|gb|EAW06346.1| tRNA pseudouridine synthase, putative [Aspergillus clavatus NRRL 1]
          Length = 568

 Score = 38.5 bits (88), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 34/124 (27%), Positives = 52/124 (41%), Gaps = 15/124 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  ++I Y G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 80  KVAVLIGYAGTGYHGMQLSDKEKTIEGDL-FAAFVAAGAISKANAADPKKSSLVRCARTD 138

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  K +N  L     I + ++ + +K F        R Y
Sbjct: 139 KGVHAAGNVVSLKLIVEDPDIV--KKINEQL--CPQIRVWDVQVTNKGFSCYQMCDSRVY 194

Query: 113 LYRI 116
            Y I
Sbjct: 195 EYLI 198


>gi|255539108|ref|XP_002510619.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223551320|gb|EEF52806.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 584

 Score = 38.5 bits (88), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 50/117 (42%), Gaps = 15/117 (12%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVHALRQ 60
           Y G GY G Q+     +I+G +E+A+F          G         + RTD GV A+ Q
Sbjct: 62  YCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVPEQDRGCPKRYDWARSARTDKGVSAVGQ 121

Query: 61  VAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           V      R +V P  L   LN+ L     I I     V   F+A+    RR Y+Y I
Sbjct: 122 VISG---RFYVDPPGLVDRLNSIL--PSQIRIFGYKRVTASFNAKKFCDRRRYVYLI 173


>gi|190349084|gb|EDK41674.2| hypothetical protein PGUG_05772 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 477

 Score = 38.5 bits (88), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 56/126 (44%), Gaps = 18/126 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           CMI  Y G+GY G Q Q N    +I+G +  A F+  G I   +           A RTD
Sbjct: 33  CMI-GYCGTGYNGMQIQNNPDVKTIEGDLFDA-FVKAGAISPENADDLKKNAFMRAARTD 90

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +N++L   D I +  +   +K F  R     R Y
Sbjct: 91  KGVHAAGNVISCKLIIEDQDIL--QRINSHL--PDQIRVWGIERTNKSFDCRKMCSSRVY 146

Query: 113 LYRIIT 118
            Y + T
Sbjct: 147 EYLLPT 152


>gi|297842357|ref|XP_002889060.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297334901|gb|EFH65319.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 458

 Score = 38.5 bits (88), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 33/123 (26%), Positives = 52/123 (42%), Gaps = 17/123 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +I  + G GY G Q+     +I+G +E+A+F        + G         + RTD 
Sbjct: 23  KVAIIFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPESIRGKPKLYDFARSARTDK 82

Query: 54  GVHALRQV--AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           GV A+ QV    F++     P      LN+ L   + I I     V   F ++    RR 
Sbjct: 83  GVSAVGQVVSGRFNV----DPPGFVDRLNSNL--PNQIRIFGYKHVTPSFSSKKFCDRRR 136

Query: 112 YLY 114
           Y+Y
Sbjct: 137 YVY 139


>gi|146412075|ref|XP_001482009.1| hypothetical protein PGUG_05772 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 477

 Score = 38.5 bits (88), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 56/126 (44%), Gaps = 18/126 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           CMI  Y G+GY G Q Q N    +I+G +  A F+  G I   +           A RTD
Sbjct: 33  CMI-GYCGTGYNGMQIQNNPDVKTIEGDLFDA-FVKAGAISPENADDLKKNAFMRAARTD 90

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +N++L   D I +  +   +K F  R     R Y
Sbjct: 91  KGVHAAGNVISCKLIIEDQDIL--QRINSHL--PDQIRVWGIERTNKSFDCRKMCSSRVY 146

Query: 113 LYRIIT 118
            Y + T
Sbjct: 147 EYLLPT 152


>gi|325190643|emb|CCA25138.1| ubiquitin fusion degradation protein putative [Albugo laibachii
           Nc14]
          Length = 585

 Score = 38.1 bits (87), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 41/129 (31%), Positives = 56/129 (43%), Gaps = 19/129 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
           R  ++  YNGS Y G Q   N  +I+  I KA++ +             +    + RTD 
Sbjct: 79  RVAIVAGYNGSDYHGVQLNPNVPTIEDEIRKAMYHIGALRASNFQDLNKIDWSRSSRTDK 138

Query: 54  GVHALRQV-AHFDLVREWV--PVI-----LCKALNAYLKISDTISILNLSIVDKQFHARF 105
           GVHA   V A   L+ E V  PV      L +ALN  L     I I +++ V   F+AR 
Sbjct: 139 GVHASTIVFAGKLLLNEDVIDPVTGRVRGLTRALNENL--PPNIRIFSVTRVCNSFNART 196

Query: 106 SAIRRSYLY 114
               R Y Y
Sbjct: 197 ECALREYEY 205


>gi|19075946|ref|NP_588446.1| tRNA pseudouridine synthase Lsp1 [Schizosaccharomyces pombe 972h-]
 gi|74627010|sp|O94396|PUS1_SCHPO RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|4008551|emb|CAA22472.1| tRNA pseudouridine synthase Lsp1 [Schizosaccharomyces pombe]
 gi|6469502|emb|CAB61835.1| pseudouridine synthase [Schizosaccharomyces pombe]
          Length = 534

 Score = 38.1 bits (87), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 53/124 (42%), Gaps = 19/124 (15%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI----------VVVHGAGRTDSGVH 56
           ++ Y GSGY G Q      +I+G +  A F+  G +          V +  A RTD GVH
Sbjct: 49  LVGYCGSGYHGMQLNPPSKTIEGDLFDA-FVKAGAVSSYNADDPKKVALARAARTDKGVH 107

Query: 57  ALRQVAHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           A   V    L+ E   +I  + + L   +++ D I  +N       F+ R     R Y Y
Sbjct: 108 AAGNVISLKLIMEDEKLIEKVNEHLPPSIRLWDVIRTIN------SFNPRTYCESRIYEY 161

Query: 115 RIIT 118
            + T
Sbjct: 162 MVPT 165


>gi|66356668|ref|XP_625512.1| Pus1p-like type II pseudousynthas TruA [Cryptosporidium parvum
          Iowa II]
 gi|46226500|gb|EAK87494.1| Pus1p-like type II pseudousynthas TruA [Cryptosporidium parvum
          Iowa II]
          Length = 501

 Score = 38.1 bits (87), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 37/86 (43%), Gaps = 22/86 (25%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGS-------SIQGSIEK-----AIFLVTGEIVVVHGA 48
          M  YCM   Y+GS Y G Q Q   +       +I+G +E       +F ++ E     G 
Sbjct: 7  MKTYCMSFGYDGSDYHGMQIQMRNNKKVEELRTIEGEMEDCLEKLGMFFLSNEQNDDQGG 66

Query: 49 ----------GRTDSGVHALRQVAHF 64
                    GRTD GVH++ QV  F
Sbjct: 67 LLKKIKWSRVGRTDKGVHSVCQVVSF 92


>gi|70941666|ref|XP_741093.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56519252|emb|CAH76348.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 493

 Score = 38.1 bits (87), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 14/94 (14%)

Query: 47  GAGRTDSGVHA---------LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV 97
           G  RTD GVHA          +++  F+   E + + L + LN  +K+   + + N    
Sbjct: 137 GVSRTDKGVHAKEYVCQYISYKKLPPFNGNLEKIKLSLNRLLNKDIKV---LGVFNAPF- 192

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
              F+ RF  + + Y Y I  R+    LEK  +W
Sbjct: 193 -NSFNVRFHNLGKIYTYNIDLRKPSQPLEKNFSW 225


>gi|224061937|ref|XP_002300673.1| predicted protein [Populus trichocarpa]
 gi|222842399|gb|EEE79946.1| predicted protein [Populus trichocarpa]
          Length = 429

 Score = 38.1 bits (87), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 66/165 (40%), Gaps = 24/165 (14%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVHALRQ 60
           Y G GY G Q+     +I+G +E+A+F          G         + RTD GV A+ Q
Sbjct: 25  YCGVGYQGMQKNPGAKTIEGDLEEALFHAGAVPEQDRGIPKRYDWARSARTDKGVSAVGQ 84

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-- 118
           V       +  P  L + L++ L  S    I     V   F+A+    RR Y+Y I    
Sbjct: 85  VVSGRFYID--PPGLVERLHSNL--SPQFRIFGYKRVTGSFNAKKFCDRRRYVYLIPVFA 140

Query: 119 --------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
                   R++ LA  +  + LI K L+C          VG+  F
Sbjct: 141 LDPCSHRDRESVLASLRSGSELI-KCLECSERGRKVAGAVGKRSF 184


>gi|219117902|ref|XP_002179737.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408790|gb|EEC48723.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 216

 Score = 38.1 bits (87), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 94/238 (39%), Gaps = 43/238 (18%)

Query: 30  SIEKAIF--LVTGEIVVVHGA------GRTDSGVHALRQVAHFDLVREWVPVILCKAL-- 79
           S+EKA+F  L T  +V    +      GRTD GV A  Q           P+   +AL  
Sbjct: 1   SVEKALFRALRTSRLVESRASSGYSRCGRTDKGVSAAGQQTD-------PPLRQQRALRE 53

Query: 80  NAYLKI-----SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
           +AY KI      D I +L    V   F ARFSA  R+Y Y    R               
Sbjct: 54  HAYDKILNNLLPDDIRVLGWIPVSDDFSARFSATSRTYRYFFRRR--------------- 98

Query: 135 KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTIDHFDVNSFGNLIEIR---VVA 190
           ++LD E MR     + G HDF  F  +  +      R ID  ++ +      +    +V 
Sbjct: 99  RTLDVEAMRQGLHRMQGTHDFRNFCKMDVEKVYNFERRIDKAEIVNMERDTGVSYFLIVG 158

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQDR-KECGPLAPPEGLYFDSVEY 246
           ++FL  QIR     L  +G G  T   +   L  AQ+  K   PLA  + L      Y
Sbjct: 159 QAFLWHQIRYMASILFAIGQGLETPELVTAMLDIAQNPGKPAYPLADEQPLVLHDCGY 216


>gi|302844654|ref|XP_002953867.1| hypothetical protein VOLCADRAFT_94649 [Volvox carteri f.
          nagariensis]
 gi|300260975|gb|EFJ45191.1| hypothetical protein VOLCADRAFT_94649 [Volvox carteri f.
          nagariensis]
          Length = 709

 Score = 38.1 bits (87), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 14/79 (17%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAG-------- 49
          M R   +  Y+G+GYFG QRQ + +   +++  +E+A+ +  G +   H           
Sbjct: 1  MQRVAFVCGYDGAGYFGLQRQPDNTGRPTVEQELERAL-VAAGALQARHAGALHKVNWSR 59

Query: 50 --RTDSGVHALRQVAHFDL 66
            RTD GV A   V   D+
Sbjct: 60 TSRTDKGVSAAANVVSLDI 78


>gi|226506356|ref|NP_001150144.1| LOC100283773 [Zea mays]
 gi|195637102|gb|ACG38019.1| tRNA pseudouridine synthase family protein [Zea mays]
          Length = 561

 Score = 38.1 bits (87), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 51/122 (41%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD 
Sbjct: 53  KVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRSAPRRYDWARAARTDK 112

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A  QV      R +V P      LNA L  +  I       V   F+A+    RR Y
Sbjct: 113 GVSAAAQVVSG---RFYVDPPGFIDRLNAQL--APQIRAYGYVRVTNSFNAKKFCDRRRY 167

Query: 113 LY 114
           LY
Sbjct: 168 LY 169


>gi|145545961|ref|XP_001458664.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124426485|emb|CAK91267.1| unnamed protein product [Paramecium tetraurelia]
          Length = 351

 Score = 38.1 bits (87), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 63/281 (22%), Positives = 107/281 (38%), Gaps = 59/281 (20%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIVVVHGA-----------GRTDSGVH 56
           YNG+ Y G Q QK G   + ++E  +F  L    +++   A            RTD GVH
Sbjct: 16  YNGANYHGLQIQK-GVEFE-TVESKLFQALKDSNLIMEQNANDLSKSGWSRGARTDKGVH 73

Query: 57  ALRQVAHFDL---------------------VREWVPVILCKALNAY-LKISDTISILNL 94
           AL       L                     +R+   V   K LN     + + I + ++
Sbjct: 74  ALCNSIAVKLCINKEFFKDEIQQNEEEIVSKLRDKQKVDYSKVLNVINSNLPNDIKVHSI 133

Query: 95  SIVDKQFHARFSAIRRSYLYRIITRQAPLAL---EKGRAWLIPKSLDCENMRIAAQHLVG 151
            +V + F  R +A  R Y Y      AP+++   +KG   L       E +    +  VG
Sbjct: 134 KLVTQGFDVRKNARYRFYEYI-----APVSIYSDKKGEEIL-------EKVSNLVKKFVG 181

Query: 152 RHDFTTF-RSIHCQASSPIRTIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLK 206
            H+F  + R +       +R I    V  F        +  +  +SF++ QIR  +G + 
Sbjct: 182 THNFHNYSRGMKYTDPQSMRYILSIQVELFKCQDREFFKFLIHGQSFIYHQIRKMMGIVI 241

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +   +   T ++        +    LAP EGL+ + + + 
Sbjct: 242 QIFQEELPDTFIDNTFFKNQLRII--LAPAEGLFLNRISFE 280


>gi|223948195|gb|ACN28181.1| unknown [Zea mays]
          Length = 562

 Score = 38.1 bits (87), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 51/122 (41%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD 
Sbjct: 53  KVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRSAPRRYDWARAARTDK 112

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A  QV      R +V P      LNA L  +  I       V   F+A+    RR Y
Sbjct: 113 GVSAAAQVVSG---RFYVDPPGFIDRLNAQL--APQIRAYGYVRVTNSFNAKKFCDRRRY 167

Query: 113 LY 114
           LY
Sbjct: 168 LY 169


>gi|212532769|ref|XP_002146541.1| tRNA pseudouridine synthase, putative [Penicillium marneffei ATCC
           18224]
 gi|210071905|gb|EEA25994.1| tRNA pseudouridine synthase, putative [Penicillium marneffei ATCC
           18224]
          Length = 571

 Score = 38.1 bits (87), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 53/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  ++I Y+G+GY G Q      +I+G +  A F+  G I   + A           RTD
Sbjct: 76  KVAVMIGYSGTGYHGMQLSPTEKTIEGDL-FAAFVAAGAISKANAADPKKSSLVRCARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E  P I+ K +N  L  S  I +     V K F        R Y
Sbjct: 135 RGVHAAGNVVSLKLIVE-DPDIVQK-INDNL--SPQIRVWGYETVTKGFSCYQLCDSRMY 190

Query: 113 LYRIIT 118
            Y I T
Sbjct: 191 EYLIPT 196


>gi|145529301|ref|XP_001450439.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124418050|emb|CAK83042.1| unnamed protein product [Paramecium tetraurelia]
          Length = 297

 Score = 38.1 bits (87), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 50/229 (21%), Positives = 91/229 (39%), Gaps = 44/229 (19%)

Query: 41  EIVVVHGAGRTDSGVHALRQVAHFDL---------------VREWVPV--ILCKALNAYL 83
           +I V  GA RTD GVHAL  V    L               V +W     +L + LN+  
Sbjct: 36  KIGVSRGA-RTDRGVHALCNVVSLKLQIDQKYCSSMTNNKLVDKWNIDWDLLIQELNS-- 92

Query: 84  KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
           ++   I +  +  V + F+ +  A +R Y Y                 + P     + ++
Sbjct: 93  QLPSDIKVNAIKHVTQSFNVKHQADQRMYNY-----------------ISPSFSTVDYVQ 135

Query: 144 IAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSFG----NLIEIRVVARSFLHTQI 198
                 +G H+F  + S       S  R I  F V +      N ++  ++  SF++ QI
Sbjct: 136 NICNQYLGTHNFHNYTSKKEYNDPSSKRFIQDFRVQNLNFHNENYLKFTILGNSFMYHQI 195

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           R  +G++  +   K   + ++     Q  +    +AP +GLY   ++++
Sbjct: 196 RKIIGTIYQIVQEKKDLSFIQDTFSQQ--QHSLYIAPQQGLYLREIKFT 242


>gi|13541142|ref|NP_110830.1| putative pseudouridylate synthase [Thermoplasma volcanium GSS1]
 gi|14324528|dbj|BAB59455.1| hypothetical protein [Thermoplasma volcanium GSS1]
          Length = 388

 Score = 38.1 bits (87), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 30/107 (28%), Positives = 50/107 (46%), Gaps = 10/107 (9%)

Query: 18  WQRQKNGSSIQGSI-EKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF------DLVREW 70
           W  +K+G SI+  I E A+ +  G+   +HG+GR D  V  L     F       ++R +
Sbjct: 178 WIHKKDGDSIESIIGEAALRIAGGKNYYLHGSGREDVDVRMLGNGREFVIEVEAPIMRTF 237

Query: 71  VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              IL + +N  +K    + I +LS VD++        + S +Y  I
Sbjct: 238 DLSILSETVNRSMK---GVEIFDLSFVDRKTVKEIKEEKHSKVYDCI 281


>gi|134080163|emb|CAK46143.1| unnamed protein product [Aspergillus niger]
          Length = 567

 Score = 38.1 bits (87), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 32/125 (25%), Positives = 56/125 (44%), Gaps = 15/125 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+G+GY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 120 KVAVLLGYSGTGYKGMQLSETEKTIEGEL-FAAFVAAGAISKANATDPKKSSLVRCARTD 178

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    L+ E   +I  + +N   K+S  I + ++ + +K F +      R Y
Sbjct: 179 KGVHAAGNIVSLKLIVEDDDII--QKINE--KLSSQIRVWDILVTNKSFSSYQLCDSRIY 234

Query: 113 LYRII 117
            Y I 
Sbjct: 235 EYLIT 239


>gi|242066426|ref|XP_002454502.1| hypothetical protein SORBIDRAFT_04g032290 [Sorghum bicolor]
 gi|241934333|gb|EES07478.1| hypothetical protein SORBIDRAFT_04g032290 [Sorghum bicolor]
          Length = 567

 Score = 37.7 bits (86), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 50/122 (40%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDS 53
           +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD 
Sbjct: 53  KVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRAAPRRYDWARAARTDK 112

Query: 54  GVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A  QV      R +V P      LNA L  +  I       V   F A+    RR Y
Sbjct: 113 GVSAAAQVVSG---RFYVDPPGFIDRLNAQL--ASQIRAYGYVRVTNSFSAKKFCDRRRY 167

Query: 113 LY 114
           LY
Sbjct: 168 LY 169


>gi|317033787|ref|XP_001395447.2| tRNA pseudouridine synthase [Aspergillus niger CBS 513.88]
          Length = 517

 Score = 37.7 bits (86), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 28/109 (25%), Positives = 51/109 (46%), Gaps = 15/109 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+G+GY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 49  KVAVLLGYSGTGYKGMQLSETEKTIEGEL-FAAFVAAGAISKANATDPKKSSLVRCARTD 107

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQF 101
            GVHA   +    L+ E   +I  + +N   K+S  I + ++ + +K F
Sbjct: 108 KGVHAAGNIVSLKLIVEDDDII--QKINE--KLSSQIRVWDILVTNKSF 152


>gi|134118796|ref|XP_771901.1| hypothetical protein CNBN0810 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50254505|gb|EAL17254.1| hypothetical protein CNBN0810 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 560

 Score = 37.7 bits (86), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 54/124 (43%), Gaps = 12/124 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
           R  ++I Y G+GY G Q Q +   +I+G +  A+           +    V +  A RTD
Sbjct: 124 RCAVLIGYCGTGYQGMQIQDHTDRTIEGEVFAALVKAGAVSADNAIDARKVDIARAARTD 183

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRR 110
           +GVHA   V    ++ E       K +  Y+   + D I +       K F+AR +A  R
Sbjct: 184 AGVHAAGNVISIKMITEPPLPEGFKDVAEYVNTFLPDQIRMWGWVRTVKSFNARTAADSR 243

Query: 111 SYLY 114
            Y Y
Sbjct: 244 IYEY 247


>gi|255553385|ref|XP_002517734.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223543132|gb|EEF44666.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 377

 Score = 37.7 bits (86), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 54/126 (42%), Gaps = 21/126 (16%)

Query: 8   IEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGV 55
           + Y G+ Y G Q+Q++    S+I+  +E AIF   G +   +G         + RTD GV
Sbjct: 60  VGYVGTDYRGLQKQEDEHSLSTIEAELECAIFKAGGILDSNYGNLHKIAWARSSRTDKGV 119

Query: 56  HALRQVAHFDL---VREWVP----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           H+L  +    +      W      + L + +N YL   D I I ++    K F  R    
Sbjct: 120 HSLATMISMKMEIPENAWKEDPNGIALAECVNYYL--PDNIRIFSILPSQKSFDPRRECN 177

Query: 109 RRSYLY 114
            R Y Y
Sbjct: 178 LRKYSY 183


>gi|253744705|gb|EET00865.1| Pseudouridylate synthase, putative [Giardia intestinalis ATCC
           50581]
          Length = 507

 Score = 37.4 bits (85), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 77/199 (38%), Gaps = 35/199 (17%)

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
           V + V +    A+N  +++ +TI +L  + VD+ F AR S   R Y+Y            
Sbjct: 199 VPQEVEIDYVSAIN--MRLPETIRVLGWAPVDENFSARHSTSSRRYIYTF---------- 246

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDF-----------TTFRSI--HCQAS---SPIR 170
            G+      SL+ + M  A   LVG HDF            TF  +   CQ      P  
Sbjct: 247 -GQVG----SLNIQRMAEACTTLVGFHDFRNICKPSLDNVKTFERVIFSCQLEIDGQPYE 301

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRK 228
                   S  + + + V   +FL+ Q+R     L  +G      + +   L       K
Sbjct: 302 CEGSRAAVSEDSSLSLVVCGSAFLYHQVRCIASLLLHIGAELEPPSIISDLLDVTRFPGK 361

Query: 229 ECGPLAPPEGLYFDSVEYS 247
              P+AP E L F+  EY+
Sbjct: 362 PDYPIAPGELLIFEKAEYT 380


>gi|70923191|ref|XP_734642.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56507573|emb|CAH84165.1| hypothetical protein PC300883.00.0 [Plasmodium chabaudi chabaudi]
          Length = 82

 Score = 37.4 bits (85), Expect = 1.7,   Method: Composition-based stats.
 Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 17/97 (17%)

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
            + I+R+YLY                + + K+ +   M  AA+  +G HDF+ F      
Sbjct: 1   LNCIQRTYLY----------------FFVNKNYNIPRMNEAAKIFLGEHDFSNFCKKRKN 44

Query: 165 ASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRS 200
             S IRTI  F++     N    ++   SFL+ Q+ +
Sbjct: 45  TISFIRTIHKFEIKRIDQNFYYFKIKGTSFLYNQVNN 81


>gi|58262434|ref|XP_568627.1| pseudouridylate synthase [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57230801|gb|AAW47110.1| pseudouridylate synthase, putative [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 560

 Score = 37.4 bits (85), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 54/124 (43%), Gaps = 12/124 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
           R  ++I Y G+GY G Q Q +   +I+G +  A+           +    V +  A RTD
Sbjct: 124 RCAVLIGYCGTGYQGMQIQDHTDRTIEGEVFAALVKAGAVSADNAIDARKVDIARAARTD 183

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRR 110
           +GVHA   V    ++ E       K +  Y+   + D I +       K F+AR +A  R
Sbjct: 184 AGVHAAGNVISIKMITEPPLPEGFKDVAEYVNTFLPDQIRMWGWVRTVKSFNARTAADSR 243

Query: 111 SYLY 114
            Y Y
Sbjct: 244 IYEY 247


>gi|254566437|ref|XP_002490329.1| tRNA:pseudouridine synthase, introduces pseudouridines at positions
           26-28, 34-36, 65, and 67 of tRNA [Pichia pastoris GS115]
 gi|238030125|emb|CAY68048.1| tRNA:pseudouridine synthase, introduces pseudouridines at positions
           26-28, 34-36, 65, and 67 of tRNA [Pichia pastoris GS115]
          Length = 509

 Score = 37.4 bits (85), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 54/122 (44%), Gaps = 15/122 (12%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTDSGVH 56
           +I Y G+GY G Q      +I+G + +A F+ +G I   +           A RTD GVH
Sbjct: 88  LIGYCGTGYHGMQLNPPQKTIEGDLFEA-FVESGAISRDNSNDLKKSSFMRAARTDKGVH 146

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   V    ++ E   ++  + +N+  K+  TI +      +K F  R     R Y Y +
Sbjct: 147 AAGNVISLKMIIEDEDIL--EKINS--KLPPTIRVWGYERTNKNFDCRKMCSSRIYEYLM 202

Query: 117 IT 118
            T
Sbjct: 203 PT 204


>gi|328350723|emb|CCA37123.1| tRNA pseudouridine synthase A [Pichia pastoris CBS 7435]
          Length = 516

 Score = 37.4 bits (85), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 54/122 (44%), Gaps = 15/122 (12%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTDSGVH 56
           +I Y G+GY G Q      +I+G + +A F+ +G I   +           A RTD GVH
Sbjct: 95  LIGYCGTGYHGMQLNPPQKTIEGDLFEA-FVESGAISRDNSNDLKKSSFMRAARTDKGVH 153

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   V    ++ E   ++  + +N+  K+  TI +      +K F  R     R Y Y +
Sbjct: 154 AAGNVISLKMIIEDEDIL--EKINS--KLPPTIRVWGYERTNKNFDCRKMCSSRIYEYLM 209

Query: 117 IT 118
            T
Sbjct: 210 PT 211


>gi|269955758|ref|YP_003325547.1| binding-protein-dependent transport systems inner membrane
           component [Xylanimonas cellulosilytica DSM 15894]
 gi|269304439|gb|ACZ29989.1| binding-protein-dependent transport systems inner membrane
           component [Xylanimonas cellulosilytica DSM 15894]
          Length = 506

 Score = 37.4 bits (85), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 1   MIRYCMIIEYNGSGYFG--WQRQKNGSSIQGS-IEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           +IRY M +    +G  G  WQ  ++ +S+ GS I   + LV G IV+  G G     V A
Sbjct: 63  VIRYFMWLGNVLTGDLGSSWQTGQSVTSMLGSAIPSTVTLVAGSIVLAIGLGILIGMVAA 122

Query: 58  LRQVAHFDLVREWVPVIL 75
           LRQ   FD    +V  +L
Sbjct: 123 LRQYTRFDYAVTFVSFVL 140


>gi|115391499|ref|XP_001213254.1| hypothetical protein ATEG_04076 [Aspergillus terreus NIH2624]
 gi|114194178|gb|EAU35878.1| hypothetical protein ATEG_04076 [Aspergillus terreus NIH2624]
          Length = 613

 Score = 37.4 bits (85), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 32/72 (44%), Gaps = 16/72 (22%)

Query: 101 FHARFSAIRRSYLYRIITRQ----------APLALEKGRAWLIPKS----LDCENMRIAA 146
           F ARFS   R Y Y                AP A +K  A  +PK     LD E MR AA
Sbjct: 275 FDARFSCRERQYKYFFTQPAFSPTPGPGGFAPRANDK--AGSVPKYREGWLDIEAMREAA 332

Query: 147 QHLVGRHDFTTF 158
           +  VGRHDF  F
Sbjct: 333 RMFVGRHDFRNF 344


>gi|217074404|gb|ACJ85562.1| unknown [Medicago truncatula]
          Length = 530

 Score = 37.4 bits (85), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 47/116 (40%), Gaps = 13/116 (11%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTDSGVHALRQ 60
           Y G GY G Q+     +I+G +E+A+++         G         + RTD GV A+ Q
Sbjct: 62  YCGVGYQGMQKNPGAKTIEGELEEALYVSGAVPEQDRGLSKRYDWARSARTDKGVSAVGQ 121

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           V       +  P      LN+ L     I I     V   F A+    RR Y+Y I
Sbjct: 122 VVSGRFYID--PPGFVDRLNSNL--PSQIRIFGFKRVTASFSAKKFCDRRRYVYLI 173


>gi|307102143|gb|EFN50538.1| hypothetical protein CHLNCDRAFT_138514 [Chlorella variabilis]
          Length = 346

 Score = 37.4 bits (85), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 62/262 (23%), Positives = 99/262 (37%), Gaps = 63/262 (24%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +  + + Y+G+G  G Q Q++ +   +I+  +E+AIF   G    +  + R + G     
Sbjct: 43  KVALFVGYSGTGRRGLQMQRSSAPEETIEDVLEEAIFQAGG----ILPSNRGNLG----- 93

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                                        + + ++  V K ++AR   IRRSY Y +   
Sbjct: 94  ----------------------------KVRVFSVQRVSKSWNARRECIRRSYSYFVPAS 125

Query: 120 QAPLALEKGRA------WLIPKSLDCENMRIA-------AQHLVGRHDFTTFRSIH-CQA 165
              LAL+ G+        L   S     +++A       A  +V RH    FR I  C+A
Sbjct: 126 VLGLALDGGKEDQRRLHLLQHASSKKGQVQVAWKFERDDADPIVRRH----FRFIEWCRA 181

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            + +  +    V      I + +   SF+  QIR  VG    V  G      LE +L   
Sbjct: 182 GTELEVL----VPGGQPCIHLSLQGSSFMLHQIRKMVGMAVAVARGNLPLELLEFSLATP 237

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    PLAPP  L      +S
Sbjct: 238 ARINL-PLAPPSTLMLTGALFS 258


>gi|150865972|ref|XP_001385404.2| pseudouridine synthase [Scheffersomyces stipitis CBS 6054]
 gi|149387228|gb|ABN67375.2| pseudouridine synthase [Scheffersomyces stipitis CBS 6054]
          Length = 465

 Score = 37.4 bits (85), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 76/202 (37%), Gaps = 56/202 (27%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNA---YLKISDTISILNLSIVD------- 98
           GRTD GV A+ QV         + +++   LN     LK +D   I  LSI++       
Sbjct: 145 GRTDKGVSAMNQV---------ISLVVRSNLNEEEQLLKENDHKEIKYLSIINALLPPDI 195

Query: 99  ----------KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQ 147
                      +F ARFS   R Y Y                 L  K  LD E M  A  
Sbjct: 196 RMTAVCLRPPPKFDARFSCDYRHYRY-----------------LFKKHDLDIELMNEACI 238

Query: 148 HLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGS 204
             +G HDF  F  I    Q ++ +R +    +     +   + +   +FL  Q+R  V  
Sbjct: 239 KYIGSHDFRNFCKIDGSKQITNYVREVYSMKIIHLKDDFYAVDLKGSAFLWHQVRCMVAI 298

Query: 205 LKLVGDGKWTST------DLEK 220
           L L+G     +T      DLEK
Sbjct: 299 LFLIGQKLEATTIIEDLFDLEK 320


>gi|322499857|emb|CBZ34930.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 696

 Score = 37.0 bits (84), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 60/130 (46%), Gaps = 21/130 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAI--FLVTGEIVVVHGAG---------RT 51
           + + Y+GSG+ G Q Q +  +   ++G + +A+    +  E+V    AG         RT
Sbjct: 29  LCVLYSGSGFRGLQIQAHAPTCHTVEGVLIQALKDAGIIAEVVRGRPAGEHHHFARSCRT 88

Query: 52  DSGVHALRQVAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    + +E    +     +C+ LN   ++  T+ + N+  +   F  R  
Sbjct: 89  DRGVHAIRNMVSLFVPKEVFEEMGQAEGICEKLN--RQLPSTVRVANVMQLSGSFIPRHC 146

Query: 107 AIRRSYLYRI 116
             RR Y Y +
Sbjct: 147 CNRRVYRYML 156


>gi|296412959|ref|XP_002836186.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295629994|emb|CAZ80377.1| unnamed protein product [Tuber melanosporum]
          Length = 454

 Score = 37.0 bits (84), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 108/269 (40%), Gaps = 44/269 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  ++I Y G+GY G Q      SI+  + +A F+  G I   +             RTD
Sbjct: 92  KVAVLIGYCGTGYRGMQLNPPHKSIESDLFEA-FVQAGAISKANSDDPKKSSLVRCARTD 150

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E  P I  K +N+YL   + I +  +      F +      R Y
Sbjct: 151 KGVHAAGNVISLKLIIE-DPDITEK-INSYL--PEQIRVWGIVRTVGSFSSYHQCDSRRY 206

Query: 113 LYRI-----ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            Y +     I       L K    + PK L  + +R   +   G H+F  F +I    + 
Sbjct: 207 EYLVPSHCFIPPHPKSYLAKKTYRISPKRL--QRVREGFRSYEGTHNFHNF-TIQKTFND 263

Query: 168 P-----IRTIDHFDVNSFGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           P     I++ +  D     N   + +RV  +SF+  QIR  VG + +V     T   LE+
Sbjct: 264 PSSKRFIKSFEVLDPIIINNTEWLSLRVHGQSFMMHQIRKMVGMVMMV---VRTGCPLER 320

Query: 221 ALQAQDRKECG------PLAPPEGLYFDS 243
             +A     CG      P AP  GL  +S
Sbjct: 321 IKEA-----CGPRVVSIPKAPSLGLLLES 344


>gi|156048366|ref|XP_001590150.1| hypothetical protein SS1G_08914 [Sclerotinia sclerotiorum 1980]
 gi|154693311|gb|EDN93049.1| hypothetical protein SS1G_08914 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 599

 Score = 37.0 bits (84), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 53/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  ++I Y G+GY G Q      +I+G + KA F+  G I   +             RTD
Sbjct: 57  KVAVMIGYAGTGYKGLQINTKEKTIEGDMFKA-FVAAGAISKANANDPKKSALVRCARTD 115

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   V+  + +N++L   D I +  +      F+       R Y
Sbjct: 116 KGVHAAGNVLSLKLITEDPNVV--ENINSHL--PDQIRVWGIERTTGSFNCYQMCDSRWY 171

Query: 113 LYRIIT 118
            Y I T
Sbjct: 172 EYLIPT 177


>gi|294655697|ref|XP_002770167.1| DEHA2C04312p [Debaryomyces hansenii CBS767]
 gi|199430534|emb|CAG85917.4| DEHA2C04312p [Debaryomyces hansenii]
          Length = 528

 Score = 36.6 bits (83), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 55/126 (43%), Gaps = 18/126 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           CMI  Y G+GY G Q Q N    +I+G + +A F+  G I   +           A RTD
Sbjct: 75  CMI-GYCGTGYNGMQIQNNLDVKTIEGDLFQA-FVKAGAISPENADDLKKNGFMRAARTD 132

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +N  L   D I +  +   +K F  R     R Y
Sbjct: 133 KGVHAAGNVISCKLIIEDEDIL--EKINKEL--PDQIRVWGIERTNKSFDCRKMCSSRVY 188

Query: 113 LYRIIT 118
            Y + T
Sbjct: 189 EYLLPT 194


>gi|307105485|gb|EFN53734.1| hypothetical protein CHLNCDRAFT_136316 [Chlorella variabilis]
          Length = 353

 Score = 36.6 bits (83), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 15/79 (18%)

Query: 42  IVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQF 101
            V +  AGRTD GVHAL Q    ++VR         ALNA  +    +   + + V + F
Sbjct: 41  TVALAVAGRTDRGVHALGQ----EVVR---------ALNA--ERPGLLRAWHAAQVPRSF 85

Query: 102 HARFSAIRRSYLYRIITRQ 120
           HA F+A  R YLY +  R+
Sbjct: 86  HATFAAKWRRYLYLLPLRE 104


>gi|260944536|ref|XP_002616566.1| hypothetical protein CLUG_03807 [Clavispora lusitaniae ATCC 42720]
 gi|238850215|gb|EEQ39679.1| hypothetical protein CLUG_03807 [Clavispora lusitaniae ATCC 42720]
          Length = 229

 Score = 36.6 bits (83), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 38/130 (29%), Positives = 56/130 (43%), Gaps = 23/130 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHG----------A 48
           MI YC      G+GY G Q Q N    +I+  I KA F+  G +   +           A
Sbjct: 1   MIGYC------GTGYNGMQIQNNPDVKTIEAEIFKA-FIAAGAVSQENSTDLKKNGFMRA 53

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            RTD GVHA   V    L+ E   ++    +N++L   + I +  +  V++ F  R    
Sbjct: 54  ARTDKGVHAAGNVISCKLILEDEDIM--HKINSHL--PEKIRLWGIERVNRSFDCRKLCS 109

Query: 109 RRSYLYRIIT 118
            R Y Y + T
Sbjct: 110 SRVYEYLLPT 119


>gi|255935685|ref|XP_002558869.1| Pc13g04330 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211583489|emb|CAP91502.1| Pc13g04330 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 548

 Score = 36.6 bits (83), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 52/122 (42%), Gaps = 15/122 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+G+GY G Q  +   +I+G +  A+  V G +   + A           RTD
Sbjct: 84  KVALLMGYSGTGYSGMQLNEQQRTIEGDLFTALVNV-GAVSKANAADPKKSSFVRCARTD 142

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    ++ E   +I  + +NA L  S  I +    +  K F        R Y
Sbjct: 143 KGVHAAGNVVSLKMIVEDEDII--QKINAEL--SPQIRVWGYEVTSKSFSCYQMCDSRVY 198

Query: 113 LY 114
            Y
Sbjct: 199 EY 200


>gi|315929089|gb|EFV08321.1| tRNA pseudouridine synthase II [Campylobacter jejuni subsp. jejuni
           305]
          Length = 58

 Score = 36.6 bits (83), Expect = 3.6,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   + Y
Sbjct: 3   ANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLYLSRICY 58


>gi|322492588|emb|CBZ27865.1| pseudouridylate synthase-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 696

 Score = 36.6 bits (83), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 59/130 (45%), Gaps = 21/130 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAI--FLVTGEIVVVHGAG---------RT 51
           + + Y+GSG+ G Q Q +  +   ++G + +A+    +  ++V    AG         RT
Sbjct: 29  LCVLYSGSGFRGLQIQAHAPTCHTVEGVLIQALKDAGIIADVVRGRPAGEHHHFARSCRT 88

Query: 52  DSGVHALRQVAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    + +E    +     +C+ LN  L    T+ + N+  +   F  R  
Sbjct: 89  DRGVHAIRNMVSLFVPKEIFEEVGQTEGICEKLNRQLPA--TVRVANVMQLSGSFIPRHC 146

Query: 107 AIRRSYLYRI 116
             RR Y Y +
Sbjct: 147 CNRRVYRYML 156


>gi|213401227|ref|XP_002171386.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|211999433|gb|EEB05093.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 503

 Score = 36.2 bits (82), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 33/124 (26%), Positives = 53/124 (42%), Gaps = 19/124 (15%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI----------VVVHGAGRTD 52
           +   ++ Y G+GY G Q      +I+G + +A F+  G +          V +  A RTD
Sbjct: 45  KVACLVGYCGTGYHGMQLNPPNKTIEGDLFEA-FVKVGAVSSYNADDPKKVALARAARTD 103

Query: 53  SGVHALRQVAHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
            GVHA   V    L+ E   +I  + + L   +++ D I  +N       F+ R     R
Sbjct: 104 KGVHAAGNVITLKLILEDENLIQKVNEVLPPTIRVWDVIRTIN------SFNPRTYCESR 157

Query: 111 SYLY 114
            Y Y
Sbjct: 158 IYEY 161


>gi|158520883|ref|YP_001528753.1| pseudouridylate synthase-like protein [Desulfococcus oleovorans
           Hxd3]
 gi|158509709|gb|ABW66676.1| Pseudouridylate synthase-like protein [Desulfococcus oleovorans
           Hxd3]
          Length = 148

 Score = 36.2 bits (82), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 29/55 (52%)

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
           F   F AI ++Y Y I++R    A+ +  AW + + L+ + +R A   + G HD 
Sbjct: 18  FEPAFQAISKTYRYWIVSRPTSAAIGRQYAWHLSRPLEIKAIRQALPLVTGTHDL 72


>gi|146089460|ref|XP_001470389.1| pseudouridylate synthase-like protein [Leishmania infantum]
 gi|134070422|emb|CAM68761.1| pseudouridylate synthase-like protein [Leishmania infantum JPCM5]
          Length = 696

 Score = 36.2 bits (82), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 60/130 (46%), Gaps = 21/130 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAI--FLVTGEIVVVHGAG---------RT 51
           + + Y+GSG+ G Q Q +  +   ++G + +A+    +  ++V    AG         RT
Sbjct: 29  LCVLYSGSGFRGLQIQAHAPTCHTVEGVLIQALKDAGIVADVVRGRPAGEHHHFARSCRT 88

Query: 52  DSGVHALRQVAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    + +E    +     +C+ LN   ++  T+ + N+  +   F  R  
Sbjct: 89  DRGVHAIRNMVSLFVPKEVFEEMGQAEGICEKLN--RQLPSTVRVANVMQLSGSFIPRHC 146

Query: 107 AIRRSYLYRI 116
             RR Y Y +
Sbjct: 147 CNRRVYRYML 156


>gi|154300700|ref|XP_001550765.1| hypothetical protein BC1G_10938 [Botryotinia fuckeliana B05.10]
 gi|150856545|gb|EDN31737.1| hypothetical protein BC1G_10938 [Botryotinia fuckeliana B05.10]
          Length = 631

 Score = 35.8 bits (81), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 53/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  ++I Y G+GY G Q      +I+G + KA F+  G I   +             RTD
Sbjct: 99  KVAVMIGYAGTGYKGLQINTKEKTIEGDMFKA-FVAAGAISKANANDPKKSALIRCARTD 157

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   V+  + +N++L   D I +  +      F+       R Y
Sbjct: 158 KGVHAAGNVLSLKLIIEDPKVV--ENINSHL--PDQIRVWGIERTTGSFNCYQMCDSRWY 213

Query: 113 LYRIIT 118
            Y I T
Sbjct: 214 EYLIPT 219


>gi|154274161|ref|XP_001537932.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
 gi|150415540|gb|EDN10893.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
          Length = 634

 Score = 35.8 bits (81), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 13/91 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA----------GRTD 52
           +  +++ Y+GSGY G Q  +   +I+G +  A F+  G I   +             RTD
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTA-FVAAGAISKANATDPKKSSLVRCARTD 180

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYL 83
            GVHA   V    L+ E   V+  + +N +L
Sbjct: 181 KGVHAAGNVVSLKLIVEDPNVV--QKINGHL 209


>gi|198427214|ref|XP_002128771.1| PREDICTED: similar to Pseudouridine synthase 1 [Ciona intestinalis]
          Length = 531

 Score = 35.8 bits (81), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 64/267 (23%), Positives = 107/267 (40%), Gaps = 36/267 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF--LVTGEIV-----------VVHGAG 49
           +  M+  Y G+ Y G Q  +    I+ +IE  +F  LV  ++V               A 
Sbjct: 70  KVAMLFAYCGANYHGLQMNRGERWIK-TIEGDLFQALVDAKVVPSNCVQEPHKMTYKSAS 128

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV    QVA   L      V L   +N +L   + I ++ +    + F+A+  A  
Sbjct: 129 RTDKGVSTCGQVASLKLRLNENVVGL---INQHL--PEDIVVMAVRRTTQGFNAQLKAEG 183

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR-------HDFTTFRSI- 161
           R+Y Y + T           ++ I      E+  +  + ++ R       H+FT+ + + 
Sbjct: 184 RTYSYTLPTFAFADYGTGNTSYKI-----TEDKLLKVKSILYRYKGTHSFHNFTSGKRMG 238

Query: 162 HCQASSPIRTIDHFDVNSFGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
              A   I   +H D     N+  I + +  +SF+  QIR  +G L  + +G        
Sbjct: 239 EMSAQRFIIEFEHGDPFLVQNVEFITLTIKGQSFMLHQIRKMIGLLIAMVNGLAKEQHFI 298

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEY 246
           +A    +  E  P AP  GL  + V Y
Sbjct: 299 RAF--SEPLEDIPKAPGTGLVLEKVHY 323


>gi|310791388|gb|EFQ26915.1| tRNA pseudouridine synthase A [Glomerella graminicola M1.001]
          Length = 614

 Score = 35.4 bits (80), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 32/126 (25%), Positives = 53/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  +++ Y+G+GY G Q      +I+G + KA F+  G I   +             RTD
Sbjct: 125 KVAVMVGYSGTGYKGMQINNEEKTIEGDLFKA-FVAAGAISKANADDHKKSSLVRCARTD 183

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++    +NA L   + I +  +   +  F    +   R Y
Sbjct: 184 KGVHAAGNVISLKLIIEDEDIV--DKINANL--PEQIRVWGIQRTNNSFSCYQTCDSRWY 239

Query: 113 LYRIIT 118
            Y + T
Sbjct: 240 EYLLPT 245


>gi|119192942|ref|XP_001247077.1| tRNA pseudouridine synthase 1, putative [Coccidioides immitis RS]
          Length = 597

 Score = 35.4 bits (80), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 52/126 (41%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  +++ Y+G+GY G Q      +I+G I  A+ +  G I   +             RTD
Sbjct: 115 KVAVLLGYSGTGYHGMQMSAKEKTIEGEIFPAL-VAAGAISKANAMDPKKSSFVRCARTD 173

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E  P ++ K  N    +S  I I  +   +K F        R Y
Sbjct: 174 KGVHAAGNVISLKLIIE-DPDLVNKVNNI---LSPQIRIWGIEPTNKGFSCYQFCDSRIY 229

Query: 113 LYRIIT 118
            Y I T
Sbjct: 230 EYLIPT 235


>gi|303312455|ref|XP_003066239.1| tRNA pseudouridine synthase, putative [Coccidioides posadasii C735
           delta SOWgp]
 gi|240105901|gb|EER24094.1| tRNA pseudouridine synthase, putative [Coccidioides posadasii C735
           delta SOWgp]
          Length = 597

 Score = 35.4 bits (80), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 52/126 (41%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  +++ Y+G+GY G Q      +I+G I  A+ +  G I   +             RTD
Sbjct: 115 KVAVLLGYSGTGYHGMQMSAKEKTIEGEIFPAL-VAAGAISKANAMDPKKSSFVRCARTD 173

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E  P ++ K  N    +S  I I  +   +K F        R Y
Sbjct: 174 KGVHAAGNVISLKLIIE-DPDLVNKVNNI---LSPQIRIWGIEPTNKGFSCYQFCDSRIY 229

Query: 113 LYRIIT 118
            Y I T
Sbjct: 230 EYLIPT 235


>gi|320033682|gb|EFW15629.1| tRNA pseudouridine synthase [Coccidioides posadasii str. Silveira]
          Length = 597

 Score = 35.4 bits (80), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 52/126 (41%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  +++ Y+G+GY G Q      +I+G I  A+ +  G I   +             RTD
Sbjct: 115 KVAVLLGYSGTGYHGMQMSAKEKTIEGEIFPAL-VAAGAISKANAMDPKKSSFVRCARTD 173

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E  P ++ K  N    +S  I I  +   +K F        R Y
Sbjct: 174 KGVHAAGNVISLKLIIE-DPDLVNKVNNI---LSPQIRIWGIEPTNKGFSCYQFCDSRIY 229

Query: 113 LYRIIT 118
            Y I T
Sbjct: 230 EYLIPT 235


>gi|169619633|ref|XP_001803229.1| hypothetical protein SNOG_13015 [Phaeosphaeria nodorum SN15]
 gi|111058695|gb|EAT79815.1| hypothetical protein SNOG_13015 [Phaeosphaeria nodorum SN15]
          Length = 621

 Score = 35.0 bits (79), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 33/126 (26%), Positives = 54/126 (42%), Gaps = 15/126 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----------AGRTD 52
           +  ++I Y+G+GY G Q      +I+G +  A F+  G I   +             RTD
Sbjct: 106 KVAVMIGYSGTGYKGMQIDNKQKTIEGDLFTA-FVAAGAISKANADDPKKSSLVRCARTD 164

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L+ E   ++  + +N++L  S+ I +  +      F    +   R Y
Sbjct: 165 KGVHAAGNVISLKLIIEEEDIV--EKINSHL--SEQIRVWGIQRTTGSFSCYQACDSRWY 220

Query: 113 LYRIIT 118
            Y I T
Sbjct: 221 EYLIPT 226


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


Results from round 2




>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 =  348 bits (894), Expect = 3e-94,   Method: Composition-based stats.
 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 =  337 bits (864), Expect = 1e-90,   Method: Composition-based stats.
 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|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 =  326 bits (837), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 146/248 (58%), Positives = 182/248 (73%), Gaps = 1/248 (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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFLQVDYP 248


>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 =  326 bits (835), Expect = 2e-87,   Method: Composition-based stats.
 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|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 =  326 bits (835), Expect = 2e-87,   Method: Composition-based stats.
 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|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 (833), Expect = 4e-87,   Method: Composition-based stats.
 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|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 =  324 bits (831), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 136/247 (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  L   D I ++    V   +H R+   +++Y Y I+  +
Sbjct: 61  VAVFDSETSIPPERISYALNQRL--PDDIVVIRSEEVSADWHPRYCNSKKTYEYHILNAK 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|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 =  321 bits (824), Expect = 4e-86,   Method: Composition-based stats.
 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 =  321 bits (824), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 148/248 (59%), Positives = 186/248 (75%), Gaps = 1/248 (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  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFMQVDYP 248


>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 =  321 bits (822), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (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  L   D I I+    V   FH R+    ++Y Y II  + P
Sbjct: 65  VFDSATSIPPERIAMALNQRL--PDDIVIVKSEEVAPDFHPRYCDCEKTYEYHIINTRTP 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 SVEYS 247
            + Y 
Sbjct: 243 EIRYP 247


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

 Score =  320 bits (821), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 123/247 (49%), Positives = 167/247 (67%), Gaps = 1/247 (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 FDSVEYS 247
              V Y 
Sbjct: 240 LTGVSYP 246


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

 Score =  320 bits (821), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 154/248 (62%), Positives = 192/248 (77%), Gaps = 1/248 (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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFLQVDYP 248


>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 =  320 bits (820), Expect = 1e-85,   Method: Composition-based stats.
 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|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 =  320 bits (820), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (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  L   D I I+    V   FH R+    ++Y Y II  + P
Sbjct: 65  VFDSATSIPPERIAMALNQRL--PDDIVIVKSEEVATDFHPRYCDCEKTYEYHIINTRTP 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 SVEYS 247
            + Y 
Sbjct: 243 EIRYP 247


>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 =  319 bits (819), Expect = 2e-85,   Method: Composition-based stats.
 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|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 =  319 bits (819), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 154/248 (62%), Positives = 193/248 (77%), Gaps = 1/248 (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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFLQVDYP 248


>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 =  319 bits (819), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 152/248 (61%), Positives = 192/248 (77%), Gaps = 1/248 (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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFLQVDYP 248


>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 =  319 bits (819), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   +++EY+G+ Y GWQ+Q N  S+Q  +EKAI+ +TGE V + GAGRTD+GVHA  QV
Sbjct: 1   MNVKILLEYDGTNYHGWQKQNNALSVQEVLEKAIYALTGERVSIIGAGRTDAGVHARGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          L  A+N+ L   + I++     V   FHAR+SA  + Y Y I     
Sbjct: 61  ANFRTNTRIPVERLPYAINSKL--PEDIAVKGAEAVPDDFHARYSAKAKVYTYSIYNAPF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  L +  ++  P  LD E MR AA+  +G HDF  FR+      + +R I   DV   G
Sbjct: 119 PSPLLRRYSYFFPLPLDVEAMRRAAKAFIGVHDFAAFRASGSSVKTSVRNITRLDVKKCG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ I V A  FL+  +R   G+L  VG GK    ++   ++++DR+  G   P  GL  
Sbjct: 179 KLLTIEVEADGFLYNMVRIIAGTLLEVGTGKKDPEEIPSIIESRDRERAGVTLPAHGLCL 238

Query: 242 DSVEY 246
           + V Y
Sbjct: 239 EKVIY 243


>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 =  319 bits (819), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ Y GWQ+QKN  ++Q +IE+AI  +TGE V + GA RTD GVHAL Q
Sbjct: 1   MRNVKLIIEYDGTNYHGWQKQKNAKTVQDTIERAIKGLTGEKVDLIGASRTDFGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN  L   D I I     VD  FHAR+ A  + Y Y I   Q
Sbjct: 61  VANFITNSGIPGDRFSYALNRML--PDDIVIKESQEVDMDFHARYKAKGKRYRYLIYNSQ 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P AL + R + +   LD E+M+ AA + +G HDF+ FRS    A + +RTI    +   
Sbjct: 119 FPSALLRHRTYHVSHKLDFESMQRAASYFLGTHDFSAFRSSGSSAKTSVRTITDVSLERE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +++  +    FL+  +R  VG+L  VG GK  + ++ + ++++ RK  G  AP EGLY
Sbjct: 179 DKIVKFEIAGDGFLYNMVRIIVGTLMEVGIGKIRADEIPQIIESRKRKRAGRTAPAEGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVEVYY 244


>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 =  319 bits (818), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 132/247 (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  L   + I I+    V + FH R+    ++Y Y I+  +
Sbjct: 61  VAVFDTHTTIPPERISYALNQRL--PEDIVIVKSEEVAEDFHPRYCDCSKTYEYHILNMR 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|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 =  319 bits (817), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 160/247 (64%), Positives = 193/247 (78%), 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  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL REW    L  ALNA+L ++ + +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|260589149|ref|ZP_05855062.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|331082565|ref|ZP_08331690.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
 gi|260540569|gb|EEX21138.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|330400543|gb|EGG80173.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 245

 Score =  319 bits (817), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG ++Q  + + +   TGE +   GA RTD+GVHAL  
Sbjct: 1   MKRVKLTVAYDGTNYCGWQVQPNGITVQEVLNQCLSEFTGENIETIGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN  L   + I I     VD  FH R+   +++Y YRI+  +
Sbjct: 61  VAVFDTEMRMPGDKFSFALNQRL--PEDIRIQKSEEVDADFHPRYVKSQKTYEYRILNCR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+  +      LD + M+ AA +L+G HDF +F     Q  + +RT+    +   
Sbjct: 119 FPIPTERFYSHFTYIPLDVDKMKEAASYLIGEHDFKSFCGTGAQVKTTVRTVKEIQIEKS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I IR+    FL+  +R   G+L  +G G +    +++ L+A+DRK+ GP AP  GL 
Sbjct: 179 GDRITIRITGEGFLYNMVRIIAGTLMDIGGGLYPPEKMKEILEAKDRKKAGPTAPARGLT 238

Query: 241 FDSVEY 246
              ++Y
Sbjct: 239 LMKIQY 244


>gi|295109363|emb|CBL23316.1| pseudouridylate synthase I [Ruminococcus obeum A2-162]
          Length = 246

 Score =  318 bits (815), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 133/246 (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  L   + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTNTRIPGEKISYALNQRL--PEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 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|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 =  317 bits (814), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 139/246 (56%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++EY+G+ Y GWQ Q+N  ++Q  ++KAI  VTGE V + GA RTD+GVHAL Q
Sbjct: 1   MRNVMIVVEYDGTNYHGWQYQENAVTVQEVLQKAIKKVTGEEVNLIGASRTDTGVHALYQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F    +     L  ALN+ L   D I ++    V+  FHAR+SA R+ Y Y I+ R+
Sbjct: 61  VANFRTNTKIPAEKLPYALNSVL--PDDIVVVQAKDVEDSFHARYSAKRKRYKYIILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+   +   W I   L  E M+ AA +L+G HDF+ F++     +S IRT+    +   
Sbjct: 119 FPMPTMRNYCWHISYPLSIEKMKKAASYLIGTHDFSAFKASGSSKTSTIRTVYDLTIEKN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+  +R  VG+L  VG GK    ++   L+++DR + G  APP+GLY
Sbjct: 179 EEFINIEIEANGFLYNMVRIIVGTLSYVGLGKIEENEVYDILKSRDRTKAGITAPPQGLY 238

Query: 241 FDSVEY 246
              + Y
Sbjct: 239 LIKIMY 244


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

 Score =  317 bits (813), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 128/247 (51%), 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  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L+   + 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|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 =  317 bits (813), Expect = 9e-85,   Method: Composition-based stats.
 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  VANFKTCTNIPTSKIPNALNSVL--PADIVIKDAFEADMDFHSRYSAKGKRYKYIIYNRR 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|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 =  317 bits (812), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 150/248 (60%), Positives = 190/248 (76%), Gaps = 1/248 (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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFLQVDYP 248


>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 =  317 bits (812), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 150/248 (60%), Positives = 190/248 (76%), Gaps = 1/248 (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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFMQVDYP 248


>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 =  316 bits (811), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 150/248 (60%), Positives = 190/248 (76%), Gaps = 1/248 (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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFMQVDYP 248


>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 =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 133/246 (54%), Gaps = 2/246 (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  IHFDTDANRAEGAWTLGLNSNL--PPDIAVRWVKQVDEGFHARFSATARRYRYVIYNHNY 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  316 bits (810), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 138/246 (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 FQMPTMRNYCWHIDYPLSIEKMKKAASYLIGTHDFSAFKASGSSKTSTIRTVYDLTIEKD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I I + A  FL+  +R  VG+L  VG GK    ++   L ++DR + G  APP+GLY
Sbjct: 179 EDFINIEIEANGFLYNMVRIIVGTLSYVGLGKIEVNEVYDILTSRDRTKAGITAPPQGLY 238

Query: 241 FDSVEY 246
              + Y
Sbjct: 239 LIKIMY 244


>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 =  315 bits (808), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 133/246 (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  L   + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 65  VAVFDTNTRIPGEKISYALNQRL--PEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 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|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 =  315 bits (808), Expect = 3e-84,   Method: Composition-based stats.
 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|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 =  315 bits (808), Expect = 3e-84,   Method: Composition-based stats.
 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|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 =  315 bits (808), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

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--PDDIAVKWAVEVPEDFHARFSATARRYRYIIFNRKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M  A Q+L+G +DF++FR+  CQ+ +P R I H +V+  G
Sbjct: 119 RSAILPKGVSHYHVDLDHEKMHEAGQYLLGENDFSSFRAAKCQSHTPWRNIHHLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A  EGLY 
Sbjct: 179 AYIIVDIQANAFVHHMVRNIVGSLIEVGQGNQPPEWIKWLLEQKDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>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 =  315 bits (808), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 156/247 (63%), Positives = 187/247 (75%), 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  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL +EW P  L  ALNA+L+++   ++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|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 =  315 bits (807), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 132/246 (53%), Gaps = 2/246 (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  IHFDTHAIRSESAWTLGLNSNL--PPDIAVRWVKEVDETFHARFSATARRYRYVIYNHNY 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>gi|303240936|ref|ZP_07327447.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
 gi|302591522|gb|EFL61259.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
          Length = 245

 Score =  315 bits (807), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 132/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ Y GWQ Q N  ++Q ++EKAI+ +TGE++ ++G+ RTD GVHA  Q
Sbjct: 1   MKNVKLIIEYDGTNYHGWQSQSNAKTVQETVEKAIYGLTGEVININGSSRTDQGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN  L   + I I     V   FHAR+ A  + Y Y I    
Sbjct: 61  VANFFTKSNIPHDRFSYALNRML--PEDIIIRKSEEVSMDFHARYCAKGKKYRYLIYNSS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P A+ + R++ +  +LD ++M+ A     G HDF+ F++      + +RTI   +++  
Sbjct: 119 FPSAIFRNRSYHVSHNLDMDSMKKAIPFFKGTHDFSAFKATGSSVKTSVRTIFDVNLSRA 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I   V    FL+  +R  VG+L  VG G+  + ++   +++ DRK  G  APP+GLY
Sbjct: 179 EDNIWFEVSGDGFLYNMVRIMVGTLVDVGMGRIKAEEIPGIIESCDRKRAGRTAPPQGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LVEVYYE 245


>gi|291548427|emb|CBL21535.1| pseudouridylate synthase I [Ruminococcus sp. SR1/5]
          Length = 245

 Score =  315 bits (807), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 132/246 (53%), 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  L   + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTESRIPGEKFSYALNQRL--PEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 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|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 =  315 bits (807), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 132/247 (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  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D ++ W P  +  ALNA L+   + 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|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 =  315 bits (807), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 130/247 (52%), 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  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L+   + 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|319404987|emb|CBI78590.1| tRNA pseudouridine synthase A [Bartonella sp. AR 15-3]
          Length = 247

 Score =  314 bits (806), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 129/247 (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  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W   I+  ALNA+L+   + 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|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 =  314 bits (806), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

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--PDDIAVKWAVEVPEDFHARFSATARRYRYIIFNRKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M  A Q+L+G +DF++FR+  CQ+ +P R I H +V+  G
Sbjct: 119 RSAILPKGVSHYHVDLDHEKMHEAGQYLLGENDFSSFRAAKCQSHTPWRNIHHLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A  EGLY 
Sbjct: 179 AYIIVDIQANAFVHHMVRNIVGSLIEVGQGNQPPEWIKWLLEQKDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>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 =  314 bits (806), Expect = 6e-84,   Method: Composition-based stats.
 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  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 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|325265188|ref|ZP_08131914.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
 gi|324029592|gb|EGB90881.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
          Length = 263

 Score =  314 bits (805), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 128/247 (51%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + K +  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLTVAYDGTNYCGWQIQPNGITIEEILNKKLSRLTGEEIRVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  L  ALN  +   + I I+    V   +H R+    ++Y Y I+  +
Sbjct: 61  VAVFDTETTIPPDRLAYALNQRM--PEDIVIVKSEEVPADWHPRYCDTVKTYEYLILNAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   + +   LD + MR AA +L G HDF +F ++       +RTI   D+   
Sbjct: 119 IPDPTRRLTTYFVSYDLDLQKMRRAAGYLSGEHDFASFCNVRTNVEDTVRTIYELDILEN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I IR+    FL+  +R  VG+L  VG G +T   ++  L+A+DR+  G  APP GL 
Sbjct: 179 GEEITIRIRGNGFLYNMVRIIVGTLLRVGRGFYTPEQVKDILEAKDRQAAGVTAPPHGLR 238

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 239 LIGIEYP 245


>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 =  314 bits (805), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+   S+Q  +EKA+ ++    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTNYFGWQRQREVKSVQEELEKALSVIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA +     I++     V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNVTRKMVAWTMGANANM--PSDIAVRWAKEVPDDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDEKKMHEAGQYLLGENDFTSFRAAHCQSRSPFRNLMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + I + A +F+H  +R+  GSL  VG G+ +   ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 NYVVIDIKANAFVHHMVRNITGSLIKVGRGEESPEWIKWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  314 bits (804), Expect = 9e-84,   Method: Composition-based stats.
 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|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 =  313 bits (803), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L     ISI +   V   F AR+SA +++Y Y I  ++
Sbjct: 61  KANFKTNSKIPTDKFPLALNSVL--PGDISIKDAVEVPLDFSARYSAKQKTYKYLIYNKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  AL +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +   
Sbjct: 119 SRPALLRNYAYHYPYELDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY
Sbjct: 179 NECIAIYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLVIESKDRTKAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVVY 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 =  313 bits (802), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   
Sbjct: 1   MRNIKLTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN+ L     I I+N   V + FHAR+    ++Y Y I+ R+
Sbjct: 61  VANFKTNSNIPGKNFKAALNSKL--PKDIVIINSEEVAEDFHARYMTTGKTYCYTILNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P ALE+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + 
Sbjct: 119 EPPALERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I+I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL 
Sbjct: 179 GNKIKIYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLC 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


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

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 128/247 (51%), 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  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L+   + 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|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 =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 132/246 (53%), 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  L   + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTNTRIPGEKISYALNQRL--PEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 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|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 =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    M IEY+G+ Y G+Q+Q   N  +IQ ++EKA+  +TGE + V GAGRTD+GVHAL
Sbjct: 1   MRNIKMTIEYDGTSYHGFQKQADQNLPTIQEALEKALRKLTGEEISVTGAGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV +F            +ALN+ L   + I   +       FHA+F A +++Y Y I  
Sbjct: 61  GQVINFYTESSIPTGNFVRALNSVL--PEDIVAKDAVEAPGDFHAQFWAKKKTYRYTIFN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P    +  +  +P  L+ +NMR AA  LVG+HDF+ FR+    A S IRT+   +V 
Sbjct: 119 DTVPSVFYRRYSLFVPCKLNVDNMRKAASFLVGQHDFSAFRAAGSTARSSIRTMYRAEVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G LI + + A  FL+  +R   G+L  +G GK    +++  + + DR   GP  PP+G
Sbjct: 179 QEGELIHVYLEANGFLYNMVRIITGTLLYIGQGKLRVEEMKDIIASGDRTLAGPTVPPQG 238

Query: 239 LYFDSVEY 246
           L    VEY
Sbjct: 239 LCLMRVEY 246


>gi|160881752|ref|YP_001560720.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
 gi|160430418|gb|ABX43981.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
          Length = 245

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q N  +I+G + + +  +  E +V+ GA RTD+GVHA   
Sbjct: 1   MKRVLLKVAYDGTNYCGWQVQPNAKTIEGVLNECLTKLLKEEIVIIGASRTDAGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         L  ALNA+L   + I I     V+  FH R+   R++Y YRI    
Sbjct: 61  VAVFDTNSRIPAEKLSYALNAHL--PEDIVIQASMEVESDFHPRYCDTRKTYEYRIYNAT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL   +  A  +   LD E MR AA +L+G HDF +F S + Q     RTI    +   
Sbjct: 119 FPLPTNRRYAHFVYYDLDLEAMRKAASYLIGEHDFVSFCSANTQVKDTTRTIYDIQIEKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI IR+    FL+  +R   G+L  VG  +W    + +AL  +DR+  GP AP +GL 
Sbjct: 179 RELIVIRIKGNGFLYNMVRIIAGTLIQVGTHQWEPERVLEALTKKDRQAAGPTAPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LVEIEY 244


>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 =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   
Sbjct: 1   MRNIKLTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN+ L     I I+N   V + FHAR+    ++Y Y I+ R+
Sbjct: 61  VANFKTNSNIPGKNFKAALNSKL--PKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P ALE+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + 
Sbjct: 119 EPPALERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I+I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL 
Sbjct: 179 GNKIKIYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLC 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>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 =  312 bits (801), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 130/246 (52%), Gaps = 2/246 (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  VHFDTNVTRKMVAWTMGANANM--PSDIAVRWAKEVSDDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q L+G +DFT+FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDEKKMHEAGQFLLGENDFTSFRAAHCQSRSPFRNLMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + I + A +F+H  +R+  GSL  VG G+ +   ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 NYVVIDIKANAFVHHMVRNITGSLIKVGRGEESPEWIKWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  312 bits (801), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 132/246 (53%), Gaps = 2/246 (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  IHFDTEANRAEGAWTLGLNSNL--PPDIAVRWVKQVDESFHARFSATARRYRYVIYNHNY 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  312 bits (801), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 93/247 (37%), Positives = 132/247 (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  L   D I +     V   FH R +   ++Y Y+I+ R+
Sbjct: 61  VAVFDTESRIPGDKICFALNQRL--PDDIRVQASEEVPLSFHPRKANCTKTYEYKILNRK 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|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 =  312 bits (801), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ++ +S+Q  +EKA+ +V  E + VH AGRTD+GVH   QV
Sbjct: 1   MRIALCIEYDGAEYYGWQRQRDVNSVQEELEKALTIVANEPIEVHCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              NA L     I++     V++ FHARF+A  R Y Y I   + 
Sbjct: 61  VHFDTTSSRKLAAWMMGANANL--PKNIAVRWAKEVNEDFHARFTATARRYRYIIYNNRL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+          +LD   M  A Q+L+G +DFT+FR++HCQ+ SP R + H  V   G
Sbjct: 119 RPAILGHGVSHYHDALDANLMHEAGQYLLGENDFTSFRAVHCQSRSPWRNLMHLKVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +F+H  +R+  GSL  VG GK     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 DFIVIDIKANAFVHHMVRNITGSLIEVGKGKQKPEWIKWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  312 bits (800), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L     IS+ +   V   F AR+SA +++Y Y I  ++
Sbjct: 61  KANFKTSSKIPTDKFPLALNSVL--PGDISVKDAVEVPLDFSARYSAKQKTYKYLIYNKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  AL +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR I +  +   
Sbjct: 119 SRPALLRNYAYYYPYELDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRHIYNAYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+   R   G++  VG GK    D+   ++++DR   G   PP GLY
Sbjct: 179 NECIAIYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTLAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVVY 244


>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 =  312 bits (800), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 130/246 (52%), Gaps = 2/246 (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  VHFDTNVNRKMVAWTMGANANM--PSDIAVRWAKEVPDDFHARFSATARRYRYIIFNHAL 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  312 bits (800), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQ +  S+QG +EKA+  V  E + V  AGRTD+GVH   QV
Sbjct: 1   MRVALGIEYDGSRYYGWQRQLDVDSVQGQLEKALSKVANEPITVQCAGRTDTGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +N  L   D I++  + +VD++FHARFSA  R Y Y I   Q 
Sbjct: 61  VHFDTNAIRKETAWTLGVNVNL--PDDIAVRWVKVVDEEFHARFSATARRYRYMIYNHQL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +        ++D + M  AAQ  VG HDFT+FR++ CQ+ +P R I   +V   G
Sbjct: 119 RPGILRSGVSHYRGNIDEDKMHQAAQLFVGEHDFTSFRALQCQSKTPFREIHEVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VG+L  +G G      +   L  +DR +    A P GLY 
Sbjct: 179 MYICVDIKANAFLHHMVRNIVGTLLEIGKGNQPKEWVNTLLALKDRSKAAATAQPNGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  312 bits (800), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 132/246 (53%), Gaps = 2/246 (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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 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 =  312 bits (799), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L     IS+ +   V   F AR+SA +++Y Y I  ++
Sbjct: 61  KANFKTNSKIPTDKFPLALNSVL--PGDISVKDAVEVPLDFSARYSAKQKTYKYLIYNKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  AL +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +   
Sbjct: 119 SRPALLRNYAYYYPYELDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY
Sbjct: 179 NECIAIYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLVIESKDRTKAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVVY 244


>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 =  311 bits (798), Expect = 4e-83,   Method: Composition-based stats.
 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|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 =  311 bits (798), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 138/247 (55%), Positives = 173/247 (70%), Gaps = 1/247 (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 FDSVEYS 247
              V+Y 
Sbjct: 240 LMQVDYE 246


>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 =  311 bits (798), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 129/247 (52%), Positives = 166/247 (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  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L+     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|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 =  311 bits (798), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 137/247 (55%), Positives = 175/247 (70%), Gaps = 1/247 (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  VAHADLAREWRPDVLRDALNAHMR-PALVAVVAAEPVPETFDARFSAIRRHYLYRIINRR 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 FDSVEYS 247
              V+Y 
Sbjct: 240 LTGVDYP 246


>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 =  311 bits (798), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   
Sbjct: 1   MRNIKLTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN+ L     I I+N   V + FHAR+    ++Y Y I+ R+
Sbjct: 61  VANFKTNSNIPGKNFKAALNSKL--PKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P ALE+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    +   
Sbjct: 119 EPPALERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIEIE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I+I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL 
Sbjct: 179 GNKIKIYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLC 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>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 =  311 bits (798), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 132/246 (53%), Gaps = 2/246 (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  VHFDTNVSRKMVAWTMGANANM--PSDIAVRWAVEVNDDFHARFSATARRYRYIIFNHAL 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 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 =  311 bits (798), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+GS ++GWQRQ+   S+Q  +EKA+  +  + V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGVEYDGSQFYGWQRQREVPSVQEHLEKALSKIANQPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+            +N +L   DTI++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDIEGSRPLRAWTMGVNTHL--PDTIAVRWAKEVPDEFHARFSATARRYRYIIYNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         LD   M  A Q+L+G +DFT+FR++ CQ+ SP R + H +V   G
Sbjct: 119 RPGILRHGVSHYHGELDETLMHEAGQYLLGENDFTSFRAVQCQSKSPWRNVHHINVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL +VG  +     ++  L+A+DR      A  EGLY 
Sbjct: 179 RFVIIDIKANAFVHHMVRNITGSLIVVGRKEQKPEWIKWLLEAKDRNLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             VEY 
Sbjct: 239 VEVEYP 244


>gi|291549528|emb|CBL25790.1| pseudouridylate synthase I [Ruminococcus torques L2-14]
          Length = 256

 Score =  311 bits (797), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q    +I+G + +AI  +T E ++V GA RTD+GVHA   
Sbjct: 1   MRRIRLRVAYDGTAYCGWQVQPEVPTIEGELNQAISRLTKEEIIVIGASRTDAGVHAKGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN  L   + I ++    V+  +H R     ++Y Y+I+  +
Sbjct: 61  VAVFDTESTIPADRFAYALNPLL--PEDIVVVASDEVEADWHPRHCDTEKTYEYKILNSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  + +   + +   L+ E MR AA++L G HDF +F ++H Q    +RTI   +V   
Sbjct: 119 FPDPMRRRDTYHVSFDLNLEKMREAAEYLKGEHDFKSFCNVHTQVEDTVRTIYDLEVEKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI IRV    FL+  +R   G+L  VG G      +   L+A+DR+  G   PP+GL 
Sbjct: 179 EELITIRVRGNGFLYNMVRILAGTLIGVGRGAIAPEQIPAILEAKDRQAAGMTVPPQGLT 238

Query: 241 FDSVEY 246
              ++Y
Sbjct: 239 LVKIDY 244


>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 =  311 bits (797), Expect = 6e-83,   Method: Composition-based stats.
 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|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 =  311 bits (797), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 131/247 (53%), Positives = 171/247 (69%), Gaps = 1/247 (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  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL ++W    +  A+NA+L    + 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 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLVGVDY 247


>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 =  311 bits (797), Expect = 6e-83,   Method: Composition-based stats.
 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|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 =  311 bits (797), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 131/247 (53%), Positives = 172/247 (69%), Gaps = 1/247 (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  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL ++W    +  A+NA+L    + 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 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLVGVDY 247


>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 =  311 bits (797), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 142/246 (57%), Gaps = 2/246 (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     +++  +  VD  FHARFSA  R+Y Y I  +  
Sbjct: 61  IHFDTEKKRKDTAWTLGVNTHL--PSDVAVAWVKKVDDDFHARFSATARNYRYIIYNKPL 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  311 bits (797), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 134/247 (54%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + 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  L     I+IL    + + FHAR+SAI + Y Y I+   
Sbjct: 61  VASFQLHSKIPAERISFALNGKL--PRDITILEAKEMPEDFHARYSAIGKRYGYCIMNNT 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 FDSVEYS 247
              V Y 
Sbjct: 239 LQKVFYP 245


>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 =  311 bits (797), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   
Sbjct: 1   MRNIKLTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN+ L     I I+N   V + FHAR+    ++Y Y I+ R+
Sbjct: 61  VANFKTNSNIPGKNFKAALNSKL--PKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P ALE+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + 
Sbjct: 119 EPPALERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I+I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL 
Sbjct: 179 GNKIKIYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKSGICVPPTGLC 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>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 =  310 bits (796), Expect = 8e-83,   Method: Composition-based stats.
 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  VVHVDLEKDWPAQTVFNALNAHLT-HEAVSILSAEVAEGDWHARFSANERRYLYRILNRR 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|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 =  310 bits (796), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS ++GWQRQ   +S+Q  +E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSKFYGWQRQAEVNSVQAELERALSIVANEPIEVQCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +N +L   D I++     V+  FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNAVRKEGAWTLGVNVHL--PDDIAVRWAMPVNDDFHARFSATARRYRYVIFNHNF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D E M  AAQ L+G  DFT+FR+I CQ+++P R +    V+  G
Sbjct: 119 RPGILRKGVSHYHGDIDVERMHDAAQALIGERDFTSFRAIGCQSNTPFRNVHKVSVSRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VGSL  +G G      +   L+A+DR +    A P GLY 
Sbjct: 179 MYIVVDIQANAFLHHMVRNIVGSLLEIGLGNQPLDWMATLLEAKDRSQAAATAKPHGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  310 bits (796), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 127/247 (51%), Positives = 167/247 (67%), Gaps = 1/247 (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 FDSVEYS 247
           F    Y 
Sbjct: 240 FVEATYP 246


>gi|154483152|ref|ZP_02025600.1| hypothetical protein EUBVEN_00853 [Eubacterium ventriosum ATCC
           27560]
 gi|149735960|gb|EDM51846.1| hypothetical protein EUBVEN_00853 [Eubacterium ventriosum ATCC
           27560]
          Length = 246

 Score =  310 bits (795), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 133/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +II Y+G+ Y GWQ Q NG +++  + KA+  +  E + V GA RTDSGVHA+  
Sbjct: 1   MKRVRLIIAYDGTNYCGWQVQINGITVEEVLNKALKDLLNEEIAVIGASRTDSGVHAMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN  L   + I I     V   +H R+    ++Y Y+I+ R+
Sbjct: 61  VAVFDTETRIPAEKISFALNQRL--PNDIRIQKSDEVPLDWHPRYRDSTKTYEYKILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L++     +   LD + M+ AA+++VG HDF +F S   Q  S +RT+    VN  
Sbjct: 119 FPDPLQRFYTHFMYMPLDEQKMKEAAEYIVGEHDFASFCSAGSQVDSTVRTVYSLSVNKR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++I IR+    FL+  +R  VG+L  VG G +    +++ ++A+DR   GP AP  GL 
Sbjct: 179 DDVISIRITGNGFLYNMVRIIVGTLIKVGLGVYPPEHVKEIIEAKDRYVAGPKAPACGLT 238

Query: 241 FDSVEYS 247
              +EYS
Sbjct: 239 LVGIEYS 245


>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 =  310 bits (794), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L     IS+ +   V   F AR+SA +++Y Y I  ++
Sbjct: 61  KANFKTSSKIPTDKFPLALNSVL--PGDISVKDAIEVSLDFSARYSAKQKTYKYLIYNKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  AL +  A+  P  LD + M+ A ++ +G +DF +F S+  ++ + +R I +  +   
Sbjct: 119 SRPALLRNYAYYYPYELDVDAMQRACEYFIGEYDFKSFCSVDSESKTTVRRIYNAYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+   R   G++  VG GK    D+   ++++DR   G   PP GLY
Sbjct: 179 NECIAIYLTANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTLAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVAY 244


>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 =  310 bits (794), Expect = 1e-82,   Method: Composition-based stats.
 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|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 =  310 bits (794), Expect = 1e-82,   Method: Composition-based stats.
 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|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 =  310 bits (794), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 104/246 (42%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQK+  S+Q  +E A+  V    V VH AGRTDSGVH   QV
Sbjct: 1   MRIALGIEYDGSKYYGWQRQKDVISVQEKLEDALSRVANHPVRVHCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V     +NA L   D I++     VD++FHARFSA  R Y Y I   Q 
Sbjct: 61  VHFDTDAVRQDVAWTLGVNANL--PDDIAVRWALEVDEEFHARFSATARRYRYIIYNSQL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           +D E M  AAQ LVG HDFT+FR+ HCQA SPI+T+ H +V    
Sbjct: 119 RPAILSAGVSHYYGDIDVELMHEAAQQLVGEHDFTSFRAKHCQAKSPIKTMHHINVIRQN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I V A +FLH  +R+  GSL  VG G    + + + L  +DR      +  EGLY 
Sbjct: 179 SYIIIDVKANAFLHHMVRNLAGSLMEVGKGNKPVSWIAELLAGKDRSVAAATSKAEGLYM 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  309 bits (793), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 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 =  309 bits (793), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 133/247 (53%), Gaps = 2/247 (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  VVHFDTEIDRADVSWVRGTNSFL--PKTISVQWAKPMPDEFHARFSAFERTYYYVLYVHP 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 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 245


>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 =  309 bits (793), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 136/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   +++EY G+ Y GWQRQKN  SIQ  +E AI  +TGE V V G+GRTD+GVHAL QV
Sbjct: 1   MNVKILLEYEGTAYSGWQRQKNAISIQEVLENAIKSITGEAVNVIGSGRTDAGVHALGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F    +     L  A+N+ L   + I + +  IV + FHARF A  + Y Y I   + 
Sbjct: 61  ANFKTQTKIPIEKLPYAINSKL--PEDIVVKHAEIVPEDFHARFWAKAKIYTYTIYNAKF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  L K  ++  P+ L+   M+ AA  L+G HDF +F + +    S +R I+  +V   G
Sbjct: 119 PSPLLKRYSYFYPRPLNVRAMKKAADMLIGTHDFASFMASNSPVKSTVRCIERLEVFQNG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++++  + A  FL+  +R   G+L  VG  K  + D+   ++++DR   G   PP+GL  
Sbjct: 179 DIVKFEIEANGFLYNMVRIIAGTLLDVGINKKKANDIISIIKSKDRSMAGKTLPPQGLCL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 IKVIY 243


>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 =  309 bits (793), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 134/246 (54%), Gaps = 2/246 (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 DSVEYS 247
             V Y 
Sbjct: 239 VHVTYP 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 =  309 bits (793), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 138/246 (56%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   
Sbjct: 1   MRNIKLIIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN+ L     I I+N   V + FHAR+    ++Y Y I+ R+
Sbjct: 61  VANFKTNSNIPGKNFKAALNSKL--PKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P ALE+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + 
Sbjct: 119 EPPALERNCVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I+I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL 
Sbjct: 179 GNKIKIYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLC 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


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

 Score =  309 bits (792), Expect = 2e-82,   Method: Composition-based stats.
 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  VAHFDLVREWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 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|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 =  309 bits (792), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 131/246 (53%), Gaps = 2/246 (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  VHFDTNVSRKMVAWTMGANANM--PSDIAVRWAVEVNDDFHARFSATARRYRYIIFNHAL 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  309 bits (792), Expect = 2e-82,   Method: Composition-based stats.
 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|187776609|ref|ZP_02993082.1| hypothetical protein CLOSPO_00123 [Clostridium sporogenes ATCC
           15579]
 gi|187775268|gb|EDU39070.1| hypothetical protein CLOSPO_00123 [Clostridium sporogenes ATCC
           15579]
          Length = 246

 Score =  309 bits (792), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 136/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EK I  +T E V + GA RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGTNYCGWQKQKNEKFITLQGTLEKVISNITKEKVEITGASRTDSGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             + +F       P  L + +N  L     I +L+   V  +FH+RF +  ++Y Y I+ 
Sbjct: 61  GYMCNFFTNSRIPPENLQRVINNNL--PPDIVVLSSEEVSSEFHSRFCSKGKTYEYTILN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +  P+A+ +   +     LD + M+IA+++ +G HDF+ F++      + +RTI  F++N
Sbjct: 119 KSEPIAIGRNYVFHFKYKLDIDKMKIASKYFIGTHDFSAFQTKGSSVKTSVRTISKFEIN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+LI+  +    FL+  +R  VG+L  +G  K     +E  ++++DR++ G   P  G
Sbjct: 179 KSGDLIKFIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIEYVIKSKDRRKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 246


>gi|158319577|ref|YP_001512084.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
 gi|158139776|gb|ABW18088.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
          Length = 248

 Score =  309 bits (792), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 131/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+GS Y GWQ Q N  +IQ  I KA+  + G+ VV+HG+GRTD+GVHA  Q
Sbjct: 1   MRNIMIEIEYDGSNYSGWQVQPNAITIQEEIMKALKKLEGKDVVIHGSGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F + R      L  A+N+ L     I+I++   V   FHAR+SAI + Y+Y I   +
Sbjct: 61  VATFLMERNIPVERLPLAMNSNL--PKDITIIDAKEVPMDFHARYSAIGKRYIYHIYESR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+ +  ++ I   LD   M  A++ L+G HDF  F S        +RTI   +  S 
Sbjct: 119 YRSAILRNYSYHINYKLDRSKMMEASKLLIGTHDFRGFMSNGSSVEDTVRTIKSLEFKSD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + +    FL+  +R   G+L  +G G      +EK L+ +DR   G  APP+GL+
Sbjct: 179 GENIYMIIEGDGFLYNMVRIITGTLVQIGAGNKPLEQIEKILKTKDRSLAGHTAPPQGLF 238

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 239 LDKVFYP 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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 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|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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 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   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 YFDSVEYS 247
           +   V+Y 
Sbjct: 241 FLIGVDYP 248


>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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+  +S+Q  +EKA+ ++    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTQYYGWQRQREVNSVQEELEKALSVIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       +      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTATRKMIAWTMGANANL--PKNIAVRWAKEVPDEFHARFSATARRYRYVIYNHMF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD   M  A Q L+G +DFT+FR++HCQ+ SP R I H +V    
Sbjct: 119 RPGILATGVSHYHGELDVARMHQAGQFLLGENDFTSFRAVHCQSRSPWRNIMHLNVTRHE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQEPEWIQWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

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     +++     V + FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTASRKMVAWTMGANANL--PSDVAVRWAKEVPEDFHARFSATARRYRYIIFNSAL 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+     +E  LQA+DRK  G  A  EGLY 
Sbjct: 179 QYVVIDIKANAFVHHMVRNITGSLICVGRGEQKPEWIEWLLQAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>gi|294497016|ref|YP_003560716.1| tRNA pseudouridine synthase A [Bacillus megaterium QM B1551]
 gi|295702381|ref|YP_003595456.1| tRNA pseudouridine synthase A [Bacillus megaterium DSM 319]
 gi|294346953|gb|ADE67282.1| tRNA pseudouridine synthase A [Bacillus megaterium QM B1551]
 gi|294800040|gb|ADF37106.1| tRNA pseudouridine synthase A [Bacillus megaterium DSM 319]
          Length = 246

 Score =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 123/247 (49%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   I+ Y+G+ + G+Q Q N  ++Q  IE  +  +  + V ++ +GRTD+ VHA  Q
Sbjct: 1   MKRLKCIVAYDGTHFSGYQVQPNKRTVQLEIEAVLEKMHNKKVPIYASGRTDTNVHAQGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           KALN+ L   D I + N+  VD  FHAR+    + Y Y I+  +
Sbjct: 61  VIHFDTNLNIPCDKWKKALNSML--PDDIVMKNVCEVDAHFHARYDVTSKEYRYHILRGE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A+  P  LD   M+ A  +L+G HDFT+F S   +    IRTI   D+   
Sbjct: 119 DRNPFTRSYAYHYPYPLDYSKMKKAITYLLGTHDFTSFCSARTEVEDKIRTIYKIDMYEE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + +  R V   FL+  +R  VG+L  VG G+     ++  L+++ R   G  AP +GLY
Sbjct: 179 NSQLVFRFVGSGFLYNMVRILVGTLLEVGQGRIEPDAIKDILESKSRPRAGKTAPSQGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LWRVFYD 245


>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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 99/246 (40%), Positives = 132/246 (53%), Gaps = 2/246 (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             +N  L   D I++    +VD+ FHARFSA  R Y Y I   Q 
Sbjct: 61  VHFDTDAIRKESAWTLGVNVSL--PDDIAVRWAKVVDEDFHARFSATARRYRYMIYNYQL 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 132/247 (53%), Gaps = 2/247 (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  VVHFDTELDRADVSWVRGTNSFL--PKTISVQWAKPMPDEFHARFSAFERTYYYVLYVHP 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 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 245


>gi|312127288|ref|YP_003992162.1| tRNA pseudouridine synthase a [Caldicellulosiruptor hydrothermalis
           108]
 gi|311777307|gb|ADQ06793.1| tRNA pseudouridine synthase A [Caldicellulosiruptor hydrothermalis
           108]
          Length = 244

 Score =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ YFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTEYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L     ISI +   V   F AR+SA +++Y Y I  + 
Sbjct: 61  KANFKTSSKIPTDKFPLALNSVL--PGDISIKDAVEVPLNFSARYSAKQKTYKYLIYNKN 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  AL +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +   
Sbjct: 119 SRPALLRNYAYYYPYQLDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNSYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY
Sbjct: 179 NECIAIYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTKAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVVY 244


>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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 97/246 (39%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

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 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  AAQ+L+G +DFT+FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILSSGVSHYHGELDEKKMHQAAQYLLGENDFTSFRATHCQSRSPWRNMMHINVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     +E  L A+DRK  G  A  EGLY 
Sbjct: 179 QYVVIDIKANAFVHHMVRNITGSLICVGRGEQEPQWIEWLLAAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 132/248 (53%), Positives = 176/248 (70%), Gaps = 1/248 (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 YFDSVEYS 247
           +   V+Y 
Sbjct: 241 FLTGVDYP 248


>gi|322514646|ref|ZP_08067676.1| tRNA pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
 gi|322119437|gb|EFX91539.1| tRNA pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
          Length = 289

 Score =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    V    AGRTDSGVH   QV
Sbjct: 28  MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSVVANAPVEAFCAGRTDSGVHGTGQV 87

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   + I++     V + FHARFSA  R Y Y I   + 
Sbjct: 88  VHFETETVRPLQSWCFGTNANL--PNDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKL 145

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  C++ +P R I H +V+  G
Sbjct: 146 RSAILPKGVSHYHHELDHQKMHEAGQFLLGENDFSSFRAAKCESHTPWRNIHHLNVSRLG 205

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 206 NYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 265

Query: 242 DSVEYS 247
             V Y 
Sbjct: 266 VDVHYP 271


>gi|146296772|ref|YP_001180543.1| tRNA pseudouridine synthase A [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|166228689|sp|A4XKB7|TRUA_CALS8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145410348|gb|ABP67352.1| tRNA pseudouridine synthase A [Caldicellulosiruptor saccharolyticus
           DSM 8903]
          Length = 244

 Score =  309 bits (791), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ YFGWQ+Q N  ++QG IE AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTNYFGWQKQPNKKTVQGVIEDAIKKITGEDVNLVGSGRTDRGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L   + ISI + + V   F AR+SA +++Y Y I   +
Sbjct: 61  KANFKTESKIPTEKFPLALNSVL--PNDISIKDAAEVSLDFSARYSAKQKTYKYLIYNHK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+     +  P  LD  +M+ + ++ +G +DF++F S   + +S +R I    +   
Sbjct: 119 FRPAILCNYVYHFPYELDLVSMQKSCEYFIGEYDFSSFCSSGSETNSKVRRIFDCYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I I + A  FL+   R   G++  VG G++  TD+   ++++DR + G   PP GLY
Sbjct: 179 NDCIAIYITANGFLYNMARIIAGTILDVGVGRFKPTDIPLIIESKDRTKAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVVY 244


>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 =  308 bits (790), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 2/247 (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  VVHFDTELDRADVSWVRGTNSFL--PKTISVQWAKPMPDEFHARFSAFERTYYYVLYVHP 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 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 245


>gi|197302933|ref|ZP_03167984.1| hypothetical protein RUMLAC_01661 [Ruminococcus lactaris ATCC
           29176]
 gi|197298014|gb|EDY32563.1| hypothetical protein RUMLAC_01661 [Ruminococcus lactaris ATCC
           29176]
          Length = 297

 Score =  308 bits (790), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q N ++I+G +   +  +TG+ V V GA RTD+GVHA   
Sbjct: 26  MKRIRLTVAYDGTDYCGWQVQNNVATIEGELNTVLTQLTGQTVKVIGASRTDAGVHARGN 85

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P     A+NA L   + I +++   V   +H R     ++Y YR++ ++
Sbjct: 86  VAVFDTESSIPPERFLYAVNALL--PEDIVVVDSCEVAADWHPRHCNTEKTYEYRVLNQK 143

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  + +   + +   LD E MR AA +L G HDF +F ++H      +RTI   +V   
Sbjct: 144 LPDPMRRRDTYFVSFPLDLERMRQAAGYLEGEHDFKSFCNVHTHVEDTVRTIYRLEVIRE 203

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N+I  RV    FL+  +R   G+L  VG G     ++   L+A+DR+  G   PP+GL 
Sbjct: 204 ENVITFRVRGNGFLYNMVRILAGTLIGVGRGLIDPEEIPAMLEAKDRQAAGMTVPPQGLT 263

Query: 241 FDSVEY 246
              ++Y
Sbjct: 264 LMKIDY 269


>gi|323703515|ref|ZP_08115161.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
 gi|323531506|gb|EGB21399.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
          Length = 249

 Score =  308 bits (790), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 87/249 (34%), Positives = 133/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + + Y+G+ Y G+Q Q+    +++Q  +E A+  V  E V V GAGRTD+GVHA 
Sbjct: 3   MKNIKLTVAYDGTNYHGFQEQRGTGLATVQEVLEAALSKVANETVQVIGAGRTDAGVHAR 62

Query: 59  RQVAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV +F      VP   +  A+N+ L   D I+++    V   FHARFSA  ++Y Y I 
Sbjct: 63  GQVVNFRSTNWPVPTEKIHLAVNSLL--PDDIAVIKAEEVPLDFHARFSATAKTYRYSIY 120

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +    L +  A+  P+ LD E MR AAQ+L+G HDF +F++        +RTI   ++
Sbjct: 121 NHRVMSPLHRLYAYHEPRPLDIEAMRQAAQYLLGTHDFKSFQAQGTPVKDTVRTIYRAEL 180

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S   LI + +    FL+  +R   G+L  VG GK +  +++  ++A++R   G   PP 
Sbjct: 181 VSEPPLIHLYLRGNGFLYNMVRIITGTLLDVGKGKKSPPEMKSIIEARNRTRAGTTVPPH 240

Query: 238 GLYFDSVEY 246
           GL    VEY
Sbjct: 241 GLCLMEVEY 249


>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 =  308 bits (790), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++   S V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWASSVPDDFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHCELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNLMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  308 bits (790), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   D I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETQAIRPLQSWCFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 179 NYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 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|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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 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|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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 134/246 (54%), Gaps = 2/246 (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 DSVEYS 247
             V Y 
Sbjct: 239 VHVTYP 244


>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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R I H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 121/247 (48%), Positives = 166/247 (67%), Gaps = 1/247 (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 FDSVEYS 247
              V Y 
Sbjct: 240 LTGVGYE 246


>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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L     ISI +       F AR+SA +++Y Y I  ++
Sbjct: 61  KANFKTSSKIPTDKFPLALNSVL--PGDISIKDAVEAPLDFSARYSARQKTYKYLIYNKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  AL +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +   
Sbjct: 119 SRPALLRNYAYYYPYQLDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY
Sbjct: 179 NECIAIYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTKAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVVY 244


>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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   D I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETQAIRPLQSWCFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 179 NYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 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  VVHVDLDKDWPAQTVFNALNAHLTR-EAVSILSAEVAEEGWHARFSANERRYLYRILNRR 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|46143880|ref|ZP_00204588.1| COG0101: Pseudouridylate synthase [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
          Length = 262

 Score =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   D I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETQAIRPLQSWCFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 179 NYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 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 =  308 bits (789), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 136/247 (55%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + I Y+GS YFGWQ+Q++  SIQ  +E+A+  +  E + +  AGRTD+GVHA  Q
Sbjct: 1   MKKIALGISYDGSRYFGWQKQQSVQSIQNELEQALSTIANEPIEIFCAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+              N +L   + I++   + V++ FHARFSA+ R Y Y I  R 
Sbjct: 61  VIHFETSASRPLQAWIFGTNVHL--PNDIAVKWSTEVNEDFHARFSALSRRYRYIIYNRP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+           LD + M IA Q+L+G +DF++FR+  CQ+ SP R + H  V+  
Sbjct: 119 QRFAILPTGITHHHYPLDEKLMHIAGQYLLGENDFSSFRAAQCQSKSPYRNVHHLQVSRI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + + + A +F+H  +R+ VGSL +VG+GK     ++  LQ +DR    P A   GLY
Sbjct: 179 GDYLIVDIQANAFVHHMVRNIVGSLLVVGEGKQKPEWIKWLLQQRDRSCAAPTAKAAGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LVKVHYP 245


>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 =  308 bits (789), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY 
Sbjct: 179 RYVVIDLKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  307 bits (788), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R I H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  307 bits (788), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 126/247 (51%), Positives = 159/247 (64%), Gaps = 1/247 (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 FDSVEYS 247
              V Y 
Sbjct: 240 LSLVAYP 246


>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 =  307 bits (788), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 134/246 (54%), Gaps = 2/246 (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     I++   + V   FHARF+A  R Y Y I     
Sbjct: 61  VHFDVNVNRKMAAWTMGVNAHL--PSDIAVRWAAEVSDDFHARFTATARRYRYVIYNHAL 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  307 bits (788), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 94/245 (38%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  RIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPISVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD             +NA L     I++  +  V   FHARFSA  R Y Y I  ++  
Sbjct: 71  HFDTTAVRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYVIYNQRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G 
Sbjct: 129 PAVLSQGVTHFYEPLDAERMQRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>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 =  307 bits (788), Expect = 6e-82,   Method: Composition-based stats.
 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  VHFDTGVERPLTAWVRGVNRFL--PPGVAVLWVQPVADDFHARFSACSRSYSYYLMNHPV 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|144900443|emb|CAM77307.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 245

 Score =  307 bits (788), Expect = 7e-82,   Method: Composition-based stats.
 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|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 =  307 bits (788), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 97/246 (39%), Positives = 134/246 (54%), Gaps = 2/246 (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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  307 bits (787), Expect = 9e-82,   Method: Composition-based stats.
 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|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 =  307 bits (787), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 123/246 (50%), Positives = 174/246 (70%), 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  VCHFDLEKPFTALKLRDALNFHLK-PAPIAVLEVEAVTEDFHARLTSTGRAYVYRIVNRR 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|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 =  307 bits (787), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 146/248 (58%), Positives = 186/248 (75%), Gaps = 1/248 (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  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 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 YFDSVEYS 247
           YF  V+Y 
Sbjct: 241 YFMQVDYP 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 =  307 bits (787), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 138/246 (56%), Gaps = 2/246 (0%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD        +    +NA L     I++  +  V++ FHARF+A  R Y Y I   + 
Sbjct: 61  VHFDTNSVRKLPVWMVGVNANL--PKNIAVRWVKEVNEDFHARFTATARRYRYIIFNNRQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+         ++LD + M  A Q+L+G +DFT+FR++ CQ+ +P R + H  V   G
Sbjct: 119 RPAIFSHGVSHYHETLDADLMHEAGQYLLGENDFTSFRAVRCQSRTPWRNLIHLKVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +F+H  +R+  GSL  VG GK     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 DFIVIDIKANAFVHHMVRNITGSLIEVGRGKQKPEWVQWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 IDVDYP 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 =  307 bits (787), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 10  VKIALGIEYDGSKYYGWQRQQEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHATGQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L     I++  +  V  +FHARFSA  R Y Y I   + 
Sbjct: 70  VHFETTAIRKDAAWTLGVNANL--PGDIAVRWVKDVPAEFHARFSATARRYRYVIYNHRL 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V  FG
Sbjct: 128 RPAVLSQGVTHYHLPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNLMHINVERFG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  +G G    + + + L A+DR      A  EGLY 
Sbjct: 188 AYIVVDIKANAFVHHMVRNIVGSLMEIGCGNQPESWMAELLAAKDRTLAAATAKAEGLYL 247

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 248 VSVDYP 253


>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 =  307 bits (787), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ    ++Q  +EKA+ +V  E + VH AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGSQYFGWQRQAEVDTVQERLEKALSIVANEPIAVHCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +N  L   D I++  + +VD +FHARF+A  R Y Y I   Q 
Sbjct: 61  VHFETNAIRKETAWTLGVNVNL--PDNIAVRWVKVVDDEFHARFTATARRYRYMIYNHQL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +      P  +D   M  AAQ+L+G  DFT+FR++HCQ+++P R +   +V   G
Sbjct: 119 RPGILRSGVSHYPGDIDESKMHQAAQYLLGEQDFTSFRAVHCQSNTPFRCVHEVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VGSL  VG G  +   +E+ L  +DR +    A P GLY 
Sbjct: 179 MYICVDIKANAFLHHMVRNIVGSLLEVGLGNQSVEWIEQLLALKDRNKAAATAKPNGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 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 =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 130/246 (52%), Gaps = 2/246 (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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 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 =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 134/247 (54%), Gaps = 2/247 (0%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+             +NA L     I++  +  V  +FHARFSA  R Y Y I   +
Sbjct: 61  VVHFETTAVRKDAAWTLGVNANL--PGDIAVRWVKDVPAEFHARFSATARRYRYVIYNHR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+           LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V  F
Sbjct: 119 LRPAVLSQGVTHYHLPLDAQRMHRAAQCLIGENDFTSFRAVQCQSRTPWRNLMHINVERF 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G    + + + L A+DR      A  EGLY
Sbjct: 179 GAYIVVDIKANAFVHHMVRNIVGSLMEIGCGNQPESWMAELLAAKDRTLAAATAKAEGLY 238

Query: 241 FDSVEYS 247
             SV+Y 
Sbjct: 239 LVSVDYP 245


>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 =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

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  VHFETNVDRKMVAWTMGANANM--PKDIAVRWATEVNEDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGHLDEKKMHEAGQYLLGENDFTSFRATHCQSHSPWRNMIHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 HYIVIDIKANAFVHHMVRNITGSLIAVGKGEQKPEWIKWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 244


>gi|296333145|ref|ZP_06875599.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305672848|ref|YP_003864519.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|296149761|gb|EFG90656.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305411091|gb|ADM36209.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. spizizenii
           str. W23]
          Length = 247

 Score =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 135/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  + + + V  +GRTDSGVHA  
Sbjct: 1   MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAEKWPYALNALL--PDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ +NMR AA+HL+G HDFT+F ++  +    +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFSYHLNVQNMREAAKHLLGTHDFTSFCAVKTEVQDKVRTIYELDWAE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK +  D++  L+A+DR+  G  AP  GL
Sbjct: 179 TDDGLQMRITGSGFLYNMVRIIAGTLLDAGIGKISPDDVKSMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLWNVFYD 246


>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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 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|312622107|ref|YP_004023720.1| tRNA pseudouridine synthase a [Caldicellulosiruptor kronotskyensis
           2002]
 gi|312202574|gb|ADQ45901.1| tRNA pseudouridine synthase A [Caldicellulosiruptor kronotskyensis
           2002]
          Length = 244

 Score =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q
Sbjct: 1   MRNILLTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        ALN+ L     ISI +   V   F AR+SA +++Y Y I  ++
Sbjct: 61  KANFKTSSKIPTDKFPLALNSVL--PGDISIKDAIEVPLDFSARYSARQKTYKYLIYNKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  AL +  A+  P  LD + M+   ++ +G +DF +F S   +A + IR + +  +   
Sbjct: 119 SRPALLRNYAYYYPYQLDVDAMQRTCEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY
Sbjct: 179 NECIAIYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTKAGKTLPPWGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVDVVY 244


>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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 139/246 (56%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +I+EY+G+ Y GWQ+QKN  ++QG+IEKAI  +T E V + G  RTDSGVHA   
Sbjct: 1   MRNIKLILEYDGTKYSGWQKQKNSVTVQGTIEKAIEAITKESVELIGCSRTDSGVHAKGY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F    +        A+NA L   + I IL+   V + FH+RF+ I ++Y Y ++ R 
Sbjct: 61  TANFFTNSKIPIERFYIAINAKL--PEDIVILSSEEVPEDFHSRFNCIGKTYCYSVLNRV 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  A+ +   + +P+ L  + M+ AA+  VG +DF  FR++  + +S +RTI   +V   
Sbjct: 119 SYPAMYRNYLYHVPRKLSIDEMKKAAESFVGTYDFNAFRNLGTEVASTVRTIHRIEVEEH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I I V    FL+  +R   G+L  VG G+  S  ++  L+++DR   G  AP  GL 
Sbjct: 179 GDIINILVTGDGFLYNMVRIIAGTLVEVGLGQKRSDQIKVILESKDRNRAGKTAPARGLS 238

Query: 241 FDSVEY 246
            D V Y
Sbjct: 239 LDKVYY 244


>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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 134/247 (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  L   + I I     +   FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTETRMPGEKISYALNQRL--PEDIRIQLSEEMPMDFHPRYCDSVKTYEYRILNRR 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|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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPIEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  RIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVLCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I  ++  
Sbjct: 71  HFETTAVRKDAAWTLGVNANL--PGDIAVRWVKNVPDDFHARFSATARRYRYVIYNQRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G 
Sbjct: 129 PAVLSQGVTHFYEPLDAERMQRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>gi|295093665|emb|CBK82756.1| pseudouridylate synthase I [Coprococcus sp. ART55/1]
          Length = 247

 Score =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q NG +++  + K +  +  E + V GA RTDSGVHAL  
Sbjct: 3   MKRVKLIVAYDGTNYCGWQVQINGITVEEVLNKTLSELCHEDIKVIGASRTDSGVHALGN 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN  L   + I I     V   FH R+    ++Y Y+I+ R+
Sbjct: 63  VAVFDTESGIPGEKFSFALNQRL--PEDIRIQESCQVADDFHPRYCDTIKTYEYKILNRR 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  +  +   LD + M+ AA  LVG HDF +F S   Q  + +RTI    ++  
Sbjct: 121 FDMPTERLYSTFVYYPLDIDKMKRAAAVLVGEHDFKSFCSSRSQVENTVRTITDITIDKA 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IR+    FL+  +R  VG+L  +G G W    +E  L+A+DR + GP A  +GL 
Sbjct: 181 GDMIHIRISGNGFLYNMVRIIVGTLMKIGLGIWPEDCMESILEAKDRTKAGPKAEAKGLT 240

Query: 241 FDSVEY 246
              ++Y
Sbjct: 241 LVEIKY 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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 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|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 =  307 bits (786), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   D I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETQAIRPLQSWCFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKP 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+ +P R + + +V+  G
Sbjct: 119 RSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHYLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 179 NYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>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 =  306 bits (785), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

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 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M +AAQ+L+G +DFT+FR+ HCQ+ SP R + H +V    
Sbjct: 119 RPGILSTGVSHYHGELDEKKMHLAAQYLLGENDFTSFRATHCQSRSPWRNMMHINVTRHN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L A+DRK  G  A  EGLY 
Sbjct: 179 QYVVIDIKANAFVHHMVRNITGSLICVGRGEQEPEWIQWLLGAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  306 bits (785), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTSAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 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 =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 97/246 (39%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG+ Y+GWQRQ++ SS+Q  +EKA+ +V  + V V  AGRTD+GVH   QV
Sbjct: 1   MKVALGIEYNGANYYGWQRQRDVSSVQEELEKALSIVANQPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+      P      +NA L     I++     V ++FHARFSA  R Y Y I     
Sbjct: 61  VHFESSVIRKPAAWTMGVNANL--PKDIAVRWAKEVHEEFHARFSATARRYRYVIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M  A Q+L+G +DFT+FR++HCQ+ SP R I H +V+  G
Sbjct: 119 RPGILSSGISHYHGELDAEKMHQAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVSRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL +VG G  +   +E  LQ +DRK  G  A  EGLY 
Sbjct: 179 PYVVIDIKANAFVHHMVRNITGSLIVVGKGDQSPEWIEWLLQQKDRKLAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>gi|165976323|ref|YP_001651916.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|307250146|ref|ZP_07532106.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307256957|ref|ZP_07538734.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|238687566|sp|B0BPI7|TRUA_ACTPJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|165876424|gb|ABY69472.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|306857811|gb|EFM89907.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306864532|gb|EFM96438.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 262

 Score =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   D I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETQAIRPLQSWCFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+ +P R + + +V+  G
Sbjct: 119 RSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHYLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 179 NYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>gi|240144416|ref|ZP_04743017.1| tRNA pseudouridine synthase A [Roseburia intestinalis L1-82]
 gi|257203524|gb|EEV01809.1| tRNA pseudouridine synthase A [Roseburia intestinalis L1-82]
          Length = 294

 Score =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  MI+ Y+G+ Y GWQ Q NG +I+  + K +  + GE +VV GA RTDSGVH+L  +
Sbjct: 48  MRVKMIVAYDGTNYKGWQVQPNGITIEEVLNKNLSNLLGEQIVVSGASRTDSGVHSLGNI 107

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FD         +  ALN  L   + I +     V+  +H R+   R++Y YRI+ R  
Sbjct: 108 AVFDTNTRMPADKIAFALNQRL--PEDIVVQGSCEVEDGWHPRYQNSRKTYEYRILNRTF 165

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
            +   +   +     LD E M+ AA +L G HDF +F +I  Q  + +RTI   DV   G
Sbjct: 166 RMPTRRLDTYFYHYPLDVEKMKKAASYLEGEHDFKSFCAIGAQVKTTVRTIYACDVEKEG 225

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IRV    FL+  +R   G+L  VG G      ++  L  +DR   GP AP  GL  
Sbjct: 226 DIITIRVTGNGFLYNMVRIIAGTLVQVGGGAIKPEAVKGILAKKDRSAAGPTAPAHGLTM 285

Query: 242 DSVEYS 247
             +E+ 
Sbjct: 286 MGIEFE 291


>gi|225376773|ref|ZP_03753994.1| hypothetical protein ROSEINA2194_02415 [Roseburia inulinivorans DSM
           16841]
 gi|225211399|gb|EEG93753.1| hypothetical protein ROSEINA2194_02415 [Roseburia inulinivorans DSM
           16841]
          Length = 247

 Score =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q NG +I+  + + +  + GE + V GA RTDSGVH++  
Sbjct: 1   MKRVKLIVAYDGTNYCGWQVQPNGITIEQVLNENLSKLLGEEITVTGASRTDSGVHSMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN  L   + I + +   V   +H R+   R++Y YRI+ R 
Sbjct: 61  VAIFDTETRMPADKISFALNQRL--PEDIVVQDSCEVPSDWHPRYQVSRKTYEYRILNRT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +   +     LD + M+ AA +LVG HDF +F ++  Q  +  RTI   +V   
Sbjct: 119 FRMPNRRLDTYFYHHKLDVDKMKQAASYLVGEHDFKSFCAVGAQVKTTTRTIYSCEVEKD 178

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G ++I IRV    FL+  +R   G+L  VG G+    ++ + L  +DR   GP AP  GL
Sbjct: 179 GNDIITIRVTGNGFLYNMVRIIAGTLIRVGGGEMAPDEIPQILGKKDRTAAGPTAPAHGL 238

Query: 240 YFDSVEY 246
               +EY
Sbjct: 239 TMMGIEY 245


>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 =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLITVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   D I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETQAIRPLQSWCFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILPKGISHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 179 NYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>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 =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSRYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGANNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 124/247 (50%), Positives = 170/247 (68%), Gaps = 1/247 (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 FDSVEYS 247
             +V+Y 
Sbjct: 240 LTAVDYP 246


>gi|320183774|gb|EFW58608.1| tRNA pseudouridine synthase A [Shigella flexneri CDC 796-83]
          Length = 270

 Score =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L   D I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PDDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 126/247 (51%), Positives = 168/247 (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  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  ++W    +  ALNA+L+     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|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 =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 128/246 (52%), Gaps = 2/246 (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--PDNIAVRWAKEVDDSFHARFSATARRYRYVIYNHNF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  306 bits (784), Expect = 2e-81,   Method: Composition-based stats.
 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|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 =  305 bits (783), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G  YFGWQRQ    S+Q  +E+A+  V  E + VH AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGRQYFGWQRQAEVDSVQAQLERALSKVANEPIRVHCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +N  L   D I++  + IVD +FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRKDSAWTLGVNVNL--PDDIAVRWVKIVDDEFHARFSATARRYRYMIYNYDF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +        ++D + M  AAQ  VG HDFT+FR++HCQ+ +P R++   +V   G
Sbjct: 119 RPGILRSGVSHYRGNIDADIMHQAAQQFVGEHDFTSFRALHCQSKTPFRSVHEVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VG+L  +G G      + + L  +DR +  P A P GLY 
Sbjct: 179 MYICVDIKANAFLHHMVRNIVGTLLEIGLGNQRPEWIPQLLDLKDRSQAAPTAKPNGLYM 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  305 bits (783), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L   D I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAPRKDAAWTLGVNANL--PDDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  305 bits (783), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 94/250 (37%), Positives = 134/250 (53%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+G+ + GWQ Q +G ++Q  +++AIF  T   +    AGRTD+GVHA  Q
Sbjct: 1   MKRIALGIEYDGTNWRGWQTQPDGMTVQDQLQEAIFRFTRTRISTMCAGRTDAGVHASEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD---KQFHARFSAIRRSYLYRII 117
           V H D   + +PV   + +NAYL    +I++     V      FHAR SA+ R Y Y I 
Sbjct: 61  VVHLDTELDRLPVSWVRGVNAYL--PSSIAVRWACEVPGGKDGFHARSSAMARRYRYLIY 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L K RA  + K LD   M+  A  L+G HDF+ FR+  CQ+ +P++T+   D+
Sbjct: 119 NSPVRSPLWKNRAGWVFKPLDIGLMQKGAGLLLGEHDFSAFRAAECQSITPVKTVKRIDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              GNLI     A +FLH  +R+ VGSL  +G G      +++ L A+DR    P   P+
Sbjct: 179 EKQGNLIVFTFEANAFLHHMVRNIVGSLVYIGKGNHPPEWMKQLLDAKDRSLAAPTFMPD 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLSRVHYE 248


>gi|163816009|ref|ZP_02207379.1| hypothetical protein COPEUT_02189 [Coprococcus eutactus ATCC 27759]
 gi|158448819|gb|EDP25814.1| hypothetical protein COPEUT_02189 [Coprococcus eutactus ATCC 27759]
          Length = 254

 Score =  305 bits (783), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +++  + K +  +  E + V GA RTDSGVHAL  
Sbjct: 10  MKRVKLVVAYDGTNYCGWQVQINGITVEEVLNKTLSELCHENIKVIGASRTDSGVHALGN 69

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN  L   + I I     V   FH R+    ++Y Y+I+ R+
Sbjct: 70  VAVFDTESGIPGEKFSFALNQRL--PEDIRIQESCQVADDFHPRYCDTIKTYEYKILNRR 127

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  +  +   LD + M+ AA  LVG HDF +F S   Q  + +RTI    ++  
Sbjct: 128 FDMPTERLYSTFVYYPLDIDKMKRAAAVLVGEHDFNSFCSTRSQVENTVRTITDITIDKV 187

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IR+    FL+  +R  VG+L  +G G W    +E  L A+DR + GP A  +GL 
Sbjct: 188 GDMIHIRISGNGFLYNMVRIIVGTLMKIGLGIWPEDCMESILAAKDRTKAGPKAEAKGLT 247

Query: 241 FDSVEY 246
              ++Y
Sbjct: 248 LVEIKY 253


>gi|220928242|ref|YP_002505151.1| tRNA pseudouridine synthase A [Clostridium cellulolyticum H10]
 gi|254789632|sp|B8I814|TRUA_CLOCE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219998570|gb|ACL75171.1| tRNA pseudouridine synthase A [Clostridium cellulolyticum H10]
          Length = 245

 Score =  305 bits (783), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 125/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + IEY+G+ Y GWQ QKN  ++Q  I+KA+  + GE V V G  RTD GVHA  Q
Sbjct: 1   MRKIRLTIEYDGTNYHGWQIQKNAKTVQEVIQKALSKLLGEDVGVTGCSRTDVGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF    +        A+N  L   D I I N   V ++FHAR+SA  + Y Y I    
Sbjct: 61  VAHFLTDSKIPGDKFSYAINNLL--PDDIVIKNSEEVPEEFHARYSAKGKKYRYLIYNSP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
              A+ + R+  +   L+   M+ AA +  G HDF  F++   Q  S +R I   +V   
Sbjct: 119 HASAIMRNRSCHVRPELNVAEMQKAAGYFKGEHDFLAFQATGGQVRSTVREIYGMEVYVK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N+I I V    FL+  +R   G+L  VG GK   +++   +   DR + G  AP +GL
Sbjct: 179 EDNMISIEVSGNGFLYNMVRIIAGTLIYVGMGKLHESEIPGIIAGLDRTKAGKTAPAQGL 238

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 239 YLVQIYY 245


>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 =  305 bits (783), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHDELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL +VG G+     ++  L  +DR      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIVVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 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 =  305 bits (783), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  305 bits (783), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 128/246 (52%), Gaps = 2/246 (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--PDNIAVRWAKEVDDSFHARFSATARRYRYVIYNHNF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>gi|323977481|gb|EGB72567.1| tRNA pseudouridine synthase A [Escherichia coli TW10509]
          Length = 270

 Score =  305 bits (782), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGANNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  305 bits (782), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 128/246 (52%), Gaps = 2/246 (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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  305 bits (782), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  + + V  AGRTD+GVH   QV 
Sbjct: 11  RIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANQPIAVCCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I  ++  
Sbjct: 71  HFETTSVRKDAAWTLGVNANL--PGDIAVRWVKDVPDDFHARFSATARRYRYIIYNQRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G 
Sbjct: 129 PAVLGQGVTHFYEPLDAERMQRAAQSLIGENDFTSFRAVQCQSRTPWRNVMHINVSRYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>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 =  305 bits (782), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 129/246 (52%), Gaps = 2/246 (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  VHFDTNVSRKMVAWTMGANANM--PSDIAVRWAVEVSDDFHARFSATARRYRYIIFNHAL 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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  305 bits (782), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 131/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+GS + GWQ Q +G+++Q  +E+A+       V    AGRTD+GVH L Q
Sbjct: 1   MKRIALGIQYDGSAFCGWQSQPHGNTVQDELERALREFAQTPVHTVVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E   V   +  N +L    TIS+     + + FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELERADVSWVRGTNTFL--PKTISVQWAKPMPEAFHARFSAFERTYYYLLYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  +   LD E MR AA HL+G HDF+ FRS  CQA +PI+ +   D+   
Sbjct: 119 VRSPMLAARAGWVHTPLDIEAMRAAAAHLIGEHDFSAFRSSQCQAKTPIKHLHQIDIEQH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +  R  A +FLH  +R+ +G L  +G  +     + + L ++DR+   P   P+GLY
Sbjct: 179 GDFVHFRFRANAFLHHMVRNLMGCLVYIGKRRRPVEWMAEVLASRDRESAAPTFMPDGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 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 =  305 bits (782), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  305 bits (782), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 131/246 (53%), Gaps = 2/246 (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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  305 bits (781), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

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  VHFETNVDRKMVAWTMGANANM--PKDIAVRWATEVNEDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGHLDEKKMHEAGQYLLGENDFTSFRATHCQSRSPWRNMIHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 HYIVIDIKANAFVHHMVRNITGSLIAVGKGEQKPEWIQWLLEAKDRKVAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  305 bits (781), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  305 bits (781), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

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--PDDIAVKWAVAVNEDFHARFSATARRYRYIIFNQKL 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M  A Q+L+G +DF++FR+  CQ+++P R I H +V+  G
Sbjct: 137 RSAILPKGVTHFHFPLDERKMHQAGQYLLGENDFSSFRAAKCQSNTPWRNIHHLNVSRQG 196

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + + + A +F+H  +R+ VG+L  +G GK      +  L+ +DR++  P A  EGLY 
Sbjct: 197 NYVIVDIQANAFVHHMVRNIVGTLLEIGQGKQPVEWAKWVLEQRDREKAAPTAKAEGLYL 256

Query: 242 DSVEYS 247
             V Y 
Sbjct: 257 VEVHYP 262


>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 =  305 bits (781), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 128/247 (51%), Positives = 168/247 (68%), Gaps = 1/247 (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  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL ++W    +  A+NA+L    + +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 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLIGVDY 247


>gi|326203861|ref|ZP_08193723.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
 gi|325985959|gb|EGD46793.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
          Length = 245

 Score =  305 bits (781), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 131/247 (53%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +IIEY+G+ Y GWQ QKN  ++Q +++KAI  + GE V V G  RTD GVHA  Q
Sbjct: 1   MRKIKIIIEYDGTNYHGWQVQKNAKTVQETVQKAISKLLGEGVGVTGCSRTDVGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF    +        A+N  L   D I I +   V ++FHAR+S   + Y Y I    
Sbjct: 61  VAHFLTDSQIPGDKFSYAINNLL--PDDIVIKHSEEVSEEFHARYSTKGKKYRYLIYNAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
            P A+ + R+  +   LD E M+ AA++ +G HDF  F++   Q  S +R I   +V+  
Sbjct: 119 HPSAIMRNRSCHVRPVLDIEQMKKAARYFIGEHDFAAFQATGGQVRSTVREIYSMEVSGK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N+I I V    FL+  +R   G+L  VG GK   +++   +   DR + G  AP +GL
Sbjct: 179 EDNMIYIEVSGNGFLYNMVRIIAGTLIYVGMGKLQESEIPGIIAGLDRTKSGKTAPAQGL 238

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 239 YLMEIYY 245


>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 =  305 bits (781), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

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--PDDIAVKWAVAVNEDFHARFSATARRYRYIIFNQKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M  A Q+L+G +DF++FR+  CQ+++P R I H +V+  G
Sbjct: 119 RSAILPKGVTHFHFPLDERKMHQAGQYLLGENDFSSFRAAKCQSNTPWRNIHHLNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + + + A +F+H  +R+ VG+L  +G G+      +  L+ +DR++  P A  EGLY 
Sbjct: 179 NYVIVDIQANAFVHHMVRNIVGTLLEIGQGRQPVEWAKWVLEQRDREKAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VEVHYP 244


>gi|118497491|ref|YP_898541.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida U112]
 gi|195536184|ref|ZP_03079191.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
 gi|254372827|ref|ZP_04988316.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|166228699|sp|A0Q6C2|TRUA_FRATN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|118423397|gb|ABK89787.1| tRNA pseudouridine synthase A [Francisella novicida U112]
 gi|151570554|gb|EDN36208.1| tRNA pseudouridine synthase A [Francisella novicida GA99-3549]
 gi|194372661|gb|EDX27372.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
          Length = 258

 Score =  305 bits (781), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGRNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    E       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSDAERPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 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 =  305 bits (781), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSRYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|332678185|gb|AEE87314.1| tRNA pseudouridine synthase A [Francisella cf. novicida Fx1]
          Length = 258

 Score =  305 bits (781), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    E       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IINFYSDAERPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>gi|254369374|ref|ZP_04985386.1| hypothetical protein FTAG_00346 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157122324|gb|EDO66464.1| hypothetical protein FTAG_00346 [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 258

 Score =  305 bits (781), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F            + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNAYRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  305 bits (781), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KVALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVLCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I  ++  
Sbjct: 71  HFETTAVRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYVIYNQRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ FG 
Sbjct: 129 PAVLSQGVTHFYEPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRFGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>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 =  305 bits (781), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

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--PDDIAVKWAVAVNEDFHARFSATARRYRYIIFNQKL 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M  A Q+L+G +DF++FR+  CQ+++P R I H +V+  G
Sbjct: 137 RSAILPKGVTHFHFPLDERKMHQAGQYLLGENDFSSFRAAKCQSNTPWRNIHHLNVSRQG 196

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + + + A +F+H  +R+ VG+L  +G GK +    +  L+ +DR++  P A  EGLY 
Sbjct: 197 NYVIVDIQANAFVHHMVRNIVGTLLEIGQGKQSVEWAKWVLEQRDREKAAPTAKAEGLYL 256

Query: 242 DSVEYS 247
             V Y 
Sbjct: 257 VEVHYP 262


>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 =  304 bits (780), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETRAQRKDAAWTLGVNANL--PGDIAVRWVKRVPADFHARFSATARRYRYVIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G 
Sbjct: 129 PAVLSHGVTHFHQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>gi|254374311|ref|ZP_04989793.1| tRNA pseudouridine synthase A [Francisella novicida GA99-3548]
 gi|151572031|gb|EDN37685.1| tRNA pseudouridine synthase A [Francisella novicida GA99-3548]
          Length = 258

 Score =  304 bits (780), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PKDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  304 bits (780), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V    
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHS 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 244


>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 =  304 bits (780), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 101/246 (41%), Positives = 139/246 (56%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+ + GWQ Q N  ++QG +EKA  +V    + V  AGRTD+GVHAL QV
Sbjct: 1   MRIALGIEYAGTDFCGWQNQPNTRTVQGELEKAASVVANHSIDVFAAGRTDTGVHALNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +NA L     I++  +  VD +F+ARF+AI+R Y Y I+ R +
Sbjct: 61  VHFDTDAIRSERGWLLGINANL--PKDINVAWMKPVDDEFNARFTAIKRRYRYLILNRLS 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+   R W     LD E M+ AA  LVG+HDF+ FR+  CQA SPI+T+D   V    
Sbjct: 119 RSAVHHNRMWWHHHPLDIERMQAAADQLVGKHDFSAFRASECQARSPIKTLDKITVRRQQ 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + V A+SFLH  +R+ VG +  +GDG          L++ DR + G  APP+GLY 
Sbjct: 179 DCIAVDVEAKSFLHHMVRNLVGVMAAIGDGSKPVDWAGDVLRSVDRSQGGVTAPPQGLYL 238

Query: 242 DSVEYS 247
             VEY 
Sbjct: 239 VDVEYP 244


>gi|226309840|ref|YP_002769734.1| tRNA pseudouridine synthase A [Brevibacillus brevis NBRC 100599]
 gi|254789606|sp|C0ZIL2|TRUA_BREBN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226092788|dbj|BAH41230.1| tRNA pseudouridine synthase A [Brevibacillus brevis NBRC 100599]
          Length = 244

 Score =  304 bits (780), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 122/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   ++ Y+G+ + G+Q Q +  ++QG IE A+  VTGE + V G+GRTD+GVHA  Q
Sbjct: 1   MKRLRCVLAYDGTDFSGFQVQPDQVTVQGEIEAALNRVTGEDIQVFGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD             LN  L   D+I I  +  VD  FHARF    + Y Y I    
Sbjct: 61  VIHFDTASNIPMDKWRFVLNNQL--PDSIVIRTVEEVDASFHARFDVQVKEYRYCIDNNP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    A  +   LD + M+ AA +LVG HDFT+F S        +RT+    V   
Sbjct: 119 VADVFRHRYADHVRFPLDVDAMQQAAHYLVGEHDFTSFCSAKTYVEDKVRTVYGLSVEKI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + +      FL+  +R  VG+L  VG GK    +L + L A DR++ G  AP +GL 
Sbjct: 179 GDEVWVTCRGNGFLYNMVRIIVGTLVEVGQGKRNPAELREILAACDREKAGKTAPAKGLT 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 MWEVVY 244


>gi|157690932|ref|YP_001485394.1| tRNA pseudouridine synthase A [Bacillus pumilus SAFR-032]
 gi|166991159|sp|A8F9B7|TRUA_BACP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157679690|gb|ABV60834.1| tRNA-pseudouridine synthase I [Bacillus pumilus SAFR-032]
          Length = 247

 Score =  304 bits (780), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 128/248 (51%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
           ++    + Y+G+ + G+Q Q    ++Q  IE A+  +    E+V +  +GRTDSGVHA  
Sbjct: 1   MKVKCTVSYDGTHFKGYQVQPGQRTVQTEIESALAKMHKQDELVPIVASGRTDSGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L   D I +L    VD+ FHARFS + + Y Y++ T 
Sbjct: 61  QVIHFDTPLSIPMERWPFALNSLL--PDDIRVLKAEEVDESFHARFSVVSKEYRYKVSTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  A   P  LD + MR AA +L+G HDFT+F + + +    +R I   +  +
Sbjct: 119 THQNVFTRQYACHFPYRLDADKMREAAGYLIGTHDFTSFCAANTEVQDKVREIYTLEWKN 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +E+RV    FL+  +R   G+L  VG GK+   +++  L A++R+  G  AP  GL
Sbjct: 179 VSDGLEMRVRGNGFLYNMVRIIAGTLLEVGSGKFHPDEIKAMLAARNREAAGKTAPSHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 239 YLWEVFYD 246


>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 =  304 bits (780), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 136/247 (55%), Gaps = 2/247 (0%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD             L     +   ISIL+   VD +FHARFSA  RSY Y I+ R 
Sbjct: 61  VVHFDTEAIRPERAWL--LGVTQSLPSDISILSAQFVDPEFHARFSATARSYRYIILNRM 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL +GR       LD   M  A QHL+G HDF++FR+  CQ+ SP+R+I+  +++  
Sbjct: 119 TRSALHRGRITWWRGPLDESAMHEAGQHLLGEHDFSSFRAKDCQSVSPVRSIESLNIHRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + + + A +FLH  +R+ VG+L  VG G+  +  L   LQA+DR   G  AP +GLY
Sbjct: 179 GEYVYMDITANAFLHHMVRNIVGTLLPVGAGERPADSLWDILQAKDRSAAGMTAPADGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LVGVRYP 245


>gi|225026395|ref|ZP_03715587.1| hypothetical protein EUBHAL_00644 [Eubacterium hallii DSM 3353]
 gi|224956284|gb|EEG37493.1| hypothetical protein EUBHAL_00644 [Eubacterium hallii DSM 3353]
          Length = 256

 Score =  304 bits (780), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 86/254 (33%), Positives = 134/254 (52%), Gaps = 10/254 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +++ Y+G+ Y GWQ Q NG +++  + K +     E + + GA RTDSGVH+   
Sbjct: 4   MKRFKLVVAYDGTNYCGWQIQPNGITVEEVLNKTLSRFLKEEIHIIGASRTDSGVHSFGN 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  LC ALN  L   + I I++   V   FH R+   R++Y Y I   +
Sbjct: 64  VAVFDSETTIPPEKLCFALNPQL--PEDIRIVSSEQVPGDFHPRYCDTRKTYEYHIQNGK 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
            PL  E+  + L+   L+ + M+ A+Q+LVG HDF +F +   QA + +RT+   +V   
Sbjct: 122 IPLPTERLYSHLVIFPLNIQAMQEASQYLVGTHDFKSFCAAKTQAQTTVRTVTGIEVEAH 181

Query: 179 --SFGNL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             S G      + IRV    FL+  +R   G+L  VG G +    +++ L+A DR + G 
Sbjct: 182 PLSEGEYPSKKVIIRVTGEGFLYNMVRIISGTLIKVGLGVYPPEHVKQILEACDRSQAGE 241

Query: 233 LAPPEGLYFDSVEY 246
             P +GL+   +EY
Sbjct: 242 TVPAKGLFLKKIEY 255


>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 =  304 bits (780), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPDSWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (780), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 126/247 (51%), Positives = 168/247 (68%), Gaps = 1/247 (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 FDSVEYS 247
           F  V + 
Sbjct: 240 FLRVRFP 246


>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 =  304 bits (780), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|56708110|ref|YP_170006.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670581|ref|YP_667138.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|224457202|ref|ZP_03665675.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370594|ref|ZP_04986599.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254874909|ref|ZP_05247619.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|62901197|sp|Q5NG36|TRUA_FRATT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123169371|sp|Q14HI8|TRUA_FRAT1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56604602|emb|CAG45654.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320914|emb|CAL09037.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|151568837|gb|EDN34491.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254840908|gb|EET19344.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159310|gb|ADA78701.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 258

 Score =  304 bits (780), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  304 bits (780), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            +  + IEY+GS Y+GWQRQ+   S+Q  +E+A+  V    V V  AGRTD+GVH   QV
Sbjct: 7   QKLALGIEYDGSRYYGWQRQQEVRSVQEKLERALSKVADHPVSVFCAGRTDAGVHGTGQV 66

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+ V +         +NA L   D I++  +  V   FHARFSA  R Y Y I  ++ 
Sbjct: 67  VHFETVAQRADAAWTLGVNANL--PDDIAVRWVKAVPDDFHARFSATARRYRYLIYNQRL 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G
Sbjct: 125 RPAILGNGVTHFYYPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVMHLNVTRHG 184

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  +G G  + + + + L A+DR      A  EGLY 
Sbjct: 185 PYVIVDIKANAFVHHMVRNIVGSLMEIGCGNQSESWMAELLAAKDRTLAAATAKAEGLYL 244

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 245 VAVDYP 250


>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 =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

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  VHFETNVDRKMVAWTMGANANM--PKDIAVRWATEVNEDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGHLDEKKMHEAGQYLLGENDFTSFRATHCQSRSPWRNMIHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +F+H  +R+  GSL  VG G      ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 HYIVIDIKANAFVHHMVRNITGSLIAVGKGDQKPEWIQWLLEAKDRKVAGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTSAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V    
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHS 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 244


>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 =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ + +S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 24  KIALGIEYDGSQYYGWQRQNDVASVQACLEKALSKVADEPIEVFCAGRTDAGVHGTGQVV 83

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I   +  
Sbjct: 84  HFTTQAIRKDAAWTMGVNANL--PPDIAVRWVKTVDEDFHARFSATARRYRYVIYNHRYR 141

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   G+
Sbjct: 142 PAVLSHGMTHFYHPLDVERMERAGQCLLGENDFTSFRAVQCQSRTPWRNVNHLKVTRHGD 201

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR   G  A  EGLY  
Sbjct: 202 YIVVDIKANAFVHHMVRNIVGSLMDVGCGNRPESWIAELLVAKDRTLAGATARAEGLYLV 261

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 262 AVDYP 266


>gi|182418813|ref|ZP_02950078.1| tRNA pseudouridine synthase A [Clostridium butyricum 5521]
 gi|237666467|ref|ZP_04526452.1| tRNA pseudouridine synthase A [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377310|gb|EDT74871.1| tRNA pseudouridine synthase A [Clostridium butyricum 5521]
 gi|237657666|gb|EEP55221.1| tRNA pseudouridine synthase A [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 244

 Score =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IE++GS + GWQ+Q  G ++Q  IE+AIF  TGE ++++G+ RTDSGVHA   
Sbjct: 1   MRNIKLTIEFDGSEFCGWQKQPKGRTVQKVIEEAIFKATGEEIIINGSSRTDSGVHAKDM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A+F            +ALN  L     +SI+    V + FHAR+S+  ++Y Y II R 
Sbjct: 61  IANFFTNSTIPGDKFREALNVRL--PKDVSIIRSEEVSEDFHARYSSKGKTYSYTIIHRY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             ++      +     LD +NMR A ++ +G HDF  F S      + +RTI    +   
Sbjct: 119 ERVSFGHQYVYHWRHDLDIDNMREACKYFIGTHDFRAFMSPGSSIKTTVRTITDLHIEQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I+I V A  FL+  +R  VG+L  VG+ K    D++  ++  +RK  G + PP GL 
Sbjct: 179 GEKIKIFVSADGFLYNMVRIIVGTLIKVGNKKLKPEDIQDIIREGNRKRAGMVVPPNGLV 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>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 =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|23097605|ref|NP_691071.1| tRNA pseudouridine synthase A [Oceanobacillus iheyensis HTE831]
 gi|38258776|sp|Q8CXP1|TRUA_OCEIH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|22775828|dbj|BAC12106.1| tRNA pseudouridine synthase A [Oceanobacillus iheyensis HTE831]
          Length = 253

 Score =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 130/249 (52%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+GS + G+Q Q +  ++QG +EKA++ +  G+ + +  +GRTD+GVHA+ 
Sbjct: 1   MERLKCTVSYDGSDFAGFQVQPDHRTVQGVLEKALYNMHKGKSIRIQASGRTDTGVHAVG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E       +ALN  L   D + I  +    ++FHAR+S   + Y Y ++  
Sbjct: 61  QVIHFDSPLEIPERNWKQALNTLL--PDDVRIQKVEKKTEEFHARYSVKEKEYHYFVLNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVN 178
           + P   ++G  +  P+ LD E M+ A Q+L G HDFT+F S       S +RT+ H   +
Sbjct: 119 EDPNVFQRGYVYHEPRKLDLERMQEACQYLEGTHDFTSFSSAKSSVKGSKVRTLYHVSCH 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  IE       FL+  +R  +  L  VG GK    D+   L +++R++ G    P+G
Sbjct: 179 QTGTNIEFIFRGSGFLYNMVRIMMSVLIDVGKGKRNPEDIIDLLASKNRQQIGKTMAPQG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLWRVSYE 247


>gi|221307961|ref|ZP_03589808.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221312282|ref|ZP_03594087.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221317216|ref|ZP_03598510.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221321479|ref|ZP_03602773.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767037|ref|NP_388029.2| tRNA pseudouridine synthase A [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|321313820|ref|YP_004206107.1| tRNA pseudouridine synthase A [Bacillus subtilis BSn5]
 gi|239938721|sp|P70973|TRUA_BACSU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225184664|emb|CAB11924.2| pseudouridylate synthase I [Bacillus subtilis subsp. subtilis str.
           168]
 gi|291482520|dbj|BAI83595.1| tRNA pseudouridine synthase A [Bacillus subtilis subsp. natto
           BEST195]
 gi|320020094|gb|ADV95080.1| tRNA pseudouridine synthase A [Bacillus subtilis BSn5]
          Length = 247

 Score =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  + + + V  +GRTDSGVHA  
Sbjct: 1   MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAERWPYALNALL--PDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ ++MR AA+HL+G HDFT+F +   +    +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFSYRLNVQDMREAAKHLIGTHDFTSFCAAKTEVQDKVRTIYELDWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK +  +++  L+A+DR+  G  AP  GL
Sbjct: 179 TADGLQMRITGSGFLYNMVRIIAGTLLDAGIGKISPDEVKSMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLWNVYYD 246


>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 =  304 bits (779), Expect = 7e-81,   Method: Composition-based stats.
 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|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 =  304 bits (779), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLAKGVTHYYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAARDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (778), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ    S+Q  +E+A+  V  E + +  AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGSRYFGWQRQAEVDSVQAQLERALSFVANEPISIQCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +N  L   D I++     VD +FHARF+A  R Y Y I   Q 
Sbjct: 61  VHFETNAVRKESAWTLGVNVNL--PDDIAVRWAKDVDDEFHARFTATARRYRYMIYNHQF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +      P  +D   M  AAQ L+G  DFT+FR+I CQ+++P R +   +V   G
Sbjct: 119 RPGILRSGVSHYPGQIDEAKMHEAAQFLLGEQDFTSFRAIQCQSNTPFRCVHEVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VGSL  VG G+   + +++ L  +DR +    A P GLY 
Sbjct: 179 MYICVDIKANAFLHHMVRNIVGSLLEVGYGRQPVSWIKELLALKDRTQAAATAKPNGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  304 bits (778), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHHQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (778), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 83/244 (34%), Positives = 134/244 (54%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              ++IEY+G+ Y GWQRQ N  SIQ  +E+AI   T     V G+ RTD+GVHA   V 
Sbjct: 6   NIKLVIEYDGTNYCGWQRQDNAESIQQKVEEAIERATKVFSKVTGSSRTDAGVHAEGFVC 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F       P    +ALN +L   + I I+    VDK+FH+RF++I + Y+Y ++T    
Sbjct: 66  NFFTESSIPPENFKEALNVFL--PEDIVIIESKEVDKEFHSRFNSIGKKYVYTVLTGSHR 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+ +   +   K+L+   M+ AA++ +G HDF+ F+       + IRTI   +++  GN
Sbjct: 124 PAIRRNYVYYFNKNLNIGQMKEAAKYFLGTHDFSAFKKSGSSVKTSIRTIKELNIDIDGN 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I+  ++   FL+  +R  VG+L  VG  ++   D++K + +++R   G  AP  GL  +
Sbjct: 184 YIKFSIIGDGFLYNMVRIIVGTLLDVGTNRFNPEDIDKIISSKNRSNAGKSAPACGLTLE 243

Query: 243 SVEY 246
            V Y
Sbjct: 244 KVFY 247


>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 =  304 bits (778), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (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 L   D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNAIRNEGAWTLGVNANL--PDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 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 =  304 bits (778), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ YFGWQRQ++  S+Q  +EKA+ ++    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYFGWQRQRDVISVQEKLEKALSIIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          NA L     I++    +V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERNMAAWTMGANANL--PKDIAVRWAKVVADDFHARFSATARRYRYVIYNHAY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M++A Q+L+G +DFT+FR++HCQ+ SP R I H +V+   
Sbjct: 119 RPGILSSGVSHYHPELDVQRMQLAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVSRHE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  VG G+     +E  L A+DRK     A  EGLY 
Sbjct: 179 RYVVVDIKANAFVHHMVRNIVGSLIEVGRGEKEPQWIEWLLAAKDRKLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 239 VAVDYP 244


>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 =  304 bits (778), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+       V     +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTALRKDVAWTLGVNANL--PGDIAVRWVKAVADDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         K LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G 
Sbjct: 129 PAVLAKGVTHYYKPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHISVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (778), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|320174675|gb|EFW49808.1| tRNA pseudouridine synthase A [Shigella dysenteriae CDC 74-1112]
          Length = 270

 Score =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTVPRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 131/247 (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  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D ++ W    +  ALNAYL+   + 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|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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (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 L   D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNAIRNEGAWTLGVNANL--PDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQ    ++Q  +E+A+  V  + + VH AGRTD+GVH   QV
Sbjct: 15  MRVALGIEYDGSKYYGWQRQLEVDTVQAQLERALSKVANQPITVHCAGRTDAGVHGTGQV 74

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +N  L   D I++  + +VD  FHARFSA  R Y Y I     
Sbjct: 75  VHFETTAIRKESAWTLGVNVNL--PDDIAVKWVKLVDDDFHARFSATARRYRYLIYNYHL 132

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         LD   M  AAQH VG HDFT+FR++HCQ+ SP R +   +V   G
Sbjct: 133 RPGILRSGVSHYRGQLDENKMHQAAQHFVGEHDFTSFRALHCQSKSPFRHVHEVNVTRQG 192

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G      + + L  +DR +  P A P GLY 
Sbjct: 193 MYLCVDIKANAFLHHMVRNIVGSLIEIGQGHQQGDWIVELLALKDRSKAAPTAKPNGLYM 252

Query: 242 DSVEYS 247
             V Y 
Sbjct: 253 VDVTYP 258


>gi|317131990|ref|YP_004091304.1| tRNA pseudouridine synthase A [Ethanoligenens harbinense YUAN-3]
 gi|315469969|gb|ADU26573.1| tRNA pseudouridine synthase A [Ethanoligenens harbinense YUAN-3]
          Length = 252

 Score =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 124/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++ ++G+ Y GWQ QKNG ++Q  ++ A+  V      V G  RTD+GVHAL  
Sbjct: 1   MRNILLLLRFDGAAYHGWQVQKNGVTVQEVLQNALETVLRHRPPVTGCSRTDAGVHALAY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             +F          L +ALNA L   D I++     V   FHAR+SA  + Y+YRI+   
Sbjct: 61  ACNFRTEHTIPCQNLVRALNACL--PDDIAVFACREVPPDFHARYSAHEKEYVYRILNAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A     +GRA  +P  LD   M  AA+  +G HDF  FR+        +RT+ H  V   
Sbjct: 119 ARDPFWRGRALHVPYPLDEAVMDKAARGFLGTHDFAGFRAAGSDVKDTVRTVFHSGVQRD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+  RV A  FL+  +R  VG+L      K    D+   + ++DR   GP AP  GLY
Sbjct: 179 GDLVLFRVRADGFLYNMVRIMVGTLLYTAQDKLQPADILAVIDSRDRTAAGPTAPAHGLY 238

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 239 LNRVFYD 245


>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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLAKGVTHYYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAARDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|324015393|gb|EGB84612.1| tRNA pseudouridine synthase A [Escherichia coli MS 60-1]
          Length = 270

 Score =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSRYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A          + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAGLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (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 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>gi|208779289|ref|ZP_03246635.1| tRNA pseudouridine synthase A [Francisella novicida FTG]
 gi|208745089|gb|EDZ91387.1| tRNA pseudouridine synthase A [Francisella novicida FTG]
          Length = 258

 Score =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    E       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSDAERPLSAWQRGVNALL--PQDIKILAVQQVDNDFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD   M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIYKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 126/246 (51%), Positives = 160/246 (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  VAHLDLSKDWPAETVKNALNFH-AQPDPVAILDCEKAGLGFDARFSAIRRHYRYKIANRL 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|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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 98/247 (39%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD              N +L     IS+L    VD  F ARFSA  R Y Y I+ R 
Sbjct: 61  VIHFDTESVRTARSWVLGGNTHL--PPEISLLWAKEVDADFSARFSARSRRYRYVILNRW 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   +       LD E M  A Q L+G  DFT+FR++ CQA SP+RT+    V   
Sbjct: 119 VRPGVLHRKVSWHHPPLDAERMHAAGQRLLGEWDFTSFRAVGCQAKSPVRTLLSLSVTRR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + V A +FLH  +R+  G L  VG+G+     + + L A+DR   G  APP GLY
Sbjct: 179 GDFIYLDVHANAFLHHMVRNIAGVLMAVGEGERPVEWVSEVLHARDRTLGGVTAPPHGLY 238

Query: 241 FDSVEYS 247
              VEY 
Sbjct: 239 LVHVEYE 245


>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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETRAQRKDAAWTLGVNANL--PGDIAVRWVKHVPADFHARFSATARRYRYVIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G 
Sbjct: 129 PAVLSHGVTHFHQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 133/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++Y+G+ + GWQ Q +G+++Q  +E+A+       V    AGRTD+GVH L Q
Sbjct: 1   MKRIALGVQYDGTAFCGWQSQPHGNTVQDELERALREFAQTPVHTVVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E   V   +  N++L    TIS+     + + FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELERADVSWVRGTNSFL--PKTISVQWAKPMPEAFHARFSAFERTYYYVLYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  +  +LD + M  AA HL+G HDF+ FRS  CQ+ +P++ +   D+   
Sbjct: 119 VRSPMLAGRAGWVHAALDIDAMHAAAAHLIGEHDFSAFRSSQCQSKTPVKHLYQIDIQQH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +  R  A +FLH  +R+ +G L  +G G+     + + L  +DR+   P   P+GLY
Sbjct: 179 GDFVHFRFRANAFLHHMVRNVMGCLVYIGKGRRPVQWMAEVLAGRDREWAAPTFMPDGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 245


>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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 2/247 (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  VVHFDTELERADISWVRGTNSFL--PKTVSVQWAKPMPEAFHARFSAFERTYYYVLYVHP 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 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 245


>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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETRAQRKDAAWTLGVNANL--PGDIAVRWVKHVPADFHARFSATARRYRYVIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G 
Sbjct: 129 PAVLSHGVTHFHQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>gi|328676060|gb|AEB28735.1| tRNA pseudouridine synthase A [Francisella cf. novicida 3523]
          Length = 258

 Score =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 127/247 (51%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  SIQ  +EKA+  +    + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSIQAELEKALSKIANRNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +       +  NA L     I IL    V+  F++RF+AI R+Y Y I    
Sbjct: 61  VVNFHSDADRPLSAWQRGANALL--PHDIKILAAQEVNDDFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKLVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 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|52078642|ref|YP_077433.1| tRNA pseudouridine synthase A [Bacillus licheniformis ATCC 14580]
 gi|52784004|ref|YP_089833.1| tRNA pseudouridine synthase A [Bacillus licheniformis ATCC 14580]
 gi|319649083|ref|ZP_08003291.1| tRNA pseudouridine synthase A [Bacillus sp. BT1B_CT2]
 gi|62901269|sp|Q65P74|TRUA_BACLD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52001853|gb|AAU21795.1| pseudouridylate synthase I [Bacillus licheniformis ATCC 14580]
 gi|52346506|gb|AAU39140.1| TruA [Bacillus licheniformis ATCC 14580]
 gi|317388783|gb|EFV69602.1| tRNA pseudouridine synthase A [Bacillus sp. BT1B_CT2]
          Length = 247

 Score =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 90/248 (36%), Positives = 136/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  ++G+Q Q    +IQ  +EKA+  +    E + V  +GRTDSGVHA+ 
Sbjct: 1   MRMKCTISYDGHLFYGYQVQPGQRTIQDELEKALQTLHKAKERIPVVSSGRTDSGVHAVG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD            ALNA L   D IS+     V+ QFHARFSA R+ Y Y I   
Sbjct: 61  QTIHFDSPLSIPEAKWPYALNALL--PDDISVRKAEAVNDQFHARFSAKRKEYRYMIYRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+ +P  LD E ++ A+++LVG HDFT+F +   +    +RT+   + + 
Sbjct: 119 RHPDVFKRYYAYHVPYDLDMEKVKEASRYLVGTHDFTSFCATKTEVKDKVRTVHELEWSD 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +++R+V   FL+  +R   G+L  VG GK++  D+EK + A++R   G  AP  GL
Sbjct: 179 TGDGLQMRIVGSGFLYNMVRIIAGTLLDVGTGKFSPGDIEKMILAKNRDAAGRTAPAHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 239 YLWRVIYD 246


>gi|283796516|ref|ZP_06345669.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
 gi|291075930|gb|EFE13294.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
 gi|295092580|emb|CBK78687.1| pseudouridylate synthase I [Clostridium cf. saccharolyticum K10]
          Length = 368

 Score =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + +A+  +  E + V GA RTDSGVHA+  
Sbjct: 1   MKRIRLTVAYDGTNYCGWQLQPNGITIEEVLNRALSELLKEEIQVVGASRTDSGVHAMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD      P  +C ALN  L   + + +     V   FH R +   ++Y Y+I+ R+
Sbjct: 61  IAVFDTESRIPPEKICFALNQRL--PEDVRVQKSEEVPLTFHPRKANCVKTYEYKILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             + L +         LD E MR AA  LVG HDF +F ++  QA   +RTI    V+  
Sbjct: 119 IDMPLNRLYCHFCYFDLDVEKMRRAAAFLVGEHDFKSFCTVRTQAEETVRTIYSLTVDRG 178

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IR+    FL+  +R   G+L  +G G W    +E+ L+A+DR   GP  P +GL
Sbjct: 179 ADDVIVIRISGSGFLYNMVRIITGTLVKIGMGVWPPEYMEEILEARDRAAAGPTIPAKGL 238

Query: 240 YFDSVEYS 247
              S+EY 
Sbjct: 239 TLVSMEYE 246


>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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ    ++Q  +EKA+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGSQYFGWQRQAEVDTVQERLEKALSIVANEPIAVQCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +N  L   D I++  + +VD +FHARF+A  R Y Y I   Q 
Sbjct: 61  VHFETNAVRKDTAWTLGVNVNL--PDNIAVRWVKVVDDEFHARFTATARRYRYMIYNHQL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +      P  +D   M  AAQ+L+G  DFT+FR++ CQ+++P R +   +V+  G
Sbjct: 119 RPGILRSGVSHYPGVIDEAKMHQAAQYLLGEQDFTSFRAVQCQSNTPFRCVHEVNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VGSL  VG G      +E+ L  +DR +    A P GLY 
Sbjct: 179 MYICVDIKANAFLHHMVRNIVGSLLEVGLGNQPIEWIEQLLALKDRNKAAATAKPNGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 98/246 (39%), Positives = 142/246 (57%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSGY GWQ Q +  +IQ +++ A+  + GE + +  AGRTD+GVHAL QV
Sbjct: 1   MRIALGIEYDGSGYNGWQSQPDVPNIQDTLQAALSRIAGENISIIAAGRTDTGVHALEQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           +  NA L     +++L    V  +FHARFSA  RSY Y +I R +
Sbjct: 61  VHFDTGIVRPLASWVRGTNALL--PKDVAVLWAHPVADEFHARFSAQARSYQYVLINRPS 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G+       LD E MR+AAQ+L+G HDF+ FRS  CQA +P++T+   D+   G
Sbjct: 119 RSAVHHGKVGWFHLPLDVEAMRMAAQNLLGEHDFSAFRSSQCQAKTPVKTLAQLDIVQQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I   + A +FLH  +R+ VG L  VG GK+    + + LQ ++RK   P   P+GLY 
Sbjct: 179 DIIIFNLTANAFLHHMVRNIVGCLLYVGKGKYPPQWMHELLQGRERKLAAPTFAPDGLYL 238

Query: 242 DSVEYS 247
             + Y 
Sbjct: 239 CHITYD 244


>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 =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 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|255284006|ref|ZP_05348561.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
 gi|255265459|gb|EET58664.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
          Length = 245

 Score =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q N  +I+  +   +  + GE + V GA RTD+GVHAL  
Sbjct: 1   MKRVKLIVAYDGTNYSGWQIQPNAVTIESMLNLHLSELLGEPIRVIGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  A+N  L     I I +   V   FH RF    ++Y YRI+ R+
Sbjct: 61  VAVFDTSARMPAEKISYAMNTRL--PQDIRIQDSCEVAADFHPRFCKTIKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +      LD ENMR A  +LVG HDF +  +   +  + +RTI   D+   
Sbjct: 119 FPDPTRRLYSLFYYYPLDVENMRRALAYLVGEHDFKSLCTHKEEVENTVRTIYEADIQKD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IR+    FL+  +R  VG+L  VG G +    +++ L A++R+  G  APP+GL 
Sbjct: 179 GDMISIRISGNGFLYNMVRIIVGTLLRVGSGYYPPEYMQELLAAKNRQAAGETAPPQGLT 238

Query: 241 FDSVEY 246
              + Y
Sbjct: 239 LLEIRY 244


>gi|209764794|gb|ACI80709.1| pseudouridylate synthase I [Escherichia coli]
          Length = 270

 Score =  303 bits (777), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNYRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 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|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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

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  VHFDTKAIRSEKAWTFGLNANL--PADIAVRWAKVVSEDFHARFSATARRYRYLIYNHPL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL          +LD   M  A Q+L+G HDF++FR+  CQ+++P R I H  V    
Sbjct: 119 RSALFPTGVTHHHVALDHRLMHQAGQYLLGEHDFSSFRAAQCQSNTPWRNIHHLHVFRQA 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  +G GK     ++  L  +DR    P A P+GLY 
Sbjct: 179 NYIIVDIQANAFVHHMVRNIVGSLLEIGSGKQPVEWMDWLLTQKDRTLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVKYP 244


>gi|194017442|ref|ZP_03056053.1| tRNA pseudouridine synthase A [Bacillus pumilus ATCC 7061]
 gi|194010714|gb|EDW20285.1| tRNA pseudouridine synthase A [Bacillus pumilus ATCC 7061]
          Length = 247

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 128/248 (51%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
           ++    + Y+G+ + G+Q Q    ++Q  IE A+  +    E++ +  +GRTDSGVHA  
Sbjct: 1   MKVKCTVSYDGTHFKGYQVQPGQRTVQTEIESALARMHKQDELIPIVASGRTDSGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L   D I +L    VD+ FHARFS + + Y Y++ T 
Sbjct: 61  QVIHFDTPLSIPMERWPFALNSLL--PDDIRVLKAEEVDESFHARFSVVSKEYRYKVSTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  A   P  LD + MR AA HL+G HDFT+F + + +    +R I   +  +
Sbjct: 119 THQNVFTRQYACHFPYRLDADKMREAAGHLIGTHDFTSFCAANTEVQDKVREIYTLEWKN 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +E+RV    FL+  +R   G+L  +G GK+   +++  L A++R+  G  AP  GL
Sbjct: 179 VSDGLEMRVRGNGFLYNMVRIIAGTLLEIGSGKFHPEEIKAMLAARNREAAGKTAPSHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 239 YLWEVFYD 246


>gi|291524335|emb|CBK89922.1| pseudouridylate synthase I [Eubacterium rectale DSM 17629]
 gi|291527615|emb|CBK93201.1| pseudouridylate synthase I [Eubacterium rectale M104/1]
          Length = 244

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  MI+ Y+G+ Y GWQ Q NG +I+  + + +  +  E + V GA RTD+GVH+L  V
Sbjct: 1   MRVKMIVAYDGTNYCGWQIQPNGITIEQVLNEHLSRLLKEDIKVTGASRTDAGVHSLGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD         +  ALN  L   + I +++   V   FH RFS  R++Y YRI+  + 
Sbjct: 61  CMFDTNTRMPAEKISYALNQKL--PEDIVVVDSCEVSDDFHPRFSKSRKTYEYRILNARF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   +     LD E M  AA++L+G HDF +F S + QA + +RTI    V+  G
Sbjct: 119 RNPTRRLDTYFYHYPLDTEKMSEAAKYLIGEHDFASFCSANSQAQTTVRTIYDCTVSKAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IRV    FL+  +R   G+L  +G     +  ++  + A DR   GP AP  GL  
Sbjct: 179 DIITIRVTGNGFLYNMVRIIAGTLVKIGGSDMPADAMKDIIAATDRAAAGPTAPAHGLTM 238

Query: 242 DSVEYS 247
             ++Y 
Sbjct: 239 IGLKYE 244


>gi|261417639|ref|YP_003251321.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC61]
 gi|319765297|ref|YP_004130798.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC52]
 gi|261374096|gb|ACX76839.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC61]
 gi|317110163|gb|ADU92655.1| tRNA pseudouridine synthase A [Geobacillus sp. Y412MC52]
          Length = 258

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 88/245 (35%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           R   II Y+G+ + G+Q Q    ++QG +E+ +  +  G+ V V  +GRTD+GVHA  QV
Sbjct: 4   RIKCIIAYDGTHFSGYQIQPGKRTVQGELEEVLRRMHKGKGVRVAASGRTDAGVHAYGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           KALNA L   D I +  +   D  FHARFSA  + Y Y++ T   
Sbjct: 64  IHFDTSLSLSSEQWKKALNAQL--PDDIVVRFVQEADADFHARFSAKAKEYRYKVWTAAE 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +      P  L  + M  A +   G HDFT+F S        +RTI    V   G
Sbjct: 122 RDVFRRHYCAWHPYPLHMDAMNEALRLFCGTHDFTSFCSAKTTIEDRVRTIYRAKVKVDG 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++E R V   FL+  +R  VG++  +G GK +  D+   L A+DR+  GP AP EGLY 
Sbjct: 182 PMLEFRFVGSGFLYNMVRIMVGTVLEIGQGKRSPADISTLLAAKDRRLAGPTAPAEGLYL 241

Query: 242 DSVEY 246
             V Y
Sbjct: 242 WRVYY 246


>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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETRAQRKDAAWTLGVNANL--PGDIAVRWVKHVPADFHARFSATARRYRYVIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G 
Sbjct: 129 PAVLSQGVTHFHQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (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  VHFETTAQRKDAAWTLGVNANL--PADIAVRWVKSVPDDFHARFSATARRYRYVIYNRRL 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 DSVEYS 247
            +V+Y 
Sbjct: 249 VAVDYP 254


>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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 5   KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 65  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLR 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 123 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 183 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 242

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 243 AVDYP 247


>gi|197117301|ref|YP_002137728.1| tRNA pseudouridine synthase A [Geobacter bemidjiensis Bem]
 gi|238690881|sp|B5EFM8|TRUA_GEOBB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|197086661|gb|ACH37932.1| tRNA pseudouridines 38,39,40 synthase [Geobacter bemidjiensis Bem]
          Length = 250

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ Y GWQ Q NG ++Q  +++A+  + GE   +HG+GRTD+GVHA   
Sbjct: 1   MRNIKLIIEYDGTAYCGWQVQPNGRTVQEVLQEALAAMLGEKTPLHGSGRTDAGVHARGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   +        + LN  L     I++     V  +FH RF A  + Y Y I+   
Sbjct: 61  VACFKTDKAMPLRAFREGLNCLL--PGDIAVREACEVPLEFHPRFDAHAKHYRYTILLDD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +   W +   LD + MR A    VG HDF  FR+ +C A + +R I   D+   
Sbjct: 119 LRSPLSRLTVWRLKGKLDIQAMRAACAAFVGEHDFAAFRASNCAAKTTVRRIYSMDLVQE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE-CGPLAPPEGL 239
           G L+ + V    FL   +R   G+L  VG GK +  D+ + LQ  DR++  G   PP+GL
Sbjct: 179 GCLLHLDVKGSGFLKNMVRIITGTLIEVGQGKKSVEDVARLLQGGDRQQNSGMTVPPQGL 238

Query: 240 YFDSVEY 246
               V Y
Sbjct: 239 CLMQVYY 245


>gi|251799612|ref|YP_003014343.1| tRNA pseudouridine synthase A [Paenibacillus sp. JDR-2]
 gi|247547238|gb|ACT04257.1| tRNA pseudouridine synthase A [Paenibacillus sp. JDR-2]
          Length = 246

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 124/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      + Y+G+ + G+Q Q  G +IQ  IE AI  +TGE +++ G+GRTD+GVHA  Q
Sbjct: 1   MRNIAATVSYDGTDFNGFQSQPYGRTIQQEIELAIKKLTGEDIIILGSGRTDAGVHANGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F             ALN  L     I IL    V + FH+R SA R++Y Y I   +
Sbjct: 61  VFNFLTESTIPAERWAIALNTRL--PKDIVILEAHEVPEAFHSRRSAKRKTYRYTIDMGK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  A+  P  L+ E M+     LVG HDFT+F SIH      +RTI    +   
Sbjct: 119 FPDVFYRRYAFHHPTPLNVEAMQKGLSFLVGEHDFTSFTSIHSTKPHHVRTIYEAYLERE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G ++ + +    FL+  IR  +G+L  VG GK    D+ + L+ + R   GP A P GL 
Sbjct: 179 GQMLHMYMTGNGFLYNMIRIVMGTLLHVGHGKLKPEDMARILEGRKRSLAGPTAMPHGLM 238

Query: 241 FDSVEYS 247
              VEY 
Sbjct: 239 LMKVEYP 245


>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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 109/247 (44%), Positives = 155/247 (62%), Gaps = 1/247 (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 FDSVEYS 247
              V Y 
Sbjct: 240 LTGVAYD 246


>gi|134301921|ref|YP_001121890.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|166228700|sp|A4IXW8|TRUA_FRATW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|134049698|gb|ABO46769.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           tularensis WY96-3418]
          Length = 258

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 131/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q S+EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQESLEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVMRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|15896350|ref|NP_349699.1| tRNA pseudouridine synthase A [Clostridium acetobutylicum ATCC 824]
 gi|30913407|sp|Q97EL1|TRUA_CLOAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|15026164|gb|AAK81039.1|AE007806_12 Pseudouridylate synthase, TRUA [Clostridium acetobutylicum ATCC
           824]
 gi|325510506|gb|ADZ22142.1| tRNA pseudouridine synthase A [Clostridium acetobutylicum EA 2018]
          Length = 244

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + +EY+G+ Y GWQ+QKN  ++Q  +EK I  +TGE + V G  RTDSGVHA   
Sbjct: 1   MKNVKLTLEYDGTNYCGWQKQKNVVTVQEEVEKIIGEITGEKIDVIGCSRTDSGVHAKAY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             +F       P      LN+ L   D I  LN   V   FH+RF    ++Y Y I+ R 
Sbjct: 61  TCNFKTNTVIPPEKFYLVLNSVL--PDDIVALNSEEVPMDFHSRFDNKGKTYSYTILNRL 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+++   +     L+C+ MR A ++++G HDFT+F+S   +  S IRTI    +   
Sbjct: 119 QRAAIDRNYVYQYGHKLNCDLMREATKYILGTHDFTSFKSTGSKVKSNIRTIYEARIVED 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N +   V    FL+  +R  VG+L  VG+ K T  +++  ++++DR + G + P +GL 
Sbjct: 179 ENKVIFYVTGDGFLYNMVRIIVGTLLEVGEEKITPLNVKTIVESKDRTKAGRVVPAKGLC 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVMY 244


>gi|89256403|ref|YP_513765.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314847|ref|YP_763570.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica OSU18]
 gi|167010425|ref|ZP_02275356.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367741|ref|ZP_04983762.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica 257]
 gi|122325138|sp|Q0BLV1|TRUA_FRATO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122999741|sp|Q2A3D7|TRUA_FRATH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|89144234|emb|CAJ79507.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129746|gb|ABI82933.1| tRNA-pseudouridine synthase I [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253552|gb|EBA52646.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica 257]
          Length = 258

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSLSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F            + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNAYRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>gi|297521911|ref|ZP_06940297.1| tRNA pseudouridine synthase A [Escherichia coli OP50]
          Length = 259

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 5   KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 65  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 123 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 183 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 242

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 243 AVDYP 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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA L   D I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETQAIRPLQSWCFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYIIFNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+          +LD + M +A Q L+G +DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILPKGVSHYHYALDHQKMHVAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLNVSRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ V SL  VG G+     ++  L  +DR    P A  EGLY 
Sbjct: 179 NYIVVDIQANAFVHHMVRNIVESLIEVGQGRQPVEWIQWLLAQRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVHYP 244


>gi|301156483|emb|CBW15954.1| pseudouridylate synthase I [Haemophilus parainfluenzae T3T1]
          Length = 264

 Score =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y GWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYNGKQYCGWQRQEKVRSVQEELEKALSFVANEKIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA L   D IS+    +VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETTAVRPEKAWAFGTNANL--PDDISVSWAKVVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+++P R + H +V   G
Sbjct: 119 RSAILPEGITHCHLDLDEKKMHQAGQFLLGENDFSSFRAAQCQSNTPWRNVHHLNVVRKG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  VG G      ++  L+ +DRK   P A PEGLY 
Sbjct: 179 QFVIVDIQANAFVHHMVRNIVGSLIEVGAGNQPVEWMKWLLEQKDRKLAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVIYP 244


>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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E V V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPVTVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   E         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETRAERKDAAWTLGVNANL--PGDIAVRWVKYVADDFHARFSATARRYRYVIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD   M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G 
Sbjct: 129 PAVLSQGVTHYHQPLDAARMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVERYGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAGNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 249 SVDYP 253


>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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 131/247 (53%), Gaps = 2/247 (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  VVHFDTELDRVDISWVRGPNAFL--PKTIGVQWAKPMPDDFHARFSAFERTYYYVLYVSP 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 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 245


>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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG        + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPERWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|187931655|ref|YP_001891639.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|238691562|sp|B2SGK2|TRUA_FRATM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|187712564|gb|ACD30861.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 258

 Score =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+ +DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEVKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 91/251 (36%), Positives = 140/251 (55%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + H D      P    +  NA+L    T+++     V + FHARFSA RR+Y Y +++  
Sbjct: 61  IVHLDTDLVREPFSWVRGTNAFL--PPTVAVRWAQAVPEDFHARFSAHRRTYYYALVSGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L  G+A  +     +SLD   M+ AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRSPLLGGKAGYVMLPPGQSLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKTLYSAE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+   +FLH  +R+ +G L  +G G+  +  + + L A+DRK   P   P
Sbjct: 179 VRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRRPAAWMAEVLAARDRKAAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E V V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPVSVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETHAVRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V  FG 
Sbjct: 129 PAVLGKGVTHYYEPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVERFGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

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  VHFDTKAIRSEKAWTFGLNANL--PADIAVRWAKVVSEDFHARFSATARRYRYLIYNHPL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL          +LD   M  A Q+L+G HDF++FR+  CQ+++P R I H  V    
Sbjct: 119 RSALFPTGVTHHHVALDHHLMHQAGQYLLGEHDFSSFRAAQCQSNTPWRNIHHLHVFRQA 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I + + A +F+H  +R+ VGSL  +G GK     ++  L  +DR    P A P+GLY 
Sbjct: 179 NYIIVDIQANAFVHHMVRNIVGSLLEIGSGKQPVEWMDWLLTQKDRTLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVKYP 244


>gi|308050321|ref|YP_003913887.1| tRNA pseudouridine synthase A [Ferrimonas balearica DSM 9799]
 gi|307632511|gb|ADN76813.1| tRNA pseudouridine synthase A [Ferrimonas balearica DSM 9799]
          Length = 263

 Score =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 124/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G GYFGWQRQ+    +Q  +E AI  V    V V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGHGYFGWQRQREVVGVQERLEAAIAKVANHPVEVACAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P      LNA L   D I++     V   FHARFSA  R Y Y I   + 
Sbjct: 61  VHFDAQFDRRPAAWTLGLNANL--PDGIAVRWAQPVSDDFHARFSATARRYRYIIFNNRL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         LD   M  A Q L+G +DF+ FR+I CQ+ +P R I H  V   G
Sbjct: 119 RPGILRHGVSHYHHPLDEALMHQAGQQLLGENDFSAFRAIQCQSRTPWRNIHHLRVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G      + + L+ +DR      A  EGLY 
Sbjct: 179 QYVIIDIKANAFVHHMVRNIAGSLMEVGMGNRPVEWIAELLEGKDRNLAAATAKAEGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  302 bits (775), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG        + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPECWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  302 bits (774), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 127/246 (51%), Gaps = 2/246 (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 L   D+++I     VD  FHAR+SA  R Y Y I   + 
Sbjct: 61  VHFDTDVQRPMTAWTQGVNANL--PDSVAIRWAKEVDDSFHARYSATARRYRYVIYNHKL 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


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

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 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|323161584|gb|EFZ47470.1| tRNA pseudouridine synthase A [Escherichia coli E128010]
          Length = 270

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG        + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPECWIAELLAAKDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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  VHFETNAVRPEKAWAFGTNANL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G HDF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGMTHCHLDLDAEKMHQAGQCLLGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 98/249 (39%), Positives = 141/249 (56%), Gaps = 5/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +++EY+G+ Y GWQRQ N  +IQ  +E++I  +T E V++HG+GRTD+GVHAL
Sbjct: 13  MTRRNIKLVLEYDGTAYRGWQRQGNLPTIQKILEESIARITQEPVILHGSGRTDAGVHAL 72

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVA+F          L + LN+ L     I I     VD++FH+R+SA  +SYLYRI+ 
Sbjct: 73  NQVANFRTSSRIPAANLLRGLNSLL--PGDIVIRETEDVDEEFHSRYSAKSKSYLYRILN 130

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 L++  AW I   LD E M  A   L G+HDFT+F +      S +RTI   ++ 
Sbjct: 131 SPVRSPLQRNSAWFIRCCLDLEKMAGAISLLCGKHDFTSFCAAGSDVKSCVRTIIRAEIE 190

Query: 179 SF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                +I I V A  FL   +R+ VG+L  +G G+ +S  +   L+A+DR   G  APP+
Sbjct: 191 RETEQVITISVEADGFLRHMVRNIVGTLVEIGAGQDSSEIMRDILEAKDRGCAGITAPPQ 250

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 251 GLFLQKVSY 259


>gi|253701944|ref|YP_003023133.1| tRNA pseudouridine synthase A [Geobacter sp. M21]
 gi|259550393|sp|C6E4S9|TRUA_GEOSM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|251776794|gb|ACT19375.1| tRNA pseudouridine synthase A [Geobacter sp. M21]
          Length = 247

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 125/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ Y GWQ Q NG ++Q ++E+A+  + G    +HG+GRTD+GVHA   
Sbjct: 1   MRNIKLIIEYDGTAYCGWQVQPNGRTVQEALEEALASMLGGKTALHGSGRTDAGVHARGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   +        + LN  L     I++     V  +FH RF A+ + Y Y ++   
Sbjct: 61  VACFQTDKGMPLRAFREGLNCLL--PADIAVREACEVPLEFHPRFDALAKHYRYTMLLDD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +  AW +   LD + MR A    VG HDF  FR+ +C A + +R I   D+   
Sbjct: 119 LRSPLSRLTAWRLKGKLDVDAMRSACAAFVGEHDFAAFRASNCAAKTTVRRIYSMDLVQE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE-CGPLAPPEGL 239
           G  + + V    FL   +R   G+L  VG GK +  D+ + L+  DR++  G   PP+GL
Sbjct: 179 GPFLHLDVKGSGFLKNMVRIITGTLIEVGQGKKSVEDVARLLKGSDRQQNSGMTVPPQGL 238

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 239 CLMQVYYP 246


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EYNG  YFGWQRQ+   S+Q  +EKA+  V  E + +  AGRTDSGVH   QV
Sbjct: 1   MKIALGVEYNGKRYFGWQRQEKVLSVQEELEKALSFVANEKIDLFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA L   D I++      D +FHARFSA  R Y Y I T   
Sbjct: 61  VHFETEVVRPERAWAFGTNANL--PDDIAVKWAKTADDEFHARFSATARRYRYLIYTNPL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M  A Q L+G +DF++FR+  CQ+ +P R + H  V   G
Sbjct: 119 RSAVLPEGVTHCHLPLDHEKMHEAGQFLLGENDFSSFRAAQCQSKTPWRNVHHLQVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G+     ++  L+ ++RK   P A P+GLY 
Sbjct: 179 RYIVVDIQANAFVHHMVRNIVGSLMEVGSGRQPVEWMKWLLEQRNRKLAAPTAKPQGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VRVTYP 244


>gi|227543592|ref|ZP_03973641.1| tRNA pseudouridine synthase A [Lactobacillus reuteri CF48-3A]
 gi|300909379|ref|ZP_07126840.1| tRNA-pseudouridine synthase I [Lactobacillus reuteri SD2112]
 gi|227186432|gb|EEI66503.1| tRNA pseudouridine synthase A [Lactobacillus reuteri CF48-3A]
 gi|300893244|gb|EFK86603.1| tRNA-pseudouridine synthase I [Lactobacillus reuteri SD2112]
          Length = 256

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 130/251 (51%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY +   Y+G+ + G+Q Q N  +++ +++ A+  +       + V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGTNFSGFQIQPNKRTVEQTLKNAVNKIAKHPNPAIPVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD+        + KALN+ L     I I    +VD  FHAR+SA R++Y YR+ 
Sbjct: 61  LNQVAHFDIPYHLSNESMRKALNSIL--PLDILIKKAELVDNDFHARYSAHRKTYRYRVD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         L+ E MR AA  LVG HDFT+F +   QA S +RTI+   +
Sbjct: 119 QGEFVNPFKRNYTSHFKYPLNLEKMRKAANDLVGTHDFTSFVASGSQAKSNVRTIESITI 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 N +        FL+ Q+R  V  L  +G  +    D+ + L+A+DR      AP
Sbjct: 179 KRDELRNEVVFDFTGNGFLYNQVRIMVAFLLEIGSNQRPVDDVSRVLEAKDRTLARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  +V+Y
Sbjct: 239 ASGLYLVNVDY 249


>gi|205372037|ref|ZP_03224854.1| tRNA pseudouridine synthase A [Bacillus coahuilensis m4-4]
          Length = 251

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 134/247 (54%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R    ++Y+G+ Y G+Q Q N  +IQG IEK +  + G+ + +  +GRTD+GVHA+ Q
Sbjct: 4   MRRIKCTVQYDGTWYAGYQVQPNSKTIQGEIEKVLEKIHGKPIRISASGRTDAGVHAIGQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   ++         N+ L   + I ++++  V   FH+RF +I + Y Y++    
Sbjct: 64  VFHFDTDTKFPVEKWLPIFNSQL--PNDIVVIHVEEVAGSFHSRFGSIEKEYRYKVYRAP 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    A+ +P SL  + M  A+++L+G HDFT+F S   +    +RTI    +   
Sbjct: 122 HKSPFLIHHAYHVPHSLSVQKMEEASRYLLGTHDFTSFCSAKTEVEDKVRTIFTISIEEE 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N++   +V   FL+  +R  +G L  VG GK    ++++ L+A+DR+  G  AP +GLY
Sbjct: 182 ENMLTFSLVGNGFLYNMVRIIIGVLIEVGQGKRAPIEVKEILEAKDRRAGGKTAPAQGLY 241

Query: 241 FDSVEYS 247
              V+YS
Sbjct: 242 LYRVKYS 248


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 129/246 (52%), Positives = 165/246 (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  VAHVDLERRWPPETVRNALNFHLR-PAPMVILACEEVDETFDARFSAKARHYLYRIVTRR 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|312109293|ref|YP_003987609.1| tRNA pseudouridine synthase A [Geobacillus sp. Y4.1MC1]
 gi|311214394|gb|ADP72998.1| tRNA pseudouridine synthase A [Geobacillus sp. Y4.1MC1]
          Length = 248

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 127/246 (51%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           R    + Y+G+ +FG+Q Q    ++QG +E+A+  +  G+ + V  +GRTD+GVHA  QV
Sbjct: 4   RIKCTLSYDGTHFFGYQIQPGKRTVQGELEQALEQIHKGKAIRVTASGRTDAGVHAYGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P    KALNA L   D I I +       FHARFSA  + Y Y++   Q 
Sbjct: 64  IHFDTFLSLSPEQWKKALNALL--PDDIVIKDAQEAAPSFHARFSATAKEYRYKVRIAQE 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   +  P  LD E M  A + + G HDFT+F S        +RTI   D+    
Sbjct: 122 RDVFLRHYCYHYPYPLDMEAMGRALRLIEGTHDFTSFCSAKTDVDDRVRTIYKADMTVRD 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+E R +   FL+  +R  VG++  VG GK +   +  AL A+DR+  G  APP+GLY 
Sbjct: 182 DLLEFRFIGNGFLYNMVRIIVGTILEVGQGKRSVDSISSALAAKDRRFAGKTAPPQGLYL 241

Query: 242 DSVEYS 247
             V Y 
Sbjct: 242 WKVYYD 247


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 135/247 (54%), Gaps = 2/247 (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  VVHFDTDLDRADFSWVRGTNAFL--PPTVAVQWAKPMPDTFHARFAAFERTYYYALYVHP 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 FDSVEYS 247
              V Y 
Sbjct: 239 LAHVGYP 245


>gi|160941032|ref|ZP_02088370.1| hypothetical protein CLOBOL_05925 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435981|gb|EDP13748.1| hypothetical protein CLOBOL_05925 [Clostridium bolteae ATCC
           BAA-613]
          Length = 247

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q    +I+  + +A+  +  E + V GA RTDSGVHA   
Sbjct: 1   MKRIRLVVAYDGTQYHGWQIQPGAVTIESVLNEALTQLMREPIQVIGASRTDSGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD   +  P  +C ALN  L   + I +     V   +H R     ++Y YRI+ R+
Sbjct: 61  VAVFDTESQMPPDKICMALNQRL--PEDIRVQVSEEVPSDWHPRKCTCIKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             + +E+  +      LD + M+ AA  L G HDF +F S+  Q +  +RT+   DV   
Sbjct: 119 INMPMERLYSHFCYYKLDVDRMQAAANMLAGEHDFKSFCSVRTQVTDTVRTVYRIDVTRN 178

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IRV    FL+  +R   G+L  VG G   + D+   L+A+DR+  GP AP  GL
Sbjct: 179 ADDIITIRVTGNGFLYNMVRIIAGTLMAVGTGHIQAEDMPSILEAKDRRAAGPTAPARGL 238

Query: 240 YFDSVEYS 247
               ++Y 
Sbjct: 239 TLIEMKYE 246


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G ++Q  +E+A+       +    AGRTD+GVH L Q
Sbjct: 1   MTRIALGIQYDGAAFCGWQSQPHGKTVQDELERALREFALTPLQTVVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELDRAEFSWVRGTNAFL--PSTVAVQWAKPMPDAFHARFSAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  I   LD + MR AA  L+G HDF+ FRS  CQ+ +P++ +   D+   
Sbjct: 119 VRSPMLASRAGWIHTPLDVDAMREAAACLIGEHDFSAFRSSECQSKTPVKHLYQIDIRPQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R  A +FLH  +R+ +G L  VG G++ +  L + L  +DR    P   P+GLY
Sbjct: 179 GDFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPAAWLSEVLHGRDRNRAAPTFMPDGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 245


>gi|54114177|gb|AAV29722.1| NT02FT0202 [synthetic construct]
          Length = 258

 Score =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MI Y + I Y G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MINYLLQIGYFGKNYCGWQRQSHSPSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F    +       + +NA L     I IL +  VD  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNADRPLSAWQRGVNALL--PQDIKILAVQQVDNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 130/247 (52%), Gaps = 2/247 (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  VVHFDTELDRVDISWVRGPNAFL--PKTIGVQWAKPMPDDFHARFSAFERTYYYVLYVSP 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 FDSVEYS 247
              V Y 
Sbjct: 239 LAQVGYP 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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 124/247 (50%), Positives = 163/247 (65%), Gaps = 1/247 (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  RAHVDIEKPLTPFKLTEALNAQLR-PAPIAVIGCEVVPDDWHARFACIGRSYEYRIVNRR 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 FDSVEYS 247
           F    Y 
Sbjct: 240 FVGAVYP 246


>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 =  302 bits (774), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y GWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYNGKQYCGWQRQEKVRSVQEELEKALSFVANEKIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA L   D IS+    +VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETTAVRPEKAWAFGTNANL--PDDISVSWAKVVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+++P R + H +V   G
Sbjct: 119 RSAILPEGITHCHLDLDEKKMHQAGQFLLGENDFSSFRAAQCQSNTPWRNVHHLNVVRKG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  VG G      ++  L+ +DRK   P A PEGLY 
Sbjct: 179 QYVIVDIQANAFVHHMVRNIVGSLIEVGAGNQPVEWMKWLLEQKDRKLAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVIYP 244


>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 =  302 bits (773), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EK++  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKSLSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A   GLY 
Sbjct: 179 RYVVIDIKANAFVHHMVRNITGSLIAVGCGEQKPEWIQWLLAQKDRTLAAATAKAGGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 244


>gi|330820903|ref|YP_004349765.1| Pseudouridylate synthase [Burkholderia gladioli BSR3]
 gi|327372898|gb|AEA64253.1| Pseudouridylate synthase [Burkholderia gladioli BSR3]
          Length = 277

 Score =  302 bits (773), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q  +E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDELERALKAFALVPLQTVVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRSDFSWVRGTNAFL--PSTVAVQWAKPMPDSFHARFAAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +   RA  +   LD E MR AA+HL+G HDF++FRS  CQ+ +P++ +   D+ + G
Sbjct: 119 RSPMLASRAGWVHTPLDIEAMREAARHLIGEHDFSSFRSSECQSKTPVKHLYQIDIRASG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  + + L A++R+   P   P+GLY 
Sbjct: 179 SFIHFRFRANAFLHHMVRNLMGCLIAVGRGRYPADWMAEVLAARNRERAAPTFAPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>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 =  302 bits (773), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ + +S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 24  KIALGIEYDGSQYYGWQRQIDVASVQACLEKALSKVADEPIEVLCAGRTDAGVHGTGQVV 83

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA L     I++  +  V + FHARFSA  R Y Y I   +  
Sbjct: 84  HFTTQAIRKDAAWTMGVNANL--PPDIAVRWVKAVHEDFHARFSATARRYRYIIYNHRYR 141

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   GN
Sbjct: 142 PAVLSHGMTHFYHPLDVERMERAGQCLLGENDFTSFRAVQCQSRTPWRNVNHLKVTRHGN 201

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR   G  A  EGLY  
Sbjct: 202 YIVVDIKANAFVHHMVRNIVGSLMDVGCGNRPESWIAELLAAKDRTLAGATARAEGLYLV 261

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 262 AVDYP 266


>gi|149377425|ref|ZP_01895168.1| tRNA pseudouridine synthase A [Marinobacter algicola DG893]
 gi|149358266|gb|EDM46745.1| tRNA pseudouridine synthase A [Marinobacter algicola DG893]
          Length = 298

 Score =  302 bits (773), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 126/246 (51%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +  EY+G G+ GWQ QK    S+QG + +A+  V    V +  AGRTD+GVHA  Q+
Sbjct: 18  RVAIAFEYDGRGFHGWQYQKSGVRSVQGELTQAVSKVADHPVELVCAGRTDAGVHASYQI 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+      P      +N  L     I++         FHARFSA  R Y Y I     
Sbjct: 78  AHFETPSVRNPRSWVMGINTSL--PQDIAVHWAGNGVDDFHARFSATYRRYRYVIYNHAV 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  G+     + LD   M  AAQ L G HDF++FR+  CQ+ SPIR ++  +V   G
Sbjct: 136 RPGILHGQVSWTFRPLDEALMHQAAQFLCGEHDFSSFRAAGCQSRSPIRFLEAIEVTRKG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I V A +FLH  +R+  G+L  VG GK     + + L+A+DR   G  APP GLY 
Sbjct: 196 DFVVIDVQANAFLHHMVRNIAGALMSVGTGKQRPEWIREILEARDRTVAGVTAPPHGLYL 255

Query: 242 DSVEYS 247
             V Y 
Sbjct: 256 VDVGYP 261


>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 =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 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|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 =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 92/251 (36%), Positives = 138/251 (54%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D      P    +  NA+L    T+++     V + FHARFSA RR+Y Y +++  
Sbjct: 61  VVHLDTDLVRDPFSWVRGTNAFL--PPTVAVRWAQEVPEDFHARFSAHRRTYYYALVSGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L  G+A  +     +SLD   M+ AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRAPLLGGKAGYVMLPPGESLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKTMYSAE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  + +R+   +FLH  +R+ +G L  +G GK     + + L A+DRK   P   P
Sbjct: 179 ARGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGKRPVAWMGEVLAARDRKVAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>gi|156502494|ref|YP_001428559.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|290953826|ref|ZP_06558447.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312837|ref|ZP_06803569.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|166228698|sp|A7NCA0|TRUA_FRATF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|156253097|gb|ABU61603.1| tRNA pseudouridine synthase A [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 258

 Score =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSLSVQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F            + +NA L     I IL +  V+  F++RF+AI R+Y Y I    
Sbjct: 61  IVNFYSNAYRPLSAWQRGVNALL--PQDIKILAVQQVNNNFNSRFTAINRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + LD + M  A ++L+G  DF++FRS  CQ+++P R I   +    
Sbjct: 119 TSSPIFAEHCLWENRELDIDKMNQACEYLLGEQDFSSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+ VGSL  VG G  +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNLVGSLLKVGLGFESPEWIKVVLEAKDRTQAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQ    ++Q  +E+A+  V  + + VH AGRTDSGVH   QV
Sbjct: 1   MRVALGIEYDGSKYYGWQRQLEVDTVQAQLERALSKVANQPISVHCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +N  L   D I++  + +VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETTAIRKESAWTLGVNVNL--PDDIAVKWVKLVDDDFHARFSATARRYRYIIYNYHL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         LD + M  AAQH VG HDFT+FR++HCQ+ +P R +   +V   G
Sbjct: 119 RPGILRSGVSHYRGQLDEDKMHHAAQHFVGEHDFTSFRALHCQSKTPFRHVHEVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G      +   L  +DR +  P A P GLY 
Sbjct: 179 MYLCVDIKANAFLHHMVRNIVGSLIEIGLGHQNEDWIVSLLALKDRSKAAPTAKPNGLYM 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 136/247 (55%), Positives = 166/247 (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  VAHVDLRRDWEPDTVRDALNAHLR-DAPVAILSAERVADDFDARFSARKRFYLYRIFNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP AL  GR W + K LD + M  AAQ LVG HDF TFRS HCQA +PIRT++  DV   
Sbjct: 120 APTALLIGRVWWVSKPLDVDAMHAAAQRLVGTHDFDTFRSAHCQAKNPIRTLEQLDVVRG 179

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 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|167759245|ref|ZP_02431372.1| hypothetical protein CLOSCI_01592 [Clostridium scindens ATCC 35704]
 gi|167663119|gb|EDS07249.1| hypothetical protein CLOSCI_01592 [Clostridium scindens ATCC 35704]
          Length = 248

 Score =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I Y+G+ Y GWQ Q NG +++  + K +  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLTIAYDGTDYCGWQIQPNGITVEEILNKKLKKLTGEDIHVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF-SAIRRSYLYRIITR 119
           VA FD         +  ALN  L   D I I++   V   +H R+   I ++Y Y I   
Sbjct: 61  VAVFDTESSIPAERMAYALNQRL--PDDIVIVSSKEVPLDWHPRYQDEILKTYEYHIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L++  +  +   ++ E MR  A +L+G HDF +F ++       +RT+    +  
Sbjct: 119 PVQNPLKRRYSAFVSFPMNVEKMREGAAYLLGEHDFVSFCNVRTSVEDTVRTVKELMIEQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I IR+    FL+  +R   G+L  VG G +  T +++ L+A++R + G  APPEGL
Sbjct: 179 EGPDITIRITGNGFLYNMVRIIAGTLIRVGRGFYEPTKVKEILEARERTQAGVTAPPEGL 238

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 239 TLVCIEYD 246


>gi|266620223|ref|ZP_06113158.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
 gi|288868186|gb|EFD00485.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
          Length = 354

 Score =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 91/241 (37%), Positives = 126/241 (52%), Gaps = 2/241 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q NG +I+  + +A+  +  E V V GA RTDSGVHA   
Sbjct: 1   MKRIKLIVAYDGTNYCGWQIQNNGRTIEEVLNEALTALLHEKVAVIGASRTDSGVHAEGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C ALN  L   + I +L    V   +H R     ++Y YRI+ R+
Sbjct: 61  VAVFDTENRMPADKICFALNQRL--PEDIRVLKSEEVPLTWHPRKCNCVKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +  A+     LD E M+ AA++LVG HDFT+F +   QA   +RTI   DV   
Sbjct: 119 IEVPTLRLYAYFCYYPLDVEKMKQAAEYLVGEHDFTSFCAPRTQAEDMVRTIYSLDVGKT 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IRV    FL+  +R   G+L  VG G W    +E+ L A+ R   GP A   GL 
Sbjct: 179 GDMITIRVSGSGFLYNMVRIIAGTLMKVGLGVWPPEHVEEILDARSRAAAGPTAVARGLT 238

Query: 241 F 241
            
Sbjct: 239 L 239


>gi|138893815|ref|YP_001124268.1| tRNA pseudouridine synthase A [Geobacillus thermodenitrificans
           NG80-2]
 gi|196250992|ref|ZP_03149674.1| tRNA pseudouridine synthase A [Geobacillus sp. G11MC16]
 gi|166228701|sp|A4IJL9|TRUA_GEOTN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|134265328|gb|ABO65523.1| tRNA pseudouridine synthase A [Geobacillus thermodenitrificans
           NG80-2]
 gi|196209464|gb|EDY04241.1| tRNA pseudouridine synthase A [Geobacillus sp. G11MC16]
          Length = 253

 Score =  302 bits (773), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            R   ++ Y+G+ + G+Q Q    ++QG  E  +  +  G+ V +  +GRTD+GVHA  Q
Sbjct: 3   RRIKCVVAYDGTYFSGYQVQPGKRTVQGEFEGVLKRMHKGDDVRITASGRTDAGVHAYGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P    KALNA L   D I++ ++   D  FHARFSA  + Y Y + T  
Sbjct: 63  VIHFDTPLALSPEQWKKALNAQL--PDDIAVRSVDEADSTFHARFSAKAKEYRYNVWTAA 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P  L  + M  A   L G HDFT+F S        +RTI   ++   
Sbjct: 121 ERDVFRRHYCAWHPYPLRVDAMSEALGLLKGTHDFTSFCSAKTVIEDRVRTIYQAEMEVD 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +++ R V   FL+  +R  VG++  VG GK    D+E  L A+DR+  GP AP EGLY
Sbjct: 181 GPMLQFRFVGSGFLYNMVRIIVGTVLEVGQGKRPPDDIEALLAAKDRRLAGPTAPAEGLY 240

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 241 LWRVYYD 247


>gi|260558318|ref|ZP_05830514.1| tRNA pseudouridine synthase [Enterococcus faecium C68]
 gi|261207023|ref|ZP_05921712.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289565342|ref|ZP_06445792.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|294615363|ref|ZP_06695236.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|294618289|ref|ZP_06697870.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
 gi|260075492|gb|EEW63798.1| tRNA pseudouridine synthase [Enterococcus faecium C68]
 gi|260078651|gb|EEW66353.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289162832|gb|EFD10682.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|291591737|gb|EFF23373.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|291595383|gb|EFF26695.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
          Length = 248

 Score =  301 bits (772), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|332970797|gb|EGK09777.1| tRNA pseudouridine synthase A [Desmospora sp. 8437]
          Length = 258

 Score =  301 bits (772), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + + Y+G+ + G+QRQ    ++QG++E+ +  VTGE + V GAGRTD+GVHAL Q
Sbjct: 1   MGKIKLTVAYDGTDFSGFQRQPGKRTVQGTLEETLTRVTGETISVTGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+           + LNA L     + +     V ++FHAR+ A  + Y Y + T  
Sbjct: 61  VIHFETSVPIPTERWVRLLNASL--PRDLLVTQAKEVPREFHARYDACWKHYRYTLDTCP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P    +      P  L  + M+ AA+HL G HDFT+F +   Q     R++ H +V   
Sbjct: 119 IPDLFRRRYQTHYPHPLSRDRMQRAARHLTGTHDFTSFSAARAQVKDRRRSLYHCEVKEV 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              ++ I VV   FL+  +R   G+L  +G GK    ++   L+A+DR   G   PPEGL
Sbjct: 179 NPGVLSIEVVGDGFLYHMVRILTGTLVEIGAGKIPPDEIRGILKAKDRSAAGKTFPPEGL 238

Query: 240 YFDSVEY 246
               V Y
Sbjct: 239 VMVEVGY 245


>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 =  301 bits (772), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

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  VHFDTEVERPLASWCFGTNAHLA--NDIAVKWAVKVAEDFHARFSATARRYRYIIFNSKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q+L+G  DF++FR+  CQ+ +P R I H +V   G
Sbjct: 119 RTAILPKGVAHYHYPLDAQKMHQAGQYLLGEQDFSSFRAAKCQSHTPWRNIHHLNVVRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + + + A +F+H  +R+ VGSL  VG G+     ++  L+ ++R+   P    EGLY 
Sbjct: 179 NYVIVDIQANAFVHHMVRNIVGSLLEVGQGRQPIEWIKWLLEQKNRQLAAPTTKAEGLYL 238

Query: 242 DSVEYS 247
            +VEY 
Sbjct: 239 VNVEYP 244


>gi|69247200|ref|ZP_00604262.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257878755|ref|ZP_05658408.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257881397|ref|ZP_05661050.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257890614|ref|ZP_05670267.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|258615179|ref|ZP_05712949.1| tRNA pseudouridine synthase A [Enterococcus faecium DO]
 gi|293562977|ref|ZP_06677444.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|314937639|ref|ZP_07844965.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|314942862|ref|ZP_07849675.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|314948002|ref|ZP_07851406.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
 gi|314950919|ref|ZP_07853988.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|314991433|ref|ZP_07856910.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|314995046|ref|ZP_07860166.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|68194965|gb|EAN09433.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257812983|gb|EEV41741.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257817055|gb|EEV44383.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257826974|gb|EEV53600.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|291605103|gb|EFF34570.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|313590772|gb|EFR69617.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|313593913|gb|EFR72758.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|313596928|gb|EFR75773.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|313598334|gb|EFR77179.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|313643016|gb|EFS07596.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|313645600|gb|EFS10180.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
          Length = 248

 Score =  301 bits (772), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        IRTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKIRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>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 =  301 bits (772), Expect = 5e-80,   Method: Composition-based stats.
 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|227550751|ref|ZP_03980800.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257887991|ref|ZP_05667644.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257893205|ref|ZP_05672858.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257896390|ref|ZP_05676043.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|293379476|ref|ZP_06625620.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
 gi|293570714|ref|ZP_06681764.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
 gi|227180069|gb|EEI61041.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257824045|gb|EEV50977.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257829584|gb|EEV56191.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257832955|gb|EEV59376.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|291609186|gb|EFF38458.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
 gi|292641999|gb|EFF60165.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
          Length = 248

 Score =  301 bits (772), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV ++FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEEFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|89100313|ref|ZP_01173178.1| pseudouridylate synthase I [Bacillus sp. NRRL B-14911]
 gi|89084934|gb|EAR64070.1| pseudouridylate synthase I [Bacillus sp. NRRL B-14911]
          Length = 245

 Score =  301 bits (772), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 117/247 (47%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+   I Y+GS + G+Q Q    ++Q  +E+A+  +  G  V +  +GRTD+GVHA  
Sbjct: 1   MQRFKCKIAYDGSQFSGYQVQPGKRTVQLEVERALAKIHKGNPVKIFASGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L     I++ +     + FHARF A  + Y Y I   
Sbjct: 61  QVIHFDSPLAIPEDRWVTALNSLL--PKDIAVESTEKAAEGFHARFDACGKEYRYFIYRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     E+  ++  P  LD   MR AA+HL+G HDF++F +        +R I    V  
Sbjct: 119 KIRSPFERHYSYHYPHPLDIRAMREAAEHLLGTHDFSSFCASRTDVEDKVREIRKVHVEE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E+      FL+  +R   G+L   G G        + +  +DR   G  AP EGL
Sbjct: 179 AGEMLELHFTGSGFLYNMVRILTGTLLEAGAGTRDPGSFPEVISGRDRSLAGKTAPAEGL 238

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 239 YLWKVFY 245


>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 =  301 bits (772), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 124/247 (50%), Positives = 166/247 (67%), Gaps = 1/247 (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 FDSVEYS 247
              V + 
Sbjct: 240 LTHVTFE 246


>gi|326792573|ref|YP_004310394.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
 gi|326543337|gb|ADZ85196.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
          Length = 245

 Score =  301 bits (772), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 132/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +I+ Y+G+ Y G+ +Q N ++IQG+++ AI  +    V   GAGRTD GVHA  Q
Sbjct: 1   MKRFKLIVAYDGTNYNGFAKQPNATTIQGTLDVAIAKIVQHEVRTLGAGRTDRGVHAFAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              FD   +     L KA+N+ L     IS+ ++  V + FH RF A R++Y Y+I+  +
Sbjct: 61  CCVFDSDTKIPADRLAKAINSQL--PADISVKSVEEVSEDFHPRFGAKRKTYRYQILNAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    A L P  LD E M+ AA  ++G HDF  F +        +R I   DV   
Sbjct: 119 IRDPFLYKYALLYPYELDVERMQEAANEMIGEHDFACFCAAGSTVKDTVRIIYSIDVKKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ I V    FL+  +R  +G+L  V + K T   ++  +++++R+  GP  PP+GL 
Sbjct: 179 GDLVSIDVCGNGFLYNMVRIIIGTLLDVNENKITKDSIKTIIESKNRELAGPTVPPQGLT 238

Query: 241 FDSVEYS 247
             ++ Y+
Sbjct: 239 MLNIVYN 245


>gi|56418673|ref|YP_145991.1| tRNA pseudouridine synthase A [Geobacillus kaustophilus HTA426]
 gi|62901182|sp|Q5L3Q7|TRUA_GEOKA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56378515|dbj|BAD74423.1| pseudouridylate synthaseI [Geobacillus kaustophilus HTA426]
          Length = 258

 Score =  301 bits (772), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            R   II Y+G+ + G+Q Q    ++QG  E+ +  +  G  V V  +GRTD+GVHA  Q
Sbjct: 3   QRIKCIIAYDGTHFSGYQIQPGKRTVQGEFEEVLRRMHKGTKVRVAASGRTDAGVHAYGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           KALNA L   D I +  +   D  FHARFSA  + Y Y++ T  
Sbjct: 63  VIHFDTPLSLSSEQWKKALNAQL--PDDIVVRFVQEADADFHARFSAKAKEYRYKVWTAA 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P SL    M  A + L G HDFT+F S        +RT+   +V + 
Sbjct: 121 ERDVFRRHYCAWHPYSLHISAMNEALRLLHGTHDFTSFCSAKTSIEDRVRTMYRAEVKAD 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G ++E R V   FL+  +R  VG++  +G GK +  D+   L A+DR+  GP AP EGLY
Sbjct: 181 GPMLEFRFVGSGFLYNMVRIIVGTVLEIGQGKRSPADISTLLAAKDRRLAGPTAPAEGLY 240

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 241 LWRVYYE 247


>gi|325567346|ref|ZP_08144013.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
 gi|325158779|gb|EGC70925.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
          Length = 248

 Score =  301 bits (772), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ + +HG+GRTD+GVHA  
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTKMNNGQPIQIHGSGRTDAGVHAQG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  ++     +   L+   +  + +++ ++ IVD  FHAR+  + ++Y +R+   
Sbjct: 61  QVIHFDFPQKRPLEKMRFGLDT--QTPEDVAVKSVEIVDDTFHARYLVVEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  LD E ++ A    +G HDFT+F +         RTI      V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLEKIQRALPDFLGTHDFTSFCATGSSVDDKTRTIHEASMAV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NDAGDELIFTFRGDGFLYKMIRIMVGTLLKIGNGRIAPDSIPAIIAQKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLVHVAYE 248


>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 =  301 bits (771), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANERINVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V  FG 
Sbjct: 129 PAVLGKGVTHYYEPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHIKVERFGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGANNQPESWIAELLAARDRTLAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|257885664|ref|ZP_05665317.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|293553909|ref|ZP_06674515.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
 gi|257821520|gb|EEV48650.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|291601961|gb|EFF32207.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
          Length = 248

 Score =  301 bits (771), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPAIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|227114786|ref|ZP_03828442.1| tRNA pseudouridine synthase A [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 283

 Score =  301 bits (771), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ + +S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 24  KIALGIEYDGSLYYGWQRQIDVASVQACLEKALSKVADEPIEVFCAGRTDAGVHGTGQVV 83

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I   +  
Sbjct: 84  HFTTHAIRKDAAWTMGVNANL--PPDIAVRWVKTVDEDFHARFSATARRYRYVIYNHRYR 141

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   G+
Sbjct: 142 PAVLSRGMTHFYHPLDVERMERAGQCLLGENDFTSFRAVQCQSRTPWRYVNHLKVTRHGD 201

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR   G  A  EGLY  
Sbjct: 202 YIVVDIKANAFVHHMVRNIVGSLMDVGCGNRPESWIAELLAAKDRTLAGATARAEGLYLV 261

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 262 AVDYP 266


>gi|212637986|ref|YP_002314506.1| Pseudouridylate synthase I [Anoxybacillus flavithermus WK1]
 gi|226708641|sp|B7GJ99|TRUA_ANOFW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|212559466|gb|ACJ32521.1| Pseudouridylate synthase I [Anoxybacillus flavithermus WK1]
          Length = 246

 Score =  301 bits (771), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 127/248 (51%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    I Y+G+ + G+Q Q+   ++QG +E+A+ ++  G+ V V+ +GRTD+ VHA  
Sbjct: 1   MRRIKCTIAYDGTNFAGYQIQQQKRTVQGELERALSIIHKGQFVRVYASGRTDATVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           KALNA L   D + +   S V   FHARFS  ++ Y YR+   
Sbjct: 61  QVIHFDTPLTIPDERWPKALNALL--PDDVIVKEASEVPSSFHARFSVKKKEYRYRVWIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  +    M  A ++L+G HDFT+F S   +    +RTI   +V  
Sbjct: 119 EK-NVFLRHYVYHHPYDVSVPAMNEALRYLIGTHDFTSFCSAKTEVDDKVRTIYEAEVVQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +  R+V   FL+  +R  VG++  VG G+  + +++  L+ ++R   G  AP  GL
Sbjct: 178 EGEELIFRLVGNGFLYNMVRIIVGTVLEVGRGERCAEEIKTILEQKNRSVAGKTAPGHGL 237

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 238 YLWHVSYD 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 =  301 bits (771), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 117/251 (46%), Positives = 161/251 (64%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           AP  ++ G  W I   LD E M+  A++LVG+HDFTTFRS  CQA SPI+++    +   
Sbjct: 120 APAIVDVGWVWQIQHDLDLELMQEGAKYLVGKHDFTTFRSSICQAQSPIKSLKEISIKEI 179

Query: 179 --SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G   E  ++ARSFLH Q+RSF+G+L+ VG G W    + +AL A+DR +CGP+ PP
Sbjct: 180 SLEHGKEFEFTIIARSFLHNQVRSFIGTLERVGSGSWDPERVHEALIAKDRSKCGPVCPP 239

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLAQVSYD 250


>gi|225377724|ref|ZP_03754945.1| hypothetical protein ROSEINA2194_03375 [Roseburia inulinivorans DSM
           16841]
 gi|225210401|gb|EEG92755.1| hypothetical protein ROSEINA2194_03375 [Roseburia inulinivorans DSM
           16841]
          Length = 245

 Score =  300 bits (770), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQ Q + G +IQG IE  +  + G  V V G+GRTD+GVHA  
Sbjct: 1   MNNYKITIQYDGTRYKGWQGQNSTGLTIQGKIEAVLGQMAGHAVEVIGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F +   +    +   LN YL   D I+++ +  VD++FH+R++A +++Y Y I   
Sbjct: 61  QVANFHIEEHFTEGKILSYLNHYL--PDDIAVIAVEQVDERFHSRYAAKKKTYRYHIHMG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     E+   +   K+LD E M+ AA +L+G HDFT+F        + +RTI   +   
Sbjct: 119 EISDVFERKYEYQYEKTLDVERMKEAASYLIGTHDFTSFCGNKKMKKTAVRTIYEINFTK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN + I      FL   +R   G+L  VGDG+    +L + L++++R+  G  AP  GL
Sbjct: 179 KGNDLWIDYRGNGFLQNMVRILTGTLIEVGDGRRAPEELPQILESKNRENAGYTAPACGL 238

Query: 240 YFDSVEY 246
               V Y
Sbjct: 239 MLMEVHY 245


>gi|167573521|ref|ZP_02366395.1| tRNA pseudouridine synthase A [Burkholderia oklahomensis C6786]
          Length = 270

 Score =  300 bits (770), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (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  VHFDTELDRADFSWVRGTNAFL--PSTVSVQWAKPMPDTFHARFAAFERTYYYALYVHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|323706484|ref|ZP_08118045.1| tRNA pseudouridine synthase A [Thermoanaerobacterium xylanolyticum
           LX-11]
 gi|323534204|gb|EGB23994.1| tRNA pseudouridine synthase A [Thermoanaerobacterium xylanolyticum
           LX-11]
          Length = 239

 Score =  300 bits (770), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 86/241 (35%), Positives = 127/241 (52%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY+G+ Y GWQ QKN  ++Q  I KAI  +T E V + G+ RTD+GVHAL QVA+F 
Sbjct: 1   MVIEYDGTNYHGWQIQKNAVTVQEVITKAIKKITSEDVNLIGSSRTDAGVHALNQVANFI 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +  ALN+ L     I I N    D  FH+R+SA  + Y Y I  R+    +
Sbjct: 61  SNCNIPLSKMPNALNSVL--PKDIVIKNAYEADMDFHSRYSAKGKRYKYIIYNRKFNSPV 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  +W I   LD + M  +  +L G HDF+ F+S        IRT+    +      +E
Sbjct: 119 YRNYSWHISDELDLDKMIESLTYLKGTHDFSAFKSSGSSVKDSIRTVRDISLRKNDFNVE 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             + A  FL+  +R  VG++  VG GK     +++ L+++DR   G  APP+GL+   + 
Sbjct: 179 FEIEADGFLYNMVRIIVGTIVDVGIGKINPIHVKEILESKDRCMAGKTAPPQGLFLTKIY 238

Query: 246 Y 246
           Y
Sbjct: 239 Y 239


>gi|257876163|ref|ZP_05655816.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257810329|gb|EEV39149.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 248

 Score =  300 bits (770), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ + +HG+GRTD+GVHA  
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTKMNNGQPIQIHGSGRTDAGVHAQG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  ++     +   L+   +  + +++  + IVD  FHAR+  + ++Y +R+   
Sbjct: 61  QVIHFDFPQKRPLEKMRFGLDT--QTPEDVAVKAVEIVDDTFHARYLVVEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  LD E ++ A    +G HDFT+F +         RTI      V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLEKIQRALPDFLGTHDFTSFCATGSSVDDKTRTIHEASMAV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NDAGDELIFTFRGDGFLYKMIRIMVGTLLKIGNGRLAPDSIPAIIAQKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLVHVAYE 248


>gi|238925343|ref|YP_002938860.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
 gi|238877019|gb|ACR76726.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
          Length = 252

 Score =  300 bits (770), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  MI+ Y+G+ Y GWQ Q NG +I+  + + +  +  E + V GA RTD+GVH+L  V
Sbjct: 9   MRVKMIVAYDGTNYCGWQIQPNGITIEQVLNEHLSRLLKEDIKVTGASRTDAGVHSLGNV 68

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD         +  ALN  L   + I +++   V   FH RFS  R++Y YRI+  + 
Sbjct: 69  CMFDTNTRMPAEKISYALNQKL--PEDIVVVDSCEVSDDFHPRFSKSRKTYEYRILNARF 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   +     LD E M  AA++L+G HDF +F S + QA + +RTI    V+  G
Sbjct: 127 RNPTRRLDTYFYHYPLDTEKMSEAAKYLIGEHDFASFCSANSQAQTTVRTIYDCTVSKAG 186

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IRV    FL+  +R   G+L  +G     +  ++  +   DR   GP AP  GL  
Sbjct: 187 DIITIRVTGNGFLYNMVRIIAGTLVKIGGSDMPADAMKDIIATTDRAAAGPTAPAHGLTM 246

Query: 242 DSVEYS 247
             ++Y 
Sbjct: 247 IGLKYE 252


>gi|257866559|ref|ZP_05646212.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257872925|ref|ZP_05652578.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257800517|gb|EEV29545.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807089|gb|EEV35911.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 248

 Score =  300 bits (770), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ + + G+GRTD+GVHA  
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTKMNNGQPIQIQGSGRTDAGVHAQG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  ++     +   L+   +  + +++ ++ IVD  FHAR+  + ++Y +R+   
Sbjct: 61  QVIHFDFPQKRPLEKMRFGLDT--QTPEDVAVKSVEIVDDTFHARYLVVEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  LD E ++ A    +G HDFT+F +         RTI      V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLEKIQRALPDFLGTHDFTSFCATGSSVDDKTRTIHEASMAV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NDAGDELIFTFRGDGFLYKMIRIMVGTLLKIGNGRLAPDSIPAIIAQKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLVHVAYE 248


>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 =  300 bits (770), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 131/246 (53%), Gaps = 2/246 (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 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|227520026|ref|ZP_03950075.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
 gi|227072574|gb|EEI10537.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
          Length = 249

 Score =  300 bits (770), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 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 =  300 bits (770), Expect = 9e-80,   Method: Composition-based stats.
 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|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 =  300 bits (770), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 130/246 (52%), Gaps = 2/246 (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 L   D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRNEGAWTLGVNANL--PDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  300 bits (770), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    ++Q ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVLEYDGSKYHGWQAQTGLHTVQQAVENALSKVADLPISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  ++         +N++L     I +     + ++FHAR+SA  R Y Y I     
Sbjct: 61  IHFDSEKQRSIRAWIHGVNSFL--PKDICVKWGKELSEEFHARYSATARRYRYVIYNSAI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL +       + LD   M  AAQ L+G +DFT+FRS+ CQ+++P+R +    VN  G
Sbjct: 119 RPALLRSNVTWQYRQLDHRLMHQAAQVLLGENDFTSFRSVECQSNTPMRNVYKLQVNRMG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A +FLH  +R+  G L  VG GK     +E+ LQA+DR+     AP  GLY 
Sbjct: 179 DLVIIDITANAFLHHMVRNIAGVLIAVGSGKRPVFWVEEVLQAKDRRLGAETAPAYGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VQVNYP 244


>gi|239623391|ref|ZP_04666422.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522357|gb|EEQ62223.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 247

 Score =  300 bits (770), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 131/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q    +I+  + +A+  + GE V V GA RTDSGVHA   
Sbjct: 1   MKRVRLVVAYDGTHYHGWQIQPGKVTIESRLNEALTSLLGEPVQVIGASRTDSGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C ALN  L   + I + +   VD  +H R     ++Y YRI+ R+
Sbjct: 61  VAVFDTSHRMPADRICMALNQRL--PEDIRVQSSEEVDPDWHPRKCRCVKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
             + +++  +     +LD E M+ AA  LVG HDF +F S+  Q +  +RTI   +V   
Sbjct: 119 IEMPMQRFYSHFCYFNLDLEKMQKAAGLLVGEHDFKSFCSVRTQVTDTVRTIYSIEVKRD 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IRV    FL+  +R   G+L  VG G+    D+   L+A+DR+  GP AP  GL
Sbjct: 179 EEDMIGIRVTGNGFLYNMVRIIAGTLMAVGMGQIAPEDMGAILEARDRRAAGPTAPARGL 238

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 239 TLIQMEYD 246


>gi|239825725|ref|YP_002948349.1| tRNA pseudouridine synthase A [Geobacillus sp. WCH70]
 gi|259550397|sp|C5D3U9|TRUA_GEOSW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239806018|gb|ACS23083.1| tRNA pseudouridine synthase A [Geobacillus sp. WCH70]
          Length = 248

 Score =  300 bits (770), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           R    + Y+G+ +FG+Q Q    ++QG +E+ +  +  G+ + V  +GRTD+GVHA  QV
Sbjct: 4   RIKCTLSYDGTHFFGYQIQPGKRTVQGELERVLEQMHKGKAIRVTASGRTDAGVHAYGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P    KALNA L   D I I ++   D  FHARFSA  + Y Y++   Q 
Sbjct: 64  IHFDTFLSLSPDQWKKALNAQL--PDDIVIKDVQEADPSFHARFSAKAKEYRYKVRIAQE 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   +  P  LD E MR A + + G HDFT+F S        +RTI   D+    
Sbjct: 122 RDVFLRNYCYHYPYPLDMEAMRHALRLIEGTHDFTSFCSAKTDVDDRVRTIYKADMAMHD 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+E   +   FL+  +R  VG++  VG GK +   +  A +A+DR+  G  APP+GLY 
Sbjct: 182 DLLEFCFIGNGFLYNMVRIIVGTILEVGQGKRSIDSISHAFEAKDRQFAGKTAPPQGLYL 241

Query: 242 DSVEYS 247
             V Y 
Sbjct: 242 WKVYYD 247


>gi|315172660|gb|EFU16677.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1346]
          Length = 249

 Score =  300 bits (769), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NEKGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|295401888|ref|ZP_06811851.1| tRNA pseudouridine synthase A [Geobacillus thermoglucosidasius
           C56-YS93]
 gi|294976018|gb|EFG51633.1| tRNA pseudouridine synthase A [Geobacillus thermoglucosidasius
           C56-YS93]
          Length = 248

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 126/246 (51%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           R    + Y+G+ +FG+Q Q    ++QG +E+A+  +  G+ + V  +GRTD+GVHA  QV
Sbjct: 4   RIKCTLSYDGTHFFGYQIQPGKRTVQGELEQALEQIHKGKAIRVTASGRTDAGVHAYGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P    KALNA L   D I I +       FHARFSA  + Y Y++   Q 
Sbjct: 64  IHFDTFLSLSPEQWKKALNALL--PDDIVIKDAQEAAPSFHARFSATAKEYRYKVRIAQE 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   +  P  LD E M  A + + G HDFT+F S        +RTI   D+    
Sbjct: 122 RDVFLRHYCYHYPYPLDMEAMGRALRLIEGTHDFTSFCSAKTDVDDRVRTIYKADMTVRD 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+E   +   FL+  +R  VG++  VG GK +   +  AL A+DR+  G  APP+GLY 
Sbjct: 182 DLLEFCFIGNGFLYNMVRIIVGTILEVGQGKRSVDSISSALAAKDRRFAGKTAPPQGLYL 241

Query: 242 DSVEYS 247
             V Y 
Sbjct: 242 WKVYYD 247


>gi|227555887|ref|ZP_03985934.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|256964165|ref|ZP_05568336.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257418666|ref|ZP_05595660.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
 gi|307274205|ref|ZP_07555413.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
 gi|227175054|gb|EEI56026.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|256954661|gb|EEU71293.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257160494|gb|EEU90454.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
 gi|306509167|gb|EFM78229.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
 gi|315573548|gb|EFU85739.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309B]
 gi|315582104|gb|EFU94295.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309A]
          Length = 249

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 118/251 (47%), Positives = 162/251 (64%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   + G+ W +   LD + M+ AA +L+G HDFTTFRS  CQA SP++T+D   V   
Sbjct: 120 APATHDAGQVWQLSHELDADAMQEAANYLIGNHDFTTFRSSICQAQSPVKTLDELTVERV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L+ VG G W   D++ AL+A+DR  CGP+ P 
Sbjct: 180 QGFSGPEIHFHVRARSFLHNQVRSFVGTLERVGAGAWDPADVKAALEARDRAACGPVCPG 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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 121/251 (48%), Positives = 159/251 (63%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   + G+ W I   LD E M+  A  L+G HDFTTFRS  CQA+SP++T+D   V   
Sbjct: 139 APATHDAGQVWQINHRLDVEAMQAGADMLLGNHDFTTFRSSICQAASPVKTLDELRVEQV 198

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   V ARSFLH Q+RSFVG+L+ VG G WT  D+  AL A+DR  CGP+ P 
Sbjct: 199 QGLSGPEVHFHVRARSFLHNQVRSFVGTLERVGAGAWTPEDVRDALAAKDRAACGPVCPG 258

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 259 HGLYLARVGYP 269


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 132/246 (53%), Gaps = 2/246 (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 FDSVEY 246
              V Y
Sbjct: 239 LLEVIY 244


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 90/251 (35%), Positives = 138/251 (54%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + H D      P    +  NA+L    T+++     V + FHARFSA RR+Y Y +++  
Sbjct: 61  IVHLDTDLVREPFSWVRGTNAFL--PSTVAVRWAQAVPEDFHARFSAHRRTYYYALVSGP 118

Query: 121 APLALEKGRAWLIPKS----LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L  G+A  +       LD   M+ AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRSPLLGGKAGYVMLPPGEWLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKTLYSAE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+   +FLH  +R+ +G L  +G G+  +  + + L A+DRK   P   P
Sbjct: 179 VRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRRPAAWMAEVLAARDRKAAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>gi|309973317|gb|ADO96518.1| tRNA pseudouridine synthase A [Haemophilus influenzae R2846]
          Length = 269

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 131/246 (53%), Gaps = 2/246 (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 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|257084178|ref|ZP_05578539.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256992208|gb|EEU79510.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 249

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 136/246 (55%), Gaps = 2/246 (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    ++++     + + FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTELDRTAFSWVRGTNAFL--PPSVAVQWAKPMPEAFHARFAAFERTYYYALYVHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|229546930|ref|ZP_04435655.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|229550518|ref|ZP_04439243.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|255971742|ref|ZP_05422328.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|255974742|ref|ZP_05425328.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|256618347|ref|ZP_05475193.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|257081530|ref|ZP_05575891.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257417608|ref|ZP_05594602.1| tRNA pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257421532|ref|ZP_05598522.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|307276430|ref|ZP_07557553.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|307278640|ref|ZP_07559710.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|312952641|ref|ZP_07771505.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|229304375|gb|EEN70371.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|229307858|gb|EEN73845.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|255962760|gb|EET95236.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|255967614|gb|EET98236.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|256597874|gb|EEU17050.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256989560|gb|EEU76862.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257159436|gb|EEU89396.1| tRNA pseudouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|257163356|gb|EEU93316.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|306504700|gb|EFM73900.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|306506910|gb|EFM76057.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|310629429|gb|EFQ12712.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|315026801|gb|EFT38733.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2137]
 gi|315147137|gb|EFT91153.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4244]
 gi|315153575|gb|EFT97591.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0031]
 gi|315156245|gb|EFU00262.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0043]
 gi|315158610|gb|EFU02627.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0312]
 gi|315168134|gb|EFU12151.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1341]
 gi|315171426|gb|EFU15443.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1342]
 gi|323479455|gb|ADX78894.1| tRNA pseudouridine synthase A [Enterococcus faecalis 62]
 gi|327534038|gb|AEA92872.1| tRNA-pseudouridine synthase I [Enterococcus faecalis OG1RF]
          Length = 249

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|293567901|ref|ZP_06679242.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
 gi|291589486|gb|EFF21293.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
          Length = 248

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + +V + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEVVSEDFHARYLVTEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +      +  A   P  LD E ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPAIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 116/248 (46%), Positives = 159/248 (64%), Gaps = 2/248 (0%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIITR 119
           V H DL R+W    +  A+NA+L I   + +L+        +HARFSA  R YLYRI+ R
Sbjct: 61  VIHADLERDWPVDTVLNAVNAHL-IKQDVCVLSAEYAPDPDWHARFSATGRGYLYRILNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    LE+ R W + KSLD E M  AAQ LVG HDFTTFR + CQ+ SP++T+D   V+ 
Sbjct: 120 RPQPVLERDRVWHVKKSLDAEAMHQAAQVLVGLHDFTTFRDVGCQSKSPVKTLDVARVSR 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG  + +   ARSFLH Q+RS  G+L  VG G+WT+ D++ AL+A+DR  CGP+AP  GL
Sbjct: 180 FGEEVHLVFQARSFLHRQVRSMAGTLVEVGLGRWTAHDVKAALEAKDRARCGPVAPSAGL 239

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 240 YLSGVRYD 247


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 86/247 (34%), 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    +I I++   V ++FHAR+S   + Y+Y++ T 
Sbjct: 61  QVVHIDYPKRIEANSLVRAMNSLL--PTSIRIVSAEAVSEEFHARYSVTGKRYIYKVTTA 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|256956829|ref|ZP_05561000.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|257078499|ref|ZP_05572860.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294781084|ref|ZP_06746435.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|300861778|ref|ZP_07107858.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|307269121|ref|ZP_07550482.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|307286980|ref|ZP_07567055.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|312901088|ref|ZP_07760376.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|256947325|gb|EEU63957.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256986529|gb|EEU73831.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294451887|gb|EFG20338.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|295112531|emb|CBL31168.1| pseudouridylate synthase I [Enterococcus sp. 7L76]
 gi|300848303|gb|EFK76060.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|306501926|gb|EFM71215.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|306514601|gb|EFM83155.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|311291760|gb|EFQ70316.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|315031173|gb|EFT43105.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0017]
 gi|315035981|gb|EFT47913.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0027]
 gi|315145370|gb|EFT89386.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2141]
 gi|315165868|gb|EFU09885.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1302]
          Length = 249

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        IRTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKIRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E V V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPVNVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V + FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTALRKDAAWTLGVNANL--PGDIAVRWVKAVPEDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAILGHGVTHFYEPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVTRHGA 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR+     A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRRLSAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P    +  AW  P  L+   MR AA+   G HDF +F        + +RTI    V   
Sbjct: 119 EPNLFIRNYAWWFPYKLNICKMREAAKFFEGEHDFRSFMKSGDHRENTVRTIYRVRVLQL 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 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|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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 140/246 (56%), Gaps = 2/246 (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  VHFDVEVERPENAWVRGVNSHL--PADIAVVWAKQVDEEFHARFSAFSRSYSYFLLTHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 TGVGYP 244


>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 =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 127/247 (51%), Positives = 168/247 (68%), Gaps = 2/247 (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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 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 YFDSVEY 246
           Y  ++EY
Sbjct: 240 YLTAIEY 246


>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 =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 124/247 (50%), Positives = 166/247 (67%), Gaps = 1/247 (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 FDSVEYS 247
           F +  Y 
Sbjct: 240 FVAATYP 246


>gi|148544665|ref|YP_001272035.1| tRNA pseudouridine synthase A [Lactobacillus reuteri DSM 20016]
 gi|184154018|ref|YP_001842359.1| tRNA pseudouridine synthase A [Lactobacillus reuteri JCM 1112]
 gi|194466922|ref|ZP_03072909.1| tRNA pseudouridine synthase A [Lactobacillus reuteri 100-23]
 gi|227363788|ref|ZP_03847895.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM2-3]
 gi|325682999|ref|ZP_08162515.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM4-1A]
 gi|166991164|sp|A5VLH4|TRUA_LACRD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|229557996|sp|B2G8U7|TRUA_LACRJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148531699|gb|ABQ83698.1| tRNA pseudouridine synthase A [Lactobacillus reuteri DSM 20016]
 gi|183225362|dbj|BAG25879.1| tRNA pseudouridine synthase A [Lactobacillus reuteri JCM 1112]
 gi|194453958|gb|EDX42855.1| tRNA pseudouridine synthase A [Lactobacillus reuteri 100-23]
 gi|227071145|gb|EEI09461.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM2-3]
 gi|324977349|gb|EGC14300.1| tRNA pseudouridine synthase A [Lactobacillus reuteri MM4-1A]
          Length = 256

 Score =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY +   Y+G+ + G+Q Q N  +++ +++ A+  +       + V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGTNFSGFQIQPNKRTVEQTLKNAVNKIAKHPTPAIPVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD+        + KALN+ L     I I    +VD  FHAR+SA R++Y YR+ 
Sbjct: 61  LNQVAHFDIPYHLSNESMRKALNSIL--PLDILIKKAELVDNDFHARYSAHRKTYRYRVD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         L+ E MR AA  LVG HDFT+F +   QA S +RTI++  +
Sbjct: 119 QGEFVNPFKRNYTSHFKYPLNLEKMRKAADDLVGTHDFTSFVASGSQAKSNVRTIENITI 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 N +        FL+ Q+R  V  L  +G  +    D+ + L+A+DR      AP
Sbjct: 179 KRDEVRNEVVFDFTGNGFLYNQVRIMVAFLLEIGSNQRPVDDVSRVLKAKDRTLARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  +V+Y
Sbjct: 239 ASGLYLVNVDY 249


>gi|308172039|ref|YP_003918744.1| pseudouridylate synthase I [Bacillus amyloliquefaciens DSM 7]
 gi|307604903|emb|CBI41274.1| pseudouridylate synthase I [Bacillus amyloliquefaciens DSM 7]
 gi|328551849|gb|AEB22341.1| tRNA pseudouridine synthase A [Bacillus amyloliquefaciens TA208]
 gi|328910104|gb|AEB61700.1| pseudouridylate synthase I [Bacillus amyloliquefaciens LL3]
          Length = 247

 Score =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  T   V V+ +GRTDS VHA  
Sbjct: 1   MRMKCTIAYDGHLFNGYQVQPGKRTVQSELEKALAVIHKTDGRVPVYSSGRTDSDVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAEKWPFALNALL--PDDIAVKTAEIADDGFHARFSAVQKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ + MR A++HL+G HDFT+F ++       +RTI   +   
Sbjct: 119 KHPDVFKRHYAYHFAYQLNVQKMREASRHLIGTHDFTSFCAVDTAVQDKVRTIYELEWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +++R+    FL+  +R   G+L   G GK++  D++  L+A+DR+  G  AP  GL
Sbjct: 179 TGDGLQMRITGNGFLYNMVRIIAGTLLDTGAGKFSPDDVKAMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  SV Y 
Sbjct: 239 YLWSVCYD 246


>gi|62901272|sp|Q65TC8|TRUA_MANSM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 263

 Score =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  YFGWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYNGKNYFGWQRQEKVHSVQAELEKALSFVANEKIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA L   D I++     V   FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAIRPEKAWAFGTNANL--PDDIAVRWAKEVPDDFHARFSATARRYRYVLYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M+ A + L+G +DF++FR+  CQ+++P R I H +V   G
Sbjct: 119 RSAILPYGITHTHLDLDEHKMQEAGRFLLGENDFSSFRAAQCQSNTPWRNIHHLNVIRRG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + + + A +F+H  +R+ VGSL  VG G      +E  L  ++RK   P A  EGLY 
Sbjct: 179 NFVIVDIKANAFVHHMVRNIVGSLMEVGCGNQPPEWIEWLLAQKNRKLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VQVTYP 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 =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 89/245 (36%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + +EY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 10  KIALGVEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 69

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L     I++  +  V + FHARFSA  R Y Y I   +  
Sbjct: 70  HFETSALRKDAAWTLGVNANL--PGDIAVRWVKAVPEDFHARFSATARRYRYIIYNHRLR 127

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+  G 
Sbjct: 128 PAVLAKGVTHYYEPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRHGA 187

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 188 YVVVDIKANAFVHHMVRNIVGSLMEVGAHHQPESWIAELLAAKDRTLAAATAKAEGLYLV 247

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 248 AVDYP 252


>gi|256960635|ref|ZP_05564806.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|293382724|ref|ZP_06628649.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|293388093|ref|ZP_06632621.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
 gi|312908619|ref|ZP_07767561.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|312909233|ref|ZP_07768090.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
 gi|256951131|gb|EEU67763.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|291079884|gb|EFE17248.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|291082544|gb|EFE19507.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
 gi|310625406|gb|EFQ08689.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|311290475|gb|EFQ69031.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
          Length = 249

 Score =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NKTGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>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 =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 101/247 (40%), Positives = 134/247 (54%), Gaps = 2/247 (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  VVHFETYSRRSKSAWTLGMNRYL--PSSICVRWARLVNKDFHARFSAISRRYCYIINNNC 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 FDSVEYS 247
              V+Y 
Sbjct: 239 LVEVKYP 245


>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 =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+QG +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 14  KIALGIEYDGSRYYGWQRQAEVGSVQGCLEAALSQVANERIDVFCAGRTDAGVHATGQVV 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I  R+  
Sbjct: 74  HFTTNAVRKDAAWTMGVNANL--PPDIAVRWVKTVDEAFHARFSATARRYRYVIYNRRFR 131

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  A Q L+G +DFT+FR++ CQ+ +P R + H  V   G+
Sbjct: 132 PAILSHGVTHYYLPLDADRMHRAGQCLLGENDFTSFRAVQCQSRTPWRNLMHLRVTRLGD 191

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      +++ L A+DR      A  +GLY  
Sbjct: 192 YVVVDIKANAFVHHMVRNIVGSLMEIGCGNQPENWMDELLAAKDRTLAAATAKADGLYLV 251

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 252 AVDYP 256


>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 =  300 bits (768), Expect = 1e-79,   Method: Composition-based stats.
 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|256855196|ref|ZP_05560557.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
 gi|307291679|ref|ZP_07571554.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|256709709|gb|EEU24756.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
 gi|306497298|gb|EFM66840.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|315028842|gb|EFT40774.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4000]
          Length = 249

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IE+ +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEETLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|154684666|ref|YP_001419827.1| tRNA pseudouridine synthase A [Bacillus amyloliquefaciens FZB42]
 gi|166228678|sp|A7Z0S0|TRUA_BACA2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|154350517|gb|ABS72596.1| TruA [Bacillus amyloliquefaciens FZB42]
          Length = 247

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  T   V V+ +GRTDS VHA  
Sbjct: 1   MRVKCTIAYDGHLFNGYQVQPGKRTVQSELEKALAVIHKTDGRVPVYSSGRTDSDVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPGEKWPFALNALL--PDDIAVKTAEIADDGFHARFSAVQKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ + MR A++HLVG HDFT+F +        +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFAYPLNVQKMREASRHLVGTHDFTSFCAADTAVQDKVRTIYELDWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK++  D++  L+A+DR+  G  AP  GL
Sbjct: 179 TVDGLQMRITGNGFLYNMVRIIAGTLLDTGAGKFSPDDVKAMLEAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  SV Y 
Sbjct: 239 YLWSVCYD 246


>gi|220930998|ref|YP_002507906.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
 gi|220931093|ref|YP_002508001.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
 gi|219992308|gb|ACL68911.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
 gi|219992403|gb|ACL69006.1| pseudouridylate synthase I [Halothermothrix orenii H 168]
          Length = 246

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 127/248 (51%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R   + +EY+G+ Y GWQ Q N   +IQG + K +F +    V + GA RTD+GVHA 
Sbjct: 1   MERNIKITVEYDGTNYSGWQIQNNTPETIQGVLSKCLFDINKSPVKLIGASRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVA+F L        +  ALN+ L     I   +   V + FHARF A  + Y+YRI+ 
Sbjct: 61  GQVANFRLKVGIPVERIPLALNSKL--PPDIVCKDAEEVTEDFHARFDARGKRYIYRILN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P    +   + IP +L+ + MR A   L+G HDF +F++      + +RTI   D+ 
Sbjct: 119 SEYPSPFLRNYTYFIPHNLNIDKMREAGSLLIGEHDFASFQASGGSNKTTVRTITKLDIY 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                I+I V    FL+  +R   G+L  VG GK T   + + L+ +DR   G  APP G
Sbjct: 179 RDQYQIKIEVCGNGFLYKMVRIIAGTLIEVGLGKRTVKSVGQLLEIKDRDRAGFTAPPRG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LTLIEVFY 246


>gi|257088682|ref|ZP_05583043.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|256997494|gb|EEU84014.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|315160761|gb|EFU04778.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0645]
 gi|315579360|gb|EFU91551.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0630]
          Length = 249

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLVRMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|237808326|ref|YP_002892766.1| tRNA pseudouridine synthase A [Tolumonas auensis DSM 9187]
 gi|259550489|sp|C4LF13|TRUA_TOLAT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|237500587|gb|ACQ93180.1| tRNA pseudouridine synthase A [Tolumonas auensis DSM 9187]
          Length = 261

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+ Y+GWQRQ+  +S+Q  +E A+  V    V +  AGRTD+GV+A  QV
Sbjct: 1   MRIALGIEYFGADYYGWQRQREVNSVQQELETALSRVANHPVEIQCAGRTDAGVNATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +NA L   D I++    +VD  FHARFSA  R Y Y I     
Sbjct: 61  IHFDTTANRQMSAWTLGINAQL--PDDIAVRWAHVVDDNFHARFSATARRYRYIIYNEPL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           L+ + M  A Q L+G  DFT+FR+  CQ+++P R I    V+  G
Sbjct: 119 RPGILAKGVSHYYHPLNADQMNEAGQLLLGERDFTSFRAAQCQSNTPFRNIMSLSVHRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + + + A +FLH  +R+ +GSL LVG G+     + + L A+DR   G  A  EGLY 
Sbjct: 179 SYVILDIQANAFLHHMVRNIMGSLLLVGTGEKPKEWIGEILDAKDRTVSGATAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>gi|153952894|ref|YP_001393659.1| tRNA pseudouridine synthase A [Clostridium kluyveri DSM 555]
 gi|189029994|sp|A5N4T0|TRUA_CLOK5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146345775|gb|EDK32311.1| TruA [Clostridium kluyveri DSM 555]
          Length = 244

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    ++IEY+G+ Y GWQRQ N  +IQ  +E+AI   TGE   V G+ RTD+GVHA   
Sbjct: 1   MKNIKLVIEYDGTNYSGWQRQYNAITIQQRLEEAIEKATGEFSPVIGSSRTDAGVHARGF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +     +   LN  L   + I++L+   VD  FH+R+    + Y Y I+T  
Sbjct: 61  VCNFFTASKIPTSNIKMVLNTLL--PEDIAVLDSKEVDSSFHSRYFTTGKEYSYTIVTGD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  + +   +   + LD E ++ + ++ +G HDF+ F+     A S IRTI    V   
Sbjct: 119 RPPVIGRQYVYYFRRKLDIEKIKNSCEYFIGTHDFSAFKKKGSTARSSIRTIKELTVLKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N+I+  +V   FL+  +R  +G+L  VG G+++   ++  L+++DR + G   P +GL 
Sbjct: 179 KNIIKFNIVGDGFLYNMVRIIIGTLLEVGLGRFSIEYVKYILESKDRAKAGKPVPAKGLC 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>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 =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 99/247 (40%), Positives = 136/247 (55%), Gaps = 2/247 (0%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E          N+ L   D + I  +      FHAR+SAI R Y Y I+ R 
Sbjct: 61  VVHFDAKVERELHTWVLGGNSNL--PDDVRITWVKPAVGDFHARYSAIARFYRYVILNRP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL + +A      LD + M  AAQHL+G+HDF+TFR+  CQ+ SP R +   DV   
Sbjct: 119 IKSALLRNQATWHHNPLDADKMHRAAQHLIGKHDFSTFRAQGCQSKSPCREMYFIDVYRD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + + I + A +FLH  +R+  G L  +G GK   +  ++ L+ ++RK  G  APP GLY
Sbjct: 179 DDKVIIDISANAFLHHMVRNIAGVLMDIGAGKQDESWTQELLEVKNRKLGGVTAPPYGLY 238

Query: 241 FDSVEYS 247
             +V Y 
Sbjct: 239 LGAVYYP 245


>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 =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 90/251 (35%), Positives = 139/251 (55%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + H D           +  NA+L    T+++     V + FHARFSA RR+Y Y +++  
Sbjct: 61  IIHLDTDLVREAFSWVRGTNAFL--PSTVAVRWAQAVPEDFHARFSAHRRTYYYALVSGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L  G+A  +     +SLD   M+ AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRSPLLGGKAGYVMLPPGESLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKTLYSAE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+   +FLH  +R+ +G L  +G G+  +  + + L A+DRK   P   P
Sbjct: 179 VRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRRPAAWMAEVLAARDRKAAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>gi|268608385|ref|ZP_06142112.1| tRNA pseudouridine synthase A [Ruminococcus flavefaciens FD-1]
          Length = 257

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 125/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I Y G+ Y G+Q Q N  ++QG++EK +  V  E V + G  RTD+GVHA   
Sbjct: 1   MRNLKVTIAYRGTNYHGFQIQNNAVTVQGTLEKHLSKVLNEPVSITGCSRTDTGVHANMF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             +         +  C+ +N  L   D ISIL+   V   FHARF    + Y+Y++   +
Sbjct: 61  CFNVKTNSRISTLGFCRGVNGEL--PDDISILSCEEVPIDFHARFDCKGKEYIYKMHCSE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +         +   +  D E  R AAQ+ VG HDF++F +     S+ +RTI  F + + 
Sbjct: 119 SKDPFAPDMKFHYRRPFDIEAARKAAQYFVGTHDFSSFCADCTNVSTTVRTIYSFKIENS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + + V    FL+  IR   G+L  V + +++  D+ + L+A+DR + G  A   GLY
Sbjct: 179 GDTVIMLVKGNGFLYNMIRIMAGTLIDVSEKRFSPDDMPRILEAKDRLQAGRTAMAHGLY 238

Query: 241 FDSVEYS 247
            + V YS
Sbjct: 239 LNRVFYS 245


>gi|256618219|ref|ZP_05475065.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256597746|gb|EEU16922.1| tRNA pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|315033638|gb|EFT45570.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0017]
          Length = 246

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILKQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKNKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|167566409|ref|ZP_02359325.1| tRNA pseudouridine synthase A [Burkholderia oklahomensis EO147]
          Length = 270

 Score =  299 bits (767), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (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  VHFDTELDRADFSWVRGTNAFL--PSTVSVQWAKPMPDTFHARFAAFERTYYYALYVHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>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 =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

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--PDDVAVRWAKVVDDDFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+++P R + H +V+  G
Sbjct: 119 RSAILPQGVTHCHLELDHQLMHQAGQALLGENDFSSFRAAQCQSNTPWRNVHHLNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G  +   L   L  +DR    P A PEGLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGCGNQSVEWLAWLLAQKDRTLAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVFYP 244


>gi|160894723|ref|ZP_02075498.1| hypothetical protein CLOL250_02274 [Clostridium sp. L2-50]
 gi|156863657|gb|EDO57088.1| hypothetical protein CLOL250_02274 [Clostridium sp. L2-50]
          Length = 245

 Score =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 125/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +I+  + + I  +  E + V GA RTD+GVHA   
Sbjct: 1   MKRVKLVVAYDGTNYHGWQVQDNGITIEEVLNRTISELVQEDIKVIGASRTDAGVHACGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN  L   D I I     VD  FH R++   ++Y Y I+ R+
Sbjct: 61  VAVFDTESRIPGDKFSFALNQRL--PDDIRIQESCEVDADFHPRYADTVKTYEYNILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  ++  A      +D E M  AA +LVG HDF +F S   Q  + +RTI   +V   
Sbjct: 119 FEMPSKRLYAAFCYYPMDIERMNQAAAYLVGEHDFKSFCSAGAQVQTTVRTIYAVNVTKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ IR+    FL+  +R   G+L  VG G      +++ L+A+DR + GP A  +GL 
Sbjct: 179 DDMVHIRITGNGFLYNMVRIIAGTLMQVGTGLMEPERVKEILEARDRSKAGPTAVAKGLT 238

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 239 LVEIRYE 245


>gi|256822702|ref|YP_003146665.1| tRNA pseudouridine synthase A [Kangiella koreensis DSM 16069]
 gi|256796241|gb|ACV26897.1| tRNA pseudouridine synthase A [Kangiella koreensis DSM 16069]
          Length = 264

 Score =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 118/247 (47%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + IEY+G  Y GWQRQ + SS+Q ++EK +  +  E + V  AGRTD+GVHA  Q
Sbjct: 1   MTKVALCIEYDGHRYHGWQRQSHASSVQQTLEKVLSTIADEPIEVSCAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HF+L  E          N  L   D I++     V   FHARFSA  R Y Y I    
Sbjct: 61  IIHFELSNERPLKAWTMGANTQL--PDDIAVRWAHSVSDDFHARFSAKARRYRYIIANTP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+ +         LD + M  A  +  G  DF  F++  CQ+ +  R I H  V   
Sbjct: 119 TRPAISRSGLTWCRAPLDIDVMNQACAYFPGEQDFAAFQAASCQSKTSFRNIHHLFVERL 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +FLH  +R+  GSL  +G         ++ L  +DR +    A P GLY
Sbjct: 179 GEYVVIDIKANAFLHHMVRNIAGSLIEIGRYNQKPEWAKQLLDGKDRTQAASTASPNGLY 238

Query: 241 FDSVEYS 247
              VEY 
Sbjct: 239 LVDVEYP 245


>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 =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 112/246 (45%), Positives = 152/246 (61%), 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 Y      + + N  +V   FHARFSAI R Y+YRII R 
Sbjct: 69  VAHFDLSKYLEPYKIIKAIN-YFVRPYDVGVWNCELVSNNFHARFSAISRHYIYRIINRT 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|118581782|ref|YP_903032.1| tRNA pseudouridine synthase A [Pelobacter propionicus DSM 2379]
 gi|166228745|sp|A1AUF4|TRUA_PELPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|118504492|gb|ABL00975.1| tRNA pseudouridine synthase A [Pelobacter propionicus DSM 2379]
          Length = 244

 Score =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 124/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ Y GWQ Q NG ++Q  +E+A+  + GE V +  +GRTD+GVHA   
Sbjct: 1   MRTIKLTIEYDGTNYAGWQVQPNGLAVQQVLEEALLRLLGERVRLRSSGRTDAGVHARAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   R           N +L   D I+IL+ +    +F     A  + Y Y I    
Sbjct: 61  VASFTTSRSLPLQAFVGGANRFL--PDDIAILSAAEAAPEFRPIQDARSKWYRYTIYNAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +  +W + + LD + M++AA H  GRHDF  FR+ +C A + +R ID   + S 
Sbjct: 119 VRSPLRRLFSWHVREPLDTDAMQLAAHHFPGRHDFAAFRASNCAAKTTLRRIDSVTIASE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI I V+   FL   +R   G+L  VG G++    +   L+  DRK+ G  AP  GL 
Sbjct: 179 GELIVIDVIGEGFLKNMVRVMAGTLVDVGRGRFEPERVAWLLENPDRKKAGVTAPACGLC 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LMDVSY 244


>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 =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 123/251 (49%), Positives = 169/251 (67%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           APL  ++G AW + ++LD + M+  A  L+GRHDFTTFRS  CQA SP++T+D   V   
Sbjct: 120 APLVHDRGNAWRVVQALDADAMQAGADRLIGRHDFTTFRSTMCQADSPVKTLDELRVETL 179

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

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 DGLYLARVGYP 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 =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 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|167577247|ref|ZP_02370121.1| tRNA pseudouridine synthase A [Burkholderia thailandensis TXDOH]
          Length = 270

 Score =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (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  VHFDTDLDRADFSWVRGTNAFL--PSTVAVQWAKPMPDTFHARFAAFERTYYYALYVHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|255974352|ref|ZP_05424938.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|257088141|ref|ZP_05582502.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
 gi|307278161|ref|ZP_07559243.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|255967224|gb|EET97846.1| tRNA pseudouridine synthase [Enterococcus faecalis T2]
 gi|256996171|gb|EEU83473.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
 gi|306505150|gb|EFM74338.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0860]
 gi|315026898|gb|EFT38830.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2137]
          Length = 246

 Score =  299 bits (766), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKNKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|170761533|ref|YP_001788787.1| tRNA pseudouridine synthase A [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169408522|gb|ACA56933.1| tRNA pseudouridine synthase A [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 246

 Score =  299 bits (766), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EK I  +T E V + G  RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGTNYCGWQKQKNEKFITLQGTLEKVISNITKEKVEIIGVSRTDSGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             V +F       P  L K +N  L     I +L+   V  +FH+RF +  ++Y Y ++ 
Sbjct: 61  GYVCNFFTNTRIPPENLQKVINNNL--PQDIVVLSSEEVSNEFHSRFCSKGKTYEYTVLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P+A+ +   +     L+ +NM+IA+++ +G HDF+ F++      + +RTI+ F+++
Sbjct: 119 SPQPIAIGRNYIFQFKDKLNIDNMKIASRYFIGTHDFSAFKTKGSSVKTSVRTINEFEID 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+  +    FL+  +R  VG L  +G  K     +E  ++++DR++ G   P  G
Sbjct: 179 KKGDFIKFTITGDGFLYNMVRIIVGILIEIGLNKREPEYVEYVIKSKDRRKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 246


>gi|315151105|gb|EFT95121.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0012]
          Length = 249

 Score =  299 bits (766), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGRSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 239 GLYLAEVRYE 248


>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 =  299 bits (766), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 118/247 (47%), Positives = 156/247 (63%), Gaps = 1/247 (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 +    + +SIL    V  +FHARFSA  R Y+YRII R+
Sbjct: 61  VAHIDLSKEFTTDKVRDAMN-HFMKDEPVSILLAEEVSDEFHARFSAYARHYIYRIIDRR 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 FDSVEYS 247
              V+Y 
Sbjct: 240 LSQVDYP 246


>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 =  299 bits (766), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G  Y GWQ Q  G ++Q +++ A+  +    V V+ AGRTD+GVHAL QV
Sbjct: 1   MRIALGVEYDGKPYCGWQSQPGGRTVQDTLQSALSHIADAPVTVNAAGRTDTGVHALEQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+           + +NA L    ++ +     V  +FHARFSA  RSY Y +I +  
Sbjct: 61  VHFETDANRPLSAWVRGVNAML--PPSVVVRWAHPVPDEFHARFSAQGRSYRYLLINKPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G+A      LD   MR AA +L+G HDF+ FR+  CQA SP++ ++  D+   G
Sbjct: 119 RSAIHAGKAGWFHLPLDIALMREAAGYLLGEHDFSAFRAAECQAKSPVKCMNKIDIYLNG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +++   + A +FLH  +R+ VG L  VG GK+    +   L ++ R    P   P+GLY 
Sbjct: 179 DVLVFDLEANAFLHHMVRNIVGCLVYVGKGKYPPAWMADLLASRTRHLAAPTFSPDGLYL 238

Query: 242 DSVEYS 247
             ++Y 
Sbjct: 239 RRIQYD 244


>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 =  299 bits (766), Expect = 3e-79,   Method: Composition-based stats.
 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|52425230|ref|YP_088367.1| tRNA pseudouridine synthase A [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307282|gb|AAU37782.1| TruA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 270

 Score =  299 bits (765), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  YFGWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   QV
Sbjct: 8   MKIALGIEYNGKNYFGWQRQEKVHSVQAELEKALSFVANEKIEVFCAGRTDSGVHGTGQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA L   D I++     V   FHARFSA  R Y Y +   + 
Sbjct: 68  VHFETNAIRPEKAWAFGTNANL--PDDIAVRWAKEVPDDFHARFSATARRYRYVLYCNKL 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M+ A + L+G +DF++FR+  CQ+++P R I H +V   G
Sbjct: 126 RSAILPYGITHTHLDLDEHKMQEAGRFLLGENDFSSFRAAQCQSNTPWRNIHHLNVIRRG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + + + A +F+H  +R+ VGSL  VG G      +E  L  ++RK   P A  EGLY 
Sbjct: 186 NFVIVDIKANAFVHHMVRNIVGSLMEVGCGNQPPEWIEWLLAQKNRKLAAPTAKAEGLYL 245

Query: 242 DSVEYS 247
             V Y 
Sbjct: 246 VQVTYP 251


>gi|315169224|gb|EFU13241.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1341]
 gi|315171531|gb|EFU15548.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1342]
          Length = 277

 Score =  299 bits (765), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 32  MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 91

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 92  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 149

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 150 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKNKKSTTRTIEKITIER 209

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 210 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 269

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 270 FLDEVYY 276


>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 =  299 bits (765), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + IEY+G+ + GWQ +Q    ++Q  +E A+  V    V V  AGRTD+GVH   
Sbjct: 1   MTRIALGIEYDGTDFRGWQTQQPGVRTVQECLEAALSKVANHPVAVVCAGRTDAGVHGTG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD              N  L     +++   + VD  FHARFSA+ R Y Y I   
Sbjct: 61  QVVHFDSEAPREMKSWIMGANTNL--PRDVTVRWATPVDDAFHARFSAVSRRYRYVIYNH 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P AL + +     + LD   MR AA +LVG HDFT +RS+HCQA SP++T+   ++  
Sbjct: 119 ARPPALFRNQVTWNYRPLDVAAMREAAAYLVGEHDFTAYRSVHCQAKSPLKTMHSLELYE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++ +   A +FL   +R+  G L  VG GK  +    + L+ +DR++    APP GL
Sbjct: 179 HGKVLVLEAHANAFLMHMVRNIAGVLMSVGAGKRPAHWAREVLEGRDRRKGAATAPPFGL 238

Query: 240 YFDSVEYS 247
           Y   +EY 
Sbjct: 239 YLVDIEYP 246


>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 =  299 bits (765), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 113/247 (45%), Positives = 156/247 (63%), Gaps = 1/247 (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 FDSVEYS 247
              V+Y 
Sbjct: 240 LTGVDYP 246


>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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 84/246 (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+     V   FHARF+A  R+Y Y +     
Sbjct: 66  VHFDTLLDRAAFSWVRGVNAFL--PPSVSVQWAKPVPPTFHARFAAFERTYFYVLYVHPV 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|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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (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  VHFDTDLDRADFSWVRGTNAFL--PSTVAVQWAKPMPDTFHARFAAFERTYYYALYVHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   +KG+ W I   LD   M+  A  L+GRHDFTTFRS  CQA+SP++T+D   V   
Sbjct: 120 APATHDKGQVWQIGHPLDVAAMQEGADMLIGRHDFTTFRSSICQAASPVKTLDELRVEQV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 113/246 (45%), Positives = 155/246 (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  VAHFNMERQFELYRIRNGINYHLKA-IPIVVLSAEAVDDAFHARFSAKKRYYEYRIINRY 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|332992505|gb|AEF02560.1| tRNA pseudouridine synthase A [Alteromonas sp. SN2]
          Length = 263

 Score =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 94/247 (38%), Positives = 132/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+G+   GWQRQK+ +S+Q  +EKA+ ++  + ++V  AGRTD+GVHA  Q
Sbjct: 1   MGRIALGIEYDGASVHGWQRQKDVASVQEYLEKALTVIANKPIIVFCAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD   E         +NA +   DTI++     V   FHARFSA  R Y Y I   +
Sbjct: 61  IVHFDSDVERPERAWTLGINANM--PDTIAVTWAKPVSDDFHARFSATHRRYRYVIYNSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+         + LD E M  AAQ LVG HDFTTFR+  CQ+ +P RT+    V+  
Sbjct: 119 MRPAILHNGVTHEYRELDAEKMHEAAQALVGEHDFTTFRASLCQSKTPHRTVSSVSVHRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + + + A +FLH  +R+  GSL  +G G+     +   L  +DR +    A P GLY
Sbjct: 179 GRYVVLDIRANAFLHHMVRNITGSLLCIGAGEQPVDWMAHLLTLKDRAKAATTAKPNGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LVDVTYP 245


>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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +++ Y+GS Y GWQ Q     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  VHFETKALRSPYSWAMGVNHFL--PADVSVSWAGAVPEDFHARYTATSRSYRYVIYNHPI 140

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E+M  A  HL+G +DF+ FR   CQ+ SP R +   +V+ FG
Sbjct: 141 RPAWLNNSVTWNYRPLDVESMSAAGAHLIGENDFSAFRGSDCQSKSPFRNLTRLEVSRFG 200

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +++ I V A +FLH  +R+  G+L  VG GK  S  +   L ++ R + G  APP GLY 
Sbjct: 201 DMVVIEVEANAFLHHMVRNISGTLMAVGTGKKPSDWVADVLASKKRSKAGVTAPPFGLYL 260

Query: 242 DSVEYS 247
            SV Y 
Sbjct: 261 TSVTYP 266


>gi|256762037|ref|ZP_05502617.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
 gi|256683288|gb|EEU22983.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
          Length = 249

 Score =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++    + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERASEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>gi|167855019|ref|ZP_02477793.1| ribonuclease G [Haemophilus parasuis 29755]
 gi|167853867|gb|EDS25107.1| ribonuclease G [Haemophilus parasuis 29755]
          Length = 262

 Score =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+G  Y GWQRQ+   S+Q  +E+A+ ++      V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYDGRRYCGWQRQQYVDSVQQRLEEALSVIANSSCEVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD          C   NA+L   + I +     V   FHARFSA+ R Y Y I   + 
Sbjct: 61  VHFDTDVNRPMQSWCLGTNAHL--PEDIVVKWAIGVSDDFHARFSALARRYRYVIYNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+          SLD E M  A Q L+G +DF++FR+  CQ+ +P R + H  V+   
Sbjct: 119 RSAILPKGISHYHYSLDHEKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLIVSRHQ 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A  EGLY 
Sbjct: 179 DYIILDIQANAFVHHMVRNIVGSLIEVGRGDKPVEWIKWLLEKRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VEVIYP 244


>gi|260893342|ref|YP_003239439.1| tRNA pseudouridine synthase A [Ammonifex degensii KC4]
 gi|260865483|gb|ACX52589.1| tRNA pseudouridine synthase A [Ammonifex degensii KC4]
          Length = 259

 Score =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 83/244 (34%), Positives = 125/244 (51%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + + Y+G+ + G+QRQ    ++QG +E+A+  +T E   V GAGRTD+GVHA  QV  
Sbjct: 6   VALKVAYDGTAFSGFQRQPGLRTVQGVLEEALARLTKETCQVKGAGRTDAGVHAEGQVVS 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F          L  ALN  L     +++L  + V +QFH R+ A+ + Y Y    R    
Sbjct: 66  FRTASSIPTPRLVPALNGLL--PPDVAVLAAAEVPEQFHPRYDAVSKVYRYTFFRRAVRC 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
            L +  A  +P+ LD E MR AA +L GRHDF  F++      S +RT+    +   G  
Sbjct: 124 PLTRFYALHVPEPLDVERMREAAAYLGGRHDFRAFQNTGRPVKSSVRTVFSCRLEEAGPF 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   + A  FL+  +R   G+L  +G GK   + +  AL+  +R+  GP APP GL    
Sbjct: 184 LYFWIEADGFLYQMVRVIAGTLLEIGRGKLEPSVILAALEKGERQLLGPTAPPHGLCLVQ 243

Query: 244 VEYS 247
           V+Y 
Sbjct: 244 VKYP 247


>gi|167840379|ref|ZP_02467063.1| tRNA pseudouridine synthase A [Burkholderia thailandensis MSMB43]
          Length = 270

 Score =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 131/246 (53%), Gaps = 2/246 (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  VHFDTDLDRADFSWVRGTNAFL--PSTIAVQWAKPMPDTFHARFAAYERTYYYALYVHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 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|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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 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 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APL +EK RA   P+ LD E M  AAQ LVGRHDFTTFRS+ CQA SP+R++D  DV  
Sbjct: 121 RAPLVIEKNRALWSPRPLDAEAMHEAAQRLVGRHDFTTFRSVQCQADSPVRSLDRLDVTR 180

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            G   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|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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 131/246 (53%), Gaps = 2/246 (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 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 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 =  298 bits (764), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (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  VHFDTDLDRADFSWVRGTNAFL--PPTVAVQWAKPMPDTFHARFAAFERTYYYALYVHPV 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 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|257899365|ref|ZP_05679018.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
 gi|257837277|gb|EEV62351.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
          Length = 248

 Score =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQRMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV ++FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRKVEIVSEEFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +      +  A   P  LD   ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 119 KPRSPFRRHYASYYPYPLDLGKIQRALPDLLGTHDFTSFCASGSSIEDKVRTIYEAKMEV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A PE
Sbjct: 179 NETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPAIIAKKDRNAAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLYEVKYE 248


>gi|16273533|ref|NP_439786.1| tRNA pseudouridine synthase A [Haemophilus influenzae Rd KW20]
 gi|260580419|ref|ZP_05848248.1| tRNA pseudouridine synthase A [Haemophilus influenzae RdAW]
 gi|1174804|sp|P45291|TRUA_HAEIN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1574492|gb|AAC23291.1| pseudouridylate synthase I (truA) [Haemophilus influenzae Rd KW20]
 gi|260093096|gb|EEW77030.1| tRNA pseudouridine synthase A [Haemophilus influenzae RdAW]
          Length = 269

 Score =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGTGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|297528514|ref|YP_003669789.1| tRNA pseudouridine synthase A [Geobacillus sp. C56-T3]
 gi|297251766|gb|ADI25212.1| tRNA pseudouridine synthase A [Geobacillus sp. C56-T3]
          Length = 258

 Score =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            R   II Y+G+ + G+Q Q    ++QG  E+ +  +  G  V V  +GRTD+GVHA  Q
Sbjct: 3   TRIKCIIAYDGTHFSGYQIQPGKRTVQGEFEEVLRRMHKGTKVRVAASGRTDAGVHAYGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           KALNA L   D I +  +   D  FHARFSA  + Y Y++ T  
Sbjct: 63  VIHFDTSLSLSSEQWKKALNAQL--PDDIVVRFVQEADADFHARFSAKAKEYRYKVWTAA 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +      P SL    M  A + L G HDFT+F S        +RT+   +V + 
Sbjct: 121 ERDVFRRHYCAWHPYSLHISAMNEALRLLHGTHDFTSFCSAKTLIEDRVRTMYRAEVKAD 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G ++E R V   FL+  +R  VG++  +G GK +  D+   L A+DR+  GP AP EGLY
Sbjct: 181 GPMLEFRFVGSGFLYNMVRIIVGTVLEIGQGKRSPADISMLLAAKDRRLAGPTAPAEGLY 240

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 241 LWRVYYE 247


>gi|222056725|ref|YP_002539087.1| tRNA pseudouridine synthase A [Geobacter sp. FRC-32]
 gi|254789637|sp|B9M6W5|TRUA_GEOSF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221566014|gb|ACM21986.1| tRNA pseudouridine synthase A [Geobacter sp. FRC-32]
          Length = 244

 Score =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 124/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ Y GWQ Q NG +IQ  IE+++  + G+ V +  +GRTD+GVHAL  
Sbjct: 1   MRNIKLIIEYDGTAYCGWQLQPNGITIQQVIEESLEKMLGQSVRLQSSGRTDAGVHALGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   ++         LN  L     I+I + S V   F+ R  AI + Y Y I   +
Sbjct: 61  VAVFKTQKDLPVRAFSDGLNCLL--PPDIAIRDASEVPLSFNPRADAISKHYRYTIYNSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +  +W +   L+ E M++ A H VG HDF  FR+ +C A + IR + H  V   
Sbjct: 119 RRSPLTRLNSWHLRGILNMELMQLGASHFVGEHDFAAFRASNCVAKTTIRRMFHVSVAKV 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I V    FL   +R   G+L  VG GK   + +   L   DR   G  APP+GL 
Sbjct: 179 GDSVIIDVHGSGFLKNMVRVIAGTLVAVGQGKLDPSAIPGLLAGGDRSASGITAPPQGLC 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LMEVFY 244


>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 =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 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  VAHFDTRAVRPASAWVRGVNALL--PPAVVVRWSTEVGDDFHARFLACERQYRYILHNAP 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|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 =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (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 L   D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRNEGAWTLGVNANL--PDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>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 =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 112/246 (45%), Positives = 152/246 (61%), 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 Y      + + N  +V   FHARFSAI R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPYKIIKAIN-YFVRPYDVGVWNCELVSNNFHARFSAISRHYIYRIINRT 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|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 =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD     +        NA L     ++IL    V++ FHARFSAI R Y Y ++ R+ 
Sbjct: 61  VHFDTTTFRLEHHWVFGGNANL--PPEVAILWAQPVNEAFHARFSAIARHYRYIVLNRRT 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+   R     + L    M+ A   LVG HDF++FR+  CQA SP+R + H +V   G
Sbjct: 119 RPAIANRRVTWYCQPLSVTKMKEAGAFLVGEHDFSSFRAKACQAKSPVRNVHHLEVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +FLH  +R+  G L  +G G+      E+ LQA+ R   G  A P+GLY 
Sbjct: 179 DWIIMDISANAFLHHMVRNIAGVLMAIGKGEQPPRWAEEVLQARCRAVGGVTARPDGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 244


>gi|329577713|gb|EGG59139.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1467]
          Length = 249

 Score =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGAHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        IRTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKIRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>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 =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

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--PDDIAVRWAKVVEDDFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+++P R + H +V   G
Sbjct: 119 RSAILPQGVTHYHLELDHQLMHGAGQALLGENDFSSFRAAQCQSNTPWRNVHHLNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A PEGLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGCGNQPVEWMKWLLEQKDRTLAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVIYP 244


>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 =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (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 L   D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETHAIRNEGAWTLGVNANL--PDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>gi|257083304|ref|ZP_05577665.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256991334|gb|EEU78636.1| tRNA pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 246

 Score =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTNKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 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 =  298 bits (763), Expect = 5e-79,   Method: Composition-based stats.
 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
             LALE+ RAW + + LD   M   A  LVGRHDFTTFR++ CQA+SP++T+D  +V   
Sbjct: 120 PDLALERNRAWRVLRPLDVAGMAEGAARLVGRHDFTTFRAVGCQAASPLKTLDRLEVEEV 179

Query: 180 --FGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 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|322418344|ref|YP_004197567.1| tRNA pseudouridine synthase A [Geobacter sp. M18]
 gi|320124731|gb|ADW12291.1| tRNA pseudouridine synthase A [Geobacter sp. M18]
          Length = 250

 Score =  298 bits (763), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 120/247 (48%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ Y GWQ Q NG ++Q  +E A+  + GE   +H +GRTD+GVHA   
Sbjct: 1   MRNIKLIIEYDGTAYSGWQVQPNGVTVQAVMEDALSRMLGERTPLHASGRTDAGVHARGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   +        + LN  L     I++   + V   FH RF A  + Y Y ++   
Sbjct: 61  VACFKTGKTMPLRAFREGLNTLL--PSDIAVREAAEVPLGFHPRFDAQAKHYRYTMLLDD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +  AW I   LD E MR A    VG HDF  FR  +C A + +R I   ++   
Sbjct: 119 LRSPLSRHTAWRIKGKLDLEAMRAACTVFVGEHDFAAFRGANCAAKTTVRRIYSMELVQE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +    FL   +R   G+L  VG G+  + D+ + L+  DR+  G   PP+GL 
Sbjct: 179 DRLLHLDIKGSGFLKNMVRIITGTLVDVGQGRLGAADVARLLKGGDRQNAGMTVPPQGLC 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LMRVFYP 245


>gi|312904650|ref|ZP_07763805.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
 gi|310632002|gb|EFQ15285.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
          Length = 249

 Score =  298 bits (763), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLVRMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP A PE
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLVGPTAHPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLAEVKYE 248


>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 =  298 bits (763), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 109/246 (44%), Positives = 150/246 (60%), 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 Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIITAIN-YFVRPYAVGVWNCELAPNNFHARFSATSRYYIYRIINRP 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|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 =  297 bits (762), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (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 L   D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETQAIRNEGAWTLGVNANL--PDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>gi|325678788|ref|ZP_08158386.1| tRNA pseudouridine synthase A [Ruminococcus albus 8]
 gi|324109292|gb|EGC03510.1| tRNA pseudouridine synthase A [Ruminococcus albus 8]
          Length = 250

 Score =  297 bits (762), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 127/247 (51%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + + Y+GSGY GWQRQ N  ++Q  +E AIF +TGE VVV G  RTD+GVHA   
Sbjct: 1   MRNFKVTLAYDGSGYHGWQRQSNALAVQEVVENAIFKLTGEKVVVQGCSRTDAGVHARMY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V   +L     P  +   LN++L   D IS++     +  FHAR+    + Y Y +   +
Sbjct: 61  VLSMELESTITPRGIQLGLNSWL--PDDISVIGCEECEAGFHARYHCKGKEYEYIVHNSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 K  A+     +D   +  AA+  VG HDF  F S  C     +RTI  FDV   
Sbjct: 119 IKDPFLKNTAFRNTYPIDEVLLDKAAKDYVGEHDFKAFCSTACDKEITVRTIYRFDVRRE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+   V    FL+  +R  VG+L  + +GK  +  + + ++++DR + G   PP+GLY
Sbjct: 179 GELVIFTVAGNGFLYNMVRIMVGTLLFINEGKIAADAIPRIIESKDRTKAGKTVPPQGLY 238

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 239 LNKVYYD 245


>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 =  297 bits (762), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+QG +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 14  KIALGIEYDGSRYYGWQRQAEVDSVQGCLEAALSQVANERIDVFCAGRTDAGVHATGQVV 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA L     I++  +  VD  FHARFSA  R Y Y I  R+  
Sbjct: 74  HFTTRAARKDAAWTMGVNANL--PPDIAVRWVKTVDDAFHARFSATARRYRYVIYNRRFR 131

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  A Q L+G +DFT+FR++ CQ+ +P R + H  V   G+
Sbjct: 132 PAILSRGVTHYYLPLDAERMHRAGQCLLGENDFTSFRAVQCQSRTPWRNLMHLRVARQGD 191

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G  +   + + L A+DR      A  +GLY  
Sbjct: 192 YVVVDIKANAFVHHMVRNIVGSLMEIGCGNQSENWMAELLAAKDRTLAAATAKADGLYLV 251

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 252 SVDYP 256


>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 =  297 bits (762), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 120/247 (48%), Positives = 159/247 (64%), Gaps = 1/247 (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  VVSFDLSKAFKADTVRDAMNAFLAR-EPVSVLAAEQVDDEFSARFSATGRMYLYRILTRR 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 FDSVEYS 247
              V Y 
Sbjct: 240 LTHVTYE 246


>gi|323703112|ref|ZP_08114766.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
 gi|323531889|gb|EGB21774.1| tRNA pseudouridine synthase A [Desulfotomaculum nigrificans DSM
           574]
          Length = 245

 Score =  297 bits (762), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQR  +   +IQG IE  +  +TGE + + G+GRTD+GVHAL 
Sbjct: 1   MRNIKLTIQYDGSRYRGWQRLGDTDVTIQGKIEAVLSRMTGEEIEIFGSGRTDTGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   L  YL   + I +  +  V  +FHAR++   + YLY+I   
Sbjct: 61  QVANFKTNSNMSTGEIMDYLYHYL--PEDIVVTRVEEVSDRFHARYNVKSKKYLYKIWNH 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +     +P+ L  + M+ AA  L+G HDF +FR+   +  S ++TI   D+  
Sbjct: 119 KYHDPFRRKFVHHVPEPLQIKAMQKAAAFLIGEHDFASFRASKSKKKSSVKTIYAIDIVK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              LI+I V    FLH  +R  VG+L  VG G      +++ L  +DR   GP AP +GL
Sbjct: 179 KDPLIKITVHGNGFLHNMVRIIVGTLVEVGLGHMRPEQVKEILSKKDRSAAGPTAPAKGL 238

Query: 240 YFDSVEY 246
           Y   VEY
Sbjct: 239 YLLEVEY 245


>gi|68249766|ref|YP_248878.1| tRNA pseudouridine synthase A [Haemophilus influenzae 86-028NP]
 gi|81335806|sp|Q4QL79|TRUA_HAEI8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|68057965|gb|AAX88218.1| tRNA pseudouridine synthase A [Haemophilus influenzae 86-028NP]
          Length = 269

 Score =  297 bits (762), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|332982675|ref|YP_004464116.1| tRNA pseudouridine synthase A [Mahella australiensis 50-1 BON]
 gi|332700353|gb|AEE97294.1| tRNA pseudouridine synthase A [Mahella australiensis 50-1 BON]
          Length = 245

 Score =  297 bits (762), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   + ++Y+G+ Y GWQ QKN  +IQ  +E+AI  +TG+   V  AGRTD GVHAL 
Sbjct: 1   MERNIKLTLQYDGTAYAGWQYQKNALTIQQVVEEAIESLTGQHSTVIAAGRTDRGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F             ALNA L   + I +++   V   FHARF A  + Y Y I   
Sbjct: 61  QVTNFKTESNIPTDRWLYALNAVL--PEDIRVIDAQDVLPSFHARFDAKGKLYRYIIWNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL +  +  + + LD + M+ AA + VG HDF++F++        +R I    + +
Sbjct: 119 PYSSALLRNFSLHVARPLDADAMKRAALYFVGTHDFSSFQASGSTVRDTVRNIWDISIQT 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +I I +    FL+  +R  VG+L  VG GK T+ D +  L+A+DRK  G  A P GL
Sbjct: 179 EGKMISISISGDGFLYNMVRIMVGTLIDVGIGKITACDAKLILEARDRKRAGKTAGPHGL 238

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 239 YLVEVYY 245


>gi|253577209|ref|ZP_04854529.1| tRNA pseudouridine synthase A [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251843453|gb|EES71481.1| tRNA pseudouridine synthase A [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 261

 Score =  297 bits (762), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 92/257 (35%), Positives = 132/257 (51%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    M + Y+G+ YFG+Q Q  G+++Q  IE AI  +TGE V +HG+GRTD+GVHA +Q
Sbjct: 1   MRNLLMTVSYDGTNYFGFQTQPGGNTVQDHIEGAIRQLTGETVKIHGSGRTDAGVHARQQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             HF           C ALNA L     I +L    V   FH+R SA R++Y Y I T +
Sbjct: 61  PFHFHTDSRIPVERWCLALNARL--PSDIRVLTAREVPLTFHSRHSAKRKTYRYTINTNR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--- 177
            P   ++   +  P  L+ + M+ +  +LVG HDFT+F S      S +RTI    +   
Sbjct: 119 FPDVFQRNYQFHHPGQLNVDAMQASLPYLVGTHDFTSFASRQSTKLSHVRTIYDARIVVD 178

Query: 178 -------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                   +   ++   V    FL   +R  VG+L  +G+GK T   ++  L+A+DR   
Sbjct: 179 SLAKIPGTTGQGIVHFYVTGSGFLQHMVRIIVGTLIEIGEGKRTPESIQAILEAKDRTAA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           GP A  +GL   SVEY 
Sbjct: 239 GPTAESKGLMLWSVEYE 255


>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 =  297 bits (762), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 96/250 (38%), Positives = 137/250 (54%), Gaps = 5/250 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD---KQFHARFSAIRRSYLYRII 117
           V H D   E +PV   + +N+YL    +I++     V      FHAR SAI R Y Y + 
Sbjct: 64  VVHLDTGLERLPVSWVRGINSYL--PSSIAVRWACEVPGGKDGFHARSSAIARRYRYLVY 121

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L K RA  + + LD E MR  A  L+G HDF+ FR+  CQ+ +P++T++   +
Sbjct: 122 NSPVRSPLWKNRAGWVFRPLDLEWMREGAGFLLGEHDFSAFRAAECQSITPVKTMNGIGI 181

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              GNLI     A +FLH  IR+ VGSL +VG G      +++ L+++DR +  P   P+
Sbjct: 182 EKQGNLIVFTFEANAFLHHMIRNIVGSLIVVGKGNRPPKWMKELLESRDRSQAAPTFMPD 241

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 242 GLYLSRVFYE 251


>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 =  297 bits (761), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 144/246 (58%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R+ + +E++GS + GWQ Q+N  S+Q ++E+A+  +  E + VHG+GRTD+GVHA  QV
Sbjct: 13  QRFRITVEFDGSAFSGWQSQQNAPSVQQALEQALAPLHNEPIRVHGSGRTDAGVHATGQV 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD           + LN   +   +I++L    V + FHAR+ A  R YLYRI TR+ 
Sbjct: 73  AHFDAPAHRDAATYLRILNV--RTPHSIAVLACQPVAESFHARYDAYYRQYLYRINTRKI 130

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P ALE+ R W  P  LD E +  A+  L+G HDF++FR+  CQ+ SP++ +        G
Sbjct: 131 PPALERSRVWHYPYLLDAERLAEASALLLGTHDFSSFRAAGCQSKSPVKFMRLIQWQQRG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  ++ + A +FL   +R+ VG+L LVG G W    + + L A+DR + GP AP  GLY 
Sbjct: 191 DEWQVSIGANAFLQHMVRNLVGTLVLVGKGDWPVARVAELLAARDRVQAGPTAPAWGLYL 250

Query: 242 DSVEYS 247
             + Y 
Sbjct: 251 THICYP 256


>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 =  297 bits (761), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 129/246 (52%), Gaps = 2/246 (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 L   D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETHAIRNEGAWTLGVNANL--PDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 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 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>gi|28212149|ref|NP_783093.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
 gi|38258761|sp|Q890R5|TRUA2_CLOTE RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|28204593|gb|AAO37030.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
          Length = 248

 Score =  297 bits (761), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 134/250 (53%), Gaps = 5/250 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M R   + +EY+G+ Y GWQ+QK+ +  +IQ SIEKAI   T E V + G+ RTD+GVHA
Sbjct: 1   MARNVRLKVEYDGTNYSGWQKQKDKNIKTIQSSIEKAIEEATKEEVELIGSSRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L   A+F             ALN +L   + I IL    V  +FH+RF  I ++Y+Y+I+
Sbjct: 61  LAYTANFKTCSTIPGEKFKHALNRFL--PEDIVILESEEVPMEFHSRFDCIGKTYVYKIL 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R     +++   + +   LD  +M  A++ L+G HDF  F+       + +RTI + ++
Sbjct: 119 NRPLFSPIQRNYIYHVKDELDINSMIEASKFLIGTHDFNAFKKSGGNLKTTVRTITNINI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               +++EI V    FL+  +R   G+L  VG  +    D+   LQ++DR + G  AP  
Sbjct: 179 LKSNDIVEIHVSGDGFLYNMVRIISGTLIEVGLSRRKPEDISIILQSKDRCKAGMCAPAR 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y+
Sbjct: 239 GLYLKELFYN 248


>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 =  297 bits (761), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 109/246 (44%), 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   MYRYKITIEYLGTHFSGWQRQAGVLSVQQILEEAIYKFSGEQVTLFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +AHFDL +   P  + KA+N Y      + + N  +V   FHARFSA  R Y+YRI+ R 
Sbjct: 61  IAHFDLSKYLEPYKIIKAIN-YFVRPYAVGVWNCELVSNNFHARFSATSRHYIYRIVNRT 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|145630935|ref|ZP_01786711.1| tRNA pseudouridine synthase A [Haemophilus influenzae R3021]
 gi|144983402|gb|EDJ90878.1| tRNA pseudouridine synthase A [Haemophilus influenzae R3021]
          Length = 269

 Score =  297 bits (761), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVYHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|225570923|ref|ZP_03779946.1| hypothetical protein CLOHYLEM_07027 [Clostridium hylemonae DSM
           15053]
 gi|225160385|gb|EEG73004.1| hypothetical protein CLOHYLEM_07027 [Clostridium hylemonae DSM
           15053]
          Length = 282

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 125/246 (50%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I Y+G+ Y GWQ Q NG +I+  +   +  +TGE + V GA RTDSGVHAL  V
Sbjct: 37  RRIRLVIAYDGTDYCGWQIQPNGITIEEVLNGVLTKLTGEDIHVIGASRTDSGVHALGNV 96

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF-SAIRRSYLYRIITRQ 120
           A FD      P  +  ALN  L     I I+    V   +H R+   + ++Y Y I    
Sbjct: 97  AVFDTASSIPPERMAYALNQRL--PKDIVIVRSDEVPAGWHPRYRDVVIKTYEYHIYNAP 154

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L++  +  I   L+ E MR  A++L+G HDF +F ++       +RT+    ++S 
Sbjct: 155 VQNPLKRRTSTHISFPLNVEKMREGAKYLIGEHDFASFCNVRTSVKDTVRTVTELRIDSD 214

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +R+    FL+  +R   G+L  VG G +    +++ L+A++R   G   PP GL 
Sbjct: 215 GPEIIMRITGNGFLYNMVRIIAGTLIRVGRGFYEPEKVKEILEAKERTGAGVTVPPNGLV 274

Query: 241 FDSVEY 246
              ++Y
Sbjct: 275 LVEIDY 280


>gi|1644206|dbj|BAA10987.1| unknown [Bacillus subtilis]
          Length = 247

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R    I Y+G  + G+Q Q    ++Q  +EKA+ ++  + + + V  +GRTDSGVHA  
Sbjct: 1   MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L   D I++    I D  FHARFSA+++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAERWPYALNALL--PDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ ++MR AA+H +G HDFT+F +   +    +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFSYRLNVQDMREAAKHPIGTHDFTSFCAAKTEVQDKVRTIYELDWTE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+    FL+  +R   G+L   G GK +  +++  L+A+DR+     AP  GL
Sbjct: 179 TADGLQMRITGSGFLYNMVRIIAGTLLDAGIGKISPDEVKSMLEAKDREAAERTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLWNVYYD 246


>gi|259500923|ref|ZP_05743825.1| tRNA pseudouridine synthase A [Lactobacillus iners DSM 13335]
 gi|302190624|ref|ZP_07266878.1| tRNA pseudouridine synthase A [Lactobacillus iners AB-1]
 gi|309803645|ref|ZP_07697735.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 11V1-d]
 gi|309804945|ref|ZP_07699003.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 09V1-c]
 gi|309806696|ref|ZP_07700691.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 03V1-b]
 gi|309808529|ref|ZP_07702428.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 01V1-a]
 gi|312871160|ref|ZP_07731258.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 3008A-a]
 gi|312872668|ref|ZP_07732733.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2062A-h1]
 gi|315653995|ref|ZP_07906911.1| tRNA pseudouridine synthase A [Lactobacillus iners ATCC 55195]
 gi|259167617|gb|EEW52112.1| tRNA pseudouridine synthase A [Lactobacillus iners DSM 13335]
 gi|308164243|gb|EFO66500.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 11V1-d]
 gi|308165705|gb|EFO67930.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 09V1-c]
 gi|308166876|gb|EFO69060.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 03V1-b]
 gi|308168357|gb|EFO70476.1| tRNA pseudouridine synthase A [Lactobacillus iners LactinV 01V1-a]
 gi|311091710|gb|EFQ50089.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2062A-h1]
 gi|311093174|gb|EFQ51520.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 3008A-a]
 gi|315488691|gb|EFU78337.1| tRNA pseudouridine synthase A [Lactobacillus iners ATCC 55195]
          Length = 260

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 88/249 (35%), Positives = 134/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD          +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A+DR++    AP  G
Sbjct: 179 QNGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKDVEDVEKIILAKDRQKARNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>gi|255654196|ref|ZP_05399605.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-23m63]
 gi|296449765|ref|ZP_06891534.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296877828|ref|ZP_06901851.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
 gi|296261363|gb|EFH08189.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296431170|gb|EFH16994.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
          Length = 243

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I+YNG  Y GWQ+Q +   IQG+IE+AI+ +T E V + G+GRTDSGVHA+ Q
Sbjct: 1   MRNIKITIQYNGKNYCGWQKQLDSLGIQGTIERAIYDITKEKVSLIGSGRTDSGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A+F          +  ALNA L     IS+++   V+  FH+R+SA  ++Y Y +   +
Sbjct: 61  IANFKTNSSISIESIPMALNAKL--PKDISVIDACEVNDDFHSRYSAKGKTYKYLVYNSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +    ++ +   LD + M   A+ L+G HDF  F S        +RTI   D+   
Sbjct: 119 FRNPILSEISYQVKYELDFDKMCSEAKLLLGTHDFKGFMSSGSSVKDTVRTIYDIDIIRK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LI   +    FL+  +R  VG+L  +G G+         +Q++ R  CG  AP +GL+
Sbjct: 179 DDLITFEISGNGFLYNMVRIIVGTLVDIGRGRIN-EPFLDIIQSKTRSRCGHTAPAQGLF 237

Query: 241 FDSVEY 246
              V Y
Sbjct: 238 LKKVHY 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 =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 96/248 (38%), Positives = 135/248 (54%), Gaps = 3/248 (1%)

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  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD + +       + L  +L   DTI I     V   FHARFSA  R+Y Y +   
Sbjct: 88  QVIHFDTLAQRPLKAWMRGLGPHL--PDTIGIRWAQDVSPGFHARFSAQSRTYRYLMSDG 145

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +  AL   +     + LD   MR  A  L+G HDFT+FR+  CQA SP+R I++  +  
Sbjct: 146 ASSPALLHDQVSWSSRPLDVALMRQGAACLIGEHDFTSFRATQCQAKSPVRRIEYLHLVR 205

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LI + + A +FLH  +R+ VG L  VG G    + +   L A+DR   G  A P GL
Sbjct: 206 RGELIVMEIRANAFLHHMVRNIVGVLMQVGAGFKKPSWVGDVLAARDRTAAGATAKPNGL 265

Query: 240 YFDSVEYS 247
           Y  +V+Y 
Sbjct: 266 YLVAVDYP 273


>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 =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 116/251 (46%), Positives = 162/251 (64%), Gaps = 5/251 (1%)

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

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

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

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLARVGYP 250


>gi|219870357|ref|YP_002474732.1| tRNA pseudouridine synthase A [Haemophilus parasuis SH0165]
 gi|254789638|sp|B8F382|TRUA_HAEPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219690561|gb|ACL31784.1| tRNA pseudouridine synthase A [Haemophilus parasuis SH0165]
          Length = 262

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+G  Y GWQRQ+   S+Q  +E+A+ ++      V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYDGCRYCGWQRQQYVDSVQQRLEEALSVIANSSCEVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD          C   NA+L   + I +     V   FHARFSA+ R Y Y I   + 
Sbjct: 61  VHFDTDVNRPMQSWCLGTNAHL--PEDIVVKWAIGVSDDFHARFSALARRYRYVIYNNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+          SLD E M  A Q L+G +DF++FR+  CQ+ +P R + H  V+   
Sbjct: 119 RSAILPKGISHYHYSLDHEKMHEAGQFLLGENDFSSFRAAKCQSHTPWRNVHHLIVSRHQ 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A  EGLY 
Sbjct: 179 DYIILDIQANAFVHHMVRNIVGSLIEVGRGDKPVEWIKWLLEKRDRTLAAPTAKAEGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VEVIYP 244


>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 =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIE++G+ + GWQRQ    ++QG +EKAI  +TGE  + +G+ RTD GVHA   
Sbjct: 1   MRNIKLIIEFDGTNFCGWQRQIKDRTVQGCLEKAILKITGEKSLTNGSSRTDGGVHAKAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F            +ALN  L   D I+++    VD  FHAR+S+  + Y Y I+ R 
Sbjct: 61  VANFITNSSIPGEKFREALNTKL--PDDIAVIKSEEVDMDFHARYSSKGKMYSYTIVNRY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             L+  K     + K L+ E+M+ A +  +G+HDF  F S    A + +RTI  F +   
Sbjct: 119 EKLSFGKQYVHHVRKELNVEDMKKACECFIGKHDFKAFMSPGSSAKTTVRTIQEFYIEKN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++I+I + A  FL+  +R  VG+L  +G GK    D++  +    RK  G   PP GL 
Sbjct: 179 EDVIKIFISADGFLYNMVRIIVGTLINIGTGKTKLEDVDNIINDGIRKRSGMCVPPNGLV 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>gi|148828368|ref|YP_001293121.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittGG]
 gi|166228702|sp|A5UIY2|TRUA_HAEIG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148719610|gb|ABR00738.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittGG]
          Length = 269

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAIRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|300857214|ref|YP_003782198.1| tRNA pseudouridine synthase A [Clostridium ljungdahlii DSM 13528]
 gi|300437329|gb|ADK17096.1| tRNA pseudouridine synthase A [Clostridium ljungdahlii DSM 13528]
          Length = 244

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ Y GWQRQ N  +IQ  +E+AI  +TG    V GA RTD+GVHA   
Sbjct: 1   MKNVMLTIEYDGTNYSGWQRQNNAMTIQQRLEEAIKKITGNFSEVIGASRTDAGVHARGF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +        ALN  L     I +LN   VD  FH+R+ ++ + Y+Y I+T  
Sbjct: 61  VCNFFTNSKMPSPNFKMALNGVL--PKDIVVLNAREVDNSFHSRYHSLGKKYVYTIVTGN 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               + +   +   + LD + M+ A ++ +G HDF+ F+     A S +RT+    +   
Sbjct: 119 NRPVIGRQYVYYFRRKLDIDKMKNACKYFIGTHDFSAFKKKGSSAKSSVRTVKELTIAQE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            NLI+  +V   FL+  +R  VG+L  VG G++T   ++  L ++DR + G   P  GL 
Sbjct: 179 DNLIKFSIVGDGFLYNMVRIIVGTLLEVGLGRFTPEYVKDILDSKDRSKAGKPVPALGLC 238

Query: 241 FDSVEY 246
            + + Y
Sbjct: 239 LEKIFY 244


>gi|259502563|ref|ZP_05745465.1| tRNA pseudouridine synthase A [Lactobacillus antri DSM 16041]
 gi|259169515|gb|EEW54010.1| tRNA pseudouridine synthase A [Lactobacillus antri DSM 16041]
          Length = 256

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 134/251 (53%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY +   Y+G+ + G+Q Q +  +++  ++ A+  +       V V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGANFSGFQIQPHKRTVEQVLKNAVNKIAKHPDPPVSVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD+  +     + KALN+ L     I +     VD+ FHAR+SA R++Y YR+ 
Sbjct: 61  LNQVAHFDIPYQLSDEAMRKALNSLL--PLDILVKKAERVDENFHARYSAHRKTYRYRVD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                   ++         +D E MR+AA+  +G HDFT+F +   QA S +RT++   V
Sbjct: 119 QGDFVDPFKRNYTAHYKVPVDIEKMRLAAKDFIGEHDFTSFVASGSQAKSNVRTVEKITV 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           N     N +        FL+ QIR  V  L  VG G+   +D+++ L A+DR +    AP
Sbjct: 179 NRDPAQNEVVFEFTGNGFLYNQIRIMVAFLLEVGSGQRPVSDVKRVLAAKDRTQARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  SV+Y
Sbjct: 239 ASGLYLVSVDY 249


>gi|301170402|emb|CBW30008.1| pseudouridylate synthase I [Haemophilus influenzae 10810]
          Length = 269

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDTEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|145637534|ref|ZP_01793192.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittHH]
 gi|145269340|gb|EDK09285.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittHH]
          Length = 269

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|145627788|ref|ZP_01783589.1| tRNA pseudouridine synthase A [Haemophilus influenzae 22.1-21]
 gi|144979563|gb|EDJ89222.1| tRNA pseudouridine synthase A [Haemophilus influenzae 22.1-21]
          Length = 269

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHEAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|325913236|ref|ZP_08175605.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 60-B]
 gi|325477500|gb|EGC80643.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 60-B]
          Length = 260

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 88/249 (35%), Positives = 134/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD          +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A+DR++    AP  G
Sbjct: 179 QHGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKDVEDVEKIILAKDRQKARNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>gi|311070796|ref|YP_003975719.1| tRNA pseudouridine synthase A [Bacillus atrophaeus 1942]
 gi|310871313|gb|ADP34788.1| tRNA pseudouridine synthase A [Bacillus atrophaeus 1942]
          Length = 247

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 133/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
           ++    I Y+G  + G+Q Q    ++Q  +EKA+ ++    + V V  +GRTDSGVHA  
Sbjct: 1   MKMKCTISYDGHLFNGYQVQPGKRTVQAELEKALAILHKSEDKVPVISSGRTDSGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA L     I++      D  FHARFSAI++ Y Y + T 
Sbjct: 61  QVIHFDTPLSIPAERWPYALNALL--PGDIAVKTAEHADDGFHARFSAIKKEYRYFVYTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++  A+     L+ + MR A++HL+G HDFT+F S + +    +RTI   D   
Sbjct: 119 KHPDVFKRHYAYHFSYRLNVQKMREASEHLIGTHDFTSFCSANTEVRDKVRTIYELDWTD 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +++R+V   FL+  +R   G+L  VG GK+++ D++  L A+DR+  G  AP  GL
Sbjct: 179 TDDGLQMRIVGSGFLYNMVRIIAGTLLDVGTGKFSADDVKGMLDAKDREAAGRTAPGHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 239 YLWHVYYD 246


>gi|309809150|ref|ZP_07703023.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 2503V10-D]
 gi|308170595|gb|EFO72615.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 2503V10-D]
          Length = 260

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 88/249 (35%), Positives = 134/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD          +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A+DR++    AP  G
Sbjct: 179 QNGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKDVEDVEKIILAKDRQQARNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>gi|329297440|ref|ZP_08254776.1| tRNA pseudouridine synthase A [Plautia stali symbiont]
          Length = 270

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V    V V  AGRTD+GVH   QV 
Sbjct: 9   KLALGIEYDGSRYYGWQRQNEVRSVQEKLEKALAKVANHPVNVFCAGRTDAGVHGTGQVV 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +N+ L   D I++  +  V + FHARFSA  R Y Y I  ++  
Sbjct: 69  HFETTLSRADSAWTLGVNSNL--PDDIAVRWVKAVPETFHARFSATARRYRYVIYNQRLR 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G 
Sbjct: 127 PAILGKGITHFYHPLDAEKMHRAAQALLGENDFTSFRAVQCQSRTPWRNVMHLYVTRQGP 186

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G    T +   L A+DR      A  EGLY  
Sbjct: 187 YVIVDIKANAFVHYMVRNIVGSLLEIGCGNQPETWMATLLAAKDRTLAAATAKAEGLYLV 246

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 247 AVDYP 251


>gi|319897314|ref|YP_004135510.1| tRNA pseudouridine synthase a [Haemophilus influenzae F3031]
 gi|317432819|emb|CBY81184.1| tRNA pseudouridine synthase A [Haemophilus influenzae F3031]
          Length = 269

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVAWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|310768198|gb|ADP13148.1| tRNA pseudouridine synthase A [Erwinia sp. Ejp617]
          Length = 271

 Score =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V    + V  AGRTD+GVH   QV 
Sbjct: 12  KLALGIEYDGSRYYGWQRQNEVRSVQEKLEKALAKVADRPIAVFCAGRTDAGVHGTGQVV 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I  ++  
Sbjct: 72  HFETTAQRKDAAWTLGVNANL--PADIAVRWVKAVADDFHARFSATARRYRYVIYNQRLR 129

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+  G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P+R + H +V+  G 
Sbjct: 130 PAILAGGVTHFYHPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPMRNVMHLNVSRHGA 189

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      + + L A+DRK     A  EGLY  
Sbjct: 190 YVVVDIKANAFVHHMVRNIVGSLIEIGCGNQPEGWMRELLVAKDRKLAAATARAEGLYLV 249

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 250 AVDYP 254


>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 =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+QG +E A+  V    + V  AGRTD+GVHA  QV 
Sbjct: 14  KIALGIEYDGSRYYGWQRQAEVDSVQGCLEAALSQVANARIDVFCAGRTDAGVHATGQVV 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I  R+  
Sbjct: 74  HFTTHAVRKDAAWTMGVNANL--PPDIAVRWVKTVDEAFHARFSATARRYRYVIYNRRFR 131

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  A Q L+G +DFT+FR++ CQ+ +P R + H  V   G+
Sbjct: 132 PAILSQGVTHYYLPLDAERMHRAGQCLLGENDFTSFRAVQCQSRTPWRNLMHLRVTRLGD 191

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      + + L A+DR      A  +GLY  
Sbjct: 192 YVVVDIKANAFVHHMVRNIVGSLMEIGCGNQPENWMAELLAAKDRTLAAATAKADGLYLV 251

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 252 AVDYP 256


>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 =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 92/251 (36%), Positives = 138/251 (54%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D      P    +  NA+L    T+++     + + FHARFSA RR+Y Y +    
Sbjct: 61  VVHLDTELVRDPFSWVRGTNAFL--PPTVAVRWAQAMPEDFHARFSAHRRTYYYALTYGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L +G+A  +     +SLD   M  AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRAPLLEGKAGYVTLPPGQSLDVTAMHEAAQVLVGEHDFSSFRAAECQAKSPVKTMYSTE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+   +FLH  +R+ +G L  +G GK  +  + + L A+DRK   P   P
Sbjct: 179 VRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGKRPAAWMGEVLAARDRKAAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>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 =  297 bits (760), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ+  +S+QG +E+A+  V    VVV  AGRTD+GVHA  QV 
Sbjct: 10  KIALGIEYDGSRYYGWQRQQEVASVQGCLEQALSKVADAPVVVFCAGRTDAGVHATGQVV 69

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +N +L     I++  +S V + FHARFSA  R Y Y I   +  
Sbjct: 70  HFETTARRKDAAWTMGVNTHL--PPDIAVRWVSEVREDFHARFSATARRYRYLIFNHRYR 127

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+ +         LD + M+ AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G 
Sbjct: 128 PAVLQQGMTHFYHPLDADRMQRAAQALLGENDFTSFRAVQCQSRTPWRNVKHVKVTRHGQ 187

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G      + + L  +DR      A  +GLY  
Sbjct: 188 YIVVDIKANAFVHHMVRNIVGSLMEIGCGNQDENWMAELLALKDRNLAAATAKADGLYLV 247

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 248 AVDYP 252


>gi|319776538|ref|YP_004139026.1| tRNA pseudouridine synthase A [Haemophilus influenzae F3047]
 gi|329124048|ref|ZP_08252595.1| tRNA pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
 gi|317451129|emb|CBY87362.1| tRNA pseudouridine synthase A [Haemophilus influenzae F3047]
 gi|327467473|gb|EGF12971.1| tRNA pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
          Length = 269

 Score =  296 bits (759), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHRAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|291562779|emb|CBL41595.1| pseudouridylate synthase I [butyrate-producing bacterium SS3/4]
          Length = 255

 Score =  296 bits (759), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 90/248 (36%), Positives = 133/248 (53%), Gaps = 5/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
              + +EY+GS Y GWQ+Q N  ++IQG +E  +F + GE + VHG+GRTD+GVHA  QV
Sbjct: 4   NIRITLEYDGSRYDGWQKQGNTDNTIQGKLENVLFRMAGEEIEVHGSGRTDAGVHARGQV 63

Query: 62  AHFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           A+F +  E  P      + LN YL   D I +L+  IV ++FH+R SA  ++Y Y + T 
Sbjct: 64  ANFHINAEICPDGEAAREYLNRYL--PDDIRVLSAKIVPERFHSRLSATSKTYGYYVETG 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 E+   +   K LD + MR AA+ L+G HDF +F +      S +R ID   +  
Sbjct: 122 DKKNVFERKYVYGCGKKLDVKAMRQAAEFLIGEHDFKSFCANRRMKKSTVRRIDEIRIVE 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +E       FL+  +R   G+L  VG G      +++ + A++R   G  APPEGL
Sbjct: 182 HGTKLEFLYTGNGFLYNMVRILTGTLLEVGSGTRRPEKMKEIIAAKNRDMAGRTAPPEGL 241

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 242 FLLHVGYE 249


>gi|172056172|ref|YP_001812632.1| tRNA pseudouridine synthase A [Exiguobacterium sibiricum 255-15]
 gi|229470753|sp|B1YH83|TRUA_EXIS2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171988693|gb|ACB59615.1| tRNA pseudouridine synthase A [Exiguobacterium sibiricum 255-15]
          Length = 249

 Score =  296 bits (759), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 132/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+   I+Y+G+ Y G+Q Q NG +IQ  +EK +  +    V V G+GRTD+ VHA  Q
Sbjct: 1   MRRFKCTIQYDGTDYSGYQVQPNGLTIQEVLEKTLGRMHKHPVKVIGSGRTDARVHAQGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P  + KALN  L   D I + +   V   F AR+  + + Y Y +  R+
Sbjct: 61  VIHFDTELSIAPASMVKALNTLL--PDDIRVRDCKEVASDFEARYDVVGKEYRYFV--RR 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A  + ++ LIP SLD   +R+   HLVG HDF++F     +  + +RTI   ++   
Sbjct: 117 TENAFRRHQSVLIPYSLDVAQIRLGLAHLVGTHDFSSFCVAKTETDNRVRTIYEAELIEQ 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +  R     FL+ QIR  VG+L  VG G++   D+++ L+A+DR   G  APP GLY
Sbjct: 177 GEELIFRFQGSGFLYNQIRIMVGTLLDVGRGRFAPDDIKRMLEAKDRNVAGVTAPPHGLY 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LWEVFYP 243


>gi|145633047|ref|ZP_01788779.1| tRNA pseudouridine synthase A [Haemophilus influenzae 3655]
 gi|144986273|gb|EDJ92852.1| tRNA pseudouridine synthase A [Haemophilus influenzae 3655]
          Length = 269

 Score =  296 bits (759), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>gi|299066408|emb|CBJ37593.1| tRNA pseudouridylate synthase I [Ralstonia solanacearum CMR15]
          Length = 274

 Score =  296 bits (759), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 91/251 (36%), Positives = 139/251 (55%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D      P    +  NA+L    T+++     + + FHARFSA RR+Y Y +    
Sbjct: 61  VIHLDTDLVRDPFSWVRGTNAFL--PPTVAVRWAQAMPEDFHARFSAHRRTYYYALTYGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L +G+A  +     +SLD   M  AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRAPLLEGKAGYVTLPPGQSLDVAAMHEAAQVLVGEHDFSSFRAAECQAKSPVKTMYSAE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+   +FLH  +R+ +G L  +G GK  +  + + L A++RK   P   P
Sbjct: 179 VRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGKRPAAWMGEVLAARERKAAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>gi|145639258|ref|ZP_01794864.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittII]
 gi|145271561|gb|EDK11472.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittII]
 gi|309751137|gb|ADO81121.1| tRNA pseudouridine synthase A [Haemophilus influenzae R2866]
          Length = 269

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (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 +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPNKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>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 =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 97/246 (39%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            + +IIEY+G+ + GWQ QK+  ++QG I  A+  +TG+ V V G+GRTD+GVHA+ QVA
Sbjct: 4   NFRLIIEYDGACFHGWQIQKDLRTVQGEITGALASITGQAVSVIGSGRTDAGVHAMAQVA 63

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F       P  L KALN  L     I I +   V   FHAR+SA  ++Y YRI+ R  P
Sbjct: 64  SFICDTRLEPGTLQKALNGILA--KDIVIHDCREVSLNFHARYSAKSKTYRYRILNRNLP 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFG 181
            AL +G AW I K LD   M  A  H++GRHDF++F       +S +R +     N +  
Sbjct: 122 AALYRGYAWHIKKPLDLGAMTAALPHILGRHDFSSFEGTGSPKASSVRHVTAATFNMAED 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   + A  FL   +R+ VG+L  VG GK T   +   L A+DR   G  AP  GL+ 
Sbjct: 182 GYLAFEITADGFLKHMVRNIVGTLVEVGLGKKTPEAVADILAAKDRSRAGATAPGHGLFL 241

Query: 242 DSVEYS 247
             V Y 
Sbjct: 242 VRVNYE 247


>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 =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 96/250 (38%), Positives = 135/250 (54%), Gaps = 6/250 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R   + IEY+GS Y GWQR     N ++IQG +E  +  +TGE V ++G+GRTD+GVH
Sbjct: 1   MKRNIRLTIEYDGSRYQGWQRLGGDSNANTIQGKLESVLSKMTGEDVNINGSGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QVA+F          +   L  YL     I I+ +S   ++FH+R +A  ++YLYRI
Sbjct: 61  AYGQVANFHTDCMMSVSEIKNYLTKYL--PSDIGIVEVSEASERFHSRLNAKEKTYLYRI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                    E+   W  P++LD + M  AA  L+G HDF  F SI     S +RTI + +
Sbjct: 119 AIPGVSNVFERKYLWYFPETLDIKKMEEAASLLIGTHDFKGFSSIKKTKKSTVRTIYNIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +      I+I      FLH  +R   G+L  VG GK    D+ KAL++  R + G  APP
Sbjct: 179 IKKTKKEIQISYTGNGFLHNMVRILTGTLVEVGCGKIKPEDITKALESTKRSDAGITAPP 238

Query: 237 EGLYFDSVEY 246
           +GL+  SVEY
Sbjct: 239 QGLFLVSVEY 248


>gi|317472004|ref|ZP_07931336.1| tRNA pseudouridine synthase A [Anaerostipes sp. 3_2_56FAA]
 gi|316900408|gb|EFV22390.1| tRNA pseudouridine synthase A [Anaerostipes sp. 3_2_56FAA]
          Length = 252

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 121/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q   ++I+G + + +  + GE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLEVAYDGTNYCGWQIQPKDTTIEGVLNEKLGSLLGEEITVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD   E     + +ALN  L   D I I + S V   FH R+   R++Y Y I   +
Sbjct: 61  VAVFDTETEIPGERIARALNQRL--PDDIVIQSSSEVKDDFHPRYQDTRKTYEYTIYNAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E MR AA+  +G HDF +F +      + +RTI   +V   
Sbjct: 119 FDNPVTARHHHFVYVPLDVERMRTAARCFLGEHDFLSFSTTGSPTKTTVRTIYECEVRQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +RV    FL+  +R   G+L  +G G+     + +      R + GP AP +GL 
Sbjct: 179 GRYITMRVTGNGFLYNMVRMMAGTLISIGRGRRDPEWVRELFLHPKRGKAGPNAPAKGLT 238

Query: 241 FDSVEY 246
             ++ Y
Sbjct: 239 LINIHY 244


>gi|257865435|ref|ZP_05645088.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257871770|ref|ZP_05651423.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257875038|ref|ZP_05654691.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|325569125|ref|ZP_08145372.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
 gi|257799369|gb|EEV28421.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257805934|gb|EEV34756.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257809204|gb|EEV38024.1| tRNA pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|325157583|gb|EGC69741.1| tRNA pseudouridine synthase A [Enterococcus casseliflavus ATCC
           12755]
          Length = 245

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  +   +IQ  +E  I L+TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYLGWQRLGDSEKTIQEKVEGVIKLLTGEEIEIVGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     + +  N YL     I +  +  V ++FHAR+ A  + Y Y +   
Sbjct: 61  QVANFKTTHQMSLPEMQQFFNRYL--PQDIVVNKIEEVPERFHARYHAKGKQYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P    +  ++  P+ LD E M+ AA+ L+G HDF  F ++     S +RTID   +  
Sbjct: 119 AIPSVFARNTSFHCPQPLDLEKMQQAAEKLIGTHDFIGFSALKKSKKSTVRTIDEITITP 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+        FLH  +R   G+L  +GDG      +++ L  + R+  G   P  GL
Sbjct: 179 EGDLLRFTFKGNGFLHKMVRILTGTLIAIGDGTLPPEVIDQVLADKVRQAAGETVPSHGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


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

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 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|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 =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS YFGWQRQ+  +S+Q  +EKA+  V    +VV  AGRTD+GV A  QV 
Sbjct: 17  RVALGIEYDGSAYFGWQRQQGVASVQECLEKALSRVANAPIVVFCAGRTDAGVSATGQVV 76

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD             +N +L     I++   + V + FHARFSA  R Y Y I   +  
Sbjct: 77  HFDTPVLRKDAAWTMGVNTHL--PKDIAVRWCANVGEDFHARFSATARRYRYVIYNNRYR 134

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+       +   LD E M++A Q L+G +DFT+FR+  CQ+ +P R + H +V+  G+
Sbjct: 135 SAILHAGVTHVHMPLDVEKMQLAGQALLGENDFTSFRASQCQSRTPWRYVMHVNVSRHGS 194

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      + + L A+DR        PEGLY  
Sbjct: 195 YVVVDIKANAFVHHMVRNIVGSLVEIGAGNQPVGWMGELLAAKDRNLAAATGKPEGLYLV 254

Query: 243 SVEYS 247
            V+Y 
Sbjct: 255 CVDYP 259


>gi|260582150|ref|ZP_05849944.1| tRNA pseudouridine synthase A [Haemophilus influenzae NT127]
 gi|260094782|gb|EEW78676.1| tRNA pseudouridine synthase A [Haemophilus influenzae NT127]
          Length = 269

 Score =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRQEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVIYP 244


>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 =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIE++GS + GWQRQ  G +IQ  IE AIF  TGE ++++G+ RTD+GVHA   
Sbjct: 1   MRNIKLIIEFDGSNFCGWQRQPKGRTIQKVIETAIFKATGEEIMINGSSRTDAGVHAREM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F            +A+N  L   + +SI+    V + FHAR+S+  ++Y Y II R 
Sbjct: 61  VANFLTNSSIPGDKFREAINTRL--PEDVSIIKSEEVSEDFHARYSSKGKTYSYTIINRY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             L+L     +     LD   MR A ++ +GRHDF  F S      +  RTI    ++  
Sbjct: 119 ERLSLGHQYLYHYKYRLDVNEMRRACEYFIGRHDFRAFMSPGSSIKTTTRTIHDLYIDQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I+I + A  FL+  +R  VG+L  +G+GK    +++  ++  +RK+ G   PP GL 
Sbjct: 179 GNEIKIFITADGFLYNMVRIIVGTLIKIGNGKLEVENIKDIIEEGNRKKAGMCVPPNGLI 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>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 =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V    + V  AGRTD+GVH   QV 
Sbjct: 12  KLALGIEYDGSRYYGWQRQNEVRSVQEKLEKALAKVADRPIAVFCAGRTDAGVHGTGQVV 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I  ++  
Sbjct: 72  HFETTAQRKDAAWTLGVNANL--PADIAVRWVKAVADDFHARFSATARRYRYVIYNQRLR 129

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+  G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P+R + H  V+  G 
Sbjct: 130 PAILAGGVTHFYHPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPMRNVMHLKVSRHGA 189

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      + + L A+DRK     A  EGLY  
Sbjct: 190 YVVVDIKANAFVHHMVRNIVGSLMEIGCGNQPEGWMRELLVAKDRKLAAATARAEGLYLV 249

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 250 AVDYP 254


>gi|221134792|ref|ZP_03561095.1| tRNA pseudouridine synthase A [Glaciecola sp. HTCC2999]
          Length = 264

 Score =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               M +EY G+ ++GWQRQ N  S+Q ++E A   V  E V +  +GRTD+GVHA  Q+
Sbjct: 3   TNIAMAVEYYGADFYGWQRQDNVPSVQQALEDAASFVADEKVNIICSGRTDAGVHATYQI 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F    +         L    K  D I++     V   FHARFSA  R Y Y I   + 
Sbjct: 63  VNFKTSAKRDEKAWT--LGVTTKTPDAIAVKWAVEVPDTFHARFSATARRYRYIIYNHRV 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P A+           LD + M  AAQ LVG HDFT+FR+  CQ+ +P R I   +V   G
Sbjct: 121 PPAILAKGLTHCYLPLDAQKMHEAAQVLVGEHDFTSFRAALCQSKTPFRNIHFVNVQRVG 180

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +FLH  +R+  GSL L+G G+   + L++ L+ +DR + G  A P GLYF
Sbjct: 181 EYVIIDIKANAFLHHMVRNIAGSLMLIGAGEQPLSWLQEILEIKDRTQAGVTAKPNGLYF 240

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 241 VDVDYP 246


>gi|147676690|ref|YP_001210905.1| tRNA pseudouridine synthase A [Pelotomaculum thermopropionicum SI]
 gi|146272787|dbj|BAF58536.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
          Length = 273

 Score =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 86/249 (34%), Positives = 133/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + I Y+G+ Y+G+Q Q+     ++Q  IE+ +  + GE + V GAGRTD+GVHA 
Sbjct: 26  MRNIKVTIAYDGTNYYGFQEQRGTKFRTVQEVIEERLSRLAGEQIRVIGAGRTDAGVHAR 85

Query: 59  RQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV +F+       P  +  ALN+ L     I+ L    V   FHARFSA+ ++Y Y I 
Sbjct: 86  GQVINFNPGNWPIPPERVAYALNSLL--PRDIAALESVEVPPSFHARFSAVAKTYRYTIY 143

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +      +  ++ +P+ LD E M+  A  L+GRHDF+ FR++     S +RT+    V
Sbjct: 144 NARVHSPFLRLYSYHVPRRLDVEAMQAGAALLIGRHDFSAFRALGTPVKSTVRTMLEACV 203

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G+L+ I + A  FL+   R   G+L  VG GK    ++   L+++D    GP AP  
Sbjct: 204 SREGDLVYIDLKADGFLYHMARMIAGTLIRVGLGKIPPGEVAAILKSRDSLRGGPTAPAR 263

Query: 238 GLYFDSVEY 246
           GL  + +EY
Sbjct: 264 GLCLEKIEY 272


>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 =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 93/247 (37%), Positives = 139/247 (56%), Gaps = 2/247 (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  VVHFDTFVQRPLNAWVRGVNAFL--PDDIAVLWASEVSDRFHARYSALERRYLYFLLNQS 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 FDSVEYS 247
              V+Y 
Sbjct: 239 LAGVKYD 245


>gi|241668494|ref|ZP_04756072.1| tRNA pseudouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877028|ref|ZP_05249738.1| tRNA pseudouridine synthetase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843049|gb|EET21463.1| tRNA pseudouridine synthetase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 258

 Score =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  SIQ  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSIQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +       +  NA L     I IL++ +VD  F++RF+A  R+Y Y I    
Sbjct: 61  VVNFHSDADRNLSSWMRGTNALL--PQDIKILDIKVVDNDFNSRFTAKNRTYNYIIYNSL 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + L+ + M  A ++L+G  DFT+FRS  CQ+++P R I   +    
Sbjct: 119 ISSPIFAEHCLWENRQLNIDKMNQACKYLLGEQDFTSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+F+GSL  VG    +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNFIGSLLKVGLEFESPEWIKLVLEAKDRTKAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>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 =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       +  NA L     I++L  S     FHAR+ A+ R YLY ++    
Sbjct: 117 LHFDTRAERPMNAWVRGANALL--PSGIALLWASPTADDFHARYCALERCYLYLLLNHPV 174

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L + R       L  E+M++ AQ LVG HDF+ FR+  CQA SP+RT+   +V   G
Sbjct: 175 RPGLHQHRVGWYHHPLRLESMQMGAQMLVGEHDFSAFRAAACQAKSPVRTLTKLEVTRVG 234

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++   + A +FLH  +R+ VG L  VG GK+    + K L+   R E  P     GLY 
Sbjct: 235 NMVAFELRANAFLHHMVRNIVGCLVYVGKGKFRPDWIGKLLENGKRSEAAPTFSASGLYL 294

Query: 242 DSVEYS 247
             V Y 
Sbjct: 295 AGVAYD 300


>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 =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 116/251 (46%), Positives = 165/251 (65%), Gaps = 5/251 (1%)

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    ++I++ + V+  +HARFSA+ R YL+RI+ R+
Sbjct: 61  VAHCDMVKDWDPFRLSEALNFHLK-PSPVAIVDCARVEDDWHARFSAVERQYLFRILIRR 119

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

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLARVGYP 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 =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 115/251 (45%), Positives = 159/251 (63%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +   W +P  LD + M  AAQ LVGRHDF+ FR+  CQA+SPIRT++  DV   
Sbjct: 120 SPAALTRAHVWHVPWPLDADLMHDAAQRLVGRHDFSAFRAAECQANSPIRTLEQLDVARA 179

Query: 181 G----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                + I +   ARSFLH Q+R+ VG+L L G  +  + D+ + L + D+  CGPLAP 
Sbjct: 180 PMALHDEIVVATAARSFLHHQVRAMVGTLMLAGCRRLAADDVAEILASGDKSRCGPLAPA 239

Query: 237 EGLYFDSVEYS 247
            GL F  V+Y 
Sbjct: 240 AGLTFVGVDYD 250


>gi|257870548|ref|ZP_05650201.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804712|gb|EEV33534.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 247

 Score =  296 bits (758), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 130/250 (52%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ NG ++Q  IEK +  +  G+ V +HG+GRTD+GVHAL 
Sbjct: 1   MVRYKATIAYDGTNFQGFQRQPNGRTVQEEIEKTLTRMNNGQAVQIHGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD         +   L+   +  + I++  + IVD+ FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDFDE-RPLEKMRFGLDT--QTPEDIAVKQVEIVDEHFHARYLVREKTYQFRVDIG 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +      +  A   P  LD   ++ A   L+G HDFT+F +        +RTI     +V
Sbjct: 118 KPRSPFRRYYASYYPYPLDLMKIQQALPDLLGTHDFTSFCATGSSVEDKVRTIHQASMEV 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N  G+ +        FL+  IR  VG+L  +G+G+  +  +   +  +DR   GP A PE
Sbjct: 178 NEAGDELLFTFRGDGFLYKMIRIMVGTLLKIGNGRLPADSIPAIIAQKDRNAAGPTAHPE 237

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 238 GLYLVRVAYE 247


>gi|325523908|gb|EGD02125.1| tRNA pseudouridine synthase A [Burkholderia sp. TJI49]
          Length = 270

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 83/246 (33%), 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    ++++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTDLDREPFSWVRGTNAFL--PPSVAVQWAKPMPDAFHARFSAFERTYYYALYVHPV 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|153853813|ref|ZP_01995169.1| hypothetical protein DORLON_01160 [Dorea longicatena DSM 13814]
 gi|149753563|gb|EDM63494.1| hypothetical protein DORLON_01160 [Dorea longicatena DSM 13814]
          Length = 246

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 123/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + K++  +TGE + + GA RTDSGVHAL  
Sbjct: 1   MKRIRIFVAYDGTNYCGWQVQPNGVTIEEKLNKSLARLTGEEIRIIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA-IRRSYLYRIITR 119
           VA FD      P     ALN  L   + I ++    V   +H R+   I ++Y Y I   
Sbjct: 61  VAVFDTESSIPPERFAYALNQRL--PEDIVVVRSDEVPADWHPRYQENISKTYEYHIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L+      +   +D E MR  A++LVG HDF +F +I       +RT+    +  
Sbjct: 119 AVPNPLKTRYCTFVSFPMDVEAMRAGAKYLVGEHDFVSFCNIRTNTQDTVRTVYDLIIEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I +R+    FL+  +R   G L  VG G +T   +++ L A+     G  APP GL
Sbjct: 179 KDDEIVLRITGNGFLYNMVRIIAGVLIRVGRGFYTPEKVKEILDAKVHTSEGATAPPNGL 238

Query: 240 YFDSVEYS 247
               ++Y+
Sbjct: 239 VLMKIDYN 246


>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 =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

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--PDDIAVRWAKVVDDDFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+++P R + H +V+  G
Sbjct: 119 RSAILPQGITHCHLELDHQLMHQAGQALLGENDFSSFRAAQCQSNTPWRNVHHLNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      L   L  QDR    P A PEGLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGCGNQPVEWLAWLLGQQDRTLAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVLYP 244


>gi|291520511|emb|CBK75732.1| pseudouridylate synthase I [Butyrivibrio fibrisolvens 16/4]
          Length = 245

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++ Y+GS Y GWQ Q NG +I+  + +A+  +  E + + GA RTD+GVH+L  V
Sbjct: 1   MRVMIVVAYDGSNYSGWQIQPNGVTIEQKLNEALTDLLQEPISIMGASRTDAGVHSLGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FD         +  ALN  L   D I +     V+  FH R++A R++Y Y+I+ R+ 
Sbjct: 61  AVFDTNSRMPADKISFALNQRL--PDDIVVQYSCQVEDDFHPRYAACRKTYEYKILNRKM 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   ++   +     LD E M  AA +L+G+HDFT+F S+  Q  S +RTI    V    
Sbjct: 119 PDPTKRKDTFHYYYDLDVEKMNEAAAYLIGQHDFTSFSSVKAQVKSRVRTIYTAKVYKED 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I IR+    FL+  +R   G+L  VG G+     + +  + ++R+  GP AP  GL  
Sbjct: 179 DVIHIRLTGDGFLYNMVRIIAGTLIKVGAGEMEPMYMLEIFRGRNRELAGPTAPAHGLTM 238

Query: 242 DSVEYS 247
             +EY 
Sbjct: 239 IGIEYE 244


>gi|315651854|ref|ZP_07904857.1| tRNA pseudouridine synthase A [Eubacterium saburreum DSM 3986]
 gi|315485856|gb|EFU76235.1| tRNA pseudouridine synthase A [Eubacterium saburreum DSM 3986]
          Length = 245

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ+Q NG +++  + +AI  +TGE + V GA RTDSGVHA   
Sbjct: 1   MRRIRLIVSYDGTNYCGWQKQPNGITVEEILNRAISKLTGEEIEVIGASRTDSGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            A+N  L   D I I     V+  +H R +   ++Y YRI+ R+
Sbjct: 61  VAVFDTNVRMAADKFAFAINQRL--PDDIRIQYSDEVESDWHPRKNDCIKTYTYRILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  A     +LD E MR A+ + +G HDFT+F S   QASSPIRT+   +V   
Sbjct: 119 IDIPTERLYAHFCYFNLDVEKMREASGYFIGTHDFTSFCSQKSQASSPIRTVFSLEVLQD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++I I V    FL+  IR   G+L  VG G +  + + + ++A++RK  G   P +GL 
Sbjct: 179 EDMITIVVRGDGFLYNMIRIIAGTLIKVGMGVYPPSHITEIMKAKERKFAGQTMPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LVEIEY 244


>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 =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ+  +S+Q S+E+A+  V    + V  AGRTD+GVHA  QV 
Sbjct: 13  KIALGIEYDGSRYYGWQRQQEVASVQASLEQALSKVANAPISVLCAGRTDAGVHATGQVV 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +N +L     I++  ++ V + FHARFSA  R Y Y I   +  
Sbjct: 73  HFETTAQRKDAAWTMGVNTHL--PPDIAVRWVTGVAEDFHARFSATARRYRYIIYNHRYR 130

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+ +         LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V  +G 
Sbjct: 131 PAVLQQGVTHFYHPLDAERMERAAQALLGENDFTSFRAVQCQSRTPWRNVKHVKVTRYGE 190

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G  +   + + L  +DR      A  EGLY  
Sbjct: 191 YIVVDIKANAFVHHMVRNIVGSLMEIGCGNQSENWMAELLALKDRNLAAATARAEGLYLV 250

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 251 SVDYP 255


>gi|331002224|ref|ZP_08325743.1| tRNA pseudouridine synthase A [Lachnospiraceae oral taxon 107 str.
           F0167]
 gi|330411318|gb|EGG90734.1| tRNA pseudouridine synthase A [Lachnospiraceae oral taxon 107 str.
           F0167]
          Length = 245

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ+Q NG +I+  +  AI  +TGE + V GA RTDSGVHA   
Sbjct: 1   MRRIRLIVSYDGTNYCGWQKQPNGITIEEVLNNAITKLTGEDIEVIGASRTDSGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD            A+N  L   + I I     V+  +H R +   ++Y YRI+ R+
Sbjct: 61  IAVFDTNARIAADKFAFAINQRL--PEDIRIQYSDEVESGWHPRKNDCIKTYTYRILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  A     +LD E MR A+ + +G HDFT+F S   QASSPIRTI   ++   
Sbjct: 119 IDIPTERLYAHFCYFNLDVEKMREASGYFIGTHDFTSFCSQKSQASSPIRTIFSLEILQD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ I +    FL+  IR   G+L  VG G +  + + + ++A++RK  G   P +GL 
Sbjct: 179 EDMVTIVIRGDGFLYNMIRIIAGTLIKVGMGVYPPSHITEIMKAKNRKLAGQTMPAKGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LVEIEY 244


>gi|210623220|ref|ZP_03293659.1| hypothetical protein CLOHIR_01609 [Clostridium hiranonis DSM 13275]
 gi|210153757|gb|EEA84763.1| hypothetical protein CLOHIR_01609 [Clostridium hiranonis DSM 13275]
          Length = 243

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + ++YNG+ Y GWQ Q N   IQG+IE AI  +TGE V ++G+GRTD+GVHAL Q
Sbjct: 1   MRNIKITVQYNGANYCGWQEQPNSPGIQGNIEYAIKEITGEKVKINGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F +  +     +  ALN+ L     ISI++   V+ +FHAR+SA  + Y Y +   +
Sbjct: 61  VANFKIESQIPVNRIPDALNSKL--PKDISIIDAEEVEDEFHARYSAKGKIYKYLVYNSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               + K  ++ +   LD E M+  A+ L+G +DF  F S        +RTI    +   
Sbjct: 119 YRNPILKDISYQVKYDLDFEKMKKEAESLIGTYDFCGFMSSGSSVKDTVRTIKSVKIEKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LI        FL+  +R   G+L  +G G+ T   +E  +++QDR + G  AP   L+
Sbjct: 179 DDLIVFEFEGNGFLYNMVRILSGTLIDIGRGRIT-ESMEDIIKSQDRSKAGHTAPGHALF 237

Query: 241 FDSVEY 246
              V Y
Sbjct: 238 LKKVFY 243


>gi|15602502|ref|NP_245574.1| tRNA pseudouridine synthase A [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|13431946|sp|P57861|TRUA_PASMU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|12720912|gb|AAK02721.1| TruA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 264

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + I+YNG  Y GWQRQ+N +S+Q  +EKAI  V  +   +  AGRTDSGVHA  QV
Sbjct: 1   MKIALGIQYNGKNYCGWQRQENVASVQEQLEKAISFVANQPCQIFCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D IS+     V   FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETDAIRAEKAWSFGVNANL--PDDISVSWAKCVTDDFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M  A Q L+G  DF++FR+  CQ+ +P R + H  V   G
Sbjct: 119 RSAILPEGVTHCHLDLDHHLMHQAGQALLGEQDFSSFRAAQCQSHTPFRNVHHLKVVRRG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      +   L  +DR+   P A PEGLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGAGHQPVEWIGWLLAQKDRRLAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVSYP 244


>gi|167627942|ref|YP_001678442.1| tRNA pseudouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|189029995|sp|B0U0B1|TRUA_FRAP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167597943|gb|ABZ87941.1| tRNA-pseudouridine synthase I [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 258

 Score =  295 bits (757), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + IEY G  Y GWQRQ +  SIQ  +EKA+  +  + + V  AGRTD+GVHA  Q
Sbjct: 1   MKNYLLQIEYFGKNYCGWQRQSHSPSIQEELEKALSKIANQNIEVTCAGRTDTGVHATSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +       +  NA L     I IL++  VD  F++RF+A  R+Y Y I    
Sbjct: 61  VVNFHSDADRNLSSWMRGTNALL--PQGIKILDIKEVDNDFNSRFTATNRTYNYIIYNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +         + L+ + M  A ++L+G  DFT+FRS  CQ+++P R I   +    
Sbjct: 119 ISSPILAEHCLWENRQLNIDKMNQACKYLLGEQDFTSFRSSQCQSNTPFRNIQKAEFIKQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I   VV  +FLH  IR+F+GSL  +G    +   ++  L+A+DR +    A   GLY
Sbjct: 179 GSFIVFEVVGNAFLHHMIRNFIGSLLKIGLEFESPEWIKLVLEAKDRTKAAETAKAHGLY 238

Query: 241 FDSVEYS 247
           F  VEY 
Sbjct: 239 FVGVEYP 245


>gi|51340814|sp|Q814C2|TRUA1_BACCR RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
          Length = 247

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 61  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 119 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 179 QDDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 239 YLWEVNYN 246


>gi|291166165|gb|EFE28211.1| tRNA pseudouridine synthase A [Filifactor alocis ATCC 35896]
          Length = 244

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 137/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               + I+Y G+ Y GWQ+Q NG SIQ  IE+AI  VTG+ V + G+GRTDSGVHAL QV
Sbjct: 3   QNILLKIQYIGTNYCGWQKQNNGKSIQQEIERAICEVTGKQVNLTGSGRTDSGVHALGQV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F +        +  A+N YL   D I I+    V+  FHAR+S+ +++Y YRI   + 
Sbjct: 63  ANFVIDTTIPVEKIKYAINYYL--PDDIRIIESKAVEDSFHARYSSKKKTYCYRINMNEI 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               EK R++ + K LD   M+  ++ L+G HDF  F+S      + +RTI   ++N   
Sbjct: 121 ESPFEKNRSYFVGKELDLSKMKEQSKFLMGEHDFAAFQSEGSSVKTTVRTIYSLEINCIN 180

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N+ EI ++   FL+  +R   G+L  +G GK     +   L  + R+  GP AP  GL+ 
Sbjct: 181 NIAEIHIIGNGFLYNMVRIIAGTLIEIGKGK--DYSIVDILNTKQRENAGPTAPACGLFM 238

Query: 242 DSVEYS 247
           + VEY 
Sbjct: 239 EKVEYD 244


>gi|332685695|ref|YP_004455469.1| tRNA pseudouridine synthase A [Melissococcus plutonius ATCC 35311]
 gi|332369704|dbj|BAK20660.1| tRNA pseudouridine synthase A [Melissococcus plutonius ATCC 35311]
          Length = 257

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 85/249 (34%), Positives = 130/249 (52%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q Q NG ++Q  +EK ++ +   + + + G+GRTD+GVHAL 
Sbjct: 1   MPRYKAIIAYDGTNFNGFQSQINGRTVQDELEKTLYKLNNNQSITIFGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD ++      L  AL+   +    IS+  +  V   FHAR+  I ++Y ++I T 
Sbjct: 61  QVIHFDYLKARDVEKLRFALDT--QSPADISVKKIEEVSNNFHARYHVIEKTYQFKIDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P S+D   +  A   L+G HDFT+F +  C   S IRTI    V+ 
Sbjct: 119 KTRDPFRRFYASYFPHSIDLAKIEKALPDLLGEHDFTSFCAAGCSVDSKIRTIYEASVSQ 178

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + I        FL+  +R  VG+L  +G GK   T + + +  ++R+  GP A PEG
Sbjct: 179 TSEDEIIFTFRGNGFLYKMVRIIVGTLLKIGQGKIKETAIPEIIAGKNRRLAGPTAHPEG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLVQVIYE 247


>gi|260438183|ref|ZP_05791999.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
 gi|292809373|gb|EFF68578.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
          Length = 250

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 77/246 (31%), Positives = 123/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+GY GWQ+Q N  +++  + KA   +  + + + GA RTD+GVH+   V
Sbjct: 1   MRVMLRVAYDGTGYSGWQKQPNAITVEEVLCKACKNLFAQDIDIIGASRTDAGVHSYGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FD+        +  ALN+ L   + I ++    V + FH R    R++Y Y+I   + 
Sbjct: 61  AVFDVDTRIPAEKISYALNSRL--PEDIRVVESRQVSENFHPRHVECRKTYEYKIWNDKF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L +  +     +LD   M  A ++ +G HDFT+F S+  Q  S IR I    V    
Sbjct: 119 ENPLVRYYSHFFYGNLDIGKMNEACRYFIGLHDFTSFCSVGSQVQSKIREIYSISVEKNN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI IRV    FL+  +R   G+L  VG G+    ++ K +  ++R+  GP AP  GL  
Sbjct: 179 RLITIRVTGNGFLYNMVRIIAGTLIKVGQGQLEPAEIPKIIDGKNRELAGPTAPARGLAL 238

Query: 242 DSVEYS 247
             + Y 
Sbjct: 239 VEINYE 244


>gi|254496537|ref|ZP_05109407.1| tRNA pseudouridine synthase A [Legionella drancourtii LLAP12]
 gi|254354236|gb|EET12901.1| tRNA pseudouridine synthase A [Legionella drancourtii LLAP12]
          Length = 262

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    ++Q ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVLEYDGSHYHGWQAQTGLHTVQQALEHALSKVADCPISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  +E          N++L  S  + +     + + F+AR+SA  R Y Y I     
Sbjct: 61  VHFDTDKERSIRAWIHGANSFL--SKDVCVKWGKELSETFNARYSATARRYRYVIYNGAI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL +       + LD   M  AAQ L+G +DFT+FRS+ CQ+++P+R I    V    
Sbjct: 119 RPALLRSNVTWQYRQLDHRLMHQAAQLLLGENDFTSFRSVECQSNTPMRNIHKLQVTRTN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A +FLH  +R+  G L  VG GK   + +++ L+A+DR+     AP  GLY 
Sbjct: 179 DLVIIDITANAFLHHMVRNIAGVLIAVGSGKHPVSWVDEVLKARDRRLGAETAPAYGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VQVTYP 244


>gi|145635070|ref|ZP_01790776.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittAA]
 gi|145267678|gb|EDK07676.1| tRNA pseudouridine synthase A [Haemophilus influenzae PittAA]
          Length = 269

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EK++  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKSLSHIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G  DF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEQDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVVYP 244


>gi|30018411|ref|NP_830042.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|206972233|ref|ZP_03233180.1| tRNA pseudouridine synthase A [Bacillus cereus AH1134]
 gi|228956583|ref|ZP_04118379.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229041047|ref|ZP_04189810.1| tRNA pseudouridine synthase A [Bacillus cereus AH676]
 gi|229125659|ref|ZP_04254691.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-Cer4]
 gi|229142948|ref|ZP_04271389.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST24]
 gi|229188427|ref|ZP_04315475.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10876]
 gi|296500975|ref|YP_003662675.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
 gi|29893951|gb|AAP07243.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|206732807|gb|EDZ49982.1| tRNA pseudouridine synthase A [Bacillus cereus AH1134]
 gi|228595101|gb|EEK52872.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10876]
 gi|228640569|gb|EEK96958.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST24]
 gi|228657851|gb|EEL13657.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-Cer4]
 gi|228727344|gb|EEL78538.1| tRNA pseudouridine synthase A [Bacillus cereus AH676]
 gi|228803148|gb|EEM49970.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|296322027|gb|ADH04955.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
          Length = 252

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>gi|219853559|ref|YP_002470681.1| hypothetical protein CKR_0216 [Clostridium kluyveri NBRC 12016]
 gi|219567283|dbj|BAH05267.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 247

 Score =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 80/244 (32%), Positives = 130/244 (53%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              ++IEY+G+ Y GWQRQ N  +IQ  +E+AI   TGE   V G+ RTD+GVHA   V 
Sbjct: 6   NIKLVIEYDGTNYSGWQRQYNAITIQQRLEEAIEKATGEFSPVIGSSRTDAGVHARGFVC 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F    +     +   LN  L   + I++L+   VD  FH+R+    + Y Y I+T   P
Sbjct: 66  NFFTASKIPTSNIKMVLNTLL--PEDIAVLDSKEVDSSFHSRYFTTGKEYSYTIVTGDRP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             + +   +   + LD E ++ + ++ +G HDF+ F+     A S IRTI    V    N
Sbjct: 124 PVIGRQYVYYFRRKLDIEKIKNSCEYFIGTHDFSAFKKKGSTARSSIRTIKELTVLKEKN 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +I+  +V   FL+  +R  +G+L  VG G+++   ++  L+++DR + G   P +GL  +
Sbjct: 184 IIKFNIVGDGFLYNMVRIIIGTLLEVGLGRFSIEYVKYILESKDRAKAGKPVPAKGLCLE 243

Query: 243 SVEY 246
            V Y
Sbjct: 244 KVFY 247


>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 =  295 bits (757), Expect = 3e-78,   Method: Composition-based stats.
 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|54294200|ref|YP_126615.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Lens]
 gi|62901233|sp|Q5WX34|TRUA_LEGPL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|53754032|emb|CAH15505.1| tRNA-pseudouridine synthase I [Legionella pneumophila str. Lens]
          Length = 262

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    +IQ ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVVEYDGSQYHGWQAQTGLHTIQQAVEFALSKVADSSISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  ++          N++L     I +     + + FHAR+SA+ R Y Y I     
Sbjct: 61  IHFDCEKDRSIRAWIHGANSFL--PKDICVKWGKEMPENFHARYSAVSRRYRYVIYNGAI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L +G      + LD   M+   Q L+G +DFT+FRS+ CQ+++P+R I    V   G
Sbjct: 119 RPGLLRGNVTWQYRQLDHRLMQQGGQCLLGENDFTSFRSVECQSNTPMRNIHQLQVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ + + A +FLH  +R+  G L  VG GK     ++  L A+DRK     AP  GLY 
Sbjct: 179 DLVVLDITANAFLHHMVRNIAGVLIAVGSGKHPVGWVKDVLNAKDRKLGAETAPSYGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VQVTYP 244


>gi|227530236|ref|ZP_03960285.1| tRNA pseudouridine synthase A [Lactobacillus vaginalis ATCC 49540]
 gi|227349848|gb|EEJ40139.1| tRNA pseudouridine synthase A [Lactobacillus vaginalis ATCC 49540]
          Length = 256

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 85/251 (33%), Positives = 129/251 (51%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY +   Y+GS + G+Q Q +  +++  ++ A+  +       + V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGSNFSGFQIQPHKRTVEQVLKNAVNKIAKHPTPEIPVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD+        + KALN+ L     I I    +VD  FHAR+SA  ++Y YR+ 
Sbjct: 61  LNQVAHFDIPYHLSNESMRKALNSIL--PLDILIKKAELVDSDFHARYSAHNKTYRYRVD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         LD   MR AA++ +G HDFT+F +   QA S +RT+   D+
Sbjct: 119 QGEFVNPFKRNYTAHFKYPLDLTLMRKAAKNFIGEHDFTSFVASGSQAKSNVRTVYKIDI 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 N +        FL+ QIR  V  L  +G  +    D+++ L A+DR +    AP
Sbjct: 179 KRDKLRNEVVFDFTGNGFLYNQIRIMVAFLLEIGSKQRPVDDVKRVLAAKDRTQARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  SV+Y
Sbjct: 239 ASGLYLVSVDY 249


>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 =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

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  VHFDTRSRRPDTAWTLGVNANL--PADIAVRWVAPVTDDFHARFSATARRYRYIIYNHPL 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL           LD  +M  A Q L+G +DFT+FR++ CQ+ SP R + H  V   G
Sbjct: 128 RPALLGRGLTHYYHPLDAPSMARAGQCLLGENDFTSFRALQCQSRSPWRNVHHLYVTRQG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  VG G    + +   L  +DR + G  A  EGLY 
Sbjct: 188 RYVVVDIKANAFVHHMVRNIVGSLLEVGCGNRPESWIADLLACRDRTQAGATARAEGLYL 247

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 248 VAVDYP 253


>gi|312870517|ref|ZP_07730636.1| tRNA pseudouridine synthase A [Lactobacillus oris PB013-T2-3]
 gi|311093979|gb|EFQ52304.1| tRNA pseudouridine synthase A [Lactobacillus oris PB013-T2-3]
          Length = 256

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 134/251 (53%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           M RY +   Y+G+ + G+Q Q +  +++  ++ A+  +       + V G+GRTD+GVHA
Sbjct: 1   MYRYKITFAYDGANFSGFQIQPHKRTVEQVLKNAVNKIAKYPDPPISVIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     + KALN+ L     I +     VD+ FHAR+SA R++Y YR+ 
Sbjct: 61  LNQVAHFDLPYQLSDESMRKALNSLL--PLDILVKKAERVDESFHARYSAHRKTYRYRVD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                   ++         +D + MR+AA+  +G HDFT+F +   QA S +RT++   V
Sbjct: 119 QGDFVDPFKRNYTAHYKVPVDIDKMRLAAKDFIGEHDFTSFVASGSQAKSNVRTVEKITV 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +     N +        FL+ QIR  V  L  VG G+   +D+++ L A+DR +    AP
Sbjct: 179 DRDPAQNEVVFEFTGNGFLYNQIRIMVAFLLEVGSGQRPVSDVKRVLAAKDRTQARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  SV+Y
Sbjct: 239 ASGLYLVSVDY 249


>gi|311029085|ref|ZP_07707175.1| Pseudouridylate synthase I [Bacillus sp. m3-13]
          Length = 248

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 131/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R   I+ Y+G+G+ G+Q QK   ++Q  +++A+  +  G  V V  +GRTD+GVHA+ 
Sbjct: 1   MNRLKCILTYDGAGFEGYQIQKEKRTVQLEVQRALSRIHKGTEVKVSASGRTDAGVHAVG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALNA+L     I +  +  V   FHARF  +++ Y Y++   
Sbjct: 61  QVLHFDSPLSIPVAAWQNALNAHL--PKDIWVKKVESVSGDFHARFDVVKKEYRYKVSLA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++ + +  P  LD E ++ A  HL+G HDFT+F S   +    +RTI   +V  
Sbjct: 119 KDFNVFDRDQVYHYPYPLDLEAVKEACGHLIGEHDFTSFCSAKTEVEDKVRTIYSLEVVR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +E R++   FL+  +R  VG+L  +G GK    D+   L+A+DR   G  AP  GL
Sbjct: 179 NGEELEFRIIGNGFLYNMVRIIVGTLLEIGQGKKLPRDIFSILEARDRGAAGKTAPAHGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLWNVVYD 246


>gi|260588018|ref|ZP_05853931.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|331082412|ref|ZP_08331538.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
 gi|260541545|gb|EEX22114.1| tRNA pseudouridine synthase A [Blautia hansenii DSM 20583]
 gi|330400898|gb|EGG80499.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 244

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 132/246 (53%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y + I+Y+GS Y GWQRQK+  ++IQG IE  +  + G  V + GAGRTD+GVHA  Q
Sbjct: 1   MNYRLDIQYDGSRYGGWQRQKDTDNTIQGKIEDVLTKMLGTEVQIQGAGRTDAGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F    E     +C+ LN YL   + I I  +S  +++FH+R +A  + Y YRI++  
Sbjct: 61  VANFHADCEKSCEEICQYLNEYL--PEDIEISKVSEAEERFHSRLNAKEKVYQYRIVSGI 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E+     + ++LD   M+ AA++L G HDF +F S      S +RTI   ++   
Sbjct: 119 HKNVFERKYQCPLHETLDVNAMQEAAKYLEGTHDFKSFCSNKKMKKSSVRTIYSIEIVDL 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I      FL+  +R   G+L  VG G+    +++  L+  DRKE G  AP  GL 
Sbjct: 179 TQEIVITYTGNGFLYNMVRILTGTLIEVGRGRRKPEEMKGILEGCDRKEAGFTAPARGLT 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LLEVRY 244


>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 =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (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  VHFETTAQRKDAAWTLGVNANL--PADIAVRWVKAVPDEFHARFSATARRYRYIIYNQRL 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 DSVEYS 247
            +V+Y 
Sbjct: 249 VAVDYP 254


>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 =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 120/252 (47%), Positives = 157/252 (62%), Gaps = 6/252 (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  VAHCDMDKAWDAFRLSEALNFHLK-PAPISIVACAQVSDDWHARFSALERRYLFRLVNRR 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 -----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                    +  V ARSFLH Q+RSFVG+L+ VG G WT  D+  AL A+DR  CGP+ P
Sbjct: 180 TRVDGAQEFQFHVRARSFLHNQVRSFVGTLERVGAGAWTPDDVTAALNARDRTACGPVCP 239

Query: 236 PEGLYFDSVEYS 247
           P GLY   V Y 
Sbjct: 240 PHGLYLAGVSYP 251


>gi|164688053|ref|ZP_02212081.1| hypothetical protein CLOBAR_01698 [Clostridium bartlettii DSM
           16795]
 gi|164602466|gb|EDQ95931.1| hypothetical protein CLOBAR_01698 [Clostridium bartlettii DSM
           16795]
          Length = 245

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    M++EY+GS + G+Q+ K N ++IQG +E  +  +  E + + G+GRTD GVHA  
Sbjct: 1   MRNIKMVVEYDGSNFKGFQKLKDNENTIQGKLESVLSQMADENIEIIGSGRTDMGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          + K L  YL    +I+I  +  VD +FH+R++A R+ YLY+I   
Sbjct: 61  QVVNFKTNSPLSLNKMHKYLYEYL--PQSIAIREIEEVDDRFHSRYNAKRKVYLYKIDNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +     +PK +D + MR  A  LVG HDFT+F S   +  S +R I    +N 
Sbjct: 119 EYPNPFNRKYTCHVPKKIDLDKMRAVADVLVGEHDFTSFCSSRSKKKSHVREIYSISINE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              LIEI V    FL+  +R   G+L   G  K T  +++  L+ +DR +    AP +GL
Sbjct: 179 NNGLIEIYVEGNGFLYNMVRIIAGTLIDAGHNKITPEEVKNLLELKDRSKSPETAPSKGL 238

Query: 240 YFDSVEY 246
           +   V+Y
Sbjct: 239 FLYRVKY 245


>gi|153938429|ref|YP_001392800.1| tRNA pseudouridine synthase A [Clostridium botulinum F str.
           Langeland]
 gi|152934325|gb|ABS39823.1| tRNA pseudouridine synthase A [Clostridium botulinum F str.
           Langeland]
 gi|295320780|gb|ADG01158.1| tRNA pseudouridine synthase A [Clostridium botulinum F str. 230613]
          Length = 246

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 135/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             + +F    +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++ 
Sbjct: 61  GYICNFFTNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P+A+ +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N
Sbjct: 119 SSQPIAIGRNYIFQFKNKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEIN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+  +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  G
Sbjct: 179 KKGDFIKFIITGDGFLYNMVRIMVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 246


>gi|170756303|ref|YP_001783087.1| tRNA pseudouridine synthase A [Clostridium botulinum B1 str. Okra]
 gi|169121515|gb|ACA45351.1| tRNA pseudouridine synthase A [Clostridium botulinum B1 str. Okra]
          Length = 246

 Score =  295 bits (756), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 135/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             + +F    +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++ 
Sbjct: 61  GYICNFFTNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P+A+ +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N
Sbjct: 119 SSQPIAIGRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEIN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+  +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  G
Sbjct: 179 KKGDFIKFIITGDGFLYNMVRIMVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 246


>gi|121534665|ref|ZP_01666486.1| tRNA pseudouridine synthase A [Thermosinus carboxydivorans Nor1]
 gi|121306685|gb|EAX47606.1| tRNA pseudouridine synthase A [Thermosinus carboxydivorans Nor1]
          Length = 250

 Score =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 123/246 (50%), Gaps = 3/246 (1%)

Query: 2   IRY-CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            RY  + + Y+G+ Y G+QRQ N  ++Q  +E+ +  + G  + V GA RTD+GVHA  Q
Sbjct: 7   QRYLKLTVAYDGTAYHGFQRQANAITVQQVLEERLATIFGHPLKVTGAARTDAGVHAYGQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F          + +A  A   +   I ++    V   FHARFSA  + YLYRI    
Sbjct: 67  VVGFATSGTIPAANIVRA--AKSVLPPDIVVVKAEEVSADFHARFSARSKIYLYRIYNAA 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  AW + + LD   M  A Q +VG HDF+ FR+      SP+RTI        
Sbjct: 125 VADPFRRNYAWHVTQPLDEAAMDTAVQTVVGTHDFSAFRAAGGPPVSPVRTIYEAGCTRE 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++E R     FL+  +R+ VG+L  VG G+ T     + L  +DR   G  APP+GLY
Sbjct: 185 GDMLEFRFWGNGFLYHMVRNLVGTLVDVGLGRLTRDGFTRILAGRDRTRAGITAPPQGLY 244

Query: 241 FDSVEY 246
              + Y
Sbjct: 245 LKEIFY 250


>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 =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 118/251 (47%), Positives = 165/251 (65%), 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   + G  W + K LD + MR AA HL+G HDFTTFRS  CQA +P++T+D  D+   
Sbjct: 120 PPATHQAGLVWQVKKPLDIDRMREAATHLIGEHDFTTFRSTICQAQTPVKTLDRVDMTEH 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  ++  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|228477786|ref|ZP_04062414.1| tRNA pseudouridine synthase A [Streptococcus salivarius SK126]
 gi|228250478|gb|EEK09692.1| tRNA pseudouridine synthase A [Streptococcus salivarius SK126]
          Length = 248

 Score =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 134/250 (53%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  +EK +  + +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEELEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I ++++ +V ++FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDVVSIELVSEEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L    M+ AA+ LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAKDLVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                          FL+ Q+R+ VG+L  +G+G+   + ++  L+++DR   GP A   
Sbjct: 179 DEKTGFYIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESRDRNLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 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|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 =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 124/251 (49%), Positives = 159/251 (63%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P   + G  W +P  LD   M+  AQHL+G HDFTTFRS  CQA SP++T+D   V   
Sbjct: 120 PPATHDAGLVWQVPHLLDVNAMQAGAQHLLGLHDFTTFRSSICQAQSPLKTLDELKVRQI 179

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLAHVTYP 250


>gi|288554758|ref|YP_003426693.1| tRNA pseudouridine synthase A [Bacillus pseudofirmus OF4]
 gi|288545918|gb|ADC49801.1| tRNA pseudouridine synthase A [Bacillus pseudofirmus OF4]
          Length = 247

 Score =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 134/248 (54%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R   II Y+G+ + G+Q Q N  ++Q  IE+A+  V  G+ V V  +GRTD+GVHA  
Sbjct: 1   MNRIACIISYDGTNFSGYQVQPNKRTVQLEIEQALKRVHKGQEVSVTASGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           KALNA L   D I +L+    +K FHAR+    + Y YR++  
Sbjct: 61  QVIHFDSPFRIPAAQWPKALNACL--PDDIRVLSAHYAEKDFHARYHTTGKEYRYRVLNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +     +  +LD + MR AA +L+G HDF+ F + +      +RT+   D+N 
Sbjct: 119 EDPDVFRRHHTAHVLYALDIDKMRQAAAYLIGTHDFSAFCAANTSVIDKVRTLYAVDINV 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +   +    FL+  +R  VG+L  VG GK T+  ++ AL+   R + G  APP+GL
Sbjct: 179 HEDELHFILRGNGFLYNMVRIIVGTLLEVGYGKRTAESVDTALRTCKRDDAGKTAPPQGL 238

Query: 240 YFDSVEYS 247
           Y  SV+Y+
Sbjct: 239 YLWSVQYN 246


>gi|52841533|ref|YP_095332.1| tRNA pseudouridine synthase A [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|54297221|ref|YP_123590.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Paris]
 gi|148358844|ref|YP_001250051.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Corby]
 gi|296106890|ref|YP_003618590.1| tRNA pseudouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
 gi|62901237|sp|Q5X5Q4|TRUA_LEGPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901247|sp|Q5ZVY6|TRUA_LEGPH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228736|sp|A5IBF5|TRUA_LEGPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52628644|gb|AAU27385.1| tRNA pseudouridine synthase A [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|53751006|emb|CAH12417.1| tRNA-pseudouridine synthase I [Legionella pneumophila str. Paris]
 gi|148280617|gb|ABQ54705.1| tRNA pseudouridine synthase A [Legionella pneumophila str. Corby]
 gi|295648791|gb|ADG24638.1| tRNA pseudouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
          Length = 262

 Score =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    +IQ ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVVEYDGSQYHGWQAQTGLHTIQQAVEFALSKVADSSISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  ++          N +L     I +     + + FHAR+SA+ R Y Y I     
Sbjct: 61  IHFDCEKDRSIRAWIHGANTFL--PKDICVKWGKEMPENFHARYSAVSRRYRYVIYNGAI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L +G      + LD   M+   Q L+G +DFT+FRS+ CQ+++P+R I    V   G
Sbjct: 119 RPGLLRGNVTWQYRQLDHRLMQQGGQCLLGENDFTSFRSVECQSNTPMRNIHQLQVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ + + A +FLH  +R+  G L  VG GK     ++  L A+DRK     AP  GLY 
Sbjct: 179 DLVVLDITANAFLHHMVRNIAGVLIAVGSGKHPVGWVKDVLNAKDRKLGAETAPSYGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VQVTYP 244


>gi|90410767|ref|ZP_01218782.1| tRNA pseudouridine synthase A [Photobacterium profundum 3TCK]
 gi|90328398|gb|EAS44696.1| tRNA pseudouridine synthase A [Photobacterium profundum 3TCK]
          Length = 261

 Score =  295 bits (756), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGAKYCGWQRQVDVDSVQERLEKALSHIANKPIAVFCAGRTDTGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +   V     +NA+L     IS+   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDVDVDRQMVAWTIGVNAHL--PRDISVRWATPVSDDFHARFSATARRYRYIIYNNAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ+LVG HDFT+ R+  CQ+ SP R + H +V+  G
Sbjct: 119 RPAIFGIGVSHYHGHLDEKKMHEAAQYLVGEHDFTSVRASQCQSRSPWRAMKHVNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+ T   ++  L+ +DR+  G  A   GLY 
Sbjct: 179 DFVIIDIKANAFVHHMVRNIAGSLIRVGRGQETPEWMKWVLEQKDRRVAGETAKAAGLYL 238

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 239 VAVDYP 244


>gi|15612730|ref|NP_241033.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Bacillus halodurans C-125]
 gi|8134764|sp|Q9Z9J0|TRUA_BACHD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|4512436|dbj|BAA75303.1| truA homologue (identity of 62% to B. subtilis ) [Bacillus
           halodurans]
 gi|10172779|dbj|BAB03886.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Bacillus halodurans C-125]
          Length = 263

 Score =  295 bits (755), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 76/240 (31%), Positives = 124/240 (51%), Gaps = 3/240 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R  + + Y+G+ + G+Q Q N  ++QG +E  +  +  G  + V  +GRTD+GVHA  
Sbjct: 1   MKRIGLKVAYDGTDFAGYQIQPNERTVQGELESVLKNIHKGMSIRVTASGRTDTGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+ HFD    +       ALN+ L     I +L  + V   FHAR+SA  + Y YR++T 
Sbjct: 61  QIVHFDTSLSFPVDRWPIALNSQL--PADICVLEAADVPADFHARYSAKTKEYRYRVLTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +   + +   LD E M+ AA  L+G HDF++F +   +    +RTI+   +  
Sbjct: 119 AQADVFRRNYTYHVRYPLDVEAMQRAAVQLLGTHDFSSFCAAKAEVEDKVRTIEDVALWR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   +    FL+  +R  VG+L  +G GK ++ ++ K L A+ R+  G  AP  GL
Sbjct: 179 EGDELIFSIRGNGFLYNMVRIIVGTLLEIGAGKRSAEEVAKILAARSREAAGKTAPGHGL 238


>gi|291562296|emb|CBL41112.1| pseudouridylate synthase I [butyrate-producing bacterium SS3/4]
          Length = 344

 Score =  295 bits (755), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 129/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + KA+  +  E V V GA RTDSGVHA   
Sbjct: 1   MRRIKLTVAYDGTAYKGWQLQPNGVTIEEMLNKALSDLLKEPVCVIGASRTDSGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD          C A+N  L   + I ++    V   +H R     ++Y Y+I+  +
Sbjct: 61  VAVFDTESRIPGDKFCYAVNRGL--PEDIRVVESEEVPLDWHPRKQNCVKTYEYQILNCK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
             +   +  A      L+ E M  AA++L+G HDF +F + + QA   +RTI   +V   
Sbjct: 119 IEIPTRRLYAHFCYYPLNVEKMNEAAKYLIGEHDFISFCAANHQAEETVRTIYGAEVKKN 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +++ IR+    FL+  +R   G+L  VG G+W    +++ L+A++RKE G  AP +GL
Sbjct: 179 DEDIVTIRLCGSGFLYNMVRIIAGTLLKVGTGEWEPEHVKEVLEARNRKEAGQTAPAKGL 238

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 239 TLVGIEYE 246


>gi|168178866|ref|ZP_02613530.1| tRNA pseudouridine synthase A [Clostridium botulinum NCTC 2916]
 gi|226950899|ref|YP_002805990.1| tRNA pseudouridine synthase A [Clostridium botulinum A2 str. Kyoto]
 gi|182670055|gb|EDT82031.1| tRNA pseudouridine synthase A [Clostridium botulinum NCTC 2916]
 gi|226843785|gb|ACO86451.1| tRNA pseudouridine synthase A [Clostridium botulinum A2 str. Kyoto]
          Length = 246

 Score =  295 bits (755), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 136/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             + +F    +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++ 
Sbjct: 61  GYICNFFTNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P+A+ +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N
Sbjct: 119 SSKPIAIGRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEIN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+  +    FL+  +R  VG+L  +G  K     ++  ++++DR++ G   P  G
Sbjct: 179 KKGDFIKFIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIKYVIKSKDRRKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 246


>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 =  295 bits (755), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 101/247 (40%), Positives = 140/247 (56%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + IEY+GS Y GWQ+QKNG S+Q  +E A+ +VT E V V  AGRTDSGVHAL Q
Sbjct: 1   MQKIALGIEYDGSRYCGWQKQKNGISVQDCVENALNIVTAESVSVFCAGRTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+   ++        +N YL    +I I  +S++ + FHARFSA+ R Y Y I   +
Sbjct: 61  VVHFETDVKYSKSAWTFGVNRYL--PRSICIRWVSLMKQDFHARFSAVSRRYYYYIYNDK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+   + W   K LD   M  AAQ+L+G +DF+ FRS  CQ+ S  R + H  V   
Sbjct: 119 IRSAILFQKTWHYTKLLDVCKMSRAAQYLLGENDFSAFRSAGCQSYSRCRNLYHLRVIRI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A SFL+  +R+ VGSL  VG G   +  + + L++  R   G  AP +GLY
Sbjct: 179 GQCVIIDIQANSFLYRMVRNIVGSLVEVGCGNRPAIWILELLKSCKRSLAGMTAPADGLY 238

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 239 LAEVKYP 245


>gi|148263121|ref|YP_001229827.1| tRNA pseudouridine synthase A [Geobacter uraniireducens Rf4]
 gi|189030134|sp|A5GB00|TRUA_GEOUR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146396621|gb|ABQ25254.1| tRNA pseudouridine synthase A [Geobacter uraniireducens Rf4]
          Length = 244

 Score =  295 bits (755), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 121/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +IIEY+G+ Y GWQ Q NG +IQ  IE ++  + GE V +H +GRTD+GVHAL  
Sbjct: 1   MRQIKLIIEYDGTNYSGWQVQPNGITIQQLIEASLATMLGEPVKLHSSGRTDAGVHALGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   +          LNA L   + I+I +       F+ R  A  + Y Y I    
Sbjct: 61  VAAFKTGKLLPLRAFSDGLNALL--PNDIAIRDAVEAPLSFNPRADAKSKHYRYTIYNAV 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +  +W +  +LD E M+ AA H VG HDF  FR+ +C A + +R +    V   
Sbjct: 119 RRSPLARLSSWHLRGALDIERMQAAASHFVGEHDFAAFRASNCAAKTTVRRLFSVSVAKD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I V    FL   +R   G+L  VG GK     +   L + DR   G  APP+GL 
Sbjct: 179 GESVIIDVHGSGFLKNMVRIIAGTLAEVGQGKKNPDAVPGLLVSGDRAASGITAPPQGLC 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LVEVFY 244


>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 =  295 bits (755), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 89/251 (35%), Positives = 135/251 (53%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D      P    +  NA+L    T+++     + + FHARFSA RR+Y Y +    
Sbjct: 61  VVHLDTDLVREPFSWVRGTNAFL--PPTVAVRWAQEMPEGFHARFSAHRRTYYYALTFGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L + +A  +     +SLD E M  AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRAPLLEDKAGYVMLPPGQSLDVEAMNEAAQVLVGEHDFSSFRAAECQAKSPVKTMYSVE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+   +FLH  +R+ +G L  +G G+   + +   L A+ R    P   P
Sbjct: 179 VRGEGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRQPVSWMGDVLAARSRVAAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>gi|322807772|emb|CBZ05347.1| tRNA pseudouridine synthase A [Clostridium botulinum H04402 065]
          Length = 246

 Score =  295 bits (755), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 135/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             + +F    +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++ 
Sbjct: 61  GYICNFFTNTKIPPENLQKVINNNL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P+A+ +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N
Sbjct: 119 SSQPIAIGRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEIN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+  +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  G
Sbjct: 179 KKGDFIKFIITGDGFLYNMVRIIVGTLIEIGLNKRKPEYIKYVIKSKDRTKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 246


>gi|228919092|ref|ZP_04082471.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228840617|gb|EEM85879.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 252

 Score =  295 bits (755), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDEIIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>gi|126697674|ref|YP_001086571.1| tRNA pseudouridine synthase 1 [Clostridium difficile 630]
 gi|254973765|ref|ZP_05270237.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-66c26]
 gi|255091155|ref|ZP_05320633.1| tRNA pseudouridine synthase 1 [Clostridium difficile CIP 107932]
 gi|255099266|ref|ZP_05328243.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-63q42]
 gi|255305049|ref|ZP_05349221.1| tRNA pseudouridine synthase 1 [Clostridium difficile ATCC 43255]
 gi|255312809|ref|ZP_05354392.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-76w55]
 gi|255515568|ref|ZP_05383244.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-97b34]
 gi|255648663|ref|ZP_05395565.1| tRNA pseudouridine synthase 1 [Clostridium difficile QCD-37x79]
 gi|260681880|ref|YP_003213165.1| tRNA pseudouridine synthase 1 [Clostridium difficile CD196]
 gi|260685478|ref|YP_003216611.1| tRNA pseudouridine synthase 1 [Clostridium difficile R20291]
 gi|306518785|ref|ZP_07405132.1| tRNA pseudouridine synthase ACD [Clostridium difficile QCD-32g58]
 gi|115249111|emb|CAJ66922.1| transfer RNA pseudouridine synthase A 1 [Clostridium difficile]
 gi|260208043|emb|CBA60248.1| tRNA pseudouridine synthase 1 [Clostridium difficile CD196]
 gi|260211494|emb|CBE01638.1| tRNA pseudouridine synthase 1 [Clostridium difficile R20291]
          Length = 243

 Score =  295 bits (755), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I+YNG  Y GWQ+Q +   IQG+IE+AI+ +T E   + G+GRTDSGVHA+ Q
Sbjct: 1   MRNIKIKIQYNGKNYCGWQKQPDSLGIQGTIERAIYDITKEETSLIGSGRTDSGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A+F +        +  ALNA L     IS++    V+  FH+R+SA  ++Y Y +   +
Sbjct: 61  IANFKINSGISIESIPMALNAKL--PKDISVIEACEVNDDFHSRYSAKGKTYKYLVYNSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +    ++ +   LD + M   A+ L+G HDF  F S        +RTI   D++  
Sbjct: 119 FRNPILSEISYQVKYELDFDKMCSEAKSLLGTHDFKGFMSSGSSVKDTVRTIYDIDISKK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LI   +    FL+  +R  VG+L  +G G+         +Q++ R  CG  AP +GL+
Sbjct: 179 DDLITFEISGNGFLYNMVRIIVGTLVDMGRGRIN-EPFLDIIQSKTRSRCGHTAPAQGLF 237

Query: 241 FDSVEY 246
              V Y
Sbjct: 238 LKKVHY 243


>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 =  295 bits (755), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 112/251 (44%), Positives = 156/251 (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  VAHCDMAKPWDPFRLSEALNFHLK-PAPVAIRACAAVADDWHARFSAVERRYTFRLLARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP  LE G+ W +   LD   M+  A HL+G HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATLEAGQVWRVMNPLDLGAMQEGAAHLLGLHDFTTFRSTMCQAASPVKTLDEIRIEEC 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|152973988|ref|YP_001373505.1| tRNA pseudouridine synthase A [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152022740|gb|ABS20510.1| tRNA pseudouridine synthase A [Bacillus cytotoxicus NVH 391-98]
          Length = 247

 Score =  295 bits (755), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 123/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 1   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I+ +    ++FHAR+  +++ Y YR++  
Sbjct: 61  QVIHFDTPLSLEEWQWGNALNTLL--PDDIVIVQVEKKTEEFHARYGVVKKEYRYRVLLS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  +D + +R A  + +G HDFT+F S        +RTI   D+  
Sbjct: 119 KTADVFRRNYVYQYPYPIDIQLIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIDLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +  R V   FL+  +R  VG+L  VG GK     + + L  QDR+  G + P  GL
Sbjct: 179 QGDELVFRFVGNGFLYNMVRIIVGTLLSVGQGKVDPDSIPEILAKQDRRFAGKMVPGHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 239 YLWQVNYN 246


>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 =  295 bits (755), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 119/251 (47%), Positives = 162/251 (64%), Gaps = 5/251 (1%)

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 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 YGLYLAHVVYE 250


>gi|218230830|ref|YP_002364991.1| tRNA pseudouridine synthase A [Bacillus cereus B4264]
 gi|228950690|ref|ZP_04112824.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|229077443|ref|ZP_04210092.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-2]
 gi|229148551|ref|ZP_04276807.1| tRNA pseudouridine synthase A [Bacillus cereus m1550]
 gi|229176742|ref|ZP_04304146.1| tRNA pseudouridine synthase A [Bacillus cereus 172560W]
 gi|218158787|gb|ACK58779.1| tRNA pseudouridine synthase A [Bacillus cereus B4264]
 gi|228606785|gb|EEK64202.1| tRNA pseudouridine synthase A [Bacillus cereus 172560W]
 gi|228634967|gb|EEK91540.1| tRNA pseudouridine synthase A [Bacillus cereus m1550]
 gi|228705869|gb|EEL58206.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-2]
 gi|228809041|gb|EEM55526.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 252

 Score =  294 bits (754), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWINALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QNDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>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 =  294 bits (754), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 121/251 (48%), Positives = 168/251 (66%), Gaps = 5/251 (1%)

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  VAHCDLRRDWDPFRLSEALNYHLK-PAPVAITACAPVAEDWHARFSALERRYLFRLLTRR 119

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

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

Query: 237 EGLYFDSVEYS 247
            GLY   VEY 
Sbjct: 240 HGLYLAGVEYP 250


>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 =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 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|297618350|ref|YP_003703509.1| tRNA pseudouridine synthase A [Syntrophothermus lipocalidus DSM
           12680]
 gi|297146187|gb|ADI02944.1| tRNA pseudouridine synthase A [Syntrophothermus lipocalidus DSM
           12680]
          Length = 244

 Score =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   ++EY G+ Y G+QRQ  G +I+G +E AI  +TGE V V  AGRTD+GVHAL Q
Sbjct: 1   MNRIKALVEYEGTRYSGFQRQPRGLTIEGELEAAICKLTGERVKVLAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD      P     ALN+ L     I +L      + FH R+ A  ++Y Y I  ++
Sbjct: 61  VIAFDTESPIPPERFAPALNSVL--PSDIRVLKSEKAKEGFHPRYQARAKAYRYLIYRQE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A+  P+ LD   M  AA+++ G HDF  F +      + +RT+    +N  
Sbjct: 119 EGRTFYRNLAYYYPQPLDLPAMAKAARYMEGTHDFMAFCASGSGVRNYVRTVFEVSINEK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              ++I V    FL+  +R  VG+L  VG  +    ++E+ L ++DR+  GP  P  GLY
Sbjct: 179 PPFLQIDVCGDGFLYNMVRIMVGTLLEVGRKRLAPEEVEQILLSRDRQRAGPTVPACGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LKRVFY 244


>gi|226322882|ref|ZP_03798400.1| hypothetical protein COPCOM_00654 [Coprococcus comes ATCC 27758]
 gi|225208668|gb|EEG91022.1| hypothetical protein COPCOM_00654 [Coprococcus comes ATCC 27758]
          Length = 256

 Score =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 119/246 (48%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + KAI  +TGE + V GA RTDSGVHA   
Sbjct: 9   MRRIRLTVAYDGTNYCGWQIQPNGITIEEVLNKAICKLTGEEIQVIGASRTDSGVHARGN 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD            ALN  L     I ++    VD  +H R+    ++Y Y II  +
Sbjct: 69  IAVFDTESRIPAERFSYALNQRL--PKDIVVVKSDEVDLNWHPRYQDTLKTYEYHIINTK 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+   + +   LD   MR  A +L G HDF  F  I   A + +RTI    +   
Sbjct: 127 VPIPTERLYNYFVSFDLDVGQMRRGAAYLEGEHDFAPFCCIRTNAKTTVRTITDLQILQS 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I IR+    FL+  +R   G L  VG G +    +++ L+  +R      APP+GL 
Sbjct: 187 GEHITIRITGNGFLYNMVRIIAGVLVRVGRGFYEPEKVKELLEGGERTREAVTAPPQGLC 246

Query: 241 FDSVEY 246
              + Y
Sbjct: 247 LMEIRY 252


>gi|325294776|ref|YP_004281290.1| tRNA pseudouridine synthase A [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325065224|gb|ADY73231.1| tRNA pseudouridine synthase A [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 250

 Score =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY G+ YFGWQ      +IQG I K +  +    V + GA RTD+GVHA  Q
Sbjct: 1   MKNIKLTIEYLGTNYFGWQILPEKPTIQGEIIKVLERILQHPVKLTGASRTDAGVHAFGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F   +E     L  ALN  L     I I+++  V  +F +R  A  + Y YRI  R+
Sbjct: 61  VANFKTKKEIPLYKLQSALNGLL--PPDIKIISVEEVPLEFDSRRWAKGKRYRYRIFNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVNS 179
            P   E  R+W +P  LD   M  A + L+G  DFT+F         +P+RT+D+ ++  
Sbjct: 119 VPSPFEYKRSWFVPYQLDISLMEKAKEFLIGTFDFTSFSKSDRNVDINPVRTVDNIEIVK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I+     RSFL   +R  V +L  VG GK    D+++  + ++RK    LAPP+GL
Sbjct: 179 KESHIDFIFYGRSFLRHMVRIMVATLVEVGKGKLRPEDIKEIREKKNRKFAPFLAPPDGL 238

Query: 240 YFDSVEYS 247
           Y + V Y 
Sbjct: 239 YLEKVYYD 246


>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 =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            +  + IEY+GS Y+GWQ+Q+  +S+QG +E+A+  V    + V  AGRTDSGVHA  QV
Sbjct: 12  QKIALGIEYDGSRYYGWQQQREVASVQGCLEQALSKVADAPINVLCAGRTDSGVHATGQV 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +N +L     I++  +S V   FHARFSAI R Y Y I   + 
Sbjct: 72  VHFETSARRKDAAWSMGVNTHL--PPDIAVRWVSAVADDFHARFSAIARRYRYIIYNHRN 129

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+ +         LD   M  AAQ L+G +DFT+FR+  CQ+ +P R + H  V   G
Sbjct: 130 RPAVLQQGVTHFYHPLDAVRMHRAAQALLGENDFTSFRAAQCQSRTPWRKVKHVKVTRQG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  +G GK     L + L  +DR      A  EGLY 
Sbjct: 190 EYIVVDIKANAFVHHMVRNIVGSLMEIGCGKRNENWLAELLALRDRNLAAATARAEGLYL 249

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 250 VSVDYP 255


>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 =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 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|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 =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 119/251 (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   MPRFALKVEYHGAPFAGWQRQKDQPSVQGAIEDALARLEPGPHTIAAAGRTDTGVHGLGQ 60

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

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

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLARVGYP 250


>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 =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

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--PDDIAVRWAKVVEDDFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+++P R + H +V   G
Sbjct: 119 RSAILPQGVTHCHLELDHQLMHDAGQALLGENDFSSFRAAQCQSNTPWRNVHHLNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG        ++  L+ +DR    P A PEGLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGCCNQPVEWMKWLLEQKDRALAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVIYP 244


>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 =  294 bits (754), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD     +        NA L     ++IL    V++ FHARFSAI R Y Y I+ R A
Sbjct: 61  VHFDTATFRLEHNWVFGGNANLL--PEVAILWAQPVNEAFHARFSAIARHYRYIILNRGA 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+   R     + L    M+ A   LVG HDF++FR+  CQA SP+R + + +V   G
Sbjct: 119 RPAIANRRVTWYCQPLSVTKMKEAGAFLVGEHDFSSFRAKACQAKSPVRNVHYLEVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +FLH  +R+  G L  +G G+      E+ LQA+ R   G  A P+GLY 
Sbjct: 179 DWIVIDISANAFLHHMVRNIAGVLMAIGKGEQPPRWAEEVLQARCRAVGGVTARPDGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VRVDYP 244


>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 =  294 bits (754), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEYNGS Y+GWQRQ+   S+QG +E A+  V    + V  AGRTD+GVHA  QV 
Sbjct: 9   RIALGIEYNGSRYYGWQRQQEVKSVQGCLEDALSKVANHPINVFCAGRTDAGVHATGQVV 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD             +N +L   + I++     VD++FHARFSA  R Y Y I   +  
Sbjct: 69  HFDTPVIRKEAAWTMGVNTHL--PEDIAVRWCKPVDEEFHARFSATARRYRYVIFNHRYR 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   GN
Sbjct: 127 PAILSSGVTHFHYPLDEKKMHEAAQALLGENDFTSFRAVQCQSRTPWRNVMHVQVTRHGN 186

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      + + L+ +DR +    A  +GLY  
Sbjct: 187 YVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDINWMAQLLELKDRTKAAATAKADGLYLV 246

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 247 SVDYP 251


>gi|312144215|ref|YP_003995661.1| tRNA pseudouridine synthase A [Halanaerobium sp. 'sapolanicus']
 gi|311904866|gb|ADQ15307.1| tRNA pseudouridine synthase A [Halanaerobium sp. 'sapolanicus']
          Length = 248

 Score =  294 bits (753), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            Y + +EY+GS Y GWQRQKN   +IQ  +E A+  +    V V G+GRTD+GVHA  Q 
Sbjct: 4   NYKITLEYDGSNYSGWQRQKNTKETIQEKLENALSKINKNKVEVIGSGRTDAGVHAAGQT 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F L  +     +  A+N +L   D I       V K FHAR+ A  + Y YRI+    
Sbjct: 64  ANFFLDIQIPTYKIPIAINTHL--PDDIICYKAEKVAKDFHARYDARGKKYRYRILNSNF 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +   + + + LD + M+  A+  +G HDF  F S      S IR I  FD+NS  
Sbjct: 122 NSVFVRNYVYKVHQRLDLDIMQKGAKIFLGSHDFAAFCSAGSSVDSTIREIYSFDINSKT 181

Query: 182 N-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           N  I+I +    FL+  +R  VG+L  +  GK    DLE+ L    R+  G  AP +GL 
Sbjct: 182 NGEIQIDISGSGFLYNMVRILVGTLIELAKGKRNLADLEEILAGTQRERAGFTAPAKGLT 241

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 242 LLEVFYD 248


>gi|148381387|ref|YP_001255928.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           3502]
 gi|153931537|ref|YP_001385762.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           19397]
 gi|153934471|ref|YP_001389169.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. Hall]
 gi|148290871|emb|CAL85007.1| tRNA pseudouridine synthase [Clostridium botulinum A str. ATCC
           3502]
 gi|152927581|gb|ABS33081.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           19397]
 gi|152930385|gb|ABS35884.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. Hall]
          Length = 246

 Score =  294 bits (753), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 135/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V GA RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGASRTDSGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             + +F    +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++ 
Sbjct: 61  GYICNFFTNTKIPPENLQKVINNIL--PPDIVVLSSEEASSEFHSRFCSKGKTYEYTVLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P+A+ +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N
Sbjct: 119 SSKPIAIGRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEIN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+  +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  G
Sbjct: 179 KKGDFIKFIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 246


>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 =  294 bits (753), Expect = 7e-78,   Method: Composition-based stats.
 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|110803601|ref|YP_698382.1| tRNA pseudouridine synthase A [Clostridium perfringens SM101]
 gi|110684102|gb|ABG87472.1| tRNA pseudouridine synthase A [Clostridium perfringens SM101]
          Length = 248

 Score =  294 bits (753), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M    + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVH
Sbjct: 1   MRNIKITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   VA+F          + K +N YL   + I +  +    ++FHARF+   ++Y Y I
Sbjct: 61  AKNYVANFKTNSLMTLEQIIKYINEYL--PEDIRVKEIREASERFHARFNVKSKTYEYTI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  +
Sbjct: 119 DNNKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP 
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPA 238

Query: 237 EGLYFDSVEY 246
            GL    + Y
Sbjct: 239 HGLCLLELNY 248


>gi|312874027|ref|ZP_07734062.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2052A-d]
 gi|312874727|ref|ZP_07734746.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2053A-b]
 gi|325912360|ref|ZP_08174756.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 143-D]
 gi|329920629|ref|ZP_08277316.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 1401G]
 gi|311089472|gb|EFQ47897.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2053A-b]
 gi|311090367|gb|EFQ48776.1| tRNA pseudouridine synthase A [Lactobacillus iners LEAF 2052A-d]
 gi|325475831|gb|EGC79001.1| tRNA pseudouridine synthase A [Lactobacillus iners UPII 143-D]
 gi|328935887|gb|EGG32347.1| tRNA pseudouridine synthase A [Lactobacillus iners SPIN 1401G]
          Length = 260

 Score =  294 bits (753), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 87/249 (34%), Positives = 134/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+G+ + G+Q+Q N  +IQG IE A+  +T G+ V+VHG+GRTD+GVHA  
Sbjct: 1   MQRYKLILAYDGTLFHGFQKQPNQRTIQGVIEDALLKMTKGKHVIVHGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD          +  ALNA +     I  L+  +V+  FH ++S   + Y Y I  
Sbjct: 61  QVIHFDYPGNVIPAKNMLLALNALM--PRDIIFLDSELVNDDFHVQYSTKAKWYRYIINQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +      P  LD   M+ AA +L+G+HDFT+F +   Q    +RTI + ++ 
Sbjct: 119 SRFTDPFRRNYTGHCPYKLDMLKMKKAATYLLGKHDFTSFAASGGQIVDKVRTIFYINLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I + V+   FL+  +R   G L  +G G+    D+EK + A++R++    AP  G
Sbjct: 179 QHGDEIVLDVIGDGFLYNMVRIITGLLIDIGHGQKEVEDVEKIILAKNRQQVRNTAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLYHVFYD 247


>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 =  294 bits (753), Expect = 7e-78,   Method: Composition-based stats.
 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|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 =  294 bits (753), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I+EY+G GY GWQ+Q +  S+Q  +E A+  +    + V  AGRTD+GVHAL QV
Sbjct: 1   MKIVLILEYDGRGYCGWQKQPDRISVQSRLESALSRIASSQIQVVAAGRTDAGVHALCQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+           +  NA L   D IS+L  S V+  FHARFSA  R+YLY +++R A
Sbjct: 61  VHFETHVIRPLTAWVRGANALL--PDDISVLWASEVNDDFHARFSATERTYLYYLLSRPA 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +G+      SLD E M+ AA+ L+G HDF+ FRS  CQA + IR +   D++   
Sbjct: 119 RPGIFQGKTGWTHYSLDLEKMQTAARFLIGEHDFSAFRSAECQAKNAIRKLVRLDISQSE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FLH  +R+ +G+L  +G GK+    ++  L  +DR    P   P+GLY 
Sbjct: 179 QFFVFEFCANAFLHHMVRNILGALIYIGQGKYPPEWIQILLGKRDRTLAAPTFSPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AGVRYD 244


>gi|18309973|ref|NP_561907.1| tRNA pseudouridine synthase A [Clostridium perfringens str. 13]
 gi|24212547|sp|Q8XLQ0|TRUA1_CLOPE RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|18144651|dbj|BAB80697.1| tRNA-pseudouridine synthase I [Clostridium perfringens str. 13]
          Length = 248

 Score =  294 bits (753), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M    + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVH
Sbjct: 1   MRNIKITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   VA+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I
Sbjct: 61  AKNYVANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  +
Sbjct: 119 DNNKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP 
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIMVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPA 238

Query: 237 EGLYFDSVEY 246
            GL    + Y
Sbjct: 239 HGLCLLELNY 248


>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 =  294 bits (753), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 135/251 (53%), Gaps = 6/251 (2%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D      P    +  NA+L    T+++     + + FHARFSA RR+Y Y +    
Sbjct: 61  VVHLDTDLVREPFSWVRGTNAFL--PPTVAVRWAQEMPEDFHARFSAHRRTYYYALTFGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               L + +A  +     +SLD   M  AAQ LVG HDF++FR+  CQA SP++T+   +
Sbjct: 119 TRAPLLEDKAGYVMLPPGQSLDVAAMNEAAQVLVGEHDFSSFRAAECQAKSPVKTMYSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+   +FLH  +R+ +G L  +G G+   + +   L A+ R    P   P
Sbjct: 179 VRGEGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRQPVSWMGDVLAARSRVAAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 239 DGLYLAEVGYP 249


>gi|54309813|ref|YP_130833.1| tRNA pseudouridine synthase A [Photobacterium profundum SS9]
 gi|51316618|sp|Q6LNU5|TRUA_PHOPR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46914251|emb|CAG21031.1| Putative tRNA pseudouridine synthase A [Photobacterium profundum
           SS9]
          Length = 261

 Score =  294 bits (753), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y GWQRQ +  S+Q  +EKA+  +  + + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGAKYCGWQRQVDVDSVQERLEKALSHIANKPIAVFCAGRTDTGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +   V     +NA+L     IS+   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDVDVDRQMVAWTIGVNAHL--PRDISVRWATQVSDDFHARFSATARRYRYIIYNSAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ+LVG HDFT+ R+  CQ+ SP R + H +V+  G
Sbjct: 119 RPAIFGVGVSHYHGHLDEKKMHEAAQYLVGEHDFTSVRASQCQSRSPWRAMKHVNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+ T   ++  L+ +DR+  G  A   GLY 
Sbjct: 179 DFVIIDIKANAFVHHMVRNIAGSLIRVGRGQETPEWMKWVLEQKDRRVAGETAKAAGLYL 238

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 239 VAVDYP 244


>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 =  294 bits (753), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 121/251 (48%), Positives = 162/251 (64%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   +KG+ W I  +LD   M+  A  L+G+HDFTTFRS  CQA+SP++T+D   V   
Sbjct: 120 APATHDKGQVWQINHTLDVAAMQAGADMLIGQHDFTTFRSSICQAASPVKTLDALRVEQV 179

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

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


>gi|225018926|ref|ZP_03708118.1| hypothetical protein CLOSTMETH_02877 [Clostridium methylpentosum
           DSM 5476]
 gi|224948306|gb|EEG29515.1| hypothetical protein CLOSTMETH_02877 [Clostridium methylpentosum
           DSM 5476]
          Length = 250

 Score =  294 bits (753), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 121/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I YNG+ Y GWQ QKN  ++Q  ++ A+  + G    V G  RTD+GVHA   
Sbjct: 3   MRNLLVKIAYNGAAYHGWQVQKNALTVQEVVQDAVEKLFGRREDVVGCSRTDTGVHANEY 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             +    ++     + + +N  L   D +++L  + V++ FHAR+    + Y+Y+I   +
Sbjct: 63  FFNMHTEKDIPCRSVMRGMNTLL--PDDVAVLGCTEVEEDFHARYCCTGKEYIYKIWNAE 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +       +    P  LD + +  A +  +G HDF+ F S        +RTI     +  
Sbjct: 121 SRNPFLHRQCLRYPFPLDIQLLNRAMERFLGTHDFSAFCSAGSDVEDRVRTITQAHASRE 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ + V    FL+  +R  VG+L  V +GK +  D+   + ++DR   G  APP GL+
Sbjct: 181 GDLVTLTVRGDGFLYNMVRILVGTLIEVQEGKLSPDDIPSVIASRDRSRAGKTAPPCGLF 240

Query: 241 FDSVEY 246
            + V Y
Sbjct: 241 LNRVFY 246


>gi|255604972|ref|XP_002538318.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223512770|gb|EEF24066.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 283

 Score =  294 bits (753), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 138/246 (56%), Gaps = 2/246 (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  AHFDTAVTRPQNAWVRGVNAFL--PTGVRVLWASEVDVEFHARFSAERRSYQYVLQVSPV 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 DSVEYS 247
             V Y 
Sbjct: 263 TGVHYD 268


>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 =  294 bits (753), Expect = 9e-78,   Method: Composition-based stats.
 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|110800554|ref|YP_695694.1| tRNA pseudouridine synthase A [Clostridium perfringens ATCC 13124]
 gi|110675201|gb|ABG84188.1| tRNA pseudouridine synthase A [Clostridium perfringens ATCC 13124]
          Length = 248

 Score =  294 bits (752), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M    + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVH
Sbjct: 1   MRNIKITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   VA+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I
Sbjct: 61  AKNYVANFKTNSLMTLEQIIEYINEYL--PEDIRVKEIREASERFHARFNVKSKTYEYTI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  +
Sbjct: 119 DNNKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP 
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPA 238

Query: 237 EGLYFDSVEY 246
            GL    + Y
Sbjct: 239 HGLCLLELNY 248


>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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 102/246 (41%), Positives = 140/246 (56%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+G+ Y GWQRQ NG S+Q  +E+++  V    V V  AGRTD+GVHA +QV
Sbjct: 1   MKIALGVEYDGTAYHGWQRQNNGISVQQVLEESLSKVANHGVQVQCAGRTDTGVHATQQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +          NA L     +S+     V   FHARFSA  R Y Y I++R +
Sbjct: 61  VHFESSAQRSIRNWILGANANL--PFDVSVRWAKQVSDDFHARFSAQGRRYRYLILSRYS 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL   RA    K LD E M+ AAQHLVGRHDF+++R++HCQA SP+RT+   +V   G
Sbjct: 119 RSALWGRRATWTHKPLDLEVMQQAAQHLVGRHDFSSYRAVHCQAKSPVRTLHSLEVGRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I V    FLH  +R+  G L  +G G+       + L+ +DR+  G  APP GLYF
Sbjct: 179 DFIYIDVHGDGFLHHMVRNIAGVLMAIGAGEAVPDWSREVLEHRDRRLGGVTAPPWGLYF 238

Query: 242 DSVEYS 247
              EY 
Sbjct: 239 VHAEYP 244


>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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 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|322381099|ref|ZP_08055102.1| tRNA pseudouridine synthase A-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154675|gb|EFX46946.1| tRNA pseudouridine synthase A-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 252

 Score =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 130/254 (51%), Gaps = 9/254 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      + Y+G+ Y G+Q Q +G+++Q  +E+AI ++TGE V +  +GRTD+GVHA  Q
Sbjct: 1   MRNLRFTLSYDGTSYSGFQTQPDGNTVQDQLEEAIHMLTGEKVKITSSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F           C ALN+ L     I +     V   FH+R SA R++Y Y I T +
Sbjct: 61  VVNFLTSSRIPVDRWCLALNSRL--PRDIVVYEAEEVSLTFHSRKSAKRKTYCYEIRTSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +      P  L+ E M+ A    +G HDFT+F +      + +RTI    +   
Sbjct: 119 FPDVFHRAFEVHYPTPLNIEAMKEALSCFIGTHDFTSFCTTRTTMENRVRTIYEARLEYL 178

Query: 181 GN-------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            +       LI+I +    FL+  +R  VG++  VG+GK  S+++   L A+DR++ GP 
Sbjct: 179 PDQDDPARGLIQIYLTGSGFLYNMVRIIVGTILQVGEGKEKSSEIPVILAAKDRRKAGPT 238

Query: 234 APPEGLYFDSVEYS 247
           A  +GL    VEY 
Sbjct: 239 AMAKGLTLWKVEYE 252


>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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

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--PDDISVSWAKIVDEDFHARFSANARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q L+G +DF++FR+  CQ+ +P R + H +V   G
Sbjct: 119 RSAILPKGITHCHLELDHQLMHQAGQVLLGENDFSSFRASQCQSHTPFRNVHHLNVIRRG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  +G G      +   L  +DR    P A PEGLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEIGAGHQPVEWMSWLLAQKDRTLAAPTAKPEGLYL 238

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 239 VNVIYP 244


>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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + ++Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGVQYDGAAFCGWQAQPHGKTVQDALERALGEFACVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+S+     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTALDRAEFSWVRGTNAFL--PPTVSVQWAKAMPDTFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAVHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY 
Sbjct: 179 HFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SPI+T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDAEAMRAGAAHLVGRHDFTTFRAAGCQAASPIKTLDALTLETV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 129/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 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  + Y Y I   
Sbjct: 61  QVAHFHTIARHPPEVFLKALNATL--PPDVRVVWAEEAPQSFHATLDAQSKRYRYVIDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  AW + + LD   M  A Q L GRHDF +F +      S +RTI    V  
Sbjct: 119 PFADPFLRRTAWHLFRPLDAPRMNRAVQALRGRHDFRSFETNWPNRMSSVRTILDVQVRR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +E+ V A  FL+  +RS  G+  LVG G    T + + L AQDR+  GP APP+GL
Sbjct: 179 IDHRVELEVEADGFLYNMVRSIAGTAVLVGLGDRPETFVAEVLHAQDRRLAGPTAPPQGL 238

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 239 FLLQVRY 245


>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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SP++T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDPEAMRAGAAHLVGRHDFTTFRAAGCQAASPVKTLDALTLETV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (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  IHLDTGADRKEISWVRGLNSYL--PTECAVRWAKVVPDEFHARFSACSRTYEYWIVNEPV 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 DSVEYS 247
             V Y 
Sbjct: 239 TGVGYP 244


>gi|167748465|ref|ZP_02420592.1| hypothetical protein ANACAC_03209 [Anaerostipes caccae DSM 14662]
 gi|167652457|gb|EDR96586.1| hypothetical protein ANACAC_03209 [Anaerostipes caccae DSM 14662]
          Length = 252

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 121/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q   ++I+G + + +  + GE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLEVAYDGTNYCGWQIQPKDTTIEGILNEKLGSLLGEEITVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD   E     + +ALN  L   D I I + S V   FH R+   R++Y Y I   +
Sbjct: 61  VAVFDTETEIPGERIARALNQRL--PDDIVIQSSSEVKDDFHPRYQDTRKTYEYTIYNAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E MR AA+  +G HDF +F +      + +RTI   +V   
Sbjct: 119 FDNPVTARHHHFVYVPLDAERMRTAARCFLGEHDFLSFSTTGSPTKTTVRTIYECEVRQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +RV    FL+  +R   G+L  +G G+     + +      R + GP AP +GL 
Sbjct: 179 GRYITMRVTGNGFLYNMVRMMAGTLISIGRGRKDPEWVRELFLHPKRGKAGPNAPAKGLT 238

Query: 241 FDSVEY 246
             ++ Y
Sbjct: 239 LINIHY 244


>gi|229170993|ref|ZP_04298594.1| tRNA pseudouridine synthase A [Bacillus cereus MM3]
 gi|228612533|gb|EEK69754.1| tRNA pseudouridine synthase A [Bacillus cereus MM3]
          Length = 252

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIKQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEISSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QGDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 143/246 (58%), Gaps = 2/246 (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  L     + +L    VD +FHARF A +RSY Y +I +  
Sbjct: 61  VHFDTEAVRSQTAWVRGVNTKL--PRGVRVLWAKEVDPRFHARFDAYQRSYQYWLINQPV 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 DSVEYS 247
             V Y 
Sbjct: 239 TGVGYD 244


>gi|168208061|ref|ZP_02634066.1| tRNA pseudouridine synthase A [Clostridium perfringens E str.
           JGS1987]
 gi|168215906|ref|ZP_02641531.1| tRNA pseudouridine synthase A [Clostridium perfringens NCTC 8239]
 gi|169341141|ref|ZP_02863234.1| tRNA pseudouridine synthase A [Clostridium perfringens C str.
           JGS1495]
 gi|169299748|gb|EDS81800.1| tRNA pseudouridine synthase A [Clostridium perfringens C str.
           JGS1495]
 gi|170660642|gb|EDT13325.1| tRNA pseudouridine synthase A [Clostridium perfringens E str.
           JGS1987]
 gi|182381869|gb|EDT79348.1| tRNA pseudouridine synthase A [Clostridium perfringens NCTC 8239]
          Length = 248

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M    + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVH
Sbjct: 1   MRNIKITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   VA+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I
Sbjct: 61  AKNYVANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  +
Sbjct: 119 DNNKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP 
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPA 238

Query: 237 EGLYFDSVEY 246
            GL    + Y
Sbjct: 239 HGLCLLELNY 248


>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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIE++G+ + GWQRQ    ++QG +E AI  +TGE  + +G+ RTD GVHA   
Sbjct: 1   MRNIKLIIEFDGTNFCGWQRQVKDRTVQGCLENAILKITGEKSLTNGSSRTDGGVHAKAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F            +ALN  L   D ISI+    VD +FHAR+S+  + Y Y I+ R 
Sbjct: 61  VANFITNSSIPGEKFREALNTKL--PDDISIIKSEEVDMEFHARYSSKGKMYSYTIVNRY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             LA  K     + K L+ E+M+ A ++ VG+HDF  F S    A + +RTI  F +   
Sbjct: 119 EKLAFGKQYLHHVRKELNVEDMKKACEYFVGKHDFKAFMSPGSSAKTTVRTITDFYIEEN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N+I I + A  FL+  +R  VG+L  VG GK    D+   +    RK  G   PP GL 
Sbjct: 179 KNVIRIFISADGFLYNMVRIIVGTLINVGTGKTKLQDVNNIINDGIRKNAGMCVPPNGLV 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 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|309389901|gb|ADO77781.1| tRNA pseudouridine synthase A [Halanaerobium praevalens DSM 2228]
          Length = 248

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 92/250 (36%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M + Y +I+EY+GS Y GWQRQKN   +IQ  IE+A+  +    V + GAGRTD+GVHA 
Sbjct: 1   MRKNYKIIVEYDGSNYSGWQRQKNTEQTIQQKIEEALTKINKSQVKIDGAGRTDAGVHAA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            Q A+F L  E  P  +  ALN  L   D I       V++ FHAR+ A  + Y YRI+ 
Sbjct: 61  GQSANFFLDVEIPPTKIPIALNTEL--PDDIICKKAIKVNQNFHARYDARGKKYRYRILN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                   +   + + K LD + M+ AA+   G HDF +F +      S +RTI   D+ 
Sbjct: 119 SNFNSVFVRNFVYNVYKKLDLKMMQKAAKIFEGSHDFASFCAAGSSVESTVRTIRSIDIY 178

Query: 179 SFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  +  I + +V   FL+  +R   G+    G GK T ++LE  LQ+ +RK  G  AP +
Sbjct: 179 AVDDSEIWLDIVGNGFLYNMVRILAGTFIETGMGKKTLSELEVILQSCNRKNAGFTAPAQ 238

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 239 GLTLMEVFYD 248


>gi|229067907|ref|ZP_04201224.1| tRNA pseudouridine synthase A [Bacillus cereus F65185]
 gi|228715266|gb|EEL67125.1| tRNA pseudouridine synthase A [Bacillus cereus F65185]
          Length = 252

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTSLSLEEWQWINALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QNDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>gi|229107828|ref|ZP_04237464.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-15]
 gi|228675677|gb|EEL30885.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-15]
          Length = 252

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 123/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q N  ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPNHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I  R V   FL+  +R  VG+L  VG GK  S  + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDSDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIE++G+ + GWQRQ    ++QG +E AI  +TGE  + +G+ RTD GVHA   
Sbjct: 1   MRNIKLIIEFDGTNFCGWQRQVKDRTVQGCLENAILKITGEKSLTNGSSRTDGGVHAKAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F            +ALN  L   D ISI+    VD +FHAR+S+  + Y Y I+ R 
Sbjct: 61  VANFITNSSIPGEKFREALNTKL--PDDISIIKSEEVDMEFHARYSSKGKMYSYTIVNRY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             LA  K     + K L+ E+M+ A ++ +G+HDF  F S    A + +RTI  F +   
Sbjct: 119 EKLAFGKQYLHHVRKELNVEDMKKACEYFLGKHDFKAFMSPGSSAKTTVRTITDFYIEEN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N+I I + A  FL+  +R  VG+L  VG GK    D+   +    RK  G   PP GL 
Sbjct: 179 KNVIRIFISADGFLYNMVRIIVGTLINVGTGKTKLQDVNNIINDGIRKNAGMCVPPNGLV 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVFY 244


>gi|78221826|ref|YP_383573.1| tRNA pseudouridine synthase A [Geobacter metallireducens GS-15]
 gi|78193081|gb|ABB30848.1| tRNA pseudouridine synthase [Geobacter metallireducens GS-15]
          Length = 256

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 124/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++EY+G+ Y GWQ Q NG S+Q  +E+A+  +  E V VH +GRTD+GVHA   
Sbjct: 13  MHTIKLVLEYDGTNYAGWQIQPNGISVQQVVEEALARLLKEPVRVHSSGRTDAGVHARGM 72

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   +          LNA L     I+++        F+ RF A  + Y Y I   +
Sbjct: 73  VAAFTTAKGLPMRAFSDGLNALL--PPDIAVMEALEAPDGFNPRFDAAGKHYRYTIHRGE 130

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +   W   ++LD   M   A H+VG HDF +FR+  C A + +R ID  D+   
Sbjct: 131 RRSPLCRHYVWHARETLDLAAMEKGASHMVGEHDFASFRTAGCAARTTVRRIDAVDLALE 190

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ I V    FL   +R  VG+L  VG G+ ++ D+    +    +  GP APP+GL 
Sbjct: 191 GDLLHIDVKGSGFLRNMVRIMVGTLVEVGRGRRSADDVALLFRYPGERFAGPTAPPQGLC 250

Query: 241 FDSVEY 246
              V Y
Sbjct: 251 LMEVYY 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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 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|229159315|ref|ZP_04287339.1| tRNA pseudouridine synthase A [Bacillus cereus R309803]
 gi|228624207|gb|EEK81009.1| tRNA pseudouridine synthase A [Bacillus cereus R309803]
          Length = 252

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QGDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (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  IHLDTGADRKEISWVRGLNSYL--PTECAVRWAKVVPDEFHARFSACSRTYEYWIVNEPV 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 DSVEYS 247
             V Y 
Sbjct: 239 TGVGYP 244


>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 =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 88/245 (35%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ+  +S+Q  +E+A+  V    + V  AGRTD+GVHA  QV 
Sbjct: 13  KIALGIEYDGSQYYGWQRQQEVASVQACLEQALSKVADAPINVLCAGRTDAGVHATGQVV 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +N +L     I++  ++ V++ FHARFSA  R Y Y I   +  
Sbjct: 73  HFETTAQRKDAAWTMGVNTHL--PPDIAVRWVTGVNEDFHARFSATARRYRYIIYNHRYR 130

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+ +         LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V  +G 
Sbjct: 131 PAVLQKGMTHFYHPLDAERMERAAQALLGENDFTSFRTVQCQSRTPWRNVKHVKVTRYGE 190

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G      + + L  +DR      A  +GLY  
Sbjct: 191 YIVVDIKANAFVHHMVRNIVGSLMEIGCGNQDENWMAELLALKDRNLAAATARADGLYLV 250

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 251 SVDYP 255


>gi|317497062|ref|ZP_07955389.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895607|gb|EFV17762.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 252

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 124/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+GY GWQ Q N  +++G + K I  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRVKLIVAYDGTGYCGWQVQPNEITVEGVLNKHISELTGEDIKVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         + KALNA L   + I I +   V   +H RF   R++Y Y     +
Sbjct: 61  VAVFDTESRIPGEKMAKALNARL--PEDIIIQDSKEVPLDYHPRFQDTRKTYEYTFYNAR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E M+ AA + +G H F +  S   Q +S +R I   DV   
Sbjct: 119 YDNPVTSRHHHFVYVPLDVEKMKEAASYFLGEHCFISMCSSKAQVTSYVREIYECDVTQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +RV    FL+  +R   G+L  VG GK     +++ L +++R   GP  P +GL 
Sbjct: 179 GRYITMRVTGSGFLYNMVRLMAGTLLEVGRGKQEPQWVKEILASKERVTPGPKLPAKGLT 238

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 239 LIQIEYP 245


>gi|184155960|ref|YP_001844300.1| tRNA pseudouridine synthase A [Lactobacillus fermentum IFO 3956]
 gi|238692990|sp|B2GDT8|TRUA_LACF3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|183227304|dbj|BAG27820.1| pseudouridylate synthase A [Lactobacillus fermentum IFO 3956]
          Length = 258

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 128/252 (50%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---VHGAGRTDSGVHA 57
           M RY +   Y+GS + G+Q Q    ++Q  +E+A+  +  +      V G+GRTD+GVHA
Sbjct: 1   MHRYKITFAYDGSNFAGFQIQPGERTVQQVLERAVNKIAKKPQPPLMVFGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     L +ALN+ L     + +   + V   FHARF A  + Y YR++
Sbjct: 61  LGQVAHFDLPYQIPGPSLVRALNSSL--PLDVLVKEATEVAPDFHARFDAHHKRYRYRVV 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D E M+ AAQ  VG HDFT+F +   QA+S +R ID   V
Sbjct: 119 GGEFTNPFKRNYTGHYKYPVDVERMQTAAQDFVGEHDFTSFVASGSQATSNVRRIDEVTV 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +    V   FL+ Q+R  V  L  +G+G+    D+ + ++A++R      AP
Sbjct: 179 VRDEENDEVVFDFVGNGFLYNQVRIMVAFLLEIGNGRRPVDDVMRVMKAKNRDLARGTAP 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ASGLYLVEVTYD 250


>gi|182625331|ref|ZP_02953105.1| tRNA pseudouridine synthase A [Clostridium perfringens D str.
           JGS1721]
 gi|177909489|gb|EDT71936.1| tRNA pseudouridine synthase A [Clostridium perfringens D str.
           JGS1721]
          Length = 248

 Score =  293 bits (751), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M    + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVH
Sbjct: 1   MRNIKITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   VA+F          + + +N YL   + I I  +    ++FHARF+   ++Y Y I
Sbjct: 61  AKNYVANFKTNSLMTLEQIIEYINEYL--PEDIRITEIREASERFHARFNVKSKTYEYTI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  +
Sbjct: 119 DNNKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP 
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPA 238

Query: 237 EGLYFDSVEY 246
            GL    + Y
Sbjct: 239 HGLCLLELNY 248


>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 =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 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|228937445|ref|ZP_04100091.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970331|ref|ZP_04130990.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228976901|ref|ZP_04137313.1| tRNA pseudouridine synthase A [Bacillus thuringiensis Bt407]
 gi|228782871|gb|EEM31037.1| tRNA pseudouridine synthase A [Bacillus thuringiensis Bt407]
 gi|228789440|gb|EEM37360.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228822278|gb|EEM68260.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|326937937|gb|AEA13833.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 252

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+ + +R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEIKKIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>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 =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 94/245 (38%), Positives = 142/245 (57%), Gaps = 2/245 (0%)

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  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD   +       + +N++L   D+I +    IV   F ARFSA+ R+Y+Y +   +  
Sbjct: 64  HFDTEVDRNLESWIRGVNSHL--PDSIRVRWSKIVPDSFSARFSAVSRTYVYLLRNERVM 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             +  GRA     +LD E+M IA + ++G HDFT+FRS  CQASSP+RT+D F +N+ G 
Sbjct: 122 SPIWSGRAGWDFHNLDVESMNIAKEKMIGTHDFTSFRSSQCQASSPVRTLDLFKINAEGP 181

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I   + A  FLH  +R+ +G++  VG G+++ + +   ++A++R    P   P+GLYF 
Sbjct: 182 FIIFTLRANGFLHHMVRNLIGTILYVGMGRFSPSKIPDLIEAKNRMFTAPTFMPDGLYFA 241

Query: 243 SVEYS 247
            V+Y 
Sbjct: 242 RVDYP 246


>gi|229194532|ref|ZP_04321335.1| tRNA pseudouridine synthase A [Bacillus cereus m1293]
 gi|228588998|gb|EEK47013.1| tRNA pseudouridine synthase A [Bacillus cereus m1293]
 gi|324324133|gb|ADY19393.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 252

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|134298133|ref|YP_001111629.1| tRNA pseudouridine synthase A [Desulfotomaculum reducens MI-1]
 gi|172044244|sp|A4J151|TRUA_DESRM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|134050833|gb|ABO48804.1| tRNA pseudouridine synthase A [Desulfotomaculum reducens MI-1]
          Length = 247

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 127/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + + Y+G+ Y G+Q Q+    ++IQ ++EKA+  +    + V GAGRTD+GVHA 
Sbjct: 1   MKNIKLTLAYDGTNYHGFQEQRGTGLATIQEALEKALSTIAQTPIQVIGAGRTDAGVHAQ 60

Query: 59  RQVAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV +F   +  VP      ALN  L     I ++    V   FHARFSA+ ++Y Y I 
Sbjct: 61  GQVVNFRSEKWPVPAEKAPLALNVLL--PGDIKVVKAEEVPMDFHARFSAVAKTYRYSIY 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +      +   +  P+ LD   M+  A +L+G +DF +F++        IRTI   D+
Sbjct: 119 HHRVMSPFHRYYCYHEPRRLDVNAMQEGAAYLLGTYDFKSFQAQGTPVKDTIRTIYRADI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                +I + +    FL+  +R   G+L  +G GK    D+ K +++++R   G  APP+
Sbjct: 179 IEDAPVINLYLRGNGFLYNMVRIITGTLLNIGFGKIKPEDMVKIIESKNRTLAGTTAPPQ 238

Query: 238 GLYFDSVEY 246
           GL    VEY
Sbjct: 239 GLCLMEVEY 247


>gi|87308089|ref|ZP_01090231.1| Pseudouridylate synthase (tRNA [Blastopirellula marina DSM 3645]
 gi|87289171|gb|EAQ81063.1| Pseudouridylate synthase (tRNA [Blastopirellula marina DSM 3645]
          Length = 260

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 131/246 (53%), Gaps = 6/246 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I+ Y+G+ Y GWQ Q +  +IQG++E+ +  +TGE + V G+GRTDSGVHA+ QV  F 
Sbjct: 11  LIVSYDGTNYAGWQIQNDQRTIQGALERTLLKITGEKIRVTGSGRTDSGVHAIGQVVSFR 70

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +  +  P ++ +ALNA L     I + +      +F+A   AI++ Y Y +   +     
Sbjct: 71  MQSQLSPDVMRRALNAEL--PPDIVVQSARNAIPEFNAIDCAIKKRYRYLLQEGRIDDVF 128

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS----FG 181
            +  AW + K L+   M+ AAQHL+G HDF +F S+  +  + +R +    V        
Sbjct: 129 SRQYAWFVKKELNFAAMQAAAQHLIGEHDFASFESVGSERMTTVRHVFDVQVLRSERHEF 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I V A  FL+  +R  VG+L  VG G+     + + L A+ R   G  AP  GLY 
Sbjct: 189 DKVAIEVEANGFLYNMVRIIVGTLVDVGKGRRPPEWVAEVLAAKKRTAGGMTAPAHGLYL 248

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 249 LRVDYP 254


>gi|317055617|ref|YP_004104084.1| tRNA pseudouridine synthase A [Ruminococcus albus 7]
 gi|315447886|gb|ADU21450.1| tRNA pseudouridine synthase A [Ruminococcus albus 7]
          Length = 245

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 85/242 (35%), Positives = 124/242 (51%), Gaps = 2/242 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M + Y+GS Y GWQRQ N  ++Q  +E AIF +TGE VVV G  RTD+GVHA   V  F 
Sbjct: 1   MTLAYDGSNYHGWQRQSNALAVQEVVEDAIFKLTGENVVVQGCSRTDAGVHAREYVLSFG 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           L        +   LN++L   D IS++     D+ FHAR+    + Y Y +   +     
Sbjct: 61  LELPINCRGIQLGLNSWL--PDDISVIGCEEADEGFHARYMCKGKEYEYIVHNSRIKDPF 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A+     +D   +  AA++ VG HDF  F S  C     +R I  FDV   G+ + 
Sbjct: 119 MRNTAFRNTYPIDEVLLDRAAKYFVGEHDFKAFCSTACDKEITVRKIYRFDVRREGDKVI 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             V    FL+  +R  VG+L  + +GK  +  + + L ++DRK+ G   PP+GLY + V 
Sbjct: 179 FTVAGNGFLYNMVRIMVGTLLFINEGKIAADAIPRILDSKDRKKAGKTVPPQGLYLNKVY 238

Query: 246 YS 247
           Y 
Sbjct: 239 YD 240


>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 =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 95/251 (37%), Positives = 139/251 (55%), Gaps = 8/251 (3%)

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  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVD------KQFHARFSAIRRSYLYRI 116
           HFD   E       + +N +L    +I++   + V         FHARFSA  R Y Y +
Sbjct: 67  HFDTTLERDMSSWVRGVNTFL--PPSIAVRWATEVAHNPDEQDNFHARFSARSRMYQYVL 124

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G+A  + + LD E MR AAQHL+G HDF+TFRS+ CQA SP++++    
Sbjct: 125 YNNPVRSPLLEGKAGWVFRKLDVERMRTAAQHLLGEHDFSTFRSVQCQAKSPVKSMYSIK 184

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+LI   + A +FLH  +R+ VGSL  VG+G      L++ L  +DRK   P   P
Sbjct: 185 IEQRGDLIMFTLHANAFLHHMVRNIVGSLIYVGNGAQQPDWLKELLDGRDRKFAAPTFMP 244

Query: 237 EGLYFDSVEYS 247
           +GLY   ++Y 
Sbjct: 245 DGLYLAKIDYD 255


>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 =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 91/243 (37%), Positives = 130/243 (53%), Gaps = 2/243 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + + Y+GS + GWQ Q  G ++Q ++E A+       V    AGRTD+GVHAL Q+ H 
Sbjct: 2   ALGLAYDGSSWQGWQTQPGGLTVQDTLESALAEFLNHPVGTICAGRTDTGVHALEQIVHL 61

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P    + LNA L    +I++     V   FHARFSA+ RSY+Y +   +    
Sbjct: 62  DTQAARRPESWVRGLNALL--PASIAVQWAKPVSDSFHARFSALSRSYVYIVRNTRVRSP 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L  GR   +  SL  + MR AA+ LVG HDF++FRS  CQA+SP+RT+    V   G+  
Sbjct: 120 LMHGRVGWVYHSLQLDPMRDAARRLVGEHDFSSFRSSQCQAASPVRTLQEASVEQHGDFY 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R  A +FLH  IR+ +G++  +G GK     +++ L  +DR+   P   P GLY   V
Sbjct: 180 LFRFQANAFLHHMIRNLMGAILYIGQGKQEPGWIDELLAQRDRRRAAPTFSPAGLYLSGV 239

Query: 245 EYS 247
            Y 
Sbjct: 240 RYP 242


>gi|163857158|ref|YP_001631456.1| tRNA pseudouridine synthase A [Bordetella petrii DSM 12804]
 gi|229557953|sp|A9IRL0|TRUA_BORPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|163260886|emb|CAP43188.1| pseudouridylate synthase I [Bordetella petrii]
          Length = 268

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 88/249 (35%), Positives = 133/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +  ++Q ++E A+    G    +    AGRTD+GVHA 
Sbjct: 1   MPRMALGLAYDGSSWQGWQTQPHRQTVQDTLEAALARFAGIDGSLPTVCAGRTDTGVHAA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H D   E       + +NA+L    +I++     V   FHARFSA  R+YLY +  
Sbjct: 61  MQVVHLDTRLERRAESWVRGVNAFL--PPSIAVQWAQPVPDDFHARFSARSRTYLYLLWR 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +    L  GRA    + LD + MR AA  L+G HDF++FRS  CQA  P+RT+   D++
Sbjct: 119 GRVRPPLWAGRAGWCFQPLDVQAMRQAASALLGEHDFSSFRSSQCQARHPVRTLHRLDID 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A +FLH  +R+ +G+L  +G G+     +   L A+DR+   P    +G
Sbjct: 179 ERGPFLVFTLRANAFLHHMVRNLMGALLQIGQGRQPVAWMPAVLAARDRRLAAPTFAADG 238

Query: 239 LYFDSVEYS 247
           LY  ++EY 
Sbjct: 239 LYLSAIEYP 247


>gi|254517504|ref|ZP_05129560.1| tRNA-pseudouridine synthase I [Clostridium sp. 7_2_43FAA]
 gi|226911253|gb|EEH96454.1| tRNA-pseudouridine synthase I [Clostridium sp. 7_2_43FAA]
          Length = 244

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 138/246 (56%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + +EY+G+ Y GWQ+QK G++IQ ++E+AI L+T E   V G+ RTD+GVHA   
Sbjct: 1   MRNIKLTLEYDGTNYLGWQKQKIGATIQETLEEAIRLLTNEESEVIGSSRTDAGVHARGF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F            +A+N  L   + I IL    V++ FH+R+SA  ++Y Y I+ R 
Sbjct: 61  VANFKTNSTIPSEKFREAINYRL--PNDIVILKSEEVEEDFHSRYSAKGKTYSYSILNRD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+ K   + + + LD E+M+ A ++ +G  DF  F+S      + +RTI    ++  
Sbjct: 119 VNSAIGKDYVYHVKRKLDVEDMKEACKYFIGTKDFMAFKSSGSSVKTTVRTISDLYIDIK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++I+I V    FL+  +R  VG+L +VG  K  S +++  ++++DRK+ G   P  GL 
Sbjct: 179 DDIIKIYVTGDGFLYNMVRIIVGTLIMVGSNKIDSREVKNIIESKDRKKAGICVPAAGLV 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LEKVYY 244


>gi|189423417|ref|YP_001950594.1| tRNA pseudouridine synthase A [Geobacter lovleyi SZ]
 gi|189419676|gb|ACD94074.1| tRNA pseudouridine synthase A [Geobacter lovleyi SZ]
          Length = 262

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 121/247 (48%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +II+Y+G+ Y GWQ Q NG SIQ ++E A+  + G+ V V  +GRTD+GVHA+  
Sbjct: 17  MRTIKLIIQYDGTNYCGWQEQTNGPSIQETVELALAKILGQRVRVQSSGRTDAGVHAVAM 76

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A F              +N +L   D I+I +   V   F A   A  ++Y Y I    
Sbjct: 77  PAVFRTESTIPLKAFVDGVNCHL--PDDIAIQSAVEVPTGFRAIGGARSKTYRYTIYNAP 134

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +  +W + + LD + M+ AA + VG HDF  FR  +C A +  R ID   +N  
Sbjct: 135 VRSPLNRRTSWHVREQLDLQAMQQAAAYFVGEHDFAAFRGANCSAVTSRRRIDAVQINQS 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI I V    FL   +R   G+L  VG G++    +   L   DR+  G  APP+GL 
Sbjct: 195 GPLITIDVTGGGFLKYMVRIMAGTLVDVGRGRFAPEHVAGLLAEPDRQRGGVTAPPQGLS 254

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 255 LLQVIYP 261


>gi|229083462|ref|ZP_04215810.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-44]
 gi|228699895|gb|EEL52532.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-44]
          Length = 252

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGENVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLTLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  +L+G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYLIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK  +  + + L  Q+RK  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLDVGQGKLDADSIPEILAKQNRKFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|167767771|ref|ZP_02439824.1| hypothetical protein CLOSS21_02306 [Clostridium sp. SS2/1]
 gi|167710510|gb|EDS21089.1| hypothetical protein CLOSS21_02306 [Clostridium sp. SS2/1]
 gi|291558888|emb|CBL37688.1| pseudouridylate synthase I [butyrate-producing bacterium SSC/2]
          Length = 252

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 125/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+GY GWQ Q N  +++G + K I  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRVKLIVAYDGTGYCGWQVQPNEITVEGVLNKHISELTGEDIKVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         + KALNA L   + I I +   V   +H RF   R++Y Y     +
Sbjct: 61  VAVFDTESRIPGEKMAKALNARL--PEDIIIQDSKEVPLDYHPRFQDTRKTYEYTFYNAR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +       +   LD E M+ AA + +G H F +  S   Q +S +R I   DV   
Sbjct: 119 YDNPVTSRHHHFVYVPLDVEKMKEAASYFLGEHCFISMCSSKAQVTSYVREIYECDVTQN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I++RV    FL+  +R   G+L  VG GK     +++ L +++R   GP  P +GL 
Sbjct: 179 GRYIKMRVTGSGFLYNMVRLMAGTLLEVGRGKQEPQWVKEILASKERVTPGPKLPAKGLT 238

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 239 LIQIEYP 245


>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 =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 126/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + IEY+G+ + GWQ +Q    ++Q  +E A+  V    V V  AGRTD+GVH   
Sbjct: 1   MTRIALGIEYDGTDFRGWQMQQSGVRTVQECLEAALSKVANHSVTVVCAGRTDAGVHGTG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD              N  L     ++I     V   FHARFSA+ R Y Y I   
Sbjct: 61  QVVHFDSDAPREMKSWIMGGNTNL--PRDVTIRWAVPVSDDFHARFSAVSRRYRYVIYNH 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P AL + +     + LD   MR AA +LVG HDFT +RS+HCQA SP++T+   ++  
Sbjct: 119 ARPPALYRSQVTWNHRPLDVAAMREAASYLVGHHDFTAYRSVHCQAKSPLKTLHSLELYE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++ +   A +FL   +R+  G L  VG GK      +  L+ +DR+     APP GL
Sbjct: 179 QGKVLVLEAHANAFLMHMVRNIAGVLMKVGAGKKPPVWAKDVLECRDRRLGAATAPPFGL 238

Query: 240 YFDSVEYS 247
           Y   +EY 
Sbjct: 239 YLVEIEYP 246


>gi|206978041|ref|ZP_03238926.1| tRNA pseudouridine synthase A [Bacillus cereus H3081.97]
 gi|217957717|ref|YP_002336261.1| tRNA pseudouridine synthase A [Bacillus cereus AH187]
 gi|229136988|ref|ZP_04265615.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST26]
 gi|206743754|gb|EDZ55176.1| tRNA pseudouridine synthase A [Bacillus cereus H3081.97]
 gi|217063029|gb|ACJ77279.1| tRNA pseudouridine synthase A [Bacillus cereus AH187]
 gi|228646526|gb|EEL02733.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST26]
          Length = 252

 Score =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE++ V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELIRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SP++T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDPEAMRAGAAHLVGRHDFTTFRAAGCQAASPVKTLDALTLETV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|227515518|ref|ZP_03945567.1| tRNA-pseudouridine synthase I [Lactobacillus fermentum ATCC 14931]
 gi|227086131|gb|EEI21443.1| tRNA-pseudouridine synthase I [Lactobacillus fermentum ATCC 14931]
          Length = 258

 Score =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 128/252 (50%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---VHGAGRTDSGVHA 57
           M RY +   Y+GS + G+Q Q    ++Q  +E+A+  +  +      V G+GRTD+GVHA
Sbjct: 1   MHRYKITFAYDGSNFAGFQVQPGERTVQQVLERAVNKIAKKPQPPLMVFGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     L +ALN+ L     + +   + V   FHARF A  + Y YR++
Sbjct: 61  LGQVAHFDLPYQIPGPSLVRALNSSL--PLDVLVKEATEVAPDFHARFDAHHKRYRYRVV 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D E M+ AAQ  VG HDFT+F +   QA+S +R ID   V
Sbjct: 119 GGEFTNPFKRNYTGHYKYPVDVERMQTAAQDFVGEHDFTSFVASGSQATSNVRRIDEVTV 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +    V   FL+ Q+R  V  L  +G+G+    D+ + ++A++R      AP
Sbjct: 179 VRDEENDEVVFDFVGNGFLYNQVRIMVAFLLEIGNGRRPVDDVMRVMKAKNRDLARGTAP 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ASGLYLVEVTYD 250


>gi|227550954|ref|ZP_03981003.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257893717|ref|ZP_05673370.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257896582|ref|ZP_05676235.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|293379717|ref|ZP_06625853.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
 gi|227179913|gb|EEI60885.1| tRNA-pseudouridine synthase I [Enterococcus faecium TX1330]
 gi|257830096|gb|EEV56703.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257833147|gb|EEV59568.1| tRNA pseudouridine synthase [Enterococcus faecium Com12]
 gi|292641715|gb|EFF59889.1| tRNA pseudouridine synthase A [Enterococcus faecium PC4.1]
          Length = 247

 Score =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +   
Sbjct: 61  QVANFKTNTEIELSEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +  
Sbjct: 119 VIPSAFERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++    V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL
Sbjct: 179 KGEMLHFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>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 =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEYNGS Y+GWQRQ+   S+QG +E+A+  +  E + V+ AGRTD+GVHA  QV 
Sbjct: 9   RIALGIEYNGSRYYGWQRQQEVKSVQGCLEEALSKIAAEPISVNCAGRTDAGVHATGQVV 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+              N +L     I++     VD++FHARFSA  R Y Y I   +  
Sbjct: 69  HFETTAIRKEAAWTMGANTHL--PPDIAVRWCKPVDEEFHARFSATARRYRYVIFNHRYR 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   GN
Sbjct: 127 PAILSNGVTHFHYPLDEKRMHQAAQALLGENDFTSFRAVQCQSRTPWRNVMHVNVTRHGN 186

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      + + L+ +DR +    A  EGLY  
Sbjct: 187 YVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDIDWMHQLLELKDRTKAAATAKAEGLYLV 246

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 247 SVDYP 251


>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 =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 122/246 (49%), Positives = 155/246 (63%), Gaps = 1/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + IEY+G+ + GWQRQ NG ++Q  +E+A F  TGE + V GAGRTDSGVHAL QV
Sbjct: 3   RRIFITIEYDGAPFVGWQRQDNGITVQQELEEAAFAFTGEKINVQGAGRTDSGVHALGQV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH D+  ++ P  + +ALNA+L     IS+L+   V    HARFSAI R YLYRI+ R+ 
Sbjct: 63  AHLDVPEKFAPNRVMEALNAHLS-HTAISVLDAYEVPDDAHARFSAIGRRYLYRILPRRQ 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P AL+ GR W   + LD + M+  A  L+GRHDF +FR+  CQA S IRT+D   V    
Sbjct: 122 PPALDAGRVWHHKQPLDADAMQAGADMLIGRHDFNSFRAAQCQAESSIRTLDILQVEQVS 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + V ARSFLH Q+R+  G+L LVG GKW   D++ AL A DR   GP APP GLY 
Sbjct: 182 AEIHLHVEARSFLHHQVRNIAGTLALVGTGKWQPDDVKAALAAADRSAAGPTAPPHGLYL 241

Query: 242 DSVEYS 247
             V Y 
Sbjct: 242 TDVFYP 247


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

 Score =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 115/251 (45%), Positives = 165/251 (65%), Gaps = 5/251 (1%)

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  VAHCDMVKDWDPFRLSEALNFHLK-PAPVAIVDCARAEDDWHARFSAVERQYLFRILIRR 119

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

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLARVGYP 250


>gi|319942390|ref|ZP_08016704.1| pseudouridylate synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804078|gb|EFW00986.1| pseudouridylate synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 269

 Score =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 87/244 (35%), Positives = 129/244 (52%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IEY G+ + GWQ Q +  S+Q ++E A+       + V  AGRTD+GVHA  QV  
Sbjct: 11  LALGIEYRGTAFNGWQVQPDHPSVQAALEAALSQFADHPISVICAGRTDTGVHATHQVVS 70

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F  V         + +NA L   +++++  +  VD++FHARFSA  R+Y Y I       
Sbjct: 71  FTSVARRPSAGWIRGVNAIL--PESVAVRWMREVDEKFHARFSARSRTYEYWIWNDPVRS 128

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
            L +G A  + + LD   M+  A  L+G HDFT+FR+  CQA +P+RTI    +   G L
Sbjct: 129 PLFEGSAGWVFRPLDEALMQRGATALIGEHDFTSFRASECQAKTPVRTISELKIVRRGAL 188

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + +R+ A +FL   +R+ VG+L  VG G+     + + L A+ R    P   P GLY   
Sbjct: 189 VGVRITANAFLQHMVRNIVGALIYVGTGRERPEWIAEVLAAKSRDAAAPTFSPAGLYLTG 248

Query: 244 VEYS 247
           V Y 
Sbjct: 249 VGYP 252


>gi|168213913|ref|ZP_02639538.1| tRNA pseudouridine synthase A [Clostridium perfringens CPE str.
           F4969]
 gi|170714597|gb|EDT26779.1| tRNA pseudouridine synthase A [Clostridium perfringens CPE str.
           F4969]
          Length = 248

 Score =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M    + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVH
Sbjct: 1   MRNIKITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   VA+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I
Sbjct: 61  AKNYVANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  +
Sbjct: 119 DNNKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP 
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIIVGTLVNVGLGKIEPKYINDILEAKERAKASEKAPA 238

Query: 237 EGLYFDSVEY 246
            GL    + Y
Sbjct: 239 HGLCLLELNY 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 =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

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 I     
Sbjct: 61  VHFETEAIRKDVAWTLGVNANL--PKDIAVRWVKQVDSSFHARFSATARHYRYIIYNGAF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M +A Q L+G  DFT+FR++HCQASSP++ I++ +++   
Sbjct: 119 RPGILGTGLSHYHMDLDVQKMHLAGQMLLGEQDFTSFRALHCQASSPVKCIEYLNISQRS 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A +FLH  +R+  GSL  +G GK     L+  L  +DR +    A P GLY 
Sbjct: 179 QFIIIDIKANAFLHHMVRNIAGSLIEIGCGKQPVDWLKTLLAYKDRSKAAATAKPGGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 98/246 (39%), Positives = 129/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + IEY GS Y GWQRQ     S+Q ++E+A+  V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGIEYKGSRYRGWQRQEAGVPSVQEALERALSKVAAEPVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANL--PADISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD   MR AAQ LVG HDFT+FR++ CQA SP++T+ H  +   G
Sbjct: 137 RPAHLAEEVTWNHRPLDIGRMREAAQVLVGTHDFTSFRAVQCQAKSPVKTMHHVRLLEHG 196

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+  G L  +G G+      ++ L+A+DR+  G  A P GLY 
Sbjct: 197 RLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLEARDRRAGGVTAHPYGLYL 256

Query: 242 DSVEYS 247
             VEY 
Sbjct: 257 VRVEYP 262


>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 =  292 bits (749), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 132/246 (53%), Gaps = 2/246 (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  VHFDVPVPRADVAWTLGVNSNL--PAGIAVRWAREVDSEFSARFSATSRRYRYIIANTRF 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 DSVEYS 247
            +V Y 
Sbjct: 239 VAVTYP 244


>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 =  292 bits (749), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS + GWQRQ +  S+Q ++E+A+  V    V V  AGRTD+GVHA  QV
Sbjct: 26  MRVALGIEYDGSRFSGWQRQSHRLSVQVALEEALSRVADHPVTVTCAGRTDAGVHATHQV 85

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +N+ L     I I  +  V + FHARF+A  RSY Y I++R  
Sbjct: 86  IHFDTTAPRPSRAWVRGVNSNL--PGDIRITWVRAVPQVFHARFAATARSYRYVILSRAV 143

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P AL + R     + L    MR+AAQ+L+G HDF+++R++ CQA  P+RT+   D+   G
Sbjct: 144 PPALHRRRVAWTYRPLQLSAMRVAAQYLLGEHDFSSYRALACQARHPVRTVHRLDITRCG 203

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +   + V A +FLH  +R+  G L  +G G        + LQA+DR   G  AP  GLY 
Sbjct: 204 DYFYVDVTANAFLHHMVRNIAGVLLSIGSGARPPQWSWEILQARDRTAGGVTAPAGGLYL 263

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 264 VAVRYP 269


>gi|222093912|ref|YP_002527962.1| tRNA pseudouridine synthase a [Bacillus cereus Q1]
 gi|221237960|gb|ACM10670.1| tRNA pseudouridine synthase A [Bacillus cereus Q1]
          Length = 247

 Score =  292 bits (749), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 61  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLLS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 119 KTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 179 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 239 YLWQVNYN 246


>gi|160935852|ref|ZP_02083227.1| hypothetical protein CLOBOL_00746 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441596|gb|EDP19306.1| hypothetical protein CLOBOL_00746 [Clostridium bolteae ATCC
           BAA-613]
          Length = 248

 Score =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +   + + Y+G+ Y GWQ+Q N   +IQG +E  +  + G  V VHG+GRTD+GVHA  Q
Sbjct: 1   MNIGVWLSYDGTRYDGWQKQGNTDRTIQGKLEAVLEKLEGSPVEVHGSGRTDAGVHAESQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F L +   P  + + +N YL   + I++    ++ ++FH+R +A+R++Y Y+I T  
Sbjct: 61  VANFHLAKNMTPDEIMRYMNRYL--PEDIAVTRACVMPERFHSRLNALRKTYRYQIETAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E+   + + + LD   M  AA  L G HD+ +F        S IRTI+       
Sbjct: 119 KKNVFERYYYYGLGQDLDVGKMEQAAAILTGTHDYKSFCGNKKMKKSTIRTIESICFYRM 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I      FL   +R   G+L  VG GK    ++   L+A DR   G  APPEGL+
Sbjct: 179 GSRIHISFTGNGFLQQMVRILSGTLIEVGTGKRKPEEMAAILEAGDRSMAGFTAPPEGLF 238

Query: 241 FDSVEY 246
            + VEY
Sbjct: 239 LEKVEY 244


>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 =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 119/251 (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   MPRFALKVEYHGKPFAGWQRQKDLPSVQGAIEDALSRLEPGAHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L +ALN +LK    ++IL+ + VD+ +HARFSAI R YL+RI+ R+
Sbjct: 61  VAHCDLQKDWDPFRLSEALNYHLK-PAPVAILDCAGVDEDWHARFSAIERQYLFRILMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   + G+ W I   LD   M+ AA HL+G HDFTTFRS  CQA+SP +T+D   + + 
Sbjct: 120 APATHDAGQVWQINHELDVAAMQEAADHLIGNHDFTTFRSSICQAASPQKTLDELRIETV 179

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLARVGYP 250


>gi|260662783|ref|ZP_05863677.1| tRNA pseudouridine synthase A [Lactobacillus fermentum 28-3-CHN]
 gi|260552864|gb|EEX25863.1| tRNA pseudouridine synthase A [Lactobacillus fermentum 28-3-CHN]
          Length = 258

 Score =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 129/252 (51%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---VHGAGRTDSGVHA 57
           M RY +   Y+GS + G+Q Q    ++Q ++E+A+  +  +      V G+GRTD+GVHA
Sbjct: 1   MHRYKITFAYDGSNFAGFQVQPGERTVQQALERAVNKIAKKPQPPLMVFGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFDL  +     L +ALN+ L     + +   + V   FHARF A  + Y YR++
Sbjct: 61  LGQVAHFDLPYQIPGPSLVRALNSSL--PLDVLVKEATEVAPDFHARFDAHHKRYRYRVV 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D E M+ AAQ  VG HDFT+F +   QA+S +R ID   V
Sbjct: 119 GGEFTNPFKRNYTGHYKYPVDVERMQTAAQDFVGEHDFTSFVASGSQATSNVRRIDEVTV 178

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +    V   FL+ Q+R  V  L  +G+G+    D+ + ++A++R      AP
Sbjct: 179 VRDEENDEVVFDFVGNGFLYNQVRIMVAFLLEIGNGRRPVDDVMRVMKAKNRDLARGTAP 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ASGLYLVEVTYD 250


>gi|322374222|ref|ZP_08048755.1| tRNA pseudouridine synthase A [Streptococcus sp. C150]
 gi|321276927|gb|EFX53999.1| tRNA pseudouridine synthase A [Streptococcus sp. C150]
          Length = 248

 Score =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 88/250 (35%), Positives = 135/250 (54%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+QRQ +  SIQ  IEK +  + +G  VVVHGAGRTD+GVHA  
Sbjct: 1   MVRYKAIISYDGTLFSGFQRQPDARSIQEEIEKTLLRLNSGTPVVVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V + FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEDFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L    M+ AA+ LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAKDLVGTHDFTGFTASGTSVENKVRTITQARVSI 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                          FL+ Q+R+ VG+L  +G+G+   + ++  L++ DR   GP A   
Sbjct: 179 DEKTGFYVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPISQVKTVLESCDRNLAGPTASGN 238

Query: 238 GLYFDSVEYS 247
           GLY   ++Y 
Sbjct: 239 GLYLKEIKYE 248


>gi|42779223|ref|NP_976470.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10987]
 gi|51316699|sp|Q73F64|TRUA1_BACC1 RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|42735138|gb|AAS39078.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10987]
          Length = 247

 Score =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 61  QVIHFDTPLSLEEWQWNNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLLS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+   +R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 119 KTADVFRRNYVYQYPYPLEINAIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 179 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 239 YLWQVNYN 246


>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 =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEYNGS Y+GWQRQ+   S+QG +E A+  +  E + V+ AGRTD+GVHA  QV 
Sbjct: 9   RIALGIEYNGSRYYGWQRQQEVQSVQGCLEAALSKIAAEPISVNCAGRTDAGVHATGQVV 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+              N +L   D I++     VD +FHARFSA  R Y Y I   +  
Sbjct: 69  HFETSAIRKEAAWTMGTNTHL--PDDIAVRWCKPVDDEFHARFSATARRYRYVIFNHRYR 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  AAQ L+G  DFT+FR++ CQ+ +P R + H +V   GN
Sbjct: 127 PAILSNGVTHFHFPLDEKRMHQAAQALLGERDFTSFRAVQCQSKTPWRNVMHVNVTRHGN 186

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      +   L+ +DR +    A  EGLY  
Sbjct: 187 YVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDIDWMAHLLELKDRTKAAATAKAEGLYLV 246

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 247 SVDYP 251


>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 =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 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 Y     ++ + N  +    FHARFSA+ R Y+YRI+ R 
Sbjct: 61  VAHFDLSKNLETHKIITAIN-YFARPYSVIVWNCEMAPNNFHARFSAVSRHYIYRILNRP 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|257900124|ref|ZP_05679777.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838036|gb|EEV63110.1| tRNA pseudouridine synthase [Enterococcus faecium Com15]
          Length = 247

 Score =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +   
Sbjct: 61  QVANFKTNSEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +  
Sbjct: 119 VIPSAFERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++    V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL
Sbjct: 179 KGEMLHFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>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 =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 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|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 =  292 bits (748), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + +EY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 27  KIALGVEYDGSRYYGWQRQNEVRSVQERLEKALSQVANEPISVFCAGRTDAGVHATGQVV 86

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +N +L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 87  HFETTAHRKDPAWTMGVNTHL--PADIAVRWVKTVADDFHARFSATARRYRYVIFNHRYR 144

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G+
Sbjct: 145 PAILSSGVTHFHYPLDAERMHQAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVSRYGD 204

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G    T + + L  +DR +    A   GLY  
Sbjct: 205 YVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDITWMAELLALKDRTKAAATAKANGLYLV 264

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 265 SVDYP 269


>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 =  292 bits (747), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 118/251 (47%), Positives = 160/251 (63%), 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  VAHCDLQKPWSPFRLSEALNFHLK-PAPVAIVDCAVVDPEWHARFSAIERQYLFRILIRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   + G+ W I   LD E M+  A HL+G HDFTTFRS  CQA SP +T+D   +   
Sbjct: 120 APATHDAGQVWQINNDLDVERMQQGANHLLGNHDFTTFRSSICQAQSPQKTLDELRIERV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|257888836|ref|ZP_05668489.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257824892|gb|EEV51822.1| tRNA pseudouridine synthase [Enterococcus faecium 1,141,733]
          Length = 246

 Score =  292 bits (747), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +   
Sbjct: 61  QVANFKTNTEIELSEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +  
Sbjct: 119 VIPSAFERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++    V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL
Sbjct: 179 KGEMLHFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKARQHAGETVPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>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 =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

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 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q +VG HDFT+FR++HCQA++P+R+I   +V    
Sbjct: 119 RPGILNSGLSHYHHLLDADKMHQAGQFIVGTHDFTSFRALHCQANTPVRSIHSLNVTRRA 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +FLH  +R+  GSL  +G        L   L+ ++R      A P GLY 
Sbjct: 179 DFIIIDIKANAFLHHMVRNIAGSLIEIGQDNQKVDWLMTLLEYKNRARAAATAKPGGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>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 =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 119/251 (47%), Positives = 159/251 (63%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   + G  W +   LD   M+ AA  L+GRHDFTTFRS  CQA+SP++T+D   V + 
Sbjct: 120 APATHDAGLVWQVGHRLDARAMQAAADLLLGRHDFTTFRSSICQAASPVKTLDELRVEAV 179

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

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


>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 =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 90/249 (36%), Positives = 137/249 (55%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +G ++Q ++E A+     TG  +    AGRTD+GVHA 
Sbjct: 1   MTRIALGLSYDGSSWQGWQTQPHGQTVQDTLEAALGQFSGTGAPLDTLCAGRTDTGVHAA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H D           + +NA+L    +ISI     V + FHARFSA  R+Y+Y +  
Sbjct: 61  MQVVHVDTHLNRRAESWVRGVNAFL--PSSISIHWAKEVGEDFHARFSARSRTYVYLLWR 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +   AL   RA    + LD   MR AAQ L+G HDF++FRS  CQA  P+R +   D+ 
Sbjct: 119 GRVRPALWAHRAGWCFQPLDVTAMRQAAQALLGEHDFSSFRSSQCQARHPVRHLTRLDIA 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +   + A +FLH  +R+ +G+L  +G G+ +   +   L+A+DR+   P   P+G
Sbjct: 179 ERGSFLVFTLQANAFLHHMVRNIMGALLQIGQGRESVDWMASLLRARDRRLGAPTFSPDG 238

Query: 239 LYFDSVEYS 247
           LY  +++Y 
Sbjct: 239 LYLSAIDYP 247


>gi|218895277|ref|YP_002443688.1| tRNA pseudouridine synthase A [Bacillus cereus G9842]
 gi|218542262|gb|ACK94656.1| tRNA pseudouridine synthase A [Bacillus cereus G9842]
          Length = 252

 Score =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    I Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTIAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>gi|85713087|ref|ZP_01044122.1| tRNA pseudouridine synthase A [Idiomarina baltica OS145]
 gi|85693073|gb|EAQ31036.1| tRNA pseudouridine synthase A [Idiomarina baltica OS145]
          Length = 261

 Score =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G  Y+GWQRQ+   S+Q  +E A+  V  + V    AGRTD+GVHA  QV
Sbjct: 1   MRIALGLEYDGRAYYGWQRQREVDSVQQRLENALSKVADQAVETVCAGRTDAGVHATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +         +N++L     I++     VD  F ARFSA  R Y Y I     
Sbjct: 61  VHFDVSTQRRAAAWTLGVNSHL--PPDIAVRWAQPVDDSFSARFSATARRYRYIIANHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M+ A   L+G HDF+ FR+  CQ+ S  R I H +V+  G
Sbjct: 119 RPGIHSHGVSHYHHPLDVDAMQAATPALLGEHDFSAFRAAQCQSHSAHREITHLNVHRRG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +FLH  +R+ VGSL ++G  +   + L + L  +DR +    A P GLY 
Sbjct: 179 DFIIVDIKANAFLHHMVRNIVGSLIVIGRHQQDPSWLGELLAGKDRTKAAATAKPGGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VEVDYP 244


>gi|293556963|ref|ZP_06675523.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
 gi|294618124|ref|ZP_06697719.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
 gi|291595614|gb|EFF26912.1| tRNA pseudouridine synthase A [Enterococcus faecium E1679]
 gi|291600783|gb|EFF31075.1| tRNA pseudouridine synthase A [Enterococcus faecium E1039]
          Length = 247

 Score =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     +   +N YL     I I  +  + ++FH+R++A+ + Y Y +   
Sbjct: 61  QVANFKTNTEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHSRYNAVGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  P+ LD + +  A + LVG HDF  F ++     S +RTID   +  
Sbjct: 119 VIPSAFERNHSFYFPQELDMDKLNAACEKLVGTHDFIGFSALKKSKKSTVRTIDELSIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++    V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL
Sbjct: 179 KGEMLHFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|168181898|ref|ZP_02616562.1| tRNA pseudouridine synthase A [Clostridium botulinum Bf]
 gi|237796908|ref|YP_002864460.1| tRNA pseudouridine synthase A [Clostridium botulinum Ba4 str. 657]
 gi|182674803|gb|EDT86764.1| tRNA pseudouridine synthase A [Clostridium botulinum Bf]
 gi|229262719|gb|ACQ53752.1| tRNA pseudouridine synthase A [Clostridium botulinum Ba4 str. 657]
          Length = 246

 Score =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQ+QKN    ++QG++EKAI  +T E + V G  RTDSGVHA 
Sbjct: 1   MKNIKLKLEYDGANYCGWQKQKNEKFITLQGTLEKAISNITKEKIEVIGVSRTDSGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             V +F    +  P  L K +N  L     I +L+      +FH+RF +  ++Y Y ++ 
Sbjct: 61  GYVCNFFTNTKIPPENLQKVINNNL--PADIVVLSSEEASNEFHSRFCSKGKTYEYTVLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P+A+ +   +     L+ +NM++A+++ +G HDF+ F++      + +RTI  F++N
Sbjct: 119 SSQPIAIGRNYIFQFKDKLNIDNMKMASRYFIGTHDFSAFKTKGSSIKTSVRTISKFEIN 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+  +    FL+  +R  VG+L  +G  K     ++  ++++DR + G   P  G
Sbjct: 179 KKGDFIKFIITGDGFLYNMVRIIVGTLIEIGLNKREPEYIKYVIKSKDRTKAGKCVPSSG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLKEVFY 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 =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 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|291522074|emb|CBK80367.1| pseudouridylate synthase I [Coprococcus catus GD/7]
          Length = 247

 Score =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 89/249 (35%), Positives = 132/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M R   ++IEY+GS Y GWQR  + +G +IQG +E  +  +TGE V + GAGRTD+GVHA
Sbjct: 1   MERNIRLLIEYDGSRYDGWQRLGKGHGVTIQGKLEDVLSKMTGEQVELIGAGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QVA+F          +   LN YL     I++  +  V ++FH+R++A  + YLYRI 
Sbjct: 61  YEQVANFHTNSNMKCWEMKYYLNRYL--PGDIAVNRVDDVPERFHSRYNAKAKKYLYRIA 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P   ++   W     LD   M+ AA  LVG HDF  F S      S +R I   D+
Sbjct: 119 IGDVPCVFDRKYTWYCFDKLDVTAMKKAAALLVGEHDFKAFCSNKRTNKSTVREIYDIDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +    ++I V    FL+  +R  VG+L  VG G+    ++   L++++R + G  A  +
Sbjct: 179 YADTRELQITVYGNGFLYNMVRIIVGTLIEVGKGERRPEEMTAILESRERTKAGATAAAQ 238

Query: 238 GLYFDSVEY 246
           GL+   VEY
Sbjct: 239 GLFLQEVEY 247


>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 =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 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|300119545|ref|ZP_07057089.1| tRNA pseudouridine synthase A [Bacillus cereus SJ1]
 gi|298723017|gb|EFI63915.1| tRNA pseudouridine synthase A [Bacillus cereus SJ1]
          Length = 252

 Score =  292 bits (747), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 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|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 =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 94/247 (38%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R + +I+EY+G+ Y GWQRQ +  +IQ  +E A+  +T +  VV+GAGRTDSGVHAL 
Sbjct: 1   MKRNFKLILEYDGTHYHGWQRQPHDLTIQEVLEGALEKITRQKCVVYGAGRTDSGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+F         +  KALN+ L     I     ++    FHAR SA+ + Y Y I   
Sbjct: 61  YVANFRCNTHLDAGVFVKALNSTL--PKDIVCKESTLAPDGFHARKSAVSKIYEYHITNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A+ +  AW + + LD E M  AA+  +G HDF+ F       ++ +R I    + S
Sbjct: 119 PTPPAVCRQYAWHVRRRLDKEAMTRAAKLFLGSHDFSAFEGAGSPKATSVRNIMQSHIQS 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + N I  RV A  FL   +R+ VG+L  +G GK     +   L + DR + GP APPEGL
Sbjct: 179 WENHIIYRVEANGFLRYMVRNIVGTLVYIGMGKIPPEAVMDILASGDRGQAGPTAPPEGL 238

Query: 240 YFDSVEY 246
           +   V+Y
Sbjct: 239 FMMCVKY 245


>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 =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 120/252 (47%), Positives = 157/252 (62%), Gaps = 6/252 (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  VAHCDMDKTWDAFRLSEALNFHLK-PAPVSIVACVQVADDWHARFSALERRYLFRLVNRR 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 PEGLYFDSVEYS 247
           P GLY  SV Y 
Sbjct: 240 PHGLYLASVGYP 251


>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 =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 101/245 (41%), Positives = 140/245 (57%), Gaps = 2/245 (0%)

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  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+              NA L   DT+S+  +  V + FHARF A+RRSY Y     ++ 
Sbjct: 64  HFETGAYRPEHAWVLGANANL--PDTVSVHWVQPVSEAFHARFGALRRSYRYVWYCSRSR 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            AL +GR      +LD E M +AA HL+GRHDF+ FR++ CQA  P+R +   DV + G 
Sbjct: 122 PALLRGRVAWSKYALDPEPMAMAAGHLLGRHDFSAFRAVACQAKHPVRELYRLDVWARGG 181

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + V A +FLH  +R+  G+L L+G G+  +T     L   DR   G  AP EGLY  
Sbjct: 182 FVYLDVCANAFLHHMVRNLAGTLALIGRGERPATWAADLLAGGDRTRAGATAPAEGLYLV 241

Query: 243 SVEYS 247
            V+Y 
Sbjct: 242 GVDYP 246


>gi|312862611|ref|ZP_07722852.1| tRNA pseudouridine synthase A [Streptococcus vestibularis F0396]
 gi|311101871|gb|EFQ60073.1| tRNA pseudouridine synthase A [Streptococcus vestibularis F0396]
          Length = 249

 Score =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  +EK +  + +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEELEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                          FL+ Q+R+ VG+L  +G+G+   + ++  L++ DR   GP A   
Sbjct: 179 DEKTGFYIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESCDRNLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|228983397|ref|ZP_04143610.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228776387|gb|EEM24740.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 252

 Score =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 111/251 (44%), Positives = 156/251 (62%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +   W +P  LD + M  AAQ L+GRHDF+ FR+  CQA+SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWHVPWPLDADLMHAAAQRLLGRHDFSAFRAAECQAASPVRTLEQLDVTRQ 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  I I   ARSFLH Q+R+  G+L L G  + ++ D+ + L  + +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCRRLSADDVAEILATKAKHRCGPLAPA 239

Query: 237 EGLYFDSVEYS 247
            GL F  V+Y 
Sbjct: 240 CGLTFVGVDYD 250


>gi|229094864|ref|ZP_04225869.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-29]
 gi|229100941|ref|ZP_04231745.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-28]
 gi|229113818|ref|ZP_04243253.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-3]
 gi|228669689|gb|EEL25096.1| tRNA pseudouridine synthase A [Bacillus cereus Rock1-3]
 gi|228682520|gb|EEL36593.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-28]
 gi|228688607|gb|EEL42480.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-29]
          Length = 252

 Score =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIFEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 142/247 (57%), Gaps = 5/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY +I++Y+G+ + G+Q Q +  ++QG I+KA+ ++T G  V++HG+GRTDSGVHA  QV
Sbjct: 5   RYKLIVQYDGTHFAGFQIQPHDRTVQGEIQKALKIMTKGIEVIIHGSGRTDSGVHAKGQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD         + +ALN+    SD I + ++SIV+ +FHAR++   + Y YR+   + 
Sbjct: 65  IHFDYPFVIPAKNMKRALNSL--TSDEIFVKDVSIVEDEFHARYNTSGKKYQYRVDLNEI 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--NS 179
           P   ++      P  LD + ++ A + L G HDF +F + H    + +RT+    V  + 
Sbjct: 123 PDPFKRLYTLHHPYPLDMDKLKNALKDLEGEHDFASFCASHSGRENKVRTVYEASVVKDD 182

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           F N +        FL+  +R FVG+L  + +G   + ++++ L+ +DR E GP A P+GL
Sbjct: 183 FNNELLFTFRGNGFLYNMVRIFVGTLLQIANGLRPADEIQRLLEVKDRNEAGPTAKPQGL 242

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 243 YLMEVYY 249


>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 =  291 bits (746), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 123/251 (49%), 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   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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SPI+T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDAEAMRAGAAHLVGRHDFTTFRAAGCQAASPIKTLDALTLETV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + 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|229153920|ref|ZP_04282050.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 4342]
 gi|228629601|gb|EEK86298.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 4342]
          Length = 252

 Score =  291 bits (746), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGIHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|69244266|ref|ZP_00602734.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257878927|ref|ZP_05658580.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257881556|ref|ZP_05661209.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257890781|ref|ZP_05670434.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|258615438|ref|ZP_05713208.1| tRNA pseudouridine synthase A [Enterococcus faecium DO]
 gi|261206813|ref|ZP_05921504.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289567364|ref|ZP_06447735.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|293563155|ref|ZP_06677615.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|293568529|ref|ZP_06679849.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
 gi|294614075|ref|ZP_06694002.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|294620867|ref|ZP_06700069.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|314939024|ref|ZP_07846289.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|314943424|ref|ZP_07850191.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|314948177|ref|ZP_07851572.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
 gi|314952740|ref|ZP_07855717.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|314991371|ref|ZP_07856849.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|314995418|ref|ZP_07860520.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|68196452|gb|EAN10879.1| tRNA pseudouridine synthase [Enterococcus faecium DO]
 gi|257813155|gb|EEV41913.1| tRNA pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257817214|gb|EEV44542.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257827141|gb|EEV53767.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|260078943|gb|EEW66643.1| tRNA pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289160842|gb|EFD08771.1| tRNA pseudouridine synthase A [Enterococcus faecium D344SRF]
 gi|291588865|gb|EFF20693.1| tRNA pseudouridine synthase A [Enterococcus faecium E1071]
 gi|291593065|gb|EFF24647.1| tRNA pseudouridine synthase A [Enterococcus faecium E1636]
 gi|291599569|gb|EFF30584.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|291604885|gb|EFF34359.1| tRNA pseudouridine synthase A [Enterococcus faecium E1162]
 gi|313590351|gb|EFR69196.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a01]
 gi|313594045|gb|EFR72890.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133B]
 gi|313595146|gb|EFR73991.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133A]
 gi|313597796|gb|EFR76641.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133C]
 gi|313641733|gb|EFS06313.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0133a04]
 gi|313645389|gb|EFS09969.1| tRNA pseudouridine synthase A [Enterococcus faecium TX0082]
          Length = 246

 Score =  291 bits (746), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     +   +N YL     I I  +  + ++FH+R++A+ + Y Y +   
Sbjct: 61  QVANFKTNTEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHSRYNAVGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  P+ LD + +  A + LVG HDF  F ++     S +RTID   +  
Sbjct: 119 VIPSAFERNHSFYFPQELDMDKLNAACEKLVGTHDFIGFSALKKSKKSTVRTIDELSIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++    V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL
Sbjct: 179 KGEMLHFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 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 =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 98/246 (39%), Positives = 130/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ     S+Q ++E+A+  V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGVEYKGSRYRGWQRQEAGVPSVQEALERALSKVAAESVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANL--PGDISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E MR AAQ LVG HDFT+FR++ CQA SP++T+ H  +   G
Sbjct: 137 RPAHMAEEVTWNHRPLDIERMREAAQVLVGTHDFTSFRAVQCQARSPVKTMHHVRLLEHG 196

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+  G L  +G G+      ++ L+A+DR+  G  A P GLY 
Sbjct: 197 RLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLEARDRRAGGVTAHPYGLYL 256

Query: 242 DSVEYS 247
             VEY 
Sbjct: 257 VRVEYP 262


>gi|49183176|ref|YP_026428.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Sterne]
 gi|49476722|ref|YP_034493.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52145077|ref|YP_081752.1| tRNA pseudouridine synthase A [Bacillus cereus E33L]
 gi|165873347|ref|ZP_02217948.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0488]
 gi|167642077|ref|ZP_02400301.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0193]
 gi|196046214|ref|ZP_03113441.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB108]
 gi|270000591|ref|YP_003329029.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Ames]
 gi|291612229|ref|YP_003541012.1| tRNA pseudouridine synthase A [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|62901423|sp|Q63H59|TRUA1_BACCZ RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|62901430|sp|Q6HPM7|TRUA1_BACHK RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|62901432|sp|Q6I4Q2|TRUA1_BACAN RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|49177103|gb|AAT52479.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Sterne]
 gi|49328278|gb|AAT58924.1| tRNA pseudouridine synthase A (pseudouridylate synthase) [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51978546|gb|AAU20096.1| tRNA-pseudouridylate synthase I [Bacillus cereus E33L]
 gi|164710915|gb|EDR16491.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0488]
 gi|167509964|gb|EDR85386.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0193]
 gi|196022959|gb|EDX61639.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB108]
 gi|224552852|gb|ACN55064.1| tRNA pseudouridine synthase A [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|269850235|gb|ACZ49980.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Ames]
          Length = 247

 Score =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 61  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 119 KTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 179 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 239 YLWQVNYN 246


>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 =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 97/246 (39%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + IEY GS Y GWQRQ     S+Q ++E+A+  V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGIEYKGSRYRGWQRQEAGVPSVQEALERALSKVAAEPVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANL--PADISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD   MR AAQ LVG HDFT+FR++ CQA SP++T+ H  +   G
Sbjct: 137 RPAHLAEEVTWNHRPLDIGRMREAAQVLVGTHDFTSFRAVQCQAKSPVKTMHHVRLLEHG 196

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+  G L  +G G+      ++ L+ +DR+  G  A P GLY 
Sbjct: 197 RLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLETRDRRAGGVTAHPYGLYL 256

Query: 242 DSVEYS 247
             VEY 
Sbjct: 257 VRVEYP 262


>gi|229015543|ref|ZP_04172540.1| tRNA pseudouridine synthase A [Bacillus cereus AH1273]
 gi|229021754|ref|ZP_04178334.1| tRNA pseudouridine synthase A [Bacillus cereus AH1272]
 gi|228739541|gb|EEL89957.1| tRNA pseudouridine synthase A [Bacillus cereus AH1272]
 gi|228745766|gb|EEL95771.1| tRNA pseudouridine synthase A [Bacillus cereus AH1273]
          Length = 252

 Score =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLAEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 131/247 (53%), Gaps = 2/247 (0%)

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  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD              N+ L     ISIL    V++ FHAR+SA+ R Y Y +   +
Sbjct: 61  VAHFDTTAYRSDHAWVFGANSNL--PHDISILWAKAVEEDFHARYSAMARRYRYIVYNHE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+ +       + LD + M+  AQ+L+G HDF++F+   CQ+ +P+R I   ++   
Sbjct: 119 IRPAILRKAIGWHYRPLDEKRMQAGAQYLIGEHDFSSFQGAGCQSRTPVRKIFQIEIYRI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             ++ I V A +FL   +R+  G L  +G G+      +  L+A+DR++ G   PP GLY
Sbjct: 179 RRMVVIEVQANAFLLHMVRNIAGVLIAIGSGEKHPDWAQTVLKAKDRRQGGVTVPPNGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LVEVNYP 245


>gi|254854197|ref|ZP_05243545.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL R2-503]
 gi|300763651|ref|ZP_07073649.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL N1-017]
 gi|258607589|gb|EEW20197.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL R2-503]
 gi|300515928|gb|EFK42977.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL N1-017]
          Length = 248

 Score =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL A       IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQAM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ +AL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISEALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|168211805|ref|ZP_02637430.1| tRNA pseudouridine synthase A [Clostridium perfringens B str. ATCC
           3626]
 gi|170710235|gb|EDT22417.1| tRNA pseudouridine synthase A [Clostridium perfringens B str. ATCC
           3626]
          Length = 248

 Score =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M    + ++Y+GS Y GWQ+Q     N S++Q  +EK +  +T E + + G GRTDSGVH
Sbjct: 1   MRNIKITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMTSEEIQLIGCGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   VA+F          + + +N YL   + I +  +    ++FHARF+   ++Y Y I
Sbjct: 61  AKNYVANFKTNSLMTLEQIIEYINEYL--PEDIRVTEIREASERFHARFNVKSKTYEYTI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +  AW + + LD E M   A++L+G HDF +F S+  +  S +RTI+  +
Sbjct: 119 DNNKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N++ I++    FL   +R  VG+L  VG GK     +   L+A++R +    AP 
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIIVGTLVDVGLGKIEPKYINDILEAKERAKASEKAPS 238

Query: 237 EGLYFDSVEY 246
            GL    + Y
Sbjct: 239 HGLCLLELNY 248


>gi|163938150|ref|YP_001643034.1| tRNA pseudouridine synthase A [Bacillus weihenstephanensis KBAB4]
 gi|163860347|gb|ABY41406.1| tRNA pseudouridine synthase A [Bacillus weihenstephanensis KBAB4]
          Length = 252

 Score =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 123/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q +  ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGIHFCGYQIQPHHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNSML--PDDIIIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|325276985|ref|ZP_08142659.1| tRNA pseudouridine synthase A [Pseudomonas sp. TJI-51]
 gi|324097881|gb|EGB96053.1| tRNA pseudouridine synthase A [Pseudomonas sp. TJI-51]
          Length = 286

 Score =  291 bits (745), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 123/246 (50%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ     S+Q ++E+A+  V  E + V  AGRTD+GVH   QV
Sbjct: 20  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPIAVVCAGRTDAGVHGCGQV 79

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N  L     IS++    +   FHARF A  R Y Y I     
Sbjct: 80  VHFDTRAVRDERAWTMGTNFNL--PHDISVVWSQPMPADFHARFKACARRYRYVIYNDPI 137

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AAQ L+G HDF+ FR+  CQA SPI+ I H  V   G
Sbjct: 138 RPAHLAEEVTWNHRPLDVERMAQAAQSLLGTHDFSAFRASQCQAKSPIKHIYHLRVTRHG 197

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + V A +FLH  +R+  G L  +G G+   +   + L+ +DR+E G  A P GLY 
Sbjct: 198 QMIVLDVRATAFLHHMVRNIAGVLMAIGSGERPVSWAREVLEGRDRREGGVTAHPYGLYL 257

Query: 242 DSVEYS 247
             VEY 
Sbjct: 258 VQVEYP 263


>gi|299820989|ref|ZP_07052878.1| tRNA-pseudouridine synthase I [Listeria grayi DSM 20601]
 gi|299818010|gb|EFI85245.1| tRNA-pseudouridine synthase I [Listeria grayi DSM 20601]
          Length = 247

 Score =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 126/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +I+ Y+GSG+ G+Q Q +  ++Q  +E+A+  +  GE V V  +GRTD+GVHA  
Sbjct: 1   MPRYKVILAYDGSGFSGYQVQPHKRTVQSELEEALLKMHKGEFVRVTASGRTDTGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       +AL         I I ++  V   FHAR+  + + Y Y I   
Sbjct: 61  QVIHFDSPLQIPNEKFQRALQRM--TPFDIGIHSVEQVPDDFHARYGTVGKEYRYVIKNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  A   P  L  E M+ A+Q L+G HDFT+F S   +  S +RTI   +   
Sbjct: 119 TDYDPFSRNFALHYPYPLSIEKMQEASQILIGEHDFTSFCSARTEQDSKVRTIYSIEFLK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG-PLAPPEG 238
               I I      FL+  +R   G+L  +G G+ T+  LEKALQA+DR +     AP +G
Sbjct: 179 EKETITICYRGDGFLYNMVRILTGALLDIGQGRMTAETLEKALQAKDRTKLPSVTAPAQG 238

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 239 LYLWEVAY 246


>gi|312866252|ref|ZP_07726471.1| tRNA pseudouridine synthase A [Streptococcus downei F0415]
 gi|311098225|gb|EFQ56450.1| tRNA pseudouridine synthase A [Streptococcus downei F0415]
          Length = 248

 Score =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+QRQ    S+Q  +EK +  + +G  V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKAIISYDGTLFAGFQRQSKERSVQEELEKTLERLNSGNPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++++  V + FHAR++   ++Y + + T 
Sbjct: 61  QVIHFDLPQTRDEEKLRFGLDT--QSPEDIDVVSVEQVPEVFHARYNPHSKTYEFLVDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  +D   M+ A   L+G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRAYATHFPYPVDLGAMQEAIADLLGTHDFTGFTASGTSVENKVRTISQAKVER 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+   + ++  L A+DR   GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTILAAKDRNLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEITYD 248


>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 =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 158/252 (62%), 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  VAQADLAKAWEPFRLAEALNYHLK-PAPIAIVACARVADDWHARFSANERRYLFRLVARR 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 -----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                       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|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 =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 125/251 (49%), Positives = 164/251 (65%), Gaps = 5/251 (1%)

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  VAHCDLERDWDPFRLSEALNYHLK-PAPIAITACTAVDAEWHARFSARQRQYLFRILCRR 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 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLAHVVYD 250


>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 =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 126/247 (51%), Positives = 170/247 (68%), Gaps = 1/247 (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 FDSVEYS 247
           F S +Y 
Sbjct: 240 FISAQYP 246


>gi|228898895|ref|ZP_04063177.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 4222]
 gi|228963242|ref|ZP_04124411.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228796500|gb|EEM43939.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228860795|gb|EEN05173.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 4222]
          Length = 252

 Score =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>gi|170689686|ref|ZP_02880864.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0465]
 gi|177656196|ref|ZP_02937177.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0174]
 gi|190567334|ref|ZP_03020248.1| tRNA pseudouridine synthase A [Bacillus anthracis Tsiankovskii-I]
 gi|196036037|ref|ZP_03103438.1| tRNA pseudouridine synthase A [Bacillus cereus W]
 gi|218901347|ref|YP_002449181.1| tRNA pseudouridine synthase A [Bacillus cereus AH820]
 gi|225862194|ref|YP_002747572.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB102]
 gi|227812815|ref|YP_002812824.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CDC 684]
 gi|228912881|ref|ZP_04076528.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228925395|ref|ZP_04088491.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228943947|ref|ZP_04106332.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229089273|ref|ZP_04220554.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-42]
 gi|229119804|ref|ZP_04249065.1| tRNA pseudouridine synthase A [Bacillus cereus 95/8201]
 gi|229182536|ref|ZP_04309787.1| tRNA pseudouridine synthase A [Bacillus cereus BGSC 6E1]
 gi|229604554|ref|YP_002864793.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0248]
 gi|254686641|ref|ZP_05150500.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CNEVA-9066]
 gi|254726279|ref|ZP_05188061.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A1055]
 gi|254735284|ref|ZP_05192992.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Western
           North America USA6153]
 gi|254739476|ref|ZP_05197174.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Kruger B]
 gi|254755530|ref|ZP_05207564.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Vollum]
 gi|301051879|ref|YP_003790090.1| tRNA pseudouridine synthase A [Bacillus anthracis CI]
 gi|170666357|gb|EDT17142.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0465]
 gi|172079844|gb|EDT64958.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0174]
 gi|190561461|gb|EDV15432.1| tRNA pseudouridine synthase A [Bacillus anthracis Tsiankovskii-I]
 gi|195991406|gb|EDX55373.1| tRNA pseudouridine synthase A [Bacillus cereus W]
 gi|218535501|gb|ACK87899.1| tRNA pseudouridine synthase A [Bacillus cereus AH820]
 gi|225789774|gb|ACO29991.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB102]
 gi|227005095|gb|ACP14838.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CDC 684]
 gi|228600991|gb|EEK58560.1| tRNA pseudouridine synthase A [Bacillus cereus BGSC 6E1]
 gi|228663705|gb|EEL19284.1| tRNA pseudouridine synthase A [Bacillus cereus 95/8201]
 gi|228694112|gb|EEL47794.1| tRNA pseudouridine synthase A [Bacillus cereus Rock3-42]
 gi|228815780|gb|EEM62016.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228834317|gb|EEM79858.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228846817|gb|EEM91822.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229268962|gb|ACQ50599.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0248]
 gi|300374048|gb|ADK02952.1| tRNA pseudouridine synthase A [Bacillus cereus biovar anthracis
           str. CI]
          Length = 252

 Score =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           +R  + IEY+G  + GWQ Q +G+++Q  + +A+  + G   VV H AGRTD+GVHA  Q
Sbjct: 1   MRIALGIEYDGRAFAGWQSQPHGNTVQDRLNRALGQIAGNRDVVTHAAGRTDAGVHAAMQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA L     ++++    V   FHARFSA  RSY Y ++T  
Sbjct: 61  VVHFDTDASRPLNAWVRGVNALL--PPEVAVVWAREVGDDFHARFSAFSRSYSYFLLTHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  G+     ++LD   MR AA  L+GRHDF++FR+  CQA SP++ +   D+   
Sbjct: 119 VRSCLLAGKVGWYHQALDVAAMREAAAGLLGRHDFSSFRASECQAKSPVKDLQRLDIIEA 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+   + A +FLH  +R+ VG+L  VG G  +  D++  L A+DR    P   P+GLY
Sbjct: 179 DGLLRFDLHADAFLHHMVRNIVGALLYVGKGALSPADMQSLLAARDRTSAPPTFMPDGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LTGVGYP 245


>gi|47570254|ref|ZP_00240905.1| tRNA pseudouridine synthase A [Bacillus cereus G9241]
 gi|47553078|gb|EAL11478.1| tRNA pseudouridine synthase A [Bacillus cereus G9241]
          Length = 247

 Score =  291 bits (745), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 1   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 61  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLLS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 119 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP  GL
Sbjct: 179 QDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 238

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 239 YLWQVNYN 246


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

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 123/246 (50%), Positives = 167/246 (67%), Gaps = 1/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +E++G+ +FG QRQK+G S+Q ++E+A   VTG+ V +H AGRTD+GVHA+   
Sbjct: 4   TRYALTLEFDGTPFFGLQRQKDGPSVQQAVEEAAQAVTGQQVTLHSAGRTDTGVHAIAMR 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           +HFD+  +  P  + +A+NA+L+    I++ +   V + +HARFS I R YLYRII R+A
Sbjct: 64  SHFDVESKLTPFRMGEAINAHLR-PAPIAVTHCEAVPEDWHARFSCIGRRYLYRIINRRA 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           PL LEK RAWL+    D E M  AAQ LVG HDFTTFRS+HCQA+SP++T+D  DV   G
Sbjct: 123 PLTLEKNRAWLVSPECDAEAMHRAAQSLVGHHDFTTFRSVHCQAASPVKTLDRLDVERAG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + V ARSFLH Q+RS VG L LVG G+W    + + L+A+DR+E G  AP  GLYF
Sbjct: 183 DEIRVHVAARSFLHHQVRSMVGCLALVGMGRWNEGRIAQVLEAKDRQELGLNAPSHGLYF 242

Query: 242 DSVEYS 247
               Y 
Sbjct: 243 VEAVYP 248


>gi|238855099|ref|ZP_04645427.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 269-3]
 gi|260664884|ref|ZP_05865735.1| tRNA pseudouridine synthase A [Lactobacillus jensenii SJ-7A-US]
 gi|282931908|ref|ZP_06337380.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
 gi|238832343|gb|EEQ24652.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 269-3]
 gi|260561367|gb|EEX27340.1| tRNA pseudouridine synthase A [Lactobacillus jensenii SJ-7A-US]
 gi|281303960|gb|EFA96090.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
          Length = 262

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 87/251 (34%), Positives = 133/251 (52%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+ M + Y+G  + G+Q+Q N  ++QG+IE+A+  ++ G+ +VVHG+GRTD+GVHAL 
Sbjct: 1   MPRFKMTMAYDGHLFHGFQKQPNQRTVQGTIEEALKKMSKGKRIVVHGSGRTDAGVHALG 60

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD          +  ALN+ +     I     SIVD+ FH ++S   + Y Y +  
Sbjct: 61  QVIHFDFPNDNIPANKMVLALNSMM--PTDIVFKEASIVDESFHVQYSTKGKWYRYIVNQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
            +     ++      P  LD   M+ AA  L+G HDFT+F +   Q    +RTI +  + 
Sbjct: 119 DRFVDPFKRFYTGHYPYKLDVSKMQEAASDLLGEHDFTSFAASGGQIIDKVRTIFYVKIW 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                N I    +   FL+  +R  VG+L  +G+G+    DLE+ + A+DR+E    AP 
Sbjct: 179 QKPEENEIVFDFIGNGFLYNMVRIMVGALLEIGNGRRPIHDLERVILAKDRQEVRNTAPA 238

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 239 SGLYLYHVFYE 249


>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 =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 96/268 (35%), Positives = 130/268 (48%), Gaps = 23/268 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y+GS Y GWQ Q NG S+Q  +EKAI  +T +   V  AGRTD+GVHAL Q
Sbjct: 1   MRNIKLTLAYDGSEYAGWQVQPNGPSVQACVEKAIEQLTQQRSPVLVAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F          L   L  +L   ++I +  +  V   FHA +SAI++ Y Y I    
Sbjct: 61  VASFQTESAIPCKNLQTGLQRFL--PESICVREVREVPPDFHATYSAIQKRYRYVIHNSA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    K       + LD + M  A Q L+G+HDF  F S +   ++ +RTI    V   
Sbjct: 119 VPYPFLKKYVSEFGRPLDSDRMHAAGQQLLGQHDFRCFESHYPNKATSVRTITELTVQRT 178

Query: 181 G---------------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           G                       I + VVA  FL+  +R+ VG+L  VG G+WTS D++
Sbjct: 179 GVWPVWGVLEQAHLSMENSTSAEFITVDVVADGFLYNMVRAIVGTLLDVGVGRWTSNDVQ 238

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           K L   DR + GP AP  GLY   V+Y 
Sbjct: 239 KILTGMDRSQAGPTAPACGLYLVQVDYP 266


>gi|332141777|ref|YP_004427515.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327551799|gb|AEA98517.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 264

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 128/247 (51%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+G+  +GWQRQ+   S+Q  +EKA+  V  E + V  AGRTD+GVHA  Q
Sbjct: 1   MGRIALGIEYDGAAVYGWQRQREVPSVQEHLEKALSTVANEPIEVQCAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+             +NA L   +++++     V   FHARFSA  R Y Y I   +
Sbjct: 61  VVHFNCDAPRSERAWTLGVNANL--PNSVAVTWAKNVADDFHARFSATHRRYRYVIHNAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+       I + LD + M +AAQ L+G  DFT+FR+  CQ+ +P R + +  V   
Sbjct: 119 MRPAILSSGVTHIHRELDEKKMHLAAQALLGEQDFTSFRAALCQSKTPFRNVTNVGVYRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +FLH  +R+  G+L  +G G+     +   L  +DR +    A P GLY
Sbjct: 179 GRYVIIDIRANAFLHHMVRNITGALVEIGAGEQDVNWIAHLLSLKDRSKSAATAKPNGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LVDVTYP 245


>gi|65317587|ref|ZP_00390546.1| COG0101: Pseudouridylate synthase [Bacillus anthracis str. A2012]
          Length = 257

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 11  MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 70

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 71  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 128

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 129 KTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 189 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 248

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 249 YLWQVNYN 256


>gi|290891783|ref|ZP_06554780.1| truA protein [Listeria monocytogenes FSL J2-071]
 gi|290558377|gb|EFD91894.1| truA protein [Listeria monocytogenes FSL J2-071]
          Length = 248

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 90/250 (36%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMNKGKTVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|148993376|ref|ZP_01822893.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP9-BS68]
 gi|168488681|ref|ZP_02712880.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP195]
 gi|147927931|gb|EDK78951.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP9-BS68]
 gi|183572616|gb|EDT93144.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP195]
 gi|332072441|gb|EGI82924.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA17570]
          Length = 249

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     +   L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIALILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 134/247 (54%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY G+ Y GWQ QK+  S+Q  +EKA+  +  E + ++ AGRTD+GVHA+ Q
Sbjct: 1   MTLLAIGIEYQGTAYCGWQHQKHCDSVQQQLEKALSYIADEPIGLNCAGRTDTGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +AHF+           + +N  L   + I +  +  + + FHARFSA+ R Y Y I  R 
Sbjct: 61  IAHFETNASRPDKAWIQGVNTQL--PNDIRVTWVKPMPEDFHARFSAVARQYRYVIFNRP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+   R     + LD + M  AAQ L+G +DF++FR+  CQAS   R + +  V+  
Sbjct: 119 VHSAILANRVTWENRPLDVKKMHAAAQDLLGENDFSSFRAAGCQASHANRNVQYLQVSRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN + + + A +FLH  +R+ VG+L  VG        + + L+ QDR + G  AP  GLY
Sbjct: 179 GNFVFVDIQANAFLHHMVRNIVGTLLEVGRLDKPVEWVSELLKKQDRTQAGMTAPAAGLY 238

Query: 241 FDSVEYS 247
           F +  Y 
Sbjct: 239 FVNALYP 245


>gi|228989350|ref|ZP_04149341.1| tRNA pseudouridine synthase A [Bacillus pseudomycoides DSM 12442]
 gi|228995533|ref|ZP_04155201.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock3-17]
 gi|228764262|gb|EEM13141.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock3-17]
 gi|228770428|gb|EEM19001.1| tRNA pseudouridine synthase A [Bacillus pseudomycoides DSM 12442]
          Length = 252

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHARG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I +  +    + FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWMNALNTML--PDDIVVRQVEKKTEDFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+ E++R A  + +G HDFT+F S        +RTI   D+  
Sbjct: 124 KNADVFRRNYVYQYPYPLEIESIRKAIPYFIGTHDFTSFCSTKTDKKDKVRTIYEIDLME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  +G GK     + + L+ QDR+  G + P  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKMVPDSIPEILKKQDRRFAGKMVPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|313906313|ref|ZP_07839656.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
 gi|313468869|gb|EFR64228.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
          Length = 271

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 84/255 (32%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +II Y+G+ Y G+Q Q NG ++Q  + +A+  +TGE +   GA RTD+GVHA   
Sbjct: 4   MKRIMLIIAYDGTNYCGFQVQPNGVTVQELVNRAVSELTGEEIRTIGASRTDAGVHARGN 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD            ALN  L   D I +     V   FH R++   ++Y YRI+ R+
Sbjct: 64  VVVFDTKARMPGDKYSYALNPRL--PDDIKVQLSREVSPDFHPRYTDTVKTYEYRILNRR 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSPIRTIDHFDVN 178
            P    +        SLD + M+ AA++L G HDF +F++          +RTI    V 
Sbjct: 122 MPDPTRRLNTLFNYFSLDADRMQAAARYLEGTHDFRSFQASGETNPDKETVRTIYSASVT 181

Query: 179 S------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                    +LI  R+    FL+  +R   G+L  +G GK    D++K + A+ R   GP
Sbjct: 182 RGNAADGNEDLITFRITGNGFLYNMVRILAGTLIEIGRGKLEPEDMKKIMDARSRDAAGP 241

Query: 233 LAPPEGLYFDSVEYS 247
            APP+GL    + Y 
Sbjct: 242 TAPPQGLTLVEIRYP 256


>gi|229074203|ref|ZP_04207249.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-18]
 gi|228708973|gb|EEL61100.1| tRNA pseudouridine synthase A [Bacillus cereus Rock4-18]
          Length = 252

 Score =  290 bits (744), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIFEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  +G GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNIGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|322411078|gb|EFY01986.1| tRNA pseudouridine synthase A [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 249

 Score =  290 bits (744), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  ++Q  IEK +  +TG + V +HGAGRTD+GVHA  
Sbjct: 1   MTRYKATISYDGTLFSGFQRQSHERTVQEEIEKTLQKLTGGQPVPIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  D I +++L+IV   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDLEKLRFALDT--QTPDDIDVVDLAIVADDFHCRYQKHSKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDMNKMQEAIKTLVGTHDFTGFTAAGTSVKNKVRTITEATLVQ 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DDKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVEQIKVILDSKNRQLAGPTPAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIHYE 248


>gi|304405587|ref|ZP_07387246.1| tRNA pseudouridine synthase A [Paenibacillus curdlanolyticus YK9]
 gi|304345626|gb|EFM11461.1| tRNA pseudouridine synthase A [Paenibacillus curdlanolyticus YK9]
          Length = 248

 Score =  290 bits (744), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 126/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   M + Y+G+ Y G+Q Q +G++IQ  +E AI  +TGE + + G+GRTD+GVHA  
Sbjct: 1   MSRNIVMTVSYDGTTYSGFQSQPSGNTIQDIVETAIHSLTGEQLRIIGSGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F             A+N  L   D I IL      + FHAR SA R++Y Y I  R
Sbjct: 61  QVFNFHTESRIPQERWALAMNTRL--PDDIVILEAWEAPEAFHARHSAKRKTYRYTIDRR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +  A+  P  L    MR A  HL+G HDFT+F SI       +RTI    +  
Sbjct: 119 KFPDVFSRMYAFHHPTPLQVGAMREALTHLIGEHDFTSFTSIQSTQPHHVRTIFEAWLEE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L+ + V    FL+  +R   G++  VG+GK    D+   L A DR   GP A   GL
Sbjct: 179 DGPLLYLFVTGNGFLYNMVRIIAGTMMWVGEGKLAPADIPAMLAAVDRTCAGPTAMAHGL 238

Query: 240 YFDSVEYS 247
              +VEY 
Sbjct: 239 MLWNVEYP 246


>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 =  290 bits (744), Expect = 9e-77,   Method: Composition-based stats.
 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|253682551|ref|ZP_04863348.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
 gi|253562263|gb|EES91715.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
          Length = 246

 Score =  290 bits (744), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   +IIEY+GS Y GWQ+QK+  ++Q  +E+AI  +T     + G  RTD+GVHA  
Sbjct: 1   MKRNVKLIIEYDGSNYSGWQKQKHSITVQQKVEEAISEITKTDTEIIGCSRTDAGVHARN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+F       P     A+N+ L     I I   S V   FHARF +  + Y+Y I+ R
Sbjct: 61  FVANFITESSVPPSKFKYAINSKL--PKDIVIKKSSEVPLDFHARFHSKGKKYVYTILNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVN 178
           + P  +++   +   K LD   M++A+++ +G H+F +F +       S +RTI + DV 
Sbjct: 119 EEPPTIDRNVMYHFNKDLDVNAMKMASKYFIGSHEFDSFYKKSGSSVKSTLRTIYYCDVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              ++I+  V+   FL+  +R   G+L   G G+    D++  + A+DR++ G   PP+G
Sbjct: 179 KCEDVIKFTVIGEGFLYNMVRIMAGTLIEAGIGRIRPEDIKAIILAKDREKAGRSLPPQG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLQEVLY 246


>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 =  290 bits (744), Expect = 9e-77,   Method: Composition-based stats.
 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|229542172|ref|ZP_04431232.1| tRNA pseudouridine synthase A [Bacillus coagulans 36D1]
 gi|229326592|gb|EEN92267.1| tRNA pseudouridine synthase A [Bacillus coagulans 36D1]
          Length = 245

 Score =  290 bits (744), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 119/247 (48%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+GS + G+Q Q    ++Q  IEKA+  +  G  V    +GRTD+GVHA+ 
Sbjct: 1   MKRVKCTVSYDGSRFAGYQVQPGQRTVQQEIEKALATLHKGRHVKTAASGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L     IS+   +  D  FHAR+S   + Y YRI   
Sbjct: 61  QVIHFDTDLSIPETSWPAALNSLL--PGDISVSKAAYADPAFHARYSVKEKEYRYRIYFS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 +   A  +  SLD E M  AA+ ++G HDFT+F S   +    IRT+       
Sbjct: 119 HVRSPFKHRYALRVWYSLDIEAMEAAAETVLGTHDFTSFCSAKTEVEDKIRTLKEIRFLQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + I      FL+  +R   G+L  +G GK    ++ + L+ ++R   G  APPEGL
Sbjct: 179 QDDELVICFKGNGFLYNMVRILTGTLLEIGSGKRDPGEMREILEKRNRIYAGKTAPPEGL 238

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 239 YLWKVSY 245


>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 =  290 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 94/250 (37%), Positives = 143/250 (57%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + ++Y+G+ + GWQ Q NG ++Q  +E A++  T + +    AGRTD+GVHAL QV
Sbjct: 12  RRIVLGVQYDGAPWQGWQTQLNGLTVQDKLEFALYKFTQQTITTACAGRTDAGVHALEQV 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD----KQFHARFSAIRRSYLYRII 117
            HFD   E       + +N +L    +I++   S V     + FHARFSA  R+Y Y + 
Sbjct: 72  VHFDTTLERDMQSWVRGVNTFL--PSSIAVRWASEVAHDPAENFHARFSARSRTYHYMLY 129

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +G+A  + ++LD   M+ AA HL+G+HDF+ FRS+ CQA SP++T+    +
Sbjct: 130 NNPVRSPLLEGKAGWVFRALDIAKMQEAAAHLLGQHDFSAFRSVQCQAKSPVKTMHAIKI 189

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+LI   V A +FLH  +R+ VGSL  VG+G    + L++ L  Q+RK   P   P+
Sbjct: 190 ERRGDLIMFTVHANAFLHHMVRNIVGSLIYVGNGTQAPSWLKEVLAGQERKFAAPTFMPD 249

Query: 238 GLYFDSVEYS 247
           GLY   ++Y 
Sbjct: 250 GLYLAKIDYD 259


>gi|167032538|ref|YP_001667769.1| tRNA pseudouridine synthase A [Pseudomonas putida GB-1]
 gi|166859026|gb|ABY97433.1| tRNA pseudouridine synthase A [Pseudomonas putida GB-1]
          Length = 286

 Score =  290 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 123/246 (50%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ     S+Q ++E+A+  V  E + V  AGRTD+GVH   Q+
Sbjct: 20  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPISVICAGRTDAGVHGCGQI 79

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N  L     IS++    +   FHARF A  R Y Y I     
Sbjct: 80  VHFDTRAVRDERAWTMGTNFNL--PHDISVVWSQPMPADFHARFKACARRYRYVIYNDPI 137

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AAQ L+G HDF+ FR+  CQA SPI+ I H  V   G
Sbjct: 138 RPAHLAEEVTWNHRPLDVERMAEAAQFLLGTHDFSAFRASQCQAKSPIKHIYHLRVTRHG 197

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + V A +FLH  +R+  G L  +G G+   T   + L+ ++R+E G  A P GLY 
Sbjct: 198 QMIVLDVRATAFLHHMVRNIAGVLMAIGAGERPVTWAREVLEGRNRREGGVTAHPYGLYL 257

Query: 242 DSVEYS 247
             VEY 
Sbjct: 258 VQVEYP 263


>gi|308270748|emb|CBX27358.1| tRNA pseudouridine synthase A [uncultured Desulfobacterium sp.]
          Length = 246

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 94/248 (37%), Positives = 137/248 (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     I I     V ++FH+R+ +  + Y Y+I+ R
Sbjct: 61  QVANFICDTNLEPDSFYRGLNSLL--PGDIIIKLCEQVCEKFHSRYDSKSKLYRYKILNR 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|149006661|ref|ZP_01830347.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP18-BS74]
 gi|147761576|gb|EDK68540.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP18-BS74]
          Length = 249

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFDGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     +   L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIALILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|118475910|ref|YP_893061.1| tRNA pseudouridine synthase A [Bacillus thuringiensis str. Al
           Hakam]
 gi|118415135|gb|ABK83554.1| tRNA pseudouridine synthase A [Bacillus thuringiensis str. Al
           Hakam]
          Length = 264

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 18  MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 77

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 78  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 135

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 136 KTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 195

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 196 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 255

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 256 YLWQVNYN 263


>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 =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 111/250 (44%), Positives = 156/250 (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+    +SIL+  +V ++F AR SAIRR Y YRI+ R+
Sbjct: 61  VAHLDLAKDWRTDTVRDALNAHLR-PQPVSILSAEVVPQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRE 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  I I   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|40063298|gb|AAR38116.1| tRNA pseudouridine synthase A [uncultured marine bacterium 578]
          Length = 247

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 136/246 (55%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK+G  ++Q  +E A+ LV    V V   GRTDSGVHA  Q
Sbjct: 1   MKIALGVEYLGTNFNGWQIQKSGIRTVQEVVESALSLVANHPVRVFCCGRTDSGVHAKEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+              N  L     ++      VD  FHARF+A  RSY Y+I    
Sbjct: 61  VIHFETDSNRSNEAWVFGGNVNL--PSDVNFSWAKDVDDDFHARFNAYARSYEYKIHNHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              +L        P+SL+ + MR AA  L+G HDF++FR   CQA SP++T+++ D+   
Sbjct: 119 VRSSLNANYYLWEPRSLNIDEMRKAANFLIGEHDFSSFRGRLCQAKSPVKTVEYLDIIES 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + + +++ A +FLH  +R+ VG+L  +G G+  +  +   L+++DR+E GP A P+GLY
Sbjct: 179 DDNLIVKIKANAFLHHMVRNIVGTLLKIGRGERDAEWMLSVLESKDRREAGPTAEPQGLY 238

Query: 241 FDSVEY 246
           F    Y
Sbjct: 239 FIKAYY 244


>gi|75764616|ref|ZP_00744060.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74487896|gb|EAO51668.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 264

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 18  MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 77

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 78  QVIHFDTPLSLEEWQWNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRVLLS 135

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 136 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 195

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 196 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 255

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 256 YLWEVNYN 263


>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 =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 127/251 (50%), Positives = 161/251 (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  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL R W    L +ALNA+L+ +   ++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 VNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 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|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 =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 110/251 (43%), Positives = 156/251 (62%), 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-PQPVAILSAEVVTQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRE 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  I I   ARSFLH Q+R+  G+L L G  + ++ D+ + L    +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCKRLSADDVAEILATGAKHRCGPLAPA 239

Query: 237 EGLYFDSVEYS 247
            GL F  V+Y 
Sbjct: 240 CGLTFVGVDYP 250


>gi|228931644|ref|ZP_04094550.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228828072|gb|EEM73800.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 252

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   + I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PNDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>gi|295398321|ref|ZP_06808363.1| tRNA pseudouridine synthase A [Aerococcus viridans ATCC 11563]
 gi|294973460|gb|EFG49245.1| tRNA pseudouridine synthase A [Aerococcus viridans ATCC 11563]
          Length = 285

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 82/249 (32%), Positives = 134/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+ + ++Y+G+ + G+Q Q NG ++Q ++EKA+ L++ G  + V G+GRTDSGVHAL 
Sbjct: 1   MPRFKVTLQYDGTPFVGFQVQPNGHTVQEALEKALKLMSKGHDIQVVGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     + +A+N+ L   D I I  +  V+  FHARF    + Y+Y++ T 
Sbjct: 61  QVIHFDYPAEIGEEAVLRAMNSIL--DDAIRITKVERVEDDFHARFHTNGKKYIYKVDTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P   D   M+ A + ++G HDF +F S     ++ +R I   +V +
Sbjct: 119 KFPSPFTRQYMYHHPYRTDVTRMQTALKDIIGVHDFKSFCSTKTDKTNFVREIYRAEVTA 178

Query: 180 FGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +   +        FL+  +R  VG+   +GDG     ++++ + A+DR E GP A   
Sbjct: 179 DPDAETLTFVFEGSGFLYNMVRILVGTTLQIGDGLRPVDEMKRLITAEDRNEAGPTAAAH 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLAEVYY 247


>gi|228905939|ref|ZP_04069836.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 200]
 gi|228853754|gb|EEM98514.1| tRNA pseudouridine synthase A [Bacillus thuringiensis IBL 200]
          Length = 252

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPKHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWNNALNTML--PDDIVIRRVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPNSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWEVNYN 251


>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 =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 95/253 (37%), Positives = 141/253 (55%), Gaps = 8/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 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    +I +++   V   FHARFSA+ R+Y Y I   
Sbjct: 82  QIVHFDTLAGRPSKAWLQGVNTHL--PFSIRVISAKEVGFDFHARFSALSRTYRYVIHVS 139

Query: 120 QAPLALEKGRAWLIPKS-----LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           Q   A        +        LD   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 PPEGLYFDSVEYS 247
           P  GLYF +V+Y 
Sbjct: 260 PAAGLYFVNVQYP 272


>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 =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 111/251 (44%), 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   MPRYALQVEYHGAPFAGWQRQADQPSVQGAIEAALARLEPGPHTIAAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA  DL ++W P  L +ALN +L+    ++I   + V + +HARFSA+ R Y++R++ R+
Sbjct: 61  VAQCDLEKDWDPFRLSEALNHHLR-PAPVAIRACARVAEDWHARFSALERRYMFRLLMRR 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|289167524|ref|YP_003445793.1| tRNA pseudouridine synthase A [Streptococcus mitis B6]
 gi|288907091|emb|CBJ21925.1| tRNA pseudouridine synthase A [Streptococcus mitis B6]
          Length = 249

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  E  + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKEQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYTKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E MR A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMREAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLTV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|169335662|ref|ZP_02862855.1| hypothetical protein ANASTE_02082 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258400|gb|EDS72366.1| hypothetical protein ANASTE_02082 [Anaerofustis stercorihominis DSM
           17244]
          Length = 244

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G  Y GWQ Q NG S++  ++ AI  +  E V ++G+GRTDSGVHAL Q
Sbjct: 1   MRNILITIEYDGKNYVGWQMQNNGISVEEKVKTAIEKLVKEEVKLYGSGRTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A F          L   +N++L   + I ++     ++ FHAR+SA  + Y+Y I  R 
Sbjct: 61  AASFYTNSNISADKLPYGINSFL--PEDIRVIKAEEKEEDFHARYSAKGKEYVYLIYNRS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               + KGRA  +   LD + M+ A++ L+G HDF  F        S +R I   D+   
Sbjct: 119 IMNPIYKGRASHVFYKLDLDKMKRASKSLIGIHDFAGFMGSGSDVKSTVREIYDIDITKD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LI+I++    FL+  +R  V SL  +G G++    +E+ L+ + R      AP  GLY
Sbjct: 179 NDLIKIKISGSGFLYNMVRIIVASLIDIGRGRFDENRIEEILETKQRSMANVTAPAVGLY 238

Query: 241 FDSVEY 246
            + V Y
Sbjct: 239 LNKVFY 244


>gi|46908770|ref|YP_015159.1| tRNA pseudouridine synthase A [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47093538|ref|ZP_00231299.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 4b
           H7858]
 gi|226225144|ref|YP_002759251.1| pseudouridylate synthase I [Listeria monocytogenes Clip81459]
 gi|254825041|ref|ZP_05230042.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-194]
 gi|254992719|ref|ZP_05274909.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J2-064]
 gi|255520577|ref|ZP_05387814.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-175]
 gi|51316671|sp|Q71WI0|TRUA_LISMF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|259550404|sp|C1KZ13|TRUA_LISMC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46882043|gb|AAT05336.1| tRNA pseudouridine synthase A [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47018098|gb|EAL08870.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 4b
           H7858]
 gi|225877606|emb|CAS06320.1| Putative pseudouridylate synthase I [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|293594283|gb|EFG02044.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-194]
 gi|328468084|gb|EGF39090.1| tRNA pseudouridine synthase A [Listeria monocytogenes 1816]
          Length = 248

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 88/250 (35%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ +AL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISEALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|148986314|ref|ZP_01819186.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP3-BS71]
 gi|147921782|gb|EDK72913.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP3-BS71]
 gi|301800423|emb|CBW33056.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae OXC141]
          Length = 249

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+++ VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQVITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFTVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


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

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   S+QG +E+A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 16  MKIALGIEYDGSRYYGWQRQQEVKSVQGCLEEALSKVADEPISVFCAGRTDAGVHATGQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +N +L     I++  +  VD+ FHARFSA  R Y Y I   + 
Sbjct: 76  VHFETSVQRKDAAWTMGVNVHL--PPDIAVRWVKTVDEGFHARFSATARRYRYIIFNHRY 133

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ ++G +DFT+FR++ CQ+ +P R + H +VN +G
Sbjct: 134 RPAVLANGVTHFHYPLDEKRMHQAAQCILGENDFTSFRAVQCQSKTPWRNVMHINVNRYG 193

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  +G G      + + L  +DR +    A   GLY 
Sbjct: 194 HYVVIDIKANAFVHHMVRNIAGSLMEIGCGNQDINWMAQLLALKDRAKAAATAKAAGLYL 253

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 254 VAVDYP 259


>gi|225028683|ref|ZP_03717875.1| hypothetical protein EUBHAL_02962 [Eubacterium hallii DSM 3353]
 gi|224953993|gb|EEG35202.1| hypothetical protein EUBHAL_02962 [Eubacterium hallii DSM 3353]
          Length = 253

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 81/252 (32%), Positives = 126/252 (50%), Gaps = 10/252 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            Y M I Y+GS Y+GW+ Q +  +IQG +E  +  + GE + V GAGRTD+GVHA   VA
Sbjct: 4   NYKMTICYDGSRYYGWEHQPDRDTIQGKLENVLTRMCGEFIDVLGAGRTDAGVHARGMVA 63

Query: 63  HFDLV--------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           +            RE  P  +   +N YL   D I++  +    ++FHAR+ A+ + Y Y
Sbjct: 64  NAVFDATDKERGGRERTPDEIRDYMNRYL--PDDIAVKEVREASERFHARYKAVGKLYRY 121

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                      ++    ++ K  D E M+ AA +L G+HD+ +F        S +R +D 
Sbjct: 122 TCYDGPVKPVFQRKYVAVLEKRPDVEKMQQAAAYLEGKHDYKSFCGNPRMKKSTVRVVDK 181

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++   G+ I        FL   +R  VG+L  VG GK     + + L+A++R+  GP A
Sbjct: 182 IEITRKGSFIYFDFHGTGFLQNMVRILVGTLLEVGKGKIKPEQIPEILEAKNRQMAGPTA 241

Query: 235 PPEGLYFDSVEY 246
           P +GL    V+Y
Sbjct: 242 PAQGLCLIKVDY 253


>gi|56961964|ref|YP_173686.1| pseudouridylate synthase I [Bacillus clausii KSM-K16]
 gi|62901228|sp|Q5WLN0|TRUA_BACSK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56908198|dbj|BAD62725.1| pseudouridylate synthase I [Bacillus clausii KSM-K16]
          Length = 261

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 125/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G+ + G+Q Q    ++Q  +E+A+  +  G  V V  +GRTD+GVHA  
Sbjct: 1   MSRMACKLSYDGTAFAGYQVQPGKRTVQSEVERALQEIHKGARVPVVASGRTDAGVHACG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P     ALN +L   D I + N ++V+  FHAR+ A  + Y Y I   
Sbjct: 61  QVLHFDTELTIAPERWVSALNTHL--PDDIVVTNAAMVEPDFHARYGAQAKEYRYYIQCG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  A  I ++LD   M+ AA+HL+G HDF+ F + +   +  +RTI H  V  
Sbjct: 119 PFENVFRRHFAVHIKQALDVPAMQTAAKHLLGTHDFSAFCAANTTVTDKVRTITHVAVQP 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + I +    FL+  +R  VG+L  +G GK  +++++  L  + R   G  AP  GL
Sbjct: 179 SEEGLLISIRGTGFLYNMVRIIVGTLLEIGTGKRVASEMKVILAGKSRNLAGKTAPAHGL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 CLYEVDY 245


>gi|16804636|ref|NP_466121.1| tRNA pseudouridine synthase A [Listeria monocytogenes EGD-e]
 gi|224499270|ref|ZP_03667619.1| tRNA pseudouridine synthase A [Listeria monocytogenes Finland 1988]
 gi|224503609|ref|ZP_03671916.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL R2-561]
 gi|254829047|ref|ZP_05233734.1| truA [Listeria monocytogenes FSL N3-165]
 gi|254830971|ref|ZP_05235626.1| tRNA pseudouridine synthase A [Listeria monocytogenes 10403S]
 gi|254899951|ref|ZP_05259875.1| tRNA pseudouridine synthase A [Listeria monocytogenes J0161]
 gi|254912843|ref|ZP_05262855.1| tRNA pseudouridine synthase A [Listeria monocytogenes J2818]
 gi|254937223|ref|ZP_05268920.1| truA [Listeria monocytogenes F6900]
 gi|255029029|ref|ZP_05300980.1| tRNA pseudouridine synthase A [Listeria monocytogenes LO28]
 gi|284800516|ref|YP_003412381.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5578]
 gi|284993702|ref|YP_003415470.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5923]
 gi|24212550|sp|Q8Y457|TRUA_LISMO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|16412086|emb|CAD00676.1| truA [Listeria monocytogenes EGD-e]
 gi|258601456|gb|EEW14781.1| truA [Listeria monocytogenes FSL N3-165]
 gi|258609828|gb|EEW22436.1| truA [Listeria monocytogenes F6900]
 gi|284056078|gb|ADB67019.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5578]
 gi|284059169|gb|ADB70108.1| tRNA pseudouridine synthase A [Listeria monocytogenes 08-5923]
 gi|293590841|gb|EFF99175.1| tRNA pseudouridine synthase A [Listeria monocytogenes J2818]
          Length = 248

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ +AL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISEALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|330721742|gb|EGG99735.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC2047]
          Length = 269

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 98/247 (39%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + IEY+GSGY GWQ Q + S ++Q  +E A+  +    V V  AGRTD+GVHA  Q
Sbjct: 9   TRVALGIEYHGSGYNGWQAQNHESITVQCELESALSKIADAPVRVFCAGRTDAGVHATGQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+++        +  N +L   D+I +     V + FHARFSA+ R Y+Y I    
Sbjct: 69  VVHFDVLKPRTENAWVRGTNTHL--PDSIRVRWAKFVPEDFHARFSAMARRYIYVIENTP 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+         + LD E M++AA +LVG HDF+++R++ CQA S I+T+ H  V   
Sbjct: 127 VHSAIMNKHFSFEDRPLDVERMQLAANYLVGEHDFSSYRTVRCQAKSAIKTVHHLKVERH 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI I + A +FLH  +R+  G L +VG GK      ++ L A+DR   G  APP GLY
Sbjct: 187 GSLIAIDIYANAFLHHMVRNVAGVLMMVGMGKAEPVWAKQVLDARDRTVGGVTAPPNGLY 246

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 247 LVGVDYP 253


>gi|302390990|ref|YP_003826810.1| tRNA pseudouridine synthase A [Acetohalobium arabaticum DSM 5501]
 gi|302203067|gb|ADL11745.1| tRNA pseudouridine synthase A [Acetohalobium arabaticum DSM 5501]
          Length = 244

 Score =  290 bits (743), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 2   IRY-CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY   II Y+G+ Y+G+Q Q +  +IQ  +E+++ ++T E   V  AGRTD GVHA  Q
Sbjct: 1   MRYLKAIIAYDGTNYYGFQHQPDVPTIQDELEESLRILTKEKNKVIVAGRTDRGVHAQNQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F          +  A N  L   + I I  +  V+  FHAR+ A  + Y YRI+ + 
Sbjct: 61  VINFKTESPIPLENIRFAWNNCL--PNDILIKEVEDVNADFHARYDAEGKIYEYRILNQP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   ++   + I + LD   M  AA+ L+G +DF++F++      + +RTI   +V   
Sbjct: 119 LPSVFKRNYTYHIKEELDSAAMAEAAECLIGTYDFSSFQASGSNVQTTVRTIQQAEVTQQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+  R+    FL+  +R  VG+L  VG G+W    + + ++A+DR   GP AP +GL 
Sbjct: 179 DRLVIFRIEGDGFLYNMVRIIVGTLIKVGTGEWEVPRMSRIIEAEDRLAAGPTAPAQGLR 238

Query: 241 FDSVEY 246
              V+Y
Sbjct: 239 LIKVKY 244


>gi|307706977|ref|ZP_07643775.1| tRNA pseudouridine synthase A [Streptococcus mitis SK321]
 gi|307617638|gb|EFN96807.1| tRNA pseudouridine synthase A [Streptococcus mitis SK321]
          Length = 249

 Score =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVVSIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLRV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     +E  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIELILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 127/246 (51%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +I EY+G  + GWQ QK    S++  + +A   V    V +  AGRTD+GVHA  QV
Sbjct: 18  RVAIIFEYDGQAFHGWQLQKSGVRSVEAELSRAAARVADHPVDLVCAGRTDAGVHASFQV 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             +N  L   D IS+         FHARFSAI R Y Y I     
Sbjct: 78  AHFDTPSVRNLRSWVMGMNTAL--PDDISVHWAGNGQGDFHARFSAIYRRYRYVIYNHPV 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +++G+     + LD E M  A+Q LVG HDF++FR+  CQ+ +P+R ++   V   G
Sbjct: 136 RPGIQRGQVSWTFRPLDAERMHRASQALVGEHDFSSFRAAGCQSRTPVRFLEQISVTRCG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I V A +FLH  +R+  G+L  VG+G+     +   L+ +DRK  G  APP GLY 
Sbjct: 196 EFVVIDVQANAFLHHMVRNIAGALMAVGNGQQPEDWIGDILECRDRKLAGVTAPPYGLYL 255

Query: 242 DSVEYS 247
             V Y 
Sbjct: 256 VDVGYP 261


>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 =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 114/250 (45%), Positives = 156/250 (62%), Gaps = 5/250 (2%)

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  VAHCDMEKAWDPFRLSEALNFHLK-PAPVAIRACAAVSDDWHARFSAHERRYLFRLLVRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP  LE G+ W +   L  E MR  A HL+G+HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATLEAGQVWRVMNPLSLEAMRAGAAHLIGQHDFTTFRSTMCQAASPVKTMDEIRIEQT 179

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

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


>gi|196041154|ref|ZP_03108450.1| tRNA pseudouridine synthase A [Bacillus cereus NVH0597-99]
 gi|196028089|gb|EDX66700.1| tRNA pseudouridine synthase A [Bacillus cereus NVH0597-99]
          Length = 252

 Score =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P SL+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYSLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 114/246 (46%), Positives = 159/246 (64%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 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|268590477|ref|ZP_06124698.1| tRNA pseudouridine synthase A [Providencia rettgeri DSM 1131]
 gi|291314156|gb|EFE54609.1| tRNA pseudouridine synthase A [Providencia rettgeri DSM 1131]
          Length = 271

 Score =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEYNGS YFGWQRQ+   S+QG +E+A+  +  E + V  AGRTD+GVHA  QV 
Sbjct: 9   RIALGIEYNGSRYFGWQRQQEVKSVQGCLEEALSKIAAEPISVFCAGRTDAGVHATGQVV 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+              N +L     I++     V ++FHARFSA  R Y Y I   +  
Sbjct: 69  HFETSAIRKEAAWTMGANTHL--PPDIAVRWCKPVAEEFHARFSATARRYRYVIFNHRYR 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  AAQ L+G  DFT+FR++ CQ+ SP R + H +V+  G+
Sbjct: 127 PAILSSGVTHFHYPLDEKRMHEAAQALLGERDFTSFRAVQCQSKSPWRNVMHVNVSRHGH 186

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G      +   L+ +DR +    A  EGLY  
Sbjct: 187 YVVVDIKANAFVHHMVRNIVGSLLEIGCGNQNIDWMAHLLELKDRTKAAATAKAEGLYLV 246

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 247 SVDYP 251


>gi|332201036|gb|EGJ15107.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA47901]
          Length = 249

 Score =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFILDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|255526720|ref|ZP_05393623.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
 gi|255509607|gb|EET85944.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
          Length = 249

 Score =  290 bits (742), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 134/251 (53%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-----GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M    M+I+Y+GS Y GWQ+Q +      S+IQ  IE  +  +TGE + V G GRTD+GV
Sbjct: 1   MRNLKMLIQYDGSRYKGWQKQNHKDNNSVSTIQDKIESVLSKMTGEDIQVVGCGRTDTGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA   VA+F          + K L  Y  + + I + +L    ++FHAR++A  ++YLY 
Sbjct: 61  HAENYVANFHTDSILTVEDMLKYL--YEFLPEDIVVKSLRDTSERFHARYNAKSKTYLYT 118

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I   +      +  A+ + ++L+   MR AA+ L G HDF +F S+     S +RTI++ 
Sbjct: 119 INNNKFRNVFNRKYAYHVEENLNLSEMRDAAEVLTGTHDFQSFTSLKSNTKSTVRTINYI 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +     +I I V   SFL   +R  VG+L  VG G    +D+EK L  + R E GP+A 
Sbjct: 179 SITEEHGMIGIEVNGNSFLLNMVRIIVGTLLDVGKGILKPSDVEKILYEKKRAEAGPMAA 238

Query: 236 PEGLYFDSVEY 246
            +GL    ++Y
Sbjct: 239 AKGLCLKDIQY 249


>gi|229009651|ref|ZP_04166877.1| tRNA pseudouridine synthase A [Bacillus mycoides DSM 2048]
 gi|229131150|ref|ZP_04260062.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST196]
 gi|229165130|ref|ZP_04292925.1| tRNA pseudouridine synthase A [Bacillus cereus AH621]
 gi|228618393|gb|EEK75423.1| tRNA pseudouridine synthase A [Bacillus cereus AH621]
 gi|228652363|gb|EEL08288.1| tRNA pseudouridine synthase A [Bacillus cereus BDRD-ST196]
 gi|228751673|gb|EEM01473.1| tRNA pseudouridine synthase A [Bacillus mycoides DSM 2048]
          Length = 252

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGIHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIIIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G+ + GWQ Q  G  +Q ++E+ +  +    V V  AGRTD+GVHAL QV
Sbjct: 1   MRVALGLEYDGAHFCGWQSQPGGCGVQDALERELARMACHPVRVIAAGRTDTGVHALAQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   E       + +NA L    ++ +L    VD +FHARFSA +R Y Y +  +  
Sbjct: 61  VHFETTTERPLNAWVRGVNAGL--PSSVRVLWAQQVDDEFHARFSARQRYYQYILFDQAV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G+     +SLD + M  AA HL+G HDF+ FR+  CQA SPIRT+   +V   G
Sbjct: 119 APAILAGKVGWFHQSLDVDAMAEAAAHLIGEHDFSAFRAAECQAKSPIRTLQQAEVRRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I       +FLH Q+R+ VG+L  VG G      +++ LQ+ DR+   P   P+GLY 
Sbjct: 179 QAILFEFSGNAFLHHQVRNMVGALVYVGKGSQPPAFIQQLLQSHDRRLAPPTFSPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 SGVGYE 244


>gi|257886188|ref|ZP_05665841.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257822044|gb|EEV49174.1| tRNA pseudouridine synthase [Enterococcus faecium 1,231,501]
          Length = 247

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     +   +N YL     I I  +  + ++FH+R++A+ + Y Y +   
Sbjct: 61  QVANFKTNTEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHSRYNAVGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  P+ LD + +  A + LVG HDF  F ++     S +RTID   +  
Sbjct: 119 VIPSAFERNHSFYFPQELDMDKLDAACEKLVGTHDFIGFSALKKSKKSTVRTIDELSIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++    V   FL+  +R  +G+L  +G G      +++  +++ R+  G   P +GL
Sbjct: 179 KGEMLHFTFVGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETVPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|255025629|ref|ZP_05297615.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J2-003]
          Length = 248

 Score =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|15901439|ref|NP_346043.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae TIGR4]
 gi|111656856|ref|ZP_01407696.1| hypothetical protein SpneT_02001886 [Streptococcus pneumoniae
           TIGR4]
 gi|149013277|ref|ZP_01834035.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP19-BS75]
 gi|168486863|ref|ZP_02711371.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1087-00]
 gi|225859353|ref|YP_002740863.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 70585]
 gi|303253960|ref|ZP_07340080.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS455]
 gi|303258528|ref|ZP_07344508.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP-BS293]
 gi|303262617|ref|ZP_07348557.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS292]
 gi|303263556|ref|ZP_07349478.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS397]
 gi|303267576|ref|ZP_07353421.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS457]
 gi|303269928|ref|ZP_07355667.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS458]
 gi|25453312|sp|Q97PL0|TRUA_STRPN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764867|sp|C1C8I7|TRUA_STRP7 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|14973090|gb|AAK75683.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae TIGR4]
 gi|147762942|gb|EDK69888.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP19-BS75]
 gi|183570198|gb|EDT90726.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1087-00]
 gi|225721425|gb|ACO17279.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 70585]
 gi|301794601|emb|CBW37047.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae INV104]
 gi|301802309|emb|CBW35063.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae INV200]
 gi|302599048|gb|EFL66074.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS455]
 gi|302636173|gb|EFL66668.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS292]
 gi|302640029|gb|EFL70484.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP-BS293]
 gi|302640531|gb|EFL70939.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS458]
 gi|302642899|gb|EFL73201.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS457]
 gi|302646594|gb|EFL76819.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae BS397]
          Length = 249

 Score =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFTVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 110/250 (44%), Positives = 156/250 (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  VAHLDLAKDWRTDTVRDALNAHLR-PQPVAILSAEVVPQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  I I   ARSFLH Q+R+  G+L L G  + ++ D+ + L    +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCNRLSADDVAEILATGAKHRCGPLAPA 239

Query: 237 EGLYFDSVEY 246
            GL F  V+Y
Sbjct: 240 CGLTFVGVDY 249


>gi|322517723|ref|ZP_08070585.1| tRNA pseudouridine synthase A [Streptococcus vestibularis ATCC
           49124]
 gi|322123654|gb|EFX95247.1| tRNA pseudouridine synthase A [Streptococcus vestibularis ATCC
           49124]
          Length = 249

 Score =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  +EK +  + +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEELEKTLLRLNSGTPVTVHGAGRTDAGVHAYE 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR++   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRNYATHYPYPLSLAPMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                          FL+ Q+R+ VG+L  +G+G+   + ++  L++ DR   GP A   
Sbjct: 179 DEKTGFYIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESCDRNLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|83591242|ref|YP_431251.1| tRNA pseudouridine synthase A [Moorella thermoacetica ATCC 39073]
 gi|123766692|sp|Q2RFT1|TRUA_MOOTA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83574156|gb|ABC20708.1| tRNA pseudouridine synthase A [Moorella thermoacetica ATCC 39073]
          Length = 246

 Score =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 118/248 (47%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + + Y+GS Y GWQ Q   +G ++QG +  A+  +TGE +    AGRTD+GVHA 
Sbjct: 1   MPCLKITLAYDGSNYAGWQVQPEAHGPTVQGEVAAALKRLTGEEITPVAAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F             ALN+ L     I+ L    V   FHAR+ A R+ Y Y I  
Sbjct: 61  GQVISFSTRARIPVERWPLALNSVL--PADIAALEAVEVAPDFHARYCAKRKWYRYTIYN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P    +  +W + + LD   M  AA +L G HDF +F +         R +    V+
Sbjct: 119 NRVPDVFCRRYSWHLRQPLDVIAMARAAAYLQGCHDFRSFCAAGSPVRHFERQVQQASVS 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I   V+A  FL+  +R  VG+L  +G  +     +   L A+ R++ GP AP  G
Sbjct: 179 QNGPFIYFDVIADGFLYHMVRIMVGTLVEIGRRRLVPEAIPAILAARSREKAGPTAPARG 238

Query: 239 LYFDSVEY 246
           L  + VEY
Sbjct: 239 LCLERVEY 246


>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 =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 89/249 (35%), Positives = 136/249 (54%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +  ++Q ++E A+    G  + V    AGRTD+GVH  
Sbjct: 2   MSRVALGLAYDGSAWQGWQTQPHRQTVQDTLESALARFCGVQDPVPTICAGRTDTGVHGA 61

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H D   +       + +NA+L    ++S+     V  +FHARFSA  R+Y+Y +  
Sbjct: 62  MQVVHLDTSLDRRMESWVRGVNAFL--PPSVSVQWAQEVSDEFHARFSARARTYVYLLWR 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +   AL  GRA    ++LD + MR AAQ LVG HDF++FRS  CQA  P+R +   D+ 
Sbjct: 120 GRVRPALWAGRAGWCFQTLDVDAMRAAAQALVGEHDFSSFRSSQCQAKHPVRHMHRLDIA 179

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A +FLH  +R+ +G+L  VG G+ +   + + L  +DR    P   P+G
Sbjct: 180 ERGPFLVFTLKANAFLHHMVRNIMGALLQVGQGRESVDWMAQLLSLRDRTRGAPTFAPDG 239

Query: 239 LYFDSVEYS 247
           LY  S++Y 
Sbjct: 240 LYLSSIDYP 248


>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 =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 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|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 =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 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|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 =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 110/251 (43%), Positives = 155/251 (61%), 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  VAHLDLAKDWRTDTVRDALNARLR-PQPVAILSAEVVPQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  I I   ARSFLH Q+R+  G+L L G  + ++ D+ + L    +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCKRLSADDVAEILATGAKHRCGPLAPA 239

Query: 237 EGLYFDSVEYS 247
            GL F  V+Y 
Sbjct: 240 CGLTFVGVDYP 250


>gi|116628993|ref|YP_814165.1| tRNA pseudouridine synthase A [Lactobacillus gasseri ATCC 33323]
 gi|238853452|ref|ZP_04643830.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 202-4]
 gi|116094575|gb|ABJ59727.1| Pseudouridylate synthase [Lactobacillus gasseri ATCC 33323]
 gi|238833892|gb|EEQ26151.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 202-4]
          Length = 264

 Score =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 87/253 (34%), Positives = 131/253 (51%), Gaps = 8/253 (3%)

Query: 1   MI--RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHA 57
           M+  RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA
Sbjct: 1   MMTTRYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHA 60

Query: 58  LRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             QV HFD   +E     +  ALNA +         +  IVD  FH ++S   + Y Y +
Sbjct: 61  KGQVIHFDYPGKEIPAKNMMLALNALM--PIDTVFFDSEIVDSDFHVQYSTKGKWYRYIV 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + +
Sbjct: 119 DQHRFTDPFNRFYTGHYPYPLDIALMKKAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVN 178

Query: 177 VNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           + S  +   I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    A
Sbjct: 179 ITSDPDNKKIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTA 238

Query: 235 PPEGLYFDSVEYS 247
           P  GLY   V Y 
Sbjct: 239 PASGLYLQHVFYE 251


>gi|270293156|ref|ZP_06199367.1| tRNA pseudouridine synthase A [Streptococcus sp. M143]
 gi|270279135|gb|EFA24981.1| tRNA pseudouridine synthase A [Streptococcus sp. M143]
          Length = 249

 Score =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ V VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAVTVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + +   
Sbjct: 61  QAIHFDLPYQMNEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M+ A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVEQMQEAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLSV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DKTGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|310823108|ref|YP_003955466.1| tRNA pseudouridine synthase a [Stigmatella aurantiaca DW4/3-1]
 gi|309396180|gb|ADO73639.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 265

 Score =  289 bits (741), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+GS Y GWQ Q+NG S+Q  + +A+  + G  V V  AGRTDSGVHA  Q
Sbjct: 1   MPRLKLTIEYDGSRYVGWQVQRNGRSVQAELGEALGRLLGGDVEVVAAGRTDSGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD  R+       + LN  L   + I+++    V   F  R  +  + Y YR+    
Sbjct: 61  VVCFDTERQLPLKAYHRGLNGLL--PEDIAVVRAEEVSAAFDPRRWSRGKRYRYRVSNLP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
           +   L +   W I   L  E M  AA  L+GRHD++ FR+  CQA+  +R +    V  +
Sbjct: 119 SRSPLRRHTHWEIYAPLQVEAMARAATSLLGRHDYSAFRASDCQAAHAVREVRRLSVEGT 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   V   +FL   +R+ VG+L  VG G+     + + L + DR   GP APP GL
Sbjct: 179 PGDAVAFVVEGTAFLKHMVRNLVGTLVEVGKGRRPEAWVAEVLASGDRTLAGPTAPPHGL 238

Query: 240 YFDSVEY 246
             + V Y
Sbjct: 239 VLEEVFY 245


>gi|320548017|ref|ZP_08042298.1| tRNA pseudouridine synthase A [Streptococcus equinus ATCC 9812]
 gi|320447363|gb|EFW88125.1| tRNA pseudouridine synthase A [Streptococcus equinus ATCC 9812]
          Length = 249

 Score =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G  + G+QRQ +  S+Q  +EK +  + +G  V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKATISYDGGLFAGFQRQPSERSVQEELEKTLQKLNSGTPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++ + +V   FH+R++   ++Y + +   
Sbjct: 61  QVVHFDLPQARDVEKLRFGLDT--QSPEDIDVVKVELVSDDFHSRYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI     D+
Sbjct: 119 RPKNPMMRHYATHYPYPLDLALMQEAIKDLVGTHDFTGFTASGTSVENKVRTITRATVDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L++++R   GP A   
Sbjct: 179 DEKTGFFVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTVLESKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYD 248


>gi|322388332|ref|ZP_08061936.1| tRNA pseudouridine synthase A [Streptococcus infantis ATCC 700779]
 gi|321141004|gb|EFX36505.1| tRNA pseudouridine synthase A [Streptococcus infantis ATCC 700779]
          Length = 249

 Score =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + +HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTKLNKGQAITIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEVVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M+ A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHYPYPLDVERMQKAVKKLEGTHDFTGFTAAGTSVEDKVRTITEASLRV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPIEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|313499900|gb|ADR61266.1| TruA [Pseudomonas putida BIRD-1]
          Length = 284

 Score =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 122/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ     S+Q ++E+A+  V  E + V  AGRTD+GVH   QV
Sbjct: 18  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPISVICAGRTDAGVHGCGQV 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N  L     IS++    +   FHARF A  R Y Y I     
Sbjct: 78  VHFDTRAVRDERAWTMGTNFNL--PHDISVVWSRPMPADFHARFKACARRYRYVIYNDPI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD + M  AAQ L+G HDF+ FR+  CQA SPI+ I H  V   G
Sbjct: 136 RPAHLAEEVTWNHRPLDVDRMAEAAQFLLGTHDFSAFRASQCQAKSPIKHIYHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + V A +FLH  +R+  G L  +G G+       + L+ ++R+E G  A P GLY 
Sbjct: 196 QMIVLDVRATAFLHHMVRNIAGVLMAIGAGERPVAWAREVLEGRNRREGGVTAHPYGLYL 255

Query: 242 DSVEYS 247
             VEY 
Sbjct: 256 VQVEYP 261


>gi|311694720|gb|ADP97593.1| tRNA pseudouridine synthase A [marine bacterium HP15]
          Length = 302

 Score =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 124/246 (50%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +  EY+G G+ GWQ QK    S++  +  A+  V    V +  AGRTD+GVHA  Q+
Sbjct: 18  RVALAFEYDGRGFHGWQLQKSGVRSVEAELTAAVAKVANHAVDLVCAGRTDAGVHASYQI 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             +N  L   D IS+         FHARFSA  R Y Y I     
Sbjct: 78  AHFDTPSVRNLRSWVMGINTAL--PDDISVHWAGNGVGDFHARFSATYRRYRYIIYNHPV 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +++G+     + LD + M  AAQ L G HDF++FR+  CQ+ +PIR ++   V    
Sbjct: 136 RPGIQRGQVSWTFRPLDADRMHRAAQALAGEHDFSSFRAAGCQSRTPIRFLERISVTRKR 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I V A +FLH  +R+  G+L  VG GK     + + L A+DR   G  APP GLY 
Sbjct: 196 DFVVIDVQANAFLHHMVRNIAGALMAVGSGKQRPEWIHEILVARDRTAAGVTAPPHGLYL 255

Query: 242 DSVEYS 247
             V Y 
Sbjct: 256 VDVGYP 261


>gi|328951883|ref|YP_004369217.1| tRNA pseudouridine synthase A [Desulfobacca acetoxidans DSM 11109]
 gi|328452207|gb|AEB08036.1| tRNA pseudouridine synthase A [Desulfobacca acetoxidans DSM 11109]
          Length = 267

 Score =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 84/245 (34%), Positives = 130/245 (53%), Gaps = 3/245 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
            C+ +EY+G+ Y GWQRQ N  +IQ  +E  +  +TG+++ +H +GRTD+GVHAL QVAH
Sbjct: 25  ICLTLEYDGTAYHGWQRQANALTIQEVVETCLARLTGQVIRLHSSGRTDAGVHALGQVAH 84

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F            + LN+ L     ++IL +      FHAR+SA  ++Y YRI+ R    
Sbjct: 85  FLTTSSLPLSAFREGLNSLL--PRDLAILKVCDAPAGFHARYSATAKTYEYRILNRPVRS 142

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-GN 182
            +     W + + LD   +R AA +++G  DF  F++      +  R +         G 
Sbjct: 143 PVHCNYCWWLARPLDQGLLRQAAGYILGEQDFAAFQASGGSVKTTTRKVMAASWEEKPGG 202

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
               ++ A  FL   +R+ VG++  VG GK +  DL++ L A+DR++ GP AP  GLY  
Sbjct: 203 WRIFQITANGFLRGMVRALVGTMVEVGWGKRSPGDLKRLLAARDRRQAGPTAPAAGLYLV 262

Query: 243 SVEYS 247
            V Y 
Sbjct: 263 EVRYD 267


>gi|293364991|ref|ZP_06611708.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
 gi|307703239|ref|ZP_07640185.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
 gi|291316441|gb|EFE56877.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
 gi|307623314|gb|EFO02305.1| tRNA pseudouridine synthase A [Streptococcus oralis ATCC 35037]
          Length = 249

 Score =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGFAFAGFQRQPHARSVQEEIEKTLTRLNKGQAIAVHGAGRTDSGVHALE 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M+ A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLSV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|306820983|ref|ZP_07454602.1| tRNA pseudouridine synthase A [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550924|gb|EFM38896.1| tRNA pseudouridine synthase A [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 245

 Score =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 134/248 (54%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I Y+G+ Y GWQRQKN  SIQ  IE AI L+  E + V  +GRTD+GVHAL Q
Sbjct: 1   MRNILLEISYDGTNYSGWQRQKNAISIQEKIEDAISLICNEEINVIASGRTDAGVHALSQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A+F            KA+N  L   D I IL+   VD+ F+ARFSA +++Y+Y I+ R+
Sbjct: 61  IANFSTSSSIDAKKFAKAINTKL--PDDIRILSSKEVDEDFNARFSAKKKTYIYHILNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNS 179
                    +  I + LD E M+  +  L+G HDFT+F +       + I+TI   D+  
Sbjct: 119 IKNPFWDKYSMHINRKLDLELMKSNSNMLIGTHDFTSFYTYEENNPKNTIKTIYSSDIVK 178

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            + +++   +    FL+  +R  VG+L  +G  +    D+ + L  +DR + G  A  +G
Sbjct: 179 IYEDILTFSITGDGFLYNMVRIIVGTLIEIGLHQKN-DDISQILMYKDRIKAGATAKAKG 237

Query: 239 LYFDSVEY 246
           L+  +VEY
Sbjct: 238 LFLKNVEY 245


>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 =  289 bits (740), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 98/244 (40%), Positives = 139/244 (56%), Gaps = 2/244 (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 VEYS 247
           VEY 
Sbjct: 247 VEYP 250


>gi|323141117|ref|ZP_08076020.1| tRNA pseudouridine synthase A [Phascolarctobacterium sp. YIT 12067]
 gi|322414383|gb|EFY05199.1| tRNA pseudouridine synthase A [Phascolarctobacterium sp. YIT 12067]
          Length = 250

 Score =  289 bits (740), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++ Y+GS Y G+Q+QKN  ++Q  +E+A+ ++ GE VV  G+GRTD+GVHAL Q
Sbjct: 1   MRTIKLVVAYDGSAYHGFQKQKNVQTVQNVLEEALTMLCGEKVVTAGSGRTDTGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F          L +A  + L   + I +++   + + FHARFSA  ++Y Y+++  +
Sbjct: 61  TVTFTTNGRIPCANLVRAAASLL--PEDIVVVSAEEMPEGFHARFSARWKTYHYKLLVNE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    AW + + L+ + M  AA+ L+G HDF+ FRS     +SPI+TI        
Sbjct: 119 HVNPFMVRYAWQLRQQLEVKAMNEAAELLLGTHDFSAFRSSGSVDTSPIKTIFAAKWQQQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I  R+    FL+  +R+ V S+  VG GK T  D    L AQ  +     AP +GLY
Sbjct: 179 GEEILFRISGDGFLYHMVRNIVWSMVQVGMGKRTVQDFAAELTAQRCEFLNEPAPAQGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAEVGY 244


>gi|229003158|ref|ZP_04161004.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock1-4]
 gi|228758121|gb|EEM07320.1| tRNA pseudouridine synthase A [Bacillus mycoides Rock1-4]
          Length = 252

 Score =  289 bits (740), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGINFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHARG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I +  +    + FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWMNALNTML--PDDIVVRQVEKKIEDFHARYGVERKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+ E++R A  + +G HDFT+F S        +RTI   D+  
Sbjct: 124 KNADVFRRNYVYQYPYPLEIESIRKAIPYFIGTHDFTSFCSTKTDKKDKVRTIYEIDLME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  +G GK     + + L+ QDR+  G + P  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSIGQGKMVPDSIPEILKKQDRRFAGKMVPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  289 bits (740), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 119/251 (47%), Positives = 163/251 (64%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP+ L++GR W +   LD + MR  AQHL+G HDFTTFRS  CQA+SPI+T+D  +++  
Sbjct: 120 APVTLDRGRVWHVRPKLDIDAMRAGAQHLIGMHDFTTFRSTICQAASPIKTLDAIEISEH 179

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLAGVSYP 250


>gi|149021302|ref|ZP_01835548.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP23-BS72]
 gi|168491513|ref|ZP_02715656.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC0288-04]
 gi|225861429|ref|YP_002742938.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298229625|ref|ZP_06963306.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae str. Canada
           MDR_19F]
 gi|298254115|ref|ZP_06977701.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae str. Canada
           MDR_19A]
 gi|298503335|ref|YP_003725275.1| tRNA-pseudouridine synthase I [Streptococcus pneumoniae
           TCH8431/19A]
 gi|254764872|sp|C1CSL6|TRUA_STRZT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|147930403|gb|EDK81387.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP23-BS72]
 gi|183574268|gb|EDT94796.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC0288-04]
 gi|225728219|gb|ACO24070.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298238930|gb|ADI70061.1| tRNA-pseudouridine synthase I [Streptococcus pneumoniae
           TCH8431/19A]
 gi|327389783|gb|EGE88128.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA04375]
 gi|332073932|gb|EGI84410.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA41301]
          Length = 249

 Score =  289 bits (740), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVAADFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|114567807|ref|YP_754961.1| pseudouridylate synthase [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|122317314|sp|Q0AUL4|TRUA_SYNWW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|114338742|gb|ABI69590.1| Pseudouridylate synthase [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
          Length = 249

 Score =  289 bits (740), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++EY+GS Y G+Q QKN +++Q  +EKAI+ ++GE   +  AGRTD+GVHA  Q
Sbjct: 1   MSRIKLLLEYDGSNYHGFQLQKNANTVQAELEKAIYRLSGERATIVCAGRTDAGVHAWGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD            ALN+ L   + I +L       +F+ RF A+++ Y Y I  ++
Sbjct: 61  VVAFDSCSTIPGDRWAYALNSQL--PEDIQVLESQETRAEFNPRFDALKKCYGYLIYRQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A    + L  E M+ AA+ L GR +F +F +    A +  R I H  ++  
Sbjct: 119 KKATFYRHYALCNTEPLKLEAMQEAAEILKGRQNFRSFCASGSSARTFEREIFHCRLSEK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + + + A  FL+  +R   G+L  VG GK+    L + + +QDR   GP APP+GLY
Sbjct: 179 GPCLLLHIAADGFLYNMVRIITGTLLEVGKGKYPPQHLREIIASQDRTRAGPTAPPQGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LLQVFYP 245


>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 =  289 bits (740), Expect = 3e-76,   Method: Composition-based stats.
 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|42518460|ref|NP_964390.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii NCC 533]
 gi|51316717|sp|Q74L59|TRUA_LACJO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|41582745|gb|AAS08356.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii NCC 533]
          Length = 263

 Score =  289 bits (740), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  Q
Sbjct: 3   TRYKLTMAYDGHLFHGFQIQPNQRTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +E     +  ALNA +            IVD+ FH ++S   + Y Y +   
Sbjct: 63  VIHFDYPGKEIPAKNMMLALNALM--PIDTVFFESEIVDEDFHVQYSTKGKWYRYVVDQH 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++  
Sbjct: 121 RFTDPFNRFYTGHYPYPLDISLMKQAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITP 180

Query: 180 FGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +   I    +   FL+  +R  VG+L  +G+ K    D+ + L+A+DR+E    AP  
Sbjct: 181 DPDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLKAKDRQEVRTTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLQQVFYE 250


>gi|171777516|ref|ZP_02919238.1| hypothetical protein STRINF_00067 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171283226|gb|EDT48650.1| hypothetical protein STRINF_00067 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 249

 Score =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G  + G+QRQ +  S+Q  +EK +  + +G+ V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKATISYDGRLFAGFQRQPSERSVQEELEKTLQRLNSGQPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++ + +V   FH+R++   ++Y + + + 
Sbjct: 61  QVVHFDLPQARDVEKLRFGLDT--QSPEDIDVVKVELVSDDFHSRYNKHSKTYEFLVDSG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI     D+
Sbjct: 119 RPKNPMMRHYATHYPYPLDLALMQEAIKDLVGTHDFTGFTASGTSVENKVRTITRATVDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L +++R   GP A   
Sbjct: 179 DEKTGFFVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTVLASKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYD 248


>gi|307709543|ref|ZP_07645997.1| tRNA pseudouridine synthase A [Streptococcus mitis SK564]
 gi|307619674|gb|EFN98796.1| tRNA pseudouridine synthase A [Streptococcus mitis SK564]
          Length = 249

 Score =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLRV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|291530837|emb|CBK96422.1| pseudouridylate synthase I [Eubacterium siraeum 70/3]
          Length = 250

 Score =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/249 (34%), Positives = 123/249 (49%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + YNG+ Y G+QRQ N +SIQ ++E+ +  +  E + ++G  RTD+GVHA   
Sbjct: 1   MRNLKVTMAYNGTAYHGYQRQNNANSIQQTVEEVLSKLLCEDITINGCSRTDTGVHARAF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +             K  NA L     I+ L+   +   FHARF +  + Y+YRI T  
Sbjct: 61  VFNVKTNCPIPCEGFIKGGNALL--PQDIAFLSCEDMPDSFHARFDSKGKEYIYRIYTGD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDVN 178
                    A   P   D E MR AA+ +VG HDF +F     +    + +RT+   DV 
Sbjct: 119 VRDVFSADTALHYPYKPDIEKMRKAARLIVGEHDFASFCKAEAKEHLLTTVRTVYSIDVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +EI+V    FLH  +R  VG+L  + +GK T  D+  AL   DR+  G   PP G
Sbjct: 179 QTGDFVEIKVCGNGFLHNMVRIIVGTLIYISEGKRTEQDIINALTKPDREFAGKTVPPCG 238

Query: 239 LYFDSVEYS 247
           LY + V Y 
Sbjct: 239 LYLNKVFYE 247


>gi|293572050|ref|ZP_06683062.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
 gi|291607912|gb|EFF37222.1| tRNA pseudouridine synthase A [Enterococcus faecium E980]
          Length = 246

 Score =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     +   +N YL     I I  +  + ++FHAR++A+ + Y Y +   
Sbjct: 61  QVANFKTNSEIGLAEMIDFMNRYL--PRDIVIKRIEEMPERFHARYNAVGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  P+ LD + +  A + L+G HDF  F ++     S +RTID   +  
Sbjct: 119 VIPSAFERNHSFYFPQELDMDKLNAACEKLMGTHDFIGFSALKKSKKSTVRTIDELSIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++    V   FL+  +R  +G+L  +G        +++  +++ R+  G   P +GL
Sbjct: 179 KGEMLHFTFVGDGFLYKMVRIIMGTLLEIGTSAMPIETIDEIFESKVRQHAGETVPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>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 =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 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|322377359|ref|ZP_08051850.1| tRNA pseudouridine synthase A [Streptococcus sp. M334]
 gi|321281559|gb|EFX58568.1| tRNA pseudouridine synthase A [Streptococcus sp. M334]
          Length = 249

 Score =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVLHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMSRYYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLKV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|225387194|ref|ZP_03756958.1| hypothetical protein CLOSTASPAR_00946 [Clostridium asparagiforme
           DSM 15981]
 gi|225046673|gb|EEG56919.1| hypothetical protein CLOSTASPAR_00946 [Clostridium asparagiforme
           DSM 15981]
          Length = 259

 Score =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 125/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q N  +I+  + KA+  +  E + V GA RTD+GVHA   
Sbjct: 7   MRRIRLVVAYDGTNYHGWQYQPNAVTIEEVLNKALTELLREPIAVIGASRTDAGVHAQGN 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C A+N  L   + I + +   V   +H R     ++Y Y+I+ R+
Sbjct: 67  VAVFDTKNRMAADKICLAVNQRL--PEDIRVQSSEEVATDWHPRKRRCVKTYEYKILNRR 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  ++   +     LD E MR AA+ ++G HDF +F S   Q +  +RT+    +   
Sbjct: 125 IEMPDKRLYTYHCYYDLDLEKMRQAAEFILGEHDFKSFCSAKTQVTDTVRTVYDLKLERD 184

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             ++I IR+    FL+  +R   G+L   G G      + + L A+DR++ GP AP +GL
Sbjct: 185 QEDVITIRITGSGFLYNMVRIIAGTLLWAGTGLIRPEAVGEILAAEDRRKAGPTAPAKGL 244

Query: 240 YFDSVEYS 247
               + Y 
Sbjct: 245 TLIRMHYP 252


>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 =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 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+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  VAHCDMDKDWDPFRLSEALNHHLR-PAPVAILRAARVADDWHARFSAYERRYIFRLLSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           APL +E G+ W +  +LD + MR  A HL+G HDFTTFRS  CQA SP++TID   +   
Sbjct: 120 APLTVENGQFWRVGHALDADLMRAGAAHLIGLHDFTTFRSSICQAKSPVKTIDEISITEI 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|49083216|gb|AAT50973.1| PA3114 [synthetic construct]
          Length = 286

 Score =  289 bits (739), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 98/246 (39%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + IEY GS Y GWQRQ     S+Q ++E+A   V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGIEYKGSRYRGWQRQEAGVPSVQEALERASSKVAAEPVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANL--PADISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD   MR AAQ LVG HDFT+FR++ CQA SP++T+ H  +   G
Sbjct: 137 RPAHLAEEVTWNHRPLDIGRMREAAQVLVGTHDFTSFRAVQCQAKSPVKTMHHVRLLEHG 196

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+  G L  +G G+      ++ L+A+DR+  G  A P GLY 
Sbjct: 197 RLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLEARDRRAGGVTAHPYGLYL 256

Query: 242 DSVEYS 247
             VEY 
Sbjct: 257 VRVEYP 262


>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 =  289 bits (739), Expect = 4e-76,   Method: Composition-based stats.
 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|148548973|ref|YP_001269075.1| tRNA pseudouridine synthase A [Pseudomonas putida F1]
 gi|148513031|gb|ABQ79891.1| tRNA pseudouridine synthase A [Pseudomonas putida F1]
          Length = 332

 Score =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 122/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ Y GWQRQ     S+Q ++E+A+  V  E + V  AGRTD+GVH   QV
Sbjct: 66  RIALGVEYKGARYRGWQRQASGVPSVQQALEQALSKVANEPISVVCAGRTDAGVHGCGQV 125

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N  L     IS++    +   FHARF A  R Y Y I     
Sbjct: 126 VHFDTRAVRDERAWTMGTNFNL--PHDISVVWSRPMPADFHARFKACARRYRYVIYNDPI 183

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD + M  AAQ L+G HDF+ FR+  CQA SPI+ I H  V   G
Sbjct: 184 RPAHLAEEVTWNHRPLDVDRMAEAAQFLLGTHDFSAFRASQCQAKSPIKHIYHLRVTRHG 243

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + V A +FLH  +R+  G L  +G G+       + L+ ++R+E G  A P GLY 
Sbjct: 244 QMIVLDVRATAFLHHMVRNIAGVLMAIGAGERPVAWAREVLEGRNRREGGVTAHPYGLYL 303

Query: 242 DSVEYS 247
             VEY 
Sbjct: 304 VQVEYP 309


>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 =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 93/247 (37%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 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|323126548|gb|ADX23845.1| tRNA pseudouridine synthase A [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 249

 Score =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  ++Q  IEK +  +  G+ V +HGAGRTD+GVHA  
Sbjct: 1   MTRYKATISYDGTLFSGFQRQSHARTVQEEIEKTLQKLASGQPVPIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  D I +++L+IV   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDLEKLRFALDT--QTPDDIDVVDLAIVADDFHCRYQKHSKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDINKMQEAIKDLVGTHDFTGFTAAGTSVENKVRTITEATLVQ 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DDKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVEQIKVILDSKNRQLAGPTPAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+G GY GWQ+Q    S+Q  +E A+  V G  + V  AGRTD+GVHAL QV
Sbjct: 12  VKIVLALEYDGRGYCGWQKQPGCLSVQSRLESALSGVAGRQIQVVAAGRTDAGVHALCQV 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H +           +  NA L     ISIL  S V   FHARFSA  R+YLY +++R A
Sbjct: 72  VHLETCVRRPLNAWIRGTNALL--PGDISILEASEVSDDFHARFSATERTYLYYLLSRPA 129

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  G+   +   LD E M++AA+ L+G+HDF+ FRS  CQ+ + IR +   +++   
Sbjct: 130 RPGIHHGKIGWVHYPLDLEKMQMAAKLLIGKHDFSAFRSSECQSRTAIRQLTRLNISQHQ 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L      A +FLH  +R+ +G L  +G GK+    +   L+ +DR    P   P+GLY 
Sbjct: 190 QLFVFEFCANAFLHHMVRNILGGLVYIGRGKYPPEWMRILLEKRDRTLAAPTFSPDGLYL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 SGVRYD 255


>gi|217966203|ref|YP_002351881.1| tRNA pseudouridine synthase A [Listeria monocytogenes HCC23]
 gi|254789639|sp|B8DB42|TRUA_LISMH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217335473|gb|ACK41267.1| tRNA pseudouridine synthase A [Listeria monocytogenes HCC23]
 gi|307572187|emb|CAR85366.1| tRNA pseudouridine synthase A [Listeria monocytogenes L99]
          Length = 248

 Score =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRDFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>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 =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 87/244 (35%), Positives = 130/244 (53%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + +E+NG+ Y GWQRQ+    +Q  +E+ +  +  E + V  AGRTD+GVH    +AH
Sbjct: 39  YALGVEFNGANYRGWQRQQEVLCVQQVLEETLSKIANEPIEVVAAGRTDAGVHGGNMLAH 98

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F    +       +  N+ L   D I+I  +  +   FHARF AI R Y Y  + +    
Sbjct: 99  FTTSAKRGVYNWLRGANSLL--PDDIAIRWIQPMPDTFHARFGAIARRYRYITLNQPQRP 156

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+       I + LD   M+ AA+H+VG HDF++FR+  CQ+  P+R I H  +   G  
Sbjct: 157 AVLNHLVTHIHEPLDLALMQQAAEHIVGTHDFSSFRAAACQSKQPVRNIHHAKLFKHGEF 216

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I   + A  FLH  +R+ +G+L  +G G+    D  + LQA+DR    P APP+GLYF +
Sbjct: 217 IVFDIQADGFLHHMVRNLMGTLFAIGKGELQPEDYLRILQAKDRTIAPPTAPPDGLYFIN 276

Query: 244 VEYS 247
             Y 
Sbjct: 277 AYYP 280


>gi|311111209|ref|ZP_07712606.1| tRNA pseudouridine synthase A [Lactobacillus gasseri MV-22]
 gi|311066363|gb|EFQ46703.1| tRNA pseudouridine synthase A [Lactobacillus gasseri MV-22]
          Length = 263

 Score =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  Q
Sbjct: 3   TRYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +E     +  ALNA +         +  IVD  FH ++S   + Y Y +   
Sbjct: 63  VIHFDYPGKEIPAKNMMLALNALM--PIDTVFFDSEIVDSDFHVQYSTKGKWYRYIVDQH 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++ S
Sbjct: 121 RFTDPFNRFYTGHYPYPLDIALMKKAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITS 180

Query: 180 FGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +   I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    AP  
Sbjct: 181 DPDNKKIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLQHVFYE 250


>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 =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 127/247 (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   MVRLALGVEYAGDRFEGWQSQRHGRTVQDALEAALSRIAGEAVKLHCAGRTDTGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD           + +N +L     +++     VD  FHARF A  R Y Y +    
Sbjct: 61  VAHFDTAAVRPLSAWIRGVNTHL--PAGVAVRWAVEVDDAFHARFLAYERRYRYVLFNAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL  GR       LD   M  AA+ LVG  DF+ FR+  CQA +P+R +    V   
Sbjct: 119 TRPALLAGRVGWFHLPLDEGAMAEAARCLVGMQDFSAFRAAECQAKTPVRDMREVRVQRS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +     A  FLH  IR+ VG+L  VG G++    L + L  +DR    P   P+GLY
Sbjct: 179 GDYLIFDFRADGFLHHMIRNLVGALVYVGKGRYPPGWLAEVLAGRDRSRAAPTFAPDGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LCGVSYP 245


>gi|170720741|ref|YP_001748429.1| tRNA pseudouridine synthase A [Pseudomonas putida W619]
 gi|169758744|gb|ACA72060.1| tRNA pseudouridine synthase A [Pseudomonas putida W619]
          Length = 284

 Score =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + +EY GS Y GWQRQ     S+Q ++E+A+  V  E + V  AGRTD+GVH   Q
Sbjct: 17  TRIALGVEYKGSRYRGWQRQASGVPSVQQALEQALSKVANEPITVVCAGRTDAGVHGCGQ 76

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD              N  L     IS++    +   FHARF A  R Y Y I    
Sbjct: 77  IVHFDTRANRDERAWTLGTNFNL--PHDISVVWSRPMPADFHARFKATARRYRYVIYNDP 134

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A          + LD E M  AAQ L+G HDF+ FR+  CQA SPI+ I H  V   
Sbjct: 135 IRPAHLAEEVTWNHRPLDVERMADAAQFLLGTHDFSAFRASQCQAKSPIKHIHHLRVTRH 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I + V A +FLH  +R+  G L  +G G+  +    + L+ ++R+E G  A P GLY
Sbjct: 195 GQMIVLDVRATAFLHHMVRNIAGVLMTIGAGERPAGWAREVLEGRNRREGGVTAHPYGLY 254

Query: 241 FDSVEYS 247
              VEY 
Sbjct: 255 LVQVEYP 261


>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 =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 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|311105424|ref|YP_003978277.1| tRNA pseudouridine synthase A [Achromobacter xylosoxidans A8]
 gi|310760113|gb|ADP15562.1| tRNA pseudouridine synthase A [Achromobacter xylosoxidans A8]
          Length = 269

 Score =  288 bits (738), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 87/249 (34%), Positives = 134/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +  ++Q ++E A+    G    V    AGRTD+GVH  
Sbjct: 1   MSRVALGLAYDGSAWQGWQTQPHRQTVQDTLEAALGSFCGVKGPVATICAGRTDTGVHGA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H D   +       + +NA+L    +IS+     V  +FHARFSA  R+Y+Y +  
Sbjct: 61  MQVVHLDTELDRRMESWVRGVNAFL--PSSISVQWAQPVSDEFHARFSARARTYVYLLWR 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +   AL  GRA    + LD + MR AA  L+G HDF++FRS  CQA  P+R +   D++
Sbjct: 119 GRVRPALWAGRAGWCFQPLDVDAMRTAANALLGEHDFSSFRSSQCQAKHPVRHLYRLDID 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A +FLH  +R+ +G+L  +G G+     + + L  +DRK   P   P+G
Sbjct: 179 ERGPFLVFTLKANAFLHHMVRNIMGALLQIGQGREPVDWMAQLLSWRDRKLGAPTFAPDG 238

Query: 239 LYFDSVEYS 247
           LY  +++Y 
Sbjct: 239 LYLSAIDYP 247


>gi|227356152|ref|ZP_03840541.1| tRNA pseudouridine synthase A [Proteus mirabilis ATCC 29906]
 gi|227163616|gb|EEI48532.1| tRNA pseudouridine synthase A [Proteus mirabilis ATCC 29906]
          Length = 289

 Score =  288 bits (738), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 27  KIALGIEYDGSHYYGWQRQNEVRSVQERLEKALSQVANEPISVFCAGRTDAGVHATGQVV 86

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +N +L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 87  HFETTAHRKDAAWTMGVNTHL--PQDIAVRWVKTVANDFHARFSATARRYRYVIFNHRYR 144

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G+
Sbjct: 145 PAILSSGVTHFHYPLDAQRMHQAAQCLLGENDFTSFRAVQCQSRTPWRNVMHVNVSRYGD 204

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G    T + + L  +DR +    A   GLY  
Sbjct: 205 YVVVDIKANAFVHHMVRNIVGSLLEIGCGNQAITWMAELLALKDRTKAAATAKANGLYLV 264

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 265 SVDYP 269


>gi|148997657|ref|ZP_01825221.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP11-BS70]
 gi|168575203|ref|ZP_02721166.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae MLV-016]
 gi|194397044|ref|YP_002038227.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae G54]
 gi|307068239|ref|YP_003877205.1| pseudouridylate synthase [Streptococcus pneumoniae AP200]
 gi|238690845|sp|B5E6N8|TRUA_STRP4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|147756156|gb|EDK63198.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP11-BS70]
 gi|183578806|gb|EDT99334.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae MLV-016]
 gi|194356711|gb|ACF55159.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae G54]
 gi|306409776|gb|ADM85203.1| Pseudouridylate synthase [Streptococcus pneumoniae AP200]
 gi|332199640|gb|EGJ13715.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA41317]
          Length = 249

 Score =  288 bits (738), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFILDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|168493506|ref|ZP_02717649.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC3059-06]
 gi|183576362|gb|EDT96890.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC3059-06]
          Length = 249

 Score =  288 bits (738), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVLHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E MR A + L G HDFT F +        IRTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMREAIKKLEGTHDFTGFTASGTSVEDKIRTITEASLTV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>gi|329666723|gb|AEB92671.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii DPC 6026]
          Length = 263

 Score =  288 bits (738), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  Q
Sbjct: 3   TRYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +E     +  ALNA +            IVD+ FH ++S   + Y Y +   
Sbjct: 63  VIHFDYPGKEIPAKNMMLALNALM--PIDTVFFESEIVDEDFHVQYSTKGKWYRYIVDQH 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++  
Sbjct: 121 RFTDPFNRFYTGHYPYPLDISLMQQAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITP 180

Query: 180 FGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +   I    +   FL+  +R  VG+L  +G+ K    D+ + L+A+DR+E    AP  
Sbjct: 181 DSDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLKAKDRQEVRTTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLQQVFYE 250


>gi|168483521|ref|ZP_02708473.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1873-00]
 gi|172043050|gb|EDT51096.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CDC1873-00]
          Length = 249

 Score =  288 bits (738), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYVFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVLHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E MR A + L G HDFT F +        IRTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMREAIKKLEGTHDFTGFTASGTSVEDKIRTITEASLTV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>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 =  288 bits (738), Expect = 5e-76,   Method: Composition-based stats.
 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|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 =  288 bits (737), Expect = 5e-76,   Method: Composition-based stats.
 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|169830466|ref|YP_001716448.1| tRNA pseudouridine synthase A [Candidatus Desulforudis audaxviator
           MP104C]
 gi|238688213|sp|B1I1B5|TRUA_DESAP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169637310|gb|ACA58816.1| tRNA pseudouridine synthase A [Candidatus Desulforudis audaxviator
           MP104C]
          Length = 250

 Score =  288 bits (737), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + + Y+G+ Y G+Q+Q      +IQ ++E+ +  ++G  + V GA RTD+GVHA 
Sbjct: 1   MPNVRLTLAYDGTAYHGFQKQSGSGLPTIQETLERCLAELSGAALKVTGASRTDAGVHAR 60

Query: 59  RQVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV +F   R       +  ALN  L     I+ L+   V   FHAR+SA+ ++Y Y + 
Sbjct: 61  GQVVNFVTGRWGIPTERIPAALNGVL--PGDIAALDAREVPADFHARYSAVAKTYSYTLY 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                   ++  +  +P++LD   MR+AA+HL+GRHDF+TF++      S +RT+   D+
Sbjct: 119 NHPVRSPFQRLYSLHVPRALDLRAMRLAARHLMGRHDFSTFQAAGRPVQSAVRTLTRADI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +   L+ +   A  FL+  +R   G+L  VG  +     L   + + DR   GP  PP 
Sbjct: 179 EAQAPLVRLVFRADGFLYNMVRIMAGTLLEVGLERLDPEALPDIIASGDRARAGPTVPPH 238

Query: 238 GLYFDSVEYS 247
           GL  + VEY 
Sbjct: 239 GLCLEEVEYD 248


>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 =  288 bits (737), Expect = 5e-76,   Method: Composition-based stats.
 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|331268447|ref|YP_004394939.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
 gi|329124997|gb|AEB74942.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
          Length = 246

 Score =  288 bits (737), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 131/248 (52%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   +IIEY+GS Y GWQ+QK+  ++Q  IE+AI  +T     + G  RTD+GVHA  
Sbjct: 1   MKKNVKLIIEYDGSNYSGWQKQKHSITVQQKIEEAISQITKTDTEIIGCSRTDAGVHARN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+F       P     A+N+ L     I I   S V   FHARF +  + Y+Y I+ R
Sbjct: 61  FVANFITNSSVPPSKFKYAINSKL--PKDIVIKKSSEVSLDFHARFHSKGKKYVYTILNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVN 178
           + P  +++   +   K L+ + M+ A+++ +G H+F +F +       S +RTI + DV 
Sbjct: 119 EEPPTIDRNVMYHFNKDLNVDAMKEASKYFIGSHEFDSFYKKSGSSVKSTLRTIYYCDVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              ++I+  V+   FL+  +R   G+L   G G+    +++  + A+DR+  G   PP+G
Sbjct: 179 KCEDVIKFTVIGEGFLYNMVRIMAGTLIEAGIGRIKPEEIKFIILAKDRERAGRSLPPQG 238

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 239 LCLQEVLY 246


>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 =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 103/246 (41%), Positives = 153/246 (62%), 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 + +    + + N  +VD  FHARFSAI R Y+YRI+ R 
Sbjct: 61  IAHFDLSKYFEPYKIIRAINYFTR-PYIVGVCNCELVDNNFHARFSAIARHYVYRILNRP 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|42559741|sp|Q7MB17|TRUA_PHOLL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 264

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   S+QG +E+A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYDGSRYYGWQRQQEVKSVQGCLEEALSKVADEPISVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +N +L     I++  +  VD+ FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETSVQRKDAAWTMGVNVHL--PPDIAVRWVKTVDEGFHARFSATARRYRYIIFNHRY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ ++G +DFT+FR++ CQ+ +P R + H +VN +G
Sbjct: 119 RPAVLANGVTHFHYPLDEKRMHQAAQCILGENDFTSFRAVQCQSKTPWRNVMHINVNRYG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  +G G      + + L  +DR +    A   GLY 
Sbjct: 179 HYVVIDIKANAFVHHMVRNIAGSLMEIGCGNQDINWMAQLLALKDRAKAAATAKAAGLYL 238

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 239 VAVDYP 244


>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 =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 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|288904465|ref|YP_003429686.1| tRNA pseudouridylate synthase I [Streptococcus gallolyticus UCN34]
 gi|306830500|ref|ZP_07463669.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|306832735|ref|ZP_07465871.1| tRNA pseudouridine synthase A [Streptococcus bovis ATCC 700338]
 gi|325977479|ref|YP_004287195.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|288731190|emb|CBI12738.1| tRNA pseudouridylate synthase I [Streptococcus gallolyticus UCN34]
 gi|304425084|gb|EFM28214.1| tRNA pseudouridine synthase A [Streptococcus bovis ATCC 700338]
 gi|304427346|gb|EFM30449.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325177407|emb|CBZ47451.1| tRNA pseudouridine synthase A [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 249

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G  + G+QRQ +  S+Q  +EK +  + +G  V VHGAGRTDSGVHA  
Sbjct: 1   MVRYKATISYDGRLFAGFQRQPSERSVQEELEKTLQKLNSGNPVKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  + I ++ +  V  +FHAR++   ++Y + +   
Sbjct: 61  QVVHFDLPQARDVEKLRFGLDT--QSPEDIDVVKVEQVSDEFHARYNKHSKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD  +M+ A + LVG HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLDLTSMQEAIKDLVGTHDFTGFTASGTSVENKVRTITRATVAI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +              FL+ Q+R+ VG+L  +G+G+   + ++  L++++R   GP A   
Sbjct: 179 DDKTGFFVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQIKTVLESKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEINYD 248


>gi|322386788|ref|ZP_08060412.1| tRNA pseudouridine synthase A [Streptococcus cristatus ATCC 51100]
 gi|321269070|gb|EFX52006.1| tRNA pseudouridine synthase A [Streptococcus cristatus ATCC 51100]
          Length = 249

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  +I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ +V+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKALISYDGHDFAGFQRQPHARSVQEEIEKTLTRINKGQPIVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++++  V + FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLPSARDEEKLRFALDT--QTPEDIDVISVEEVTEDFHARYKPHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   M  A + L G HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLEIPLMEQAIKALEGTHDFTGFTASGTSVENKVRTITKASLTF 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +E+ L+ +DR+  GP A P 
Sbjct: 179 DAQRNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVNQIERILEEKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|167750462|ref|ZP_02422589.1| hypothetical protein EUBSIR_01438 [Eubacterium siraeum DSM 15702]
 gi|167656613|gb|EDS00743.1| hypothetical protein EUBSIR_01438 [Eubacterium siraeum DSM 15702]
          Length = 250

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 123/249 (49%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + YNG+ Y G+QRQ N +SIQ ++E+ +  +  E + ++G  RTD+GVHA   
Sbjct: 1   MRNLKVTMAYNGTAYHGYQRQNNANSIQQTVEEVLSKLLCEDITINGCSRTDTGVHARAF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +             K  NA L     I+ L+   +   FHARF +  + Y+Y+I T  
Sbjct: 61  VFNVKTNCPIPCEGFIKGGNALL--PQDIAFLSCEDMPDSFHARFDSKGKEYIYKIYTGD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDVN 178
                    A   P   D E MR AA+ +VG HDF +F     +    + +RT+   DV 
Sbjct: 119 VRDVFSADTALHYPYKPDIEKMRKAARLIVGEHDFASFCKAEAKEHLLTTVRTVYSIDVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +EI+V    FLH  +R  VG+L  + +GK T  D+  AL   DR+  G   PP G
Sbjct: 179 QTGDFVEIKVCGNGFLHNMVRIIVGTLIYISEGKRTEQDIINALTKPDREFAGKTVPPCG 238

Query: 239 LYFDSVEYS 247
           LY + V Y 
Sbjct: 239 LYLNKVFYE 247


>gi|319945640|ref|ZP_08019892.1| tRNA pseudouridine synthase A [Streptococcus australis ATCC 700641]
 gi|319748239|gb|EFW00481.1| tRNA pseudouridine synthase A [Streptococcus australis ATCC 700641]
          Length = 248

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 123/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  S+Q  IEK +  +  G  V +HGAGRTD+GVHAL 
Sbjct: 1   MTRYKATISYDGTLFAGFQRQPHARSVQEEIEKTLMRLNQGNPVTIHGAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L  AL+   +  + I  + +  V   FH+R+    ++Y + +   
Sbjct: 61  QVIHFDLPQPRDEEKLRFALDT--QTPEDIDFIRVEQVPDDFHSRYQKHSKTYEFIVDYG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD   M+ A Q L G HDFT F +        +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDVAKMQAAIQKLEGTHDFTGFTASGTSVEDKVRTITEARLVE 178

Query: 180 FGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ QIR+ VG+L  +G+G+     ++  L+ +DR   GP A P 
Sbjct: 179 DAEHHRLVFTFSGNGFLYKQIRNMVGTLLKIGNGRMPVDQIDLILEKKDRNLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|15903494|ref|NP_359044.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae R6]
 gi|116516785|ref|YP_816881.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae D39]
 gi|148988650|ref|ZP_01820083.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP6-BS73]
 gi|149004327|ref|ZP_01829087.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS69]
 gi|169833383|ref|YP_001694996.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182684548|ref|YP_001836295.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CGSP14]
 gi|221232354|ref|YP_002511507.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae ATCC
           700669]
 gi|225855038|ref|YP_002736550.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae JJA]
 gi|237649225|ref|ZP_04523477.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CCRI 1974]
 gi|237822076|ref|ZP_04597921.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CCRI
           1974M2]
 gi|307127806|ref|YP_003879837.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 670-6B]
 gi|38258775|sp|Q8CWQ1|TRUA_STRR6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122278273|sp|Q04JF7|TRUA_STRP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238688376|sp|B1ID11|TRUA_STRPI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238691180|sp|B2IRB1|TRUA_STRPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764868|sp|B8ZM12|TRUA_STRPJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764870|sp|C1CFH9|TRUA_STRZJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|15459107|gb|AAL00255.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae R6]
 gi|116077361|gb|ABJ55081.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae D39]
 gi|147757704|gb|EDK64720.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP14-BS69]
 gi|147925851|gb|EDK76926.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae SP6-BS73]
 gi|168995885|gb|ACA36497.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182629882|gb|ACB90830.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae CGSP14]
 gi|220674815|emb|CAR69389.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae ATCC
           700669]
 gi|225723432|gb|ACO19285.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae JJA]
 gi|306484868|gb|ADM91737.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae 670-6B]
 gi|332072765|gb|EGI83246.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA17545]
 gi|332200155|gb|EGJ14228.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae GA47368]
          Length = 249

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|315612755|ref|ZP_07887666.1| tRNA pseudouridine synthase A [Streptococcus sanguinis ATCC 49296]
 gi|315314865|gb|EFU62906.1| tRNA pseudouridine synthase A [Streptococcus sanguinis ATCC 49296]
          Length = 274

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 26  MTRYKATISYDGFAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 85

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + +   
Sbjct: 86  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEFIVDRG 143

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M++A + L G HDFT F +        +RTI      V
Sbjct: 144 RPKNPMRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTSVEDKVRTITEARLSV 203

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 204 DETGQFLTFSFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILKKKDRQLAGPTAAPN 263

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 264 GLYLKEIRYE 273


>gi|158320711|ref|YP_001513218.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
 gi|158140910|gb|ABW19222.1| tRNA pseudouridine synthase A [Alkaliphilus oremlandii OhILAs]
          Length = 245

 Score =  288 bits (737), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 80/247 (32%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    ++IEY+GS Y GWQR K+   +IQG IEK +  +TG  V + G+GRTD+GVHA  
Sbjct: 1   MRNIKLVIEYDGSRYDGWQRLKDSEQTIQGKIEKVLNEMTGSSVEIIGSGRTDAGVHAKN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+A+F          +   +N YL     I +  +  V  +FH+R++A ++ Y Y +   
Sbjct: 61  QIANFKTKSSMSIRDIHNYMNHYL--PQDIVVKEVKEVSDRFHSRYNAQKKKYTYYVWNH 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P A ++  ++  P++LD + M  AA  L+G HDF  F S+     S +RTI+   +  
Sbjct: 119 RIPSAFQRKYSYYFPETLDLQRMEAAANQLLGTHDFIGFSSVKKAKKSTVRTIEEITIVQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +++E   +   FLH  IR  +G+L  +G  +   + +++   ++ R   G  AP +GL
Sbjct: 179 NNHMLEFSFIGDGFLHNMIRILMGTLLEIGTREKDISCIDEIFTSKTRAMAGKTAPAQGL 238

Query: 240 YFDSVEY 246
           + + V Y
Sbjct: 239 FLEEVYY 245


>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 =  287 bits (736), Expect = 6e-76,   Method: Composition-based stats.
 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|291528184|emb|CBK93770.1| pseudouridylate synthase I [Eubacterium rectale M104/1]
          Length = 254

 Score =  287 bits (736), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 130/246 (52%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
             Y +I+ Y+G+ Y GWQ QK+   +IQG ++  +  + G+ V V G+GRTD+GVHA+ Q
Sbjct: 6   QNYKIIVAYDGTRYKGWQVQKSTDDTIQGKLQHVLSTLAGKPVEVIGSGRTDAGVHAVGQ 65

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F + + +    +   LN +L     I++ ++S V  +FHAR++A+ ++Y+Y I T  
Sbjct: 66  VASFHMPKHFSKDEIFIWLNEHL--PADIAVTDISNVPDRFHARYNAVSKTYVYTIHTGI 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   +   K LD + M+ AA +L+G HDF  F        S +RTI   D+   
Sbjct: 124 VSDVFRRKYVYDYDKPLDTDRMKKAAAYLLGEHDFKAFCGNKHMKKSTVRTIFSIDIEKT 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I      FL   IR   G+L  VGDG+     +   L ++DR + G  AP  GL 
Sbjct: 184 GADIVISYTGDGFLQNMIRIITGTLIEVGDGRKNPDAVMGILASKDRAQAGYTAPACGLS 243

Query: 241 FDSVEY 246
            + V+Y
Sbjct: 244 LERVDY 249


>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 =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 116/247 (46%), Positives = 157/247 (63%), Gaps = 1/247 (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 FDSVEYS 247
              V Y 
Sbjct: 240 LTGVTYE 246


>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 =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 95/245 (38%), Positives = 134/245 (54%), Gaps = 2/245 (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 SVEYS 247
           SV+Y 
Sbjct: 250 SVDYP 254


>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 =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 116/251 (46%), Positives = 164/251 (65%), Gaps = 5/251 (1%)

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  VAHCDMERDWDPFRLSEALNFHLK-PAPVAIVNCAQVADDWHARFDAVERQYLFRLMSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           APL  + G+ W +   LD + M+  A  L+G+HDFTTFRS  CQA SP++T+D   V   
Sbjct: 120 APLTSDAGQMWRVKHPLDADAMQAGADQLLGQHDFTTFRSSICQAKSPVKTLDALRVEAL 179

Query: 179 --SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             + G      V ARSFLH Q+RSFVG+L+ VG   WT  D+ KAL A+DR  CGP+ PP
Sbjct: 180 PHANGTEYRFHVRARSFLHNQVRSFVGTLERVGAEAWTPDDVGKALAAKDRSACGPVCPP 239

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


>gi|229053988|ref|ZP_04195422.1| tRNA pseudouridine synthase A [Bacillus cereus AH603]
 gi|228721406|gb|EEL72927.1| tRNA pseudouridine synthase A [Bacillus cereus AH603]
          Length = 252

 Score =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MERIKCTVAYDGIHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   ++ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIIIRQVEKKTEEFHARYGVEKKEYRYRVLLS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI    +  
Sbjct: 124 KTADVFRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIGLIE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +  R V   FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GL
Sbjct: 184 QDDELIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGL 243

Query: 240 YFDSVEYS 247
           Y   V Y+
Sbjct: 244 YLWQVNYN 251


>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 =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 98/244 (40%), Positives = 139/244 (56%), Gaps = 2/244 (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 VEYS 247
           VEY 
Sbjct: 247 VEYP 250


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

 Score =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 120/248 (48%), Positives = 169/248 (68%), Gaps = 2/248 (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  VAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL    +  V +  A+NA+L+    +++++ S+    FHARFSAI RSY Y I+ R
Sbjct: 61  VAHIDLATDRFDAVTVMNAINAHLR-PLPVAVVSASVASPDFHARFSAIWRSYRYVIVNR 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 YFDSVEYS 247
              +V Y 
Sbjct: 240 TLTAVGYP 247


>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 =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 121/251 (48%), Positives = 160/251 (63%), 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  VAHADMQRDWDPFRLAEALNYHLK-PAPVAITACARAHDDFHARFSATWRSYTYRMICRR 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|256847793|ref|ZP_05553238.1| tRNA pseudouridine synthase A [Lactobacillus coleohominis
           101-4-CHN]
 gi|256715482|gb|EEU30458.1| tRNA pseudouridine synthase A [Lactobacillus coleohominis
           101-4-CHN]
          Length = 253

 Score =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 85/251 (33%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           MIRY +   Y+G+ + G+Q Q +  +I+ +++  +  +       + + G+GRTD+GVHA
Sbjct: 1   MIRYKITFAYDGTNFSGFQIQPHKRTIEQTLKTIVNRMAKNPDPAISIIGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVAHFD         + +ALN+ L     I +    IV  +FHAR++A R+ Y YR+ 
Sbjct: 61  LNQVAHFDFPYHIPEQSMVRALNSQL--PLDIIVKKAEIVSNEFHARYNAHRKRYRYRVT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +     ++         +D  +M  AAQ LVG HDFT+F +   QA S IRTI    V
Sbjct: 119 QGEFVDPFKRNYTAHFKYPVDIAHMNRAAQDLVGTHDFTSFVASGSQAKSNIRTIYEAKV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +    V   FL+ Q+R  V  L  +G G+    D+++ L A+DR+E    AP
Sbjct: 179 YYEDHDHEVIFEFVGNGFLYNQVRIMVALLLEIGSGQRPVDDVQRVLAARDRQEARMTAP 238

Query: 236 PEGLYFDSVEY 246
             GLY  +V+Y
Sbjct: 239 ASGLYLVNVDY 249


>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 =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 117/247 (47%), Positives = 165/247 (66%), Gaps = 1/247 (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 FDSVEYS 247
           F + EY 
Sbjct: 240 FVAAEYP 246


>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 =  287 bits (736), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R    +EY GS + GWQ Q+   ++Q ++E+A+  V  + + V  AGRTD+GVHA  QV
Sbjct: 1   MRIAFGVEYEGSSFCGWQSQRGVPTVQATLEEAVSKVANQPITVITAGRTDAGVHAAAQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD     +        N  L     + +L    VD+ FHARFSA+ R Y Y I+ R+ 
Sbjct: 61  VHFDTTASRLEHNWIFGCNMNL--PPEVVVLWAQPVDETFHARFSAVARHYRYVILNRRV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+   R       L    MR    HL+G HDF++FR+  CQA SPIR +   +V    
Sbjct: 119 RPAIANRRVTWYCHPLSVSRMREGGAHLIGEHDFSSFRAKACQAKSPIRNVHRLEVRRQE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +FLH  +R+  G L  VG G+     +E+ LQA+ R      A P+GLY 
Sbjct: 179 DFVVIDISANAFLHHMVRNIAGVLMAVGKGEQPPCWVEEVLQARCRALGSVTARPDGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 MGVDYP 244


>gi|323143617|ref|ZP_08078294.1| tRNA pseudouridine synthase A [Succinatimonas hippei YIT 12066]
 gi|322416680|gb|EFY07337.1| tRNA pseudouridine synthase A [Succinatimonas hippei YIT 12066]
          Length = 261

 Score =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY G  Y G+QRQ N  ++QG +EKA+ ++  E V +  AGRTD+GV+A  QV
Sbjct: 1   MRVALGVEYEGWNYAGFQRQPNAVTVQGELEKALSIIADEPVSLVCAGRTDAGVNATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D+ ++     L    N  L     I+I    IV + FHARFSA  R Y Y I     
Sbjct: 61  IHIDITKDRSEKALLLGTNTKL--PSDIAITWAKIVSEDFHARFSARARRYRYIIQNTMH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +      +     D E M+ AA+ L+G HDF +F+    Q+SS  R + + +++  G
Sbjct: 119 RPGVLNKGVSVYHGDYDIELMQKAAKILIGEHDFASFKGADEQSSSTFRCVHYIEISRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I   + A +FL+  +R+ VGSL LVG    ++   E+A +A++R   GP A P+GLY 
Sbjct: 179 PFIVFDIAANAFLNHMVRNIVGSLLLVGSKVKSTAWFEEAFKARNRDAAGPTAHPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 VDVTYP 244


>gi|289422511|ref|ZP_06424354.1| tRNA pseudouridine synthase A [Peptostreptococcus anaerobius 653-L]
 gi|289157083|gb|EFD05705.1| tRNA pseudouridine synthase A [Peptostreptococcus anaerobius 653-L]
          Length = 243

 Score =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 124/246 (50%), Gaps = 3/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y G+ Y GWQRQK+   IQG +E A   V    + V G+GRTD+GVHAL Q
Sbjct: 1   MKNIRIKVAYQGTNYCGWQRQKDSLGIQGELEYAGQKVFASKIDVTGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F +        + + LN  L     I++L    VD+ FH+RFSA  ++Y Y+I   +
Sbjct: 61  VANFKVETTIPIDKIPEVLNNKL--PKDIAVLEAVEVDEDFHSRFSAHNKTYRYQIYPSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 K   + +   LD + M+   + LVG HDF  F S      + +R I    V   
Sbjct: 119 IRSPFYKDTCYQVKSPLDLDRMKKEVKGLVGVHDFVGFMSSGSSVKTTVREIYDAKVFEE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI + +    FL+  +R   G+L  +G G      +   L+++DR   G  APP+GL+
Sbjct: 179 GDLIVLELTGNGFLYNMVRIIAGTLVDMGRGHIG-DSMVDILESKDRGRAGHTAPPQGLF 237

Query: 241 FDSVEY 246
              VEY
Sbjct: 238 LKEVEY 243


>gi|307702068|ref|ZP_07639075.1| tRNA pseudouridine synthase A [Streptococcus mitis NCTC 12261]
 gi|307616555|gb|EFN95745.1| tRNA pseudouridine synthase A [Streptococcus mitis NCTC 12261]
          Length = 249

 Score =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQTHARSVQEEIEKTLTRLNKGKAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M+ A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLRV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|224369316|ref|YP_002603480.1| TruA1 [Desulfobacterium autotrophicum HRM2]
 gi|223692033|gb|ACN15316.1| TruA1 [Desulfobacterium autotrophicum HRM2]
          Length = 246

 Score =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 121/246 (49%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
             + + +EY+G+ Y GWQ Q N  ++Q  IEKA+  +  + + + G+GRTD+GVHAL QV
Sbjct: 3   TNFKLTLEYDGTPYSGWQVQNNCPTVQEEIEKALSRMLNQPIRISGSGRTDAGVHALGQV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          L ++LN+ LK    I +     VD+ FH+R+SA  + Y Y  + R+ 
Sbjct: 63  ANFQAATTIGAAQLKRSLNSLLKGP--IVVHECRKVDQSFHSRYSARAKEYHYHFLNRED 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
           P  + +   W I   L    M      + G HDF  F       S+ +RT+         
Sbjct: 121 PCGVGRNYVWHIRTPLSIPAMEECCPIITGTHDFKAFEGSGSPRSTTVRTLFSTGFERTA 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +    ++    FL   +R+ VG+L L G GK T  + +  L+ +DR   G  AP +GL+
Sbjct: 181 EDRFTFKIKGDGFLRFMVRNIVGTLVLAGAGKITPENFKTILEGKDRGRAGATAPAKGLF 240

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


>gi|317471507|ref|ZP_07930858.1| tRNA pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316901002|gb|EFV22965.1| tRNA pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 249

 Score =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 131/251 (52%), Gaps = 7/251 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M++    + IEY+G+ Y GWQ+     N S+IQG +E  +  +TGE + + G+GRTD+GV
Sbjct: 1   MMKRNIRLKIEYDGTRYQGWQKLGKNANASTIQGKLESVLSKMTGESIQIIGSGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  Q+A+F     +    + + L  YL     I I+    V ++FH+R +A +++Y YR
Sbjct: 61  HACGQIANFHTDCSFSCREIKEYLTKYL--PSDIGIVTADEVSERFHSRLNAKQKTYQYR 118

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I         E+   W  P++L+ E M  AA   +G HDF  F S+     S +RTI   
Sbjct: 119 IAIPGTVNVFERKYLWKYPETLNIEKMNKAAAFCLGTHDFLGFSSVKKTKKSTVRTIYSI 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +    + I +      FL+  +R   G+L  +G G      +    Q++DRK+ G  AP
Sbjct: 179 VIEEEHSEIRLSFTGDGFLYNMVRILTGTLAEIGAGSRDPESIFHVFQSKDRKDAGITAP 238

Query: 236 PEGLYFDSVEY 246
           P+GL+  +VEY
Sbjct: 239 PQGLFLMNVEY 249


>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 =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 111/246 (45%), Positives = 157/246 (63%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + IEYNGS + GWQ+QK+  +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|167746683|ref|ZP_02418810.1| hypothetical protein ANACAC_01394 [Anaerostipes caccae DSM 14662]
 gi|167653643|gb|EDR97772.1| hypothetical protein ANACAC_01394 [Anaerostipes caccae DSM 14662]
          Length = 249

 Score =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 130/251 (51%), Gaps = 7/251 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M++    + IEY+G+ Y GWQ+     N S+IQG +E  +  +TGE + + G+GRTD+GV
Sbjct: 1   MMKRNIRLKIEYDGTRYQGWQKLGKNANASTIQGKLESVLSKMTGESIQIIGSGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  Q+A+F     +    + + L  YL     I I+    V ++FH+R +A +++Y YR
Sbjct: 61  HACGQIANFHTDCSFSCREIKEYLTKYL--PSDIGIVTADEVSERFHSRLNAKQKTYQYR 118

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I         E+   W  P++L+ E M  AA   +G HDF  F S+     S +RTI   
Sbjct: 119 IAIPGTVNVFERKYLWKYPETLNIEKMNKAAAFCLGTHDFLGFSSVKKTKKSTVRTIYSI 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +    + I +      FL+  +R   G+L  +G G      +    Q++DRK+ G  AP
Sbjct: 179 VIEEEHSEIRLSFTGDGFLYNMVRILTGTLAEIGAGTRDPESIFHVFQSKDRKDAGITAP 238

Query: 236 PEGLYFDSVEY 246
           P GL+  +VEY
Sbjct: 239 PHGLFLMNVEY 249


>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 =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 100/247 (40%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 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    +IS+     V + FHARFSA  R Y Y I    
Sbjct: 61  VVHFDTHAMRTPRAWIHGANAAL--PHSISVRWSQEVPEHFHARFSAYARRYCYVIYNHP 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 FDSVEYS 247
           F   +Y 
Sbjct: 239 FMEAQYP 245


>gi|302873576|ref|YP_003842209.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|307688243|ref|ZP_07630689.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|302576433|gb|ADL50445.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
          Length = 245

 Score =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 134/248 (54%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G  Y GWQ+  +   +IQ  +EK +  +  E V V G+GRTD+GVHA +
Sbjct: 1   MNNYKLTIQYDGKNYRGWQKLSDSDKTIQSKLEKVLSTLVDEEVNVIGSGRTDAGVHARK 60

Query: 60  QVAHFDLVREWVPVILCKAL-NAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           Q+A+F   ++         L + Y  + + I + +   VD++FHAR++A ++ Y YRI  
Sbjct: 61  QIANFHTEKDL---KWKDVLKHCYTYLPEDIVVKSCDKVDEKFHARYNAKKKIYTYRICN 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                A E+  ++L+ K L+ + M  A+++ +G HDF +F S+  +  S +R I    +N
Sbjct: 118 SAFGDAFERKYSYLVDKKLNIDKMLAASKYFIGIHDFKSFTSMKSKKKSTVREIYDISIN 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+++EI  +   FLH  IR   G+L  VG GK    ++   +   +R + G  AP  G
Sbjct: 178 CIGDMVEITYIGEGFLHNMIRILTGTLIEVGLGKMKIDEIPTIMDGLERSDAGFTAPAHG 237

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 238 LFLVDVIY 245


>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 =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 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|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 =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 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|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 =  287 bits (736), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 123/251 (49%), Positives = 167/251 (66%), Gaps = 5/251 (1%)

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  VAHCDLVRDWDPFRLSEALNYHLK-PAPIAITACTVVDADWHARFSARQRQYLFRILCRR 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 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 YGLYLAHVVYD 250


>gi|311086513|gb|ADP66594.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. TLW03
           (Acyrthosiphon pisum)]
          Length = 266

 Score =  287 bits (735), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 98/244 (40%), Positives = 139/244 (56%), Gaps = 2/244 (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 VEYS 247
           VEY 
Sbjct: 247 VEYP 250


>gi|160894208|ref|ZP_02074986.1| hypothetical protein CLOL250_01762 [Clostridium sp. L2-50]
 gi|156864241|gb|EDO57672.1| hypothetical protein CLOL250_01762 [Clostridium sp. L2-50]
          Length = 273

 Score =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 86/249 (34%), Positives = 132/249 (53%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y  +I Y+G+ Y GW+ +K+  +IQG IE  + L+ GE V ++GAGRTD+GVHA   
Sbjct: 25  MQNYRFLIAYDGTRYHGWEHKKDVVTIQGKIESVLSLMAGEEVRINGAGRTDAGVHARAM 84

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA   +  +  P  +   +N YL   D I IL ++   ++FHARF+A  + Y Y I   +
Sbjct: 85  VASGPVPTDKTPEEIRDYMNHYL--PDDICILEVTPAAERFHARFNAKGKHYRYTIYRGR 142

Query: 121 APLALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                ++   W + +  ++DCE MR AA +LVG HDF +F        S +R +   D+ 
Sbjct: 143 LKPVFDRKYVWTLDEGETIDCERMRKAAAYLVGEHDFKSFCGNKQMKKSTVRKLFAIDIK 202

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + +      FL   +R   G+L  VG G+     +E+ L  + R+  GP APP+G
Sbjct: 203 EDGDYVILDFYGAGFLQNMVRILTGTLVEVGAGRMEPAYMEEVLTGRCRQLAGPTAPPQG 262

Query: 239 LYFDSVEYS 247
           L    V+Y 
Sbjct: 263 LCLMQVDYE 271


>gi|262198313|ref|YP_003269522.1| tRNA pseudouridine synthase A [Haliangium ochraceum DSM 14365]
 gi|262081660|gb|ACY17629.1| tRNA pseudouridine synthase A [Haliangium ochraceum DSM 14365]
          Length = 264

 Score =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 88/245 (35%), Positives = 127/245 (51%), Gaps = 3/245 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             +++EY+G+G  GWQRQ N  ++Q  +E A+  + G  V + GA RTD+GVHAL QVAH
Sbjct: 7   IRLVLEYDGTGLSGWQRQNNAPTVQAHVEDALSSMLGRAVQIVGASRTDAGVHALGQVAH 66

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P    + LN  L     I+++  + V   FHARF +  + Y Y + TR A  
Sbjct: 67  FRTGSSIPPHGFLRGLNGKL--PPAIAVVACAEVRADFHARFDSRGKHYRYALHTRAARA 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-GN 182
            L + RAW  P+ LD   M  AAQ ++G  DF  FR+  C A +  R +D   ++    +
Sbjct: 125 PLLRERAWHCPRPLDLAAMERAAQAMLGERDFQAFRASGCTAKTSRRRVDRVALSRPAAD 184

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI I V   +FL   +R   G+L  VG G+  + ++   L ++DR   G  AP  GL   
Sbjct: 185 LIHIDVYGNAFLRNMVRIMAGTLVDVGLGRLAADEISSILDSRDRTCAGRTAPAHGLTLV 244

Query: 243 SVEYS 247
            V Y 
Sbjct: 245 EVFYP 249


>gi|119475872|ref|ZP_01616224.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2143]
 gi|119450499|gb|EAW31733.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2143]
          Length = 288

 Score =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+GS Y GWQ Q     +++Q ++EKA+  V    V+V  AGRTD+GVHA  Q
Sbjct: 27  RVALCVSYDGSAYHGWQSQRKPQVATVQETLEKALSSVANANVIVQCAGRTDTGVHASHQ 86

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD           +  N  L    +I+I     V  +F+ARFSA  R Y Y I+ R 
Sbjct: 87  IVHFDSPSARGEKAWVRGGNTNL--PSSIAIQWAKPVSAKFNARFSATARRYRYVILNRP 144

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A  A+           LD  +M  AAQ LVG  DFT++R+  CQ+ +P+R I   DV+  
Sbjct: 145 ARSAILSAGVTWQRYPLDEISMHEAAQALVGELDFTSYRAAACQSKTPMRNIHRVDVSRQ 204

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ I + A +FLH  +R+  G L  +G G   +   E+ L A+DR      APP GLY
Sbjct: 205 GDLVIIDIQANAFLHHMVRNIAGVLMAIGTGAKPTVWAEEVLLAKDRSVAAATAPPHGLY 264

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 265 LIGVTYP 271


>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 =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 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|90416037|ref|ZP_01223970.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2207]
 gi|90332411|gb|EAS47608.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2207]
          Length = 285

 Score =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 87/245 (35%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY  ++ Y+GS + G+Q+QK+  S+Q  +E+A+  V    ++V  AGRTD+ VHA  QV 
Sbjct: 26  RYAAVVSYDGSAFCGFQKQKHSPSVQQELERALSSVANAEIIVSCAGRTDTAVHASYQVI 85

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD           K  N+ L   D+I++L    V++ FHARFSA  R+Y Y I +  A 
Sbjct: 86  HFDTQALRTGRNWVKGSNSQL--PDSIALLWADEVNETFHARFSATSRTYRYVIHSAPAR 143

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+       + K L+   M+ A Q+L+G  DF+ FR   CQ+ SP R I    +   G 
Sbjct: 144 PAILSQGVTWVRKPLNTAAMQEACQYLLGEQDFSAFRGAGCQSLSPNRNITSAKIIQAGE 203

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI   V A +F+   +R+ +GSL  VG G+     + + ++ +DR +    A P+GLY  
Sbjct: 204 LIVFEVTANAFVLHMVRNIIGSLMEVGFGRRDPGWIGQLIKGRDRTKSAATASPKGLYLV 263

Query: 243 SVEYS 247
            V Y 
Sbjct: 264 QVGYP 268


>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 =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 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|310829551|ref|YP_003961908.1| hypothetical protein ELI_4001 [Eubacterium limosum KIST612]
 gi|308741285|gb|ADO38945.1| hypothetical protein ELI_4001 [Eubacterium limosum KIST612]
          Length = 244

 Score =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 120/246 (48%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    MII Y G+ Y GWQRQ N  +++ ++  AI  VTGE V ++G+GRTD+GVHAL Q
Sbjct: 1   MKNIQMIIAYKGTRYAGWQRQPNAPTVEEALTGAIKAVTGETVTLYGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHF       P     ALN  L     I +L+     + FH+R+SA  + Y Y++    
Sbjct: 61  SAHFHTESRVPPERFAAALNTRL--PGDIRVLSSCEAPEGFHSRYSAKGKVYTYQLYLNP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    +W +   +D   M+ A+   +G HDF  F +        +RTI        
Sbjct: 119 VLSPFYAEYSWHVNYPVDVSRMKAASAAFLGEHDFCGFMAAGSSVRGTVRTIRAITFEQE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+ I      FL+  +R   G+L  +G G+  +  L   + + DRK+ G  APP+GL+
Sbjct: 179 GALLRITYTGNGFLYNMVRIMTGTLAEIGMGRIKAEALPGIIASCDRKQAGMTAPPQGLF 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LREVLY 244


>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 =  287 bits (735), Expect = 9e-76,   Method: Composition-based stats.
 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|225857220|ref|YP_002738731.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae P1031]
 gi|254764871|sp|C1CLU3|TRUA_STRZP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225725422|gb|ACO21274.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae P1031]
          Length = 249

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQSHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQIDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     +   L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIALILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|197285647|ref|YP_002151519.1| tRNA pseudouridine synthase A [Proteus mirabilis HI4320]
 gi|194683134|emb|CAR43721.1| tRNA pseudouridine synthase A [Proteus mirabilis HI4320]
          Length = 281

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 19  KIALGIEYDGSHYYGWQRQNEVRSVQERLEKALSQVANEPISVFCAGRTDAGVHATGQVV 78

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +N +L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 79  HFETTAHRKDAAWTMGVNTHL--PQDIAVRWVKTVANDFHARFSATARRYRYVIFNHRYR 136

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G+
Sbjct: 137 PAILSSGVTHFHYPLDAQRMHQAAQCLLGENDFTSFRAVQCQSRTPWRNVMHVNVSRYGD 196

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G    T + + L  +DR +    A   GLY  
Sbjct: 197 YVVVDIKANAFVHHMVRNIVGSLLEIGCGNQAITWMAELLALKDRTKAAATAKANGLYLV 256

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 257 SVDYP 261


>gi|268318882|ref|YP_003292538.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii FI9785]
 gi|262397257|emb|CAX66271.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii FI9785]
          Length = 263

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  Q
Sbjct: 3   TRYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +E     +  ALNA +            IVD+ FH ++S   + Y Y +   
Sbjct: 63  VIHFDYPGKEIPAKNMMLALNALM--PIDTVFFESEIVDEDFHVQYSTKGKWYRYVVDQH 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++  
Sbjct: 121 RFTDPFNRFYTGHYPYPLDISLMQQAARDLIGEHDFTSFAASGGQIVDKVRTIYYVNITP 180

Query: 180 FGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +   I    +   FL+  +R  VG+L  +G+ K    D+ + L+A+DR+E    AP  
Sbjct: 181 DPDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNQKRPVDDIPRVLKAKDRQEVRTTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLQHVFYE 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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 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|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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 138/246 (56%), 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  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA F+        + +  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 EK-DVFKRNYVWHFKYKLNIEAMRIAARYLEGEHDFSSFKK-GNDKKNPIRTVYRIRILN 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|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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 135/247 (54%), Positives = 173/247 (70%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R+ +IIEY+G  + GWQRQ+NG SIQ  +E+A+  + +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|254253654|ref|ZP_04946971.1| Pseudouridylate synthase [Burkholderia dolosa AUO158]
 gi|124898299|gb|EAY70142.1| Pseudouridylate synthase [Burkholderia dolosa AUO158]
          Length = 271

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 132/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L Q
Sbjct: 1   MMRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       +  NA+L    ++++     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTDLDRADFSWVRGTNAFL--PPSVAVQWAKPMPDTFHARFSAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  +   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   
Sbjct: 119 VRSPMLAGRAGWVHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R  A +FLH  +R+ +G L  VG G++ +  +   L  +DR    P    +GLY
Sbjct: 179 GHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGRDRDLAAPTFMADGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LAHVGYP 245


>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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 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|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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 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|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 =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 141/248 (56%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>gi|290475958|ref|YP_003468853.1| pseudouridylate synthase I [Xenorhabdus bovienii SS-2004]
 gi|289175286|emb|CBJ82089.1| pseudouridylate synthase I [Xenorhabdus bovienii SS-2004]
          Length = 279

 Score =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 16  VKIALGIEYDGSRYYGWQRQQEVKSVQECLEKALSKVADEPISVFCAGRTDAGVHATGQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF    +         +N++L     I++  +  VD +FHARFSA  R Y Y I   + 
Sbjct: 76  VHFKTSAQRKDAAWTMGVNSHL--PPDIAVRWVKTVDDEFHARFSATARRYRYIIFNHRY 133

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M  AAQ L+G +DFT+FR++ CQ++SP R + H +V+  G
Sbjct: 134 RPAVLAQGVTHFHYLLDERKMHEAAQSLLGENDFTSFRAVQCQSNSPWRNMMHINVSRHG 193

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + + + A +F+H  +R+ VGSL  +G        + + L  +DR +    A  EGLY 
Sbjct: 194 HYVVVDIKANAFVHHMVRNIVGSLLEIGCSNQDIGWMAELLALKDRTKAAATAKAEGLYL 253

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 254 VAVDYP 259


>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 =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

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  VHFDTDANRDISAFYLGMNSVL--PDAVAVRWAQEVSLDFHARFSATARRYRYVILNQNN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + K         LD + M  A  +L+G +DFT+FR++HCQ+++P R I H  V+ FG
Sbjct: 119 RPGILKNGISHYHLPLDADAMNQACSYLLGENDFTSFRAVHCQSNTPFRNIMHLRVDRFG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +FLH  +R+  G L  +G GK+ ++ ++  L+ +DR +    A   GLY 
Sbjct: 179 DYVVIDIKANAFLHHMVRNITGCLIDIGIGKYPASWMKDVLELKDRTKASATAKAAGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


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

 Score =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 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|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 =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 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|126667385|ref|ZP_01738357.1| tRNA pseudouridine synthase A [Marinobacter sp. ELB17]
 gi|126628141|gb|EAZ98766.1| tRNA pseudouridine synthase A [Marinobacter sp. ELB17]
          Length = 303

 Score =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  ++ EY+G  + GWQ+QK+G  ++Q  + KA   V    V +  AGRTD+GVHA  Q+
Sbjct: 18  RVALVFEYDGREFHGWQQQKSGIRAVQQQLAKAASKVADHDVELVCAGRTDAGVHASYQL 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +N  L     IS+         FHARFSA+ R Y Y I     
Sbjct: 78  VHFDTPSLRTMRSWVMGINTAL--PFDISVRWAGQCQGDFHARFSAVYRRYRYIIYNNPV 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +++G+     + L+ ENM  AAQ LVG HDF+ FR+  CQ+ SPIR +    V   G
Sbjct: 136 RPGIQRGQVSWNFRPLNAENMHQAAQALVGEHDFSAFRAAGCQSHSPIRFLQSISVTRKG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I V A +FLH  +R+  G+L  VG  +     + + L  +DR++ G  APP+GLY 
Sbjct: 196 DYLVIDVQANAFLHHMVRNIAGALMAVGCQEQAPDWIGQILATKDRRQAGVTAPPDGLYL 255

Query: 242 DSVEYS 247
             V Y 
Sbjct: 256 VDVGYP 261


>gi|324324528|gb|ADY19788.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 245

 Score =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 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|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 =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y G+ Y GWQ QKN  +++ ++EKAI  V G  V   GAGRTD+GVHA   
Sbjct: 1   MRNIALKLMYVGTAYHGWQIQKNAVTVEETLEKAIASVVGHPVKCTGAGRTDAGVHAENY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A+F          L  A+N  L   + I ++  + V   F+A  S I++ Y YRI   +
Sbjct: 61  IANFRTTSTIPCDRLPLAVNTRL--PEDIVVVKATEVHDGFNAIGSCIKKEYTYRIYNSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A    RAW  PK LD + M+ AA   VG HDF   +S+  +  S +RT+ +F++   
Sbjct: 119 IRNAFFVNRAWFYPKHLDEKVMQAAADRFVGTHDFAAVQSVGTEVQSTVRTVHYFNMTRS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++IE RV A  FL+  +R+ VG+     +GK+    +   L+ + R   GP APP GLY
Sbjct: 179 GDMIECRVCANGFLYNMVRAMVGTCVYAAEGKFPPEAVSDILEGRCRTAAGPTAPPGGLY 238

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 239 MTKLWYE 245


>gi|313891575|ref|ZP_07825185.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
 gi|313120034|gb|EFR43216.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
          Length = 244

 Score =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y MIIEY+G+ Y GWQ+QK+   ++QG IEKA   VTGE V + GAGRTDSGVHA  Q
Sbjct: 1   MNYKMIIEYDGTRYEGWQKQKHSDETLQGKIEKAFEKVTGENVQIIGAGRTDSGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +  L  +     L   LN  L   D I I   + V+++FH+RF A  + Y Y +    
Sbjct: 61  VVNVHLPYDLNAENLKNELNEIL--PDDIYIKQCTEVEEKFHSRFHAKSKIYEYNLRIGS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +K   W   K L  E M+ AA+ L G HDFT F +      S +RT+   ++++ 
Sbjct: 119 NKDVFQKRFIWQFAKPLCIEKMKRAAEILQGTHDFTAFCNNKNFKKSAVRTVYSIEISTS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ +R     FL   IR  VG+L  VG+ K  +  L   L+++ R   G  APP+GL 
Sbjct: 179 NDILHLRFCGDGFLQGMIRIMVGTLVEVGENKRDADSLYDVLKSKQRSNAGFTAPPQGLT 238

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 239 LISVQY 244


>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 =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 138/246 (56%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   SIQG +E+A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYDGSQYYGWQRQQEVKSIQGCLEQALSKVADEPISVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +NA+L     I++  +  VD+ FHARFSA  R Y Y I   + 
Sbjct: 61  VHFETSAQRKDAAWTMGVNAHL--PADIAVRWVKTVDEDFHARFSATARRYRYIIFNHRY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ+L+G +DFT+FR++ CQ+ +P R + H +VN +G
Sbjct: 119 RPAVLASGVTHFYYPLDEKRMHQAAQYLLGENDFTSFRAVQCQSKTPWRNVMHINVNRYG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  +G G      + + L  +DR +    A   GLY 
Sbjct: 179 HYVVIDIKANAFVHHMVRNIAGSLMEIGCGNQDINWMARLLALKDRTKAAATAKSAGLYL 238

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 239 VAVDYP 244


>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 =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 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|238923689|ref|YP_002937205.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
 gi|238875364|gb|ACR75071.1| tRNA pseudouridine synthase A [Eubacterium rectale ATCC 33656]
          Length = 276

 Score =  287 bits (734), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
             Y +I+ Y+G+ Y GWQ QK+   +IQG ++  +  + G+ V V G+GRTD+GVHA+ Q
Sbjct: 28  QNYKIIVAYDGTRYKGWQVQKSTDDTIQGKLQHVLSTLAGKPVEVIGSGRTDAGVHAVGQ 87

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F + + +    +   LN +L     I++ ++S V  +FHAR++A+ ++Y+Y I T  
Sbjct: 88  VASFHMPKHFSKDEIFIWLNEHL--PADIAVTDISNVPDRFHARYNAVSKTYVYTIHTGI 145

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   +   K LD + M+ AA +L+G HDF  F        S +RTI   D+   
Sbjct: 146 VSDVFRRKYVYDYDKPLDTDRMKKAAAYLLGEHDFKAFCGNRHMKKSTVRTIFSIDIEKT 205

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I      FL   IR   G+L  VGDG+     + + L ++DR + G  AP  GL 
Sbjct: 206 GADIVISYTGDGFLQNMIRIITGTLIEVGDGRKNPDAVMEILASKDRAQAGYTAPACGLR 265

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


>gi|254931132|ref|ZP_05264491.1| tRNA pseudouridine synthase A [Listeria monocytogenes HPB2262]
 gi|293582680|gb|EFF94712.1| tRNA pseudouridine synthase A [Listeria monocytogenes HPB2262]
 gi|328469771|gb|EGF40688.1| tRNA pseudouridine synthase A [Listeria monocytogenes 220]
 gi|332313028|gb|EGJ26123.1| tRNA pseudouridine synthase A 1 [Listeria monocytogenes str. Scott
           A]
          Length = 248

 Score =  286 bits (733), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRIKASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G  + +  D+ +AL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQDRISPDDISEALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>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 =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 139/248 (56%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 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 =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 128/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ     ++Q ++EKA+  V    + +  AGRTD+GVHA  QV
Sbjct: 8   RVALGVEYKGSRYSGWQRQSTGVLTVQETLEKALSKVADSPISLQCAGRTDAGVHACGQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +          N  L     IS+    I+   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQVDRSLKAWVMGANINL--PHDISVSWAKIMPAHFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AAQ+L+G HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 126 RPAHLNEEITWNHRPLDVERMAEAAQYLIGTHDFSAFRAGQCQAKSPIKQMHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + + A +FLH  +R+  G L  +G G+     +++ L++++R+  G  A P GLY 
Sbjct: 186 KMIVLDIRANAFLHHMVRNIAGVLMTIGAGERPVEWMKEVLESRERRSGGVTAHPFGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VQVEY 250


>gi|322806167|emb|CBZ03735.1| tRNA pseudouridine synthase A [Clostridium botulinum H04402 065]
          Length = 246

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 140/248 (56%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>gi|283781972|ref|YP_003372727.1| tRNA pseudouridine synthase A [Pirellula staleyi DSM 6068]
 gi|283440425|gb|ADB18867.1| tRNA pseudouridine synthase A [Pirellula staleyi DSM 6068]
          Length = 285

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 79/251 (31%), Positives = 123/251 (49%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + + Y+G+ + GWQ Q N  ++Q  +EKA+  +TG       +GRTD+GVHAL Q
Sbjct: 1   MRTFKLTLAYDGTNFGGWQWQPNRRTVQDELEKAVETITGVRSRFVASGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F       P  L K LNA  K+ D I I ++  V   FH    A+R+ Y Y +    
Sbjct: 61  VAAFSSETGIDPAGLLKGLNA--KVPDDIFIFDVVEVPLAFHPIRDAVRKRYRYVVQDGP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++  AW + + LD + M  A++ L+G HDF +F++      +  R +    V   
Sbjct: 119 LRDIFDRQYAWHVRQPLDEQAMLEASRLLLGEHDFASFQTSGSSRLTTERNVLDISVERV 178

Query: 181 GN----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  + + V A  FL   +R+ VG+L  VG G        + L+++DR+  G  AP 
Sbjct: 179 DGARTSRVHVEVEADGFLFNMVRNIVGTLVEVGKGTRPVAWTREVLESRDRRRAGMTAPA 238

Query: 237 EGLYFDSVEYS 247
           +GL+   V Y 
Sbjct: 239 QGLFMIGVHYD 249


>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 =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 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|55820220|ref|YP_138662.1| tRNA pseudouridine synthase A [Streptococcus thermophilus LMG
           18311]
 gi|55822111|ref|YP_140552.1| tRNA pseudouridine synthase A [Streptococcus thermophilus CNRZ1066]
 gi|62901189|sp|Q5M1T6|TRUA_STRT1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901193|sp|Q5M6C9|TRUA_STRT2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|55736205|gb|AAV59847.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Streptococcus thermophilus LMG 18311]
 gi|55738096|gb|AAV61737.1| tRNA pseudouridine synthase A (pseudouridylate synthase I)
           [Streptococcus thermophilus CNRZ1066]
          Length = 248

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  IEK +  + +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEEIEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYSKHIKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRNYAIHYPYPLSLALMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                          FL+ Q+R+ VG+L  +G+G+   + ++  L+++DR   GP     
Sbjct: 179 DEKTGFYVFAFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQVKTVLESRDRNLAGPTVAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|322392372|ref|ZP_08065833.1| tRNA pseudouridine synthase A [Streptococcus peroris ATCC 700780]
 gi|321144907|gb|EFX40307.1| tRNA pseudouridine synthase A [Streptococcus peroris ATCC 700780]
          Length = 249

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALR 59
           M RY  +I Y+G  + G+QRQ +  S+Q  IEK +  +   + V +HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAVISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGLGVTIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMEEEKLRFALDT--QSPEDIDVISVEIVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+ A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHYPYPLDVERMQKAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLKV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPIEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|315154834|gb|EFT98850.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0043]
          Length = 277

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 32  MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILKQMTGEPIEIIGSGRTDAGTHARG 91

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 92  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 149

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 150 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 209

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 210 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 269

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 270 FLDEVYY 276


>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 =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 99/246 (40%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R+ + +EY+G G  GWQRQK+G S+QG +E A+  V  + V +  AGRTD+GVHA  QV
Sbjct: 4   QRWALGVEYDGRGLLGWQRQKDGPSVQGHLEAALSFVANDGVELTCAGRTDAGVHATAQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             +N+ L   D I++     V+  FHARF A  R Y Y I  R  
Sbjct: 64  AHFDTSAVRERHSWVLGVNSRL--PDGIALRWAEPVNDDFHARFKACGRRYRYVIANRAV 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ALE GR     + LD   M  AAQ  VG HDF++ R+  CQA SPIR +    V   G
Sbjct: 122 RPALEAGRVAWWRRPLDTARMHDAAQTFVGEHDFSSLRAAGCQAKSPIREVHSIAVQRRG 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + + + A +FLH  +R+  G L  +GDG+       + L A+DR+  G  AP  GLYF
Sbjct: 182 SYVVLDIHANAFLHHMVRNIAGVLLAIGDGREEPGWAAQILAARDRRVSGITAPAGGLYF 241

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 242 VHVDYP 247


>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 =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 128/247 (51%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + +EY+G+ + G+QRQ K   ++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 QMPSALARERTWWVPKPLDANAMQQGLAHFLGEHDFKAFATQ--ERRGTVRTLYRARLER 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 YFDSVEY 246
           YF +  Y
Sbjct: 237 YFVAAGY 243


>gi|315283801|ref|ZP_07871873.1| tRNA pseudouridine synthase A [Listeria marthii FSL S4-120]
 gi|313612551|gb|EFR86621.1| tRNA pseudouridine synthase A [Listeria marthii FSL S4-120]
          Length = 248

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLRVEEVADDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  L+   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KVFDPFSRNFALHYPYELNLAKMKLASERLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  ++ +AL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPEEITEALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|307705317|ref|ZP_07642179.1| tRNA pseudouridine synthase A [Streptococcus mitis SK597]
 gi|307621104|gb|EFO00179.1| tRNA pseudouridine synthase A [Streptococcus mitis SK597]
          Length = 249

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M++A + L G HDFT F +        IRTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTNVEDKIRTITEASLRV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A   
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIDLILEKKDRQLAGPTAASN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|225871229|ref|YP_002747176.1| tRNA pseudouridine synthase A [Streptococcus equi subsp. equi 4047]
 gi|254764866|sp|C0M8L4|TRUA_STRE4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225700633|emb|CAW95185.1| tRNA pseudouridine synthase A [Streptococcus equi subsp. equi 4047]
          Length = 249

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+QRQ    ++Q  IEK +  +TG + + +HGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGTLFSGFQRQSQARTVQEEIEKTLQKLTGGQGIQIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++  P  L  AL+   +  D I +++L I    FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLEQKRDPEKLRFALDT--QTPDDIDVISLEIAADDFHARYHKHFKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDIAKMQAAIKDLVGTHDFTGFTAAGTSVKNKVRTITAATLTQ 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     +   L++++R+  GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRLPIEQIRLVLESKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|313606591|gb|EFR83384.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL F2-208]
          Length = 248

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIITYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSDLDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G+HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDISKMKLASKRLIGKHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|241895121|ref|ZP_04782417.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
 gi|241871617|gb|EER75368.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
          Length = 249

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 80/251 (31%), Positives = 123/251 (49%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHA 57
           M RY   I Y+G+ +FGWQ Q N  ++Q  +E  +  +     E + V G+GRTD+ VHA
Sbjct: 1   MPRYKATIAYDGTDFFGWQVQPNKRTVQAEMELVVNKMAKNPAEHIRVQGSGRTDARVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QVAHFDL  +     + K L+  L     I I  +  V   FHA+F+A  ++Y YR  
Sbjct: 61  KGQVAHFDLPFDIPADAVRKGLSTML--PYDIGIKKVEKVSDDFHAQFNAHNKTYFYRFS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF-- 175
           T +     ++       + L+ E M+ A    VG HD+ +F +   Q  + +RT+     
Sbjct: 119 TSEYIDPFKRNYTGHWHRRLNPELMQQAIGDYVGEHDWLSFVASGYQQKTTVRTVYSAKM 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V      I        FL+ QIR  VG L  +G+G     D+++  + +DR++    AP
Sbjct: 179 WVKPEEEEIWFEFSGNGFLYNQIRIMVGVLLEIGNGVRPVDDIKRLFEVKDRQQAQFTAP 238

Query: 236 PEGLYFDSVEY 246
            +GLY   V+Y
Sbjct: 239 AQGLYLMDVKY 249


>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 =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 96/252 (38%), Positives = 135/252 (53%), Gaps = 7/252 (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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVN- 178
            P   E  R+W + ++L  E MR A Q LVG HDFTTF     +   +PIRTID  ++  
Sbjct: 119 VPSPFEFRRSWYLRRTLSVEPMREATQFLVGTHDFTTFSKSERKREVNPIRTIDKIEITN 178

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G L+E+    RSFL   +R  V +L  VG G+    ++++ LQA+DR     LAP
Sbjct: 179 KEWEEGVLVELLFTGRSFLRHMVRVIVATLVKVGTGEVKPQEVKEMLQAKDRSRAPFLAP 238

Query: 236 PEGLYFDSVEYS 247
           P+GLY + V Y 
Sbjct: 239 PDGLYLERVFYD 250


>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 =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 139/248 (56%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>gi|227888821|ref|ZP_04006626.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii ATCC 33200]
 gi|227850658|gb|EEJ60744.1| tRNA pseudouridine synthase A [Lactobacillus johnsonii ATCC 33200]
          Length = 263

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 128/250 (51%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  Q
Sbjct: 3   TRYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +E     +  ALNA +            IVD+ FH ++S   + Y Y +   
Sbjct: 63  VIHFDYPGKEIPAKNMMLALNALM--PIDTVFFESEIVDEDFHVQYSTKGKWYRYVVDQH 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + ++  
Sbjct: 121 RFTDPFNRFYTGHYPYPLDISLMQQAARDLIGEHDFTSFAASGGQIVDKVRTIYYVNITP 180

Query: 180 FGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +   I    +   FL+  +R  VG+L  +G+ K    D+ + L+ +DR+E    AP  
Sbjct: 181 DPDKKQIIFDFIGNGFLYNMVRILVGTLLEIGNQKRPVDDIPRVLKTKDRQEVRTTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLQHVFYE 250


>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 =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 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|315173151|gb|EFU17168.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1346]
          Length = 877

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 632 MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 691

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 692 QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 749

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 750 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 809

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 810 NGKMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 869

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 870 FLDEVYY 876


>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 =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 103/248 (41%), Positives = 145/248 (58%), Gaps = 4/248 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           R+ + IEY+G+GY GWQ+Q +G+SIQG IE A   +     V    AGRTD+GVHA   V
Sbjct: 22  RWALRIEYDGTGYLGWQKQNDGTSIQGLIEAAASKLVRNRPVPSITAGRTDAGVHAAGMV 81

Query: 62  AH--FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            H  F          +   +  +LK    + +L  + V  +++ARFSA  RSY Y I+ R
Sbjct: 82  IHLDFPDDAPIDARQIRDGMGYHLK-PHRVVVLETAKVGPEWNARFSATWRSYRYTILNR 140

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            A   L + R W I + LD + M+ AA HL+G HDFT+FR++ CQA SPIRT+D  +++ 
Sbjct: 141 PARPGLMENRVWHIKRPLDVDLMQQAANHLLGPHDFTSFRAVACQARSPIRTLDVLNIHR 200

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L+ I   ARSFLH Q+R+  G+L ++G  +W    + + L+A+DR   G  APPEGL
Sbjct: 201 DGELVMIDTKARSFLHHQVRNMAGTLMMIGSRQWPVEKIIEILEAKDRCAAGQTAPPEGL 260

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 261 CLMDVGYP 268


>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 =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 138/247 (55%), Gaps = 2/247 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + ++Y+G+ + GWQ Q +G+++Q  +++A+F  T   +  H AGRTD+GVHA+ QV 
Sbjct: 5   RLVLGVQYDGTPWHGWQTQLSGNTVQDRLQQALFKFTQSDITTHCAGRTDTGVHAIEQVV 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDK--QFHARFSAIRRSYLYRIITRQ 120
           HFD   +       + LN +L  S  +    ++ +D   +FHARFSA  R+Y Y +    
Sbjct: 65  HFDTPLDRPISSWVRGLNTHLPPSIAVRWATVARLDPQHEFHARFSARSRTYHYLLYNNP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L   +A  + + LD + MR AAQ L+G HDFT FRS  CQA SP++ +    +   
Sbjct: 125 VRSPLWNDKAGWVFRPLDLDRMREAAQSLIGTHDFTAFRSADCQAKSPVKMMHEIAITRR 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LI I++ A +FLH  +R+ VGSL  VG G+     L + +  +DR    P   P+GLY
Sbjct: 185 DDLIVIKLHANAFLHHMVRNLVGSLIYVGTGRQPVDWLSELILQKDRHLAAPTFSPDGLY 244

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 245 LAKIDYD 251


>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 =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 125/246 (50%), Gaps = 2/246 (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  VHFETDAKRPLSAWVRGVNAHL--PATIRVEWAHAVDDDFHARFSAFSRSYQYLLYNAPV 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 DSVEYS 247
             V Y 
Sbjct: 239 TDVGYD 244


>gi|297582482|ref|YP_003698262.1| tRNA pseudouridine synthase A [Bacillus selenitireducens MLS10]
 gi|297140939|gb|ADH97696.1| tRNA pseudouridine synthase A [Bacillus selenitireducens MLS10]
          Length = 261

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M R  + IEY+GSG+ G+Q+Q N  ++QG +E+A+ ++   E      +GRTD+GVH +R
Sbjct: 1   MRRMLIRIEYDGSGFNGYQKQPNARTVQGELERALSVMHKAESWPCTSSGRTDTGVHGVR 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD            ALN+ L   D I +L    VD  FHAR+  + + Y YR+ T 
Sbjct: 61  QPVHFDSPLTIPDERWPMALNSLL--PDDIQVLGAMEVDASFHARYDTVGKVYRYRVDTA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P ++D E MR AA+HL G HDFT+  S        +RT+    +  
Sbjct: 119 KRQTVFRRSFAAHFPGNMDIEAMREAAKHLEGTHDFTSLSSPKTDVKDKVRTLFAVSLEE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +  ++      FL+  +R  +G+L  VG G W    +   ++ Q+R+  GP AP  GL
Sbjct: 179 REDGFDVVFAGSGFLYQMVRILMGTLIKVGSGDWPPDVIPAIIEKQERQAAGPTAPGHGL 238

Query: 240 YFDSVEY 246
           Y + V Y
Sbjct: 239 YLEDVFY 245


>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 =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 99/248 (39%), Positives = 138/248 (55%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
            R+   +EYNG+ + GWQ+QK+  G S+Q ++EKAI  V    V V  AGRTD+GVHA  
Sbjct: 29  RRFVAGVEYNGALFKGWQKQKHYAGPSVQEALEKAISRVANHTVDVVCAGRTDAGVHASA 88

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD             +N  L   D + +  +    + FHARFSA+ R Y Y I+ +
Sbjct: 89  QVIHFDTSAVRDERAWKLGINTNL--PDGVCVNWIMPAPQDFHARFSAVARRYRYFIMNK 146

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q    L         + LD E M  AAQ+L+G HDFT+FR+  CQA   +RT+ +  V  
Sbjct: 147 QVKPGLMHDGVSWWRRPLDAEKMHEAAQYLLGEHDFTSFRAKDCQARHAVRTMKYISVKR 206

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + + V A +FL+  +R+ VG L  +G+GK      E+ L AQDR++ G  AP EGL
Sbjct: 207 LNDWVIVEVCANAFLYHMVRNIVGVLLPIGEGKKPVEWCEQVLAAQDRRQAGVTAPGEGL 266

Query: 240 YFDSVEYS 247
           YF +VEY 
Sbjct: 267 YFVNVEYP 274


>gi|331266815|ref|YP_004326445.1| tRNA pseudouridine synthase A [Streptococcus oralis Uo5]
 gi|326683487|emb|CBZ01105.1| tRNA pseudouridine synthase A [Streptococcus oralis Uo5]
          Length = 249

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++ + IV   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVILIEIVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    L +  A   P  LD E M++A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPLRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLSV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNDRMPVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|300903709|ref|ZP_07121624.1| tRNA pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300404291|gb|EFJ87829.1| tRNA pseudouridine synthase A [Escherichia coli MS 84-1]
          Length = 270

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTRAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>gi|170289026|ref|YP_001739264.1| tRNA pseudouridine synthase A [Thermotoga sp. RQ2]
 gi|238688847|sp|B1LB83|TRUA_THESQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|170176529|gb|ACB09581.1| tRNA pseudouridine synthase A [Thermotoga sp. RQ2]
          Length = 245

 Score =  286 bits (732), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 127/246 (51%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+          +  A+NA L   D + +  +  V K FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIKNAMNANL--PDDVYVKEVFEVSKNFHPRFDVKKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR AA++L G HDFT+F         P+RTI    +  
Sbjct: 119 KQKNVFLRKYVWWFPYELDLDAMRKAAKYLEGTHDFTSF-KTGSDERDPVRTIYRIRILR 177

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|293374636|ref|ZP_06620951.1| tRNA pseudouridine synthase A [Turicibacter sanguinis PC909]
 gi|325845439|ref|ZP_08168732.1| tRNA pseudouridine synthase A [Turicibacter sp. HGF1]
 gi|292646726|gb|EFF64721.1| tRNA pseudouridine synthase A [Turicibacter sanguinis PC909]
 gi|325488545|gb|EGC90961.1| tRNA pseudouridine synthase A [Turicibacter sp. HGF1]
          Length = 258

 Score =  285 bits (731), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 130/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R    + Y+G+ + G+QRQ    ++QG IE A+  ++ + V +H +GRTD+GVHA  Q
Sbjct: 1   MKRIKCTVAYDGTLFNGYQRQPGQRTVQGEIEAALEKISKQPVTIHSSGRTDTGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD V         +ALN+ L   + I I++   V  +FH+R+    + Y YR+   +
Sbjct: 61  VFHFDSVVNMDGSRYVRALNSIL--PEDIYIIDSQEVHPEFHSRYHGKVKEYRYRLSLNE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +++   +    SLD E MR A  +L+G H+FT+F   +      +RTI   D+   
Sbjct: 119 Y-NPMKRNYVYYHRFSLDVEKMREAMTYLLGTHNFTSFCG-NLDDIDKVRTIYQADLIDE 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              +    V   FL   IR  VG+L  +G+GK    D++  ++A++RK  G  A P+GLY
Sbjct: 177 DGELTFIFVGNGFLRYMIRIMVGTLIQIGEGKKKPEDIKTIIEAKNRKLAGHTAKPQGLY 236

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 237 LQRVDYP 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 =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 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|148245016|ref|YP_001219710.1| tRNA pseudouridine synthase A [Candidatus Vesicomyosocius okutanii
           HA]
 gi|146326843|dbj|BAF61986.1| tRNA pseudouridine synthase A [Candidatus Vesicomyosocius okutanii
           HA]
          Length = 247

 Score =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK N  ++Q  IE+A+  V  + V V  +GRTD+GVHA  Q
Sbjct: 1   MKLALGVEYLGTHFHGWQCQKSNIRTVQQVIEQALSSVANQPVRVFCSGRTDTGVHATCQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+   +          N +L     ++   +  VD  FHARFS I R Y Y+I   +
Sbjct: 61  VIHFETNIKRKNKAWLFGGNVHL--PSDVNFTWVKPVDDNFHARFSVITRQYNYKIHNTK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              ++    +   P+ LD   M  A Q+L G+H+F+ FR   CQA SPI+ I+   +   
Sbjct: 119 IRSSIIATHSLWEPRKLDIVAMNKAGQYLTGKHNFSAFRGSLCQAKSPIKNIEFIKLTKH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I + + A +FLH  +R+ VG+L  VG G+     + + L ++ RK+ GP APP+GLY
Sbjct: 179 DDNILLDIKANAFLHHMVRNIVGTLLKVGKGEKPIEWVREVLNSKQRKQAGPTAPPQGLY 238

Query: 241 FDSVEY 246
           F    Y
Sbjct: 239 FIRAFY 244


>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 =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSG+ GWQ Q    +IQ  +E+A+  V    V V  AGRTD+GVHA+ QV
Sbjct: 1   MRIALGIEYDGSGFAGWQWQNGKRTIQAEVERALSRVADAPVRVTCAGRTDAGVHAIEQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             L A   + + + IL +   +  FHAR SAI R Y Y I+ R  
Sbjct: 61  AHFDTESRRSERSWL--LGANTALPEDVRILWVRETEPHFHARLSAIARYYRYEILNRPM 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL   +       LD E MR  A +LVG HDF++FR+  CQ+ SP R +    V   G
Sbjct: 119 RSALRPRQFTWCHAPLDVERMREGAAYLVGEHDFSSFRAQQCQSRSPFRRVHFLHVRREG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+  G L  VG GK     + + L  +DR + G  APP+GLY 
Sbjct: 179 ERVIMEIAANAFVHHMVRNIAGVLMAVGAGKRDPAWVGELLAMRDRAKGGVTAPPDGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 GGVCYP 244


>gi|293388406|ref|ZP_06632914.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
 gi|291082181|gb|EFE19144.1| tRNA pseudouridine synthase A [Enterococcus faecalis S613]
          Length = 280

 Score =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 35  MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 94

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 95  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 152

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 153 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 212

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 213 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 272

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 273 FLDEVYY 279


>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 =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 98/248 (39%), Positives = 139/248 (56%), Gaps = 3/248 (1%)

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  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD +         + +N +L   D + +     V   FHARFSA+ R+Y Y I T 
Sbjct: 82  QVIHFDTLSSRPLKAWLQGVNTHL--PDAVRVTWAMPVSFHFHARFSALSRTYHYWIQTE 139

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +      SLD E M++AA+ L+G HDF++FR+  CQA SP+R I       
Sbjct: 140 PVRSALFSQQLTWTGHSLDVERMQLAAESLLGEHDFSSFRAAQCQAHSPVREIQAVSFER 199

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           +GNLI  RV A +FLH  +R+ +GSL LVG G  + + +E+ L A+DR    P A P GL
Sbjct: 200 YGNLILFRVRANAFLHHMVRNLIGSLMLVGRGLQSPSWIEQLLAARDRTLAAPTAAPWGL 259

Query: 240 YFDSVEYS 247
              +VEY 
Sbjct: 260 SLVAVEYP 267


>gi|225867856|ref|YP_002743804.1| tRNA pseudouridine synthase A [Streptococcus equi subsp.
           zooepidemicus]
 gi|259550446|sp|C0MFQ1|TRUA_STRS7 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225701132|emb|CAW98001.1| tRNA pseudouridine synthase A [Streptococcus equi subsp.
           zooepidemicus]
          Length = 249

 Score =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+QRQ    ++Q  IEK +  +TG + + +HGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGTLFSGFQRQSQARTVQEEIEKTLQKLTGGQGIQIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++  P  L  AL+   +  D I +++L      FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLEQKRDPEKLRFALDT--QTPDDIDVISLEAAADDFHARYHKHFKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDIAKMQAAIKDLVGTHDFTGFTAAGTSVKNKVRTITAATLTQ 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     +   L++++R+  GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRLPIEQIRLVLESKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|77919497|ref|YP_357312.1| tRNA pseudouridine synthase A [Pelobacter carbinolicus DSM 2380]
 gi|123756611|sp|Q3A3B5|TRUA_PELCD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|77545580|gb|ABA89142.1| tRNA pseudouridine synthase A [Pelobacter carbinolicus DSM 2380]
          Length = 252

 Score =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +IIEY+G+ Y GWQRQ NG S+Q  +E+A+  V G    +  +GRTD+GVHA   
Sbjct: 1   MSVVRLIIEYDGTPYVGWQRQPNGLSVQQVVEEALAKVCGGPHSLVSSGRTDAGVHARGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF   +        + +N +L     I++ + +++   FHAR+SA+ + Y Y I    
Sbjct: 61  VAHFVTPQPLPMAAYREGVNRFL--PAQIAVRDAALMPDDFHARYSAVGKWYRYSIYRSP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    +W +   LD + MR AA+ LVGRHDF  FR+  C A + +R +   D+   
Sbjct: 119 VRSPLACRFSWHVRTVLDLQAMRQAARLLVGRHDFAAFRASGCAARTTVREVFSVDIVDA 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + V    FL   +R  VG+L  VG G     ++   L    RK+ G  AP +GL 
Sbjct: 179 EEWVYVDVRGSGFLRNMVRIMVGTLVEVGRGARPPEEVGAMLAGGCRKQSGITAPAQGLC 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LMEVAY 244


>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 =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 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|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 =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 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|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 =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 95/252 (37%), Positives = 135/252 (53%), Gaps = 8/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI----VVVHGAGRTDSGVH 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  ALGQVVHFDLDFEIHPLALAKALNSILN--KDIRVVAVSQVAPDFHARYHAIGKAYLYRI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            T+  P   ++      P   D   M+ A   LVG+HDFT+F S H      +RTI    
Sbjct: 119 DTQAYPDPFKRFYTLHHPYRYDLGKMQRALTDLVGQHDFTSFCSTHSDKEDKVRTIKFAT 178

Query: 177 VNSF--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +        +   +    FL+  +R  VG+L  +GDG     + ++ L  +DR + GP A
Sbjct: 179 IEEDLVNQELRFMIAGNGFLYNMVRIIVGTLLQIGDGLKPVDEFKRLLAVKDRNQAGPTA 238

Query: 235 PPEGLYFDSVEY 246
            P GLY   V+Y
Sbjct: 239 DPSGLYLYRVDY 250


>gi|256958303|ref|ZP_05562474.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|257078388|ref|ZP_05572749.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257420509|ref|ZP_05597499.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|294780153|ref|ZP_06745525.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|307268416|ref|ZP_07549794.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|256948799|gb|EEU65431.1| tRNA pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256986418|gb|EEU73720.1| tRNA pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257162333|gb|EEU92293.1| tRNA pseudouridine synthase [Enterococcus faecalis X98]
 gi|294452696|gb|EFG21126.1| tRNA pseudouridine synthase A [Enterococcus faecalis PC1.1]
 gi|306515223|gb|EFM83760.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4248]
 gi|315036592|gb|EFT48524.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0027]
 gi|329575477|gb|EGG57017.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1467]
          Length = 246

 Score =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILKQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|266623132|ref|ZP_06116067.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
 gi|288865107|gb|EFC97405.1| tRNA pseudouridine synthase A [Clostridium hathewayi DSM 13479]
          Length = 404

 Score =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 135/246 (54%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            Y ++++Y+GS Y GWQ+Q N G++IQG +E  +  +TG  V VHG+GRTD+GVHAL Q 
Sbjct: 158 NYKIVLQYDGSRYDGWQKQGNTGNTIQGKLEGILLKLTGRPVEVHGSGRTDAGVHALAQT 217

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          +    N YL   + I++L++  V  +FH+R +A++++YLYRI     
Sbjct: 218 ANFHADTGMTEDQIRAYFNQYL--PEDIAVLSVEKVQDKFHSRLNAVQKTYLYRIEMGPK 275

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E+   + + K L  + M+ AA  ++G HDF +F        S +RTI    +   G
Sbjct: 276 KDVFERKYCYGLGKQLSADRMKEAAACVLGEHDFKSFCGNKKMKKSTVRTISDITIEKEG 335

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + IR     FL+  +R   G+L  +G  + +  ++++ L   DR+  G  APPEGL+ 
Sbjct: 336 TKLLIRYTGNGFLYHMVRILTGTLIEIGLEERSPQEMKEILLKLDRQAAGFTAPPEGLFL 395

Query: 242 DSVEYS 247
           + V Y 
Sbjct: 396 ERVMYE 401


>gi|327536150|gb|AEA94984.1| tRNA-pseudouridine synthase I [Enterococcus faecalis OG1RF]
          Length = 246

 Score =  285 bits (731), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +  R
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|227554442|ref|ZP_03984489.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|229547551|ref|ZP_04436276.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|255970776|ref|ZP_05421362.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|256761150|ref|ZP_05501730.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
 gi|256960384|ref|ZP_05564555.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|257080567|ref|ZP_05574928.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|293384357|ref|ZP_06630242.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|307274425|ref|ZP_07555609.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|307287287|ref|ZP_07567351.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|307289762|ref|ZP_07569700.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|312902050|ref|ZP_07761311.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|312908558|ref|ZP_07767502.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|312908972|ref|ZP_07767834.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
 gi|312951751|ref|ZP_07770643.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|227176427|gb|EEI57399.1| tRNA-pseudouridine synthase I [Enterococcus faecalis HH22]
 gi|229307324|gb|EEN73311.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX1322]
 gi|255961794|gb|EET94270.1| tRNA pseudouridine synthase [Enterococcus faecalis T1]
 gi|256682401|gb|EEU22096.1| tRNA pseudouridine synthase [Enterococcus faecalis T3]
 gi|256950880|gb|EEU67512.1| tRNA pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256988597|gb|EEU75899.1| tRNA pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|291078349|gb|EFE15713.1| tRNA pseudouridine synthase A [Enterococcus faecalis R712]
 gi|306499218|gb|EFM68695.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0411]
 gi|306501620|gb|EFM70914.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0109]
 gi|306508935|gb|EFM78021.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2134]
 gi|310625525|gb|EFQ08808.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 512]
 gi|310630239|gb|EFQ13522.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0102]
 gi|311290672|gb|EFQ69228.1| tRNA pseudouridine synthase A [Enterococcus faecalis DAPTO 516]
 gi|311290832|gb|EFQ69388.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0470]
 gi|315030617|gb|EFT42549.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4000]
 gi|315148974|gb|EFT92990.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX4244]
 gi|315153400|gb|EFT97416.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0031]
 gi|315160015|gb|EFU04032.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0312]
 gi|315166006|gb|EFU10023.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX1302]
 gi|315575028|gb|EFU87219.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309B]
 gi|315581086|gb|EFU93277.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0309A]
 gi|323478960|gb|ADX78399.1| tRNA pseudouridine synthase A [Enterococcus faecalis 62]
          Length = 246

 Score =  285 bits (730), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>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 =  285 bits (730), Expect = 3e-75,   Method: Composition-based stats.
 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|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 =  285 bits (730), Expect = 3e-75,   Method: Composition-based stats.
 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|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 =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 128/246 (52%), Gaps = 2/246 (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  VHFDAAVERSMFAWVRGTNSFL--PSAVAVRWARPVADDFHARFSAYARRYRYLLINRAH 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 DSVEYS 247
            +V Y 
Sbjct: 239 FAVRYP 244


>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 =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 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|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 =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 91/249 (36%), Positives = 138/249 (55%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +G ++Q  +E A+      G  V    AGRTD+GVHA 
Sbjct: 1   MSRIALGLAYDGSAWQGWQTQPHGVTVQDQVEAALASFAGGGGPVATVCAGRTDTGVHAA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H D   +       + +NA+L    +I +     V + FHARFSA  R+Y+Y +  
Sbjct: 61  MQVIHLDTDLQRRDESWVRGVNAFL--PPSIVVQWARPVSEAFHARFSARSRTYVYLLWR 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 LYFDSVEYS 247
           LY  ++EY 
Sbjct: 239 LYLSAIEYP 247


>gi|309798794|ref|ZP_07693058.1| tRNA pseudouridine synthase A [Streptococcus infantis SK1302]
 gi|308117611|gb|EFO55023.1| tRNA pseudouridine synthase A [Streptococcus infantis SK1302]
          Length = 249

 Score =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IE  +  +  G+ + +HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEITLTKLNKGQAITIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M++A + L G HDFT F +        +RTI      V
Sbjct: 119 RPKNPMRRHYATHYPYPLDVERMQLAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLRV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPIEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|227517362|ref|ZP_03947411.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
 gi|227075232|gb|EEI13195.1| tRNA-pseudouridine synthase I [Enterococcus faecalis TX0104]
          Length = 277

 Score =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 32  MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 91

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 92  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 149

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 150 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 209

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 210 DGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 269

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 270 FLDEVYY 276


>gi|238927931|ref|ZP_04659691.1| tRNA-pseudouridine synthase I [Selenomonas flueggei ATCC 43531]
 gi|238884264|gb|EEQ47902.1| tRNA-pseudouridine synthase I [Selenomonas flueggei ATCC 43531]
          Length = 256

 Score =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 79/252 (31%), Positives = 126/252 (50%), Gaps = 8/252 (3%)

Query: 1   MIR-----YCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M++       + I Y+G+ Y G+QRQ     ++Q  +E A+  + GE+V +  AGRTD+G
Sbjct: 1   MMKQRARNIALTIAYDGTNYHGFQRQTPPVLAVQNVLEGALAKICGEMVELAAAGRTDAG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  QV +F          L +A+N  L     I +       ++F AR SA  ++Y+Y
Sbjct: 61  VHAYGQVVNFFTDGRIPTEHLPRAVNGLL--PPDIVVSQAWEAPREFSARHSATGKAYVY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           RI   + P    +  AW + + LD E M      L G HD+++FR+      SP+RT+D 
Sbjct: 119 RIEECRVPNPFTRNYAWQVFQPLDHEAMHAVLLLLKGTHDYSSFRAAGGAPMSPVRTLDE 178

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +      + I V    FL+  +R+ V +   VG G+ + +   +   A+DR+   P A
Sbjct: 179 IRLTEEEGRLSIYVHGTGFLYHMVRNIVSTAAAVGMGRISPSRFAEIFAARDRRLAPPTA 238

Query: 235 PPEGLYFDSVEY 246
           P  GLY  +V+Y
Sbjct: 239 PACGLYLLAVDY 250


>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 =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 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|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 =  285 bits (730), Expect = 4e-75,   Method: Composition-based stats.
 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|315149110|gb|EFT93126.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0012]
          Length = 246

 Score =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 SGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|95928687|ref|ZP_01311433.1| tRNA pseudouridine synthase A [Desulfuromonas acetoxidans DSM 684]
 gi|95135032|gb|EAT16685.1| tRNA pseudouridine synthase A [Desulfuromonas acetoxidans DSM 684]
          Length = 251

 Score =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 124/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R C+ +EY+G+ Y GWQ Q N  ++Q  IE A+  V G  V V+ +GRTD+GVHA+  
Sbjct: 1   MPRLCLTVEYDGTSYGGWQVQPNAQTVQEQIESALAQVIGASVRVYSSGRTDAGVHAIDM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD+          + +N +L     I +  +  V   FHARF A  + Y YR+   +
Sbjct: 61  KAHFDVETLLPLSAYREGVNRFL--PQDIVVRQVCRVADDFHARFDAQGKWYRYRLYRGR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +  +W +   LD E M  AA  LVG HDF  F++  C A++  RT+    +   
Sbjct: 119 IRSPLHRLTSWHVAGGLDVEAMTQAADALVGTHDFAAFQASGCAAATTQRTLFEVLLIDE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I V    FL   +R  VGSL  VG  K T+  L + L +  R   G  AP +GL 
Sbjct: 179 GDELIIDVRGSGFLKNMVRIIVGSLVEVGRAKLTAGQLAEILASGQRCRAGLTAPAQGLC 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LMQVWYE 245


>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 =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 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|163790163|ref|ZP_02184597.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
 gi|159874654|gb|EDP68724.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
          Length = 279

 Score =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 137/247 (55%), Gaps = 5/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY MII+Y+G+ + G+Q Q N  ++QG I+KA+ ++T G  +++HG+GRTDSGVHA  QV
Sbjct: 5   RYKMIIQYDGTHFAGFQIQPNDRTVQGEIQKALKIMTKGLEIIIHGSGRTDSGVHAKGQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD         + +ALN+     D + +  ++IVD  FHAR++   + Y YR+     
Sbjct: 65  IHFDYPILLPVENMQRALNSLTT--DELFVEKVAIVDTNFHARYNTSGKKYQYRVDLNAI 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-- 179
           P   ++      P  +D E ++ A + L G HDF++F + +    + +RT+    V    
Sbjct: 123 PNPFKRLYTLHHPYPIDMEKLQNALKDLEGEHDFSSFCASNSGRENKVRTVYEASVVKDI 182

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           F N +        FL+  +R FVG+L  + +G   + ++++ L  +DR E GP A P+GL
Sbjct: 183 FNNELIFTFSGNGFLYNMVRIFVGTLLQIANGLRPADEIKRLLAVKDRNEAGPTAKPQGL 242

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 243 YLMEVYY 249


>gi|116749101|ref|YP_845788.1| tRNA pseudouridine synthase A [Syntrophobacter fumaroxidans MPOB]
 gi|116698165|gb|ABK17353.1| tRNA pseudouridine synthase A [Syntrophobacter fumaroxidans MPOB]
          Length = 261

 Score =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 84/245 (34%), Positives = 130/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            + +I+EY+GS Y GWQRQ    +IQ  +E  + ++    V V  +GRTD+GVHA  QV 
Sbjct: 11  NFKLILEYDGSHYHGWQRQLGVLTIQEVLESRLEVMLQSPVGVRASGRTDAGVHACGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F +     P  + + +N+ L     I +L+  +  + FHARFSA  ++Y Y I+ R   
Sbjct: 71  NFHVHTRLRPEEILRGINSLL--PPDIVVLHAEVAAESFHARFSATGKTYEYHILNRPIR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            AL++  AW +P+ L+ + MR     L+GRHDF  F +   +  S  RTI   D++   N
Sbjct: 129 SALQRRYAWHVPQPLEPQRMRECLGSLLGRHDFAAFMASGSKVKSTERTIRRADLDCLEN 188

Query: 183 -LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + +   A  FL   +R+ VG++  VG G     +    L ++DRK  G  AP  GL+ 
Sbjct: 189 GEMRLVFEANGFLRHMVRNLVGTIVEVGRGVRAPEEFLDILSSRDRKRAGMTAPAHGLFL 248

Query: 242 DSVEY 246
            +V Y
Sbjct: 249 TAVHY 253


>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 =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 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|225175641|ref|ZP_03729635.1| tRNA pseudouridine synthase A [Dethiobacter alkaliphilus AHT 1]
 gi|225168970|gb|EEG77770.1| tRNA pseudouridine synthase A [Dethiobacter alkaliphilus AHT 1]
          Length = 246

 Score =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y+G+GY G+Q QKN  ++Q  +E+AI  V G+ V +  +GRTD+GVHA  Q
Sbjct: 1   MPNIKLTLGYDGTGYHGFQLQKNAVTVQQKLEEAIEKVMGQKVRITASGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F       P  +  ALNA L     I I    IV   FHARF A+ ++Y Y I    
Sbjct: 61  VINFFAQTGIPPQRIPHALNAVL--PRDIVIYAAEIVSDSFHARFDAVGKTYTYTIDNGA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +  A+ +   LD   M+ AA  L G+HDFT+F +      + +R +   DV   
Sbjct: 119 HPQVLSRHHAYHVRFPLDANLMKQAAATLQGKHDFTSFMASGSSVKTTVRNLYRLDVEIN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I   A  FL+  +R   G+L  VG GK    +L   + A++R   G   P  GL 
Sbjct: 179 WPYITITAAADGFLYNMVRIIAGTLIEVGRGKRD-HNLGPVIDAKNRHRAGWTVPAHGLV 237

Query: 241 FDSVEYS 247
              VEY+
Sbjct: 238 LREVEYN 244


>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 =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 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|222100131|ref|YP_002534699.1| tRNA pseudouridine synthase A [Thermotoga neapolitana DSM 4359]
 gi|254764873|sp|B9K8Q0|TRUA_THENN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221572521|gb|ACM23333.1| tRNA pseudouridine synthase A [Thermotoga neapolitana DSM 4359]
          Length = 245

 Score =  285 bits (729), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 129/246 (52%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   I+EY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MRRVAAIVEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+          +  A+NA L   D + +  +  V K FH RF   +R Y Y I T 
Sbjct: 61  LIAFNCPNDRMTTEDIKNAMNANL--PDDVYVKKVFEVPKNFHPRFDVKKRIYHYFIHTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  AW  P  LD E MR AA++L G HDFT+F         P+RTI    + S
Sbjct: 119 REKNVFLRKYAWWFPYELDLEAMRKAAKYLEGTHDFTSF-KTGSDERDPVRTIYRIRILS 177

Query: 180 FG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            G ++I IRV  RSFL   +R+ V +L  VG  +W    L++ L+A+DR      AP  G
Sbjct: 178 LGKDMILIRVEGRSFLRRMVRNIVAALVKVGLRQWEPEKLKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>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 =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 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|282852680|ref|ZP_06262022.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 224-1]
 gi|282556422|gb|EFB62042.1| tRNA pseudouridine synthase A [Lactobacillus gasseri 224-1]
          Length = 258

 Score =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 130/251 (51%), Gaps = 8/251 (3%)

Query: 1   MI--RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHA 57
           M+  RY + + Y+G  + G+Q Q N  ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA
Sbjct: 1   MMTTRYKLTMAYDGHLFHGFQIQPNERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHA 60

Query: 58  LRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             QV HFD   +E     +  ALNA +         +  IVD  FH ++S   + Y Y +
Sbjct: 61  KGQVIHFDYPGKEIPAKNMMLALNALM--PIDTVFFDSEIVDSDFHVQYSTKGKWYRYIV 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +      +      P  LD   M+ AA+ L+G HDFT+F +   Q    +RTI + +
Sbjct: 119 DQHRFTDPFNRFYTGHYPYPLDIALMKKAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVN 178

Query: 177 VNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           + S  +   I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    A
Sbjct: 179 ITSDPDNKKIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTA 238

Query: 235 PPEGLYFDSVE 245
           P  GLY   V 
Sbjct: 239 PASGLYLQHVF 249


>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 =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 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|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 =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 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|329121886|ref|ZP_08250501.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
 gi|327467824|gb|EGF13316.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
          Length = 244

 Score =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y MIIEY+G+ Y GWQ+QK+   ++QG IEKA   VTGE V + GAGRTDSGVHA  Q
Sbjct: 1   MNYKMIIEYDGTRYEGWQKQKHSDETLQGKIEKAFEKVTGENVQIIGAGRTDSGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+  L  +     L   LN  L   D I I     V+++FH+RF A  + Y Y +    
Sbjct: 61  VANVHLPYDLNAENLKNELNEIL--PDDIYIKQCIEVEEKFHSRFHAKSKIYEYNLRIGS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +K   W   K L  E M+ AA+ L G HDFT F +      S +RT+   ++++ 
Sbjct: 119 NKDVFQKRFIWQFAKPLCIEKMKRAAEILQGTHDFTAFCNNKHFKKSAVRTVYSIEISTS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +++ +R     FL   IR  VG+L  VG+ K  +  L   L+++ R   G  APP+GL 
Sbjct: 179 NDILHLRFCGDGFLQGMIRIMVGTLVEVGENKRDADSLYDVLKSKQRSNAGFTAPPQGLT 238

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 239 LISVQY 244


>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 =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 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|104780847|ref|YP_607345.1| tRNA pseudouridine synthase A [Pseudomonas entomophila L48]
 gi|95109834|emb|CAK14539.1| tRNA-pseudouridine synthase I [Pseudomonas entomophila L48]
          Length = 284

 Score =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + +EY GS Y GWQRQ     S+Q ++E+A+  V  E + V  AGRTD+GVH   Q
Sbjct: 17  TRIALGVEYKGSRYRGWQRQASGVPSVQQALEQALSTVANEPITVVCAGRTDAGVHGCGQ 76

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD              N  L     IS++  + +   FHARF A  R Y Y I    
Sbjct: 77  IVHFDTRAVRDERAWTLGTNFNL--PHDISVVWSAPMPAHFHARFKATARRYRYVIYNDP 134

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A          + LD   M  AA++L+G HDF+ FR+  CQA SPI+ I H  V   
Sbjct: 135 IRPAHLAEEVTWNHRPLDVTRMAEAARYLLGTHDFSAFRASQCQAKSPIKHIHHLRVTRH 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I + V A +FLH  +R+  G L  +G G+       + L+ ++R+E G  A P GLY
Sbjct: 195 GQMIVLDVRATAFLHHMVRNIAGVLMTIGAGERPVEWAREVLEGRNRREGGVTAHPYGLY 254

Query: 241 FDSVEYS 247
              VEY 
Sbjct: 255 LVQVEYP 261


>gi|326938210|gb|AEA14106.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 245

 Score =  285 bits (729), Expect = 5e-75,   Method: Composition-based stats.
 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|295319272|gb|ADF99649.1| tRNA pseudouridine synthase A [Clostridium botulinum F str. 230613]
          Length = 246

 Score =  284 bits (728), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 138/248 (55%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>gi|291279383|ref|YP_003496218.1| tRNA pseudouridine synthase A [Deferribacter desulfuricans SSM1]
 gi|290754085|dbj|BAI80462.1| tRNA pseudouridine synthase A [Deferribacter desulfuricans SSM1]
          Length = 244

 Score =  284 bits (728), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +   ++EY+G+ +FGWQRQK+  ++QG IE A+  +    + + G+GRTD+GVHA+ Q
Sbjct: 1   MYKKKCVVEYDGTYFFGWQRQKDLRTVQGVIEAALSKIYKSSINIVGSGRTDTGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF   R      +   LN+ L   + + I ++  VD  FHA+ SAI ++Y+Y+I   Q
Sbjct: 61  VFHFVSERYLENRSVLLGLNSVL--PEDVVIKHVEDVDLSFHAQKSAISKTYIYKIYNYQ 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL + RAW I  ++D + +    +   G  DF+          +P+RTI++      
Sbjct: 119 IRSALFRNRAWWIRDNIDVDLLNEYLKFFKGEKDFSAMCLKRSVPENPVRTINYIFAKRD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I + A  FLH  +R+ VG++  +     +   +E+ L+++DRK  G  APP+GLY
Sbjct: 179 GDFINIEINANGFLHNMVRNIVGTVIDLYSDNSSPEKIEEILKSKDRKNAGRTAPPQGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LKEVFY 244


>gi|317048970|ref|YP_004116618.1| tRNA pseudouridine synthase A [Pantoea sp. At-9b]
 gi|316950587|gb|ADU70062.1| tRNA pseudouridine synthase A [Pantoea sp. At-9b]
          Length = 268

 Score =  284 bits (728), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 89/245 (36%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V    V V  AGRTD+GVH   QV 
Sbjct: 9   KLALGIEYDGSRYYGWQRQQEVRSVQEKLEKALSKVANHDVSVFCAGRTDAGVHGTGQVV 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V + FHARFSA  R Y Y I  ++  
Sbjct: 69  HFETTSQRADGAWTLGVNANL--PPDIAVRWVKAVPETFHARFSATARRYRYVIYNQRLR 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 127 PAILGSGVTHFYHPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVMHLNVTRQGP 186

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G    + +   L A+DR      A  EGLY  
Sbjct: 187 YVIVDIKANAFVHHMVRNIVGSLMEIGCGNQPESWMATLLAAKDRTLAAATARAEGLYLV 246

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 247 AVDYP 251


>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 =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 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|323340405|ref|ZP_08080662.1| tRNA pseudouridine synthase A [Lactobacillus ruminis ATCC 25644]
 gi|323092181|gb|EFZ34796.1| tRNA pseudouridine synthase A [Lactobacillus ruminis ATCC 25644]
          Length = 250

 Score =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 124/250 (49%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
            RY + + Y+G+ + G+Q Q N  ++Q  +E A+  ++   + + ++G+GRTD+GVHAL 
Sbjct: 3   RRYKITLAYDGTNFAGFQVQPNQRTVQSVLEAAVNKMSKNSDYITIYGSGRTDAGVHALG 62

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +     + K LN+ L       ++   IV   FHARF+   + Y+YR+   
Sbjct: 63  QVVHFDFPHDIPAEGMLKGLNSML--PLACEVVGCEIVPNDFHARFTTHGKRYMYRVSRG 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++         LD E ++ A   LVG HDF++F +   Q  + +RTI    V  
Sbjct: 121 RFTNPFKRFYTGHYKYPLDIEKIKEAMPDLVGTHDFSSFVASGSQTKNHVRTIYEATVRE 180

Query: 180 --FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + I        FL+ Q+R  V +L  +G+GK    D  +  + +DR EC   AP  
Sbjct: 181 DKENDEIIFEFCGNGFLYNQVRIMVATLLEIGNGKRPVHDFLRLYEVKDRNECRETAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLKEVYYD 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 =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 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|187779482|ref|ZP_02995955.1| hypothetical protein CLOSPO_03078 [Clostridium sporogenes ATCC
           15579]
 gi|187773107|gb|EDU36909.1| hypothetical protein CLOSPO_03078 [Clostridium sporogenes ATCC
           15579]
          Length = 246

 Score =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 138/248 (55%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + + G+GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIGSGRTDAGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTNFQGSTNEILNYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ +P++LD E M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHVPQTLDIEAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++I  +   FLH  IR   G+L  +G    +  +++  L+A+DR++    AP +GL
Sbjct: 179 KDGYVDIVYLGSGFLHKMIRILTGTLIEIGLHNLSPMNVKTILEAEDRRKASSTAPSQGL 238

Query: 240 YFDSVEYS 247
           +  SV Y 
Sbjct: 239 FMTSVTYE 246


>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 =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 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   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 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTIDHFDVN 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|302669997|ref|YP_003829957.1| tRNA pseudouridine synthase A TruA1 [Butyrivibrio proteoclasticus
           B316]
 gi|302394470|gb|ADL33375.1| tRNA pseudouridine synthase A TruA1 [Butyrivibrio proteoclasticus
           B316]
          Length = 262

 Score =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 122/246 (49%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + + Y+G+ Y GW  Q +   +I+G + +AI  +TGE V V GA RTD+GVHA   
Sbjct: 5   RRIMLTVSYDGTAYNGWAEQTSTPNTIEGELNRAIERLTGEPVHVIGASRTDAGVHAYGN 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN   ++   I I+N   V   FH R     ++Y YRI   Q
Sbjct: 65  VAVFDTASSIPGDRFVFALN--HELPQDIRIVNSREVATSFHPRHCDTEKTYEYRIFNSQ 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++         LD   M  AA +LVG HDFT+F ++  QA S +RTI    V   
Sbjct: 123 IMDPTKRFYTCHFSMPLDIGRMNAAAHYLVGEHDFTSFCNVESQALSHVRTIKDIRVTRN 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I V    FL+  +R   G+L  +G GK T  +++  L  + R   GP AP EGL+
Sbjct: 183 GDEVVISVTGNGFLYNMVRIIAGTLMQIGRGKGTPAEVKDILDKKYRGAAGPTAPAEGLF 242

Query: 241 FDSVEY 246
              VEY
Sbjct: 243 L--VEY 246


>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 =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 113/247 (45%), Positives = 156/247 (63%), Gaps = 1/247 (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 FDSVEYS 247
              V+Y 
Sbjct: 240 LTGVDYP 246


>gi|315925222|ref|ZP_07921436.1| tRNA pseudouridine synthase A [Pseudoramibacter alactolyticus ATCC
           23263]
 gi|315621456|gb|EFV01423.1| tRNA pseudouridine synthase A [Pseudoramibacter alactolyticus ATCC
           23263]
          Length = 249

 Score =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 118/246 (47%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    ++I Y G+ Y GWQRQ+N  SI  +I  AI  VTGE V ++GAGRTD+GVHA  Q
Sbjct: 1   MRNIALVIAYKGTRYAGWQRQQNAVSIDETIGDAIAAVTGERVTLYGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F             ALNA+L     I I     V   FH+R+ A  ++Y YR+    
Sbjct: 61  RANFKTRVRMPADRFAPALNAHL--PRDIRIQKSFEVPADFHSRYGAKEKTYCYRVWAAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L     W +   L+ + MR  A  LVG HDF TF +    A + +R ID   +   
Sbjct: 119 VADPLTDDFCWHVRFPLNVDAMRRGAAVLVGTHDFKTFMASGSGAKTTVRRIDAIGIEQK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I        FL+  +R   G+L  +G G+     +   L A+ R   G  AP  GL 
Sbjct: 179 GRMITFTFCGTGFLYNMVRIIAGTLVEMGSGRRDPESMAAILAAKGRTAAGATAPARGLT 238

Query: 241 FDSVEY 246
            ++V Y
Sbjct: 239 LEAVAY 244


>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 =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 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|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 =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 140/248 (56%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>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 =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 138/248 (55%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>gi|256962868|ref|ZP_05567039.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|307274272|ref|ZP_07555473.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
 gi|256953364|gb|EEU69996.1| tRNA pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|306509045|gb|EFM78114.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0855]
          Length = 246

 Score =  284 bits (728), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMERACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>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 =  284 bits (728), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 97/245 (39%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 20  KIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVLCAGRTDAGVHATGQVV 79

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF    E         +N++L     I++  +  VD  FHARFSA  R Y Y I   +  
Sbjct: 80  HFITTAERKNAAWTMGVNSHL--PPDIAVRWVKTVDDGFHARFSATARRYRYIIFNHRYR 137

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G HDFT+FR+I CQ+ +P R + H  V   G 
Sbjct: 138 PAVLAQGVTHCYMPLDAEKMEQAAQCLLGEHDFTSFRAIQCQSRTPWRNVKHVKVTRHGA 197

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G  + T + + L  +DR      A  EGLY  
Sbjct: 198 YIVVDIKANAFVHHMVRNIVGSLIEIGCGNQSVTWMAELLALKDRARAAATAKAEGLYLV 257

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 258 SVDYP 262


>gi|229548121|ref|ZP_04436846.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|257091270|ref|ZP_05585631.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257417169|ref|ZP_05594163.1| tRNA pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|300861430|ref|ZP_07107514.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|312905329|ref|ZP_07764444.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
 gi|229306807|gb|EEN72803.1| tRNA-pseudouridine synthase I [Enterococcus faecalis ATCC 29200]
 gi|257000082|gb|EEU86602.1| tRNA pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257158997|gb|EEU88957.1| tRNA pseudouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|295114364|emb|CBL33001.1| pseudouridylate synthase I [Enterococcus sp. 7L76]
 gi|300848891|gb|EFK76644.1| tRNA pseudouridine synthase A [Enterococcus faecalis TUSoD Ef11]
 gi|310631353|gb|EFQ14636.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0635]
 gi|315145838|gb|EFT89854.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX2141]
 gi|315162508|gb|EFU06525.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0645]
 gi|315578608|gb|EFU90799.1| tRNA pseudouridine synthase A [Enterococcus faecalis TX0630]
          Length = 246

 Score =  284 bits (728), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYLGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|319939850|ref|ZP_08014205.1| tRNA pseudouridine synthase A [Streptococcus anginosus 1_2_62CV]
 gi|319810861|gb|EFW07180.1| tRNA pseudouridine synthase A [Streptococcus anginosus 1_2_62CV]
          Length = 249

 Score =  284 bits (728), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ V+VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHDFAGFQRQPHARSVQEEIEKTLTKINRGKPVIVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  + I  +++  V++ FH+R+    + Y + +   
Sbjct: 61  QVIHFDLPQKRDEEKLRFALDT--QTPEDIDFISVEEVNEDFHSRYWKHSKIYEFIVDVG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD   ++ A   L G HDFT F +      + +RTI     D 
Sbjct: 119 RPKNPMMRHYATHFPYPLDISLIKNAIAKLEGTHDFTGFTASGTSVENKVRTITEARLDF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N +        FL+ QIR+ VG+L  +G+G+     +++ L  ++R   GP A P 
Sbjct: 179 DEKRNFLIFTFSGNGFLYKQIRNMVGTLLKIGNGRMPVEQIDRILTEKNRHLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|332970004|gb|EGK09003.1| tRNA pseudouridine synthase A [Psychrobacter sp. 1501(2011)]
          Length = 314

 Score =  284 bits (728), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 87/244 (35%), Positives = 129/244 (52%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + IE+NGS Y GWQRQ+    +Q  +E+ +  +  E + V  AGRTD+GVH    +AH
Sbjct: 52  YALGIEFNGSNYRGWQRQQEVLCVQQVLEETLSKIANEPIEVVAAGRTDAGVHGGNMLAH 111

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F            +  N+ L   D I+I  +  +   FHARF AI R Y Y  + +    
Sbjct: 112 FKTSANRGVYNWLRGANSLL--PDDIAIRWIQPMPDDFHARFGAIARRYRYITLNQPQRP 169

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+       I + LD   M+ AA H+VG+HDF++FR+  CQ++ P+R I H  +   G  
Sbjct: 170 AVLNHLVTHIHEPLDLAKMQQAAAHIVGQHDFSSFRAAACQSNQPVRNIHHAKLFQHGQF 229

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I   + A  FLH  +R+ +G+L  +G G+    D  + L+A+DR    P A P+GLYF +
Sbjct: 230 IVFDIQADGFLHHMVRNLMGTLFAIGKGELQPMDYLRILEAKDRTIAPPTASPDGLYFIN 289

Query: 244 VEYS 247
             Y 
Sbjct: 290 AYYP 293


>gi|317492661|ref|ZP_07951088.1| tRNA pseudouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919411|gb|EFV40743.1| tRNA pseudouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 285

 Score =  284 bits (728), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 89/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y GWQRQ +  S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 26  KIALGIEYDGSQYAGWQRQSDAPSVQECLEKALSKVACEPITVSCAGRTDAGVHATGQVV 85

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +N ++     I++  +  V + FHARFSA  R Y Y I   +  
Sbjct: 86  HFETHVARKDAAWTMGVNTHM--PKDIAVRWVKSVSEDFHARFSATARRYRYVIYNHRYR 143

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+ +         LD E M  A Q L+G +DFT+FR+  CQ+ +P R + H  V   G+
Sbjct: 144 QAVLQNGLTHFYHHLDAERMERAGQALLGENDFTSFRASQCQSRTPWRNVSHLKVTRLGD 203

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  +G G    + + + L A+DRK     A   GLY  
Sbjct: 204 YVIVDIKANAFVHHMVRNIVGSLMEIGCGNQPESWMAELLAAKDRKLAAATAKAAGLYLV 263

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 264 SVDYP 268


>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 =  284 bits (728), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 96/246 (39%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R+ + +EY+G+G+ GWQRQ +  S+QG +E A+  V    + V  AGRTD+GVHAL QV
Sbjct: 10  TRWALGLEYDGNGFCGWQRQLDQDSVQGVVEAALSRVAQCPISVVVAGRTDTGVHALCQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P    +  N  L     +++    +V   FHARFSA  R Y Y I+ R+ 
Sbjct: 70  VHFDSPVLRRPEAWVRGANTAL--PAGVALRWARVVPDSFHARFSATARRYRYVILNRRE 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL +     I   LD E M+ AAQ L+G HDF+ FR+  CQA SP+R +    V   G
Sbjct: 128 KSALWRNHTAWIYSPLDVEAMQAAAQTLLGTHDFSAFRAAACQAKSPVRNLCQLRVVRRG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +LI +   A  FLH  +R+ VG L  +G          + L ++DR   G  APP GLYF
Sbjct: 188 DLIAVDAEANGFLHHMVRNLVGVLIAIGKADRPVDWAAEVLASRDRCRAGVTAPPGGLYF 247

Query: 242 DSVEYS 247
            +  Y 
Sbjct: 248 VAPRYP 253


>gi|253689176|ref|YP_003018366.1| tRNA pseudouridine synthase A [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251755754|gb|ACT13830.1| tRNA pseudouridine synthase A [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 283

 Score =  284 bits (727), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ + +S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 24  KIALGIEYDGSQYYGWQRQSDVASVQACLEKALSKVADEPIEVFCAGRTDAGVHGTGQVV 83

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA L     I++  +  V++ FHARFSA  R Y Y I   +  
Sbjct: 84  HFTTQAIRKDAAWTMGVNANL--PPDIAVRWVKTVEEDFHARFSATARRYRYVIYNHRYR 141

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD + M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   G+
Sbjct: 142 PAVLSHGMTHFYHPLDVDRMERAGQCLLGENDFTSFRAVQCQSRTPWRYVNHLKVTRHGD 201

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 202 YIVVDIKANAFVHHMVRNIVGSLMEVGCGNRPESWIAELLAAKDRTLAAATARAEGLYLV 261

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 262 AVDYP 266


>gi|312868117|ref|ZP_07728321.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis F0405]
 gi|322390938|ref|ZP_08064444.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis ATCC
           903]
 gi|311096521|gb|EFQ54761.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis F0405]
 gi|321142313|gb|EFX37785.1| tRNA pseudouridine synthase A [Streptococcus parasanguinis ATCC
           903]
          Length = 248

 Score =  284 bits (727), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  S+Q  IEK +  +  G  V VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGTLFAGFQRQPHARSVQEEIEKTLTRLNQGTPVTVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L  AL+   +  + I  + +  V+  FH+R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDEEKLRFALDT--QTPEDIDFIRVEQVEDDFHSRYKKHSKTYEFIVDYG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD E M+ A Q L G HDFT F +        +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDVEKMQAAIQKLEGTHDFTGFTASGTSVEDKVRTITEARLVE 178

Query: 180 FGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR   GP A P 
Sbjct: 179 DAEHHRLVFTFSGNGFLYKQIRNMVGTLLKIGNDRMPIEQIDLILEKKDRNLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|260856362|ref|YP_003230253.1| pseudouridylate synthase I [Escherichia coli O26:H11 str. 11368]
 gi|257755011|dbj|BAI26513.1| pseudouridylate synthase I [Escherichia coli O26:H11 str. 11368]
 gi|323156469|gb|EFZ42624.1| tRNA pseudouridine synthase A [Escherichia coli EPECa14]
          Length = 270

 Score =  284 bits (727), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 90/245 (36%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   +  
Sbjct: 71  HFETTAQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLR 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G 
Sbjct: 129 PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVMRHGP 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTRAAATAKAEGLYLV 248

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 249 AVDYP 253


>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 =  284 bits (727), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 139/248 (56%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>gi|306825673|ref|ZP_07459012.1| tRNA pseudouridine synthase A [Streptococcus sp. oral taxon 071
           str. 73H25AP]
 gi|304432034|gb|EFM35011.1| tRNA pseudouridine synthase A [Streptococcus sp. oral taxon 071
           str. 73H25AP]
          Length = 261

 Score =  284 bits (727), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G  + VHGAGRTDSGVHAL 
Sbjct: 13  MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGHAITVHGAGRTDSGVHALG 72

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL+ +     L  AL+   +  + I ++++ +V   FH R++   ++Y + +   
Sbjct: 73  QVIHFDLLYQMDEEKLRFALDT--QSPEDIDVISMELVADDFHCRYAKHSKTYEFIVDRG 130

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M++A + L G HDFT F +        +RTI   +  V
Sbjct: 131 RPKNPMRRHYATHFPYPLDVERMQMAIKKLEGTHDFTGFTASGTSVEDKVRTITEANLTV 190

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 191 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 250

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 251 GLYLKEIRYE 260


>gi|168705501|ref|ZP_02737778.1| tRNA pseudouridine synthase A [Gemmata obscuriglobus UQM 2246]
          Length = 263

 Score =  284 bits (727), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 93/248 (37%), Positives = 135/248 (54%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALR 59
           M    +II Y+G+ +FGWQ Q    ++Q ++EKAI  +T E  V ++ +GRTDSGVHA+ 
Sbjct: 1   MRNLKLIIRYDGTDFFGWQTQPGRRTVQETVEKAIAEITREPRVRLNCSGRTDSGVHAVG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+     +    +L KA+NA L   + + +  ++   + F A   A+R+ Y Y +   
Sbjct: 61  QVANVYTASKLSCAVLLKAINAKL--PEDVGVREVTEAPQSFCANKDAVRKMYRYVVQDG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  AW + + L+ E M  A++ LVGRHDF  F +      + +RTI H  VN 
Sbjct: 119 RLQDPFLRKYAWFVRQHLNAEAMARASRCLVGRHDFRCFETEWPNRLTSVRTITHLSVNR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG  I I V A  FL+  +R+  GSL  VG G W  T +   L A DR+  GP APPEGL
Sbjct: 179 FGECIWIDVEANGFLYNMVRAIAGSLVQVGRGFWPETQIADVLHAMDRRLAGPTAPPEGL 238

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 239 FLMRVTYP 246


>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 =  284 bits (727), Expect = 9e-75,   Method: Composition-based stats.
 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   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 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTIDHFDVN 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|227824316|ref|ZP_03989148.1| tRNA pseudouridine synthase A [Acidaminococcus sp. D21]
 gi|226904815|gb|EEH90733.1| tRNA pseudouridine synthase A [Acidaminococcus sp. D21]
          Length = 253

 Score =  284 bits (727), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 85/249 (34%), Positives = 124/249 (49%), Gaps = 4/249 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M +    ++ Y+G+ Y G+QRQK+ G  +Q  +EKA+     E + +  AGRTD+GVHAL
Sbjct: 1   MKKTIMAVVAYDGTNYQGFQRQKDYGVGVQQVLEKALSTALHEDISIKAAGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F+      P    +AL   L     I+I    I    FHARF A+ ++Y Y ++ 
Sbjct: 61  GQVISFETSSPIPPENYRRALQHLL--PPDIAIREAFIKPDGFHARFDALDKTYRYTVLY 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P    +  AW +  SL    M  AA  LVG HDF++F++   + +SP+RT+      
Sbjct: 119 APLPDPCARRYAWEVRSSLTLAAMNEAAALLVGTHDFSSFKNQGSEKTSPVRTLYEAYWT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                    +    FL+  +R+ VG L  VG G+WT  D    + A+DRK+ G  AP  G
Sbjct: 179 QEKERFTFTIRGDGFLYRMVRNIVGCLVKVGTGEWTVADFAAVMAAKDRKKAGVAAPACG 238

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 239 LSLVHVSYP 247


>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 =  284 bits (726), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 97/245 (39%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 20  KIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVLCAGRTDAGVHATGQVV 79

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF    E         +N++L     I++  +  VD  FHARFSA  R Y Y I   +  
Sbjct: 80  HFITTAERKDAAWTMGVNSHL--PPDIAVRWVKTVDDGFHARFSATARRYRYIIFNHRYR 137

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G HDFT+FR+I CQ+ +P R + H  V   G 
Sbjct: 138 PAVLAQGVTHCYMPLDAEKMAQAAQCLLGEHDFTSFRAIQCQSRTPWRNVKHVKVTRHGA 197

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G  + T + + L  +DR      A  EGLY  
Sbjct: 198 YIVVDIKANAFVHHMVRNIVGSLIEIGCGNQSVTWMAELLALKDRARAAATAKAEGLYLV 257

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 258 SVDYP 262


>gi|304398239|ref|ZP_07380113.1| tRNA pseudouridine synthase A [Pantoea sp. aB]
 gi|304354105|gb|EFM18478.1| tRNA pseudouridine synthase A [Pantoea sp. aB]
          Length = 267

 Score =  284 bits (726), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            +  + IEY+GS Y+GWQRQ    S+Q  +E+A+  V    V +  AGRTD+GVH   QV
Sbjct: 7   QKLALGIEYDGSRYYGWQRQNEVRSVQEKVERALSKVADHPVSIFCAGRTDAGVHGTGQV 66

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +NA L     I++  +  V  +FHARFSA  R Y Y I  ++ 
Sbjct: 67  VHFETTSQRPDGAWTLGVNANL--PPDIAVRWVKAVPDEFHARFSATARRYRYLIYNQRL 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G
Sbjct: 125 RPAVLAQGVTHFYHPLDAEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVIHLNVTRQG 184

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  +G G    + +   L A+DR      A  EGLY 
Sbjct: 185 PYVIVDIKANAFVHHMVRNIVGSLMEIGCGNKPESWMATLLAAKDRTLAAATARAEGLYL 244

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 245 VAVDYP 250


>gi|16801808|ref|NP_472076.1| tRNA pseudouridine synthase A [Listeria innocua Clip11262]
 gi|24212565|sp|Q927P1|TRUA_LISIN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|16415283|emb|CAC97973.1| truA [Listeria innocua Clip11262]
 gi|313616961|gb|EFR89587.1| tRNA pseudouridine synthase A [Listeria innocua FSL S4-378]
          Length = 248

 Score =  284 bits (726), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 90/250 (36%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG+FG+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFFGYQVQPNTRTVQAEIEKALEKMHKGKSVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y I   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEAPADFHARFGTVGKEYRYVIKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M+ A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDIAKMKQASERLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
                + I      FL+  +R   G+L   G G+ +  D+ KAL A DR K     APP+
Sbjct: 179 EDAETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLAHDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>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 =  284 bits (726), Expect = 9e-75,   Method: Composition-based stats.
 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|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 =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 127/245 (51%), Gaps = 2/245 (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  HFDAPVERDEFSWVRGTNRYL--PDDVAVQWCRRVDARFHARNSAQGRRYRFVILEAPVR 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 SVEYS 247
              Y 
Sbjct: 254 GPYYD 258


>gi|153839728|ref|ZP_01992395.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
 gi|149746752|gb|EDM57740.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
          Length = 246

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 88/233 (37%), Positives = 123/233 (52%), Gaps = 2/233 (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  VHFDTNVNRKMVAWTMGANANM--PSDIAVRWAKEVPDDFHARFSATARRYRYIIFNHAL 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 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           + + I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A
Sbjct: 179 DYVVIDIKANAFVHHMVRNITGSLIKVGRGEEKPEWIKWLLEAKDRKLAGATA 231


>gi|331007056|ref|ZP_08330287.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC1989]
 gi|330419141|gb|EGG93576.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC1989]
          Length = 286

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 137/248 (55%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + IEY G  + G+Q Q +   ++Q ++E A+ LV  E + +  AGRTD+GVHA  
Sbjct: 24  MQRVALGIEYAGHVFHGFQSQPHDEKTVQSALENALSLVANEPIKLVCAGRTDAGVHATN 83

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+ HFD + +       +  NA L   D ++I     V   FH+RFSA  R+Y Y I   
Sbjct: 84  QIVHFDTLAKRKDTAWLRGANAKL--PDGVAIRWAQDVSCDFHSRFSAKHRTYRYVIYNS 141

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   AL K       +SLD + M  A+Q LVGRHDF  FR+  CQA++ IR + +  V+ 
Sbjct: 142 RTHSALLKNFVTWDRRSLDIDAMAEASQALVGRHDFNAFRASQCQANNAIRDMHYIKVHR 201

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I I V A +FL+  +R+ VG L  +  G+   +  ++ L+++DR+  G  A P+GL
Sbjct: 202 QNDFIVIEVQATAFLYHMVRNIVGVLSTIAAGEKPVSWAKEVLESKDRRCGGITASPDGL 261

Query: 240 YFDSVEYS 247
           Y  +VEY 
Sbjct: 262 YLVAVEYD 269


>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 =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 143/246 (58%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            Y M++EY+GS Y GWQ+Q N   +IQG IE+ +  +TG+ V VHG+GRTD+GVHAL QV
Sbjct: 4   NYRMVLEYDGSRYDGWQKQGNTEQTIQGKIEQVLERMTGQAVEVHGSGRTDAGVHALAQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F +  +     + + LN YL   + I ++ L    ++FH+R +A  ++YLYRI   + 
Sbjct: 64  ANFHMDGKMASKEIQEYLNQYL--PEDIRVITLEPAKERFHSRLNAQEKTYLYRIEMGER 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E+   + + KSL+ E M  A+ +L G HDF +F S      S +R +   +    G
Sbjct: 122 KQVFERKYIYGLYKSLNVEAMERASAYLTGEHDFKSFCSNRKMKKSTVRVLKEIEFEQQG 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + IR     FL+  +R   G+L  VG G+  + D++  L+A+DR + G  APPEGL+ 
Sbjct: 182 SRLLIRYTGNGFLYNMVRIITGTLIEVGLGQRKAEDMKGILEAKDRNQAGFTAPPEGLFL 241

Query: 242 DSVEYS 247
           + V Y+
Sbjct: 242 EQVRYN 247


>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 =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 126/247 (51%), Positives = 169/247 (68%), Gaps = 1/247 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R+ + +E+NG  Y G+QRQ +G S+Q ++E+A+  VTGE V ++ AGRTD+GVHAL   
Sbjct: 6   TRFALTLEWNGGPYMGFQRQSHGPSVQQAVEEAVHSVTGEAVALNAAGRTDTGVHALGMR 65

Query: 62  AHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFDL R + P  + +ALNA L+++   +++L+   V   +HARFS   R+Y YRII R+
Sbjct: 66  AHFDLSRAFDPFRMMEALNARLRLAGHPVAVLDCIEVAPDWHARFSCTGRAYEYRIINRR 125

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL L+ GRAW I K LD   M  AAQ LVG HDFTTFRS+HCQ++SP++T+D  DV   
Sbjct: 126 APLTLDLGRAWRIAKPLDETVMHEAAQLLVGHHDFTTFRSVHCQSASPLKTLDRLDVRRD 185

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + +   ARSFLH Q+RS VG L LVG G+W+   L +AL A+DR   G  APPEGLY
Sbjct: 186 GDRVIVEAAARSFLHHQVRSMVGCLALVGQGQWSVAQLGEALAAKDRSRLGLNAPPEGLY 245

Query: 241 FDSVEYS 247
           F S +Y 
Sbjct: 246 FVSAQYP 252


>gi|195978825|ref|YP_002124069.1| tRNA pseudouridine synthase A [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|238689837|sp|B4U545|TRUA_STREM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|195975530|gb|ACG63056.1| tRNA pseudouridine synthase A TruA [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 249

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+QRQ    ++Q  IEK +  +TG + + +HGAG TD+GVHA  
Sbjct: 1   MTRYKAIISYDGTLFSGFQRQSQARTVQEEIEKTLQKLTGGQGIQIHGAGITDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++  P  L  AL+   +  D I +++L I    FHAR+    ++Y + +   
Sbjct: 61  QVIHFDLEQKRDPEKLRFALDT--QTPDDIDVISLEIAADDFHARYHKHFKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDIAKMQAAIKDLVGTHDFTGFTAAGTSVKNKVRTITAATLTQ 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     +   L++++R+  GP A   
Sbjct: 179 DPKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRLPIEQIRLVLESKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|313622273|gb|EFR92777.1| tRNA pseudouridine synthase A [Listeria innocua FSL J1-023]
          Length = 248

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 92/250 (36%), Positives = 125/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG+FG+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFFGYQVQPNTRTVQAEIEKALEKMHKGKSVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  I + Y Y I   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEAQADFHARFGTIGKEYRYVIKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD E M+ A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDIEKMKQASERLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
                + I      FL+  +R   G+L   G G+ +  D+ KAL A DR K     APP+
Sbjct: 179 EDAETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLAHDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>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 =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 121/251 (48%), 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   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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           AP   ++GR W +P  LD   MR AA HLVGRHDFTTFR+I CQA+SP++T+D   +   
Sbjct: 120 APEVHDRGRVWRVPHPLDGAAMREAAAHLVGRHDFTTFRAIGCQAASPVKTLDELTLETV 179

Query: 179 --SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G     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|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 =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 137/246 (55%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 16  VKIALGIEYDGSRYYGWQRQQEVRSVQECLEKALSQVANEPISVFCAGRTDAGVHATGQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +N +L     I++  +  VD +FHARFSA  R Y Y I   + 
Sbjct: 76  VHFETSAQRKDAAWTMGVNTHL--PSNIAVRWIKTVDDEFHARFSATARRYRYVIFNHRY 133

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  AAQ L+G +DFT+FR++ CQ++SP R + H +V+  G
Sbjct: 134 RPAVLAQGIMHFHSPLDEKKMHEAAQSLLGENDFTSFRAVQCQSNSPWRNMMHINVSRHG 193

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +F+H  +R+ VGSL  +G G      + + L  +DR +    A  +GLY 
Sbjct: 194 HYIVVDIKANAFVHHMVRNIVGSLLEIGCGNQNIGWMAELLTLKDRTKAAATAKADGLYL 253

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 254 VAVDYP 259


>gi|257417873|ref|ZP_05594867.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
 gi|257159701|gb|EEU89661.1| tRNA pseudouridine synthase [Enterococcus faecalis T11]
          Length = 246

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE++ + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGELIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+  G  AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGAGETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|313636153|gb|EFS02014.1| tRNA pseudouridine synthase A [Listeria seeligeri FSL S4-171]
          Length = 248

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRFKAIISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDISAEKFQKALQVM--TPFDISFLIVEEAPADFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  L+ E M++A++ LVG HDFT+F S   +  S +RT+   D   
Sbjct: 119 KVFDPFSRNFALHYPYELNLEKMKLASERLVGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
             +  + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR K     APP+
Sbjct: 179 EDDETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>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 =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 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|256854698|ref|ZP_05560062.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
 gi|256710258|gb|EEU25302.1| tRNA pseudouridine synthase [Enterococcus faecalis T8]
          Length = 246

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  N   +IQG IE  +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYSGWQRLGNSEKTIQGKIESILTQMTGEPIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  ++ + ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSSLTTTEMLSFLNRYL--PGDIVVKEVTEMPERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P A E+  ++  PK+LD E M  A Q L+G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPNAFERYHSFHFPKALDQEKMEQACQKLIGTHDFIGFSALKKTKKSTTRTIEKITIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +++   V   FLH  +R  VG+L  +G G      +++    + R+     AP +GL
Sbjct: 179 NGEMLQFTFVGNGFLHKMVRILVGTLLEIGAGTKELAIIDELFATKVREGASETAPAQGL 238

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 239 FLDEVYY 245


>gi|318606505|emb|CBY28003.1| tRNA pseudouridine synthase A [Yersinia enterocolitica subsp.
           palearctica Y11]
          Length = 280

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 97/245 (39%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 20  KIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVLCAGRTDAGVHATGQVV 79

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF    E         +N++L     I++  +  VD  FHARFSA  R Y Y I   +  
Sbjct: 80  HFITTAERKNAAWTMGVNSHL--PPDIAVRWVKTVDDGFHARFSATARRYRYIIFNHRYR 137

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G HDFT+FR+I CQ+ +P R + H  V   G 
Sbjct: 138 PAVLAQGVTHCYMPLDAEKMEQAAQCLLGEHDFTSFRAIQCQSRTPWRNVKHVKVTRHGA 197

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G  + T + + L  +DR      A  EGLY  
Sbjct: 198 YIVVDIKANAFVHHMVRNIVGSLIEIGCGNQSVTWMAELLALKDRARAAATAKAEGLYLV 257

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 258 SVDYP 262


>gi|332970287|gb|EGK09279.1| tRNA pseudouridine synthase A [Kingella kingae ATCC 23330]
          Length = 265

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 89/253 (35%), Positives = 137/253 (54%), Gaps = 8/253 (3%)

Query: 1   MI-----RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M+     R+ + + Y+GS +FGWQ+Q +G  ++Q ++E A+  + GE +    AGRTD+G
Sbjct: 1   MMQPQTQRFALTVSYDGSQFFGWQKQADGVVTVQAALEHALSCIAGEPIATIAAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  Q+ HFD           + +NA+L   D +++L    V+  FHARF A  R Y Y
Sbjct: 61  VHATGQIVHFDTQAHRPLSAWVRGVNAHL--PDGVAVLAAQAVEPAFHARFDATGRRYRY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            + +      L   RA     +L+ + M+ A   L+G HDF++FR+  CQA SPI+T+  
Sbjct: 119 LLESAPVRSPLLYRRAGWTHYALNTDPMQAAMNLLLGEHDFSSFRAAQCQAKSPIKTMYA 178

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G LI++   A +FLH  +R+ VG+L  VG G+ +  D    L  + R    P  
Sbjct: 179 AQLQRAGCLIKLDFHANAFLHHMVRNLVGALVYVGCGRLSVADFADLLAQKSRLTAPPTF 238

Query: 235 PPEGLYFDSVEYS 247
            P+GLYF  V+Y 
Sbjct: 239 MPDGLYFVGVDYP 251


>gi|281412654|ref|YP_003346733.1| tRNA pseudouridine synthase A [Thermotoga naphthophila RKU-10]
 gi|281373757|gb|ADA67319.1| tRNA pseudouridine synthase A [Thermotoga naphthophila RKU-10]
          Length = 245

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 126/246 (51%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+          +  A+NA L   D + +  +  V   FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIKNAMNANL--PDDVYVKEVFEVPVNFHPRFDVTKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR AA++L G HDFT+F         P+RTI    +  
Sbjct: 119 RQKNVFLRKYVWWFPYELDLDAMRKAAKYLEGTHDFTSF-KTGSDERDPVRTIYRIRILR 177

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|289435864|ref|YP_003465736.1| tRNA pseudouridine synthase A [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|289172108|emb|CBH28654.1| tRNA pseudouridine synthase A [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
          Length = 248

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q +  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPDTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDISAEKFQKALQVM--TPFDISFLIVEEAPADFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-N 178
           +      +  A   P  L+ E M++A++ LVG HDFT+F S   +  S +RT+   D   
Sbjct: 119 KVFDPFSRNFALHYPYELNLEKMKLASERLVGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
              + + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR K     APP+
Sbjct: 179 EEDDTLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|315640131|ref|ZP_07895253.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
 gi|315484108|gb|EFU74582.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
          Length = 248

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 128/248 (51%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY  II Y+G+ + G+QRQ  G ++Q  +E+ +  +  + +VVHG+GRTD+ VHAL Q
Sbjct: 3   MVRYKAIIAYDGTLFHGFQRQPQGRTVQEELERTLSKMASQPIVVHGSGRTDAHVHALGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  +E     +  A++   +  + I++  + IVD+ FHAR+    + Y + +   +
Sbjct: 63  VIHFDYPKERPLEKMRFAMDT--QTPEDIAVKQVEIVDELFHARYLVQEKVYEFHVQIGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A   P  LD   +  A   L+G HDF+ F +        +RTI    +   
Sbjct: 121 PRSPFRRHYASYYPYPLDLAKIERALPDLLGTHDFSAFCASGSSVEDKVRTIYEATMVHD 180

Query: 181 G--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + +        FL+  IR  VG+L  +G+G+   T L K + ++DR   GP A PEG
Sbjct: 181 EALSELVFTFRGDGFLYKMIRILVGTLLKIGNGRLEETSLPKIIASKDRNCAGPTAHPEG 240

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 241 LYLKEVKY 248


>gi|168186842|ref|ZP_02621477.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
 gi|169295253|gb|EDS77386.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
          Length = 245

 Score =  283 bits (725), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 74/247 (29%), Positives = 122/247 (49%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+G+ Y GWQ+   N ++IQ  IE  +  + GE V +  +GRTD+GVHA  
Sbjct: 1   MRNIKLTIQYDGTRYKGWQKLGNNDTTIQHKIESVLNELLGEKVSLMASGRTDAGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    E     + K L  YL     I + +++     FH+R++   + Y YRI   
Sbjct: 61  QVANFKTDSEISNDEIFKYLYKYL--PQDIVVTSVNNASDNFHSRYNVKEKVYTYRIHNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ I + LD + M+ A++  +G HDF +F ++  +  S ++ I+      
Sbjct: 119 EVHDVFTRKYSYHIKEKLDLKKMKEASKLFIGEHDFKSFTALKSKKKSTVKAINSITFRK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N IEI      FL+  IR  VG+L   G  K +  +++  +  +DR      AP  GL
Sbjct: 179 KENDIEIVFSGNGFLYKMIRILVGTLIQAGLNKISLDEIQNIMDKKDRNIAPETAPAHGL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 TLTEVKY 245


>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 =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 95/245 (38%), Positives = 129/245 (52%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQVERSMKAWVMGANINL--PHDVSVSWAKVMPAHFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AAQ+LVG HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 136 RPAHLNEEITWNHRPLDVERMAEAAQYLVGVHDFSAFRAGQCQAKSPIKELHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + + A +FLH  +R+  G L  +G G+     +++ L ++ R+  G  A P GLY 
Sbjct: 196 KMIVLDIRASAFLHHMVRNIAGVLMTIGAGERPVEWIKEVLDSRIRRSGGVTAHPFGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VQVEY 260


>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 =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 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|269468479|gb|EEZ80140.1| pseudouridylate synthase [uncultured SUP05 cluster bacterium]
          Length = 247

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK+G  ++Q  +E+A+  V    V V  +GRTD+GVHAL Q
Sbjct: 1   MKLALGVEYLGTNFHGWQLQKSGIRTVQQVVEQALSSVADHPVRVFCSGRTDAGVHALEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+   +          N  L     ++      V+  FHARF A  R Y Y+I    
Sbjct: 61  VIHFETTAKREDKAWVLGGNVNL--PFDVNFKWAKQVNDDFHARFDAHARQYHYKIHNTP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A++        ++LD + M  AA+ L+G HDF++FR   CQA SPI+T++   +   
Sbjct: 119 VRSAVKHAYTLWESRTLDIKLMNQAAECLIGEHDFSSFRGSLCQAKSPIKTVEFIRLTQS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I + + A +FLH  +R+ VG+L  VG G+  S  ++  L A+DRK+ G  A P+GLY
Sbjct: 179 GNGILLDIKANAFLHHMVRNIVGTLIKVGKGEQDSAWVKTVLDAKDRKQAGVTAEPQGLY 238

Query: 241 FDSVEYS 247
           F    Y 
Sbjct: 239 FVKAFYD 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 =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 107/246 (43%), Positives = 153/246 (62%), Gaps = 4/246 (1%)

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  AHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD       P  +  A+N +LK    I +L + IVD+ F ARFSAIRR Y Y+I  R+
Sbjct: 61  FHFDARESTLQPFQIVNAVNYHLKE-KLIVLLKIEIVDETFDARFSAIRRHYQYKITNRK 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PLA+ K R+W +P++L+ + +R  AQ+LVG+HDF +FRS  C AS+ IRT+D  +V   
Sbjct: 120 TPLAVFKNRSWHVPQTLNLDLIREQAQYLVGKHDFQSFRSSKCGASNAIRTLDRLEVEKN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +     A+SFLH Q+R  VG+L  +  GK     + + L  ++R+  GP APP GLY
Sbjct: 180 GEEMIFHASAKSFLHHQVRIMVGTLVAIASGKL--MSVTEILSKKNRRYAGPTAPPCGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LLKVDY 243


>gi|116627085|ref|YP_819704.1| tRNA pseudouridine synthase A [Streptococcus thermophilus LMD-9]
 gi|122268312|sp|Q03MR4|TRUA_STRTD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116100362|gb|ABJ65508.1| Pseudouridylate synthase [Streptococcus thermophilus LMD-9]
          Length = 248

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  IEK +  + +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEEIEKTLLRLNSGIPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLPQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYSKHIKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRNYAIHYPYPLSLALMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                          FL+ Q+R+ VG+L  +G+G+   +  +  L+++DR   GP     
Sbjct: 179 DEKTGFYVFAFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQAKTVLESRDRNLAGPTVAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|306829107|ref|ZP_07462297.1| tRNA pseudouridine synthase A [Streptococcus mitis ATCC 6249]
 gi|304428193|gb|EFM31283.1| tRNA pseudouridine synthase A [Streptococcus mitis ATCC 6249]
          Length = 249

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++ + IV   FH R++   + Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVILIEIVADDFHCRYAKHSKIYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +    + +  A   P  LD E M+IA + L G HDFT F +      + +RTI      V
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVENKVRTITEASLTV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 179 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMLVEQIDLILEKKDRQLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|258646098|ref|ZP_05733567.1| tRNA pseudouridine synthase A [Dialister invisus DSM 15470]
 gi|260403476|gb|EEW97023.1| tRNA pseudouridine synthase A [Dialister invisus DSM 15470]
          Length = 265

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 113/246 (45%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y G+ Y G+QRQ+N  ++Q  +E A+  +TG    ++ A RTD+GVHA  Q
Sbjct: 1   MRNIRITLAYEGTAYSGFQRQENSITVQEILETALQKLTGTKTTLYFAARTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F             ALN  L     I +     V   F  R +   ++Y Y +   +
Sbjct: 61  ECTFYTESSIPGDRFIFALNILL--PPDIRVTESREVPYDFSVRRNNYGKTYGYLLTEEK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 K   W   + LD   M  AA+ L G HDFT+FR  +   +SP+RTI    +   
Sbjct: 119 DCPPFFKRYTWQTGRKLDISKMEKAAEVLSGTHDFTSFRGNNSVPASPVRTIHDIRIIKK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +   I V    FL+  +R+  G+L   G GK T  DL + L+A+DRK  G  AP  GL 
Sbjct: 179 HHFFHIFVTGEGFLYHMVRNIAGALADAGTGKLTPKDLREILEAKDRKFLGATAPAHGLC 238

Query: 241 FDSVEY 246
              V +
Sbjct: 239 LLKVYF 244


>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 =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 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|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 =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 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|206562845|ref|YP_002233608.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia J2315]
 gi|198038885|emb|CAR54847.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia J2315]
          Length = 271

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 130/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + I+Y+G+ + GWQ Q +G ++Q  +E A+       +    AGRTD+GVH L Q
Sbjct: 1   MMRIALGIQYDGAAFCGWQAQPHGKTVQDRLEHALAEFARVPLHTTVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       +  NA+L    T+S+     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELEREVFSWVRGTNAFL--PPTVSVQWAKPMPDTFHARFSAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  I   LD + MR AA +L+G HDF++FRS  CQ+ +P++ +   DV   
Sbjct: 119 VRSPMLAGRAGWIHTPLDDDAMRAAAAYLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRA 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY
Sbjct: 179 GHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LAHVGYP 245


>gi|312277540|gb|ADQ62197.1| tRNA pseudouridine synthase A [Streptococcus thermophilus ND03]
          Length = 248

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ N  SIQ  IEK +  + +G  V VHGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQPNARSIQEEIEKTLLRLNSGTPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E  P  L   L+   +  D I I+++ +V ++FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLSQERDPEKLRFGLDT--QCPDDIDIVSIELVSEEFHARYSKHIKTYEFLVDAG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L    M+ AA  LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRNYAIHYPYPLSLALMQEAAMELVGTHDFTGFTASGTSVENKVRTITQASVSI 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                          FL+ Q+R+ VG+L  +G+G+   +  +  L+++DR   GP     
Sbjct: 179 DEKTGFYVFAFSGNGFLYKQVRNMVGTLLKIGNGRMPVSQAKTVLESRDRNLAGPTVAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|256852067|ref|ZP_05557454.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 27-2-CHN]
 gi|260661364|ref|ZP_05862277.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 115-3-CHN]
 gi|256615479|gb|EEU20669.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 27-2-CHN]
 gi|260547819|gb|EEX23796.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 115-3-CHN]
          Length = 262

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 132/251 (52%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+ M + Y+G  + G+Q+Q N  ++QG+IE+A+  +  G+ +VVHG+GRTD+GVHAL 
Sbjct: 1   MPRFKMTMAYDGHLFHGFQKQPNQRTVQGTIEEALKKMAKGQRIVVHGSGRTDAGVHALG 60

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD          +  ALN+ +     I   +  IV++ FH ++S   + Y Y +  
Sbjct: 61  QVIHFDFPNDNIPANRMVLALNSMM--PTDIIFKDAEIVNEDFHVQYSTHGKWYRYIVNQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
            +     ++      P  L+   M+ AA  L+G HDFT+F +   Q    +RTI +  + 
Sbjct: 119 DRFVDPFKRFYTGHYPYKLNVSKMQEAALDLLGEHDFTSFAASGGQIIDKVRTIYYVKIW 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             S  N I    +   FL+  +R  VG+L  +G+ +    DL++ + A+DR+E    AP 
Sbjct: 179 QKSEENEIIFDFIGNGFLYNMVRIMVGALLEIGNERRPVHDLKRVILAKDRQEVINTAPA 238

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 239 SGLYLYHVFYE 249


>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 =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 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|39997968|ref|NP_953919.1| tRNA pseudouridine synthase A [Geobacter sulfurreducens PCA]
 gi|42559718|sp|P60350|TRUA_GEOSL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|39984913|gb|AAR36269.1| tRNA pseudouridine synthase A [Geobacter sulfurreducens PCA]
 gi|298506909|gb|ADI85632.1| tRNA pseudouridines 38,39,40 synthase [Geobacter sulfurreducens
           KN400]
          Length = 244

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +I+EY+G+ Y GWQ Q NG SIQ  +E A+  +  E V +  +GRTD+GVHA   
Sbjct: 1   MRTIKLILEYDGTNYAGWQLQPNGLSIQEVVEGALARLLKEPVRLRASGRTDAGVHARGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD  R          LNA L     I++ +       F+ RF+A  + Y Y I   +
Sbjct: 61  VAAFDTDRSIPLRAFSDGLNALL--PPDIAVRSADEALPGFNPRFAATGKHYRYTIHRGE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L + ++W +  +L+   MR AA+HL G  DF +FR+  C A + IR +D  +++  
Sbjct: 119 RRSPLVRLQSWHVRGALNLAAMREAARHLTGERDFASFRTAGCAARTTIRRVDAVEISDD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G ++ + V    FL   +R  VG+L  VG GK T   + + +        GP APP+GL 
Sbjct: 179 GEMLTVDVHGSGFLRNMVRIMVGTLVEVGRGKLTPEHVAQMVVCPGVVPAGPTAPPQGLC 238

Query: 241 FDSVEY 246
              V +
Sbjct: 239 LQKVRF 244


>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 =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 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|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 =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  +++EY+G+G+ GWQRQ +  S+Q ++E A+  +    V V  AGRTD+GVHA  QV
Sbjct: 8   QRIALVLEYDGTGFSGWQRQDDAPSVQEALEGAVSRIANHPVAVVCAGRTDAGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              NA L   +T+S+ +   VD  FHAR+ A RR Y Y  + R+A
Sbjct: 68  VHFDTTASRPLHAWVLGTNAQL--PETVSVRSAHAVDADFHARYQAQRRGYRYVFLCRRA 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL + R       LD   M  AAQ LVG HDF+ FR+  CQA   +R +   DV+  G
Sbjct: 126 RPALLRHRVAWTHHELDEGRMHRAAQALVGEHDFSAFRAAACQAPHAVREVYRLDVHRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ I + A +F+H  +R+  G+L  VG G+         L A DR   G  AP  GLY 
Sbjct: 186 ELLFIDIEANAFVHHMVRNIAGTLMAVGTGEQPEHWPAGLLAAGDRTRSGMTAPAAGLYL 245

Query: 242 DSVEYS 247
             V Y 
Sbjct: 246 TRVVYP 251


>gi|251781741|ref|YP_002996043.1| tRNA pseudouridine synthase A [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390370|dbj|BAH80829.1| phosphomethylpyrimidine kinase [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 249

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  ++Q  IEK +  +   + V +HGAGRTD+GVHA  
Sbjct: 1   MTRYRATISYDGTLFSGFQRQSHARTVQEEIEKTLQKLASVQPVPIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +    I +++L+IV   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDLEKLRFALDT--QTPADIDVVDLAIVADDFHCRYQKHSKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD   M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRHYATHYPYPLDINKMQEAIKDLVGTHDFTGFTAAGTSVENKVRTITEATLVQ 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DDKTGFLVFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVEQIKVILDSKNRQLAGPTPAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|225075428|ref|ZP_03718627.1| hypothetical protein NEIFLAOT_00433 [Neisseria flavescens
           NRL30031/H210]
 gi|224953246|gb|EEG34455.1| hypothetical protein NEIFLAOT_00433 [Neisseria flavescens
           NRL30031/H210]
          Length = 281

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  
Sbjct: 12  MQRWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALSSIAGEQINTIVAGRTDTGVHATA 71

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           + +NA+L   D +++L    V   FHARF A  R Y Y + + 
Sbjct: 72  QVVHFDTSVSRPEQAWVRGVNAHL--PDGVAVLVAQKVAPHFHARFDAYGRHYRYLLESS 129

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GR       LD   MR AA  L G HDF++FR+  CQA SP++T+    ++ 
Sbjct: 130 PVRSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPVKTLYSTKISG 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + + +   +FLH  +R+ +G+L  VG G+ +  + E    A+ R +  P    +GL
Sbjct: 190 TSRYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFESVFHAKSRLKAPPTFMSDGL 249

Query: 240 YFDSVEYS 247
           Y   V+Y 
Sbjct: 250 YLTGVDYP 257


>gi|25010174|ref|NP_734569.1| tRNA pseudouridine synthase A [Streptococcus agalactiae NEM316]
 gi|77414646|ref|ZP_00790784.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 515]
 gi|42559816|sp|Q8E7Q5|TRUA_STRA3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|23094525|emb|CAD45744.1| Unknown [Streptococcus agalactiae NEM316]
 gi|77159310|gb|EAO70483.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 515]
 gi|319744038|gb|EFV96416.1| tRNA pseudouridine synthase A [Streptococcus agalactiae ATCC 13813]
          Length = 258

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  + +G  V++HGAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A   
Sbjct: 179 EASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>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 =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 114/247 (46%), Positives = 151/247 (61%), Gaps = 2/247 (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 FDSVEYS 247
            + V+Y 
Sbjct: 239 LERVDYP 245


>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 =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 116/251 (46%), Positives = 164/251 (65%), 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 +   +++  + V + +HARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDLVKDWEPFKLMGAVNYHLKPAPV-AVVACAQVAEDWHARFSALERRYLFRLLMRR 119

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

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|116873964|ref|YP_850745.1| tRNA pseudouridine synthase A [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|123466636|sp|A0ALT4|TRUA_LISW6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116742842|emb|CAK21966.1| tRNA pseudouridine synthase A [Listeria welshimeri serovar 6b str.
           SLCC5334]
          Length = 248

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 88/250 (35%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQIQPNARTVQAEIEKALKKMHKGKNVRITASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSDLDITADKFQKALQVM--TPFDISFLTVDEAPADFHARFGTVGKEYRYIVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A   P  LD   M++A++ L+G HDFT+F S   +  S +RT+   D   
Sbjct: 119 KIFDPFSRNFALHYPYELDIAKMKLASECLIGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
                + I      FL+  +R   G+L   G G+ +S D+ +AL A+DR K     APP+
Sbjct: 179 EDEETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISSEDITEALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>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 =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 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|295093425|emb|CBK82516.1| pseudouridylate synthase I [Coprococcus sp. ART55/1]
          Length = 247

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 128/249 (51%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+ Y     Y+G+ Y GW+ + N  +++G IE  +  +    V +HGAGRTD+GVHA   
Sbjct: 1   MVNYRFTFSYDGTRYHGWESKTNADTVEGRIEAVLTRMVDAKVDIHGAGRTDAGVHARAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+  L  +  P  +   LN YL     I  L++++   +FHAR +A  + Y Y +    
Sbjct: 61  VANGRLETDKTPEEIKDYLNRYL--PADICALDVAVAGDRFHARLNATGKVYEYTLYVGA 118

Query: 121 APLALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                ++   W +P+  +LD + M+ AA +LVG+HDF +F   +    S +RTI   D+ 
Sbjct: 119 EKPVFDRNYVWCVPQGSALDVDVMKKAASYLVGKHDFRSFCGNNKMKKSTVRTIYDVDIV 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + +R     FL   +R   G+L  VG G  ++  + + +   DR+  GP APP G
Sbjct: 179 KEGDYVRMRFHGNGFLQNMVRILTGTLVEVGYGNMSAEHIPEIIAGMDRQLAGPTAPPHG 238

Query: 239 LYFDSVEYS 247
           L    VEY 
Sbjct: 239 LCLMKVEYD 247


>gi|258592098|emb|CBE68403.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [NC10 bacterium 'Dutch
           sediment']
          Length = 263

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 129/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + IEY+G+ Y GWQ Q   ++IQG+++ A+  + G+ V V GAGRTD+GVHA  Q
Sbjct: 1   MTTFKLTIEYDGTDYHGWQVQPGMTTIQGTLQGAVARIVGKDVHVMGAGRTDAGVHAHGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA         P    +AL + L     I +  +  +D  FHA++SA  + Y Y ++TR 
Sbjct: 61  VASLRTEFHHPPDTFRRALTSVL--PSDIVVTAVEEMDDDFHAQYSAQWKRYRYSLLTRP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P A+E+     +P  L  + M +AA  LVG HDF+ F++ H  A SP+RT+   +    
Sbjct: 119 YPSAIERRYTLFVPYPLQTDAMAVAAGSLVGTHDFSAFQAAHSSAESPVRTVLVAEFRQH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +   +VA  FL   IR  +G+L  +G G+     L    + +DR +      P GL 
Sbjct: 179 GDHLLFEIVADGFLRHMIRIIMGTLLDIGRGRLQVEALHIIREGRDRNQASKTISPHGLC 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LLEVGY 244


>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 =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 110/246 (44%), Positives = 147/246 (59%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY   +EY G+G+ GWQ+Q +  S+Q  +E  +  +  E + V+ AGRTD+GVHAL QV
Sbjct: 1   MRYKATVEYVGTGFSGWQKQMSAPSVQEELESVLSFLLKEKIAVNVAGRTDAGVHALGQV 60

Query: 62  AHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFD       P  +  A+N +LK    I +L + IVD+ F ARFSAIRR Y YRII R+
Sbjct: 61  FHFDARESTLQPFQIVNAVNYHLKE-KLIVLLKIEIVDETFDARFSAIRRHYQYRIINRK 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P A+ + R W +P  L+ + MR  AQHLVGRHDF +FRS  C AS+ IRT+D  +V   
Sbjct: 120 MPPAVFRNRCWHVPWKLNLDFMREQAQHLVGRHDFQSFRSSKCGASNAIRTLDRLEVEKN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I     A+SFLH Q+R  VG+L  +  GK  S    + L  ++R   GP AP  GLY
Sbjct: 180 GEEIIFHASAKSFLHHQVRIMVGTLVAIASGKLVSA--TEILSKRNRCYAGPTAPSCGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LLKVDY 243


>gi|168187780|ref|ZP_02622415.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
 gi|169294335|gb|EDS76468.1| tRNA pseudouridine synthase A [Clostridium botulinum C str. Eklund]
          Length = 246

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 137/248 (55%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   ++IEY+GS Y GWQ+QK+  ++Q  IE+AIF +T + + + G  RTD+GVHA  
Sbjct: 1   MKRNIKLVIEYDGSNYSGWQKQKHSMTVQQRIEEAIFDITKQNIEIIGCSRTDAGVHARN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+F +     P     A+N+ L     I I     V   FHARF +  + Y+Y I+ R
Sbjct: 61  FVANFIIDSNIPPEKFKYAINSKL--PKDIVIKKSCEVPIDFHARFQSKGKKYVYTILNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVN 178
           + P  +++G  +   K LD + M+ A+++ +G H+F +F +       S +RTI + DV 
Sbjct: 119 EEPPTIDRGVVYHFNKKLDVDLMKSASKYFIGSHEFDSFYKKAGSSVKSTLRTIYYCDVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              ++I+I V+   FL+  +R   G+L  VG  +    D++  + A+DR+  G   PP+G
Sbjct: 179 KVDDIIKIIVIGEGFLYNMVRIMAGTLVEVGITRIKPEDIKTIILAKDRERAGRSLPPQG 238

Query: 239 LYFDSVEY 246
           L  + V Y
Sbjct: 239 LCLEEVLY 246


>gi|76787537|ref|YP_328824.1| tRNA pseudouridine synthase A [Streptococcus agalactiae A909]
 gi|123602597|sp|Q3K3S9|TRUA_STRA1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76562594|gb|ABA45178.1| tRNA pseudouridine synthase A [Streptococcus agalactiae A909]
          Length = 258

 Score =  282 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  + +G  V++HGAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMKEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A   
Sbjct: 179 EASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>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 =  282 bits (723), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 93/248 (37%), Positives = 133/248 (53%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + + YNGS +FG+Q+Q     +IQ ++E A+  + GE V +  AGRTD+GVHA  
Sbjct: 1   MTRYALTLSYNGSAFFGFQKQAAGIPTIQTALEHALAQIAGEPVAITAAGRTDTGVHATA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           + +NA+L   D I++L+   V   FHARF A  R Y Y + + 
Sbjct: 61  QVVHFDSHATRPLTAWVRGVNAHL--PDGIAVLHAQAVAPDFHARFDACGRHYRYLLQSA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GRA      LD   M+ AA  L+G HDF++FR+  CQA SP++T+     + 
Sbjct: 119 PVRSPLLVGRAGWTHYPLDMAAMQKAAALLLGEHDFSSFRAAECQAKSPVKTVYAIAFSG 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I+I   A +FLH  +R+ VG+L  VG G+    +  +   AQ R    P    +GL
Sbjct: 179 CPSFIKIDFHANAFLHHMVRNIVGALVYVGCGRLAVGEFAEMFAAQSRLTAPPTFMADGL 238

Query: 240 YFDSVEYS 247
           YF  V+Y 
Sbjct: 239 YFTGVDYP 246


>gi|241759308|ref|ZP_04757414.1| tRNA pseudouridine synthase A [Neisseria flavescens SK114]
 gi|241320444|gb|EER56741.1| tRNA pseudouridine synthase A [Neisseria flavescens SK114]
          Length = 270

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  
Sbjct: 1   MQRWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALSSIAGEQINTIVAGRTDTGVHATA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD           + +NA+L   D +++L    V   FHARF A  R Y Y + + 
Sbjct: 61  QVVHFDTSVSRPEQAWVRGVNAHL--PDGVAVLVAQKVAPHFHARFDAYGRHYRYLLESS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GR       LD   MR AA  L G HDF++FR+  CQA SPI+T+    ++ 
Sbjct: 119 PVRSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPIKTLYRTSISG 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + + +   +FLH  +R+ +G+L  VG G+ +  + E    A+ R +  P    +GL
Sbjct: 179 TSRYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFESVFHAKSRLKAPPTFMSDGL 238

Query: 240 YFDSVEYS 247
           Y   V+Y 
Sbjct: 239 YLTGVDYP 246


>gi|238917621|ref|YP_002931138.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
 gi|238872981|gb|ACR72691.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
          Length = 249

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 123/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y MII Y+G+ Y+GW+ Q     +IQG +E  +  +TG  V V GAGRTD+GVHA  
Sbjct: 1   MKNYKMIITYDGTRYYGWEHQPTTDMTIQGKLESVLSAMTGTEVEVIGAGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+  +  +     +C  +N YL   + I +  + I   +FH+R++A  ++Y Y     
Sbjct: 61  MVANAHMETKMKEDDICDYMNRYL--PEDICVQEVRIASDRFHSRYNAQGKTYCYTCYVG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +    +I   LD E M+ AA  L G HD+ +F        S +R I   DV+ 
Sbjct: 119 DKKPVFNRKYVNIIEGKLDVEAMKKAADILTGEHDYASFCGNPKMKKSTVREIYSIDVSL 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + +      FL   +R   G+L  VG GK T   + + L+ ++R   G  AP +GL
Sbjct: 179 KGSFLNLTYHGSGFLQYMVRILSGTLLEVGQGKRTPESMYELLEERNRSLAGATAPAKGL 238

Query: 240 YFDSVEYS 247
               V+YS
Sbjct: 239 CLLKVDYS 246


>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 =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 96/245 (39%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ     S+Q ++EKA+  V    VVV  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYRGWQRQASGVPSVQETLEKALSRVADSPVVVSCAGRTDAGVHACGQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N  L     IS+     +   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAVRSMKAWVMGANINL--PHDISVSWAKEMPAHFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA  LVG HDF+ FR+  CQA SPI+ I H  V   G
Sbjct: 126 RPAHLNEEITWNHRPLDIERMAQAAAFLVGTHDFSAFRAGQCQAKSPIKEIHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + + A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 186 KMIVLDIRASAFLHHMVRNIAGVLMTIGAGERPVEWAREVLESRIRRTGGVTAHPFGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VQVEY 250


>gi|297205058|ref|ZP_06922454.1| tRNA-pseudouridine synthase I [Lactobacillus jensenii JV-V16]
 gi|297149636|gb|EFH29933.1| tRNA-pseudouridine synthase I [Lactobacillus jensenii JV-V16]
          Length = 262

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 132/251 (52%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+ M + Y+G  + G+Q+Q N  ++QG+IE+A+  +  G+ +VVHG+GRTD+GVHAL 
Sbjct: 1   MPRFKMTMAYDGHLFHGFQKQPNQRTVQGTIEEALKKMAKGQRIVVHGSGRTDAGVHALG 60

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFD          +  ALN+ +     I   +  IV++ FH ++S   + Y Y +  
Sbjct: 61  QVIHFDFPNDNIPANRMVLALNSMM--PTDIIFKDAEIVNEDFHVQYSTHGKWYRYIVNQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
            +     ++      P  L+   M+ AA  L+G HDFT+F +   Q    +RTI +  + 
Sbjct: 119 DRFVDPFKRFYTGHYPYKLNVSKMQEAALDLLGEHDFTSFAASGGQIIDKVRTIYYVKIW 178

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             S  N I    +   FL+  +R  VG+L  +G+ +    DL++ + A+DR+E    AP 
Sbjct: 179 QKSEENEIIFDFIGNGFLYNMVRIMVGALLEIGNERRPVHDLKRVILAKDRQEVRNTAPA 238

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 239 SGLYLYHVFYE 249


>gi|326202743|ref|ZP_08192611.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
 gi|325987327|gb|EGD48155.1| tRNA pseudouridine synthase A [Clostridium papyrosolvens DSM 2782]
          Length = 247

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 137/248 (55%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y +I++Y+GS Y GWQ+ K+   SIQG IE  +  ++GE + V G GRTD+G HA  
Sbjct: 1   MKNYKIIVQYDGSKYKGWQKLKDSDLSIQGKIETVLSKMSGEEIQVIGCGRTDAGTHAEN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+F       P ++   L  Y  +   I + ++  VD++FHA+ +A  ++Y+Y I   
Sbjct: 61  YVANFHTNSRMSPKLILNHL--YEFLPQDIVVRSVEEVDERFHAQHNAKAKTYVYSITKG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++   + LD   M+ AA++L+G HDF +F S+   + S IRTI+  D+  
Sbjct: 119 KFRNVFNRKYSFHSEEKLDLVQMKNAAEYLIGTHDFQSFTSLKEGSKSTIRTINSLDIIE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +IEI +    FL    R  VG+L  VG  K  + D++K L  + R E  P+A P+GL
Sbjct: 179 NGMVIEIIINGNDFLLHMARLVVGALLEVGKNKIKAIDVQKILNEKKRTEAVPMAQPKGL 238

Query: 240 YFDSVEYS 247
               V+YS
Sbjct: 239 CLRDVKYS 246


>gi|229825283|ref|ZP_04451352.1| hypothetical protein GCWU000182_00637 [Abiotrophia defectiva ATCC
           49176]
 gi|229790655|gb|EEP26769.1| hypothetical protein GCWU000182_00637 [Abiotrophia defectiva ATCC
           49176]
          Length = 249

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +++ Y+G+ Y G+Q Q    +++G +  A+  + GE +V+ GA RTD+GVHA   
Sbjct: 1   MKRFKLVVAYDGTAYCGYQYQPELPTVEGFVNDALSELLGENIVIIGASRTDAGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         L  ALN  L   D I I+    V   FH R + I ++Y YRI T +
Sbjct: 61  VAVFDSDTRIPAEKLALALNTKLA--DDIRIMESLEVAADFHPRKNVIDKTYEYRINTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++  ++ +  +LD E MR AA+++ GRHDFT+F S        +RT+   DV   
Sbjct: 119 ISFPTDRLYSYNVKHNLDIEAMREAAKYIEGRHDFTSFCSAKTDKEDKVRTVFQIDVEET 178

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + IRV    FL+  +R   G+L  VG+GK +  ++   ++ +DR   G   P +GL
Sbjct: 179 LRSELIIRVRGDGFLYNMVRIIAGTLVKVGEGKISPNEIPSIIERKDRGHLGTTLPAKGL 238

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 239 FLMGIRY 245


>gi|24378608|ref|NP_720563.1| tRNA pseudouridine synthase A [Streptococcus mutans UA159]
 gi|38258780|sp|Q8DWH1|TRUA_STRMU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|24376463|gb|AAN57869.1|AE014860_6 putative tRNA pseudouridine synthase A [Streptococcus mutans UA159]
          Length = 249

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           MIRY  II Y+G+ + G+QRQ    ++Q  IEK +  + +G+ V +HGAGRTD+GVHA  
Sbjct: 1   MIRYKAIISYDGTNFSGFQRQPQVRTVQEEIEKTLLRLNSGQAVKIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L   L+   +  D I ++ +  V   FHAR+   R++Y + +   
Sbjct: 61  QVIHFDLPQQRDLEKLRFGLDT--QTPDDIDVIQVEQVADDFHARYQKHRKTYEFLVDLG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    L +  A   P  +D   ++ A + L G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPLMRHYATHFPYKVDFSVVKAAIKKLRGTHDFTGFTASGTSVENKVRTISRATVEK 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     +++ L++ DR   GP A   
Sbjct: 179 DDKTGFLIFTFTGSGFLYKQVRNMVGTLLKIGNGRMPIDQIDRILESGDRSLAGPTAASN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYD 248


>gi|118444045|ref|YP_877232.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
 gi|118134501|gb|ABK61545.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
          Length = 246

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 87/245 (35%), Positives = 138/245 (56%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              ++IEY+GS Y GWQ+QK+  +IQ  IE+AIF +T + + V+G  RTD+GVHA   VA
Sbjct: 4   NIKLVIEYDGSNYSGWQKQKHSMTIQQRIEEAIFDITKQKIEVNGCSRTDAGVHARNFVA 63

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F +     P     A+N+ L     I I N   V   FHARF +  + Y+Y I+ R+ P
Sbjct: 64  NFIIDSSIPPEKFKYAMNSKL--PKDIVIKNSCEVPMDFHARFQSKGKKYVYTILNREEP 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFG 181
             +++G  +   K LD + MR A+++ +G H+F +F +       S +RTI + DV    
Sbjct: 122 PTIDRGVVYHFNKKLDVDLMRSASKYFIGSHEFDSFYKKAGSSVKSTLRTIYYCDVTKVD 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I+I V+   FL+  +R   G+L  VG  +    D++  + A+DR++ G   PP+GL  
Sbjct: 182 DIIKIIVIGEGFLYNMVRIIAGTLVEVGIARIKPEDIKNIILAKDREKAGRSLPPQGLCL 241

Query: 242 DSVEY 246
           + V Y
Sbjct: 242 EEVLY 246


>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 =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 100/249 (40%), Positives = 143/249 (57%), Gaps = 4/249 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M +   +++EYNGS Y GWQ QK    S+Q ++EKA+ ++    V V  AGRTDSGVHA 
Sbjct: 1   MTKKVVLVVEYNGSEYKGWQAQKFGVPSVQENLEKALAIIANHPVKVVCAGRTDSGVHAS 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HF+   E         +N +L     I+++  S V   FHARFSA+ R Y Y I +
Sbjct: 61  AQVVHFETDVERNERAWTLGVNTHL--PSDITVVAASPVSNDFHARFSALSRRYRYVIYS 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                A+         K+LD   M+ AA+  +G HDF++FR++ CQA +PIRTI +F+V+
Sbjct: 119 SDFCPAILSKGITWTYKNLDVSAMKEAAKVFLGTHDFSSFRAVGCQAKTPIRTILNFEVH 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I + V A +FLH  IR+F G L  +G G+   +  ++ L+A+DR + G  APP G
Sbjct: 179 QLGQYIVLDVRANAFLHHMIRNFAGVLMSIGAGEKPVSWAKQTLEAKDRTKGGITAPPTG 238

Query: 239 LYFDSVEYS 247
           LYF   +Y 
Sbjct: 239 LYFVDAQYP 247


>gi|255067233|ref|ZP_05319088.1| tRNA pseudouridine synthase A [Neisseria sicca ATCC 29256]
 gi|255048601|gb|EET44065.1| tRNA pseudouridine synthase A [Neisseria sicca ATCC 29256]
          Length = 272

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 80/247 (32%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q  +E A+  + GE +    AGRTD+GVHA  Q
Sbjct: 14  QRWALTLSYDGSRFYGWQKQADGLPTVQTVLESALSQIAGETIRTIVAGRTDTGVHATAQ 73

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NAYL   + +++L    V   FHARF A  R Y Y + +  
Sbjct: 74  VVHFDTQVARPEQAWVRGVNAYL--PEGVAVLFAQQVAPHFHARFDAYGRRYRYLLESSP 131

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               + +G+       LD E M+ AA  L G HDF++FR++ CQA SP++T+    ++  
Sbjct: 132 VRSPILQGKVGWTHLKLDPEKMQQAALLLEGEHDFSSFRAVECQAKSPVKTLYSAKISGT 191

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              +++ +   +FLH  +R+ +G+L  VG G+ + +  +  ++ + R +  P   P+GLY
Sbjct: 192 PQFLKLDLHGNAFLHHMVRNIMGALVYVGSGRLSISGFQDLIEERSRLKAPPTFMPDGLY 251

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 252 LTGVDYP 258


>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 =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 113/245 (46%), Positives = 152/245 (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  HLDLAKALPPDNVRDGLNAYLR-PAPVSILLAQPVSPDFHARFQCHRRHYLYRLLDRRSP 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|166033550|ref|ZP_02236379.1| hypothetical protein DORFOR_03276 [Dorea formicigenerans ATCC
           27755]
 gi|166026735|gb|EDR45492.1| hypothetical protein DORFOR_03276 [Dorea formicigenerans ATCC
           27755]
          Length = 266

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 80/267 (29%), Positives = 124/267 (46%), Gaps = 22/267 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +I+  + + I  +TGE + + GA RTDSGVHAL  
Sbjct: 1   MRRIRIVVAYDGTNYCGWQIQPNGITIEEILNRQISKLTGEDIRIIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF-SAIRRSYLYRIITR 119
           VA FD            ALN  +   + I I+    V   +H R+ + I ++Y Y I   
Sbjct: 61  VAVFDTESRIPGDRFAYALNQKM--PEDIVIVRSDEVQIDWHPRYQNEISKTYEYHIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    L+   +  +   LD E MR  A++++G HDF +F ++   A   +RT+    +  
Sbjct: 119 KVRNPLKNRYSTFVSFDLDVEKMRQGAKYILGEHDFASFCNVRTNAKDTVRTVHEITIKE 178

Query: 179 ------------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
                                  I IRV    FL+  +R   G+L  VG G +    +  
Sbjct: 179 IPMDKFQASNWGQENSNLENEKEIVIRVTGNGFLYNMVRIIAGTLIRVGRGFYEPEKIRD 238

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            L+A++    G  APP GL   S++Y 
Sbjct: 239 ILEAKEHTSEGITAPPNGLVLVSIDYP 265


>gi|148270348|ref|YP_001244808.1| tRNA pseudouridine synthase ACD [Thermotoga petrophila RKU-1]
 gi|166229847|sp|A5IM09|TRUA_THEP1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|147735892|gb|ABQ47232.1| tRNA pseudouridine synthase A [Thermotoga petrophila RKU-1]
          Length = 245

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 126/246 (51%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + + +  AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYIQAAGRTDTGVHANGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+          +  A+NA L   D + +  +  V   FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIRNAMNANL--PDDVYVKEVFEVPVNFHPRFDVTKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR A ++L G HDFT+F         P+RTI    +  
Sbjct: 119 RQKNVFLRKYVWWFPYELDLDAMRKAVKYLEGTHDFTSF-KTGSDERDPVRTIYRIRILR 177

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>gi|330962608|gb|EGH62868.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 274

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 95/245 (38%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     IS+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERSLKAWVMGANINL--PHDISVSWARVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA HLVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAAHLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWAREVLESKVRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VQVEY 250


>gi|292670303|ref|ZP_06603729.1| tRNA pseudouridine synthase A [Selenomonas noxia ATCC 43541]
 gi|292648034|gb|EFF66006.1| tRNA pseudouridine synthase A [Selenomonas noxia ATCC 43541]
          Length = 260

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 81/254 (31%), Positives = 127/254 (50%), Gaps = 9/254 (3%)

Query: 1   MIR-----YCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M++       + I Y+G+ Y G+QRQ     ++Q ++E A+  V GE V +  AGRTD+G
Sbjct: 1   MMKRRARNLALKIAYDGTRYHGFQRQSPPVVAVQNALEAALAEVCGETVELAAAGRTDAG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  QV +F          L +A+N  L     I++ +     + F AR SA  ++Y+Y
Sbjct: 61  VHACGQVVNFFTDGRIPTERLPRAVNGLL--PPDIAVTDAWEAARDFSARHSAKGKAYVY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R+     P    +  AW I + LD E MR A   LVG HD+++FR+      SP+RTID 
Sbjct: 119 RMEQCTVPNPFTRNYAWQIFRPLDVEAMRAALAMLVGTHDYSSFRAAGGAPMSPVRTIDE 178

Query: 175 FDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             +   G   +   +    FL+  +R+ + ++  VG  + +     +   A+DR+   P 
Sbjct: 179 IRLEDEGEGRLSCYLHGNGFLYHMVRNIMSTVVSVGQERISVGRFAEIFAARDRRLASPT 238

Query: 234 APPEGLYFDSVEYS 247
           AP  GLY   V+Y 
Sbjct: 239 APACGLYLLHVDYD 252


>gi|284009291|emb|CBA76427.1| tRNA pseudouridine synthase A [Arsenophonus nasoniae]
          Length = 270

 Score =  282 bits (722), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 97/247 (39%), Positives = 133/247 (53%), Gaps = 2/247 (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  VIHFETSVIRKDSAWTMGVNSHL--PADIAVRWSKDVEPDFHARFSATARRYRYIIFNHR 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 FDSVEYS 247
             +V+Y 
Sbjct: 247 LVAVDYP 253


>gi|325129355|gb|EGC52190.1| tRNA pseudouridine synthase A [Neisseria meningitidis OX99.30304]
          Length = 265

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALENALAQIAGEAVSTIVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESVP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>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 =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 117/250 (46%), Positives = 155/250 (62%), Gaps = 5/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSS-IQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
            R+ + IEY+G  + GWQRQ +G + +QG +E A   +TG   V+   AGRTDSGVHA  
Sbjct: 29  RRWAVRIEYDGRDFVGWQRQASGLTSVQGVLEAAATRLTGGRPVISITAGRTDSGVHATG 88

Query: 60  QVAHFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           QVAH D   +       +  ALN ++K    ++IL    V   + ARFSAI RSY YRII
Sbjct: 89  QVAHLDFPDDIPLSSTAVRDALNYHMK-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 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 268 GLYLTGVAYP 277


>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 =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 113/248 (45%), Positives = 157/248 (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 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTIDHFDVN 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|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 =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 137/248 (55%), Gaps = 3/248 (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 YFDSVEYS 247
           +  SV+Y 
Sbjct: 239 FMTSVDYE 246


>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 =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 137/246 (55%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +  +++EY+GS Y GWQ QK +  ++Q  +E A+  +    V V  AGRTD+GVHA  QV
Sbjct: 5   KVVLVVEYDGSRYKGWQAQKFDVDTVQEKLEYALSKIANHSVGVICAGRTDAGVHASSQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   E         +N +L     IS++  + V  +FHARFSA+ R Y Y I   + 
Sbjct: 65  VHFETASERPIRAWTLGVNTHL--PPDISVVAANYVADEFHARFSALTRRYRYVIYQSEF 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+         K L  + M+ AA   +G HDF+++R+I CQA SPIRT+ +F VN FG
Sbjct: 123 RPAIMAKGVTWTYKDLSEQKMQQAAACFIGTHDFSSYRAIGCQARSPIRTVLNFSVNKFG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  IR+F G L  +G G+      ++ L A+DR + G  APP GLYF
Sbjct: 183 QYIVLDIRANAFLHHMIRNFAGVLMAIGAGEKPVQWAKQVLDAKDRTQGGVTAPPHGLYF 242

Query: 242 DSVEYS 247
              +Y 
Sbjct: 243 VDAQYP 248


>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 =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 96/245 (39%), Positives = 137/245 (55%), Gaps = 3/245 (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 LVIIDITANSFLYHMVRNIVGSLIQINDNTKK-NYIKKILDKKDRNYAGPTVSARGLYLF 244

Query: 243 SVEYS 247
            V+Y 
Sbjct: 245 FVKYP 249


>gi|296877377|ref|ZP_06901416.1| tRNA-pseudouridine synthase I [Streptococcus parasanguinis ATCC
           15912]
 gi|296431616|gb|EFH17424.1| tRNA-pseudouridine synthase I [Streptococcus parasanguinis ATCC
           15912]
          Length = 251

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+QRQ +  S+Q  IEK +  +  G  V VHGAGRTDSGVHAL 
Sbjct: 4   MTRYKATISYDGTLFAGFQRQPHARSVQEEIEKTLTRLNQGTPVTVHGAGRTDSGVHALG 63

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I  + +  V   FH+R+    ++Y + +   
Sbjct: 64  QVIHFDLPQERDEEKLRFALDT--QTPEDIDFIRVEQVAADFHSRYKKHSKTYEFIVDYG 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  LD E M+ A Q L G HDFT F +        +RTI    +  
Sbjct: 122 RPKNPMMRHYATHYPYPLDVEKMQAAIQKLEGTHDFTGFTASGTSVEDKVRTITEARLVE 181

Query: 180 FGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR   GP A P 
Sbjct: 182 DAEHHRLVFTFSGNGFLYKQIRNMVGTLLKIGNDRMPIEQIDLILEQKDRNLAGPTAAPN 241

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 242 GLYLKEIRYE 251


>gi|308187626|ref|YP_003931757.1| pseudouridylate synthase I [Pantoea vagans C9-1]
 gi|308058136|gb|ADO10308.1| pseudouridylate synthase I [Pantoea vagans C9-1]
          Length = 267

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            +  + IEY+GS Y+GWQRQ    S+Q  +E+A+  V    V +  AGRTD+GVH   QV
Sbjct: 7   QKLALGIEYDGSRYYGWQRQNEVRSVQEKVERALSKVADHPVSIFCAGRTDAGVHGTGQV 66

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +NA L     I++  +  V  +FHARFSA  R Y Y I  ++ 
Sbjct: 67  VHFETTSQRPDGAWTLGVNANL--PADIAVRWVKAVPDEFHARFSATARRYRYLIYNQRL 124

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G
Sbjct: 125 RPAVLAQGVTHFYHPLDAEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVIHLNVTRQG 184

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  +G G    + +   L A+DR      A  EGLY 
Sbjct: 185 PYVIVDIKANAFVHHMVRNIVGSLMEIGCGNKPESWMATLLAAKDRTLAAATARAEGLYL 244

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 245 VAVDYP 250


>gi|325133363|gb|EGC56028.1| tRNA pseudouridine synthase A [Neisseria meningitidis M13399]
          Length = 265

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALENALAQIAGEAVSTIVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWIRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


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

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 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|261393361|emb|CAX50997.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I; tRNA
           pseudouridylate synthase I) [Neisseria meningitidis
           8013]
          Length = 265

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|77409358|ref|ZP_00786059.1| tRNA pseudouridine synthase A [Streptococcus agalactiae COH1]
 gi|77172030|gb|EAO75198.1| tRNA pseudouridine synthase A [Streptococcus agalactiae COH1]
          Length = 258

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  + +G  V+++GAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIYGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A   
Sbjct: 179 EASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>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 =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|328957471|ref|YP_004374857.1| tRNA pseudouridine synthase A [Carnobacterium sp. 17-4]
 gi|328673795|gb|AEB29841.1| tRNA pseudouridine synthase A [Carnobacterium sp. 17-4]
          Length = 246

 Score =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    M IEY+G  Y GWQR  +   +IQG IE  +  +TG    + G+GRTD+G HA  
Sbjct: 1   MRNIKMTIEYDGGRYLGWQRLSDSDKTIQGKIENILTAMTGTKTEIIGSGRTDAGAHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  L  V ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTTSTMEFPAMLDHLNRYL--PRDIVVKKLEEVPERFHARYNASGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P   ++  ++  P  LD + M  A   LVG HDF  F S+     S +RTID   ++ 
Sbjct: 119 SIPSVFDRNFSYDFPGELDIDKMNEACNKLVGTHDFIGFSSLKKSKKSTVRTIDEIKIHK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+        FL+  IR  +G+L  +G G    + ++   ++  R + G   P +GL
Sbjct: 179 EGDLLHFTFKGEGFLYKMIRIIMGTLLEIGSGMADPSSIDAIFKSGIRSDAGMTVPSQGL 238

Query: 240 YFDSVEYS 247
           + D V Y 
Sbjct: 239 FLDEVYYD 246


>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 =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERSMKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 136 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 196 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPIEWAREVLESRIRRTGGVTAHPYGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VGVEY 260


>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 =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|313631806|gb|EFR98984.1| tRNA pseudouridine synthase A [Listeria seeligeri FSL N1-067]
          Length = 248

 Score =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 90/250 (36%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +      FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDISAEKFQKALQVM--TPFDISFLIVEEALADFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-N 178
           +      +  A   P  L+ E M++A++ LVG HDFT+F S   +  S +RT+   D   
Sbjct: 119 KVFDPFSRNFALHYPYELNLEKMKLASERLVGEHDFTSFCSARTERDSKVRTLYSIDFYE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPPE 237
              + + I      FL+  +R   G+L   G G+ +  D+ KAL A+DR K     APP+
Sbjct: 179 EDDDTLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLARDRQKLISKTAPPQ 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLWRVDYE 248


>gi|330901134|gb|EGH32553.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 284

 Score =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERTLKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 136 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 196 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAHPYGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VGVEY 260


>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 =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|325127315|gb|EGC50250.1| tRNA pseudouridine synthase A [Neisseria meningitidis N1568]
          Length = 265

 Score =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAVRPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIGQMRQAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|167770549|ref|ZP_02442602.1| hypothetical protein ANACOL_01895 [Anaerotruncus colihominis DSM
           17241]
 gi|167667144|gb|EDS11274.1| hypothetical protein ANACOL_01895 [Anaerotruncus colihominis DSM
           17241]
          Length = 246

 Score =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 110/247 (44%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I Y G+ Y G+Q Q+N  ++  +++ A+  + GE + + G  RTD+GVHA   
Sbjct: 1   MRHLLLTIRYRGTRYHGYQVQQNAVTVAQTVQDAVERIFGERLPIKGCSRTDAGVHANCF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                         + +A+N +L     I++     V + FH R+    + YLYRI    
Sbjct: 61  ALTLRTASVMACDAVVRAMNVHL--PSDIAVTGCREVPEAFHPRYDCKGKRYLYRIYNGT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    A      LD   M  AAQ  VG HDF  F S        +RT+    V   
Sbjct: 119 VRDPFSADLALFWKYPLDERRMDAAAQGFVGTHDFAAFCSSGSGVQDTVRTVTDASVTRH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +   V    FL+  +R  VG+L     G +T  D+   L+ +DR   GP APP GLY
Sbjct: 179 GDFVIYSVTGNGFLYNMVRIMVGTLLEAARGVYTPADVLHMLEGRDRSAAGPTAPPHGLY 238

Query: 241 FDSVEYS 247
            D+V Y 
Sbjct: 239 LDAVFYD 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 =  281 bits (720), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIGQMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>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 =  281 bits (720), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGESVATTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTAAARPQQAWIRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRQAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|149797294|ref|YP_001294664.1| tRNA-pseudouridine synthase A [Symbiobacterium thermophilum IAM
           14863]
          Length = 267

 Score =  281 bits (720), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 125/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA--GRTDSGVHAL 58
           M    +I+ Y+G+ Y G+QRQ NG +IQ  +E+A+  VTGE  +  GA  GRTD+GVHA 
Sbjct: 1   MRTIKLILAYDGTAYAGFQRQPNGITIQQRLEEALRAVTGEPDLRIGAAAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H              ALN +L   D I+++        FHAR+ A  + Y Y    
Sbjct: 61  GQVVHLRTYATIPIDRWPAALNGHL--PDDIAVIGAEEAPPDFHARYWAREKRYRYTFCL 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
               L + +  ++   + +D + MR AA  LVGRHDF  FR+    A + +RTI    + 
Sbjct: 119 SPYRLPMARLYSYHWHRPVDVDAMRRAAALLVGRHDFAAFRATGGSARTTVRTITRLTLT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + + V A  FL+  +R   G+L  VG G+ +   + +AL+   R++ G   PP G
Sbjct: 179 EEPPFLHLDVTADGFLYNMVRIIAGTLLEVGAGRRSLDRVAQALRHGRREDAGRTLPPHG 238

Query: 239 LYFDSVEY 246
           L  + V Y
Sbjct: 239 LCLEEVVY 246


>gi|145588955|ref|YP_001155552.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|226708658|sp|A4SWX4|TRUA_POLSQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145047361|gb|ABP33988.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
          Length = 275

 Score =  281 bits (720), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 86/255 (33%), Positives = 134/255 (52%), Gaps = 11/255 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-----IVVVHGAGRTDSGVH 56
           +R  + ++Y+GS Y GWQ Q +  +IQ  +EKA+    GE      V    AGRTD+GVH
Sbjct: 1   MRIALGLQYDGSPYAGWQTQLHQPTIQDELEKALTAFIGEEAKAFPVHTITAGRTDTGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV HFD           + +N +L    +I +     V ++F ARFSA  R+Y+Y +
Sbjct: 61  ALGQVVHFDTNVGREDFSWVRGVNTFL--PKSIVVNWAKEVPEEFSARFSAYERTYIYAL 118

Query: 117 ITRQAPLALEKGRAWLI----PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
                   +   RA  +     + LD E M+ +A+ L+G HDF++FRS  CQ+ +P++TI
Sbjct: 119 HAGPCRSPIVNARAGYLMLPPDQFLDVEAMKKSAECLIGEHDFSSFRSSECQSKTPVKTI 178

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              D+ S    +  R+   +FLH  IR+ VG    +G G+  S  + + L A++R+   P
Sbjct: 179 YAIDIISQEPWVYFRIRGNAFLHHMIRNIVGCFLQIGQGRQQSGWMAEVLTAKNRQIAAP 238

Query: 233 LAPPEGLYFDSVEYS 247
               +GLY   ++Y 
Sbjct: 239 TFMADGLYLAKIKYP 253


>gi|22536285|ref|NP_687136.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 2603V/R]
 gi|76798489|ref|ZP_00780725.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 18RS21]
 gi|77412040|ref|ZP_00788367.1| tRNA pseudouridine synthase A [Streptococcus agalactiae CJB111]
 gi|42559812|sp|Q8CX20|TRUA_STRA5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|22533107|gb|AAM99008.1|AE014196_4 tRNA pseudouridine synthase A [Streptococcus agalactiae 2603V/R]
 gi|76586154|gb|EAO62676.1| tRNA pseudouridine synthase A [Streptococcus agalactiae 18RS21]
 gi|77161897|gb|EAO72881.1| tRNA pseudouridine synthase A [Streptococcus agalactiae CJB111]
          Length = 258

 Score =  281 bits (720), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  + +G  V++HGAGRTD GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDVGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A   
Sbjct: 179 EASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|295103893|emb|CBL01437.1| pseudouridylate synthase I [Faecalibacterium prausnitzii SL3/3]
          Length = 254

 Score =  281 bits (720), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + + + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL   
Sbjct: 1   MNFLLTLAYDGTNYCGFQVQPNGRSVAATFQDALEAVLGSRPDIKGCSRTDAGVHALGFR 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F       P  L  ALN +L     I +L +  V + FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPPQKLPLALNQHL--PPDIRVLAVQTVPEDFHARYAAHTKTYLYRIHNHPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDVN 178
               +      +P+ LD   M+ AAQ  VG HDF    +    A      +RTI    V 
Sbjct: 119 DSPFDAAYYTRVPRRLDESAMQAAAQQFVGTHDFLALCAAGSSAAAHGDTVRTITDCHVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ ++I V A  +L+  +R   G+L  VG G+  + D+   L ++DR   GP  P +G
Sbjct: 179 RRGDEVDIEVTADGYLYNMVRILAGTLCEVGAGRLRAADIPAILASRDRSRAGPTLPAKG 238

Query: 239 LYFDSVEYS 247
           L+   VEY 
Sbjct: 239 LFLKRVEYP 247


>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 =  281 bits (720), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 140/245 (57%), Gaps = 3/245 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + + Y GSG+ GWQRQ    ++Q ++E+A+  +  E + V GAGRTD+GVHA  QVA 
Sbjct: 8   YKLTLSYCGSGFHGWQRQGELPTVQRALEEAVAKIWEEPIPVEGAGRTDAGVHAKGQVAS 67

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F   R+  P +L +ALN +L   DT+ + +  IV ++F ARF A+ ++Y Y +       
Sbjct: 68  FAAPRKLEPEVLKRALNYHL--PDTVRVWDARIVPREFSARFDAVSKTYQYLLWNDPVMD 125

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGN 182
               GRAW IP+++D E M  AA+  +G+H+F  F  +      +P+RT+        G+
Sbjct: 126 PFYLGRAWHIPRAMDVEMMNEAARLFLGKHNFAAFVSNPGMPVKNPVRTVLDCFFLEQGS 185

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           L+   V A  FL+  +R+ VG+L  VG G+ +  +L+K  + Q R E    APP GLY  
Sbjct: 186 LVFFNVKADGFLYRMVRNMVGALVKVGLGRLSRQELKKIFENQKRIEAFAAAPPWGLYLL 245

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 246 AVDYP 250


>gi|290579596|ref|YP_003483988.1| putative tRNA pseudouridine synthase A [Streptococcus mutans
           NN2025]
 gi|254996495|dbj|BAH87096.1| putative tRNA pseudouridine synthase A [Streptococcus mutans
           NN2025]
          Length = 249

 Score =  281 bits (719), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           MIRY  II Y+G+ + G+QRQ    ++Q  IEK +  + +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MIRYKAIISYDGTNFSGFQRQPQMRTVQEEIEKTLLRLNSGQAVKVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L   L+   +  D I ++ +  V   FHAR+   R++Y + +   
Sbjct: 61  QVIHFDLPQQRDLEKLRFGLDT--QTPDDIDVIQVEQVADDFHARYQKHRKTYEFLVDLG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    L +  A   P  +D   ++ A + L G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPLMRHYATHFPYKVDFSVVKAAIKKLRGTHDFTGFTASGTSVENKVRTISRATVEK 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ Q+R+ VG+L  +G+G+     +++ L++ DR   GP A   
Sbjct: 179 DEKTGFLIFTFTGSGFLYKQVRNMVGTLLKIGNGRMPIDQIDRILESGDRSLAGPTAASN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYD 248


>gi|291533595|emb|CBL06708.1| pseudouridylate synthase I [Megamonas hypermegale ART12/1]
          Length = 256

 Score =  281 bits (719), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 73/251 (29%), Positives = 126/251 (50%), Gaps = 7/251 (2%)

Query: 1   MIR-----YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M++       + + Y+G+ Y G+QRQ    ++Q  +E A+F + G+ + +  AGRTD+GV
Sbjct: 8   MMKARRRNIKLTLSYDGTNYHGFQRQTKVVAVQNVLEGALFKLFGDSIELAAAGRTDAGV 67

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA+ QV +F          + +A N  L   D I +L     D+ F A  S   + Y+Y+
Sbjct: 68  HAIGQVVNFFTDGTIPIQNVVRAGNRLL--PDDIVLLKAEEADRDFSALHSVKSKIYIYK 125

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +   +          W + K L+ E+M+ A +++ G HDF++FRS     +SPIR I   
Sbjct: 126 VFENELADPFMSRFYWHVNKKLNLEDMQEALKYIEGEHDFSSFRSAGGNDTSPIREIYEA 185

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 N+   +     FL+  +R+ +G +  +G G+    ++ K ++A++R   G +AP
Sbjct: 186 SCTKENNVYTFKFWGSGFLYHMVRNIMGLMINIGLGRVDKHEVPKIIEAKNRALAGKMAP 245

Query: 236 PEGLYFDSVEY 246
             GLY   V Y
Sbjct: 246 ANGLYLQKVYY 256


>gi|254248703|ref|ZP_04942023.1| Pseudouridylate synthase [Burkholderia cenocepacia PC184]
 gi|124875204|gb|EAY65194.1| Pseudouridylate synthase [Burkholderia cenocepacia PC184]
          Length = 271

 Score =  281 bits (719), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + I+Y+G+ + GWQ Q +G ++Q  +E A+       +    AGRTD+GVH L Q
Sbjct: 1   MMRIALGIQYDGAAFCGWQAQPHGKTVQNRLEHALAEFARVPLHTTVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       +  NA+L    T+S+     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTDLEREVFSWVRGTNAFL--PPTVSVQWAKPMPDTFHARFSAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   
Sbjct: 119 VRSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRA 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY
Sbjct: 179 GYFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LAHVGYP 245


>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 =  281 bits (719), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ +++ Y+GS +FGWQ+Q  G  ++Q  +E AI  + GE + V  AGRTD+GVHA+ Q
Sbjct: 13  QRWILVLSYDGSRFFGWQKQAEGIPTVQAELESAISKIAGENISVTVAGRTDTGVHAVAQ 72

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P    + +NAYL   D +++L        FHARF A  R Y Y + +  
Sbjct: 73  VVHFDTAVFRPPQAWVRGVNAYL--PDGVAVLCAQTTQPHFHARFDAFGRRYRYLLQSAP 130

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L KGRA      L+ E MR AA  LVG HDF++FR+  CQA SP++TI   ++   
Sbjct: 131 VRSPLMKGRAGWTHLPLNLERMRQAAALLVGEHDFSSFRAAECQAKSPVKTIYSTEIGGG 190

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              +   +   +FLH  +R+ +G+L  VG G+         ++ + R +  P    +GLY
Sbjct: 191 AEWLYFDIHGNAFLHHMVRNIMGALVYVGCGRLDVGQFADLIKERSRLKAPPTFMSDGLY 250

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 251 LTGVDYP 257


>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 =  281 bits (719), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E M  AA  LVG  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMCRAASLLVGEQDFSSFRAAGCQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|330952706|gb|EGH52966.1| tRNA pseudouridine synthase A [Pseudomonas syringae Cit 7]
          Length = 274

 Score =  281 bits (719), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERTMKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VGVEY 250


>gi|323490654|ref|ZP_08095859.1| tRNA pseudouridine synthase A [Planococcus donghaensis MPA1U2]
 gi|323395746|gb|EGA88587.1| tRNA pseudouridine synthase A [Planococcus donghaensis MPA1U2]
          Length = 247

 Score =  281 bits (719), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 126/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    I Y+GSG+ G+Q Q +  ++Q  + K +  +  G+++ V  +GRTD+ VHA  
Sbjct: 1   MKRLKATIAYDGSGFAGYQVQPDSRTVQLELMKVLETIHKGKVIQVVASGRTDAKVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD       +   KALN  L   + I + ++  VD  FHAR+    ++Y Y+    
Sbjct: 61  QVIHFDTELSIPIIGWLKALNVLL--PEDIRVHSIEEVDTSFHARYHTTGKTYRYKWDRS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q      +     + + LD E M+ A+Q +VG HDF++F + +      +RT+   D   
Sbjct: 119 QIISPFTRSLMVHVKQPLDVEAMKKASQAIVGTHDFSSFCAANTAVVDKVRTVRRLDFEE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN + + +    FL+  +R   G+L  VG G+  + +LE  + A DR   G  AP  GL
Sbjct: 179 HGNELHMVIEGTGFLYNMVRIIAGTLAEVGMGRRKAEELEDIVSATDRDAAGITAPAHGL 238

Query: 240 YFDSVEYS 247
           Y ++V Y 
Sbjct: 239 YLENVMYE 246


>gi|332638011|ref|ZP_08416874.1| tRNA pseudouridine synthase A [Weissella cibaria KACC 11862]
          Length = 249

 Score =  281 bits (719), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 78/251 (31%), Positives = 125/251 (49%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY   I Y+G+ ++GWQ Q    ++Q  +EK +  +  +    + V G+GRTD+ VHA
Sbjct: 1   MPRYKATISYDGTEFYGWQVQPGKRTVQLEMEKVVNKMAKDPADHIRVQGSGRTDARVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV HFDL  +     + K L+  L     I I ++  VD+ FHA+FSA  ++Y YR+ 
Sbjct: 61  QGQVVHFDLPFDIPNEAVRKGLSTML--PYDIGIKSVEKVDESFHAQFSAHNKTYRYRLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF-- 175
           T +     ++       + +D   M+ A    VG HD+ +F +   Q  + +RT+     
Sbjct: 119 TTEFIDPFKRNYTGHWHRRIDTSLMQQAIGDYVGEHDWLSFVASGFQQKTTVRTVYSAKM 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + I        FL+ QIR  VG L  +G+G     D+++    +DR++    AP
Sbjct: 179 WEKPEEDEIWFEFTGNGFLYNQIRIMVGVLLEIGNGSRPVDDIQRLFAVKDRQQARFTAP 238

Query: 236 PEGLYFDSVEY 246
            +GLY  SV+Y
Sbjct: 239 AQGLYLMSVDY 249


>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 =  281 bits (719), Expect = 7e-74,   Method: Composition-based stats.
 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|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 =  281 bits (719), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERTTKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M +AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 136 RPAHLNQEITWNHRPLDVERMALAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 196 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWARDVLESRVRRTGGVTAHPYGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VQVEY 260


>gi|325206941|gb|ADZ02394.1| tRNA pseudouridine synthase A [Neisseria meningitidis M04-240196]
          Length = 265

 Score =  281 bits (719), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTIVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTAAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESVP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|15644322|ref|NP_229374.1| tRNA pseudouridine synthase ACD [Thermotoga maritima MSB8]
 gi|8134772|sp|Q9X1R0|TRUA_THEMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|4982143|gb|AAD36641.1|AE001802_10 pseudouridylate synthase I [Thermotoga maritima MSB8]
          Length = 245

 Score =  281 bits (719), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 125/246 (50%), Gaps = 5/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R   +IEY+GS +FG+Q Q +  ++QG IE A+  +  + +    AGRTD+GVHA  Q
Sbjct: 1   MKRVAAVIEYDGSNFFGYQGQPDVRTVQGVIEDALERIFKQRIYTQAAGRTDTGVHANGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  F+          +  A+NA L   D + +  +  V   FH RF   +R Y Y I+T 
Sbjct: 61  LIAFNCPNDRMTTEDIRNAMNANL--PDDVYVKEVFEVPVNFHPRFDVTKRIYHYFILTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W  P  LD + MR A ++L G HDFT+F         P+RTI    +  
Sbjct: 119 RQKNVFLRKYVWWFPYELDLDAMRKAVKYLEGTHDFTSF-KTGSDERDPVRTIYRIRILR 177

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+ IRV  RSFL   +R+ V +L  VG  +W    +++ L+A+DR      AP  G
Sbjct: 178 LKNDLVLIRVEGRSFLRRMVRNIVAALVKVGLKQWEPEKMKEVLEARDRSAAAGTAPAHG 237

Query: 239 LYFDSV 244
           LYF  V
Sbjct: 238 LYFYKV 243


>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 =  280 bits (718), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERTMKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M +AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 136 RPAHLNQEITWNHRPLDVERMALAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 196 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWARDVLESRVRRTGGVTAHPYGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VQVEY 260


>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 =  280 bits (718), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQTALETALAQIAGEFVATTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAVRPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>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 =  280 bits (718), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTAAVRPAQAWIRGVNAHL--PEGIAVLHARQVAPGFHARFDASGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLELDIGPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|330973842|gb|EGH73908.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 274

 Score =  280 bits (718), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERSMKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPIEWAREVLESRIRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VGVEY 250


>gi|307244438|ref|ZP_07526548.1| tRNA pseudouridine synthase A [Peptostreptococcus stomatis DSM
           17678]
 gi|306492195|gb|EFM64238.1| tRNA pseudouridine synthase A [Peptostreptococcus stomatis DSM
           17678]
          Length = 253

 Score =  280 bits (718), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 125/246 (50%), Gaps = 4/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQV 61
              +++ Y G+ Y GWQ+Q +   IQG +E A      +  + + G+GRTD+GVHAL QV
Sbjct: 5   NIMLVVAYEGTRYCGWQKQPDSPGIQGELEYACTQAFNKKNINITGSGRTDAGVHALGQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F +        + + LN  L     I++L    V  +FHAR SA +++Y Y+I   + 
Sbjct: 65  ANFTVDTTIPVDKIPEVLNNRL--PKDIAVLRAQEVKSEFHARHSAHKKTYRYQIYPSRI 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                K  A+ +   LD + M+    HL+G+HDF  F S      S +RTI   D+   G
Sbjct: 123 RSPFLKDFAYQVKYDLDLDRMKEEIIHLLGQHDFKGFMSSGSDIKSTVRTIYRADIYKRG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +LI I V    FL+  +R   G++  +G GK T   L   + +  R   G  APP+GL+ 
Sbjct: 183 DLIVIEVEGNGFLYNMVRIIAGTMVDIGRGKIT-ESLRDIIGSGVRARAGHTAPPQGLFL 241

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 242 VGVDYP 247


>gi|242239994|ref|YP_002988175.1| tRNA pseudouridine synthase A [Dickeya dadantii Ech703]
 gi|242132051|gb|ACS86353.1| tRNA pseudouridine synthase A [Dickeya dadantii Ech703]
          Length = 275

 Score =  280 bits (718), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 91/245 (37%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 14  KIALGIEYDGSRYYGWQRQAEVESVQECLEKALSNVANEPISVFCAGRTDAGVHATGQVV 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +NA+L     I++  ++ VD+ FHARFSA  R Y Y I   +  
Sbjct: 74  HFTTGAVRKDAAWTMGVNAHL--PSDIAVRWVTTVDEAFHARFSATARRYRYVIYNHRYR 131

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD   M  A Q L+G +DFT+FR++ CQ+ +P R + H  V   G 
Sbjct: 132 PAILSHGVTHYHLPLDAARMERAGQCLLGENDFTSFRAVQCQSRTPWRNVKHLKVMRHGA 191

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  VG G      + + L A+DR      A  +GLY  
Sbjct: 192 YIVVDIKANAFVHHMVRNIVGSLMEVGCGNQPEGWIAELLAAKDRTLAAATARADGLYLV 251

Query: 243 SVEYS 247
           +V+Y 
Sbjct: 252 AVDYP 256


>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 =  280 bits (718), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERTLKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VGVEY 250


>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 =  280 bits (718), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+          + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDITAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAGCQAKSPVKTIYRTDLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|172062883|ref|YP_001810534.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MC40-6]
 gi|238692865|sp|B1Z1N7|TRUA_BURA4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171995400|gb|ACB66318.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MC40-6]
          Length = 270

 Score =  280 bits (718), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDALERALGEFACVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRTDFSWVRGTNAFL--PSTVSVQWAKPMPDTFHARFAAFERTYYYVLYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY 
Sbjct: 179 HFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRTLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|90962375|ref|YP_536291.1| tRNA pseudouridine synthase A [Lactobacillus salivarius UCC118]
 gi|301300240|ref|ZP_07206452.1| tRNA pseudouridine synthase A [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|123391325|sp|Q1WSC1|TRUA_LACS1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|90821569|gb|ABE00208.1| tRNA pseudouridine synthase A [Lactobacillus salivarius UCC118]
 gi|300215017|gb|ADJ79433.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Lactobacillus salivarius
           CECT 5713]
 gi|300852181|gb|EFK79853.1| tRNA pseudouridine synthase A [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 256

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 124/250 (49%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
            R+ + + Y+G+ + G+Q Q N  ++Q  +EKAI  ++   E + V+G+GRTDSGVHAL 
Sbjct: 3   QRFKVTLAYDGTNFAGFQAQPNQRTVQFVLEKAINKMSKKDEYITVYGSGRTDSGVHALG 62

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD         + + LN+ L       +++  IV   FH+R++   + YLYR+   
Sbjct: 63  QVVHFDFPHPISAKGMLRGLNSML--PLDCEVVDCKIVPNDFHSRYTTHGKRYLYRVSRG 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++         LD E ++ A   + G HD+++F +   QA S +RTI    V  
Sbjct: 121 EFVNPFKRLYTGHYKYPLDIEKIKEAMPDVEGTHDYSSFVASGSQAKSHVRTIYEAKVYE 180

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + I        FL+ Q+R  V +L  +G+GK    D  +  + +DR +    AP  
Sbjct: 181 DKVNDEIVFEFYGNGFLYNQVRIMVATLLEIGNGKRPVHDFLRLYEVKDRSQARQTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLKEVYYD 250


>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 =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            RY + + Y+GS +FGWQ+Q  G  ++Q ++E A+  + GE V V  AGRTD+GVHA  Q
Sbjct: 7   TRYALTLAYDGSRFFGWQKQAEGVATVQAALEHALSQIAGEPVSVIAAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       + +NA+L     +++    I D  FHARF A  R Y Y + +  
Sbjct: 67  VVHFDSRADRPLSAWVRGVNAHL--PQGVAVHKAQIADSAFHARFDASGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  GRA     +L+ + MR AAQ LVG HDF++FR+  CQA SP++T+    +   
Sbjct: 125 VRSPLLYGRAGWTHYALNDDAMRQAAQLLVGEHDFSSFRAAQCQAKSPVKTMYAVHLQRT 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+++ + A +FLH  +R+ +G+L  VG G+ +     + ++ + R    P   P+GLY
Sbjct: 185 GSLLKLDLHANAFLHHMVRNIMGALVYVGCGRLSVAQFGELIETRSRLYAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|255655803|ref|ZP_05401212.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-23m63]
 gi|296450959|ref|ZP_06892706.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296879075|ref|ZP_06903071.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
 gi|296260177|gb|EFH07025.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP08]
 gi|296429948|gb|EFH15799.1| tRNA-pseudouridine synthase I [Clostridium difficile NAP07]
          Length = 245

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    MI+ Y+GS Y G+Q+   N  +IQ  +E  +  +T E V + G+GRTD G HA  
Sbjct: 1   MRNIKMIVAYDGSRYKGYQKLGDNNMTIQEKLENVLSKMTNETVEIIGSGRTDMGAHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          + K L  YL   + I +  +  VD++FH+R++   ++Y+YRI   
Sbjct: 61  QVVNFRTNCMDSLDKIQKYLYEYL--PEDIVVKAVEEVDERFHSRYNVKSKTYMYRIDNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A  + K LD + MR A+++LVG HDFT+F S   +  S +R I   ++  
Sbjct: 119 KYHNPFIRKYATHVSKKLDLDRMRKASEYLVGEHDFTSFASSKSKKKSNVREIYSINIKE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N+IEI V    FL+  +R  VG+L  VG  +    D++  L+++DR +    AP +GL
Sbjct: 179 DDNIIEIYVEGNGFLYNMVRIIVGALIDVGLKRRAPQDIKYMLESRDRCQSSDTAPAKGL 238

Query: 240 YFDSVEY 246
               V Y
Sbjct: 239 CLWKVRY 245


>gi|170703047|ref|ZP_02893873.1| tRNA pseudouridine synthase A [Burkholderia ambifaria IOP40-10]
 gi|170132039|gb|EDT00541.1| tRNA pseudouridine synthase A [Burkholderia ambifaria IOP40-10]
          Length = 270

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDALERALGEFACVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRTDFSWVRGTNAFL--PSTVSVQWAKPMPDTFHARFAAFERTYYYVLYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DRK   P    +GLY 
Sbjct: 179 HFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRKLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>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 =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTAAVRPVQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIGQMRQAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|330878235|gb|EGH12384.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 274

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 94/245 (38%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERSLKAWVMGANINL--PHDVSVSWAKVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPIKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VQVEY 250


>gi|15675714|ref|NP_269888.1| tRNA pseudouridine synthase A [Streptococcus pyogenes M1 GAS]
 gi|19746822|ref|NP_607958.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS8232]
 gi|50914971|ref|YP_060943.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10394]
 gi|71904268|ref|YP_281071.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS6180]
 gi|71911430|ref|YP_282980.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS5005]
 gi|94989250|ref|YP_597351.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS9429]
 gi|94991194|ref|YP_599294.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10270]
 gi|94993138|ref|YP_601237.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS2096]
 gi|94995068|ref|YP_603166.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10750]
 gi|139473113|ref|YP_001127828.1| tRNA pseudouridine synthase A [Streptococcus pyogenes str.
           Manfredo]
 gi|209560051|ref|YP_002286523.1| tRNA pseudouridine synthase A [Streptococcus pyogenes NZ131]
 gi|54039783|sp|P65851|TRUA_STRP8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54042088|sp|P65850|TRUA_STRP1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901238|sp|Q5XA03|TRUA_STRP6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122986813|sp|Q1J4W4|TRUA_STRPF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122986985|sp|Q1JF09|TRUA_STRPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123257716|sp|Q1J9W8|TRUA_STRPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123258127|sp|Q1JK16|TRUA_STRPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123775214|sp|Q48RE4|TRUA_STRPM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166229842|sp|A2RCK6|TRUA_STRPG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238057736|sp|B5XIG6|TRUA_STRPZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|13622931|gb|AAK34609.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes M1
           GAS]
 gi|19749059|gb|AAL98457.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes
           MGAS8232]
 gi|50904045|gb|AAT87760.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10394]
 gi|71803363|gb|AAX72716.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS6180]
 gi|71854212|gb|AAZ52235.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS5005]
 gi|94542758|gb|ABF32807.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS9429]
 gi|94544702|gb|ABF34750.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10270]
 gi|94546646|gb|ABF36693.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS2096]
 gi|94548576|gb|ABF38622.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS10750]
 gi|134271359|emb|CAM29579.1| tRNA pseudouridine synthase A [Streptococcus pyogenes str.
           Manfredo]
 gi|209541252|gb|ACI61828.1| tRNA pseudouridine synthase A [Streptococcus pyogenes NZ131]
          Length = 249

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ++  ++Q  IEK ++ +  G  +++HGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQRHLRTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I ++N+  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQEQEVEKLRFALDT--QTPEDIDVVNIEKVADDFHCRYQKHLKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +      P +L+ + M+ A   LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRHYTTHYPYTLNIKLMQEAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSR 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DEKTDFLVFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPTISGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>gi|291288851|ref|YP_003505667.1| tRNA pseudouridine synthase A [Denitrovibrio acetiphilus DSM 12809]
 gi|290886011|gb|ADD69711.1| tRNA pseudouridine synthase A [Denitrovibrio acetiphilus DSM 12809]
          Length = 245

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 127/242 (52%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +I+EY G+ + GWQ Q NG ++Q  + KA+  +    V V G+GRTDSGVHAL QVA+F
Sbjct: 6   KLIVEYVGTDFAGWQVQPNGRTVQEELHKALSKMYKTKVTVIGSGRTDSGVHALGQVANF 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              R   P  +   LN+ L   + ISI ++  V + FHA+ +A+ ++YLYRI   +   A
Sbjct: 66  RTERYIPPENVHMGLNSML--PEDISISSVEDVPEDFHAQLNAVSKTYLYRIFPSRVRSA 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           +  GR W +   L+ + M    ++  G HDFT+F        + +R I++        +I
Sbjct: 124 MLAGRTWWVKDELNYKRMCELLKYFEGEHDFTSFCVQTSLRENNVRRINNIRCYREDKVI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I +    FLH  +R   G++       +    +++A++ +DR + GP A   GLY   V
Sbjct: 184 CIEINGNGFLHNMVRIIAGTVVEALRKGYGDEYIKEAIEGRDRSKAGPTAHAAGLYLKKV 243

Query: 245 EY 246
            Y
Sbjct: 244 YY 245


>gi|261409491|ref|YP_003245732.1| tRNA pseudouridine synthase A [Paenibacillus sp. Y412MC10]
 gi|329922021|ref|ZP_08277814.1| tRNA pseudouridine synthase A [Paenibacillus sp. HGF5]
 gi|261285954|gb|ACX67925.1| tRNA pseudouridine synthase A [Paenibacillus sp. Y412MC10]
 gi|328942404|gb|EGG38668.1| tRNA pseudouridine synthase A [Paenibacillus sp. HGF5]
          Length = 263

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 83/257 (32%), Positives = 122/257 (47%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    M + Y+G+ Y G+Q Q  G +IQ  +E+AI  ++GE + +  +GRTD+GVHA  Q
Sbjct: 1   MRNLLMKVSYDGTDYNGFQTQPGGHTIQDYLEEAIRRLSGEQLKITASGRTDAGVHARAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F           C ALN +L   + I + +   V  +FH+R +A R++Y + I   Q
Sbjct: 61  VFNFYTASPIPVERWCMALNTWL--PEDIVVSDAMEVPMEFHSRHAAKRKTYRFTINANQ 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
            P    +         LD   M     HL+G HDFTTF S      S +RTI    +   
Sbjct: 119 YPDLFNRRYQIHHHGKLDIAAMEQGLSHLIGTHDFTTFASRKSTKPSHVRTIFDAWIEKD 178

Query: 179 --------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                       +I   V    FL   +R  +G+L  VG+GK    D++  L+AQ+R   
Sbjct: 179 TSMCRPGTRDQGIIHTYVSGNGFLQHMVRIIMGTLIEVGEGKRHPDDMKVILEAQNRAAA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           GP A  +GL    V+Y 
Sbjct: 239 GPTAMGKGLMLWEVDYD 255


>gi|167629501|ref|YP_001680000.1| tRNA pseudouridine synthase a [Heliobacterium modesticaldum Ice1]
 gi|167592241|gb|ABZ83989.1| tRNA pseudouridine synthase a [Heliobacterium modesticaldum Ice1]
          Length = 259

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 119/246 (48%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
            R  + + Y+G+ Y G+Q Q+N    +IQ ++ +AI ++TGE V V+ AGRTD+GVHA  
Sbjct: 4   RRLKLTVAYDGTCYHGFQTQENPALPTIQDALVRAIKVLTGEEVKVNCAGRTDAGVHARG 63

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  F             A+NA L     ++++    V   FH+RF A+ + Y Y I   
Sbjct: 64  QVVDFVTSSPIPDDRFPFAMNAIL--PPDVAVVAAKTVPLAFHSRFGALGKHYRYTIYNH 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +  +  +   L  E M  AAQ  VG HDF  F +        +RT+   D+  
Sbjct: 122 RIPSPFHRRYSHQVFPPLQFEAMAAAAQCFVGTHDFRGFCATGSPVKDFVRTVYRCDLTR 181

Query: 180 FGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + + V+   FL+  IR   G+L  VG GK    ++   + ++DR   G  APP+G
Sbjct: 182 QEEHRLVLDVMGNGFLYNMIRIIAGTLIDVGKGKIALEEIPAIIASRDRTRAGMTAPPQG 241

Query: 239 LYFDSV 244
           L    V
Sbjct: 242 LCLMKV 247


>gi|146307739|ref|YP_001188204.1| tRNA pseudouridine synthase A [Pseudomonas mendocina ymp]
 gi|145575940|gb|ABP85472.1| tRNA pseudouridine synthase A [Pseudomonas mendocina ymp]
          Length = 287

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 126/247 (51%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           R  + +EY G+ Y G+QRQ  N +SIQG +E A+  V G E + +  AGRTD+ VHA  Q
Sbjct: 19  RIALGLEYKGARYRGFQRQAGNVASIQGCLESALSKVAGGEPINIMCAGRTDASVHASGQ 78

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E          N  L   + IS+    ++   FHARFSA+ R Y Y I    
Sbjct: 79  VVHFDTAVERPLHAWIMGANMNL--PNDISVTWARVMPAHFHARFSAMARRYRYVIYNDP 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A          + LD   MR AA+ LVG HDF+ FR+  CQA SPI+T+ H  V   
Sbjct: 137 IRPAHMAEEVTWNHRPLDVTRMREAARALVGTHDFSAFRATQCQAKSPIKTVHHLQVIEH 196

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +FLH  +R+  G L  +G G+       + L+  DR+  G  A P GLY
Sbjct: 197 GCFIVLDIRANAFLHHMVRNIAGVLMAIGAGERPVEWAREVLERADRRSGGVTAHPYGLY 256

Query: 241 FDSVEYS 247
              VEY 
Sbjct: 257 LVQVEYP 263


>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 =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRAGLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|126699393|ref|YP_001088290.1| tRNA pseudouridine synthase A [Clostridium difficile 630]
 gi|254975421|ref|ZP_05271893.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-66c26]
 gi|255092808|ref|ZP_05322286.1| tRNA pseudouridine synthase A [Clostridium difficile CIP 107932]
 gi|255100921|ref|ZP_05329898.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-63q42]
 gi|255306811|ref|ZP_05350982.1| tRNA pseudouridine synthase A [Clostridium difficile ATCC 43255]
 gi|255314550|ref|ZP_05356133.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-76w55]
 gi|255517225|ref|ZP_05384901.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-97b34]
 gi|255650331|ref|ZP_05397233.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-37x79]
 gi|260683444|ref|YP_003214729.1| tRNA pseudouridine synthase A [Clostridium difficile CD196]
 gi|260687040|ref|YP_003218173.1| tRNA pseudouridine synthase A [Clostridium difficile R20291]
 gi|306520297|ref|ZP_07406644.1| tRNA pseudouridine synthase A [Clostridium difficile QCD-32g58]
 gi|115250830|emb|CAJ68654.1| Pseudouridylate synthase (tRNA pseudouridine synthase A)
           [Clostridium difficile]
 gi|260209607|emb|CBA63265.1| tRNA pseudouridine synthase 2 [Clostridium difficile CD196]
 gi|260213056|emb|CBE04418.1| tRNA pseudouridine synthase 2 [Clostridium difficile R20291]
          Length = 245

 Score =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    MI+ Y+GS Y G+Q+   N  +IQ  +E  +  +T E V + G+GRTD G HA  
Sbjct: 1   MRNIKMIVAYDGSRYKGYQKLGDNNMTIQEKLENVLSKMTNETVEIIGSGRTDMGAHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          + K L  YL   + I +  +  VD++FH+R++   ++Y+Y+I   
Sbjct: 61  QVVNFRTNCMDSLDKIQKYLYEYL--PEDIVVKTVEEVDERFHSRYNVKSKTYMYKIDNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  A  + K LD + MR A+++LVG HDFT+F S   +  S +R I   ++  
Sbjct: 119 KYHNPFIRKYATHVSKKLDLDRMRKASEYLVGEHDFTSFASSKSKKKSNVREIYSINIKE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N+IEI V    FL+  +R  VG+L  VG  +    D++  L+++DR +    AP +GL
Sbjct: 179 DDNVIEIYVEGNGFLYNMVRIIVGALIDVGLKRRAPQDIKYMLESKDRCQSSDTAPAKGL 238

Query: 240 YFDSVEY 246
               V Y
Sbjct: 239 CLWKVTY 245


>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 =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERTMKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M +AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMALAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWARDVLESRVRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VQVEY 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 =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDASGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAASLLVGEQDFSSFRAAGCQAKSPVKTIYRTGLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|306826655|ref|ZP_07459958.1| tRNA pseudouridine synthase A [Streptococcus pyogenes ATCC 10782]
 gi|304431103|gb|EFM34109.1| tRNA pseudouridine synthase A [Streptococcus pyogenes ATCC 10782]
          Length = 249

 Score =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ++  ++Q  IEK ++ +  G  +++HGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQRHLRTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I ++N+  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQEQEVEKLRFALDT--QTPEDIDVVNIKKVADDFHCRYQKHLKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +      P +L+ + M+ A   LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRHYTTHYPYTLNIKLMQEAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSR 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DEKTDFLVFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPTISGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>gi|325135431|gb|EGC58051.1| tRNA pseudouridine synthase A [Neisseria meningitidis M0579]
          Length = 265

 Score =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGESVATTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKHRAGWTHLKLDIGQMRQAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|302060553|ref|ZP_07252094.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato K40]
          Length = 284

 Score =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 94/245 (38%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERSLKAWVMGANINL--PHDVSVSWARVMPATFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 136 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPIKQLHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 196 KMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAHPYGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VQVEY 260


>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 =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI    +   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAGCQAKSPVKTIYRAGLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|302187262|ref|ZP_07263935.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. syringae
           642]
          Length = 274

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERTMKAWVMGANINL--PHDVSVTWARVMPAAFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA+ LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAEFLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VGVEY 250


>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 =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI    +   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAGCQAKSPVKTIYRAGLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>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 =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTAAVRPAQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRTGLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|221212470|ref|ZP_03585447.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD1]
 gi|221167569|gb|EEE00039.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD1]
          Length = 270

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G+++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGNTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFL--PPTVAVQWAKPMPDAFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLDGRAGWIHTPLDDDAMRAAAAHLLGEHDFSAFRSSECQSKTPVKHVYEIDIRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  +   L  +DR    P    +GLY 
Sbjct: 179 HFLHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGRDRNRAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|304438671|ref|ZP_07398609.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 149 str.
           67H29BP]
 gi|304368320|gb|EFM22007.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 149 str.
           67H29BP]
          Length = 275

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 79/254 (31%), Positives = 127/254 (50%), Gaps = 9/254 (3%)

Query: 1   MIR-----YCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M++       + + Y+G+ Y G+QRQ     ++Q  +E A+  V GE V +  AGRTD+G
Sbjct: 1   MMKARARNIALKVAYDGTNYHGFQRQTPPIRAVQNVLEAALAQVCGETVELASAGRTDAG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  QV +F          L +A+N  L     I +       + F AR SA  ++Y+Y
Sbjct: 61  VHAYGQVVNFFTDGRIPTERLPRAVNGLL--PPDIVVSEAWEAARDFSARHSATGKAYVY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           R+   + P    +  AW I + LD + MR A   L G HD+++FR+      SP+RT+D 
Sbjct: 119 RMKECRVPDPFTRSYAWQIFQPLDYDAMRAALHLLEGTHDYSSFRAAGGAPMSPVRTLDT 178

Query: 175 FDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             + + G   + + +    FL+  +R+ V +   VG G+ +     +   A+DR+   P 
Sbjct: 179 IRLTAEGEGRLSLYIHGTGFLYHMVRNIVSTAVAVGTGRISKDRFAEIFAARDRRLAPPT 238

Query: 234 APPEGLYFDSVEYS 247
           AP  GLY  +V+Y 
Sbjct: 239 APAGGLYLLAVDYD 252


>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 =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 113/244 (46%), Positives = 154/244 (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  KDWDPFRLSEALNFHLK-PAPVAIRACARVADDWHARFSAVERRYLFRILMRRAPATLEE 119

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN----SFGNL 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|313114592|ref|ZP_07800100.1| tRNA pseudouridine synthase A [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310623056|gb|EFQ06503.1| tRNA pseudouridine synthase A [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 248

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + + + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL   
Sbjct: 1   MNFLLTLAYDGTNYCGFQVQPNGRSVAQTFQDALQAVLGSRPDIKGCSRTDAGVHALGFK 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F          L  ALN +L     I +L+  +V + FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPAAKLPLALNQHL--PPDIRVLDAQVVPEDFHARYAAHTKTYLYRIHNHPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDVN 178
               +      +P+ LD   M+ AAQ  VGRHDF    +    A      +RTI    V 
Sbjct: 119 DSPFDAAYYTRVPRHLDEARMQAAAQQFVGRHDFLALCAAGSSAAAHGDTVRTITDCHVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+I V A  +L+  +R   G+L   G G+    ++   L+++DR   GP  P +G
Sbjct: 179 REGDEIDIEVTADGYLYNMVRILAGTLCEAGAGRLDPAEIPAILESRDRSRAGPTLPAKG 238

Query: 239 LYFDSVEYS 247
           L+   VEY 
Sbjct: 239 LFLKCVEYD 247


>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 =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 136/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALENALAQIAGESVATTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD V         + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTVAVRPQQAWVRGVNAHL--PEGIAVLHAQQVAPEFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA +L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIGPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|257440210|ref|ZP_05615965.1| tRNA pseudouridine synthase A [Faecalibacterium prausnitzii A2-165]
 gi|257197244|gb|EEU95528.1| tRNA pseudouridine synthase A [Faecalibacterium prausnitzii A2-165]
          Length = 249

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 125/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + + Y+G+ Y G+Q Q NG S+  + +  +  V      + G  RTD+GVHAL  
Sbjct: 1   MQNYLLTLAYDGTNYCGFQVQPNGRSVAQTFQDGLEAVLHSRPDIKGCSRTDAGVHALGF 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             +F       P  L  A+N +L     I +L   +V ++FHAR++A  ++YLYRI    
Sbjct: 61  ALNFHAETRIPPEKLPLAINQHL--PPDIRVLCARVVPEEFHARYAAHTKTYLYRIHNHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDV 177
                ++     +P+ LD + M+ AA+  VG+HDF    +    A      +RTI    V
Sbjct: 119 IDSPFDEKYYTRVPRRLDVDAMQRAAEQFVGKHDFLALCAAGSSAAAHGDTVRTITDCHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ ++I V A  +L+  +R   G+L  VG G+     +   L ++DR + GP  P +
Sbjct: 179 TRKGDEVDIEVTADGYLYNMVRILAGTLCEVGAGRMQPDAIPGILASRDRSQAGPTLPAK 238

Query: 238 GLYFDSVEYS 247
           GL+ + V+Y 
Sbjct: 239 GLFLEKVDYD 248


>gi|115358097|ref|YP_775235.1| tRNA pseudouridine synthase A [Burkholderia ambifaria AMMD]
 gi|122321799|sp|Q0BAC2|TRUA_BURCM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|115283385|gb|ABI88901.1| tRNA pseudouridine synthase A [Burkholderia ambifaria AMMD]
          Length = 270

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + ++Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGVQYDGAAFCGWQAQPHGKTVQDALERALGEFACVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+S+     + + FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRTDFSWVRGTNAFL--PSTVSVQWAKPMPETFHARFAAFERTYYYVLYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY 
Sbjct: 179 HFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRTLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|303238754|ref|ZP_07325286.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
 gi|302593633|gb|EFL63349.1| tRNA pseudouridine synthase A [Acetivibrio cellulolyticus CD2]
          Length = 245

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 127/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    ++I+Y+GS Y GWQR  +   +IQG +E+ +  ++ E + + G+GRTD+GVHA +
Sbjct: 1   MRNIKLVIQYDGSKYRGWQRLGDSDKTIQGKLEQVLSQMSNEKIELIGSGRTDAGVHAFK 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +   L  YL   + I +++   VD  FH+R     + YLYRI   
Sbjct: 61  QVANFHTKSDLAEDAMLDYLYKYL--PEDIVVIDAEEVDNMFHSRHHVKGKKYLYRIWNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +     I + LD   MR AA+H  G HDF++F S+  +  S  R I   ++  
Sbjct: 119 KRHNPFMRKHCTHIAEPLDIRLMRNAAEHFTGMHDFSSFTSLKTKNKSKEREIFSVEIEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              +++I      FL+   R   G+L  VG G+  + ++ K L  +DRK  GP AP  GL
Sbjct: 179 ENEIMDIVFYGNGFLYNMARIMAGTLIEVGAGRINADNIPKILAKKDRKLAGPTAPTNGL 238

Query: 240 YFDSVEY 246
               VEY
Sbjct: 239 ILYDVEY 245


>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 =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD + E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTLAERSLKAWVMGANINL--PHDVSVTWARVMPANFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA+ LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 136 RPAHLNQEITWNHRPLDVERMAQAAEFLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 196 KMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAHPYGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VQVEY 260


>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 =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESVP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIGPMRRAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|77406326|ref|ZP_00783390.1| tRNA pseudouridine synthase A [Streptococcus agalactiae H36B]
 gi|77175064|gb|EAO77869.1| tRNA pseudouridine synthase A [Streptococcus agalactiae H36B]
          Length = 258

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GS + G+QRQ N  ++Q  IE+ +  + +G  V++HGAGRTD+GVHA  
Sbjct: 1   MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +      L   L+   +  D I I+ +  V   FH R+    ++Y   +   
Sbjct: 61  QVIHFDLPQARDVEKLRFGLDT--QCPDDIDIVKVEQVSDDFHCRYDKHIKTYEILVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  +  E M+ A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRNYATHYPYPVIIELMKEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  NL+        FL+ Q+R+ VG+L  +G+G+   + ++  LQA++R   GP A   
Sbjct: 179 EASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|330966232|gb|EGH66492.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 274

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 94/245 (38%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERSLKAWVMGANINL--PHDVSVSWARVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPIKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VQVEY 250


>gi|262282044|ref|ZP_06059813.1| tRNA pseudouridine synthase A [Streptococcus sp. 2_1_36FAA]
 gi|262262498|gb|EEY81195.1| tRNA pseudouridine synthase A [Streptococcus sp. 2_1_36FAA]
          Length = 249

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FHAR++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVERVSDDFHARYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRYYATHYPYPLELSLLEEAITQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPIEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|332532285|ref|ZP_08408166.1| tRNA pseudouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038383|gb|EGI74828.1| tRNA pseudouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 264

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG  Y GWQRQ + +S+Q  +EKA+  +    V V  AGRTD+GVH   Q+
Sbjct: 1   MRVALGVEYNGVRYSGWQRQSHVNSVQQEVEKALSRICNHPVEVVCAGRTDAGVHGTGQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+       V     +N  L     I+I     V   FHARFSA  R Y Y I     
Sbjct: 61  IHFETEASRDMVAFTMGMNTLL--PKDIAIRFAQPVAVDFHARFSATARRYRYIIYNSPF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M+ A Q+L+G HDFT+FR+IHCQA++P RTI H  V   G
Sbjct: 119 RGAVLSEGVTHFHHPLDEVKMQEACQYLIGTHDFTSFRAIHCQANTPTRTIHHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +FLH  +R+  GSL  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 CYVIIDIKANAFLHHMVRNITGSLMDIGIHKQQPIWLKELLDCKERAKASATAKAAGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>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 =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 90/251 (35%), Positives = 138/251 (54%), Gaps = 8/251 (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 EQVIEFSTTAQRPPTAWVRGANAHL--PDTVAVRWAAPLAPDADFDARFSARERTYWYVL 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 EGLYFDSVEYS 247
            GLY  SV Y 
Sbjct: 279 GGLYLASVRYD 289


>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 =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 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  VIHFDSNTNLDEYTITSALNHYLKK-ELISILSTEIVDDNFDARRSAILRTYEYLIINRA 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|157150719|ref|YP_001449723.1| tRNA pseudouridine synthase A [Streptococcus gordonii str. Challis
           substr. CH1]
 gi|189030148|sp|A8AVB3|TRUA_STRGC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157075513|gb|ABV10196.1| tRNA pseudouridine synthase A [Streptococcus gordonii str. Challis
           substr. CH1]
          Length = 249

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDGEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLLEEAITQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 111/249 (44%), Positives = 158/249 (63%), Gaps = 4/249 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R+ + +EY+G+G  GWQRQK+G S+Q  +E+A   +     V    AGRTDSGVHAL Q
Sbjct: 10  QRWAVKLEYDGTGLVGWQRQKSGLSVQSLLEEAAARLANNRPVSSITAGRTDSGVHALAQ 69

Query: 61  VAH--FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAH  F     +    + + L+ +LK    + +L+ + VD  + ARFSAI RSY YRI+ 
Sbjct: 70  VAHLDFPADVRFSRHSVREGLSYHLK-PHNVVVLDAAQVDTDWSARFSAIWRSYQYRILN 128

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R++   L  G+ W +  +LD E M+ AA  LVG HDFT+FR++ CQA SP+RT+D  +++
Sbjct: 129 RRSRPTLLAGQVWHVKSTLDVEKMQEAANILVGSHDFTSFRAVACQAHSPMRTLDQLEIS 188

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + +   ARSFLH Q+R+ VG+LKLVG G W    + +AL+A++R   GP APPEG
Sbjct: 189 RHGDEVIVFAKARSFLHHQVRNMVGTLKLVGIGAWQPERVAEALEARNRCAAGPTAPPEG 248

Query: 239 LYFDSVEYS 247
           LY + V Y 
Sbjct: 249 LYLNGVGYD 257


>gi|227891575|ref|ZP_04009380.1| tRNA pseudouridine synthase A [Lactobacillus salivarius ATCC 11741]
 gi|227866722|gb|EEJ74143.1| tRNA pseudouridine synthase A [Lactobacillus salivarius ATCC 11741]
          Length = 256

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 124/250 (49%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
            R+ + + Y+G+ + G+Q Q N  ++Q  +EKAI  ++   E + V+G+GRTDSGVHAL 
Sbjct: 3   QRFKVTLAYDGTNFAGFQAQPNQRTVQFVLEKAINKMSKKDEYITVYGSGRTDSGVHALG 62

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD         + + LN+ L       +++  IV   FH+R++   + YLYR+   
Sbjct: 63  QVVHFDFPHPISAKGMLRGLNSML--PLDCEVVDCKIVPNDFHSRYTTHGKRYLYRVSRG 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++         LD E ++ A   + G HD+++F +   QA S +RTI    V  
Sbjct: 121 EFVNPFKRLYTGHYKYPLDIEKIKEAMPDVEGTHDYSSFVASGSQAKSHVRTIYEAKVYE 180

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + I        FL+ Q+R  V +L  +G+GK    D  +  + +DR +    AP  
Sbjct: 181 DKVNDEIVFEFYGNGFLYNQVRIMVATLLEIGNGKRPVHDFLRLYKVKDRSQARQTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLKEVYYD 250


>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 =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 127/246 (51%), Gaps = 2/246 (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  VHFDTTSIRPLTAWVRGVNAHL--PETVRVEWAHEVDEDFHARFSAFSRSYQYLLYNAPV 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 DSVEYS 247
             V Y 
Sbjct: 239 TGVGYD 244


>gi|191639397|ref|YP_001988563.1| tRNA pseudouridine synthase A [Lactobacillus casei BL23]
 gi|239630320|ref|ZP_04673351.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|301067471|ref|YP_003789494.1| pseudouridylate synthase [Lactobacillus casei str. Zhang]
 gi|238693010|sp|B3WAI6|TRUA_LACCB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|190713699|emb|CAQ67705.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Lactobacillus casei BL23]
 gi|239527932|gb|EEQ66933.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|300439878|gb|ADK19644.1| Pseudouridylate synthase [Lactobacillus casei str. Zhang]
 gi|327383485|gb|AEA54961.1| tRNA pseudouridine synthase A 1 [Lactobacillus casei LC2W]
 gi|327386676|gb|AEA58150.1| tRNA pseudouridine synthase A 1 [Lactobacillus casei BD-II]
          Length = 247

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +T G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMTKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + KA+N+ +     I IL   IVD  FHAR+SA  + YLYR+   
Sbjct: 61  QVISFDYPGNIPAESMLKAMNSLM--PLDIEILKAEIVDADFHARYSAKGKRYLYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVQRIEVALKDLVGTHDFTSFAASGGVIVDKVRTIYEATVRE 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N I        FL+  +R  V +   +G+G+    D ++    +DR++    AP  
Sbjct: 179 DPVTNEIIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFAVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>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 =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 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|91200879|emb|CAJ73934.1| strongly similar to tRNA pseudouridine synthase I [Candidatus
           Kuenenia stuttgartiensis]
          Length = 244

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY G+ Y GWQ QKN  S+Q ++  A+  V  E V +HGAGRTD+GVHAL Q
Sbjct: 1   MRNVRLTIEYEGTNYAGWQWQKNAISVQETLTHAVRTVIREEVEIHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F          L +A+N +L     I+I +++ +++ FHAR+SA  + Y Y ++   
Sbjct: 61  VANFKTYSAIPAKQLLRAINFHL--PQDITIKDVADMEEGFHARYSATSKVYRYTVLNDW 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              +L +   ++    LD   M  AAQ+L+G HDFT+F +        IRTI + ++   
Sbjct: 119 LRTSLNRNFCYVYGFPLDLSKMMTAAQYLIGTHDFTSFTTKALDNKDRIRTIKNLEIQKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   V A  FL+  +R+ VG+L  +G GK     + K L+  +R + GP AP +GL 
Sbjct: 179 GKYIYFVVEANGFLYKMVRTIVGTLLEIGRGKMDVYLIRKLLETGNRDDAGPTAPAKGLC 238

Query: 241 FDSVEY 246
              V+Y
Sbjct: 239 MKEVKY 244


>gi|330943525|gb|EGH45866.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 284

 Score =  279 bits (715), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 126/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERTLKAWVMGANINL--PHDVSVTWARVMPATFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H  V   G
Sbjct: 136 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHLRVTHHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 196 KMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAHPYGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VGVEY 260


>gi|325141434|gb|EGC63912.1| tRNA pseudouridine synthase A [Neisseria meningitidis 961-5945]
          Length = 265

 Score =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 134/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTIVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTAAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESVP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIGPMRRAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 SGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|118602946|ref|YP_904161.1| tRNA pseudouridine synthase A [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
 gi|118567885|gb|ABL02690.1| tRNA pseudouridine synthase A [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
          Length = 247

 Score =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + + Y G+ + GWQ Q  N  ++Q  +E+A+  V    V V  +GRTD+GVHA  Q
Sbjct: 1   MKIALGVAYLGTNFHGWQCQKPNIRTVQQVVEQALSSVANHPVRVFCSGRTDAGVHATCQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+   +    +     NA L     ++   +  V+  FHARFSAI R Y Y+I   +
Sbjct: 61  VIHFETNIKRENKVWLFGGNANL--PSDVNFTWVKHVNDNFHARFSAIARQYNYKIHNTK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              ++    +    K LD   M  A+++L+G+H+F+ FR   CQA S I+TI+   +N  
Sbjct: 119 VRCSIITAHSLWESKKLDIMAMNKASKYLIGKHNFSAFRGSLCQAKSSIKTIEFIKLNKC 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I + + A +FLH  +R+ VG+L  VG G+ +   +++ L  + RK+  P AP  GLY
Sbjct: 179 DDNILLDIKADAFLHHMVRNIVGTLLKVGKGEKSIEWVKEILDNKQRKQAAPAAPSHGLY 238

Query: 241 FDSVEYS 247
           F    YS
Sbjct: 239 FIKAFYS 245


>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 =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 142/247 (57%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            RY + + YNGS ++GWQ+Q  +  ++Q ++E A+ ++  + + V  AGRTD+GVHA  Q
Sbjct: 3   TRYVLTLAYNGSAFYGWQKQTADVPTVQSALEHALSVIAQQPIKVTAAGRTDTGVHATAQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + +++L+   V  +FHARF A  R Y Y +    
Sbjct: 63  VVHFDSDANRPISAWVRGVNAHL--PNDVAVLHAQAVASEFHARFDAFARRYRYVLQFAP 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  GRA     +LD  N++ A Q L+G HDF++FR+  CQA SPI+T+   D+ + 
Sbjct: 121 VRSPLLVGRAGWTHYNLDINNIQAACQFLLGEHDFSSFRAAECQAKSPIKTMYSIDIQAM 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI++   A +FLH  IR+ VG+L  VG G+ +  +  + ++ + R +  P   P+GLY
Sbjct: 181 GDLIKLDFHANAFLHHMIRNIVGALVYVGSGRLSVNEFAELIEKRSRLDAPPTFMPDGLY 240

Query: 241 FDSVEYS 247
           F   +Y 
Sbjct: 241 FAGADYP 247


>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 =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/242 (38%), Positives = 136/242 (56%), Gaps = 2/242 (0%)

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  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                         N  L     + +     VD  FHARFSA  R Y Y+I+ R+    +
Sbjct: 61  TTATRSERSWVLGANVNL--PPDVGVRWAHPVDDGFHARFSAQARHYRYQILARRTRSPI 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           ++ RA  + ++LD E MRIAA  LVG HDF++FR++ CQA SPIR + + D++    LI 
Sbjct: 119 QRDRAVWVHEALDLERMRIAAVALVGEHDFSSFRAVACQAKSPIRRVLYLDLSEREGLIT 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + + A  FLH  +R+  G L  +G G+ +     + L+ +DR+  G  A P+GLYF   +
Sbjct: 179 LAIGANGFLHHMVRNIAGVLMAIGRGEASVDWTRELLEVRDRRLGGVTAQPQGLYFVRAD 238

Query: 246 YS 247
           Y 
Sbjct: 239 YP 240


>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 =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNG  Y+GWQRQ++  SIQ  +E A+  +  E + V  AGRTD+GVHA  QV 
Sbjct: 16  KIALGIEYNGYRYYGWQRQEHVPSIQSCLEHALSKIANESITVCCAGRTDAGVHATAQVV 75

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF        V     +N YL     I++     V+K FHARFSA  R Y Y I   +  
Sbjct: 76  HFLTKAVRKEVSWIMGVNTYL--PPDITVRWAKKVEKDFHARFSATARRYRYLIFNDRHR 133

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG- 181
            AL           LD + M  AAQ ++G +DF++FR+  CQ+ +P R + H  V+ FG 
Sbjct: 134 PALFSEGLAHYSMPLDEKKMERAAQCVLGENDFSSFRAAQCQSKTPWRYVHHLKVSRFGM 193

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +FLH  +R+ VGSL  VG G+     + + L  +DR +    A   GLY 
Sbjct: 194 HYIMVDIKANAFLHHMVRNIVGSLIEVGIGRQNEHWIAQLLALKDRTQAAVTAKASGLYL 253

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 254 VSVDYP 259


>gi|294637213|ref|ZP_06715519.1| tRNA pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
 gi|291089602|gb|EFE22163.1| tRNA pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
          Length = 275

 Score =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 90/244 (36%), Positives = 126/244 (51%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IEY+GS Y GWQRQ+   S+Q  +E A+  V  E V V  AGRTD+GVHA  QV H
Sbjct: 17  IALGIEYDGSRYAGWQRQQEVDSVQARLEAALSRVASEPVTVFCAGRTDAGVHATGQVVH 76

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              +NA+L     I++  +  V   FHARFSA  R Y Y I   +   
Sbjct: 77  FTTHASRQEGAWTMGVNAHL--PKDIAVRWVKAVSADFHARFSATARRYRYVIYNHRYRP 134

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+ +         LD E M  A Q L+G +DF++FR+  CQ+ +P R + H  VN +G  
Sbjct: 135 AVLQSGVTHFYHPLDAERMARAGQALLGENDFSSFRAAQCQSRTPWRNVSHLWVNRYGPY 194

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A +F+H  +R+ VGSL  VG G      + + L A+DR      A   GLY  +
Sbjct: 195 VVVDIKANAFVHHMVRNIVGSLLEVGCGNQPEGWIAELLAARDRTLAAATAKAAGLYLVA 254

Query: 244 VEYS 247
           V+Y 
Sbjct: 255 VDYP 258


>gi|239624119|ref|ZP_04667150.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522150|gb|EEQ62016.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 249

 Score =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y + + Y+G+ Y GWQ+Q N   +IQG +E+ +  + GE V V G+GRTD+GVHA  Q
Sbjct: 1   MNYIIWLSYDGTRYDGWQKQGNTEKTIQGKLERVLEKLDGEPVEVRGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F L  +  P  + + LN YL   + I++  +    ++FH+R +A+R++Y Y+I    
Sbjct: 61  VADFQLKGKRAPEEVMEYLNRYL--PEDIAVWRIQTAPERFHSRLNAVRKTYRYQIELGP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   + + + LD  +M  A  +L G  DF +F        S +RT++       
Sbjct: 119 KKDVFRRSYYYGLGQELDVASMERAVAYLTGTRDFKSFCGNKKMKKSTVRTLESIRFERL 178

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +  + I      FL   +R   G+L  VG G+    D+   L+A DR+  G  APPEGL
Sbjct: 179 EDTRLHISFTGNGFLQQMVRILTGTLIEVGQGRRKPEDIRSILEALDRQAAGFTAPPEGL 238

Query: 240 YFDSVEY 246
           + + VEY
Sbjct: 239 FLEKVEY 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 =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 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|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 =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 94/245 (38%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 68  VHFDTQAERSLKAWVMGANINL--PHDVSVSWARVMPATFHARFKAIARRYRYVIYNDQI 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AA++LVG HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 126 RPAHLNQEITWNHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPIKQLHHLRVTRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A P GLY 
Sbjct: 186 KMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAHPYGLYL 245

Query: 242 DSVEY 246
             VEY
Sbjct: 246 VQVEY 250


>gi|297620615|ref|YP_003708752.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
 gi|297375916|gb|ADI37746.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
          Length = 254

 Score =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 133/249 (53%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +Y +II Y+G+ Y GWQ Q N  SIQ  +E+ + ++T     + GAGRTD+GVHA+ Q
Sbjct: 1   MKKYKLIIAYDGTQYSGWQMQPNALSIQEVLEEKLKVLTKTRTSLTGAGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF +   + P +L  +      +   I I+++  V   FHAR+SA  + Y Y +    
Sbjct: 61  VAHFKVEAPFNPSLLRLS--LNGLLPKDIRIMDVEEVPLDFHARYSATNKIYYYHLNLGP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---RSIHCQASSPIRTIDHFDV 177
                EK  +W I  SL+ E ++    +L+G H+F+ F    +      +PIRT+    V
Sbjct: 119 VQDPFEKQYSWNITNSLNMELLKKGISYLIGTHNFSAFANEANQGAAKKNPIRTLKRISV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + +     SFL+  +R+  G+L  V  GK +  +++K L+++DR+  G  AP +
Sbjct: 179 VPERIGMRLEFEGESFLYKMVRNMTGTLIDVAKGKLSPEEIKKILESKDRRNAGRAAPAK 238

Query: 238 GLYFDSVEY 246
           GL+   ++Y
Sbjct: 239 GLFLVRIDY 247


>gi|149926375|ref|ZP_01914636.1| tRNA pseudouridine synthase A [Limnobacter sp. MED105]
 gi|149824738|gb|EDM83952.1| tRNA pseudouridine synthase A [Limnobacter sp. MED105]
          Length = 254

 Score =  279 bits (714), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G  + GWQ Q +G ++Q  + KAI  +  E + +  AGRTD+GVHA +Q
Sbjct: 1   MNRVVLGLCYDGHEFEGWQTQPHGRTVQDYLTKAIEAIAQEPIALTCAGRTDTGVHARQQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       K +N  L    +IS+     +D  FHARFSA+ R+Y Y   +  
Sbjct: 61  VVHFDTAAERPLTAWVKGVNNSL--PSSISVQGAKQIDSGFHARFSAVSRTYRYYFYSAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                ++     +   LD   MR AA  L+G HDF+ FR+  CQA+SP+RT+   ++   
Sbjct: 119 VRDPFKR-FMTWVHYPLDLAAMRRAAVCLLGTHDFSAFRASQCQAASPVRTLYALNLIEA 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +     +   +FLH  +R+ +GSL  VG  + +   L+  L +++R       P +GL 
Sbjct: 178 DDHCYFEIHGNAFLHHMVRNLMGSLMEVGQHRQSEAWLQDVLVSKNRSLAAKTYPAQGLS 237

Query: 241 FDSVEYS 247
             ++EY 
Sbjct: 238 LWNIEYP 244


>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 =  279 bits (714), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  +I+ Y+GS +FGWQ+Q  G  ++Q ++E+A+  + GE + V  AGRTD+GVHA  Q
Sbjct: 7   TRRALIVAYDGSRFFGWQKQAGGVPTVQAALEEALSGIAGERIAVTAAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       +  N+ L   + +++L +  V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTAAERPGQAWVRGTNSLL--PEGVAVLRVHNVPPHFHARFDACGRRYRYVLQSAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  GRA      LD   MR AA  LVG HDF++FR+  CQA SP++T+    ++  
Sbjct: 125 VRSPLLAGRAGWTHTPLDPAPMREAAALLVGTHDFSSFRAAECQAKSPVKTLYSVRLSGT 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + +   +FLH  +R+ VG+L  VG G+ +     + + A+ R +  P   P+GLY
Sbjct: 185 ARFMALDLHGNAFLHHMVRNIVGALVYVGSGRLSVAGFAELIAAKSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
               +Y 
Sbjct: 245 LTGADYP 251


>gi|258540648|ref|YP_003175147.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus Lc 705]
 gi|257152324|emb|CAR91296.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus Lc 705]
          Length = 247

 Score =  279 bits (714), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 121/249 (48%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + +A+N+ +     I IL   IV   FHAR+SA  + Y YR+   
Sbjct: 61  QVISFDYPGNIPAESMLRAMNSLM--PLDIEILKAEIVAADFHARYSAKGKRYRYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEE 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  
Sbjct: 179 DPATNELIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|199598865|ref|ZP_03212276.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus HN001]
 gi|199590277|gb|EDY98372.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus HN001]
          Length = 247

 Score =  279 bits (714), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 121/249 (48%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + +A+N+ +     I IL   IV   FHAR+SA  + Y YR+   
Sbjct: 61  QVISFDYPGNIPAESMLRAMNSLM--PLDIEILKAEIVAADFHARYSAKGKRYRYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEE 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  
Sbjct: 179 DPAADELIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|221196945|ref|ZP_03569992.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2M]
 gi|221203615|ref|ZP_03576634.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2]
 gi|221177549|gb|EEE09977.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2]
 gi|221183499|gb|EEE15899.1| tRNA pseudouridine synthase A [Burkholderia multivorans CGD2M]
          Length = 270

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 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   MRIALGIQYDGAAFCGWQAQPHGNTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFL--PPTVAVQWAKPMPDAFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLDGRAGWIHTPLDDDAMRAAAAHLLGEHDFSAFRSSECQSKTPVKHVYEIDIRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  +   L   DR    P    +GLY 
Sbjct: 179 HFLHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGCDRNRAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|118443953|ref|YP_878363.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
 gi|118134409|gb|ABK61453.1| tRNA pseudouridine synthase A [Clostridium novyi NT]
          Length = 245

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 73/247 (29%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+G+ Y GWQ+   N ++IQ  IE  +  +  E V +  +GRTD+GVHA  
Sbjct: 1   MRNIKLTIQYDGTRYKGWQKLGNNDNTIQHKIESVLGELLKEEVALIASGRTDAGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          + K L  YL     I + +++   + FH+R++   + Y YRI   
Sbjct: 61  QVANFKTDSRISNDEISKYLYKYL--PQDIVVKSVNEASENFHSRYNVKEKVYTYRIHNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ + + LD + M+ A++  +G HDF +F ++  +  S ++TI+      
Sbjct: 119 EVHDVFTRKYSYHVREKLDLKKMKEASKLFIGEHDFKSFTALKSKKKSTVKTINSITFRK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + IEI      FL+  IR  VG+L  VG  K +  D++  +  +DR      AP  GL
Sbjct: 179 KEDDIEIVFSGNGFLYKMIRILVGTLVEVGLNKISIDDVKDVMDKKDRSIAPETAPAHGL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 TLTEVKY 245


>gi|3915176|sp|Q45557|TRUA_BACSV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|289265|gb|AAA73188.1| unknown [Bacillus sp. KSM-64]
          Length = 244

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 133/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y ++I+Y+G  Y GWQR  NG ++IQG IE  +  + G  + + G+GRTD+GVHAL 
Sbjct: 1   MNNYKLMIQYDGGRYKGWQRLGNGENTIQGKIETVLSEMVGRKIEIIGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+  L   +    + + LN YL     IS+  +++V  +FH+R++A  ++YLY+I   
Sbjct: 61  QVANVKLSENFTVKEVKEYLNRYL--PHDISVTEVTLVPDRFHSRYNAKDKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  +  I K L  +NM  A+Q  VG HDFT F +   +  +  RTI    +  
Sbjct: 119 DYTHPFMRKYSLHIEKKLHIDNMVKASQLFVGEHDFTAFSNAKSKKKTNTRTIHSITIQD 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I+IRV    FL+  +R  VG+L  VG G+     +   L+++DR + G  A   GL
Sbjct: 179 NQGFIDIRVCGDGFLYNMVRKMVGTLIEVGLGEKEPEQVLTILESKDRSQAGF-ADATGL 237

Query: 240 YFDSVEY 246
           Y + + +
Sbjct: 238 YLEGISF 244


>gi|258509450|ref|YP_003172201.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus GG]
 gi|257149377|emb|CAR88350.1| tRNA pseudouridine synthase A [Lactobacillus rhamnosus GG]
 gi|259650729|dbj|BAI42891.1| tRNA pseudouridine synthase [Lactobacillus rhamnosus GG]
          Length = 247

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 121/249 (48%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + +A+N+ +     I IL   IV   FHAR+SA  + Y YR+   
Sbjct: 61  QVISFDYPGNIPAESMLRAMNSLM--PLDIEILKAEIVAADFHARYSAKGKRYRYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEE 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  
Sbjct: 179 DPAANELVFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|116495915|ref|YP_807649.1| tRNA pseudouridine synthase A [Lactobacillus casei ATCC 334]
 gi|122262685|sp|Q035B5|TRUA_LACC3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116106065|gb|ABJ71207.1| Pseudouridylate synthase [Lactobacillus casei ATCC 334]
          Length = 247

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +T G+ V V G+GRTDSGVHAL 
Sbjct: 1   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMTKGQPVHVDGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + KA+N+ +     I IL   IVD  FHAR+SA  + YLYR+   
Sbjct: 61  QVISFDYPGNIPAESMLKAMNSLM--PLDIEILKAEIVDADFHARYSAKGKRYLYRVARG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 119 YYTNPFNRLYTGHYPYKLDVQRIEVALKDLVGTHDFTSFAASGGVIVDKVRTIYEATVRE 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N I        FL+  +R  V +   +G+G+    D ++    +DR++    AP  
Sbjct: 179 DSVTNEIIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFAVKDRQQARGTAPAS 238

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 239 GLYLKEVYY 247


>gi|154249373|ref|YP_001410198.1| tRNA pseudouridine synthase ACD [Fervidobacterium nodosum Rt17-B1]
 gi|171769414|sp|A7HKV8|TRUA_FERNB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|154153309|gb|ABS60541.1| tRNA pseudouridine synthase A [Fervidobacterium nodosum Rt17-B1]
          Length = 246

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 130/246 (52%), Gaps = 4/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +   Y+G+ +FG+Q Q N  ++QG +EKA+  V    +  + AGRTD+GVHA  Q
Sbjct: 1   MRRVAIEFSYDGTDFFGYQIQNNVRTVQGELEKALEKVFKIHIDTYAAGRTDTGVHANGQ 60

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V  FD   + +    +  A+NA L     I I  +      F+ R+ A RR Y Y I T 
Sbjct: 61  VVSFDCPNDRLMENDIKNAINANL--PGDIYIKKVWFTHPTFNPRYEAKRRIYHYYIDTS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++     +   W  P  LD E MRIAA++L+G HDF +F     + +  IRTI++  +  
Sbjct: 119 KSKNLFTRRYVWWFPYELDIEKMRIAAKYLIGEHDFISFSKKGEENTKTIRTINNLRIIE 178

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N LI IRV   SFL   +RS V +L  VG G W    +++ L+++DR +   LAP  G
Sbjct: 179 IKNGLILIRVEGISFLRGMVRSIVANLVRVGTGIWEPEKVKEVLESKDRSKSAGLAPAHG 238

Query: 239 LYFDSV 244
           L+   V
Sbjct: 239 LFLYKV 244


>gi|261401977|ref|ZP_05988102.1| tRNA pseudouridine synthase A [Neisseria lactamica ATCC 23970]
 gi|269207832|gb|EEZ74287.1| tRNA pseudouridine synthase A [Neisseria lactamica ATCC 23970]
          Length = 267

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 129/247 (52%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 9   QRWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGESVATTVAGRTDTGVHATAQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           +  NA L   + I++L+       FHARF A  R Y Y + +  
Sbjct: 69  VVHFDTAARRPAQAWIRGTNAAL--PEGIAVLHARQTSPGFHARFDAYGRHYRYLLESSP 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 127 VRSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQT 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY
Sbjct: 187 GGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSTLIRERSRLKAPPTFMPDGLY 246

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 247 LTGVDYP 253


>gi|21911175|ref|NP_665443.1| tRNA pseudouridine synthase A [Streptococcus pyogenes MGAS315]
 gi|28895139|ref|NP_801489.1| tRNA pseudouridine synthase A [Streptococcus pyogenes SSI-1]
 gi|25453306|sp|Q8K5W2|TRUA_STRP3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21905386|gb|AAM80246.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes
           MGAS315]
 gi|28810384|dbj|BAC63322.1| putative tRNA pseudouridine synthase A [Streptococcus pyogenes
           SSI-1]
          Length = 249

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 131/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY   I Y+G+ + G+QRQ++  ++Q  IEK ++ +  G  +++HGAGRTD+GVHA  
Sbjct: 1   MVRYKATISYDGTLFSGFQRQRHLRTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL +E     L  AL+   +  + I ++N+  V   FH R+    ++Y + +   
Sbjct: 61  QVIHFDLPQEQEVEKLRFALDT--QTPEDIDVVNIEKVADDFHCRYQKHLKTYEFLVDNG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +      P +L+ + M+ A   LVG HDFT F +      + +RTI    V+ 
Sbjct: 119 RPKNPMMRHYTTHYPYTLNIKLMQDAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSR 178

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + +        FL+ Q+R+ VG+L  +G+G+     ++  L +++R+  GP     
Sbjct: 179 DEKTDFLVFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPTISGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEICYE 248


>gi|46445962|ref|YP_007327.1| putative tRNA pseudouridylate synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
 gi|51316632|sp|Q6MEE7|TRUA1_PARUW RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|46399603|emb|CAF23052.1| putative tRNA pseudouridylate synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 256

 Score =  279 bits (713), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 82/251 (32%), Positives = 129/251 (51%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQ Q N SSIQ  I++A+ ++   E VV+ G+GRTD+GVHA  
Sbjct: 1   MHCYKLTIAYDGTNYSGWQIQPNASSIQQKIQEALCILLKKEKVVLVGSGRTDAGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAHF          L  +LN  L     I I  +  V  +FH+++SAIR+ Y Y +   
Sbjct: 61  QVAHFHFQDYIDLSRLHVSLNGLL--PRDIRIKAVEPVSPRFHSQYSAIRKEYHYYLHLN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS---IHCQASSPIRTIDHFD 176
           +     ++  +W   + +D   ++ AA    G HDFT+F +       A +P+RT+   D
Sbjct: 119 KVMDPFQRLYSWHFQRKIDVNILKKAAILFTGTHDFTSFANEAHRGTAAKNPVRTLYRLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +      + +      FL+  +R+ VG+L  V   K    ++ +   A++R++    APP
Sbjct: 179 IKPNEGGLRLEFEGDGFLYKMVRNIVGTLMDVASHKRAIEEINQIFAAKNRRQASLAAPP 238

Query: 237 EGLYFDSVEYS 247
           EGL+   V Y 
Sbjct: 239 EGLFLIQVFYE 249


>gi|325689043|gb|EGD31051.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK115]
          Length = 249

 Score =  279 bits (713), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAEHNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|295102064|emb|CBK99609.1| pseudouridylate synthase I [Faecalibacterium prausnitzii L2-6]
          Length = 251

 Score =  279 bits (713), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 122/249 (48%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL  +
Sbjct: 1   MNYLLKLSYDGTNYCGFQVQPNGRSVAAAFQDALEAVLGCRPDIKGCSRTDAGVHALGFM 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F          L  ALN +L     I  L   +V   FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPAAKLPLALNQHL--PPDIRALEARVVPDDFHARYAAHTKTYLYRIHNSPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS---SPIRTIDHFDVN 178
                      +P  LD + M+ AAQ+ VG+HDF    +    A+     +RTI   DV 
Sbjct: 119 DSPFAARYYTKVPGRLDADRMQQAAQYFVGKHDFLALCASGSSAAAHGDTVRTITACDVQ 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I+I V A  +L+  +R   G+L   G G+     +   L +++RK  GP    +G
Sbjct: 179 RRGDDIDITVTADGYLYNMVRILAGTLCEAGAGRLAPEAVPGILASRERKNAGPTLAAKG 238

Query: 239 LYFDSVEYS 247
           L+  SV+Y 
Sbjct: 239 LFLKSVDYD 247


>gi|227533991|ref|ZP_03964040.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I)
           [Lactobacillus paracasei subsp. paracasei ATCC 25302]
 gi|227188368|gb|EEI68435.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I)
           [Lactobacillus paracasei subsp. paracasei ATCC 25302]
          Length = 254

 Score =  279 bits (713), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ + G+Q Q    ++QG ++KA+  +T G+ V V G+GRTDSGVHAL 
Sbjct: 8   MTHYKVTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMTKGQPVHVDGSGRTDSGVHALG 67

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  FD         + KA+N+ +     I IL   IVD  FHAR+SA  + YLYR+   
Sbjct: 68  QVISFDYPGNIPAESMLKAMNSLM--PLDIEILKAEIVDADFHARYSAKGKRYLYRVARG 125

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +      P  LD + + +A + LVG HDFT+F +        +RTI    V  
Sbjct: 126 YYTNPFNRLYTGHYPYKLDVQRIEVALKDLVGTHDFTSFAASGGVIVDKVRTIYEATVRE 185

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N I        FL+  +R  V +   +G+G+    D ++    +DR++    AP  
Sbjct: 186 DPVTNEIIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFAVKDRQQARGTAPAS 245

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 246 GLYLKEVYY 254


>gi|296315347|ref|ZP_06865288.1| tRNA pseudouridine synthase A [Neisseria polysaccharea ATCC 43768]
 gi|296837693|gb|EFH21631.1| tRNA pseudouridine synthase A [Neisseria polysaccharea ATCC 43768]
          Length = 267

 Score =  278 bits (712), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 129/247 (52%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 9   QRWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGEAVSTIVAGRTDTGVHATAQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           +  NA L   + I++L+       FHARF A  R Y Y + +  
Sbjct: 69  VVHFDTAARRPAQAWIRGTNAVL--PEGIAVLHARQTAPGFHARFDAYGRHYRYLLESSP 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 127 VRSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQA 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 187 GGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSALIQERSRLKAPPTFMPDGLY 246

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 247 LTGVDYP 253


>gi|315221272|ref|ZP_07863195.1| tRNA pseudouridine synthase A [Streptococcus anginosus F0211]
 gi|315189631|gb|EFU23323.1| tRNA pseudouridine synthase A [Streptococcus anginosus F0211]
          Length = 249

 Score =  278 bits (712), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  + +G  VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGHGFAGFQRQLHARSVQEEIEKTLTKINSGASVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  + I  +++  V++ FH+R+    ++Y + +   
Sbjct: 61  QVIHFDLPQKRDGEKLRFALDT--QTPEDIDFISVEEVNEAFHSRYCKHSKTYEFIVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD   +  A + L G HDFT F +      + IRTI    +  
Sbjct: 119 RPKNPMMRYYATHYPYPLDLSLIEEAIEKLEGTHDFTGFTASGTSVENKIRTITEARLVF 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N +        FL+ QIR+ VG+L  +G+G+     +++ L  +DR   GP A P 
Sbjct: 179 DEKRNFLMFTFSGNGFLYKQIRNMVGTLLKIGNGRMPVEQIDRILTEKDRHLAGPTAAPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|291542954|emb|CBL16064.1| pseudouridylate synthase I [Ruminococcus bromii L2-63]
          Length = 266

 Score =  278 bits (712), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               + I Y+G  + GWQ Q+N  ++Q + + A+  + G    V G  RTDSGVHA    
Sbjct: 11  RNLLLTISYDGKEFHGWQIQQNAMTVQEAFQTALSKIIGNDFDVKGCSRTDSGVHANMYC 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                     P  L  ALN +L    +I++L+   V   FHAR+S   + Y+Y+I   + 
Sbjct: 71  ISLKTEHPIKPERLKAALNRWL--PLSIAVLDCKEVAPDFHARYSCTSKEYIYKIWNSEV 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTIDHFDVNSF 180
                 G A      +D   +  AAQ  VGRHDFT+F ++  +    + R +  F V   
Sbjct: 129 RNPFLDGYALHYRYKIDENLLDKAAQAYVGRHDFTSFCTLDNREKGDMTRNVKAFSVTRE 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ ++V A  FL+  +R  VG+L  +  GK    ++   ++ ++RK  GP A   GLY
Sbjct: 189 GDLVTMKVEADGFLYNMVRIMVGTLLRIQQGKIAPDEIPSIIEKKNRKYSGPTAQACGLY 248

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 249 LNCVNYE 255


>gi|217077259|ref|YP_002334977.1| tRNA pseudouridine synthase A [Thermosipho africanus TCF52B]
 gi|226708660|sp|B7IHS2|TRUA_THEAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217037114|gb|ACJ75636.1| tRNA pseudouridine synthase A [Thermosipho africanus TCF52B]
          Length = 244

 Score =  278 bits (712), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 130/246 (52%), Gaps = 6/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +   Y+G+ +FG+Q Q N  ++QG +E A+  +  E +    AGRTD+GVHA  Q
Sbjct: 1   MKRFAIEFAYDGTKFFGYQGQPNVRTVQGDLEDALERIFKERIYTQAAGRTDAGVHANGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA F+          +  ALNA L   D I +    +VDK F+ RF+A +R Y Y I T 
Sbjct: 61  VAAFNCPIERLTETDIKNALNANL--PDDIYVKKAWVVDKSFNPRFAATKRIYHYFISTN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   W     LD E MR AA  L G HDF++F+       +P+RTI    + +
Sbjct: 119 EK-DVFMRNYVWNFRYDLDIEAMRKAASFLEGEHDFSSFKK-GKDEKNPVRTIYRIRILT 176

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               LI IRV  RSFL + +R+ VGSL  VG G+W    + + L+ + R+E    APP G
Sbjct: 177 LKKGLILIRVEGRSFLRSMVRNIVGSLVRVGLGQWKPEKILEVLEKRSRQEAAGTAPPHG 236

Query: 239 LYFDSV 244
           LY   V
Sbjct: 237 LYLYKV 242


>gi|223935594|ref|ZP_03627510.1| tRNA pseudouridine synthase A [bacterium Ellin514]
 gi|223895602|gb|EEF62047.1| tRNA pseudouridine synthase A [bacterium Ellin514]
          Length = 270

 Score =  278 bits (712), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 134/248 (54%), Gaps = 6/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           ++ + I Y+G  Y GWQ QK+G  +Q  +E+A+  +   +  +H + RTD+GVHA+  VA
Sbjct: 5   KFKLTIAYDGKNYSGWQVQKSGIGVQQRVEEALTKLFPSVGRIHSSSRTDTGVHAIGMVA 64

Query: 63  HFDLVR---EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           H ++ +         L  A+NA+L   + I +++   V   FHARF A  + Y Y +  +
Sbjct: 65  HMEIPKAEFRMTSEKLALAINAHL--PEDIRVMSAQKVAADFHARFDAAGKQYRYFVWNQ 122

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVN 178
            A   L + +AW +PK LD + MR AA+   G+HDF +F +    +  S +RT+   D+ 
Sbjct: 123 TAMNPLLREQAWQVPKELDLKAMRSAAKLFPGKHDFRSFAASRNYEVESTVRTLARCDIK 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+L+   +    FL+   R  VG+L  VG GK  + D++K L+ +DR+  G  AP  G
Sbjct: 183 KSGSLLTFIIEGDGFLYKMCRGIVGTLVQVGQGKIAAADIKKILETRDRRVAGMTAPAHG 242

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 243 LVLWKVFY 250


>gi|313669058|ref|YP_004049342.1| tRNA pseudouridine synthase [Neisseria lactamica ST-640]
 gi|313006520|emb|CBN87984.1| tRNA pseudouridine synthase [Neisseria lactamica 020-06]
          Length = 267

 Score =  278 bits (712), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 129/247 (52%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 9   QRWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGEAVSTIVAGRTDTGVHATAQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           +  NA L   + I++L+       FHARF A  R Y Y + +  
Sbjct: 69  VVHFDTAARRPAQAWIRGTNAAL--PEGIAVLHARQTAPGFHARFDAYGRHYRYLLESSP 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 127 VRSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQT 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY
Sbjct: 187 GGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSALIRERSRLKAPPTFMPDGLY 246

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 247 LTGVDYP 253


>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 =  278 bits (712), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+          + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDITAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRTGLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|260887817|ref|ZP_05899080.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
 gi|330838710|ref|YP_004413290.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
 gi|260862493|gb|EEX76993.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
 gi|329746474|gb|AEB99830.1| tRNA pseudouridine synthase A [Selenomonas sputigena ATCC 35185]
          Length = 258

 Score =  278 bits (712), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 125/247 (50%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
              C+ + Y+G+ Y G+QRQ     ++Q  +E+ + LV G+ + +  AGRTD+GVHA+ Q
Sbjct: 14  RNVCLTVAYDGTAYHGFQRQSPPIRAVQNVLEEKLALVFGDAIELAAAGRTDAGVHAMGQ 73

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F          + +A+N+ L     I +       + F AR SA  +SY+YRI    
Sbjct: 74  VVNFFTDGRIPTERIVRAMNSVL--PPDIVVKAAREEGRDFSARHSAKSKSYIYRIQEGD 131

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P    +  AW +   LD   M  AA  L+G HDF+ FR+       P+RT+   +    
Sbjct: 132 TPNPFSERYAWYVGTPLDLAAMNEAAALLLGTHDFSAFRAAGGAPMLPVRTMYSAEGRRI 191

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  IE R  A  FL+   R+ VG+L  VG G+ T  D    L +++RK     AP  GL
Sbjct: 192 EGERIEFRFHANGFLYHMARNIVGTLVDVGKGRRTRADFAAILASRERKRASATAPACGL 251

Query: 240 YFDSVEY 246
           + +SVEY
Sbjct: 252 FLESVEY 258


>gi|325686853|gb|EGD28878.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK72]
 gi|332359857|gb|EGJ37671.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1056]
          Length = 249

 Score =  278 bits (711), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I  +++  V + FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEDRDEEKLRFALDT--QTPEDIDFISVEQVSEDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|326803064|ref|YP_004320882.1| tRNA pseudouridine synthase A [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650503|gb|AEA00686.1| tRNA pseudouridine synthase A [Aerococcus urinae ACS-120-V-Col10a]
          Length = 264

 Score =  278 bits (711), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 91/251 (36%), Positives = 129/251 (51%), Gaps = 6/251 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHAL 58
           M  RY   I Y+G+ Y G+Q Q NG SIQ ++EKA+ L+T G+ + V+G+GRTDSGVHAL
Sbjct: 1   MPQRYKATIAYDGTPYVGFQVQPNGPSIQAALEKALKLMTKGQEIPVYGSGRTDSGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   E     L +ALN+ L   D I +  +  V+K FHAR+ A R++YLY++  
Sbjct: 61  GQVVHFDYPSEIETEGLLRALNSIL--DDAICVKTVEPVEKHFHARYHAQRKAYLYKVSL 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  E+      P   D   ++ A   L+G H+F +F S     +   R I   +  
Sbjct: 119 APFVSPFERHYVLHHPYRTDVSRIQAALPALIGAHNFKSFCSTKTDKTVFDREIYRAECQ 178

Query: 179 S--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G  +        FL+  +R  VG+   +GDG     +L   L+ QDR   GP A  
Sbjct: 179 ASWDGQTLTFYFEGNGFLYNMVRIIVGTCLQIGDGLRPVENLSDLLRIQDRNAAGPTAKA 238

Query: 237 EGLYFDSVEYS 247
            GLY   V+Y 
Sbjct: 239 HGLYLHHVDYP 249


>gi|224477189|ref|YP_002634795.1| tRNA pseudouridine synthase A [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|254764865|sp|B9DM46|TRUA_STACT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|222421796|emb|CAL28610.1| putative tRNA pseudouridine synthase A [Staphylococcus carnosus
           subsp. carnosus TM300]
          Length = 267

 Score =  278 bits (711), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 81/244 (33%), Positives = 119/244 (48%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q++G ++Q   EK +  +    V +H + RTD GVHA+ Q 
Sbjct: 1   MRILVKISYQGSNFLGFQIQQHGRTVQQQFEKILKRMHKRHVRIHPSSRTDRGVHAIEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   D I +  +SIVD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIAPDKWQYAMNSAL--PDDIYVNEVSIVDDDFHCRYDCVGKRYRYKVYQGKH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                 G       SLD E M  AAQ  +G HDFT F S   +  S  RT+   ++    
Sbjct: 119 RDVFMSGLKTFYADSLDLEKMNEAAQQFIGTHDFTGFCSQKTEVESKERTLYQSEIIKTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N  +  V    FL+  +R  V  L  VG GK    ++   L+A+DRK+    AP EGLY 
Sbjct: 179 NGFDYIVTGSGFLYNMVRVLVAFLIEVGKGKRQPEEVPILLEAKDRKQVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|325697516|gb|EGD39402.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK160]
          Length = 249

 Score =  278 bits (711), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYNFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSNDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A  HL G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAHLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|294101662|ref|YP_003553520.1| tRNA pseudouridine synthase A [Aminobacterium colombiense DSM
           12261]
 gi|293616642|gb|ADE56796.1| tRNA pseudouridine synthase A [Aminobacterium colombiense DSM
           12261]
          Length = 271

 Score =  278 bits (711), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 90/248 (36%), Positives = 127/248 (51%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY  ++ Y+G+ + GWQRQ   +S+Q S+E+A+  +    + +  AGRTD GVH+  QV
Sbjct: 1   MRYAAVVSYDGTAFCGWQRQLGVASVQQSLEEALSKLCATSIPIVAAGRTDGGVHSRGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F L   W P  L  A+N YL   +T+ I+ +  V++ F ARF A+ R Y Y I    A
Sbjct: 61  ISFSLPSFWEPRRLVLAINFYL--PETVRIMGVFPVEESFSARFCALWREYRYYIWHGPA 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  RAW      D   ++ A ++L G H+F  F  I       +RTI        G
Sbjct: 119 FPPYLAQRAWWNRWQWDKTAVKKACEYLEGTHNFKAFCPIKECPEDTVRTILRIKYLRSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGL 239
           +L  I V   SFL   +RS VGSL LVG GK     +++ L  + +DR   G  AP  GL
Sbjct: 179 HLSVITVRGNSFLMNMVRSIVGSLDLVGKGKNDPEWIKELLDDEKKDRTYAGMTAPAHGL 238

Query: 240 YFDSVEYS 247
           YF  V Y+
Sbjct: 239 YFWKVCYN 246


>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 =  278 bits (711), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPGFHARFDAYGRHYRYLLESAP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI    +   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAECQAKSPVKTIYRTGLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|324989944|gb|EGC21886.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK353]
          Length = 249

 Score =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPDERDEEKLRFALDT--QTPEDIDFISVERVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELRLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITDAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTADPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 128/247 (51%), Positives = 164/247 (66%), Gaps = 1/247 (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  RAHADIAKDMTPFRLMEALNARLR-PAPVAILACETVPDDWHARFSCTGRSYVYRIVNRR 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 FDSVEYS 247
           F S  Y 
Sbjct: 240 FVSAHYP 246


>gi|291557656|emb|CBL34773.1| pseudouridylate synthase I [Eubacterium siraeum V10Sc8a]
          Length = 243

 Score =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 84/242 (34%), Positives = 120/242 (49%), Gaps = 4/242 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + YNG+ Y G+QRQ N +SIQ ++E+ +  +  E + ++G  RTD+GVHA   V +    
Sbjct: 1   MAYNGTAYHGYQRQNNANSIQQTVEEVLSKLLCEDITINGCSRTDTGVHARAFVFNVKTT 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                    K  NA L     I+ L+   +   FHARF +  + Y+YRI T         
Sbjct: 61  CPIPCEGFIKGGNALL--PQDIAFLSCEDMPDSFHARFDSKGKEYIYRIYTGDVRDVFSA 118

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDVNSFGNLIE 185
             A   P   D E MR AA+ +VG HDF +F     +    S +RT+   DV   G+ +E
Sbjct: 119 DTALHYPYKPDIEKMRKAARLIVGEHDFASFCKAEAKEHLLSTVRTVYSIDVEQTGDFVE 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I+V    FLH  +R  VG+L  + +GK T  D+  AL   DR+  G    P GLY + V 
Sbjct: 179 IKVCGNGFLHNMVRIIVGTLIYISEGKRTEQDIINALTKPDREFAGKTVSPCGLYLNKVF 238

Query: 246 YS 247
           Y 
Sbjct: 239 YE 240


>gi|257454808|ref|ZP_05620059.1| tRNA pseudouridine synthase A [Enhydrobacter aerosaccus SK60]
 gi|257447741|gb|EEV22733.1| tRNA pseudouridine synthase A [Enhydrobacter aerosaccus SK60]
          Length = 268

 Score =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 83/244 (34%), Positives = 130/244 (53%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + IE+ G+ Y GWQRQ+   SIQ  +E A+  +  E + V  AGRTD+GVHA   +AH
Sbjct: 6   YAISIEFIGTRYRGWQRQQEVDSIQQHVEAALSKIANEPIEVIAAGRTDAGVHASNMIAH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P    +A N+ L   D I++  + ++  +FHARFSAI R Y Y  +      
Sbjct: 66  FQTSATRQPYNWLRAANSLL--PDDIAVRWIQVMPAEFHARFSAIARRYRYITLNHPFRP 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+   +       L+ + M+ AA +L G HDFT+FR+  CQ++ P+R +    +   G L
Sbjct: 124 AILNQQITHEYAPLNVQLMQQAATYLEGTHDFTSFRAASCQSNQPVRHVHFAKLIQHGEL 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A  FLH  +R+ +G+L  +G G+     +E  L +++R      A  +GLYF +
Sbjct: 184 LVLDIQADGFLHHMVRNIMGTLFEIGRGEKPVAWIEALLLSKNRSLAAATASADGLYFIN 243

Query: 244 VEYS 247
             Y 
Sbjct: 244 ALYP 247


>gi|325199128|gb|ADY94584.1| tRNA pseudouridine synthase A [Neisseria meningitidis G2136]
          Length = 265

 Score =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAVRPQQAWIRGVNAHL--PEGIAVLHARQVALEFHARFDAYGRHYRYLLESSP 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA +L+G  DF++FR+  CQA SPI+TI   ++   
Sbjct: 125 VRSPLLKNRAGWTHLKLDIGPMRQAATYLIGEQDFSSFRAAECQAKSPIKTIYRANLTQS 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 185 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 244

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 245 LTGVDYP 251


>gi|161521167|ref|YP_001584594.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
 gi|189352656|ref|YP_001948283.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
 gi|42559801|sp|Q83WJ5|TRUA_BURM1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|28971662|dbj|BAC65262.1| tRNA pseudouridine synthase [Burkholderia multivorans]
 gi|160345217|gb|ABX18302.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
 gi|189336678|dbj|BAG45747.1| tRNA pseudouridine synthase A [Burkholderia multivorans ATCC 17616]
          Length = 270

 Score =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G+++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGNTVQDALERALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFL--PPTVAVQWAKSMPDAFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLDGRAGWIHTPLDDDAMRAAAAHLLGEHDFSAFRSSECQSKTPVKHLYEIDIRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  +   L  +DR    P    +GLY 
Sbjct: 179 HFLHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWVADVLAGRDRNRAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|107026755|ref|YP_624266.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia AU 1054]
 gi|116692053|ref|YP_837586.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia HI2424]
 gi|170735954|ref|YP_001777214.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia MC0-3]
 gi|123370548|sp|Q1BM62|TRUA_BURCA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123464580|sp|A0AZ67|TRUA_BURCH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238688629|sp|B1K370|TRUA_BURCC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|105896129|gb|ABF79293.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia AU 1054]
 gi|116650053|gb|ABK10693.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia HI2424]
 gi|169818142|gb|ACA92724.1| tRNA pseudouridine synthase A [Burkholderia cenocepacia MC0-3]
          Length = 270

 Score =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 129/246 (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   MRIALGIQYDGAAFCGWQAQPHGKTVQDRLEHALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       +  NA+L    T+S+     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTDLEREVFSWVRGTNAFL--PSTVSVQWAKPMPDTFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY 
Sbjct: 179 HFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|309378319|emb|CBX23065.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 267

 Score =  278 bits (711), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 129/247 (52%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 9   QRWALTLSYDGSRFYGWQKQAGGVPTVQTALEDALAQIAGEAVSTIVAGRTDTGVHATAQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           +  NA L   + I++L+       FHARF A  R Y Y + +  
Sbjct: 69  VVHFDTAARRPAQAWIRGTNAAL--PEGIAVLHARQTAPGFHARFDAYGRHYRYLLESSP 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI    +   
Sbjct: 127 VRSPLLKNRAGWTHLKLDIGPMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYSATLAQT 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY
Sbjct: 187 GGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFSTLIRERSRLKAPPTFMPDGLY 246

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 247 LTGVDYP 253


>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 =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 131/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  V  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKVANEPIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+ L     ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTHAIRPETGWLRGANSQL--PKDISIQWIKLMDESFHARFKATARRYRYIIYNT 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|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 =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 124/246 (50%), Gaps = 2/246 (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  VHLDTEIEREPFSWVRGTNRYL--PPDIAVQWCRPVDAAFHARNSARGRRYAYLLLESPV 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 DSVEYS 247
              +Y 
Sbjct: 239 LGPQYD 244


>gi|56478134|ref|YP_159723.1| tRNA pseudouridine synthase A [Aromatoleum aromaticum EbN1]
 gi|62901200|sp|Q5P1J2|TRUA_AZOSE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56314177|emb|CAI08822.1| pseudouridylate synthase A [Aromatoleum aromaticum EbN1]
          Length = 264

 Score =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 85/245 (34%), Positives = 123/245 (50%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY GS + G+Q Q +G ++Q  +E AI  +    V +H AGRTD+GVHA  QV
Sbjct: 1   MRIVLGVEYAGSAFEGFQSQAHGRTVQDHLEAAIGHIAAHPVRLHCAGRTDAGVHATAQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +N+ L     + +   +     FHARF A+ R Y Y +     
Sbjct: 61  VHFDTESVRPNSGWVRGVNSRLSSP--VVVRWATEAGDGFHARFCAVSRRYRYILHNSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL  GR       LD   M  AA+ L G HDF+ FR+  CQA SP++ +    V   G
Sbjct: 119 RPALLAGRVGWFHPPLDEIAMAEAARCLEGWHDFSAFRAAGCQAKSPVKLMHEVRVQRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +     A +FLH  +R+ VG+L  VG G+ ++  L + L A+DR         +GLY 
Sbjct: 179 DYVVFDFWANAFLHHMVRNLVGALVYVGKGRHSAAWLAEVLAARDRSLAALTFSADGLYL 238

Query: 242 DSVEY 246
             VEY
Sbjct: 239 CGVEY 243


>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 =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 94/245 (38%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ     ++Q ++EKA+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYRGWQRQASGVPTVQETLEKALSKVADSSVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERTMKAWVMGANINL--PHDVSVSWAKVMPAHFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AAQHLVG HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 136 RPAHLNEEITWNHRPLDAERMAEAAQHLVGVHDFSAFRAGQCQAKSPIKEVHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + + A +FLH  +R+  G L  +G G+       + L+++ R+  G  A P GLY 
Sbjct: 196 KMIVLDIRAGAFLHHMVRNIAGVLMTIGTGERPVDWAREVLESRIRRTGGVTAHPFGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VDVEY 260


>gi|78062974|ref|YP_372882.1| tRNA pseudouridine synthase A [Burkholderia sp. 383]
 gi|123728751|sp|Q393X8|TRUA_BURS3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|77970859|gb|ABB12238.1| Pseudouridylate synthase [Burkholderia sp. 383]
          Length = 270

 Score =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 86/246 (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   MRIALGIQYDGAAFCGWQAQPHGKTVQDRLEHALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     + + FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTDLDREVFSWVRGTNAFL--PSTVAVQWAKPMPETFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY 
Sbjct: 179 HFVHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|33519947|ref|NP_878779.1| tRNA pseudouridine synthase A [Candidatus Blochmannia floridanus]
 gi|42559760|sp|Q7U356|TRUA_BLOFL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33504293|emb|CAD83185.1| tRNA pseudouridine synthase A [Candidatus Blochmannia floridanus]
          Length = 252

 Score =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 94/247 (38%), Positives = 132/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + +EY+GS Y GWQ+QK  SSIQ  +E A+  V+ E ++V   GRTDSGVHAL Q
Sbjct: 1   MQKLVLGVEYDGSMYCGWQKQKCVSSIQSCLEYALSKVSSESILVFCGGRTDSGVHALEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HF+   +         +N +L   + I +  +S VD  FHARFSAI R Y Y I   +
Sbjct: 61  IVHFETQLKCSRSAWTLGVNCHL--PNDICVRWVSEVDNSFHARFSAISRRYCYFIYNNR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+   R W   + LD   M  AAQ+L+G +DF+ FRS   Q+ S  R I H  V   
Sbjct: 119 IRSAVFCKRVWSYSRFLDVNKMSKAAQYLLGENDFSVFRSSGSQSCSTNRNIYHLRVIRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I + A +FL+  +R+ VGSL  VG G    T + + L+          AP  GLY
Sbjct: 179 GHYVVIDIRANAFLYRMVRNIVGSLVEVGCGNKPVTWILELLKNYRGSLNRITAPASGLY 238

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 239 LVEIKYP 245


>gi|74317934|ref|YP_315674.1| tRNA pseudouridine synthase A [Thiobacillus denitrificans ATCC
           25259]
 gi|123759044|sp|Q3SHL7|TRUA_THIDA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|74057429|gb|AAZ97869.1| tRNA pseudouridine synthase [Thiobacillus denitrificans ATCC 25259]
          Length = 260

 Score =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 123/247 (49%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + +EY G G+ GWQ Q     +Q ++EKA+  + GE + V  AGRTD+GVHA  Q
Sbjct: 1   MMRIAVGLEYRGVGFCGWQSQPQACGVQDAVEKAVSAIAGEAITVTAAGRTDTGVHAALQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD           + +N++L     +++L    VD +FHARF+A  R Y Y ++   
Sbjct: 61  IVHFDTTSVRPLTAWVRGVNSHL--PAGVAVLWAREVDAEFHARFAAFERGYRYVLLNHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  G      + LD   M  AA  L+GRHDF+ FR+  CQA SP++ +    +   
Sbjct: 119 VRPGLNAGLVGWHHRPLDVACMNRAASPLIGRHDFSAFRAAECQARSPVKELRRALIERR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +     A  FLH  +R+ +G L  +G G      L + L  +DR    P     GLY
Sbjct: 179 GDYLLCDFRADGFLHHMVRNLMGCLVQIGAGGRPPEWLHEVLAGRDRTRAAPTFEAAGLY 238

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 239 LTHIRYP 245


>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 =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 131/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  V  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKVANEPIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+ L     ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTHAIRPETGWLRGANSQL--PKDISIQWIKLMDESFHARFKATARRYRYIIYNT 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|295425622|ref|ZP_06818309.1| tRNA pseudouridine synthase A [Lactobacillus amylolyticus DSM
           11664]
 gi|295064638|gb|EFG55559.1| tRNA pseudouridine synthase A [Lactobacillus amylolyticus DSM
           11664]
          Length = 262

 Score =  277 bits (710), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 128/250 (51%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M++ Y+G  + G+Q Q N  ++QG++E+A+  +T G+ V+V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMLMAYDGHLFHGFQVQPNQRTVQGTVEEALKKMTKGKRVIVEGSGRTDAGVHAMGQ 62

Query: 61  VAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V  FD     +P   +  ALN+ +     I      I    FH R+S   + Y YR+   
Sbjct: 63  VIQFDYPGNRIPAEKMILALNSMM--PMDIIFKECEIASPDFHVRYSIKGKWYRYRMSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 ++      P  +D   M+ AA+ L+G+HDFT+F +   Q  + +RT+ + +V  
Sbjct: 121 HFVNPFKRFYTGHYPYPIDVSKMKEAAKDLLGKHDFTSFAASGGQIKNKVRTMYYVNVEK 180

Query: 180 FG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +    +   FL+  +R  V +L  +G GK    D  + ++A+DR +    AP  
Sbjct: 181 NESQNELVFDFICSGFLYNMVRILVATLLEIGSGKRPVHDFPRIIKAKDRLQVTQTAPAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>gi|171321983|ref|ZP_02910866.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MEX-5]
 gi|171092713|gb|EDT37998.1| tRNA pseudouridine synthase A [Burkholderia ambifaria MEX-5]
          Length = 270

 Score =  277 bits (710), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQDALERALGEFACVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRTDFSWVRGTNAFL--PSTVSVQWAKPMADTFHARFAAFERTYYYVLYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV   G
Sbjct: 119 RSPMLAGRAGWIHTPLDDDAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDVRRAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +GLY 
Sbjct: 179 HFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|325261709|ref|ZP_08128447.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
 gi|324033163|gb|EGB94440.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
          Length = 248

 Score =  277 bits (710), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 126/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+GS Y GWQRQK+   ++QG +E+A+  VTG    + G+GRTD GVHA  
Sbjct: 1   MRTYKLTVVYDGSRYQGWQRQKSTEKTVQGILERAVTEVTGRQTEIDGSGRTDGGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +      C +LN  L   + I +  + +V   FHAR++A  + Y Y I TR
Sbjct: 61  QTASMVLPGKVEETGFCASLNNAL--PEDIRVKEMKLVKNGFHARYNAKGKRYEYFIDTR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P  L+   M  AA++L+G HDF  F     +  S IRTI    +  
Sbjct: 119 EKPDVFTRKYCYHYPYELNIPAMEEAAEYLIGTHDFAGFTDKKDE-MSTIRTIYDIIIEK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I +      FL+  +R   G+L  +G G+    +   AL+A DR+  G LAP  GL
Sbjct: 178 QDSKIRMEFYGTGFLYHMVRILTGTLLEIGTGEKRPHEAAAALEAGDREYAGFLAPARGL 237

Query: 240 YFDSVEYS 247
           +   V Y+
Sbjct: 238 FLKEVYYN 245


>gi|283795894|ref|ZP_06345047.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
 gi|291076529|gb|EFE13893.1| tRNA pseudouridine synthase A [Clostridium sp. M62/1]
          Length = 275

 Score =  277 bits (710), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 87/269 (32%), Positives = 141/269 (52%), Gaps = 24/269 (8%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R   ++++Y+GS Y GWQ+Q N  ++IQG +E  +  + GE V +HG+GRTD+GVHAL
Sbjct: 1   MYRNIKIVLQYDGSRYDGWQKQGNTKNTIQGKLEAVLEKLAGEPVEIHGSGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPV--------------------ILCKALNAYLKISDTISILNLSIVD 98
            QVA+F L    +                       +   LN YL   + I++++   V 
Sbjct: 61  GQVANFRLEERCLEELVDKTPEKKENGGKASSVSAAVMDYLNRYL--PEDIAVISAMEVP 118

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           ++FH+R +A+ ++YLY+I T       E+   + + + LD   M+ AA+ L+G HDF  F
Sbjct: 119 ERFHSRLNAVEKTYLYQIETAGRKNVFERKYIYGLGEELDLLAMKEAAKLLLGSHDFRAF 178

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            S      S +R +   +++  G+ + +      FL+  +R   G+L  +G  + T   +
Sbjct: 179 SSAKRMKKSTVRELRKIEIHRDGSRVLLEFTGNGFLYNMVRILTGTLIEIGLHRRTVDSV 238

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            KAL++QDR+  G  AP EGL   SV Y 
Sbjct: 239 RKALESQDRENAGFTAPAEGLLLKSVRYD 267


>gi|328944888|gb|EGG39047.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1087]
          Length = 249

 Score =  277 bits (709), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYNFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSNDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 180 FGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERKFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|269139760|ref|YP_003296461.1| tRNA pseudouridine synthase A [Edwardsiella tarda EIB202]
 gi|267985421|gb|ACY85250.1| tRNA pseudouridine synthase A [Edwardsiella tarda EIB202]
 gi|304559626|gb|ADM42290.1| tRNA pseudouridine synthase A [Edwardsiella tarda FL6-60]
          Length = 275

 Score =  277 bits (709), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 88/244 (36%), Positives = 125/244 (51%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IEY+GS Y GWQRQ+   S+Q  +E A+  V  E V V  AGRTD+GVHA  QV H
Sbjct: 17  LALGIEYDGSRYAGWQRQREVDSVQARLEAALSRVASEPVTVFCAGRTDAGVHATGQVVH 76

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              +NA+L     +++  +  V   FHARFSA  R Y Y I   +   
Sbjct: 77  FTTHALRQEGAWTMGVNAHL--PKDVAVRWVKSVSPDFHARFSATARRYRYVIYNHRYRP 134

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+ +         LD E M  A Q L+G +DF+ FR+  CQ+ +P R + H  VN +G  
Sbjct: 135 AVLQSGVTHCYLPLDAERMARAGQALLGENDFSAFRAAQCQSRTPWRNVSHLRVNRYGPY 194

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A +F+H  +R+ VGSL  VG G    + + + L  +DR      A   GLY  +
Sbjct: 195 VVVDIKANAFVHHMVRNIVGSLLEVGCGNQPESWIAELLAGRDRTLAAATAKAAGLYLVA 254

Query: 244 VEYS 247
           V+Y 
Sbjct: 255 VDYP 258


>gi|160934132|ref|ZP_02081519.1| hypothetical protein CLOLEP_02995 [Clostridium leptum DSM 753]
 gi|156866805|gb|EDO60177.1| hypothetical protein CLOLEP_02995 [Clostridium leptum DSM 753]
          Length = 251

 Score =  277 bits (709), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 117/247 (47%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               + I Y+G  Y GWQ Q+N  S+Q   + A+  V G+   V G  RTDSGVHA +  
Sbjct: 4   RNLLLTIAYDGRAYHGWQIQENALSVQEVFQGALRQVIGDDFDVKGCSRTDSGVHANQYC 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                        L  ALN +L     +++     V   FHAR+S   + Y Y I     
Sbjct: 64  ISLKTGHRIPCERLVAALNRFL--PMDMAVKGCRSVSLDFHARYSCKGKEYQYLIWNDPV 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSF 180
                 GRA+     LD + +  AAQ  VG+HDFT+F ++ H +  +  R +    V+  
Sbjct: 122 RNPFLDGRAFHYWYPLDTDMLNQAAQAFVGKHDFTSFCTLDHRERDNMERMVKCCSVSRE 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+  RV A  FL+  +R  VG+L  +  GK     +   L+A+DR + GP A   GLY
Sbjct: 182 GSLVTFRVEADGFLYNMVRIMVGTLLRIAQGKIPEDGIPAILEAKDRSKAGPTARACGLY 241

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 242 LNRVFYE 248


>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 =  277 bits (709), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 95/245 (38%), Positives = 128/245 (52%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++EKA+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYRGWQRQASGVLTVQETLEKALSKVADSPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E          N  L     +S+    ++   FHARF AI R Y Y I   Q 
Sbjct: 78  VHFDTQAERSMKAWVMGANINL--PHDVSVSWAKVMPAHFHARFKAIARRYRYVIYNDQI 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A          + LD E M  AAQHLVG HDF+ FR+  CQA SPI+ + H  V   G
Sbjct: 136 RPAHLNEEITWNHRPLDAERMAEAAQHLVGVHDFSAFRAGQCQAKSPIKEVHHLRVTRHG 195

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + + A +FLH  +R+  G L  +G G+      ++ L+++ R+  G  A P GLY 
Sbjct: 196 KMIVLDIRAGAFLHHMVRNIAGVLMTIGTGERPVAWAKEVLESRVRRTGGVTAHPFGLYL 255

Query: 242 DSVEY 246
             VEY
Sbjct: 256 VDVEY 260


>gi|119471543|ref|ZP_01613957.1| tRNA pseudouridine synthase A [Alteromonadales bacterium TW-7]
 gi|119445486|gb|EAW26772.1| tRNA pseudouridine synthase A [Alteromonadales bacterium TW-7]
          Length = 264

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ Y GWQRQ + +S+Q  +EKA+  +    V +  AGRTD+GVH   QV
Sbjct: 1   MRVALGVEYNGARYSGWQRQSHVNSVQQEVEKALSSICNHPVEIVCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+       V     +N  L     I+I     V + FHARFSA  R Y Y I     
Sbjct: 61  VHFETNASREMVAFTMGMNTLL--PKDIAIRFAQPVVEDFHARFSATARRYRYVIYNYPY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M+ A QHL+G HDFT+FR++HCQA++  RTI H  V   G
Sbjct: 119 RGAVMNEGVTHFHHKLDEKVMQEACQHLIGEHDFTSFRALHCQANTAKRTIHHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +FLH  +R+  G L  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 DYVVIDIKANAFLHHMVRNITGCLMDIGLHKHQPVWLKELLDLKERAKASATAKAAGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>gi|125718790|ref|YP_001035923.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK36]
 gi|166229844|sp|A3CQB8|TRUA_STRSV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|125498707|gb|ABN45373.1| tRNA pseudouridine synthase A, putative [Streptococcus sanguinis
           SK36]
          Length = 249

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G  VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGRPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEDRDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRF 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPIEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|51596937|ref|YP_071128.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186896018|ref|YP_001873130.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis PB1/+]
 gi|51590219|emb|CAH21856.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186699044|gb|ACC89673.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis PB1/+]
          Length = 299

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 37  KIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQVV 96

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + +  
Sbjct: 97  HFVTSAVRKDAAWTMGVNSHL--PADIAVRWVKTVDNDFHARFSATARRYRYIIFSHRYR 154

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G 
Sbjct: 155 PAILAQGVTHCYMPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRHGA 214

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY  
Sbjct: 215 YIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLYLV 274

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 275 SVDYP 279


>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 =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 88/249 (35%), Positives = 137/249 (55%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+GS Y GWQ Q + +++Q  +E AI    G  ++   AGRTD+GVHAL QV 
Sbjct: 5   RIAIGLHYDGSAYSGWQSQPHRNTVQDHLEDAIERFAGVRLLTTVAGRTDAGVHALGQVI 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H D   +       + +NA+L    +I++     VD+ FHARF A  R Y Y + T    
Sbjct: 65  HLDTELDRDRFSWVRGVNAFL--PPSIALQWAEPVDENFHARFLAYERMYYYALYTGPHR 122

Query: 123 LALEKGRAWL----IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
             +  GRA        + 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 LYFDSVEYS 247
           LY   V+Y 
Sbjct: 243 LYLVDVKYP 251


>gi|160879036|ref|YP_001558004.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
 gi|160427702|gb|ABX41265.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
          Length = 248

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 121/249 (48%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    +IIEY+GS Y GWQ+Q       +IQ  +E  +  +  E V V GA RT++GVHA
Sbjct: 1   MRNIQLIIEYDGSRYDGWQKQAGNQKSITIQDKLEDVLNKMENETVTVIGAARTEAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            +QVA F    +     + + LN +L     I++L    V ++FHA F+A    Y Y+I 
Sbjct: 61  YKQVASFMTNSKLKVYEIKQYLNRFL--PRDIAVLEALEVPERFHASFNAGSFEYEYKIS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P   E+   +   K  D   M+ AA++LVG+HDF  F        S  R I   ++
Sbjct: 119 IGEVPSVFERKYNYYCFKRPDIAKMKEAAKYLVGKHDFKAFSDNKRMKKSTEREIYSLEI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I I V    F    +R  VG+L  VG  K    D+++ L+++DR + G     +
Sbjct: 179 YGDEKEIVITVHGDDFWPHMVRIMVGTLLDVGLSKIEPMDIKRILESKDRDKAGETIEAK 238

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 239 GLFLTEVHY 247


>gi|218245114|ref|YP_002370485.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8801]
 gi|226708647|sp|B7K222|TRUA_CYAP8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|218165592|gb|ACK64329.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8801]
          Length = 293

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 116/247 (46%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y GS + GWQ Q N  ++Q  IE AI  V GE V +HGAGRTD+GVHA  QV
Sbjct: 10  QRVALVIQYLGSRFHGWQWQPNQRTVQAEIENAIAEVLGETVTLHGAGRTDAGVHAAAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+V           LNA L   + I I   + V   +HARFSA  R Y Y   T Q 
Sbjct: 70  AHFDMVSPIPASRWVDILNARL--PEDILIRGSAQVPLTWHARFSAQWRRYRYTFYTEQR 127

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    K  +W      LD   M+ A   L+GRH    F     +       +     +  
Sbjct: 128 PNLFVKPYSWHYYHFPLDESLMQQALNPLLGRHHLAAFHRAGSRRDHSWVEVQSTHCHRQ 187

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A  FL+  +R  VG L  VG GK +  +  +  + Q R+     AP +GL 
Sbjct: 188 GPFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLENFTEIWRKQQREAVKYAAPAKGLC 247

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 248 LLRVGYE 254


>gi|291544350|emb|CBL17459.1| pseudouridylate synthase I [Ruminococcus sp. 18P13]
          Length = 273

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 125/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M     ++ Y G+ Y G+QRQ N  ++Q ++E+A+  V      ++G  RTD+GVHA + 
Sbjct: 1   MRTLKCMMAYRGTKYHGFQRQDNAHTVQEAVEQALGSVLNHPATIYGCSRTDTGVHARQY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F   R   P+ L + +N  L   D IS+L+       FHAR++   + YLY I   +
Sbjct: 61  CFSFQTERPIQPLNLVRGVNGRL--PDDISLLSAEDAALSFHARYACRGKEYLYLIHNSE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P    +  A    + +D   ++  A   +G HDF +F S   Q +S +RTI  F V   
Sbjct: 119 SPNPFLRDLACHHRRPIDPALLQACADRFIGTHDFKSFCSAQAQRTSTVRTIYDFSVEMS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + V    FL+  IR  VG++  V DGK   +DL+  L A+DR+  G  A   GLY
Sbjct: 179 GDSIILLVKGDGFLYNMIRILVGTMLQVNDGKLKLSDLDGILAARDRRCAGKTAMACGLY 238

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 239 LNRVFYD 245


>gi|282882119|ref|ZP_06290760.1| tRNA pseudouridine synthase A [Peptoniphilus lacrimalis 315-B]
 gi|281298149|gb|EFA90604.1| tRNA pseudouridine synthase A [Peptoniphilus lacrimalis 315-B]
          Length = 243

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 120/245 (48%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   + + Y+G+ Y G+Q Q    +I+G + KAI     +   ++ AGRTD GVHAL Q 
Sbjct: 1   MNILIKVTYDGTNYHGYQVQNKLKTIEGELSKAINNTLKKETKIYSAGRTDRGVHALGQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F          L + +N +L   D IS+++   V   FHARFSA  + Y Y +   + 
Sbjct: 61  VNFYTDTTIDLGNLPRVINFHL--PDDISVISAKEVPFDFHARFSAKEKIYRYVVYNNKY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+   RA+  P SLD   M  + ++L+G+ DF +F          IRTI    V    
Sbjct: 119 RNAIYHNRAYQYPFSLDLSLMNESFKYLIGQKDFKSFMGRDAIVKDTIRTIYSIKVKKDN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I      +SFL   IR  +G+   +G GK     +++ L+ Q+RK  GP AP  GLY 
Sbjct: 179 KFIYFDFQGKSFLKNMIRIIMGTAIEIGRGKKDPIFMKEVLEKQNRKYAGPTAPSCGLYL 238

Query: 242 DSVEY 246
            ++ Y
Sbjct: 239 MNILY 243


>gi|330718940|ref|ZP_08313540.1| tRNA pseudouridine synthase A [Leuconostoc fallax KCTC 3537]
          Length = 250

 Score =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 126/252 (50%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHA 57
           M RY  I+ Y+GSG+FG+Q Q +  ++QG + K +  +       + V GA RTD+GVHA
Sbjct: 1   MPRYKAIVSYDGSGFFGFQVQNDVRTVQGELNKVVNQMAKNPATPIRVIGASRTDTGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV +FDL        + K LN  L     I I  + IV+  FHARF++  + Y YR+ 
Sbjct: 61  LGQVINFDLPFNIPAASVRKGLNTLL--PRDIMIREVEIVNDDFHARFNSHHKRYFYRLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T+      ++  A      LD + +  A   L+G HDF +F +   Q  + IR I   D+
Sbjct: 119 TQDFVDPFKRKYAGHFHWPLDIQRIEKALPDLLGEHDFASFAASGNQTQTTIRRITRADI 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                   I       +FL+ QIR  VG L  +G GK    D+++ ++ +DR +    A 
Sbjct: 179 INKPDEQEIVFIFEGNAFLYNQIRIMVGVLLEIGTGKRPVHDIQRLIEVKDRSQARFTAA 238

Query: 236 PEGLYFDSVEYS 247
             GLY D + YS
Sbjct: 239 AAGLYLDEISYS 250


>gi|269213866|ref|ZP_05983015.2| tRNA pseudouridine synthase A [Neisseria cinerea ATCC 14685]
 gi|269145225|gb|EEZ71643.1| tRNA pseudouridine synthase A [Neisseria cinerea ATCC 14685]
          Length = 277

 Score =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 131/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 19  QRWALTLSYDGSRFYGWQKQAGGVPTVQTALENALAQIAGEAVSTIVAGRTDTGVHATAQ 78

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA L   + I++L+      +FHARF A  R Y Y + +  
Sbjct: 79  VVHFDTAAVRPAQAWIRGVNANL--PEGIAVLHAQQAAPEFHARFDAYGRHYRYLLESSP 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K R       LD E MR AA  LVG  DF++FR+  CQA SP++TI   ++   
Sbjct: 137 VRSPLLKHRVGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAECQAKSPVKTIYSAEIAYG 196

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + +   +FLH  +R+ +G+L  VG G+ +       ++ + R +  P   P+GLY
Sbjct: 197 RGLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVDGFAALIRERSRLKAPPTFMPDGLY 256

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 257 LTGIDYP 263


>gi|257058139|ref|YP_003136027.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8802]
 gi|256588305|gb|ACU99191.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 8802]
          Length = 293

 Score =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 116/247 (46%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y GS + GWQ Q N  ++Q  IE AI  V GE V +HGAGRTD+GVHA  QV
Sbjct: 10  QRVALVIQYLGSRFHGWQWQPNQRTVQAEIENAIAEVLGETVTLHGAGRTDAGVHAAAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+V           LNA L   + I I   + V   +HARFSA  R Y Y   T Q 
Sbjct: 70  AHFDMVSPIPASRWVDILNARL--PEDILIRGSAQVPLTWHARFSAQWRRYRYTFYTEQR 127

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    K  +W      LD   M+ A   L+GRH    F     +       +     +  
Sbjct: 128 PNLFVKPYSWHYYHFPLDESLMQQALNPLLGRHHLAAFHRAGSRRDHSWVEVQSTHCHRQ 187

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A  FL+  +R  VG L  VG GK +  +  +  + Q R+     AP +GL 
Sbjct: 188 GPFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLENFTEIWRKQQREAVKYAAPAKGLC 247

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 248 LLRVGYE 254


>gi|291460751|ref|ZP_06600141.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
 gi|291416710|gb|EFE90429.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
          Length = 266

 Score =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 81/252 (32%), Positives = 126/252 (50%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R  + I Y+G+ Y GWQ Q+  S+I+G + +A+  L+ GE + + GA RTD+GVHA +
Sbjct: 1   MRRIRLDIAYDGTNYHGWQYQEGQSTIEGELRRALSELLPGEEIGLTGASRTDAGVHARQ 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             A FD            ALN  L   + I IL      + FH RFS  ++ Y YRI   
Sbjct: 61  NTACFDTKSRIPGANFSMALNCRL--PEDIRILRSMEAGEDFHPRFSPHKKVYEYRIGRS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA----SSPIRTIDHF 175
           + P  L++   +     L    MR+AA+ LVG HDF +F +   Q      + +RT+   
Sbjct: 119 RIPDPLKRLYCFPFSFPLSLSEMRLAAEELVGEHDFRSFANPDSQVLMHGGAAVRTLYEL 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   G  + +      FL+  IR   G+L  +G G+  + ++ + L A+DR+  G  AP
Sbjct: 179 SLREEGEELILHFEGSGFLYHMIRILTGTLLEIGSGRRRAAEIPEILAARDRRRAGFTAP 238

Query: 236 PEGLYFDSVEYS 247
            +GL   ++ Y 
Sbjct: 239 AKGLCLLALCYE 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 =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 125/247 (50%), Positives = 161/247 (65%), Gaps = 1/247 (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 FDSVEYS 247
           F    Y 
Sbjct: 240 FVRARYP 246


>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 =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 94/242 (38%), Positives = 133/242 (54%), Gaps = 2/242 (0%)

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  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                         NA L     I++  +  V + FHARF A+ R Y Y ++ + +   L
Sbjct: 61  PPAPRSEKAWVFGANANL--PRDIAVRWVMPVGEDFHARFKALARRYRYVLLNQPSRPVL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E+         LD E M  AAQ LVG HDF++FR+  CQ+ +P R +   +V+  G L+ 
Sbjct: 119 ERANVTWCRDPLDAEAMHEAAQVLVGEHDFSSFRAAGCQSKTPWRHLHFIEVHRHGPLVV 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + V   +FLH  IR+  G+L  VG G+  +  L + L  +DR +    AP  GL+F    
Sbjct: 179 VDVQGNAFLHHMIRNIAGALVTVGRGEQGADYLARLLALRDRTQGDVTAPACGLHFVDSL 238

Query: 246 YS 247
           Y 
Sbjct: 239 YD 240


>gi|299138466|ref|ZP_07031645.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX8]
 gi|298599712|gb|EFI55871.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX8]
          Length = 271

 Score =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 95/271 (35%), Positives = 135/271 (49%), Gaps = 26/271 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + + Y+G+ + GWQ Q    ++QGS+  A+  VTGE V+  G+GRTDSGVHAL Q
Sbjct: 1   MNHWKLTLSYDGTLFHGWQVQPELPTVQGSLALALKYVTGESVLPQGSGRTDSGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           V  F L     P  L +ALN  L    +I IL   +VD+ FHAR SA R++Y YRI  R 
Sbjct: 61  VTSFALETSIPPANLQRALNRAL--PPSIRILTAELVDESFHARHSARRKTYEYRIFERR 118

Query: 120 -------QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-------- 164
                  +         AW     L  E M+ A+++L G HDFT+F +   +        
Sbjct: 119 TAASPSERICSPFLAPYAWDCRWQLAIEPMQEASKYLCGTHDFTSFAASDPERGLREEES 178

Query: 165 --------ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                     +P++T+          L+  RV    FLH  +R+ VG+L  VG G     
Sbjct: 179 DDANGKAHGPNPVKTLLQAGWAHEDGLLVYRVTGSGFLHHMVRNIVGTLADVGRGSLAVD 238

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++ + L A++R   GP AP  GL+  SVEY 
Sbjct: 239 EIPRILAARNRTAAGPTAPACGLFLHSVEYD 269


>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 =  277 bits (708), Expect = 1e-72,   Method: Composition-based stats.
 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|319639209|ref|ZP_07993960.1| tRNA pseudouridine synthase A [Neisseria mucosa C102]
 gi|317399393|gb|EFV80063.1| tRNA pseudouridine synthase A [Neisseria mucosa C102]
          Length = 281

 Score =  276 bits (707), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  Q
Sbjct: 13  QRWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALTSIAGERINTIVAGRTDTGVHATAQ 72

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   D +++L    V   F+ARF A  R Y Y + +  
Sbjct: 73  VVHFDTSVSRPEQAWVRGVNAHL--PDGVAVLLAQKVAPHFNARFDAYGRHYRYLLESSP 130

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  GR       LD   MR AA  L G HDF++FR+  CQA SPI+T+    ++  
Sbjct: 131 VRSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPIKTLYSTKISGT 190

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + +   +FLH  +R+ +G+L  VG G+ +  + E    A+ R    P    +GLY
Sbjct: 191 SRYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFESVFHAKSRLMAPPTFMSDGLY 250

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 251 LTGVDYP 257


>gi|171463727|ref|YP_001797840.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|226708657|sp|B1XV49|TRUA_POLNS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171193265|gb|ACB44226.1| tRNA pseudouridine synthase A [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 276

 Score =  276 bits (707), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 90/256 (35%), Positives = 134/256 (52%), Gaps = 12/256 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE------IVVVHGAGRTDSGV 55
           +R  + ++Y+GS Y GWQ Q N +++Q  +EKAI    GE       +    AGRTD+GV
Sbjct: 1   MRIALGLQYDGSPYSGWQTQVNHNTVQNELEKAISAFVGEQACVVKPINTITAGRTDTGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HAL QV HFD   E       + +N++L  S  I I     V ++F ARFSA  R Y+Y 
Sbjct: 61  HALGQVVHFDTNVEREDFSWVRGVNSFLSSS--IVINWAKPVSEEFCARFSAYEREYIYA 118

Query: 116 IITRQAPLALEKGRAWLIPKS----LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           +        +   RA  +        D E M+ +A+ L+G HDF++FRS  CQ+ +PI+T
Sbjct: 119 LHAGPCRSPMAHSRAGYLMLPPSQWFDIEAMQKSAECLIGEHDFSSFRSSECQSKTPIKT 178

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           I   ++ S    +  R+   +FLH  IR+ VG    +G GK TS  + + L A++R+   
Sbjct: 179 IYLIEIISKQPWLYFRIRGNAFLHHMIRNLVGCFLQIGQGKQTSQWMAEVLAAKNRQIAA 238

Query: 232 PLAPPEGLYFDSVEYS 247
           P    +GLY   + Y 
Sbjct: 239 PTFMADGLYLAKITYP 254


>gi|77360999|ref|YP_340574.1| tRNA pseudouridine synthase A [Pseudoalteromonas haloplanktis
           TAC125]
 gi|123587603|sp|Q3IF40|TRUA_PSEHT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76875910|emb|CAI87131.1| tRNA pseudouridylate synthase I [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 264

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ Y GWQRQ + +S+Q  +E A+  +    V +  AGRTD+GVH   QV
Sbjct: 1   MRVALGVEYNGARYSGWQRQSHVNSVQQEVETALSRICNHPVAIVCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V     +N  L     I+I     V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTDAPRDMVAFTLGMNTLL--PKDIAIRFAQPVADDFHARFSATARRYRYVIYNNPL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+          +LD   M+ A Q+L+G++DFT+FR+IHCQA++ IRTI H  V   G
Sbjct: 119 RGAVLNEGVTHFHHTLDETKMQEACQYLIGKYDFTSFRAIHCQANTAIRTIQHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +FLH  +R+  G L  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 SYVIIDIKANAFLHHMVRNITGCLMDIGLHKQQPVWLKELLDLKERAKASATAKAAGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>gi|325695572|gb|EGD37472.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK150]
          Length = 249

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|332366230|gb|EGJ43985.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK355]
          Length = 249

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYDFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L+ +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILEEKDRYLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|325124398|gb|ADY83921.1| tRNA-pseudouridine synthase I [Acinetobacter calcoaceticus PHEA-2]
          Length = 265

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 93/248 (37%), Positives = 132/248 (53%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKIADEPIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+ L     ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTNAIRPETGWLRGANSQL--PKDISIQWIKLMDENFHARFKATARRYRYIIYNA 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|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 =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 91/276 (32%), Positives = 135/276 (48%), Gaps = 32/276 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + ++Y+G+ + GWQ Q +  ++Q  +E A+   + + +    AGRTDSGVHAL Q+
Sbjct: 12  RRVVLGVQYDGASWQGWQTQPHRQTVQDQLEAALQRFSTQPIATTCAGRTDSGVHALEQI 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDK---------------------- 99
            HFD           +  NA+L    TI++     +                        
Sbjct: 72  VHFDTPIARDSFSWVRGTNAFL--PPTIAVRWACELPYVDDAAIASAASQAAELHGADRA 129

Query: 100 --------QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
                    FHARFSAI R+Y Y +        L  G+A    + LD + M  AAQHL+G
Sbjct: 130 GADSLSQFGFHARFSAIARTYHYVLYNHAVRTPLLAGKAGWTFRPLDADRMHRAAQHLIG 189

Query: 152 RHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
            HDFT+FR++ CQA SP+R ++   V   G++I   + A +FLH  +R+ VGSL +VG G
Sbjct: 190 EHDFTSFRAVECQAKSPVRKMESIAVRRHGDMIVFTLKANAFLHHMVRNIVGSLVVVGSG 249

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           K     + + L  +DR    P   P+GLY   V+Y 
Sbjct: 250 KQEPDWMGQVLALRDRSRAAPTFMPDGLYLARVDYP 285


>gi|315641606|ref|ZP_07896674.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
 gi|315482647|gb|EFU73175.1| tRNA pseudouridine synthase A [Enterococcus italicus DSM 15952]
          Length = 248

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 127/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    +IIEY+G+ Y GWQR  +   +IQG +EK +  +TGE + + G+GRTD+G HA  
Sbjct: 1   MRNIKLIIEYDGTRYQGWQRLGDSDKTIQGKLEKIVSQLTGETIELIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +      YL     I + ++  V ++FHAR++A+ + Y Y +   
Sbjct: 61  QVANFKTNCNKSLEEMHHFFLTYL--PKDIVVTSIDEVPERFHARYNAVSKQYSYYVRHA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P A ++   + + + LD E M  A   L G HDF  F ++     S +RTI+  ++  
Sbjct: 119 ELPSAFDRNYHFYVAEPLDWEAMTEACLRLTGAHDFLGFSALKKSKKSTVRTIESIEMEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              +I        FL+  +R  +G++  VG G+ T   ++   QA+ R+  G   P +GL
Sbjct: 179 EEAMIRFVFRGDGFLYKMVRIMMGTILAVGKGEMTVNQIDDIFQAKIRQAAGETVPAQGL 238

Query: 240 YFDSVEYS 247
           + D V Y 
Sbjct: 239 FLDGVFYE 246


>gi|22125494|ref|NP_668917.1| tRNA pseudouridine synthase A [Yersinia pestis KIM 10]
 gi|45442187|ref|NP_993726.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Microtus str.
           91001]
 gi|108808073|ref|YP_651989.1| tRNA pseudouridine synthase A [Yersinia pestis Antiqua]
 gi|108812343|ref|YP_648110.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|145599273|ref|YP_001163349.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides F]
 gi|162419146|ref|YP_001604969.1| tRNA pseudouridine synthase A [Yersinia pestis Angola]
 gi|165925379|ref|ZP_02221211.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165937079|ref|ZP_02225644.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166008316|ref|ZP_02229214.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166214223|ref|ZP_02240258.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167398935|ref|ZP_02304459.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167421195|ref|ZP_02312948.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167424547|ref|ZP_02316300.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167469280|ref|ZP_02333984.1| tRNA pseudouridine synthase A [Yersinia pestis FV-1]
 gi|170023770|ref|YP_001720275.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis YPIII]
 gi|229838336|ref|ZP_04458495.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229895366|ref|ZP_04510539.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides A]
 gi|229898902|ref|ZP_04514047.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229902698|ref|ZP_04517815.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|270490127|ref|ZP_06207201.1| tRNA pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294504649|ref|YP_003568711.1| tRNA pseudouridine synthase A [Yersinia pestis Z176003]
 gi|21958390|gb|AAM85168.1|AE013763_2 pseudouridylate synthase I [Yersinia pestis KIM 10]
 gi|45437051|gb|AAS62603.1| pseudouridylate synthase I [Yersinia pestis biovar Microtus str.
           91001]
 gi|108775991|gb|ABG18510.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|108779986|gb|ABG14044.1| tRNA pseudouridine synthase A [Yersinia pestis Antiqua]
 gi|145210969|gb|ABP40376.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides F]
 gi|162351961|gb|ABX85909.1| tRNA pseudouridine synthase A [Yersinia pestis Angola]
 gi|165914942|gb|EDR33554.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165922986|gb|EDR40137.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165992698|gb|EDR44999.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166204579|gb|EDR49059.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166960684|gb|EDR56705.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167051439|gb|EDR62847.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167056429|gb|EDR66198.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169750304|gb|ACA67822.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis YPIII]
 gi|229680145|gb|EEO76244.1| tRNA pseudouridine synthase A [Yersinia pestis Nepal516]
 gi|229688450|gb|EEO80521.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229694702|gb|EEO84749.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229701674|gb|EEO89700.1| tRNA pseudouridine synthase A [Yersinia pestis Pestoides A]
 gi|262362710|gb|ACY59431.1| tRNA pseudouridine synthase A [Yersinia pestis D106004]
 gi|270338631|gb|EFA49408.1| tRNA pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294355108|gb|ADE65449.1| tRNA pseudouridine synthase A [Yersinia pestis Z176003]
 gi|320014566|gb|ADV98137.1| tRNA pseudouridine synthase A [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 293

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 31  KIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQVV 90

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + +  
Sbjct: 91  HFVTSAVRKDAAWTMGVNSHL--PADIAVRWVKTVDNDFHARFSATARRYRYIIFSHRYR 148

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G 
Sbjct: 149 PAILAQGVTHCYMPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRHGA 208

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY  
Sbjct: 209 YIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLYLV 268

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 269 SVDYP 273


>gi|329768896|ref|ZP_08260324.1| tRNA pseudouridine synthase A [Gemella sanguinis M325]
 gi|328837259|gb|EGF86896.1| tRNA pseudouridine synthase A [Gemella sanguinis M325]
          Length = 262

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 73/249 (29%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +I  Y+GS Y G+Q Q N +++Q  IEK++  +  + V ++ +GRTDSGVHA  QV
Sbjct: 1   MRVVLICRYDGSRYHGFQIQPNNNTVQEEIEKSLRKIHKKNVRIYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           KA+NA   I   I I++  +V+ +FH R+++I+++Y Y++   + 
Sbjct: 61  LHFDTDLNIPTDGWVKAINAM--IPKDIRIVSAKVVNDEFHVRYNSIKKTYSYKLYLGRE 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
                         + + +  + A ++ +G HDF++F S +      +RTI  F ++   
Sbjct: 119 IDPFLINYVGQHKFNFNFDKAKEALKYFIGEHDFSSFCSKNTSVEDKVRTIYSFKMDRDN 178

Query: 181 --GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N+I   +    FL+  +R  +G+++ V  GK+    +++ L  ++R   GP A   G
Sbjct: 179 QNDNIINFEITGNGFLYNMVRIIIGTVQDVAAGKYEPEYIQEILAKKERSFSGPKADASG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLKEVLYD 247


>gi|262366637|gb|ACY63194.1| tRNA pseudouridine synthase A [Yersinia pestis D182038]
          Length = 293

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 93/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV 
Sbjct: 31  KIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQVV 90

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + +  
Sbjct: 91  HFVTSAVRKDAAWTMGVNSHL--PADIAVRWVKTVDNDFHARFSATARRYRYIIFSHRYR 148

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+           LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G 
Sbjct: 149 PAILAQGVTHCYMPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRHGA 208

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY  
Sbjct: 209 YIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLYLV 268

Query: 243 SVEYS 247
           SV+Y 
Sbjct: 269 SVDYP 273


>gi|325107879|ref|YP_004268947.1| tRNA pseudouridine synthase A [Planctomyces brasiliensis DSM 5305]
 gi|324968147|gb|ADY58925.1| tRNA pseudouridine synthase A [Planctomyces brasiliensis DSM 5305]
          Length = 278

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 89/265 (33%), Positives = 131/265 (49%), Gaps = 21/265 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               + + Y+GSGY+GWQ Q +  +IQ  +E+AI  +TG    V GAGRTD+GVHA+ QV
Sbjct: 4   RNIKLTLSYDGSGYYGWQVQPDRPTIQEHLERAIGNITGTPSRVAGAGRTDTGVHAIGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A F             AL + L   D I I         FHA +++  + Y Y ++  + 
Sbjct: 64  ACFRTESNIPAERFRPALQSQL--PDDIVIWKSEEAADDFHAGYASRWKQYRYLVLNEEI 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-- 179
           P    +  A  I   LD + M  AA  LVG+HDF +F S     ++ +RT+ H  VN   
Sbjct: 122 PRPQMRRYATRIGTRLDLDAMNEAASALVGKHDFRSFESQFPNKATSVRTVLHCRVNEAE 181

Query: 180 -----------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
                             G  + + + A  FL+  +R+ +G+L  +G G W ++  ++ L
Sbjct: 182 TCPLWQPGLGGQRFGQAVGRCVYLDIAADGFLYNMVRAIMGTLLKIGIGSWPASAGKEVL 241

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
           +A DR+  GP APPEGLY   VEY 
Sbjct: 242 EAMDRRVAGPTAPPEGLYLMHVEYD 266


>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 =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 136/248 (54%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  +++EY+G+ + G+Q Q  G  ++QG +E A+  + G    V  AGRTDSGVHAL 
Sbjct: 1   MRRLKLVLEYDGTDFAGFQLQARGERTVQGVLEAALARIPGARPKVTAAGRTDSGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H+D         + +ALNA L     + +L    V   +HAR+SA  R YLYR++ R
Sbjct: 61  MPVHYDTEDTVPVERVPQALNALL--PPDVRVLEAEEVPPDWHARYSARWRRYLYRVLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P AL++ R W +P+  D   +  AA+ LVG HDF  F   + +  + +R +    V +
Sbjct: 119 RQPTALDRHRVWWVPQPFDFPAIAAAARTLVGEHDFGAF--ANREKRATVRRLYQAHVEA 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + +  V   F+  Q+R+ VG+L  VG G+    D+ + L+  +R E G  APP+GL
Sbjct: 177 VGGELHLHFVGSGFVRGQVRAMVGTLVEVGLGRRPPEDVARLLENPERSEGGATAPPQGL 236

Query: 240 YFDSVEYS 247
           YF +  YS
Sbjct: 237 YFVAAGYS 244


>gi|313892355|ref|ZP_07825947.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
 gi|329121372|ref|ZP_08249998.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
 gi|313119214|gb|EFR42414.1| tRNA pseudouridine synthase A [Dialister microaerophilus UPII
           345-E]
 gi|327469781|gb|EGF15247.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
          Length = 266

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 123/247 (49%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y+G+ Y G+QRQ+NG ++Q ++EK +  +TG    ++   RTD+GVHA  Q
Sbjct: 1   MRNIWITVSYDGTEYAGFQRQENGFTVQEALEKVLKKLTGVHTTIYFVARTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F             A+N+ L     I +L    + + F  R +   ++Y Y +   +
Sbjct: 61  ECTFYTESSIPSERFKNAMNSLL--PCDIRVLKSKEMYEDFSVRKTNYGKTYAYILSEDK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   W   + LD + M+  A+ L G+HDFT+FR  +   + P+R I+   +   
Sbjct: 119 DINPFLRKYVWYTGRKLDLQKMKEVAKVLEGKHDFTSFRGNNSVPADPVRFINEVRIIRK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LI + V    FL+  +R+ VG+    G G  T   +++ L+A+DRK+ G  APP+GL 
Sbjct: 179 NSLIFVYVTGEGFLYHMVRNMVGAFVDAGRGIMTPERIKEILKAKDRKKLGVTAPPQGLA 238

Query: 241 FDSVEYS 247
              V + 
Sbjct: 239 LLKVYFE 245


>gi|146320154|ref|YP_001199865.1| tRNA pseudouridine synthase A [Streptococcus suis 98HAH33]
 gi|253751190|ref|YP_003024331.1| tRNA pseudouridine synthase A [Streptococcus suis SC84]
 gi|253753091|ref|YP_003026231.1| tRNA pseudouridine synthase A [Streptococcus suis P1/7]
 gi|253754913|ref|YP_003028053.1| tRNA pseudouridine synthase A [Streptococcus suis BM407]
 gi|166229843|sp|A4VZC6|TRUA_STRS2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145690960|gb|ABP91465.1| Pseudouridylate synthase [Streptococcus suis 98HAH33]
 gi|251815479|emb|CAZ51057.1| tRNA pseudouridine synthase A [Streptococcus suis SC84]
 gi|251817377|emb|CAZ55113.1| tRNA pseudouridine synthase A [Streptococcus suis BM407]
 gi|251819336|emb|CAR44702.1| tRNA pseudouridine synthase A [Streptococcus suis P1/7]
 gi|319757459|gb|ADV69401.1| tRNA pseudouridine synthase A [Streptococcus suis JS14]
          Length = 249

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  + +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQPHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   + S+ I ++++  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTSEDIDVVSVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTITVASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   
Sbjct: 179 DQQRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRGLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|257868757|ref|ZP_05648410.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257802921|gb|EEV31743.1| tRNA pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 246

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G  Y GWQR  +   +IQ  IE  +  +T E + + G+GRTD+G HA  
Sbjct: 1   MRNIKLTIEYDGKRYLGWQRLGDSDRTIQEKIESILTQMTNEKIEIIGSGRTDAGTHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +  P  + + LN YL     I I  ++   ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTASDLSPEKMLQFLNRYL--PQDIVIKEVAEASERFHARYNATGKQYSYYVWNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P   E+ R++  P+ LD + M+ A +  +G HDF  F ++     S  RTI+   +  
Sbjct: 119 PIPTVFERHRSFHCPQELDWDKMQAACEKFIGTHDFIGFSALKKTKKSTTRTIEELSLTR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+++  R     FL+  +R   G++  +G G    + +++    Q RK  G   P +GL
Sbjct: 179 EGDMLRFRFKGDGFLYKMVRIITGTILEIGAGTMDISAIDEIFTNQVRKAAGETVPSQGL 238

Query: 240 YFDSVEY 246
           + D+V Y
Sbjct: 239 FLDAVYY 245


>gi|254480499|ref|ZP_05093746.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2148]
 gi|214039082|gb|EEB79742.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2148]
          Length = 277

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 127/247 (51%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R    IEYNG+ Y GWQ Q + +  ++Q  +E A+  V    + VH AGRTD+GVH   Q
Sbjct: 11  RIACRIEYNGARYNGWQSQPHLNVLTVQQELESALSSVADHPLRVHCAGRTDTGVHGHCQ 70

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD      P      L A   ++  + +   ++V + FHARF A+ R Y Y I    
Sbjct: 71  IVHFDAPAARAPKAWV--LGANASMAKDVRVHWATVVPESFHARFCAVARRYRYVIANTL 128

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+  G+       LD   M  AAQ L+G  DF+ FR+  CQ++SP+R +    V   
Sbjct: 129 VRPAVLVGQVSWYRYPLDAAIMDKAAQSLLGEQDFSAFRAAACQSNSPMRNVHSVAVRRI 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ + + A +FLH  +R+ VGSL  VG G+     + + L A+DR +    A P GLY
Sbjct: 189 GDLVVVDIQANAFLHHMVRNIVGSLLAVGSGRKPEAWIGQLLAARDRTQAADTAAPHGLY 248

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 249 LADVLYP 255


>gi|226322792|ref|ZP_03798310.1| hypothetical protein COPCOM_00564 [Coprococcus comes ATCC 27758]
 gi|225208773|gb|EEG91127.1| hypothetical protein COPCOM_00564 [Coprococcus comes ATCC 27758]
          Length = 259

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 133/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+G+ Y GWQRQ+N   ++QG +E+ I  + G+  VV G+GRTDSGVHAL 
Sbjct: 1   MNTYRITVAYDGTAYRGWQRQENTELTVQGILERRISEIAGKKTVVSGSGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q     L +E       K LNA L   + I +L++S   + FHAR SA+ + Y Y+I  R
Sbjct: 61  QECSLYLEQEIDMDSFKKQLNALL--PEDIRVLDISREKRDFHARKSAVGKCYEYQIDLR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +   +  P  +D   M  AA++L+G HDF+ F  +  +    +RTI    +  
Sbjct: 119 DKMEVFHRKYRFHFPHPVDIAAMEQAAEYLMGTHDFSAFTDLK-EDKDTVRTIYAVGIVY 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + +  +   FL+  +R   G+L  VG GK  + ++ + L+A+DRK+ G  AP +GL
Sbjct: 178 EKDTLTLSWIGDGFLYHMVRILTGTLLDVGIGKIKAEEIPEILKAKDRKKSGFPAPAKGL 237

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 238 FLGRVFY 244


>gi|323350454|ref|ZP_08086117.1| tRNA pseudouridine synthase A [Streptococcus sanguinis VMC66]
 gi|322123391|gb|EFX95069.1| tRNA pseudouridine synthase A [Streptococcus sanguinis VMC66]
          Length = 249

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +    +   FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFLGNGFLYKQIRNMVGTLLKIGNKRMPVEQVQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|258513673|ref|YP_003189895.1| tRNA pseudouridine synthase A [Desulfotomaculum acetoxidans DSM
           771]
 gi|257777378|gb|ACV61272.1| tRNA pseudouridine synthase A [Desulfotomaculum acetoxidans DSM
           771]
          Length = 250

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 126/252 (50%), Gaps = 8/252 (3%)

Query: 1   MIR---YCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R     +I+ Y+G+ Y G+Q QK     +IQG +++ +  +  E + V  AGRTDSGV
Sbjct: 1   MNRGRNIKVILAYDGTNYHGFQIQKGKRLPTIQGVLQRELSHLAKETITVTTAGRTDSGV 60

Query: 56  HALRQVAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           HA  QV +F      +P   +  ALN+ L     I  L+   VD  FHAR+SA+ ++Y Y
Sbjct: 61  HARGQVFNFFTGNWQIPVDRVIYALNSVL--PPDIRALSAEEVDLGFHARYSALAKTYCY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I   Q      +  ++     LD ++MR A  H+ G HDF +F +      S IRTI  
Sbjct: 119 YISRDQIVSPFTRLYSYQYNYPLDLDDMRQAVLHITGEHDFKSFMASGSLVKSTIRTIYQ 178

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            D+     ++        FL+  +R   G+L  VG GK   +++E  L+  DRK  G   
Sbjct: 179 IDLIEKDKMLIFTFRGNGFLYHMVRIITGTLLQVGTGKIHYSEIETILKKCDRKSAGATV 238

Query: 235 PPEGLYFDSVEY 246
           P  GL+ + VEY
Sbjct: 239 PALGLFLERVEY 250


>gi|146317967|ref|YP_001197679.1| tRNA pseudouridine synthase A [Streptococcus suis 05ZYH33]
 gi|166229845|sp|A4VT40|TRUA_STRSY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145688773|gb|ABP89279.1| Pseudouridylate synthase [Streptococcus suis 05ZYH33]
          Length = 249

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  + +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQPHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   + S+ I ++++  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTSEDIDVVSVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDNVRTITVASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   
Sbjct: 179 DQQRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRGLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>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 =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 92/251 (36%), Positives = 137/251 (54%), 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    +I++     VD+ FHARF A  R Y Y + T  
Sbjct: 61  VIHLDTALEREPFSWVRGVNAFL--PPSIALQWALPVDQGFHARFLAFERMYYYALYTGP 118

Query: 121 APLALEKGRAWL----IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             + L  GRA        + 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|317123065|ref|YP_004103068.1| tRNA pseudouridine synthase A [Thermaerobacter marianensis DSM
           12885]
 gi|315593045|gb|ADU52341.1| tRNA pseudouridine synthase A [Thermaerobacter marianensis DSM
           12885]
          Length = 298

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 80/244 (32%), Positives = 113/244 (46%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
              ++ Y+G+ + GWQRQ    ++Q  +E A+  + G  V V  AGRTD+GVHA  QV H
Sbjct: 46  LRAVLAYDGTDFAGWQRQPRQRTVQQVVEDALERLLGHPVRVTAAGRTDAGVHARAQVIH 105

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           +   R +    L  AL   L     +  +        FHAR+SA R++Y Y +     P 
Sbjct: 106 WRTPRPFPVDRLVPALRGLL--PADVVAVEAGEAPPGFHARYSARRKTYAYHVWRDPVPD 163

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
            L +   W +P  LD + M  AA+ L G HDF  F++         RT+    V   G L
Sbjct: 164 PLHRRWQWHLPLDLDVDAMVEAARRLEGTHDFAPFKAAGSPVRRTRRTLYRCAVEERGPL 223

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   + A  FL    R  VG+L  +G G+W +  +E  L    R   GP AP  GL    
Sbjct: 224 LRFVLEADGFLMHMARGIVGTLVEIGRGRWQADRVEAILAEGRRDLAGPTAPAHGLVLWQ 283

Query: 244 VEYS 247
           V Y 
Sbjct: 284 VVYD 287


>gi|326790769|ref|YP_004308590.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
 gi|326541533|gb|ADZ83392.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
          Length = 246

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 122/248 (49%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y + I Y+GS Y G+Q+Q      +IQG +E  +     E + +  +GRTD+GVH+ 
Sbjct: 1   MTNYKLTIAYDGSKYNGFQKQSKHPEKTIQGRLENVLTQCFEEDIQIIASGRTDAGVHSK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV +F       P  +   L+ YL     I+IL LSI   +FHAR++ +R+ Y Y I  
Sbjct: 61  GQVCNFHAEHYLEPTTVLNYLSNYL--PQDIAILELSIASPRFHARYNVLRKCYTYTIDN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                      A+ +   LD   M+ AA +L+G HDF  F S+  +  S  R + + D+ 
Sbjct: 119 GLFANPFTLKYAYHLASPLDISRMQAAANYLLGTHDFKAFTSLKSKTKSTTRHLFNIDIT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G++I++      FL   +R   G+L  VG G+ +  ++   L  Q R E G  AP  G
Sbjct: 179 QEGSMIKLTYEGNGFLQHMVRILTGTLIEVGLGERSPEEMLVLLNNQIRSEAGFTAPAHG 238

Query: 239 LYFDSVEY 246
           L    V+Y
Sbjct: 239 LCMQRVDY 246


>gi|332359236|gb|EGJ37057.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK49]
          Length = 249

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 180 FGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERKFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|327462829|gb|EGF09151.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1057]
          Length = 249

 Score =  276 bits (706), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVERVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELSLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRH 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLFKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|329116632|ref|ZP_08245349.1| tRNA pseudouridine synthase A [Streptococcus parauberis NCFD 2020]
 gi|326907037|gb|EGE53951.1| tRNA pseudouridine synthase A [Streptococcus parauberis NCFD 2020]
          Length = 249

 Score =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+GSG+ G+QRQ +  S+Q  IEK +  +  G+++ +HGAGRTD+GVHA  
Sbjct: 1   MTRYKATISYDGSGFSGFQRQPHARSVQEEIEKTLLKLYKGQVIKIHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     +  AL+   +  D I  + +  V   +H R+   +++Y + +   
Sbjct: 61  QVIHFDLPLERDIEKIRFALDT--QTPDDIDFIKVEKVADDYHCRYLKHKKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  LD   M  A + LVG HDFT F +      + +RTI    +  
Sbjct: 119 RPKNPMMRNYATHYPYPLDISLMDEAIKDLVGTHDFTGFTASGTSIENKVRTISEAKLTY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ Q+R+ VG+L  +G+ +   + +++ L+ ++R+  GP A   
Sbjct: 179 DAKRNFLIFSFTGNGFLYKQVRNMVGTLLKIGNQRMPVSQVQRILEEKNRQLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|330502915|ref|YP_004379784.1| tRNA pseudouridine synthase A [Pseudomonas mendocina NK-01]
 gi|328917201|gb|AEB58032.1| tRNA pseudouridine synthase A [Pseudomonas mendocina NK-01]
          Length = 287

 Score =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 121/247 (48%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQ 60
           R  + +EY G+ Y G+QRQ     SIQG +E A+  V G   V +H AGRTD+ VH+  Q
Sbjct: 19  RVALGLEYKGARYRGFQRQGGKVASIQGCLEDALSKVAGGAPVTIHCAGRTDASVHSSGQ 78

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E          N  L     IS+    ++   FHARFSA+ R Y Y I    
Sbjct: 79  VVHFDTTVERSLHAWVMGANMNL--PSDISVTWAKVMPAHFHARFSAMARRYRYVIYNDP 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A          + LD   MR AA  LVG HDF+ FR+  CQA SPI+T+ H  +   
Sbjct: 137 IRPAHMAEEVTWNHRPLDVARMREAALALVGTHDFSAFRATRCQAKSPIKTVHHLQLIEH 196

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +FLH  +R+  G L  +G G+       + L+  DR   G  A P GLY
Sbjct: 197 GRFIVLDIRANAFLHHMVRNIAGVLMTIGAGERPPEWAREVLERGDRHSGGVTAHPYGLY 256

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 257 LVQVDYP 263


>gi|254883215|ref|ZP_05255925.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_3_47FAA]
 gi|254836008|gb|EET16317.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_3_47FAA]
          Length = 263

 Score =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 123/247 (49%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +
Sbjct: 7   MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMI 66

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+ 
Sbjct: 67  AHFDYDRELDCVQITEKLNRLL--PPDIAVYAVKRVKDDAHARFDATYRTYKYYVTTRK- 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-F 180
                +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     
Sbjct: 124 -DPFNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVS 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+
Sbjct: 183 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALF 242

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 243 LVDVGYP 249


>gi|313888069|ref|ZP_07821747.1| tRNA pseudouridine synthase A [Peptoniphilus harei ACS-146-V-Sch2b]
 gi|312846024|gb|EFR33407.1| tRNA pseudouridine synthase A [Peptoniphilus harei ACS-146-V-Sch2b]
          Length = 244

 Score =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 122/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I Y+G+ + G+Q Q N  +++G +   I       V +  AGRTD GVHA  Q
Sbjct: 1   MKNILIKINYDGTNFHGFQLQPNERTVEGELNLGIEKTVKHPVKIFYAGRTDRGVHAEGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F          L K LN  L   + +S+++   V   FHARF A  + Y Y +   +
Sbjct: 61  YANFYSDTTIDIGNLPKVLNFNL--PEDVSVVDAKYVPDAFHARFDAKLKKYRYVVHRSR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL + RA+  P  +D + MR A   L+G HDF +F          IR+I+  DV   
Sbjct: 119 YRHALLRNRAYEYPYDVDPDRMREALASLIGEHDFNSFMGRGAIVKDSIRSIERIDVIED 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +    VA+SFL   IR   G++  +G G+     +++AL+ + RK  GP AP  GLY
Sbjct: 179 GDFLYFDFVAKSFLKNMIRIVTGTVLEIGRGQREIEYMKEALEKKSRKAAGPTAPACGLY 238

Query: 241 FDSVEY 246
              V+Y
Sbjct: 239 LLDVKY 244


>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 =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 93/248 (37%), Positives = 132/248 (53%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  +  E +V+HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKIADEPIVLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+ L     ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTNAIRPETGWLRGANSQL--PKDISIQWIKLMDENFHARFKATARRYRYIIYNA 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|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 =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 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|78780010|ref|YP_398122.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9312]
 gi|123768929|sp|Q318K9|TRUA_PROM9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78713509|gb|ABB50686.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9312]
          Length = 268

 Score =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 124/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS Y GWQRQKN +++Q ++E+A+F +T ++V    AGRTD+GVHA  Q
Sbjct: 1   MKRIALLVQYDGSNYSGWQRQKNATTVQETLERALFKITHQVVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF++            LN  L     I IL    V   +H+ +SA+ R Y Y I   +
Sbjct: 61  VVHFNIDCVIPANSYSDILNGLL--PSAIRILESVEVKDSWHSCYSAMYRHYRYVINNSK 118

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD   M  A++ + G HDF  F+    Q  + I  I + ++  
Sbjct: 119 FPNLFINNWSWHRYQKILDEVLMSNASKLMEGEHDFFAFQKSGSQRKNSITKIKNVEIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +          Q + +    AP +GL
Sbjct: 179 VEDLILVDIKATGFLYGMVRLIVGQLVLVGEKKISPEIFTDIWVNQKKNDVKESAPAKGL 238

Query: 240 YFDSVEYS 247
            F +  Y 
Sbjct: 239 CFVNAVYE 246


>gi|146282143|ref|YP_001172296.1| tRNA pseudouridine synthase A [Pseudomonas stutzeri A1501]
 gi|145570348|gb|ABP79454.1| tRNA-pseudouridine synthase I [Pseudomonas stutzeri A1501]
          Length = 286

 Score =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 99/247 (40%), Positives = 127/247 (51%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           R  + +EY GS Y G+QRQ+    SIQ S+E A+  V G   V +  AGRTD+ VHA  Q
Sbjct: 19  RIALGVEYKGSRYRGFQRQRAGVPSIQESLENALTRVAGGHPVTLSCAGRTDALVHASGQ 78

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E          N  L     IS+     +   F ARFSA+ R Y Y I   Q
Sbjct: 79  VVHFDTPVERSMHAWVMGANMNL--PPDISVTWAKKMPPHFDARFSAMARRYRYVIYNDQ 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A          + LD E MR AA  LVG HDF+ FR+  CQA SPI+TI H ++  F
Sbjct: 137 IRPAHMAEEVTWNHRPLDIERMRAAAAALVGTHDFSAFRARQCQAKSPIKTIHHLELLQF 196

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI I V A +FLH  +R+F G L  +G G+       + L+++ R+  G  A P GLY
Sbjct: 197 GRLIVIDVRANAFLHHMVRNFAGVLMTIGAGERPVEWAAQVLESRVRRTGGVTAHPYGLY 256

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 257 LVEVDYP 263


>gi|317403279|gb|EFV83796.1| pseudouridylate synthase I [Achromobacter xylosoxidans C54]
          Length = 268

 Score =  275 bits (705), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 85/244 (34%), Positives = 132/244 (54%), Gaps = 4/244 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALRQVAH 63
           M + Y+GS + GWQ Q +  ++Q ++E A+    G  + V    AGRTD+GVH   QV H
Sbjct: 1   MGLAYDGSAWQGWQTQPHRQTVQDTLEAALAQFCGVTDAVPTICAGRTDTGVHGAMQVIH 60

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            D   +       + +NA+L    +IS+     V   FHARFSA  R+Y+Y +   +   
Sbjct: 61  LDTTLDRRMESWVRGVNAFL--PSSISVQWAKAVPDAFHARFSARARTYVYLLWRGRVRP 118

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           AL  GRA    + LD   MR AA  L+G HDF++FRS  CQA  P+R +   D++  G  
Sbjct: 119 ALWAGRAGWCYQPLDVGAMRAAANALLGEHDFSSFRSSQCQAKHPVRIMHRLDIDERGPF 178

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   + A +FLH  +R+ +G+L  +G G+ +   + + L  +DR+   P   P+GLY  +
Sbjct: 179 LVFTLRANAFLHHMVRNIMGALLQIGQGRESVDWMAQLLSWRDRRRGAPTFSPDGLYLSA 238

Query: 244 VEYS 247
           ++Y 
Sbjct: 239 IDYP 242


>gi|149365240|ref|ZP_01887275.1| tRNA pseudouridine synthase A [Yersinia pestis CA88-4125]
 gi|153950548|ref|YP_001400399.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
 gi|218929838|ref|YP_002347713.1| tRNA pseudouridine synthase A [Yersinia pestis CO92]
 gi|25009503|sp|Q8ZD27|TRUA_YERPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901277|sp|Q668W9|TRUA_YERPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166991167|sp|A7FGM1|TRUA_YERP3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|115348449|emb|CAL21385.1| tRNA pseudouridine synthase A [Yersinia pestis CO92]
 gi|149291653|gb|EDM41727.1| tRNA pseudouridine synthase A [Yersinia pestis CA88-4125]
 gi|152962043|gb|ABS49504.1| tRNA pseudouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
          Length = 264

 Score =  275 bits (704), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF              +N++L     I++  +  VD  FHARFSA  R Y Y I + + 
Sbjct: 61  VHFVTSAVRKDAAWTMGVNSHL--PADIAVRWVKTVDNDFHARFSATARRYRYIIFSHRY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G
Sbjct: 119 RPAILAQGVTHCYMPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  +G G    T + + L  +DR      A  +GLY 
Sbjct: 179 AYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKADGLYL 238

Query: 242 DSVEYS 247
            SV+Y 
Sbjct: 239 VSVDYP 244


>gi|258512640|ref|YP_003186074.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257479366|gb|ACV59685.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
          Length = 262

 Score =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  +++ Y+GSG+ G+ RQ+   ++QG +E  +  + G  ++V G+GRTD GVHA  QV
Sbjct: 5   RRIRLVLGYDGSGFHGFARQEGLRTVQGVLEDELRRMLGVDILVEGSGRTDRGVHARAQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFDL        +   L   L     +   +   VD+ FHARFS +R++Y Y +     
Sbjct: 65  VHFDLPYGPPADRMVHVLRRRL--PADLLPRDAGEVDEGFHARFSVVRKTYRYTLDLAPL 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P       +W  P+ LD   M+ AA+HL+G HDFT+F +   +    +R ID  +    G
Sbjct: 123 PSLYWYRFSWHHPEPLDLAAMQEAARHLLGEHDFTSFCAAEARQRDKVRRIDRVEFRQDG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I      FL   +R  VG+L  VG G+     +   L+A+DR+  G  APP GL  
Sbjct: 183 SRLHIEFEGNGFLQYMVRILVGTLVKVGRGQERPDRIPLILEARDRRLAGETAPPHGLCL 242

Query: 242 DSVEYS 247
            +VEY 
Sbjct: 243 WNVEYP 248


>gi|313672355|ref|YP_004050466.1| tRNA pseudouridine synthase a [Calditerrivibrio nitroreducens DSM
           19672]
 gi|312939111|gb|ADR18303.1| tRNA pseudouridine synthase A [Calditerrivibrio nitroreducens DSM
           19672]
          Length = 248

 Score =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 79/242 (32%), Positives = 130/242 (53%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
              +EY+G+ + GWQ QK   ++Q  IE A+  +  + + + G+GRTD+GVHAL QV +F
Sbjct: 9   KCTVEYDGTEFHGWQFQKGLVTVQSEIEAALSKIYKKQIHIIGSGRTDAGVHALAQVFNF 68

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              +      L   LN+ L    +I I  +  VD  FHA+ SA  ++YLY+I+  + P A
Sbjct: 69  RAEKYIESEPLNLGLNSLL--PRSIIIKKVEDVDVNFHAQKSAKSKTYLYKILNSELPSA 126

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             + R W +  S+D E         VG  DF+   ++     + +RTI+  +V    ++I
Sbjct: 127 FLRNRVWWVRNSIDIEIFSEILSQFVGTFDFSAMCTMKSLKENSVRTINFINVYKTEHII 186

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FLH  +R+ +G+   +   K   + + + ++++DRK+ GP APP+GLY   V
Sbjct: 187 NIEINANGFLHNMVRNIIGTAFFIYRKKLHPSTVMEIIESRDRKKGGPTAPPQGLYLKEV 246

Query: 245 EY 246
            Y
Sbjct: 247 FY 248


>gi|294778889|ref|ZP_06744305.1| tRNA pseudouridine synthase A [Bacteroides vulgatus PC510]
 gi|294447198|gb|EFG15782.1| tRNA pseudouridine synthase A [Bacteroides vulgatus PC510]
          Length = 257

 Score =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 123/247 (49%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +
Sbjct: 1   MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+ 
Sbjct: 61  AHFDYDRELDCVQITEKLNRLL--PPDIAVYAVKRVKDDAHARFDATYRTYKYYVTTRK- 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-F 180
                +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     
Sbjct: 118 -DPFNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVS 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+
Sbjct: 177 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALF 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LVDVGYP 243


>gi|260881651|ref|ZP_05404943.2| tRNA pseudouridine synthase A [Mitsuokella multacida DSM 20544]
 gi|260848088|gb|EEX68095.1| tRNA pseudouridine synthase A [Mitsuokella multacida DSM 20544]
          Length = 264

 Score =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 123/247 (49%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
               + + Y+G+ Y G+QRQ     ++Q  +E+ +  + G+ + +  AGRTD+GVHA  Q
Sbjct: 14  RNIVLKVAYDGTAYHGFQRQTPPIVAVQNILEEKLQTIFGDTIELAAAGRTDAGVHAYGQ 73

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F          + +A N+ L   D I +      D  F AR SA  ++Y+YRI   +
Sbjct: 74  VVNFFTDGRIPVDRIARAANSLL--PDDIVVRAAGEADTDFSARHSAKSKTYVYRIQQGE 131

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P  +    AW I + LD   MR A   ++G HDF+ FR+      SP+RT+    +   
Sbjct: 132 VPDPMTARYAWYIRRPLDVAAMREALGAILGTHDFSAFRASGGAPMSPVRTMYEATIEEA 191

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +  R+    FL+  +R+ +G+L  VG G  T     + L+ +DR +    AP  GL
Sbjct: 192 AGQQLICRIHGSGFLYHMVRNIIGTLANVGLGVLTPARFGEILEGRDRTKASATAPACGL 251

Query: 240 YFDSVEY 246
           Y + V+Y
Sbjct: 252 YLEHVDY 258


>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 =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 139/251 (55%), Gaps = 6/251 (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    +I++     VD+ FHARF A  R Y Y + T  
Sbjct: 61  VIHLDTTLDRTTFSWVRGINAFL--PPSIALQWARPVDESFHARFLAFERMYYYALYTGP 118

Query: 121 APLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             + L  GRA  +     + 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 EGLYFDSVEYS 247
           +GLY   V+Y 
Sbjct: 239 DGLYLADVKYP 249


>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 =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 118/249 (47%), Positives = 151/249 (60%), Gaps = 6/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           R+ +++EY+G G+ GWQRQK     SIQG +E A   +T G  V    AGRTD+GVHA  
Sbjct: 21  RWAVLMEYDGRGFVGWQRQKTTGLLSIQGLLEDAATRLTNGHDVRSITAGRTDAGVHASG 80

Query: 60  QVAH--FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           QVAH  F          +   LN Y+K    + +L    V  Q++ARFSAI R+Y YRI+
Sbjct: 81  QVAHLDFPADVTLSSATVRDGLNFYMK-PHPVVVLMARPVLPQWNARFSAISRAYRYRIL 139

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R A  ALE G+ W +   LD + MR AA HL+GRHDFT+FR+  CQA SP+RT+D  DV
Sbjct: 140 NRAARPALEDGQVWHVRAPLDVDGMRQAAAHLLGRHDFTSFRATACQARSPVRTLDRLDV 199

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  + I   ARSFLH Q+R+  G+LKLVG+G+W    +  AL A DR+  GP APPE
Sbjct: 200 KREGEYVVIEAAARSFLHHQVRNMAGTLKLVGEGRWEPAQVAHALAACDRRAAGPTAPPE 259

Query: 238 GLYFDSVEY 246
           GL    V Y
Sbjct: 260 GLCLTGVGY 268


>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 =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 91/251 (36%), Positives = 134/251 (53%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GWQ Q + +++Q  +E AI    G  ++   AGRTD+GVHAL Q
Sbjct: 1   MNRIALGLHYDGAAFSGWQSQPHRNTVQDHLEDAIERFAGVRLLTTVAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D      P    + +NA+L    +I++     VD  FHARF A  R Y Y + T  
Sbjct: 61  VIHLDTELVREPFSWVRGVNAFL--PPSIALQWALPVDVGFHARFLAYERMYYYALYTGP 118

Query: 121 APLALEKGRAWL----IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             + +  GRA        + LD E MR AA HL+G HDF+ FR+  CQA SP++T+    
Sbjct: 119 HRVPMVHGRAGYQMLPPGQRLDVEAMRAAAAHLIGEHDFSAFRAAECQAKSPVKTMYDVT 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   GN + +R  A +FLH  +R+ +G L  VG  ++    + + L  +DRK   P   P
Sbjct: 179 IRDDGNWVFLRFRASAFLHHMVRNLMGCLVAVGRRRYPPDWMAQVLAGRDRKLAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V+Y 
Sbjct: 239 DGLYLVGVKYP 249


>gi|225025215|ref|ZP_03714407.1| hypothetical protein EIKCOROL_02112 [Eikenella corrodens ATCC
           23834]
 gi|224941973|gb|EEG23182.1| hypothetical protein EIKCOROL_02112 [Eikenella corrodens ATCC
           23834]
          Length = 269

 Score =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + + Y+GS +FGWQ+Q +G  ++Q ++E A+  +  E + V  AGRTD+GVHA  QV
Sbjct: 8   RRALFVSYDGSRFFGWQKQADGIATVQSALEAALSELAQERISVVTAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA L   + +++  +  V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDSAARRPDQAWVRGVNALL--PEGVAVWRVQDVAPEFHARFDACGRRYRYLLQSAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L  GRA     +LD   MR AA  LVG HDF++FR+  CQA SP++T+    +    
Sbjct: 126 RSPLLVGRAGWTHYALDMAAMRQAAALLVGEHDFSSFRAAECQAKSPVKTLYRVALCGTP 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ +     +FLH  +R+ +G+L  VG GK +       L A+ RK   P   P+GLY 
Sbjct: 186 ELMAVDFHGNAFLHHMVRNLMGALVYVGCGKLSVDGFAGLLAARSRKLAPPTFMPDGLYL 245

Query: 242 DSVEYS 247
             ++Y 
Sbjct: 246 TGIDYP 251


>gi|126658015|ref|ZP_01729167.1| tRNA pseudouridine synthase A [Cyanothece sp. CCY0110]
 gi|126620653|gb|EAZ91370.1| tRNA pseudouridine synthase A [Cyanothece sp. CCY0110]
          Length = 285

 Score =  275 bits (704), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 118/246 (47%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y GS + GWQRQ N  ++Q  IE +I  V G    +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYQGSRFHGWQRQPNQRTVQEVIESSIAEVLGYHTPIHGAGRTDAGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD +    P    + LN  L   D I I   + V   +HARFSA+ R Y Y   T + P
Sbjct: 72  HFDYISPIPPQRWVEILNQRL--PDDILIRGCAEVSLTWHARFSALWRRYRYSFYTDKCP 129

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W      LD E M+ A   L+GRH    FR            +        G
Sbjct: 130 NLFVRPFSWHYYYEPLDAELMQKALTPLLGRHHLAAFRRAGSHRHHSWVEVQETRCYRQG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK + T+  +  Q Q R++    AP +GL  
Sbjct: 190 QFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLTNFTEIWQNQRREQVKYSAPAKGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|323485798|ref|ZP_08091133.1| tRNA pseudouridine synthase A [Clostridium symbiosum WAL-14163]
 gi|323693150|ref|ZP_08107368.1| pseudouridylate synthase [Clostridium symbiosum WAL-14673]
 gi|323400786|gb|EGA93149.1| tRNA pseudouridine synthase A [Clostridium symbiosum WAL-14163]
 gi|323502633|gb|EGB18477.1| pseudouridylate synthase [Clostridium symbiosum WAL-14673]
          Length = 265

 Score =  275 bits (703), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 86/255 (33%), Positives = 135/255 (52%), Gaps = 12/255 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
              ++++Y+G+ Y GWQ+Q N   ++QG +E  +  + G  V VHG+GRTD+GVHAL QV
Sbjct: 5   NIRILLQYDGTRYDGWQKQGNTQQTVQGKLEAVLSCLAGGPVEVHGSGRTDAGVHALGQV 64

Query: 62  AHFDLV---------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           A+F L               + +   LN YL   + I +L       +FH+R +A+ ++Y
Sbjct: 65  ANFHLPLSVFCGSQTEAADMIRIKNYLNEYL--PEDIRVLVAEEARPRFHSRLNALSKTY 122

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YRI T       E+   + + K  D E M+ AA  LVG HDF  F S+     S +RTI
Sbjct: 123 IYRIETADKNDVFERKYRYGLGKEPDLEIMKRAASILVGTHDFRAFSSLKKTKKSTVRTI 182

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           +  D+   G  +EI +    FL+  +R  VG+L   G  + +   +++AL++ DR   G 
Sbjct: 183 NRIDIRRDGTQLEILLEGNGFLYNMVRIIVGTLVEAGLLERSVQSVKEALESLDRSLAGR 242

Query: 233 LAPPEGLYFDSVEYS 247
            AP +GL+  +V Y 
Sbjct: 243 TAPAKGLFLAAVAYE 257


>gi|315127206|ref|YP_004069209.1| tRNA pseudouridine synthase A [Pseudoalteromonas sp. SM9913]
 gi|315015720|gb|ADT69058.1| tRNA pseudouridine synthase A [Pseudoalteromonas sp. SM9913]
          Length = 264

 Score =  275 bits (703), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ Y GWQRQ + +S+Q  +EKA+  +    V +  AGRTD+GVH   QV
Sbjct: 1   MRVALGVEYNGARYSGWQRQSHVNSVQQEVEKALSRICNHPVEIVCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V     +N  L     I+I     V + FHARFSA  R Y Y I     
Sbjct: 61  VHFDTHAEREMVAFTLGMNTLL--PKDIAIRFAQPVAEDFHARFSATARRYRYVIYNYAF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD   M+ A Q+L+G HDFT+FR++HCQA++  RTI H  V   G
Sbjct: 119 RGAVLNEGVTHFHHPLDEVKMQQACQYLLGEHDFTSFRALHCQANTATRTIHHLSVQRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +FLH  +R+  G L  +G  K     L++ L  ++R +    A   GLY 
Sbjct: 179 AYVIIDIKANAFLHHMVRNITGCLMDIGLHKHEPIWLKELLDVKERAKASATAKAAGLYL 238

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 239 VDVDYP 244


>gi|262375036|ref|ZP_06068270.1| tRNA pseudouridine synthase A [Acinetobacter lwoffii SH145]
 gi|262310049|gb|EEY91178.1| tRNA pseudouridine synthase A [Acinetobacter lwoffii SH145]
          Length = 265

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + IE+ G  Y GWQ +Q   +S+Q +IEK +  V  + + +HGAGRTD+GVHA  
Sbjct: 1   MQRFAVGIEFCGMHYRGWQTQQPGVASVQETIEKVLSKVADQPISLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D  FHARF A  R Y Y +   
Sbjct: 61  MVAHFDTDAVRSERGWLMGCNSQL--PKDISIQWIKEMDHSFHARFKAQARRYRYVVYNH 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   +   LD E M  AA+   G H+F +FR+  CQ++ P+R + H  +  
Sbjct: 119 PVRPALLHKQVTHVYAPLDVEQMIYAAKKFEGTHNFESFRAAACQSNQPVRHVSHCRLIQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ +G L  +G G + +  ++    A+DRK  G  AP +GL
Sbjct: 179 HGQYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYAADHIDNIFAAEDRKAAGVTAPADGL 238

Query: 240 YFDSVEYS 247
           YF   +Y 
Sbjct: 239 YFIHADYP 246


>gi|224542274|ref|ZP_03682813.1| hypothetical protein CATMIT_01449 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524816|gb|EEF93921.1| hypothetical protein CATMIT_01449 [Catenibacterium mitsuokai DSM
           15897]
          Length = 245

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   I+ Y+G+ ++GWQ Q +  ++Q  I+KAI+ +T E V +H +GRTD+GVHA+ QV
Sbjct: 1   MRIKCIVTYDGTHFYGWQIQPDKRTVQEEIQKAIYKITHEEVTIHSSGRTDAGVHAVGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+ +E       +ALN +L   D I I +  IVD+ FHAR+SA ++ Y Y + T+  
Sbjct: 61  FHFDINKEIPEKQWIRALNNFL--PDDIYIKDSFIVDESFHARYSAKKKEYRYLVSTKPY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +E+   +   +SLD E MR  A+  +G HDF +F   +      IR I+  D+    
Sbjct: 119 -NPIERLYVYQHNRSLDIEAMRECAKIFLGEHDFASFCVFNG-LGDTIRVIETIDIQEKD 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++ +R +   F    +R   G+L  VG    T   +E  L ++ +K+C   A PEGLY 
Sbjct: 177 GIVTMRFIGNGFRRYMVRLITGALIQVGSHWRTKEFVEDLLNSKGKKKCLFKAKPEGLYL 236

Query: 242 DSVEYS 247
             V Y 
Sbjct: 237 QEVYYE 242


>gi|324992392|gb|EGC24313.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK405]
 gi|324996086|gb|EGC27997.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK678]
 gi|327460621|gb|EGF06956.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1]
 gi|327472350|gb|EGF17781.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK408]
 gi|327488890|gb|EGF20688.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1058]
          Length = 249

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFISVEQVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMLVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>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 =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 110/248 (44%), Positives = 146/248 (58%), Gaps = 1/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALR 59
           M R+ + +EY+G G+ GWQRQ+NG S+Q  +E A   + G  V     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 YFDSVEYS 247
              +V Y 
Sbjct: 241 VLVAVRYE 248


>gi|116515069|ref|YP_802698.1| hypothetical protein BCc_129 [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256923|gb|ABJ90605.1| pseudouridylate synthase I [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 269

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +++   +EY+GS Y GWQ+QK+  +IQ  IE A+  +    + V  AGRTD GVHA+ Q+
Sbjct: 1   MKFVFGVEYDGSIYHGWQKQKSVLTIQECIEHALSKIANSKIEVICAGRTDKGVHAITQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF  +      +    LN+ L     I++L L  V   FHARFSA+ RSY Y I  R+ 
Sbjct: 61  VHFSSLIIRNEEVWFTGLNSLL--PKNITVLWLKKVSSNFHARFSALSRSYRYIIFNRKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             +  K   + +   LD   M+ ++Q L+G HDF++F+S  CQ+ S  + I    +    
Sbjct: 119 RSSFLKNYYFHVRNFLDIYKMKTSSQFLIGNHDFSSFKSSGCQSFSSRKNIFSLIIYRIN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A SFL+  +R+ VG L LVG  K     ++  LQ +D K+     P +GLYF
Sbjct: 179 DFIIIDITANSFLYHMVRNIVGCLILVGLSKKKPEWVQYILQKKDIKKTYSTVPAQGLYF 238

Query: 242 DSVEYS 247
               Y 
Sbjct: 239 LFASYP 244


>gi|327480383|gb|AEA83693.1| tRNA pseudouridine synthase A [Pseudomonas stutzeri DSM 4166]
          Length = 275

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 99/247 (40%), Positives = 127/247 (51%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           R  + +EY GS Y G+QRQ+    SIQ S+E A+  V G   V +  AGRTD+ VHA  Q
Sbjct: 8   RIALGVEYKGSRYRGFQRQRAGVPSIQESLENALTRVAGGHPVTLSCAGRTDALVHASGQ 67

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E          N  L     IS+     +   F ARFSA+ R Y Y I   Q
Sbjct: 68  VVHFDTPVERSMHAWVMGANMNL--PPDISVTWAKKMPPHFDARFSAMARRYRYVIYNDQ 125

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A          + LD E MR AA  LVG HDF+ FR+  CQA SPI+TI H ++  F
Sbjct: 126 IRPAHMAEEVTWNHRPLDIERMRAAAAALVGTHDFSAFRARQCQAKSPIKTIHHLELLQF 185

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI I V A +FLH  +R+F G L  +G G+       + L+++ R+  G  A P GLY
Sbjct: 186 GRLIVIDVRANAFLHHMVRNFAGVLMTIGAGERPVEWAAQVLESRVRRTGGVTAHPYGLY 245

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 246 LVEVDYP 252


>gi|257088005|ref|ZP_05582366.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
 gi|256996035|gb|EEU83337.1| tRNA pseudouridine synthase [Enterococcus faecalis D6]
          Length = 234

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 123/236 (52%), Gaps = 5/236 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G+ + G+Q+Q N  ++Q  IEK +  +  G  V V G+GRTD+GVHA+ 
Sbjct: 1   MPRYKAIIAYDGTHFHGFQKQPNERTVQEEIEKTLARMNNGHSVTVFGSGRTDAGVHAMG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD  +E     +  AL+   +  + I++ ++  V + FHAR+  I ++Y +++   
Sbjct: 61  QVIHFDYPQERPLEKMRFALDT--QTPEDIAVRSVERVSEDFHARYHVIEKTYQFKVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +      +  A   P  +D E ++ A   L+G HDFT+F +        +RTI      V
Sbjct: 119 KPRSPFRRFYASYFPYPIDLEKIQQALPDLLGTHDFTSFCASGSSVEDKVRTIHEASVHV 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           N  G+ +        FL+  IR  VG+L  +G+G+   T +   + A+DR   GP 
Sbjct: 179 NETGDELTFTFRGDGFLYKMIRILVGTLLKIGNGRLEPTAIPAIIAAKDRNLAGPT 234


>gi|254514517|ref|ZP_05126578.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR5-3]
 gi|219676760|gb|EED33125.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR5-3]
          Length = 272

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 91/249 (36%), Positives = 130/249 (52%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
            R  + IEY+GS Y GWQ Q       ++Q  +E A+  +    V V  AGRTD+GVHA 
Sbjct: 6   QRVALKIEYDGSAYSGWQSQPQLPKVRTVQTEVEVALSKIANSPVRVFCAGRTDTGVHAA 65

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            Q  HFD   +          NA L     + + +   V + FHAR SA+ R Y Y I  
Sbjct: 66  AQWLHFDAPCDRSLKAWIVGANAQL--PLDVRLTDGLSVAEDFHARHSAVARQYDYLIAN 123

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P AL   R   + + LD   MR + Q L+G  DF+ FR+  CQ+++P+R ++   V 
Sbjct: 124 TRTPSALLANRMVWVRQPLDANLMRCSLQALLGEQDFSAFRAASCQSTTPMRFMESTQVF 183

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G++I+IRVVA +FLH  +R+ VGS   VG  +  +  L + L  +DR +    APP+G
Sbjct: 184 RRGDIIQIRVVANAFLHHMVRNIVGSCLQVGLCEQPAGWLGELLAGRDRTQAAATAPPQG 243

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 244 LYLTGVRYP 252


>gi|300362359|ref|ZP_07058535.1| tRNA-pseudouridine synthase I [Lactobacillus gasseri JV-V03]
 gi|300353350|gb|EFJ69222.1| tRNA-pseudouridine synthase I [Lactobacillus gasseri JV-V03]
          Length = 255

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 82/244 (33%), Positives = 127/244 (52%), Gaps = 6/244 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVAHFDL 66
           + Y+G  + G+Q Q    ++QG IE+A+  +T G+ VVVHG+GRTD+GVHA  QV HFD 
Sbjct: 1   MAYDGHLFHGFQIQPKERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQVIHFDY 60

Query: 67  V-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             +E     +  ALNA +         +  IV+  FH ++S   + Y Y +   +     
Sbjct: 61  PGKEIPAKNMMLALNALM--PIDTVFFDSEIVNSDFHVQYSTKGKWYRYIVDQHRFTDPF 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN--L 183
            +      P  LD + M+ AA+ L+G+HDFT+F +   Q    +RTI + ++ S  +   
Sbjct: 119 NRFYTGHYPYPLDIDLMQRAAKDLIGKHDFTSFAASGGQIVDKVRTIYYVNITSDPDNKK 178

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I    +   FL+  +R  VG+L  +G+ K    D+ + L A+DR+E    AP  GLY   
Sbjct: 179 IIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRTTAPASGLYLQH 238

Query: 244 VEYS 247
           V Y 
Sbjct: 239 VFYE 242


>gi|261364797|ref|ZP_05977680.1| tRNA pseudouridine synthase A [Neisseria mucosa ATCC 25996]
 gi|288566820|gb|EFC88380.1| tRNA pseudouridine synthase A [Neisseria mucosa ATCC 25996]
          Length = 270

 Score =  275 bits (703), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ +I+ Y+GS ++GWQ+Q  G  ++Q ++E A+  +  E +    AGRTD+GVHA  QV
Sbjct: 13  RWALILSYDGSRFYGWQKQAGGLPTVQTTLEYALSQIASENIRTIVAGRTDTGVHATAQV 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + +S+L    V   FHARF A  R Y Y + +   
Sbjct: 73  IHFDTTVVRPEQAWVRGVNAHL--PEGVSVLFAQQVASHFHARFDAYGRRYRYLLESSPV 130

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +GR       LD + M+ AA  L G HDF++FR+  CQA SPI+T+    ++   
Sbjct: 131 RSPILQGRVGWTHLKLDPDKMQQAALLLEGEHDFSSFRAAECQAKSPIKTLYSAKISGTP 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +++ +   +FLH  +R+ +G+L  VG G+ + +  +  +  + R +  P   P+GLY 
Sbjct: 191 QFLKLDLHGNAFLHHMVRNIMGALVYVGSGRLSVSGFQTLIGERSRLKAPPTFMPDGLYL 250

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 251 TGVDYP 256


>gi|225388793|ref|ZP_03758517.1| hypothetical protein CLOSTASPAR_02531 [Clostridium asparagiforme
           DSM 15981]
 gi|225045068|gb|EEG55314.1| hypothetical protein CLOSTASPAR_02531 [Clostridium asparagiforme
           DSM 15981]
          Length = 250

 Score =  275 bits (703), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 89/249 (35%), Positives = 131/249 (52%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y MI++Y+G+ Y GWQRQ N   +IQG +E  +  +  E + VHG+GRTD GVHA  Q
Sbjct: 1   MNYKMILQYDGTRYDGWQRQGNTDRTIQGKLEAVLGRLAEETLEVHGSGRTDGGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F L +   P  +   LN YL   + I +L L+   ++FH+R +A R++Y Y+I    
Sbjct: 61  VANFHLKQAREPEEIRAYLNRYL--PEDICVLELTAAPERFHSRLNACRKTYRYQIWMDG 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
                ++   + + K LD   M  AA  L+G HDF +F        S +RTI    +   
Sbjct: 119 KTDVFQRDYFYGLGKQLDIGQMERAAGTLLGTHDFKSFCGNKKMKKSTVRTITAIRLIRL 178

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + + V    FL   +R   G+L  VG GK  +  LE  L+ ++R   G  APPEG
Sbjct: 179 CDGKALAVDVTGNGFLQQMVRILAGTLIEVGLGKREADSLEAVLELKERSAAGFTAPPEG 238

Query: 239 LYFDSVEYS 247
           L   +V+Y 
Sbjct: 239 LCLMNVQYE 247


>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 =  274 bits (702), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 132/248 (53%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKIADESIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD       +   +  N+ L     ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTNAIRPEMGWLRGANSQL--PKDISIQWIKLMDENFHARFKATARRYRYVIYNA 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|163791438|ref|ZP_02185847.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
 gi|159873302|gb|EDP67397.1| tRNA pseudouridine synthase A [Carnobacterium sp. AT7]
          Length = 246

 Score =  274 bits (702), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    M +EY+G+ Y GWQR  +   +IQG IE  I  +TG    + G+GRTD+G HA  
Sbjct: 1   MRNIKMTVEYDGARYLGWQRLTDSDKTIQGKIENTITAMTGTKTEIVGSGRTDAGAHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          +   LN YL     I +  L  V ++FHAR++A  + Y Y +   
Sbjct: 61  QVANFKTESTMELQAMLDHLNRYL--PRDIVVKKLEEVPERFHARYNASGKKYSYYVWNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P   E+  ++     LD + M  A   LVG+HDF  F S+     S +RTI+   ++ 
Sbjct: 119 SVPSVFERNFSYEYAGDLDIDKMNKACDKLVGKHDFIGFSSLKKSKKSTVRTINEIKIHK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+    +   FL+  IR  +G++  +G G      ++   ++  R E G   P +GL
Sbjct: 179 EGDLLHFTFIGEGFLYKMIRIIMGTILEIGAGTTELESIDAIFKSGIRSEAGMTVPSQGL 238

Query: 240 YFDSVEYS 247
           + D V Y 
Sbjct: 239 FLDEVYYD 246


>gi|300814956|ref|ZP_07095184.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300510926|gb|EFK38198.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 243

 Score =  274 bits (702), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 120/245 (48%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   + + Y+G+ Y G+Q Q    +I+G + KAI     +   ++ AGRTD GVHAL Q 
Sbjct: 1   MNILIKVTYDGTNYHGYQIQNKLKTIEGELSKAINDTLKKETKIYSAGRTDRGVHALGQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F          L + +N +L   D IS+++   V   FHARFSA  + Y Y +   + 
Sbjct: 61  VNFYTDTTIDLGNLPRVINFHL--PDDISVISAKEVPFDFHARFSAREKIYRYVVYNNKY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+   RA+  P SLD   M  + ++L+G+ DF +F          IRTI    V    
Sbjct: 119 RNAIYHNRAYQYPFSLDLSLMNESFKYLIGQKDFKSFMGRDAIVKDTIRTIYSIKVKKDN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I      +SFL   IR  +G+   +G GK     +++ L+ Q+RK  GP AP  GLY 
Sbjct: 179 KFIYFDFQGKSFLKNMIRIIMGTAIEIGRGKKDPIFMKEVLEKQNRKYAGPTAPSCGLYL 238

Query: 242 DSVEY 246
            ++ Y
Sbjct: 239 MNILY 243


>gi|218289976|ref|ZP_03494153.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           LAA1]
 gi|218239961|gb|EED07148.1| tRNA pseudouridine synthase A [Alicyclobacillus acidocaldarius
           LAA1]
          Length = 262

 Score =  274 bits (702), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 127/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  +++ Y+GSG+ G+ RQ+   ++QG +E  +  + G  +VV G+GRTD GVHA  QV
Sbjct: 5   RRIRLVLGYDGSGFHGFARQEGLRTVQGVLEDELRRMLGVDIVVEGSGRTDRGVHARAQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFDL        +   L  + ++   +       VD  FHARFS +R++Y Y +     
Sbjct: 65  VHFDLPYGPPADRMVHVL--HRRLPADLLPRQADEVDDGFHARFSVVRKTYRYTLDLAPL 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P       +W +P+ LD   M+ AA+HL+G HDFT+F +        +R ID  +    G
Sbjct: 123 PSLYWYRFSWHLPEYLDLAAMQEAARHLLGEHDFTSFCAAEAPQRDKVRRIDRVEFRQDG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I      FL   +R  VG+L  VG GK     +   L+A+DR+  G  APP GL  
Sbjct: 183 SRLHIEFEGNGFLQYMVRILVGTLVKVGRGKERPDRIPLILEARDRRLAGETAPPHGLCL 242

Query: 242 DSVEYS 247
            +VEY 
Sbjct: 243 WNVEYP 248


>gi|258422666|ref|ZP_05685571.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9635]
 gi|257847077|gb|EEV71086.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9635]
          Length = 267

 Score =  274 bits (702), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 123/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNKAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>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 =  274 bits (702), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + IE+ G+ Y GWQ +Q    S+Q +IEK +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRFAIGIEFCGTHYRGWQTQQTGVISVQETIEKVLSKIANEPISLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D+ FHARF A  R Y Y +   
Sbjct: 61  MVAHFDSSALRSERGWLMGSNSQL--PKDISIQWIKAMDQDFHARFKAQARRYRYVVYNH 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +      +LD   M  AAQ   G H+F +FR+  CQ++ P+R + H  +  
Sbjct: 119 PQRPALMHKQVTHAYYALDVAKMMQAAQKFEGTHNFESFRAAACQSNQPVRHVSHCRLIQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ +G L  +G G +    +E    A+DRK  G  APP+GL
Sbjct: 179 HGPYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEVEHIEAIFAAEDRKAAGITAPPDGL 238

Query: 240 YFDSVEYS 247
           YF   +Y 
Sbjct: 239 YFIHADYP 246


>gi|160887061|ref|ZP_02068064.1| hypothetical protein BACOVA_05075 [Bacteroides ovatus ATCC 8483]
 gi|156107472|gb|EDO09217.1| hypothetical protein BACOVA_05075 [Bacteroides ovatus ATCC 8483]
          Length = 267

 Score =  274 bits (702), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLL--PPDISVYRVCRVRPDTHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +      + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 EDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 237 FLVNVEYP 244


>gi|150005081|ref|YP_001299825.1| tRNA pseudouridine synthase A [Bacteroides vulgatus ATCC 8482]
 gi|149933505|gb|ABR40203.1| tRNA pseudouridine synthase A [Bacteroides vulgatus ATCC 8482]
          Length = 267

 Score =  274 bits (702), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 123/247 (49%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +
Sbjct: 11  MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMI 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+ 
Sbjct: 71  AHFDYDRELDCVQITEKLNRLL--PPDIAVYAVKRVKDDAHARFDATYRTYKYYVTTRK- 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-F 180
                +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     
Sbjct: 128 -DPFNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVS 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+
Sbjct: 187 GTEWVFIIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALF 246

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 247 LVDVGYP 253


>gi|261380083|ref|ZP_05984656.1| tRNA pseudouridine synthase A [Neisseria subflava NJ9703]
 gi|284797300|gb|EFC52647.1| tRNA pseudouridine synthase A [Neisseria subflava NJ9703]
          Length = 281

 Score =  274 bits (701), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 129/247 (52%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q     ++Q ++E+A+  + GE +    AGRTD+GVHA  Q
Sbjct: 13  QRWALTLSYDGSRFYGWQKQAGDLPTVQTALEQALTSIAGEQINTIVAGRTDTGVHATAQ 72

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + +NA+L   D +++L    V   F+ARF A  R Y Y + +  
Sbjct: 73  VVHFDTSVSRPEQAWVRGVNAHL--PDGVAVLLAQKVAPHFNARFDAYGRHYRYLLESSP 130

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L  GR       LD   MR AA  L G HDF++FR+  CQA SPI+T+    ++  
Sbjct: 131 VCSPLLVGRVGWTHLKLDLNLMRQAAALLEGEHDFSSFRAAECQAKSPIKTLYRASISGT 190

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + +   +FLH  +R+ +G+L  VG G+ +  + +    A+ R +  P    +GLY
Sbjct: 191 PRYLCLDLHGNAFLHHMVRNIMGALVYVGSGRISVDEFQSIFYARSRLKAPPTFMSDGLY 250

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 251 LTGVDYP 257


>gi|51245176|ref|YP_065060.1| tRNA pseudouridine synthase A [Desulfotalea psychrophila LSv54]
 gi|62901428|sp|Q6ANM1|TRUA1_DESPS RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|50876213|emb|CAG36053.1| related to tRNA pseudouridine synthase A [Desulfotalea psychrophila
           LSv54]
          Length = 251

 Score =  274 bits (701), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 82/253 (32%), Positives = 125/253 (49%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M   C++I ++G+ Y GWQ+Q + ++IQG IE  +  ++ + + +HGAGRTD+GVHA   
Sbjct: 1   MRNICLLIAFDGTDYSGWQKQHHANTIQGEIEARLKRLSVKEISLHGAGRTDAGVHADGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHF            +ALN  L     I IL +  +   FHARF+A  + Y YR+ T  
Sbjct: 61  TAHFHTDTRLTCNDFQRALNRML--PGAIRILQVREMADDFHARFAATGKEYHYRLFTGG 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS------PIRTIDH 174
                ++       K +D E M+   Q ++G HDF++F +   +  +       +RTI  
Sbjct: 119 VIPPQKRLYMLHQEKPIDQEAMQKCLQIIIGTHDFSSFENTGSRDKTRTGGKGAVRTILE 178

Query: 175 FDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                F  +      +   FL   +R+ VGS+  VG GK +    E+AL+ +DR   GP 
Sbjct: 179 ARYEQFEEDSWHFVFIGDGFLRNMVRNIVGSILEVGRGKESVEWFEQALKEKDRNAAGPT 238

Query: 234 APPEGLYFDSVEY 246
           AP  GL    V Y
Sbjct: 239 APAHGLKLFQVFY 251


>gi|82751809|ref|YP_417550.1| tRNA pseudouridine synthase A [Staphylococcus aureus RF122]
 gi|123727496|sp|Q2YYM7|TRUA_STAAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|82657340|emb|CAI81781.1| tRNA pseudouridine synthase A [Staphylococcus aureus RF122]
          Length = 267

 Score =  274 bits (701), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L     I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PVDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               ++G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQRGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|15605190|ref|NP_219976.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D/UW-3/CX]
 gi|8134751|sp|O84469|TRUA_CHLTR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3328897|gb|AAC68063.1| Pseudouridylate Synthase I [Chlamydia trachomatis D/UW-3/CX]
 gi|296436918|gb|ADH19088.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/11222]
 gi|297748594|gb|ADI51140.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-EC]
 gi|297749474|gb|ADI52152.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-LC]
          Length = 267

 Score =  274 bits (701), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 129/251 (51%), Gaps = 6/251 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   + I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  
Sbjct: 1   MTKKIVLQIAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQG 60

Query: 60  QVAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           Q+AHF          P  + K LNA L     I I +  + D+ FH+RFSAI + Y Y +
Sbjct: 61  QIAHFHCPDHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDEDFHSRFSAIAKEYRYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                PL   +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D
Sbjct: 119 SLLPKPLPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   +L+ +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP
Sbjct: 179 LSEQEHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>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 =  274 bits (701), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 118/251 (47%), Positives = 156/251 (62%), Gaps = 5/251 (1%)

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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   + G  W +   LD E M+ AA  LVG+HDFTTFRS  CQA SP++T+D  DV   
Sbjct: 120 APAVHQAGLVWQVKHRLDVEAMQAAADLLVGKHDFTTFRSTICQAVSPVKTLDRLDVREV 179

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

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLAHVSYP 250


>gi|49484433|ref|YP_041657.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257423704|ref|ZP_05600133.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257426382|ref|ZP_05602784.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257429022|ref|ZP_05605409.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257431668|ref|ZP_05608031.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257434628|ref|ZP_05610679.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M876]
 gi|282902120|ref|ZP_06310013.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C160]
 gi|282909528|ref|ZP_06317341.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911780|ref|ZP_06319576.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282915068|ref|ZP_06322845.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M899]
 gi|282925699|ref|ZP_06333347.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C101]
 gi|283958992|ref|ZP_06376435.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|293497472|ref|ZP_06665326.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293511047|ref|ZP_06669744.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M809]
 gi|293549653|ref|ZP_06672325.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M1015]
 gi|295428801|ref|ZP_06821425.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297589714|ref|ZP_06948355.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|56749728|sp|Q6GEL6|TRUA_STAAR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|49242562|emb|CAG41283.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|257272722|gb|EEV04824.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257276013|gb|EEV07464.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257279503|gb|EEV10090.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257282547|gb|EEV12679.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257285224|gb|EEV15340.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M876]
 gi|282312528|gb|EFB42932.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C101]
 gi|282320789|gb|EFB51123.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M899]
 gi|282323476|gb|EFB53792.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326638|gb|EFB56938.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282596579|gb|EFC01538.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C160]
 gi|283789551|gb|EFC28376.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|290918700|gb|EFD95776.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291096403|gb|EFE26661.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466034|gb|EFF08563.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127150|gb|EFG56792.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297578225|gb|EFH96938.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|312437370|gb|ADQ76441.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|315193148|gb|EFU23548.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 264

 Score =  274 bits (701), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRIHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|170077660|ref|YP_001734298.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7002]
 gi|238689046|sp|B1XJI2|TRUA_SYNP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169885329|gb|ACA99042.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7002]
          Length = 274

 Score =  274 bits (701), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 115/246 (46%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ    ++Q  IE+ I  V G+ + +HGAGRTDSGVHA  Q A
Sbjct: 11  RIALVIQYIGTHFCGWQRQTAERTVQAVIEETISTVVGQKITIHGAGRTDSGVHAAGQFA 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+           K LN  L     I+I     V + +HA+FSA  R Y Y I T   P
Sbjct: 71  HFECESLIPGYKWAKILNDRL--PPDINIRGACEVSQDWHAQFSAQWRRYRYTIYTHPTP 128

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  AW   +  LD   ++ A   L+G H    F+    + S     +   + +  G
Sbjct: 129 NLFIQPYAWHYYQAPLDETLIQAALTPLLGEHHLAAFQRTGSKRSHAWVNVQAAECSRRG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A  FL+  +R  VG L  +G GK +    +   + + R      AP +GL  
Sbjct: 189 SFIHIEIQANGFLYGMVRLLVGMLVDIGQGKLSLAQFQDIWKNEKRHLVKYSAPAKGLCL 248

Query: 242 DSVEYS 247
             V Y 
Sbjct: 249 LRVGYP 254


>gi|323699460|ref|ZP_08111372.1| tRNA pseudouridine synthase A [Desulfovibrio sp. ND132]
 gi|323459392|gb|EGB15257.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans ND132]
          Length = 251

 Score =  274 bits (701), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 117/248 (47%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y G+ + GWQ Q    ++QG +E+A+  + G  V VHG+GRTD+GVHAL Q
Sbjct: 3   MTRIRLTLAYEGTDFCGWQVQPADRTVQGEVERALATILGRAVRVHGSGRTDAGVHALGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           + LN  L     + +L+ + V   FHAR+ A+ ++Y Y +   +
Sbjct: 63  VVHFDCPDGRTGFPWQRGLNGIL--PRDVRVLDAAEVPDDFHARYGAVSKTYEYCLWHER 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
                ++ R       +D   M  AA  L+G HDF  F+++     S +RT+     +  
Sbjct: 121 GFCLPQRRRFVWNCGPVDFARMEAAAGLLLGEHDFAAFQNVGTDVDSTVRTVTEISRHAG 180

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +    R  A  FL   +R+ VG L   G GK     +   L+A DR       PP+G
Sbjct: 181 PTAHESVWRFTADGFLKQMVRNLVGCLVACGRGKLDLDGVRVILEAGDRTLAPATVPPQG 240

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 241 LTLVRVAY 248


>gi|282920794|ref|ZP_06328512.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C427]
 gi|282315209|gb|EFB45593.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           C427]
          Length = 264

 Score =  274 bits (701), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 123/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRIHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G++  +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRYEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|222152501|ref|YP_002561676.1| tRNA pseudouridine synthase A [Streptococcus uberis 0140J]
 gi|254764869|sp|B9DTJ0|TRUA_STRU0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|222113312|emb|CAR40884.1| tRNA pseudouridine synthase A [Streptococcus uberis 0140J]
          Length = 250

 Score =  274 bits (701), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 132/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GS + G+QRQ +  S+Q  IEK +  +T G+ + VHGAGRTDSGVHA  
Sbjct: 1   MTRYKAIISYDGSQFQGFQRQSHARSVQEEIEKTLTKLTNGKEIKVHGAGRTDSGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL ++     L  AL+   +  + I  +++  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLDQDRDLEKLRFALDT--QSPEDIDFISVEKVSDDFHSRYTKHLKTYEFIVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +    + +  A   P  LD +N+++A + L+G HDFT F +      + +RTI    V  
Sbjct: 119 RPKNPMMRHYATHFPYPLDLDNIQLAIKDLIGTHDFTGFTASGATIENKVRTIIDASVRY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +        FL+ Q+R+ VG+L  +G+ +     ++  L+ +DR+  GP     
Sbjct: 179 EEDKNFLIFTFTGNGFLYKQVRNMVGTLLKIGNNRMPVDQIKTILEKKDRQLAGPTPAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|94677014|ref|YP_588808.1| tRNA pseudouridine synthase A [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94220164|gb|ABF14323.1| tRNA pseudouridine synthase A [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 267

 Score =  274 bits (701), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 126/246 (51%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + I YNGS Y+GWQRQK   S+Q S+E+A+ +V  E + V  AGRTD+GVHA  QV 
Sbjct: 8   KIALGIAYNGSLYYGWQRQKELPSVQASLERALSIVANEKISVFCAGRTDTGVHATGQVV 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+ V           +NA L    +I++     V   FHARFSA  RSY Y I      
Sbjct: 68  HFETVALRTNKAWTLGVNANL--PASIAVRWAMTVTLNFHARFSATARSYRYIIYNHPLR 125

Query: 123 LALEKGRAW-LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
            A+     +    + LD   M  A Q L+G  DFT+FR+  C + +P R +    V   G
Sbjct: 126 PAMLGSSGYMHFYQPLDPLKMDRAGQCLLGERDFTSFRAQQCTSRTPWRNLHQLIVKRHG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +FL+  +R+ VG L  +G GK     +   L  +DR   G  A  +GLY 
Sbjct: 186 SYIIVDITANAFLYRMVRNIVGCLIEIGSGKKPENWIADLLARRDRSLAGITARAKGLYL 245

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 246 VNVYYP 251


>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 =  274 bits (701), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 136/246 (55%), Gaps = 3/246 (1%)

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 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+         K LD   M+ AA+  VG+HDF++FR++ CQA +P+RTI +F++   G
Sbjct: 123 RPAIMSKEVTWTHKKLDILKMQQAAKVFVGKHDFSSFRAVGCQAHTPVRTILNFEIYQSG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  IR+F G L  +G G+   +   K L A+DR + G   PPEGLYF
Sbjct: 183 QYIVLDIRANAFLHHMIRNFAGVLMTIGAGEEEVSWASKVLAAKDRTKGGITGPPEGLYF 242

Query: 242 DSVEYS 247
              EY 
Sbjct: 243 VDAEYP 248


>gi|299148560|ref|ZP_07041622.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_23]
 gi|298513321|gb|EFI37208.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_23]
          Length = 267

 Score =  274 bits (701), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     ISI  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLL--PPDISIYRVCRVRPDTHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +      + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 EDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 237 FLVNVEYP 244


>gi|325288607|ref|YP_004264788.1| tRNA pseudouridine synthase A [Syntrophobotulus glycolicus DSM
           8271]
 gi|324964008|gb|ADY54787.1| tRNA pseudouridine synthase A [Syntrophobotulus glycolicus DSM
           8271]
          Length = 267

 Score =  274 bits (701), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 123/249 (49%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M   C+ + Y+G+ Y G+Q Q   +G +IQG +EKA   +  E + +  AGRTD GVHA 
Sbjct: 1   MNNICLRLAYDGTQYHGFQSQPEEHGKTIQGELEKAWKRLAQEEIKIVTAGRTDKGVHAA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV +F          +  A+N+ L   + I IL   +V  +F+AR SA  + Y Y+I  
Sbjct: 61  GQVINFKSAARIPQDKIPIAMNSVL--PEEIRILEAKLVGAEFNARTSAYWKRYDYKIEN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           ++      +  +   P  LD   MR AA  + G+HDF TF +    A S +RT+ H  V 
Sbjct: 119 KRTADVFTRLYSLHEPVPLDLNKMRQAAARIEGKHDFKTFSAAGSNAKSFVRTVYHCKVQ 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           S    I +  +   FL+  +R   G+L  VG GK    D+   L++++R   G    P G
Sbjct: 179 SSSGYITVTCIGNGFLYNMVRIITGTLLYVGKGKIVPEDMPGILKSRNRALAGKTVSPAG 238

Query: 239 LYFDSVEYS 247
           L    ++Y 
Sbjct: 239 LVLRYIDYD 247


>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 =  274 bits (700), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 115/251 (45%), Positives = 165/251 (65%), Gaps = 5/251 (1%)

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+ +   ++L  + V + FHARFSA+ RSYL+R++ R+
Sbjct: 61  VAHVDLARDWDPFRLSEALNAHLRPAPV-AVLAAARVGEDFHARFSALERSYLFRLLVRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G  W +   LD E MR  A++L+G+HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATHDAGLVWRVMNPLDVEAMREGAKYLIGKHDFTTFRSTMCQAASPVKTLDEITIEES 179

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

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


>gi|282906560|ref|ZP_06314408.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282329459|gb|EFB58980.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Btn1260]
          Length = 264

 Score =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRIHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP+ LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPEPLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLHQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|329730365|gb|EGG66755.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           21193]
          Length = 267

 Score =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 123/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTDLNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|238920608|ref|YP_002934123.1| tRNA pseudouridine synthase A, [Edwardsiella ictaluri 93-146]
 gi|238870177|gb|ACR69888.1| tRNA pseudouridine synthase A, putative [Edwardsiella ictaluri
           93-146]
          Length = 275

 Score =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 87/244 (35%), Positives = 125/244 (51%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IEY+GS Y GWQRQ+   S+Q  +E A+  V  E V V  AGRTD+GVHA  QV H
Sbjct: 17  LALGIEYDGSRYAGWQRQREVDSVQARLEAALSRVASEPVTVFCAGRTDAGVHATGQVVH 76

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              +NA+L     +++  +  V   FHARFSA  R Y Y I   +   
Sbjct: 77  FTTHALRQEGAWTMGVNAHL--PKDVAVRWVKDVSPDFHARFSATARRYRYVIYNHRYRP 134

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+ +         LD E M  A Q L+G +DF+ FR+  CQ+ +P R + H  V+ +G+ 
Sbjct: 135 AVLQSGVTHFYLPLDAERMARAGQALLGENDFSAFRAAQCQSRTPWRNVSHLRVDRYGSY 194

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A +F+H  +R+ VGSL  VG G    + +   L  +DR      A   GLY  +
Sbjct: 195 VVVDIKANAFVHHMVRNIVGSLLEVGCGNQPESWIAGLLAGRDRTLAAATAKAAGLYLVA 254

Query: 244 VEYS 247
           V+Y 
Sbjct: 255 VDYP 258


>gi|293380407|ref|ZP_06626478.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 214-1]
 gi|290923090|gb|EFE00022.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 214-1]
          Length = 262

 Score =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  A+N+ +     I   N  IV+  FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILAMNSMM--PTDIIFNNCQIVNDDFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 ++      P  LD E M+IAAQ L+G+HDFT+F +   Q    +RTI +  +  
Sbjct: 121 HFVNPFKRFYTGHFPYPLDIEKMQIAAQDLLGKHDFTSFAASGGQIEDKVRTIYYVKITE 180

Query: 180 F--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   
Sbjct: 181 DKKDNEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLQRVIAAKDRQEVRQTAHAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>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 =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 94/242 (38%), Positives = 132/242 (54%), Gaps = 2/242 (0%)

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  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                         NA L     +++  +  V   FHAR SA+ R Y Y I+ + +   L
Sbjct: 61  APVTRTQKAWLFGANANL--PRDVAVRWVVPVADDFHARLSALARRYRYVILNQPSRPVL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E+  A    + LD E M  AAQ LVG HDF++FR+  CQ+ S  R +   +V  +G L+ 
Sbjct: 119 ERANATWCREPLDAERMHAAAQALVGEHDFSSFRAAGCQSKSRWRHVHFIEVRRYGQLVV 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I + A +FLH  IR+  G+L  VG G  ++  L + L  +DR +    AP  GL+F    
Sbjct: 179 IDIQANAFLHHMIRNIAGALVAVGRGDHSTGYLGELLALRDRTQGNVTAPGCGLHFVDAL 238

Query: 246 YS 247
           Y 
Sbjct: 239 YD 240


>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 =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 90/248 (36%), Positives = 129/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G  Y GWQ +Q    SIQ +IEK +  +  E +++HGAGRTD+GVHA  
Sbjct: 2   MQRYAVGIEFCGIRYRGWQTQQAGVPSIQETIEKVLSKIADEPIILHGAGRTDAGVHATN 61

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  ++  FHARF A  R Y Y +   
Sbjct: 62  MVAHFDTNAIRPQRGWLMGANSQL--PKDISIQWIKEMNTDFHARFKATARRYRYVVYNT 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   + ++LD + M +AA+   G H+F TFR+  CQ+S P+R + H  +  
Sbjct: 120 LNRPALLHKQVTHVYQTLDVDKMMLAARKFEGTHNFETFRAASCQSSQPVRHLSHCRLTR 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ +G L  +G G +    ++    AQDRK  G  AP +GL
Sbjct: 180 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGCYEIEHIDTMFAAQDRKAAGVTAPADGL 239

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 240 YFIQAYYP 247


>gi|223933386|ref|ZP_03625373.1| tRNA pseudouridine synthase A [Streptococcus suis 89/1591]
 gi|330832153|ref|YP_004400978.1| tRNA pseudouridine synthase A [Streptococcus suis ST3]
 gi|223897953|gb|EEF64327.1| tRNA pseudouridine synthase A [Streptococcus suis 89/1591]
 gi|329306376|gb|AEB80792.1| tRNA pseudouridine synthase A [Streptococcus suis ST3]
          Length = 249

 Score =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  + +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQTHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++ +  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTPEDIDVVQVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTIKAASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +        FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   
Sbjct: 179 DQRRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRGLAGPTAAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|270285538|ref|ZP_06194932.1| tRNA pseudouridine synthase A [Chlamydia muridarum Nigg]
 gi|270289549|ref|ZP_06195851.1| tRNA pseudouridine synthase A [Chlamydia muridarum Weiss]
 gi|301336935|ref|ZP_07225137.1| tRNA pseudouridine synthase A [Chlamydia muridarum MopnTet14]
 gi|13431951|sp|Q9PJT0|TRUA_CHLMU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 267

 Score =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 131/251 (52%), Gaps = 6/251 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   + I Y G+ Y GWQ Q N  SIQ  +E  +  ++   + V  +GRTD+GVHA  
Sbjct: 1   MTKKIILRIAYQGTAYSGWQYQPNALSIQEVLETLLQKISRTRISVIASGRTDAGVHAQG 60

Query: 60  QVAHFDLVREW---VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QVAHF          P  + K LNA L     I I ++   ++ FH+RFSAI + Y Y +
Sbjct: 61  QVAHFCCPDHPHFSDPGQIKKMLNALL--PHDIVIRDVIATNEDFHSRFSAITKEYHYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                PL   +   +     L  E+MR AA++LVG HDF +F ++  + SS +RT+   D
Sbjct: 119 SLLPKPLPHHRLFCFSPRHKLCLESMREAAKYLVGTHDFASFANLGREYSSTVRTLYALD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    +L+ +      FL+  +R+ VG+L  +G GK+    L + L+ +DRK+  P APP
Sbjct: 179 LLEQEHLVTVICKGNGFLYKMVRNIVGALLDIGKGKYPPEHLLEMLEKKDRKKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>gi|327182857|gb|AEA31304.1| tRNA pseudouridine synthase A [Lactobacillus amylovorus GRL 1118]
          Length = 264

 Score =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMSYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  ALN+ +     I   +  IVD+ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILALNSMM--PTDIVFTDCQIVDENFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                 ++         LD + M+ AA+ L+G HDFT+F +   Q    +RTI + ++  
Sbjct: 121 HFVNPFKRFYTGHFQYHLDIKKMQEAAKDLLGTHDFTSFAASGGQIEDKVRTIYYVNIRK 180

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   N I    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   
Sbjct: 181 NEEENEIIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLKRVILAKDRQEVRQTAQAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>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 =  274 bits (700), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D++FHARF A  R Y Y +   
Sbjct: 61  MVAHFDTTAIRPERGWIMGANSQL--PKDISIQWIKQMDEEFHARFKATARRYRYVVYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H  +  
Sbjct: 119 PHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKHCRLFQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRKAAGITAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCYYP 246


>gi|222150476|ref|YP_002559629.1| tRNA pseudouridine synthase A [Macrococcus caseolyticus JCSC5402]
 gi|222119598|dbj|BAH16933.1| tRNA pseudouridine synthase A [Macrococcus caseolyticus JCSC5402]
          Length = 273

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 77/245 (31%), Positives = 122/245 (49%), Gaps = 2/245 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++YNG  + G+Q Q  G ++Q  +E+ +  +  + V +H + RTD GVHA  Q
Sbjct: 1   MERILLQLQYNGVNFQGFQIQNEGRTVQYELERILKRMHKQFVRIHPSSRTDKGVHARMQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             HFD            A N+ L   D I I  ++ + + FH+R+  I ++Y Y++   +
Sbjct: 61  YVHFDTPLSIPESKWQHAFNSAL--PDDIYITQVTKISEHFHSRYDCIGKAYRYKVYVAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  G+   I   LD + M  AAQH +G HDFT+F S   +  +  RT+  F+V   
Sbjct: 119 HRNVMHSGQITHIKTKLDVKRMNDAAQHFLGTHDFTSFCSAKTEIENKERTLYRFEVTET 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
               +  V+   FL+  +R  V  L  VG G+     +   +QAQDR + G  AP EGLY
Sbjct: 179 AEGYDFYVIGSGFLYNMVRIMVQYLIDVGTGQKDGDSIPAIIQAQDRTKAGKTAPAEGLY 238

Query: 241 FDSVE 245
            + + 
Sbjct: 239 LEKIY 243


>gi|120609904|ref|YP_969582.1| tRNA pseudouridine synthase A [Acidovorax citrulli AAC00-1]
 gi|166228672|sp|A1TLH0|TRUA_ACIAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120588368|gb|ABM31808.1| tRNA pseudouridine synthase A [Acidovorax citrulli AAC00-1]
          Length = 278

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 88/264 (33%), Positives = 128/264 (48%), Gaps = 20/264 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNGS Y GWQ Q  G+++Q  +E A+       V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGSAYRGWQSQPGGATVQDRLEAALARFATHEVSTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E  P    +  N +L     I++     V + FH+R SA  R Y Y ++    
Sbjct: 61  VHFDTPLERTPFSWVRGTNTFL--PPDIAVQWARPVPEAFHSRASATARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +  +LD + MR AA+HL+G HDFT+FR+  CQA SP++T+   ++   G
Sbjct: 119 RPSVEAGRVGWVFHALDGDAMRAAARHLLGEHDFTSFRASACQAKSPVKTLRRIEITQRG 178

Query: 182 N------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                                       +FLH  +R+ +G L  VG G+  +  +   LQ
Sbjct: 179 TGGVPAGQAPGDRGDVPTCYWRFEFEGNAFLHHMVRNIMGCLVAVGQGQHPADWMHAVLQ 238

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           A+ R    P   P+GLYF    Y 
Sbjct: 239 ARSRDAAAPTFSPDGLYFLGPLYD 262


>gi|300776045|ref|ZP_07085904.1| tRNA-pseudouridine synthase I [Chryseobacterium gleum ATCC 35910]
 gi|300505178|gb|EFK36317.1| tRNA-pseudouridine synthase I [Chryseobacterium gleum ATCC 35910]
          Length = 250

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 86/245 (35%), Positives = 121/245 (49%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY +   YNG  YFG+Q Q +  S+Q  +EKA+  +  E +   GAGRTD+GVHA +  A
Sbjct: 9   RYFIEFSYNGKNYFGYQIQPDAISVQEELEKALSTILREEIKTTGAGRTDTGVHAKKIFA 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD  +E     L + LN++L     ISI  +  V   FHARF A  R+Y Y I   + P
Sbjct: 69  HFDTEKELD-DQLPRRLNSFL--PPDISIKRIFPVKDDFHARFDATYRTYEYYISLEKNP 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E        +SLD + M  A + L    DFT+F  +     + I  I   +    G 
Sbjct: 126 FTQESAWQHW-KRSLDVDAMNEACKILFEYEDFTSFAKLKTDNKTNICKIYKAEWEQNGA 184

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            ++  V A  FL   +R+ VG++  +G GK    DL K ++ ++R   G  AP  GLY  
Sbjct: 185 ELKFTVSANRFLRNMVRAIVGTMVEIGTGKLKPEDLRKVIEDKNRNAAGTSAPGHGLYLV 244

Query: 243 SVEYS 247
            V Y 
Sbjct: 245 DVGYE 249


>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 =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D++FHARF A  R Y Y +   
Sbjct: 61  MVAHFDTNAIRPERGWIMGANSQL--PKDISIQWIKQMDEEFHARFKATARRYRYVVYNA 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+ +G L  +G G +    ++    A+DRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRKAAGITAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCYYP 246


>gi|28211488|ref|NP_782432.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
 gi|42559805|sp|Q893H3|TRUA1_CLOTE RecName: Full=tRNA pseudouridine synthase A 1; AltName: Full=tRNA
           pseudouridylate synthase I 1; AltName: Full=tRNA-uridine
           isomerase I 1
 gi|28203929|gb|AAO36369.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
          Length = 245

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    MI+EY+G+ Y GWQ+QK +  +IQ  IE  +  +TGE + V G GRTD+GVHA  
Sbjct: 1   MRNLKMILEYDGTRYKGWQKQKKDVLTIQDKIETVLSKMTGEDIQVIGCGRTDAGVHAEN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA+F    ++    +   L  Y  + + I +  +    ++FHAR++   ++Y+YRI   
Sbjct: 61  YVANFHTNCDFTVDYMLDYL--YEFLPEDIVVKTMKDTSERFHARYNVKSKTYVYRINNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      K  A+   + L+   M+ AA+ L+G HDF +F  +   + S IR I + ++  
Sbjct: 119 KFRSVFNKKYAYHDNEKLNISAMKDAAEFLIGTHDFKSFTRLKSNSKSTIRAIKYINITE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              +I I V    FL   +R   G+L  VG       D+EK L  + R +   + P +GL
Sbjct: 179 NQGIISIEVNGNGFLLNMVRIVAGALLEVGKENIKPIDIEKMLNEKKRADASLILPAKGL 238

Query: 240 YFDSVEY 246
               ++Y
Sbjct: 239 CLKDIQY 245


>gi|15925209|ref|NP_372743.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15927799|ref|NP_375332.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           N315]
 gi|148268659|ref|YP_001247602.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH9]
 gi|150394724|ref|YP_001317399.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH1]
 gi|156980534|ref|YP_001442793.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253316980|ref|ZP_04840193.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. CF-Marseille]
 gi|253734372|ref|ZP_04868537.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|255006999|ref|ZP_05145600.2| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu50-omega]
 gi|257794565|ref|ZP_05643544.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9781]
 gi|258408833|ref|ZP_05681117.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9763]
 gi|258422432|ref|ZP_05685344.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9719]
 gi|258439820|ref|ZP_05690566.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9299]
 gi|258442624|ref|ZP_05691184.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8115]
 gi|258446678|ref|ZP_05694833.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6300]
 gi|258450204|ref|ZP_05698296.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6224]
 gi|258455424|ref|ZP_05703384.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5937]
 gi|269203852|ref|YP_003283121.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ED98]
 gi|282893658|ref|ZP_06301890.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8117]
 gi|282926765|ref|ZP_06334392.1| tRNA pseudouridine synthase A [Staphylococcus aureus A10102]
 gi|295404895|ref|ZP_06814708.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8819]
 gi|296275990|ref|ZP_06858497.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MR1]
 gi|297243953|ref|ZP_06927843.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8796]
 gi|54039782|sp|P65849|TRUA_STAAN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54042087|sp|P65848|TRUA_STAAM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166229841|sp|A7X5B5|TRUA_STAA1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189029998|sp|A5IV03|TRUA_STAA9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030146|sp|A6U3U4|TRUA_STAA2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|13702019|dbj|BAB43311.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           N315]
 gi|14247992|dbj|BAB58381.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|147741728|gb|ABQ50026.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH9]
 gi|149947176|gb|ABR53112.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           JH1]
 gi|156722669|dbj|BAF79086.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253727689|gb|EES96418.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257788537|gb|EEV26877.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9781]
 gi|257840516|gb|EEV64976.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9763]
 gi|257841863|gb|EEV66300.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9719]
 gi|257847596|gb|EEV71598.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9299]
 gi|257851745|gb|EEV75679.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8115]
 gi|257854746|gb|EEV77694.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6300]
 gi|257856296|gb|EEV79205.1| tRNA pseudouridine synthase A [Staphylococcus aureus A6224]
 gi|257862635|gb|EEV85403.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5937]
 gi|262076142|gb|ACY12115.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ED98]
 gi|282591216|gb|EFB96289.1| tRNA pseudouridine synthase A [Staphylococcus aureus A10102]
 gi|282763716|gb|EFC03844.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8117]
 gi|283471441|emb|CAQ50652.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ST398]
 gi|285817881|gb|ADC38368.1| tRNA pseudouridine synthase A [Staphylococcus aureus 04-02981]
 gi|294969840|gb|EFG45858.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8819]
 gi|297178731|gb|EFH37976.1| tRNA pseudouridine synthase A [Staphylococcus aureus A8796]
 gi|312830568|emb|CBX35410.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ECT-R 2]
 gi|315129701|gb|EFT85692.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|329723462|gb|EGG59991.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           21172]
          Length = 267

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 123/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|332365537|gb|EGJ43297.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK1059]
          Length = 249

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQPHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V   FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVERVSDDFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELGLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMLVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|326316049|ref|YP_004233721.1| tRNA pseudouridine synthase A [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323372885|gb|ADX45154.1| tRNA pseudouridine synthase A [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 278

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 87/264 (32%), Positives = 129/264 (48%), Gaps = 20/264 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNGS Y GWQ Q  G+++Q  +E A+       V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGSAYRGWQSQPGGATVQDRLEAALARFATHEVSTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   + +P    +  N +L     I++     V + FH+R SA  R Y Y ++    
Sbjct: 61  VHFDTPLDRMPFSWVRGTNTFL--PPDIAVQWARPVPEAFHSRASATARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +  +LD + MR AA+HL+G HDFT+FR+  CQA SP++T+   ++   G
Sbjct: 119 RPSVESGRVGWVFHALDGDAMRAAARHLLGEHDFTSFRASACQAKSPVKTLRRIEITQRG 178

Query: 182 N------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                                       +FLH  +R+ +G L  VG G+  +  +   LQ
Sbjct: 179 TGGVPAGQASGDRGDVPTCYWRFEFEGNAFLHHMVRNIMGCLVAVGQGQHPADWMHAVLQ 238

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           A+ R    P   P+GLYF    Y 
Sbjct: 239 ARSRDAAAPTFSPDGLYFLGPLYD 262


>gi|154502979|ref|ZP_02040039.1| hypothetical protein RUMGNA_00801 [Ruminococcus gnavus ATCC 29149]
 gi|153796518|gb|EDN78938.1| hypothetical protein RUMGNA_00801 [Ruminococcus gnavus ATCC 29149]
          Length = 244

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+GS Y GWQRQ N   +IQG +E+A     G  V V G+GRTD GVHA  
Sbjct: 1   MRTYKLTIAYDGSRYQGWQRQSNTDKTIQGLLEQAASEAAGYPVEVQGSGRTDGGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +       + +N  L     I ++ + +V   FHAR SA+ + Y Y I  R
Sbjct: 61  QTASVILRGKVQESEFLQNMNRLL--PLDIRVIEMELVKNGFHARLSAVGKCYEYWIDMR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  PK L+ E M+ AA  L+GR+DF  F     +  S IRTI    V  
Sbjct: 119 EKPDVFMRKYTYHYPKELNIEAMQRAADDLIGRYDFAAFTDKK-EEKSTIRTIYAIIVEV 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I      F++  +R   G+L  VGDG+ T   ++ AL  +DR + G LAP  GL
Sbjct: 178 QGDKLRIEYRGSGFMYHMVRILTGTLLEVGDGRRTPESVKAALAGRDRADAGFLAPARGL 237

Query: 240 YFDSVEY 246
               V Y
Sbjct: 238 TLKEVYY 244


>gi|315037561|ref|YP_004031129.1| tRNA pseudouridine synthase A [Lactobacillus amylovorus GRL 1112]
 gi|325956034|ref|YP_004286644.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus 30SC]
 gi|312275694|gb|ADQ58334.1| tRNA pseudouridine synthase A [Lactobacillus amylovorus GRL 1112]
 gi|325332599|gb|ADZ06507.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus 30SC]
          Length = 264

 Score =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMSYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  ALN+ +     I   +  IVD+ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILALNSMM--PTDIVFTDCQIVDENFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                 ++         LD + M+ AA+ L+G HDFT+F +   Q    +RTI + ++  
Sbjct: 121 HFVNPFKRFYTGHFQYHLDIKKMQEAAKDLLGTHDFTSFAASGGQIEDKVRTIYYVNIRK 180

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N   N I    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   
Sbjct: 181 NEEENEIIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLKRVILAKDRQEVRQTAQAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>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 =  273 bits (699), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D++FHARF A  R Y Y +   
Sbjct: 61  MVAHFDTNAIRPERGWIMGANSQL--PKDISIQWIKQMDEEFHARFKATARRYRYVVYNA 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+ +G L  +G G +    ++    A+DRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDAMFAAEDRKAAGITAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCYYP 246


>gi|293369414|ref|ZP_06615999.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CMC 3f]
 gi|292635581|gb|EFF54088.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CMC 3f]
          Length = 267

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     ISI  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLL--PPDISIYRVCRVRPDTHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +      + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 DDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRVIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 237 FLVNVEYP 244


>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 =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 119/254 (46%), Positives = 158/254 (62%), Gaps = 8/254 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHA 57
           M R+ ++IEY+GS + GWQ Q    S+Q +IE A+  +         +  AGRTD+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  TGQVAHADLARDWDPFRLSEALNWHLK-PAPVAILAAARVADDFHARFSAHERRYLFRLV 119

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R+APL  ++GRAW +P  LD   MR  A HL+GRHDFTTFRS  CQA+SP++T+D   +
Sbjct: 120 ARRAPLTHDRGRAWQVPHRLDLAAMRAGAAHLLGRHDFTTFRSTMCQANSPVKTLDELTI 179

Query: 178 NS----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           +      G      + ARSFLH Q+RS VG+L+ VG G W    + +AL A DR  CGP+
Sbjct: 180 DEAEIPQGREYRFFLRARSFLHNQVRSIVGTLERVGAGAWPPGRVAEALAACDRAACGPV 239

Query: 234 APPEGLYFDSVEYS 247
            PP+GLY   V Y 
Sbjct: 240 CPPQGLYLTGVGYE 253


>gi|295694868|ref|YP_003588106.1| tRNA pseudouridine synthase A [Bacillus tusciae DSM 2912]
 gi|295410470|gb|ADG04962.1| tRNA pseudouridine synthase A [Bacillus tusciae DSM 2912]
          Length = 277

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +     + Y+G+ Y G+QRQ    ++QG +E A+  + G  V + GAGRTD+GVHA  QV
Sbjct: 1   MYVKAKVGYDGTDYHGFQRQPGLRTVQGVLEGALGELAGREVSIVGAGRTDAGVHARGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F+                  ++ + + + NL    + FH RFSA+ + Y Y +     
Sbjct: 61  IAFEWPGPIP--WQRLERVLLRRLPEDLVVSNLEPAPESFHPRFSAVGKCYRYTLDQGVY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +   W +P  +D  +MR AA    G HD+T+F +      + +RT+    +    
Sbjct: 119 PSVFLRRYTWHVPTQMDLGSMRRAALAAAGTHDYTSFCAASTPVQNKVRTVYAIRLAEEP 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + V    FL+  +R  VG+L  VG GK +   +   L A+DR+  G  AP +GL  
Sbjct: 179 PFVHLYVFGNGFLYQMVRILVGTLVEVGIGKRSVESISGILAARDRRAAGVTAPAKGLTL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 WDVYYE 244


>gi|229552739|ref|ZP_04441464.1| tRNA-pseudouridine synthase I [Lactobacillus rhamnosus LMS2-1]
 gi|229313945|gb|EEN79918.1| tRNA-pseudouridine synthase I [Lactobacillus rhamnosus LMS2-1]
          Length = 242

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 119/244 (48%), Gaps = 5/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVAHF 64
           M + Y+G+ + G+Q Q    ++QG ++KA+  +  G+ V V G+GRTDSGVHAL QV  F
Sbjct: 1   MTLAYDGTNFAGYQVQPKQRTVQGVLQKALTKMAKGQPVHVDGSGRTDSGVHALGQVISF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D         + +A+N+ +     I IL   IV   FHAR+SA  + Y YR+        
Sbjct: 61  DYPGNIPAESMLRAMNSLM--PLDIEILKAEIVAADFHARYSAKGKRYRYRVARGYYTNP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG--N 182
             +      P  LD + + +A + LVG HDFT+F +        +RTI    V      N
Sbjct: 119 FNRLYTGHYPYKLDVKRIEVALKDLVGTHDFTSFAASGGVIKDKVRTIYEATVEEDPATN 178

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +        FL+  +R  V +   +G+G+    D ++  + +DR++    AP  GLY  
Sbjct: 179 ELIFEFYGNGFLYNMVRILVATALEIGNGRRDVHDFQRLFEVKDRQQARGTAPASGLYLK 238

Query: 243 SVEY 246
            V Y
Sbjct: 239 EVYY 242


>gi|313893105|ref|ZP_07826682.1| tRNA pseudouridine synthase A [Veillonella sp. oral taxon 158 str.
           F0412]
 gi|313442458|gb|EFR60873.1| tRNA pseudouridine synthase A [Veillonella sp. oral taxon 158 str.
           F0412]
          Length = 261

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 74/248 (29%), Positives = 123/248 (49%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    +I+ Y+G+   G+Q+Q N    ++QG +E  +  +  E + ++GA RTD+GVHA 
Sbjct: 1   MRNIRIIVAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSKICNEPIQIYGASRTDAGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F          + +A+ A+  I   I +L    +   +  R++   + Y+Y I  
Sbjct: 61  FQVCTFQTSGAIPAENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYVYTIHN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +     L K   W + K L+ E M+ A   L+G HDFTT +  +   + P++TI    V 
Sbjct: 119 QLIANPLTKRYHWHVKKPLNIELMQAAGNELLGTHDFTTLKGTNSTPADPVKTIMGIQVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + I VV   FL+  +R+  G L  VG G+    D++  L A+DR+  G  AP +G
Sbjct: 179 GEGPHVTISVVGDGFLYHMVRNIAGLLVDVGLGRRKVEDIKGYLAAKDRRVIGKTAPAQG 238

Query: 239 LYFDSVEY 246
           L  + + +
Sbjct: 239 LCLEEIFF 246


>gi|239814424|ref|YP_002943334.1| tRNA pseudouridine synthase A [Variovorax paradoxus S110]
 gi|259550491|sp|C5CSH0|TRUA_VARPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239801001|gb|ACS18068.1| tRNA pseudouridine synthase A [Variovorax paradoxus S110]
          Length = 270

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 88/250 (35%), Positives = 127/250 (50%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I YNG  Y GWQ Q++G ++Q  +E A+     + +    AGRTD+GVHAL QV
Sbjct: 1   MRLALGIRYNGQAYEGWQSQRSGRTVQDKLEAALAKFAAQPIGTLCAGRTDAGVHALMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E  P    +  N +L   D I++     V  +FH R SA+ R YLY +     
Sbjct: 61  VHFDTTVEREPFSWMRGTNRFL--PDDIAVQWAQPVPDEFHCRASALARRYLYVLSQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             +L+ GR       LD + MR AA  LVG+HDF++FR+  CQA SP++ +   ++   G
Sbjct: 119 RPSLDSGRVGWSMHPLDGDAMRAAAALLVGKHDFSSFRASACQARSPVKDLRRIEITRVG 178

Query: 182 N----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +           A +FLH  IR+ +G L  +G G      + + L+A+ RK   P     
Sbjct: 179 SGDRCRWHFEFEADAFLHHMIRNLMGCLVRIGRGDERPEWITEVLEARSRKVAAPTFSAN 238

Query: 238 GLYFDSVEYS 247
           GLYF    Y 
Sbjct: 239 GLYFLGPLYD 248


>gi|315649669|ref|ZP_07902753.1| tRNA pseudouridine synthase A [Paenibacillus vortex V453]
 gi|315274857|gb|EFU38233.1| tRNA pseudouridine synthase A [Paenibacillus vortex V453]
          Length = 266

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 82/257 (31%), Positives = 123/257 (47%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    M + Y+G+ Y G+Q Q  G +IQ  +E AI  ++GE + +  +GRTD+GVHA  Q
Sbjct: 1   MRNLLMRVSYDGTDYNGFQTQPGGHTIQDYLEDAIHRLSGEQLKIIASGRTDAGVHARAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F           C ALN +L   + I + +   V  +FH+R +A R++Y Y I   Q
Sbjct: 61  VFNFYTASPIPLERWCMALNTWL--PEDIVVSDAMEVPMEFHSRHAAKRKTYRYTINANQ 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +         LD   M    +HL+G +D+TTF S     SS +RTI        
Sbjct: 119 HPDLFNRRYQIHHYGQLDIPAMEQGLRHLIGTYDYTTFASRKSTKSSHVRTIFDAWFERD 178

Query: 181 GNL----------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            ++          I   +    FL   +R  +G+L  VG+GK    D++  L+A++R   
Sbjct: 179 TSMCRPGTRDQGVIHTYLSGNGFLQHMVRIIMGTLIEVGEGKRHPDDMKIILEAKNRAAA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           GP A  +GL    VEY 
Sbjct: 239 GPTAMGKGLMLWEVEYD 255


>gi|58336660|ref|YP_193245.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus NCFM]
 gi|227903218|ref|ZP_04021023.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus ATCC 4796]
 gi|62901152|sp|Q5FM60|TRUA_LACAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|58253977|gb|AAV42214.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus NCFM]
 gi|227869023|gb|EEJ76444.1| tRNA pseudouridine synthase A [Lactobacillus acidophilus ATCC 4796]
          Length = 262

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 133/250 (53%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG++E A+  +T G+ ++V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTVEDALKKMTKGKRIIVQGSGRTDAGVHAIGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +E     +  ALN+ +     I   +  IVD+ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKEIPANRMILALNSMM--PTDIVFTDCQIVDEDFHARYSIKGKWYRYRLSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
                 ++      P  LD E MRIAAQ L+G+HDFT+F +   Q    +RTI + ++  
Sbjct: 121 YFVNPFKRFYTGHFPYQLDLEKMRIAAQDLLGKHDFTSFAASGGQIKDKVRTIYYINITK 180

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N I    +   FL+  +R  V +L  +G+ +    DL + + A+DR+E    A   
Sbjct: 181 DEKENEIVFDFIGSGFLYNMVRIMVAALLEIGNERRPLHDLRRVIAAKDRQEVRQTAQGS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>gi|237802891|ref|YP_002888085.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
 gi|237804813|ref|YP_002888967.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|255311275|ref|ZP_05353845.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 6276]
 gi|255317577|ref|ZP_05358823.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 6276s]
 gi|231273113|emb|CAX10026.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231274125|emb|CAX10919.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
          Length = 267

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 128/251 (50%), Gaps = 6/251 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   + I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  
Sbjct: 1   MTKKIVLQIAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQG 60

Query: 60  QVAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           Q+AHF          P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +
Sbjct: 61  QIAHFHCPDHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                PL   +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D
Sbjct: 119 SLLPKPLPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   +L+ +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP
Sbjct: 179 LSEQEHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>gi|108758714|ref|YP_633269.1| tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
 gi|30913405|sp|Q93NE2|TRUA_MYXXA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|14517923|gb|AAK64428.1|AF377337_4 pseudouridine synthase TruA [Myxococcus xanthus]
 gi|108462594|gb|ABF87779.1| tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
          Length = 265

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + +EY G+ Y GWQ Q NG SIQ  +E  +  + G  V V  AGRTD+GVHA  Q
Sbjct: 1   MPRLKLTLEYEGTRYVGWQVQPNGPSIQSVLESGLERLLGARVSVASAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD  R          LN  L     +++++   V + F  R  +  + Y YR+  R+
Sbjct: 61  VACFDSPRVLPMKAYVMGLNGLL--PPDVAVVDAVEVAEDFDPRRWSRGKRYRYRVSNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
               L +   W +   LD E MR AA HL+GRHDF+ FR+  CQA   +R I    V  +
Sbjct: 119 TRSPLRRMTHWEVFAPLDVEAMRQAAAHLLGRHDFSAFRAADCQAKHAVREIRSLAVEGT 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   V   +FL   +R+  G+L  VG G+  ++ + + L +Q+RK  GP APP+GL
Sbjct: 179 SGDAVSFVVEGTAFLKHMVRNLAGTLVEVGKGRRPASWVAEVLASQERKRAGPTAPPQGL 238

Query: 240 YFDSVEY 246
             + V Y
Sbjct: 239 VLEEVFY 245


>gi|323463783|gb|ADX75936.1| tRNA pseudouridine synthase A [Staphylococcus pseudintermedius
           ED99]
          Length = 267

 Score =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/245 (33%), Positives = 121/245 (49%), Gaps = 2/245 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I YNG+ + G+Q Q  G +IQG  EK +  +  + V +H + RTD GVHA  Q
Sbjct: 1   MQRVLVKISYNGAQFLGFQIQNQGRTIQGYFEKILKRMHQQHVRIHPSSRTDRGVHAKAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             HFD      P     A+N+ L   D I + ++S +D+ FH R+  + + Y Y I   +
Sbjct: 61  YFHFDTHLNITPERWQHAMNSAL--PDDIYVHDVSFIDRDFHCRYDCVGKRYRYSIYQAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                        PK+LD E M+ AAQ+ VG H+FTTF S   +  S  RTI    +   
Sbjct: 119 HRNPFWSQLKTFEPKALDIEAMQRAAQYFVGTHNFTTFCSQKTEVESKERTIYESRIEQT 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I+  +    FL+  +R  +  L  VG GK ++ D+   L  QDR      AP EGLY
Sbjct: 179 ADGIDFVITGSGFLYNMVRVIMAYLLEVGKGKRSADDVSNLLAQQDRNLVPHTAPAEGLY 238

Query: 241 FDSVE 245
            + + 
Sbjct: 239 LEKIY 243


>gi|76789199|ref|YP_328285.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|123606852|sp|Q3KLN5|TRUA_CHLTA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76167729|gb|AAX50737.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
          Length = 267

 Score =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 128/251 (50%), Gaps = 6/251 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   + I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  
Sbjct: 1   MTKKIVLQIAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQG 60

Query: 60  QVAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           Q+AHF          P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +
Sbjct: 61  QIAHFHCPDHPHFTDPRQIQKMLNALL--PHDIVIHDAVMTDGDFHSRFSAIAKEYRYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                PL   +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D
Sbjct: 119 SLLPKPLPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   +L+ +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP
Sbjct: 179 LSEQEHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>gi|295692190|ref|YP_003600800.1| tRNA pseudouridine synthase a [Lactobacillus crispatus ST1]
 gi|295030296|emb|CBL49775.1| tRNA pseudouridine synthase A [Lactobacillus crispatus ST1]
          Length = 262

 Score =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 134/250 (53%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGQRVIVQGSGRTDAGVHAVGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  A+N+ +     I   +  IVD+ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILAMNSMM--PTDIIFDDCQIVDENFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
                 ++      P  LD E M++AAQ L+G+HDFT+F +   Q  + +RTI + ++  
Sbjct: 121 HFVNPFKRFYTGHFPYPLDIEKMQVAAQDLLGKHDFTSFAASGGQIENKVRTIYYVNITK 180

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   
Sbjct: 181 DEKENEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPIHDLQRVIAAKDRQEVRQTAHAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>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 =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 117/251 (46%), Positives = 162/251 (64%), Gaps = 5/251 (1%)

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  VAHCDLERGWQAFRLSEALNYHLK-PAPVAIVDCAIVEGDWHARFSAVERRYLFRLVARR 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 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLAGVGYP 250


>gi|323440101|gb|EGA97816.1| tRNA pseudouridine synthase A [Staphylococcus aureus O11]
 gi|323442775|gb|EGB00401.1| tRNA pseudouridine synthase A [Staphylococcus aureus O46]
          Length = 267

 Score =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 124/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M+ AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMKRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEILKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHDVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|327468298|gb|EGF13783.1| tRNA pseudouridine synthase A [Streptococcus sanguinis SK330]
          Length = 249

 Score =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G G+ G+QRQ +  S+Q  IEK +  +  G+ VV+HGAGRTDSGVHAL 
Sbjct: 1   MTRYKAIISYDGYGFAGFQRQLHARSVQEEIEKTLTRINKGQPVVIHGAGRTDSGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  E     L  AL+   +  + I  + +  V  +FH+R++   ++Y + +   
Sbjct: 61  QVLHFDLPEERDEEKLRFALDT--QTPEDIDFIRVEQVSDEFHSRYNKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  L+   +  A   L G HDFT F +        +RTI    V  
Sbjct: 119 RPKNPMMRHYATHYPYPLELRLIEEAIAQLEGTHDFTGFTASGTSVEDKVRTITEAKVRY 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +  N +        FL+ QIR+ VG+L  +G+ +     +++ L  +DR   GP A P 
Sbjct: 179 DAERNFLVFTFSGNGFLYKQIRNMVGTLLKIGNKRMPVEQIQRILAEKDRHLAGPTAGPN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIRYE 248


>gi|170017912|ref|YP_001728831.1| tRNA pseudouridine synthase A [Leuconostoc citreum KM20]
 gi|238688937|sp|B1MVY3|TRUA_LEUCK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169804769|gb|ACA83387.1| tRNA pseudouridine synthase A [Leuconostoc citreum KM20]
          Length = 260

 Score =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 85/256 (33%), Positives = 128/256 (50%), Gaps = 12/256 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-----GSSIQGSIEKAIFLVTGEIVV---VHGAGRTD 52
           M RY  I+ Y+GS +FG+Q Q         ++QG + KA+  +  + V    V GA RTD
Sbjct: 1   MTRYKAIVAYDGSNFFGFQVQTKSGVEVQRTVQGELNKAVNQMAKQPVTPIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL  +  PV + K LN  L     I I  ++ V   FHARFS   + Y
Sbjct: 61  TGVHAFGQVVHFDLPFDINPVGVSKGLNTLL--PRDILIKAVTKVSDDFHARFSTHAKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            YR+ T       ++         LD   ++ A   L+G HDF +F +   Q +S +RTI
Sbjct: 119 FYRVSTTAFTDPFKRHYTGHFHWHLDTSRIQEALPDLIGEHDFASFAASGNQTASTVRTI 178

Query: 173 DHFDVNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
               +    +   +       +FL+ QIR  VG L  +G+G+    D+++ +  +DR++ 
Sbjct: 179 TSAQLIEKPDEQELVFVFEGNAFLYNQIRIMVGVLLEIGNGRREIHDIQRLIAVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEY 246
              AP  GLY D ++Y
Sbjct: 239 RFTAPASGLYLDEIDY 254


>gi|313890306|ref|ZP_07823938.1| tRNA pseudouridine synthase A [Streptococcus pseudoporcinus SPIN
           20026]
 gi|313121292|gb|EFR44399.1| tRNA pseudouridine synthase A [Streptococcus pseudoporcinus SPIN
           20026]
          Length = 249

 Score =  272 bits (697), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 128/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           MIRY  II Y+GS + G+QRQ N  +IQ  IEK +  +  G+ + + GAGRTD+GVHA  
Sbjct: 1   MIRYKAIISYDGSQFSGFQRQTNARTIQEEIEKTLMRLNKGKTITIQGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++++  V   FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLAERRDLEKLRFALDT--QTPEDIDVISVEEVSNDFHARYSKHLKTYEFIVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  LD   +++A + LVG HDFT F +      + +RT+   D N 
Sbjct: 119 RPKNPMMRQYATHYPYPLDFSLIKLAIKDLVGTHDFTGFTAAGTSVENKVRTLYQADCNF 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S    +        FL+ Q+R+ VG+L  +G+ +     +   L+ ++R+  GP     
Sbjct: 179 DSHRQFLIFTFTGNGFLYKQVRNMVGTLLKIGNQRMPVEQVRIILEQKNRQLAGPTIAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>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 =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 129/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE  +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIELVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D++FHARF A  R Y Y +   
Sbjct: 61  MVAHFDTNAIRPERGWIMGANSQL--PKDISIQWIKQMDEEFHARFKATARRYRYVVYNA 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+ +G L  +G G +    ++    A+DRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDAMFAAEDRKAAGITAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCYYP 246


>gi|296435991|gb|ADH18165.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/9768]
 gi|296437852|gb|ADH20013.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/11074]
 gi|297140352|gb|ADH97110.1| tRNA pseudouridine synthase A [Chlamydia trachomatis G/9301]
          Length = 267

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 87/251 (34%), Positives = 128/251 (50%), Gaps = 6/251 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   + I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  
Sbjct: 1   MTKKIVLQIAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQG 60

Query: 60  QVAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           Q+AHF          P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +
Sbjct: 61  QIAHFHCPDHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P+   +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D
Sbjct: 119 SLLPKPVPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   +L+ +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP
Sbjct: 179 LSEQEHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>gi|116511297|ref|YP_808513.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           SK11]
 gi|123320604|sp|Q031N1|TRUA_LACLS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116106951|gb|ABJ72091.1| Pseudouridylate synthase [Lactococcus lactis subsp. cremoris SK11]
          Length = 253

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 123/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+Q Q N  ++Q  IEK +  +   E V++ G+GRTDSGVHA  
Sbjct: 1   MTRYKATIAYDGTDFAGFQSQTNQRTVQEEIEKVLSKLNSFEPVILQGSGRTDSGVHAFG 60

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFDL  +      L   L+   +    I++  + +V   +HAR+    ++Y Y +  
Sbjct: 61  QVIHFDLNGKARDLERLRFGLDT--QTPADIAVKKVELVPDDWHARYQKHEKTYEYYLEN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                   +         L+ E M+ A   LVG+HDFT F +        +RTI   ++ 
Sbjct: 119 SVTRSPFHRHSKAYFRYPLNFELMQGAMAKLVGQHDFTGFTASGSSVDDKVRTIYQAEII 178

Query: 179 S-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                  +       FL+ Q+R+ VG++  +G+ +   + ++K L +++R   GP A PE
Sbjct: 179 QLDKENFKFIFRGNGFLYKQVRNMVGTVIKIGNDRMPVSQIDKILTSKNRNFAGPTAAPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLKEVKYE 248


>gi|319893169|ref|YP_004150044.1| tRNA pseudouridine synthase A [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162865|gb|ADV06408.1| tRNA pseudouridine synthase A [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 267

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 83/245 (33%), Positives = 121/245 (49%), Gaps = 2/245 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I YNG+ + G+Q Q  G +IQG  EK +  +  + V +H + RTD GVHA  Q
Sbjct: 1   MQRVLVKISYNGAQFLGFQIQNQGRTIQGYFEKILKRMHQQHVRIHPSSRTDRGVHAKAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             HFD      P     A+N+ L   D I + ++S +D+ FH R+  + + Y Y I   +
Sbjct: 61  YFHFDTHLNITPERWQHAMNSAL--PDDIYVHDVSFIDRDFHCRYDCVGKRYRYSIYQAE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                        PK+LD E M+ AAQ+ VG H+FTTF S   +  S  RTI    V   
Sbjct: 119 HRNPFWSQLKTFEPKALDIEAMQRAAQYFVGTHNFTTFCSQKTEVESKERTIYESRVEQT 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I+  +    FL+  +R  +  L  VG G+ ++ D+   L  QDR      AP EGLY
Sbjct: 179 ADGIDFVITGSGFLYNMVRVIMAYLLEVGKGRRSADDVPNLLAQQDRNLVPHTAPAEGLY 238

Query: 241 FDSVE 245
            + + 
Sbjct: 239 LEKIY 243


>gi|57650803|ref|YP_187018.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           COL]
 gi|87160970|ref|YP_494808.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|88196131|ref|YP_500948.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|151222333|ref|YP_001333155.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|161510423|ref|YP_001576082.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|221140179|ref|ZP_03564672.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. JKD6009]
 gi|258450785|ref|ZP_05698844.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5948]
 gi|262048488|ref|ZP_06021372.1| tRNA pseudouridine synthase A [Staphylococcus aureus D30]
 gi|262052013|ref|ZP_06024224.1| tRNA pseudouridine synthase A [Staphylococcus aureus 930918-3]
 gi|282922088|ref|ZP_06329784.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9765]
 gi|284025245|ref|ZP_06379643.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           132]
 gi|294848752|ref|ZP_06789497.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9754]
 gi|304379403|ref|ZP_07362138.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|62901165|sp|Q5HDY9|TRUA_STAAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123098008|sp|Q2FW37|TRUA_STAA8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123763262|sp|Q2FES0|TRUA_STAA3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|172049003|sp|A6QJ61|TRUA_STAAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030147|sp|A8Z326|TRUA_STAAT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57284989|gb|AAW37083.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           COL]
 gi|87126944|gb|ABD21458.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87203689|gb|ABD31499.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|150375133|dbj|BAF68393.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160369232|gb|ABX30203.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|257861568|gb|EEV84370.1| tRNA pseudouridine synthase A [Staphylococcus aureus A5948]
 gi|259160068|gb|EEW45101.1| tRNA pseudouridine synthase A [Staphylococcus aureus 930918-3]
 gi|259163346|gb|EEW47904.1| tRNA pseudouridine synthase A [Staphylococcus aureus D30]
 gi|269941808|emb|CBI50218.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|282593556|gb|EFB98549.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9765]
 gi|294824131|gb|EFG40555.1| tRNA pseudouridine synthase A [Staphylococcus aureus A9754]
 gi|302752092|gb|ADL66269.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304341935|gb|EFM07839.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|315198251|gb|EFU28582.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320140243|gb|EFW32102.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320143513|gb|EFW35294.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MRSA177]
 gi|329314902|gb|AEB89315.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           T0131]
 gi|329732055|gb|EGG68410.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           21189]
          Length = 267

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD   M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLGKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|270291103|ref|ZP_06197326.1| tRNA pseudouridine synthase A [Pediococcus acidilactici 7_4]
 gi|304385383|ref|ZP_07367728.1| tRNA pseudouridine synthase A [Pediococcus acidilactici DSM 20284]
 gi|270280499|gb|EFA26334.1| tRNA pseudouridine synthase A [Pediococcus acidilactici 7_4]
 gi|304328590|gb|EFL95811.1| tRNA pseudouridine synthase A [Pediococcus acidilactici DSM 20284]
          Length = 248

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 120/250 (48%), Gaps = 7/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHAL 58
           +RY + + Y+G+ + G+Q Q N  +++G +++A+  +       + + G+GRTD+GVHA 
Sbjct: 1   MRYKITMAYDGTNFAGFQAQPNQRTVEGVLKRAVNKIAKNPQPEIPIFGSGRTDAGVHAF 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFDL  E     +  ALN+ L       +  + IVD+ FHARF+   + Y YR+  
Sbjct: 61  GQVVHFDLPIEMTANNMLHALNSIL--PLDTQVKKVEIVDEDFHARFTTHGKRYQYRMAL 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +     ++         +  E ++ A + L G HDF++F +    A + +RTI      
Sbjct: 119 GEFVDPFKRNYTGHWKFPISIELIQQAIKDLEGTHDFSSFVASGSTAKNHVRTIYEAKAW 178

Query: 179 SFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                N I        FL+  +R  V  L  +G  +    D+ + L  +DR +    AP 
Sbjct: 179 KDEAQNEIIFEFYGNGFLYNMVRIMVAVLVEIGSKRRPVDDIPRLLAVKDRNQARGTAPA 238

Query: 237 EGLYFDSVEY 246
            GLY   V+Y
Sbjct: 239 SGLYLKEVDY 248


>gi|310644170|ref|YP_003948929.1| tRNA pseudouridine synthase a [Paenibacillus polymyxa SC2]
 gi|309249121|gb|ADO58688.1| tRNA pseudouridine synthase A [Paenibacillus polymyxa SC2]
          Length = 261

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 85/257 (33%), Positives = 127/257 (49%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M   CM + Y+G+ Y G+Q Q +G++IQ  +E AI+ +TGE + + G+GRTD+GVHA  Q
Sbjct: 1   MRNLCMKVNYDGTHYDGFQTQPSGNTIQDCLENAIYSLTGERLKITGSGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F           C ALNA+L     I + +   V   FHAR  A R++Y Y I   +
Sbjct: 61  VFNFHTESPIPIHRWCLALNAWL--PRDIIVTDAREVPLSFHARRMAKRKTYRYSINANR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
            P    +      P +LD   M     HLVG  D+T+F S   Q ++ +RTI    +   
Sbjct: 119 FPDIFHRRTQAHHPTNLDVRAMEKGLAHLVGTFDYTSFASRRSQKTNHVRTIYEAYITVD 178

Query: 179 --------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                       +I   +    FL   +R  +G+L  VG+GK +  D+   L+A++R + 
Sbjct: 179 HSFSRPGSDDQGIIHTYITGSGFLQHMVRIIMGTLLEVGEGKKSPDDIPSILEAKNRSKA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           GP A    L   +VEY 
Sbjct: 239 GPTAVGHALTLWNVEYE 255


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

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 119/241 (49%), Gaps = 6/241 (2%)

Query: 8   IEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + Y+G+ Y G+Q Q+   N  +IQ  + +AI ++TGE V +  AGRTD+GVHA  QV  F
Sbjct: 1   MSYDGTSYHGFQTQEDPTNLPTIQDELMRAIQVLTGEEVKITCAGRTDAGVHARGQVVDF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                        A+N+ L     I+++    V + FH+RF A+ + Y Y I   +    
Sbjct: 61  LTTSRIPDEKFPLAMNSLL--PKDIAVVKAETVAEDFHSRFGALGKHYRYSIYNHRIHSP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFGNL 183
                ++ +   L    M+ AA + VG HDF  F +        +RTI H  +  +  NL
Sbjct: 119 FHHRYSYQVYPPLHVAAMQEAAGYFVGTHDFRGFCATGSPVKDFVRTIWHCTLTVTEENL 178

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + V+   FL+  +R   G+L  VG GK     + + + ++DR + G  APP+GL    
Sbjct: 179 LLMDVMGDGFLYNMVRIITGTLVDVGKGKIAPESIPQIIASRDRTQAGTTAPPQGLALLE 238

Query: 244 V 244
           V
Sbjct: 239 V 239


>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 =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 96/247 (38%), Positives = 136/247 (55%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           RY + +EY+G+ Y GWQ Q+  +  SIQ ++EKA+  +    V V  AGRTD+ V+A  Q
Sbjct: 23  RYALCVEYSGAEYRGWQIQREGDVPSIQATVEKALSKIANAPVSVICAGRTDARVNATYQ 82

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD              N  L   D I+I     V + FHARFSA+ R Y Y I +  
Sbjct: 83  IIHFDSPVRRDERAWVMGTNTNL--PDDIAIQWAKQVPESFHARFSALERRYRYLIYSNP 140

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+         K +D   M+ A +HLVG HDFT++R++ CQA SP+RT+  F+V   
Sbjct: 141 VKPAILPKGITWTYKEMDVARMQEAVKHLVGEHDFTSYRAVGCQAHSPVRTVKEFNVYRE 200

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+ + V A +FLH  IR+F G L  +G G+      ++ L A+DR++ G  APP GLY
Sbjct: 201 GRLVILDVRANAFLHHMIRNFAGVLMTIGCGEAEPIWAKEVLDARDRRQGGVTAPPFGLY 260

Query: 241 FDSVEYS 247
           F   +Y 
Sbjct: 261 FVDAKYP 267


>gi|78045100|ref|YP_361085.1| tRNA pseudouridine synthase A [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77997215|gb|ABB16114.1| tRNA pseudouridine synthase A [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 246

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 123/246 (50%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
             + + I Y+G+ + G+Q+QKN   +IQG +E+ +  +  E V V GAGRTD+GVHAL Q
Sbjct: 5   PNFKLTIAYDGTNFAGFQKQKNTPQTIQGILEEKLHKILKEPVKVIGAGRTDAGVHALGQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F    +     + + LN  L     I +L   IV   FHAR+SA ++ Y Y +    
Sbjct: 65  VVNFSAPWKAPVDKIPEILNNTL--PTAIRVLEAEIVPDDFHARYSARKKEYRYYLYYGP 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  AW +P+ LD E +  A ++L+G HDF+ F +      +PI+T+        
Sbjct: 123 -PSPFYERYAWALPQKLDREKVAKALEYLIGTHDFSGFGAAGSSGKNPIKTMFEASYRED 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L     VA SFL+   R   G+L  +G        + + L   ++K  G  AP  GL+
Sbjct: 182 GFLGYFTFVADSFLYKMARILTGTLVEIGLNGH-PERVREILTTGNKKLAGKTAPAHGLF 240

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


>gi|255507054|ref|ZP_05382693.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D(s)2923]
 gi|289525508|emb|CBJ14985.1| tRNA pseudouridine synthase A [Chlamydia trachomatis Sweden2]
 gi|296435064|gb|ADH17242.1| tRNA pseudouridine synthase A [Chlamydia trachomatis E/150]
 gi|296438784|gb|ADH20937.1| tRNA pseudouridine synthase A [Chlamydia trachomatis E/11023]
          Length = 267

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 128/251 (50%), Gaps = 6/251 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  +  + I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  
Sbjct: 1   MTEKIVLQIAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQG 60

Query: 60  QVAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           Q+AHF          P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +
Sbjct: 61  QIAHFHCPDHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                PL   +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D
Sbjct: 119 SLLPKPLPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   +L+ +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP
Sbjct: 179 LSEQEHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEYLLDMLATKDRRKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>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 =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 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 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP+  ++G+ W +   LD   MR  A  L+G HDFTTFR+  CQA SP++T+D   +   
Sbjct: 120 APVVHDRGKVWQVQNPLDVAAMREGAAQLIGLHDFTTFRAAMCQAKSPVKTLDEITIEEI 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 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|32472096|ref|NP_865090.1| tRNA pseudouridine synthase A [Rhodopirellula baltica SH 1]
 gi|42559754|sp|Q7TU07|TRUA_RHOBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|32397468|emb|CAD72774.1| tRNA pseudouridine synthase A [Rhodopirellula baltica SH 1]
          Length = 276

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 76/254 (29%), Positives = 119/254 (46%), Gaps = 14/254 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y+G+ Y GWQ Q    SIQ  +E+ I  + G  V V G+GRTD+GVHA+ QVA   
Sbjct: 12  LTVAYDGTEYCGWQVQPEQRSIQSELERVIRPLAGRPVRVLGSGRTDAGVHAIGQVARCV 71

Query: 66  LVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           L       V L +A+N+ L   + I +  +    ++FH    A  + Y Y +    +   
Sbjct: 72  LPVWKADTVALQRAINSKL--PNDIRVKAVRETRERFHPIADATGKQYQYLVQVGGSRDP 129

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS----- 179
                   +   +D   M+ AA   VGRHDF  F+    +  S +RTI            
Sbjct: 130 FANRFVNRVGGPIDHSAMQSAAAKFVGRHDFKAFQGTGAERPSTVRTIHSARWIPRVATG 189

Query: 180 ------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                  G      +    FL+  +R+ +G++  VG GK +   +++ L ++DRK  GP 
Sbjct: 190 PTGAELEGEHWCFEIDGEGFLYNMVRNLMGTMLEVGRGKKSPNWIDEVLASRDRKMAGPT 249

Query: 234 APPEGLYFDSVEYS 247
           APP+GL+   V+Y 
Sbjct: 250 APPQGLFLCRVDYP 263


>gi|29349645|ref|NP_813148.1| tRNA pseudouridine synthase A [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253569984|ref|ZP_04847393.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_6]
 gi|42559809|sp|Q89ZY4|TRUA_BACTN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|29341555|gb|AAO79342.1| tRNA pseudouridine synthase A [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251840365|gb|EES68447.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_6]
          Length = 269

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 90/250 (36%), Positives = 121/250 (48%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NGSS+Q  + KA+       V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGSSVQECLMKALSTFLRRDVEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDHEDVLDTVTVADKLNRLL--PPDISVYRVRQVKPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   + +  SLD E M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRYRVYGSLDYERMNEAARTLFEYIDFTSFSKLHTDVKTNICHISHAEWTKM 176

Query: 181 GNL---IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                     + A  FL   +R+ VG+L  VG GK T     K ++ QDR + G  AP  
Sbjct: 177 EGEDTTWVFTIRADRFLRNMVRAIVGTLLEVGRGKLTVEGFRKVIEQQDRCKAGTSAPGN 236

Query: 238 GLYFDSVEYS 247
            L+  +VEY 
Sbjct: 237 ALFLVNVEYP 246


>gi|239500845|ref|ZP_04660155.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB900]
          Length = 265

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ +Q   +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D++FHARF A  R Y Y +   
Sbjct: 61  MVAHFDTNAIRQERGWIMGANSQL--PKDISIQWIKQMDEEFHARFKATARRYRYVVYNA 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+ +G L  +G G +    ++    A+DRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRKAAGITAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCYYP 246


>gi|302333855|gb|ADL24048.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JKD6159]
          Length = 267

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ   G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFKGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  +  L  VG G+   +D+ K L++++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLLAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|206889178|ref|YP_002249342.1| tRNA pseudouridine synthase A [Thermodesulfovibrio yellowstonii DSM
           11347]
 gi|238057737|sp|B5YGE4|TRUA_THEYD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|206741116|gb|ACI20173.1| tRNA pseudouridine synthase A [Thermodesulfovibrio yellowstonii DSM
           11347]
          Length = 254

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 86/257 (33%), Positives = 126/257 (49%), Gaps = 14/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+   M I+Y+G+ YFGWQRQ+ G +IQ +IE+ +  +    + + GAGRTD+GVHAL Q
Sbjct: 1   MVNIKMTIQYDGTNYFGWQRQRKGRTIQATIEECLRKIFQREIKIRGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F    +    IL K LN+ L   + I I+ L  V+  FH + S  R+SY+Y +   +
Sbjct: 61  VATFKAELKMSLDILKKVLNSLL--PNDIKIIKLENVEDSFHPQHSVKRKSYIYYLCFDE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF----- 175
                 +   W  P  LD   M  A     G  DFT F        + IRT+  F     
Sbjct: 119 ECSCFIQRYVWHYPWKLDLSLMEEALSLFTGTKDFTAFSGS-TDVKNKIRTVHDFTMQLL 177

Query: 176 ------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                 D+   GN I+ R+ A  FL   +R+ VG +  +G GK     +++A ++  R  
Sbjct: 178 TKLCFMDMCLNGNFIKFRIEADGFLRYMVRNLVGCIIEIGKGKLRIESIQEAFESGKRPS 237

Query: 230 CGPLAPPEGLYFDSVEY 246
               AP  GL+ + V Y
Sbjct: 238 TMQTAPSNGLFLEKVIY 254


>gi|256849152|ref|ZP_05554585.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-1A-US]
 gi|262047168|ref|ZP_06020126.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-3A-US]
 gi|256713928|gb|EEU28916.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-1A-US]
 gi|260572413|gb|EEX28975.1| tRNA pseudouridine synthase A [Lactobacillus crispatus MV-3A-US]
          Length = 262

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  A+N+ +     I   N  IV+  FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILAMNSMM--PTDIIFNNCQIVNDDFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 ++      P  LD E M+IAAQ L+G+HDFT+F +   +    +RTI +  +  
Sbjct: 121 HFVNPFKRFYTGHFPYPLDIEKMQIAAQDLLGKHDFTSFAASGGRIEDKVRTIYYVKITE 180

Query: 180 F--GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   
Sbjct: 181 DKKDNEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLQRVIAAKDRQEVRQTAHAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>gi|229830208|ref|ZP_04456277.1| hypothetical protein GCWU000342_02317 [Shuttleworthia satelles DSM
           14600]
 gi|229791506|gb|EEP27620.1| hypothetical protein GCWU000342_02317 [Shuttleworthia satelles DSM
           14600]
          Length = 267

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 81/243 (33%), Positives = 122/243 (50%), Gaps = 3/243 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
              I Y+G+ Y GWQ Q NG S+Q  +   +  + GE +   GA RTD+GVH++     F
Sbjct: 2   RATIAYDGTEYCGWQVQPNGISVQEVVNAGLSKLLGEEITCVGASRTDAGVHSMGNEILF 61

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +         +  ALN YL   + I     S+    FH RFS   ++Y YRI+ R+ P+ 
Sbjct: 62  ETKTRIPADKIAYALNQYL--PEDIVCQGSSLAADDFHPRFSESYKTYEYRILNRRFPMP 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-GNL 183
             +  +      LD + M+ AA  L+G HDF++F SIH Q+ + +RTI    V+    +L
Sbjct: 120 TMRRDSLFYHYDLDEKRMQEAADCLLGEHDFSSFASIHTQSKTRVRTIYQALVSRNADDL 179

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I IR+    FL+  +R   G+L  VG G  +    ++ L   +R+  GP AP  GL    
Sbjct: 180 ITIRLCGDGFLYNMVRIIAGTLIEVGAGITSPRAFQQILDGMNRELAGPTAPAHGLTQVG 239

Query: 244 VEY 246
           + Y
Sbjct: 240 LHY 242


>gi|73662003|ref|YP_300784.1| tRNA pseudouridine synthase A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|123761549|sp|Q49ZD7|TRUA_STAS1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|72494518|dbj|BAE17839.1| tRNA pseudouridine synthase A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 267

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 80/244 (32%), Positives = 121/244 (49%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q++G +IQ   EK +  +    V +H + RTD GVHA+ Q 
Sbjct: 1   MRVLVNISYQGSQFLGFQIQQHGRTIQQQFEKILKRMHKHEVRIHPSSRTDRGVHAIEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + ++S V+  FH R+  + +SY Y+I     
Sbjct: 61  FHFDTELNIPEQQWQYAMNRAL--PDDIYVNDVSFVNDDFHCRYDCVGKSYRYKIYQSAH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                 G    +P+ LD E M +AAQH +G HDFT F S   +  S IRT+    +    
Sbjct: 119 KDPFLCGLKTYVPEQLDIEKMNMAAQHFIGTHDFTGFCSQKTEVESKIRTLYESRIEKTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  +  L  VG GK    ++ + L+A+DR +    AP EGLY 
Sbjct: 179 SGFDYIVTGSGFLYNMVRVLIAFLIEVGKGKREPQEVPQLLEARDRNQVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|260171626|ref|ZP_05758038.1| tRNA pseudouridine synthase A [Bacteroides sp. D2]
          Length = 267

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 119/248 (47%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     ISI  +  V    H RF A  R+Y Y + T +
Sbjct: 61  VAHFDSDELLDTTSVTDKLNRLL--PPDISIYRVCRVRPDAHVRFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   L+ E M  AA  L   +DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRLYNQLNYERMNEAAHILFEYNDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +      + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 EDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 237 FLVNVEYP 244


>gi|226945473|ref|YP_002800546.1| tRNA pseudouridine synthase A [Azotobacter vinelandii DJ]
 gi|226720400|gb|ACO79571.1| tRNA pseudouridine synthase A [Azotobacter vinelandii DJ]
          Length = 288

 Score =  272 bits (696), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 123/247 (49%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQ 60
           R  + +EY G+ Y G+QRQ    +SIQ ++E A+  V G   + V  AGRTD+ VHA  Q
Sbjct: 20  RVALGLEYRGARYHGFQRQNPRVASIQAALESALSRVAGGVPLNVVCAGRTDALVHASGQ 79

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E          N  L     IS+     +   FHARFSA  R Y Y I    
Sbjct: 80  VVHFDTPIERSMHAWTMGANMNL--PADISVAWAREMPAHFHARFSATARRYRYVIYNDP 137

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A          + LD E MR AA+ LVG HDF+ FR+  CQA SPI+T+ H  +   
Sbjct: 138 IRPAHMAEEVTWNHRPLDIERMRQAARPLVGCHDFSAFRASQCQARSPIKTVHHLQLIRH 197

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LI + + A +FLH  +R+  G L  +G G+       + L+ + R + G  A P GLY
Sbjct: 198 GRLIVLDIRANAFLHHMVRNIAGVLMTIGAGERPVEWAREVLEGRQRHKGGVTAHPYGLY 257

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 258 LVQVDYP 264


>gi|255348836|ref|ZP_05380843.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 70]
 gi|255503376|ref|ZP_05381766.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 70s]
          Length = 267

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 87/251 (34%), Positives = 128/251 (50%), Gaps = 6/251 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   + I Y G+ Y GWQ Q N  SIQ  +E  +  + G  + V  +GRTD+GVHA  
Sbjct: 1   MTKKIVLQIAYQGTSYSGWQYQPNALSIQEVLETILKKIAGFRISVISSGRTDAGVHAQG 60

Query: 60  QVAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           Q+AHF          P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +
Sbjct: 61  QIAHFHCPDHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P+   +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D
Sbjct: 119 SLLPKPVPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   +L+ +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP
Sbjct: 179 LSEQEHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEYLLDMLATKDRRKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>gi|218440649|ref|YP_002378978.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7424]
 gi|218173377|gb|ACK72110.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7424]
          Length = 306

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 122/247 (49%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ + GWQRQ N  ++Q  IE+AI +V G+ V +HGAGRTD+GVHA  QV
Sbjct: 11  QRVALVIQYLGTHFHGWQRQPNRRTVQEEIERAIAVVIGQPVTLHGAGRTDTGVHAAAQV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD +    P      LN+ L   D I +   + V  ++HARFSA  R Y Y I T + 
Sbjct: 71  AHFDQISPIPPGRWASILNSRL--PDDIIVRASNRVCDRWHARFSACWRRYRYTIYTDKQ 128

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    K  +W      L+   M+ A   L+G+H    F   +   +     I        
Sbjct: 129 PNLFIKPFSWHYYHQPLEESLMQSALDPLLGKHHLAAFHRANSARTHSWVEIQAAHCYRI 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A  FL+  +R  VG L  VG+ + +  D  +  Q Q R+E    AP +GL 
Sbjct: 189 GPFVHIEIQANGFLYGMVRLLVGMLIEVGNKQRSIEDFTRIWQNQRREEVKYAAPAKGLC 248

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 249 LLRVGYP 255


>gi|150392315|ref|YP_001322364.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
 gi|149952177|gb|ABR50705.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
          Length = 246

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 124/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    MI+EY+G+ Y GWQRQ     +IQG +E  I  + G+   + G+GRTD+G HA  
Sbjct: 1   MRNIRMIVEYDGTKYRGWQRQTATDMTIQGKLEHVISEMVGKKTEIVGSGRTDAGAHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F          + + +N YL     I +  L     +FH+R++   + Y+YRI   
Sbjct: 61  QVANFHTKSTLSIKEMYQYINQYL--PQDIVVKELKEAGPRFHSRYNVKGKKYVYRIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  ++ +P++L+ E M+ AA  LVG +DF  F S+     + +RTI+   +  
Sbjct: 119 STASVFHRKHSYHVPQALNLELMQEAAAKLVGTYDFLPFSSVKKSEKTTVRTIESITIEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +EI +V   FL+  +R   G+L  +G  K   T +++      R+  G   P +GL
Sbjct: 179 KDAFVEITIVGDGFLYNMVRIITGTLIEIGSKKKKPTYIDEIFSVGKRQNAGETVPSQGL 238

Query: 240 YFDSVEYS 247
           +   V Y+
Sbjct: 239 FLIEVYYN 246


>gi|295698698|ref|YP_003603353.1| tRNA pseudouridine synthase A [Candidatus Riesia pediculicola USDA]
 gi|291157129|gb|ADD79574.1| tRNA pseudouridine synthase A [Candidatus Riesia pediculicola USDA]
          Length = 255

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 94/247 (38%), Positives = 139/247 (56%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + I+Y+GS Y GWQ+QKNG  SIQ  +E ++  +T E +  +  GRTDSGVHA  QV
Sbjct: 4   RVALGIQYDGSRYHGWQKQKNGLDSIQKRLESSLKKLTDEDIKTYCGGRTDSGVHAFGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+  +    V+    +N +L     IS+L +  V  +FHARFSAI R Y Y I  ++ 
Sbjct: 64  VHFETYKIRKDVVWVSGVNHFL--PKDISVLWVKPVSHRFHARFSAISRHYRYLIFNKEI 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSF 180
             A+ +     I K LD ++M  AAQ L+G +D  +F S   ++  S  R I + +V  F
Sbjct: 122 RPAIFRSNVLHISKKLDYKDMNKAAQCLLGENDLISFISFDRRSFRSTKRNIRYINVKRF 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + + I +VA SF +  +R+ VGSL  VG GK  +  ++K +  +DR + GP    +GLY
Sbjct: 182 DSYVIIDIVANSFAYNMVRNIVGSLIEVGLGKKGTEWIKKLIDLKDRTKSGPKVHSKGLY 241

Query: 241 FDSVEYS 247
              + YS
Sbjct: 242 LMHINYS 248


>gi|323465853|gb|ADX69540.1| tRNA pseudouridine synthase A [Lactobacillus helveticus H10]
          Length = 262

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 133/250 (53%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG+IE A+  ++ G+ ++V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMSKGKRIIVQGSGRTDAGVHAIGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  ALN+ +     I   N  IV++ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILALNSMM--PTDIIFNNCEIVNENFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                 ++        +LD   M+ AA+ L+G+HDFT+F +   Q    +RTI + ++  
Sbjct: 121 HFVNPFKRFYTGHFSYALDVGKMQEAAKDLLGKHDFTSFAASGGQIEDKVRTIYYVNIAK 180

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N I    +   FL+  +R  V +L  +G+G+    DL++ + A+DR+E    A   
Sbjct: 181 DEKENEIVFDFIGSGFLYNMVRIMVAALLEIGNGRRPVHDLKRVIAAKDRQEVRQTAQAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>gi|161506903|ref|YP_001576857.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DPC 4571]
 gi|260102386|ref|ZP_05752623.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DSM 20075]
 gi|172048171|sp|A8YTB0|TRUA_LACH4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160347892|gb|ABX26566.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DPC 4571]
 gi|260083830|gb|EEW67950.1| tRNA pseudouridine synthase A [Lactobacillus helveticus DSM 20075]
          Length = 263

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 133/250 (53%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG++E A+  +T G+ ++V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTVEDALKKMTKGKRIIVQGSGRTDAGVHAIGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  ALN+ +     I   N  IV++ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILALNSMM--PTDIIFNNCEIVNENFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
                 ++        +LD   M+ AA+ L+G+HDFT+F +   Q    +RTI + ++  
Sbjct: 121 HFVNPFKRFYTGHFSYALDVGKMQEAAKDLLGKHDFTSFAASGGQIEDKVRTIYYVNIAK 180

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N I    +   FL+  +R  V +L  +G+G+    DL++ + A+DR+E    A   
Sbjct: 181 DEKENEIVFDFIGSGFLYNMVRIMVAALLEIGNGRRPVHDLKRVIAAKDRQEVRQTAQAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>gi|255693609|ref|ZP_05417284.1| tRNA pseudouridine synthase A [Bacteroides finegoldii DSM 17565]
 gi|260620585|gb|EEX43456.1| tRNA pseudouridine synthase A [Bacteroides finegoldii DSM 17565]
          Length = 254

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 119/248 (47%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +  A+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMNALSTFLRREIEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  +  V  + HARF A  R+Y Y + T +
Sbjct: 61  VAHFDYDEPLDTESVADKLNRLL--PPDISVYRVCRVRPEAHARFDATARTYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +     +   LD E M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRCRVYSPLDYERMNEAAKVLFEYTDFTSFSKLHTDVKTNICHITHAEWTRE 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +      + A  FL   +R+ VG+L  VG GK +     + ++ +DR + G  AP + L
Sbjct: 177 EDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLSIEGFRRIIEQKDRCKAGTSAPGQAL 236

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 237 FLVNVEYP 244


>gi|253681679|ref|ZP_04862476.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
 gi|253561391|gb|EES90843.1| tRNA pseudouridine synthase A [Clostridium botulinum D str. 1873]
          Length = 245

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 80/247 (32%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+G+ Y GWQ+  +  ++IQ  IE  +  + GE V +  +GRTD+GVHA  
Sbjct: 1   MRNIKLTIQYDGTRYKGWQKLGDADNTIQYKIESVLNELLGEEVSLIASGRTDAGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+A+F          + K    YL     I I N+S   + FH+R++  ++ Y Y I   
Sbjct: 61  QIANFKTNSNVTNDTILKHCYKYL--PQDIVITNISDASENFHSRYNVKKKIYTYNIYNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  ++ I ++LD + M+ A++  +G HDF +F ++  +  S ++TID      
Sbjct: 119 PVHDVFTRKYSYHIKETLDIKKMKEASKLFIGEHDFKSFTALKSKKKSTVKTIDSITFKK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N IEI      FL+  IR  VGSL  VG GK T  DL+  +  +DR      AP  GL
Sbjct: 179 KDNNIEIIFTGNGFLYKMIRILVGSLINVGLGKLTIEDLQNIMNKKDRSIAPETAPAHGL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 ILTEVKY 245


>gi|163787684|ref|ZP_02182131.1| putative tRNA pseudouridine synthase A [Flavobacteriales bacterium
           ALC-1]
 gi|159877572|gb|EDP71629.1| putative tRNA pseudouridine synthase A [Flavobacteriales bacterium
           ALC-1]
          Length = 252

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 118/246 (47%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  Y GWQ Q N  S+Q  +EKA+  +    V V GAGRTD+GVHA +  
Sbjct: 1   MRFFIELSYNGKEYHGWQNQPNAISVQEVLEKALSTILKAEVSVMGAGRTDAGVHASQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +E+    +   LN+YL     I++  +  V    HARF A  R+Y Y+I T + 
Sbjct: 61  AHFDFEKEFEYKDVVYKLNSYL--PKDIAVSTIFEVKPDAHARFEAKSRTYHYKISTSK- 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +   A+ +   LD E M  A + L    DF  F   +    +    I         
Sbjct: 118 -NVFDYDFAYQVQLPLDVEAMNTACKILFEYKDFQCFSKSNTDVKTYNCDIKEAFWTQNS 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG++  +G GK    DL K + +++R E G   P  GLY 
Sbjct: 177 NQLIFTITADRFLRNMVRAIVGTMVNIGLGKLKPEDLHKIIASKNRSEAGFSVPAHGLYL 236

Query: 242 DSVEYS 247
             + Y 
Sbjct: 237 AKIVYP 242


>gi|319792244|ref|YP_004153884.1| tRNA pseudouridine synthase a [Variovorax paradoxus EPS]
 gi|315594707|gb|ADU35773.1| tRNA pseudouridine synthase A [Variovorax paradoxus EPS]
          Length = 273

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 87/253 (34%), Positives = 127/253 (50%), Gaps = 9/253 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHAL 58
           +R  + I YNG  Y GWQ Q++G ++Q  +E A+     +    +    AGRTD+GVHAL
Sbjct: 1   MRLALGIRYNGQAYEGWQSQRSGRTVQDKLEAALAKFAADPSGRIGTLCAGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   E  P    +  N +L   D I++     V  +FH R SA+ R YLY +  
Sbjct: 61  MQVVHFDTEIEREPFSWMRGTNRFL--PDDIAVQWAQPVPDEFHCRASALARRYLYVLSQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                +L+ GR       LD + MR AA  L+G HDF++FR+  CQA SP++ +   ++ 
Sbjct: 119 SPVRPSLDSGRVGWSMHPLDGDAMRKAAAVLIGTHDFSSFRASACQAKSPVKNLRRIEIT 178

Query: 179 SFGN----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             G+           A +FLH  IR+ +G L  +G G      + + L+A+ RK   P  
Sbjct: 179 RVGDGERCRWHFEFEADAFLHHMIRNLMGCLVRIGRGDERPEWIAEVLEARSRKVAAPTF 238

Query: 235 PPEGLYFDSVEYS 247
             +GLYF    Y 
Sbjct: 239 SADGLYFLGPLYD 251


>gi|229027990|ref|ZP_04184143.1| tRNA pseudouridine synthase A [Bacillus cereus AH1271]
 gi|228733378|gb|EEL84207.1| tRNA pseudouridine synthase A [Bacillus cereus AH1271]
          Length = 235

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 115/235 (48%), Gaps = 3/235 (1%)

Query: 14  GYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP 72
            + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  QV HFD       
Sbjct: 2   HFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKGQVIHFDTPLSLEE 61

Query: 73  VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWL 132
                ALN  L   D I I  +    ++FHAR+   R+ Y YR++  +      +   + 
Sbjct: 62  WQWSNALNTML--PDDIVIRQVEKKTEEFHARYGVERKEYRYRVLLSKTADVFRRNYVYQ 119

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARS 192
            P  L+  ++R A  + +G HDFT+F S        +RTI   ++    + +  R V   
Sbjct: 120 YPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIEQDDELIFRFVGNG 179

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           FL+  +R  VG+L  VG GK     + + L  Q+R+  G +AP  GLY   V Y+
Sbjct: 180 FLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMAPGHGLYLWQVNYN 234


>gi|331269740|ref|YP_004396232.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
 gi|329126290|gb|AEB76235.1| tRNA pseudouridine synthase A [Clostridium botulinum BKT015925]
          Length = 245

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+G+ Y GWQ+  N  ++IQ  +E  +  + GE + +  +GRTD+GVHA  
Sbjct: 1   MRNIKLTIQYDGTRYKGWQKLGNTDNTIQCKVENVLNELLGEEISLIASGRTDAGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+A+F          + K    YL     I + N++   + FH+R++  ++ Y Y I   
Sbjct: 61  QIANFKTDSNVSNDTILKHCYKYL--PHDIVVTNVADASENFHSRYNVKKKIYTYNICNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  ++ + ++LD + M+ A++  +G HDF +F ++  +  S ++TID      
Sbjct: 119 PVHDVFTRKYSYHVKETLDIKKMKEASKLFIGEHDFKSFTALKSKKKSTVKTIDSISFKK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N IE+      FL+  IR  VGSL  VG GK T  DLE  +  +DR      AP  GL
Sbjct: 179 KDNNIEVIFTGNGFLYKMIRILVGSLINVGLGKLTIEDLENIMNEKDRSIAPETAPAHGL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 ILTEVKY 245


>gi|160872663|ref|ZP_02062795.1| tRNA pseudouridine synthase A [Rickettsiella grylli]
 gi|159121462|gb|EDP46800.1| tRNA pseudouridine synthase A [Rickettsiella grylli]
          Length = 264

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R    I Y G  Y GWQ Q     IQ  +E+AI  V    V +  AGRTD GVHAL QV
Sbjct: 1   MRIAFGISYQGGAYHGWQSQTKLPCIQTYLERAISRVADHSVRLQCAGRTDKGVHALSQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N+YL     I +  + +V+  FHARFSA+ R Y Y I  R  
Sbjct: 61  VHFDTDVWRSKKSWLFGSNSYL--PPDIRVNWVQVVEDTFHARFSALARRYRYIIYNRHL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL           L+ ++M  AAQ+LVG HDF++FR+  CQA+  +R I H  V   G
Sbjct: 119 KSALWNAYTSHCCYPLNEKDMHRAAQYLVGEHDFSSFRAASCQANHALREIQHIQVKRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + + + A +FLH  +R+    L L+G GK ++   ++ L AQ+RK     A P GLY 
Sbjct: 179 DYVIMDIQANAFLHHMVRNISAVLMLIGQGKKSTLWAQEVLFAQNRKMADVTASPTGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 SHVIYP 244


>gi|237715548|ref|ZP_04546029.1| tRNA pseudouridine synthase A [Bacteroides sp. D1]
 gi|262408556|ref|ZP_06085102.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_22]
 gi|294643196|ref|ZP_06721024.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CC 2a]
 gi|294809320|ref|ZP_06768031.1| tRNA pseudouridine synthase A [Bacteroides xylanisolvens SD CC 1b]
 gi|229444257|gb|EEO50048.1| tRNA pseudouridine synthase A [Bacteroides sp. D1]
 gi|262353421|gb|EEZ02515.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_22]
 gi|292641462|gb|EFF59652.1| tRNA pseudouridine synthase A [Bacteroides ovatus SD CC 2a]
 gi|294443478|gb|EFG12234.1| tRNA pseudouridine synthase A [Bacteroides xylanisolvens SD CC 1b]
          Length = 249

 Score =  272 bits (695), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  +  V+   HARF A  R+Y Y + T +
Sbjct: 61  VAHFDFDELLDEVSVADKLNRLL--PPDISVYRVCRVNPDAHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   LD   M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRVYNQLDYALMNEAARTLFEYTDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +      + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 DDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRVIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 237 FLVNVEYP 244


>gi|253729885|ref|ZP_04864050.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253726332|gb|EES95061.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 267

 Score =  272 bits (695), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 78/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L+ ++RK     AP EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLELKNRKNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|319952056|ref|YP_004163323.1| tRNA pseudouridine synthase a [Cellulophaga algicola DSM 14237]
 gi|319420716|gb|ADV47825.1| tRNA pseudouridine synthase A [Cellulophaga algicola DSM 14237]
          Length = 250

 Score =  271 bits (694), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 126/246 (51%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G  Y GWQ+Q N  ++QG +E A+  +    +++ GAGRTD+GVHA    
Sbjct: 1   MRYFIRFSYFGKHYHGWQKQPNAVTVQGVLEDALSKLLANEIILMGAGRTDAGVHAKELY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             LNA+L     I+IL++  V +  HARF+A+ R+Y Y I+ ++ 
Sbjct: 61  AHFDFEEIPNKENFVFRLNAFL--PKDIAILDVFQVPEDAHARFNAVARTYEYWIVQQKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P       A LI   LD   M  AAQ  +   DF  F   +   ++    + + +     
Sbjct: 119 P--FLTNHAHLIKYPLDINKMNEAAQVFLSHIDFECFSKSNTAVNTFNCDVKYAEWKVTD 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++   + A  FL   +R+ VG+L  VG GK   ++++  L+++DR + G  AP +GLY 
Sbjct: 177 GILVFTITADRFLRNMVRAIVGTLLEVGLGKIDISNVKAILKSKDRSKAGASAPAKGLYL 236

Query: 242 DSVEYS 247
            SV Y 
Sbjct: 237 TSVLYP 242


>gi|116617361|ref|YP_817732.1| pseudouridylate synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
 gi|122272438|sp|Q03ZL3|TRUA_LEUMM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116096208|gb|ABJ61359.1| Pseudouridylate synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
          Length = 255

 Score =  271 bits (694), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 80/257 (31%), Positives = 128/257 (49%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTD 52
           M RY  +I Y+G+ +FG+Q Q     ++  ++QG + K I  +       + V GA RTD
Sbjct: 1   MPRYKAVIAYDGAEFFGFQLQTKNGVESVRTVQGELNKVINKMAKNPSPQIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL     P  + K +N  L     + + ++  V   FHARF+   + Y
Sbjct: 61  TGVHAFGQVVHFDLPFNIDPEGVRKGMNTLL--PFDVVVNHVEHVSDDFHARFNTHSKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YR+ T       ++         LD   ++ A   L+G HDF +F +   + ++ IR I
Sbjct: 119 IYRVSTTDYKDPFKRKYTGHFHWKLDINRIKAALPDLLGEHDFASFAASGNETATTIRLI 178

Query: 173 DHFDVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              DV+     + I       +FL+ QIR  VG L  +G GK    D+ + ++ +DR++ 
Sbjct: 179 TRADVDEKPEEHEIVFTFEGNAFLYNQIRIMVGVLLEIGTGKRPVHDIVRLIEVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
              AP  GLY D ++Y+
Sbjct: 239 RYTAPASGLYLDEIDYN 255


>gi|326559413|gb|EGE09838.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 46P47B1]
 gi|326564997|gb|EGE15197.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 103P14B1]
 gi|326566051|gb|EGE16211.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 12P80B1]
 gi|326572448|gb|EGE22440.1| tRNA pseudouridine synthase A [Moraxella catarrhalis BC8]
 gi|326572505|gb|EGE22494.1| tRNA pseudouridine synthase A [Moraxella catarrhalis CO72]
 gi|326574101|gb|EGE24049.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 101P30B1]
 gi|326576065|gb|EGE25984.1| tRNA pseudouridine synthase A [Moraxella catarrhalis O35E]
          Length = 268

 Score =  271 bits (694), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 83/243 (34%), Positives = 133/243 (54%), Gaps = 2/243 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IE+ G+ Y GWQRQ+    +Q  IEKA+  +  E + +  AGRTD+GVHA   +AH
Sbjct: 6   LAVGIEFIGTRYRGWQRQEEVIGVQAVIEKALSTIANESIELIAAGRTDAGVHAGNMIAH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F    E       +  N+ L   D I++  +  +   FHARFSAI R Y Y  + +    
Sbjct: 66  FVTHAERSAHSWLRGTNSLL--PDDIALRWVQPMPDDFHARFSAIARRYRYITLNQPYRP 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+ + +       LD + M IA+Q +VG HDF++FR+  CQ++ P+RT+ H ++   G+ 
Sbjct: 124 AILRHQVTHEYTKLDIDAMIIASQFIVGTHDFSSFRAAACQSNQPVRTVTHANLFQHGSY 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A  FLH  +R+ +G+L  VG G+ +     + + A++R    P A  +GLYF +
Sbjct: 184 LILDIQADGFLHHMVRNIMGALFAVGRGEISPETFYELMLAKNRTLAPPTASADGLYFIN 243

Query: 244 VEY 246
             Y
Sbjct: 244 AYY 246


>gi|81429336|ref|YP_396337.1| tRNA pseudouridine synthase A [Lactobacillus sakei subsp. sakei
           23K]
 gi|123742201|sp|Q38UV3|TRUA_LACSS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78610979|emb|CAI56031.1| tRNA pseudouridylate synthase A (Pseudouridylate synthase I)
           [Lactobacillus sakei subsp. sakei 23K]
          Length = 249

 Score =  271 bits (694), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 128/248 (51%), Gaps = 5/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY + + Y+G+ + G+Q Q    ++QG++EKA+  ++ G  + V+G+GRTDSGVHA+ Q
Sbjct: 3   QRYRVTVAYDGTDFAGFQVQPKQRTVQGTLEKALTKMSKGAYIQVYGSGRTDSGVHAMGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E     + +ALN+ L     + +++  + D  FHARFS + + Y+YR+    
Sbjct: 63  VVHFDYPSELPAKSMLRALNSLL--PLDMEVVDSQLADDDFHARFSTVGKRYMYRVDLGH 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
                ++      P  +D E ++ A   ++G HD+T+F +        +RTI    V  N
Sbjct: 121 YTNPFKRRYTGHYPYPIDVERIKAALSDVMGTHDYTSFAAAGGVIKDKVRTIYEATVVYN 180

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N +        FL+  +R  V +L  +G+G+    D  +  + +DR++    AP  G
Sbjct: 181 EAENELIFEFHGNGFLYNMVRILVATLLEIGNGRRDVHDFLRLYEVKDRQQARSTAPASG 240

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 241 LYLKEVYY 248


>gi|116490689|ref|YP_810233.1| pseudouridylate synthase [Oenococcus oeni PSU-1]
 gi|290890104|ref|ZP_06553187.1| hypothetical protein AWRIB429_0577 [Oenococcus oeni AWRIB429]
 gi|122277127|sp|Q04G54|TRUA_OENOB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116091414|gb|ABJ56568.1| Pseudouridylate synthase [Oenococcus oeni PSU-1]
 gi|290480295|gb|EFD88936.1| hypothetical protein AWRIB429_0577 [Oenococcus oeni AWRIB429]
          Length = 252

 Score =  271 bits (694), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 72/251 (28%), Positives = 121/251 (48%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y + I Y+G  + G+Q Q      ++Q  + K +  +    + V GA RTD+GVHA 
Sbjct: 1   MQNYKVTISYDGHYFEGFQTQNRPGSRTVQDELIKVVSKMAKTKIKVIGASRTDAGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV +F    +     +   +N+ L     I +  +  V   F+AR S+ R+ YLYR+ T
Sbjct: 61  GQVINFIFPFDLNEKAILMGMNSQL--PTDILVKKVEKVPINFNARHSSHRKRYLYRVST 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-- 176
            +     ++        +LD   ++ A   L+G HDF++F +   Q ++ IRT+   +  
Sbjct: 119 SKFIDPFKRFYTGHYFWNLDTNKIQEALPDLIGEHDFSSFAASGNQTATTIRTVTKAELK 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    N +       +FL+ QIR  VG L  +G+G     D+ + ++ +DR++    AP 
Sbjct: 179 IFPKNNELLFTFEGNAFLYNQIRIMVGVLLEIGNGTRPVHDIIRLIKIKDRQQARFTAPA 238

Query: 237 EGLYFDSVEYS 247
            GLY D V Y 
Sbjct: 239 SGLYLDEVYYE 249


>gi|227431309|ref|ZP_03913362.1| pseudouridylate synthase [Leuconostoc mesenteroides subsp. cremoris
           ATCC 19254]
 gi|227352902|gb|EEJ43075.1| pseudouridylate synthase [Leuconostoc mesenteroides subsp. cremoris
           ATCC 19254]
          Length = 255

 Score =  271 bits (693), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 80/257 (31%), Positives = 128/257 (49%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTD 52
           M RY  +I Y+G+ +FG+Q Q     ++  ++QG + K I  +       + V GA RTD
Sbjct: 1   MPRYKAVIAYDGAEFFGFQLQTKNGVESVRTVQGELNKVINKMAKNPSPQIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL     P  + K +N  L     + + ++  V   FHARF+   + Y
Sbjct: 61  TGVHAFGQVIHFDLPFNIDPEGVRKGMNTLL--PFDVVVNHVEHVSDDFHARFNTHSKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YR+ T       ++         LD   ++ A   L+G HDF +F +   + ++ IR I
Sbjct: 119 IYRVSTTDYKDPFKRKYTGHFHWKLDINRIKAALPDLLGEHDFASFAASGNETATTIRLI 178

Query: 173 DHFDVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              DV+     + I       +FL+ QIR  VG L  +G GK    D+ + ++ +DR++ 
Sbjct: 179 TRADVDEKPEEHEIVFTFEGNAFLYNQIRIMVGVLLEIGTGKRPVHDIVRLIEVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
              AP  GLY D ++Y+
Sbjct: 239 RYTAPASGLYLDEIDYN 255


>gi|15672468|ref|NP_266642.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281490978|ref|YP_003352958.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           KF147]
 gi|13878837|sp|Q9CI80|TRUA_LACLA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|12723367|gb|AAK04584.1|AE006284_2 tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281374736|gb|ADA64256.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           KF147]
 gi|326406013|gb|ADZ63084.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis
           CV56]
          Length = 253

 Score =  271 bits (693), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+Q Q N  ++Q  IEK +  +   E V++ G+GRTDSGVHA  
Sbjct: 1   MTRYKATIAYDGTDFAGFQSQTNQRTVQKEIEKILTKLNSFEPVILQGSGRTDSGVHAFG 60

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFDL  +      L   L+   +    I++  + +V   +HAR+    ++Y Y +  
Sbjct: 61  QVIHFDLKGKVRDLERLRFGLDT--QTPADIAVKKVELVPDDWHARYQKHEKTYEYYLEN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  ++         L+ E M+ A   LVG HDFT F +        +RTI   ++ 
Sbjct: 119 SITRSPFQRHSKAYFRYPLNFERMQEAMSKLVGEHDFTGFTASGSSVDDKVRTIYQAEII 178

Query: 179 S-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                  +       FL+ Q+R+ VG++  +G+ +   + ++K L +++R   GP A PE
Sbjct: 179 RLDEENFKFIFRGNGFLYKQVRNMVGTVIKIGNDRMPVSQIDKILTSKNRDFAGPTAAPE 238

Query: 238 GLYFDSVEY 246
           GLY   V+Y
Sbjct: 239 GLYLKEVKY 247


>gi|89900579|ref|YP_523050.1| tRNA pseudouridine synthase A [Rhodoferax ferrireducens T118]
 gi|123278889|sp|Q21XI4|TRUA_RHOFD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|89345316|gb|ABD69519.1| tRNA pseudouridine synthase A [Rhodoferax ferrireducens T118]
          Length = 260

 Score =  271 bits (693), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 84/245 (34%), Positives = 124/245 (50%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +  ++Q  +E A+  +    V    AGRTD+GVH L QV
Sbjct: 1   MRLALGVSYNGQAYQGWQSQLSRQTVQDQLEMALSKLASHRVSTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  NA L     I++     V  +FH R SA+ R Y Y ++    
Sbjct: 61  IHFDTPLDRAPNSWVRGTNALL--PRDIAVEWARPVPPEFHCRASALSRRYAYILLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             +++ G+     K L+   M+ AA HL+G HDF++FR+  CQA SP++ +   D++  G
Sbjct: 119 RPSIDAGQVGWTFKPLEQVAMQQAASHLLGEHDFSSFRASACQALSPVKMLQRLDISRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FLH  IR+ +G L  VG GK     L++ L A++R    P     GLYF
Sbjct: 179 ACWRFEFEANAFLHHMIRNIMGCLITVGQGKKPPEWLKEVLLARNRNVAAPTFSAHGLYF 238

Query: 242 DSVEY 246
               Y
Sbjct: 239 LGPRY 243


>gi|303231239|ref|ZP_07317977.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-049-V-Sch6]
 gi|302514146|gb|EFL56150.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-049-V-Sch6]
          Length = 261

 Score =  271 bits (693), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 73/248 (29%), Positives = 123/248 (49%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    +I+ Y+G+   G+Q+Q    G ++QG++EKA+ ++  E + ++GA RTD+GVHA 
Sbjct: 1   MRNIRLIVAYDGTDLAGYQKQPADKGITVQGALEKALSIICAEPIQIYGASRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F          + +A  A+L     I +     +   +  R +   + Y+Y I  
Sbjct: 61  FQVCAFQTSGSIPVENIPRATIAHL--PKDIVVTEAIEIPLDWKPRHNIFGKEYIYSIYN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R+    + +   W + K LD E M  A + L G HDF+T +  +     P++TI    + 
Sbjct: 119 REIADPMGQRYHWHVKKPLDVEAMHQAGKALEGTHDFSTLKGANTTPVDPVKTIYAIGIK 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                I+I VV   FL+  +R+  G L  VG G+ +   + + L A+DRK  G  AP +G
Sbjct: 179 EKAGRIDISVVGDGFLYHMVRNIAGLLVDVGLGRKSVAQIPELLAAKDRKRIGKTAPAQG 238

Query: 239 LYFDSVEY 246
           L  + + +
Sbjct: 239 LVLEEIFF 246


>gi|298383909|ref|ZP_06993470.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_14]
 gi|298263513|gb|EFI06376.1| tRNA pseudouridine synthase A [Bacteroides sp. 1_1_14]
          Length = 269

 Score =  271 bits (693), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 90/250 (36%), Positives = 120/250 (48%), Gaps = 7/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NGSS+Q  + KA+       V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGSSVQECLMKALSTFLRRDVEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDHEDVLDTVTVADKLNRLL--PPDISVYRVRQVKPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +     +  SLD E M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRCRVYGSLDYERMNEAARTLFEYIDFTSFSKLHTDVKTNICHISHAEWTKM 176

Query: 181 GNL---IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                     + A  FL   +R+ VG+L  VG GK T     K ++ QDR + G  AP  
Sbjct: 177 EGEDTTWVFTIRADRFLRNMVRAIVGTLLEVGRGKLTVEGFRKVIEQQDRCKAGTSAPGN 236

Query: 238 GLYFDSVEYS 247
            L+  +VEY 
Sbjct: 237 ALFLVNVEYP 246


>gi|254412106|ref|ZP_05025881.1| tRNA pseudouridine synthase A [Microcoleus chthonoplastes PCC 7420]
 gi|196181072|gb|EDX76061.1| tRNA pseudouridine synthase A [Microcoleus chthonoplastes PCC 7420]
          Length = 283

 Score =  271 bits (693), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 113/247 (45%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ + GWQRQ +  ++Q  IE+ +  V G+ V +HGAGRTD+GVHA  QV
Sbjct: 10  QRIALVIQYLGTKFSGWQRQPHHRTVQAEIEQVLSTVEGKPVTLHGAGRTDTGVHAAAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+  R          LN+ L   + I I   + V   +HARFSAI R Y Y I T   
Sbjct: 70  AHFNSSRPIPGERWMPILNSRL--PEDILIRASAPVPANWHARFSAIWRRYRYSIYTDAC 127

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +   W      LD   ++ A   L G+H    F   +        T+        
Sbjct: 128 PNLFVRPFCWHYYHAPLDEHRIQEALNPLWGKHHLAAFHRANSGRKHSWVTVQDTHCYRN 187

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I + A  FL+  +R  VG L  VG G     +  +    Q R+     AP +GL 
Sbjct: 188 GSFIHIEIQADGFLYGMVRLLVGMLVEVGRGNLNPHEFTQLWVNQQRERIKYSAPAKGLC 247

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 248 LLRVGYP 254


>gi|88799996|ref|ZP_01115567.1| tRNA-pseudouridine synthase I [Reinekea sp. MED297]
 gi|88777274|gb|EAR08478.1| tRNA-pseudouridine synthase I [Reinekea sp. MED297]
          Length = 286

 Score =  271 bits (693), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 93/246 (37%), Positives = 126/246 (51%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY G+ + GWQ QK   S+IQ ++E AI  V  E V    AGRTD+GVHA  Q+
Sbjct: 15  RIVLCLEYKGTAFHGWQIQKSGVSTIQAALEAAIAKVADEPVSTIVAGRTDAGVHATNQI 74

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +         +N  L   D IS+  ++ VD+ FHARFSA  R+Y + I     
Sbjct: 75  VHFDTRAQRSDYGWKMGINGRL--PDDISVKWVTQVDEHFHARFSAQERAYRFIIHNNWV 132

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL           LD   M+ AA  L+G HDF++FR+  CQA SP+RT+    V  FG
Sbjct: 133 KSALLHEVTTWEQYELDVGLMQQAANRLLGTHDFSSFRAAECQAHSPVRTLRELTVARFG 192

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I+  A  FLH  +R+ VG +  +G G+         L  +DR+  G  A   GLYF
Sbjct: 193 EFIVIQARADGFLHHMVRNLVGVMLPIGRGRKPVDWASDVLNYKDRRRGGVTAKGNGLYF 252

Query: 242 DSVEYS 247
               Y+
Sbjct: 253 VRASYN 258


>gi|313207118|ref|YP_004046295.1| tRNA pseudouridine synthase a [Riemerella anatipestifer DSM 15868]
 gi|312446434|gb|ADQ82789.1| tRNA pseudouridine synthase A [Riemerella anatipestifer DSM 15868]
          Length = 246

 Score =  271 bits (693), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RYC+   YNG  YFG+Q Q    S+Q ++E+A+  +  E +   GAGRTD+GVHA + 
Sbjct: 1   MSRYCIEFSYNGEKYFGYQIQPKQISVQETLEQALSTILREEIKTTGAGRTDTGVHAKKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD        +L K LN++L     IS+  L  V   FHARF A  R+Y Y I   +
Sbjct: 61  FAHFDTDLILEEELLPKRLNSFL--PPDISVKRLFRVSSDFHARFDATYRTYEYYISLEK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P        +   + L+ E M  A + L    DFT+F  ++    + +  I        
Sbjct: 119 NPFTQNSAWGYW-RRPLNLEAMNEACKILFEYTDFTSFSKLNTDTKTNLCEIYKAFWVQE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  ++  + A  FL   +R+ VG++  +G GK    DL K ++A++R   G  AP +GL+
Sbjct: 178 GTELKFTISANRFLRNMVRAIVGTMVDIGSGKIAPQDLRKVIEAKERNAAGTSAPAQGLF 237

Query: 241 FDSVEYS 247
              V Y+
Sbjct: 238 LVDVGYN 244


>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 =  271 bits (693), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 95/279 (34%), Positives = 146/279 (52%), Gaps = 33/279 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + GWQRQ+   ++QG++E A     G+ V   G+ RTD+GVHALR V
Sbjct: 28  QRYLVGIEYIGTRFSGWQRQEGVRTVQGTLEDAFSSFMGQSVSTTGSSRTDAGVHALRNV 87

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIR 109
            H DL R              P ++ +A+N +L+  S  + +++   V   FHARF A  
Sbjct: 88  FHVDLARTSKRKPGELLAPHPPDVIVRAVNHFLQRESADVQVVDARFVPPDFHARFRAKE 147

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YRI+         E+ RAW + + L+   M+ A Q L+G HDF++FR+  CQA+SP
Sbjct: 148 RTYYYRILAGSCRASLFERDRAWHVEEPLNLIAMQSACQVLLGTHDFSSFRASGCQAASP 207

Query: 169 IRTIDHFDVNSFGNL--------------------IEIRVVARSFLHTQIRSFVGSLKLV 208
           ++T++   +    +                       +   A+SFL+ Q+R  VG+LK V
Sbjct: 208 VKTLEELSIRETVSWPHLLTGCSSNAQSSNPDLKSYVVTARAQSFLYHQVRLMVGTLKGV 267

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G GK T+ D+ K L+ +      P+AP  GL+   V+Y 
Sbjct: 268 GAGKRTAEDVRKILEGRSISLALPMAPASGLFLADVKYD 306


>gi|308070945|ref|YP_003872550.1| tRNA pseudouridine synthase A [Paenibacillus polymyxa E681]
 gi|305860224|gb|ADM72012.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I)
           [Paenibacillus polymyxa E681]
          Length = 261

 Score =  271 bits (693), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 88/257 (34%), Positives = 128/257 (49%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M   CM + Y+G+ Y G+Q Q NG++IQ  +E AI+ +TGE + + G+GRTD+GVHA  Q
Sbjct: 1   MRNLCMKVNYDGTHYDGFQTQPNGNTIQDCLEHAIYSLTGERLKITGSGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F           C ALNA+L     I + +   V   FHAR  A R++Y Y I   +
Sbjct: 61  VFNFHTESPIPLQRWCLALNAWL--PRDIIVTDAREVPLSFHARRMAKRKTYRYSINANR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
            P    +      P SLD   M     HLVG  D+T+F S   Q ++ +RTI    +   
Sbjct: 119 FPDIFHRRTQVHHPTSLDVRAMEEGLAHLVGTFDYTSFASRRSQKTNHVRTIYEAYMTVD 178

Query: 179 --------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                       +I   +    FL   +R  +G+L  VG+GK +S D+   L+A++R + 
Sbjct: 179 HSFSRPDSDDQGIIHTYITGSGFLQHMVRIIMGTLLEVGEGKKSSDDIPSILEAKNRSKA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           GP A    L   +VEY 
Sbjct: 239 GPTAVGHALTLWNVEYD 255


>gi|329767334|ref|ZP_08258859.1| tRNA pseudouridine synthase A [Gemella haemolysans M341]
 gi|328836023|gb|EGF85714.1| tRNA pseudouridine synthase A [Gemella haemolysans M341]
          Length = 265

 Score =  270 bits (692), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 126/249 (50%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS Y G+Q Q N ++IQ  IEK++  +  + V ++ +GRTDSGVHA  QV
Sbjct: 1   MRIALLCRYDGSNYHGFQIQPNNNTIQEEIEKSLKKINKKDVRLYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V   KALNA   I   I I+  + V + FH R+++ +++Y Y++   + 
Sbjct: 61  LHFDTDLNIPDVAWVKALNA--TIPKDIRIVGATTVSEDFHVRYNSTQKTYYYKLYIGRE 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
                           + E  + + ++ +G HDF++F S +      +RTI    +    
Sbjct: 119 IDPFLLNYVGKHSFDFNFEKAQESLKYFIGEHDFSSFCSKNSSVEDKVRTIYSLTMGKDP 178

Query: 181 --GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N++   +    FL+  +R  +G+++ V  GK+ +  +++ L  ++R+  GP A   G
Sbjct: 179 INPNIVNFEITGNGFLYNMVRIIIGTIQNVAAGKYEADYIKEILDKKERQFAGPKADAAG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLKEVVYD 247


>gi|125623329|ref|YP_001031812.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|166228735|sp|A2RIH1|TRUA_LACLM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|124492137|emb|CAL97066.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|300070076|gb|ADJ59476.1| tRNA pseudouridine synthase A [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 253

 Score =  270 bits (692), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 123/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G+ + G+Q Q N  ++Q  IEK +  +   E V++ G+GRTDSGVHA  
Sbjct: 1   MTRYKATIAYDGTDFAGFQSQTNQRTVQEEIEKVLSKLNSFEPVILQGSGRTDSGVHAFG 60

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HFDL  +      L   L+   +    I++  + +V   +HAR+    ++Y Y +  
Sbjct: 61  QVIHFDLNGKARDLERLRFGLDT--QTPADIAVKKVELVPDDWHARYQKHEKTYEYYLEN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                   +         L+ E M+ A   LVG+HDFT F +        +RTI   ++ 
Sbjct: 119 SVTRSPFHRHSKAYFRYPLNFERMQGAMVKLVGQHDFTGFTASGSSVDDKVRTIYQAEII 178

Query: 179 S-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                  +       FL+ Q+R+ VG++  +G+ +   + ++K L +++R   GP A PE
Sbjct: 179 QLDKENFKFIFRGNGFLYKQVRNMVGTVIKIGNDRMPVSQIDKILTSKNRNFAGPTAAPE 238

Query: 238 GLYFDSVEYS 247
           GLY   V+Y 
Sbjct: 239 GLYLKEVKYE 248


>gi|224024234|ref|ZP_03642600.1| hypothetical protein BACCOPRO_00957 [Bacteroides coprophilus DSM
           18228]
 gi|224017456|gb|EEF75468.1| hypothetical protein BACCOPRO_00957 [Bacteroides coprophilus DSM
           18228]
          Length = 249

 Score =  270 bits (692), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + ++G+ Y GWQ Q NG+S+Q ++ KA+       + V GAGRTD+GVHA   
Sbjct: 1   MFRYFIYLSFDGTNYHGWQIQPNGASVQETLMKALSTFLRREIEVVGAGRTDAGVHARLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD   E    ++   LN  L     I++  +  V  + HARF A  R+Y Y I TR+
Sbjct: 61  VAHFDFDTELDGEVVTDKLNRLL--PPDIAVYGVRRVKPEAHARFDATSRTYKYYIHTRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +G +W I + LD E M  AAQ L    DFT+F  +H    +    I        
Sbjct: 119 --DPFRRGYSWRIFQPLDFERMNEAAQTLFDYTDFTSFSKLHTDVKTNNCRIMLARWEQT 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G+      + A  FL   +R+ VG+L  VG GK T     + ++ ++R   G   P   L
Sbjct: 177 GDGEWVFTIRADRFLRNMVRAVVGTLVEVGRGKLTVDGFRRVIEEKNRCSAGTSVPGHAL 236

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 237 YLTDVSYP 244


>gi|298482201|ref|ZP_07000389.1| tRNA pseudouridine synthase A [Bacteroides sp. D22]
 gi|298271758|gb|EFI13331.1| tRNA pseudouridine synthase A [Bacteroides sp. D22]
          Length = 249

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 120/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       + +   LN  L     ISI  +  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDFDEPLDEISVADKLNRLL--PPDISIYRVCRVRPDAHARFDATARTYKYYVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W +   LD   M  AA+ L    DFT+F  +H    + I  I H +    
Sbjct: 119 YP--FNRQYRWRVYNQLDYALMNEAARTLFEYTDFTSFSKLHTDVKTNICHITHAEWTQE 176

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +      + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L
Sbjct: 177 DDATWVFTIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRVIEQQDRCKAGTSAPGQAL 236

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 237 FLVNVEYP 244


>gi|315022484|gb|EFT35511.1| tRNA pseudouridine synthase A [Riemerella anatipestifer RA-YM]
 gi|325335444|gb|ADZ11718.1| Pseudouridylate synthase [Riemerella anatipestifer RA-GD]
          Length = 246

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 125/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RYC+   YNG  YFG+Q Q    S+Q ++E+A+  +  E +   GAGRTD+GVHA + 
Sbjct: 1   MLRYCIEFSYNGEKYFGYQIQPKQISVQETLEQALSTILREEIKTTGAGRTDTGVHAKKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD        +L K LN++L     IS+  L  V   FHARF A  R+Y Y I   +
Sbjct: 61  FAHFDTDLILEEELLPKRLNSFL--PPDISVKRLFRVSSDFHARFDATYRTYEYYISLEK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P        +   + L+ E M  A + L    DFT+F  ++    + +  I        
Sbjct: 119 NPFTQNSAWGYW-RRPLNLEAMNEACKILFEYTDFTSFSKLNTDTKTNLCEIYKAFWVQE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  ++  + A  FL   +R+ VG++  +G GK    DL K ++A++R   G  AP +GL+
Sbjct: 178 GAELKFTISANRFLRNMVRAIVGTMVDIGSGKIAPQDLRKVIEAKERNAAGTSAPAQGLF 237

Query: 241 FDSVEYS 247
              V Y+
Sbjct: 238 LVDVGYN 244


>gi|290968602|ref|ZP_06560140.1| tRNA pseudouridine synthase A [Megasphaera genomosp. type_1 str.
           28L]
 gi|290781255|gb|EFD93845.1| tRNA pseudouridine synthase A [Megasphaera genomosp. type_1 str.
           28L]
          Length = 264

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 84/244 (34%), Positives = 127/244 (52%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
             C+I+ Y+G+ + G+QRQ N SSIQ  IE+A+  +  E + V+GA RTD+GVHA  QV 
Sbjct: 6   NICLIVAYDGTDFHGFQRQTNASSIQQYIEEALTRIFQEPITVYGAARTDAGVHARGQVV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F          +  A+ AYL    TI++L    +   F  R     + Y YRI+ R  P
Sbjct: 66  NFYASGSIPVDKIPYAMKAYL--PPTIAVLQAREMASHFSVRHDNCGKHYCYRIVNRAVP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              +   +W I K LD E MR  A  L+G HDF+ F   +    +PI+T+    +    +
Sbjct: 124 DPFQLRYSWFIRKPLDVEAMRQGANILLGTHDFSAFEGKNTTPMNPIKTMYAVQIQKNRD 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +EI V+   FL+  +R+  G L  +G  ++T+    + L+  DRK+ G  AP  GL  +
Sbjct: 184 NVEIHVIGDGFLYHMVRNMAGGLADIGLHRFTTIHFRRILKGLDRKKLGATAPAGGLCLE 243

Query: 243 SVEY 246
            V Y
Sbjct: 244 EVFY 247


>gi|229823506|ref|ZP_04449575.1| hypothetical protein GCWU000282_00804 [Catonella morbi ATCC 51271]
 gi|229786950|gb|EEP23064.1| hypothetical protein GCWU000282_00804 [Catonella morbi ATCC 51271]
          Length = 257

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 86/253 (33%), Positives = 128/253 (50%), Gaps = 8/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
           M RY + + Y+GS + G+Q Q NG SIQ +++ A+  +     G  +    +GRTDSGVH
Sbjct: 1   MPRYAIQLAYDGSRFVGYQVQPNGPSIQANLDAALIKMAKCPEGVTIPTVASGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV HFD         + +ALNA L     I ++ ++ V   FHAR+ AI + Y YR+
Sbjct: 61  ALGQVVHFDYPAPMPQQAMQRALNALL--DPAIKVVAVARVADDFHARYHAIGKEYRYRV 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--H 174
                    ++  +   P   D + +  A + +VG HDFT+F S        +RT+    
Sbjct: 119 DIGAYANPFKRLYSLHHPYRYDLDRINQALEAVVGTHDFTSFCSTKTDKEDKVRTVHLAR 178

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              +     +  +     FL+  IR  VG+   +GDG     +LE+ +Q Q+RKE GP A
Sbjct: 179 VWEDRDQQELVFQFRGTGFLYNMIRILVGTSLQIGDGLRPVNELERLIQVQNRKEAGPTA 238

Query: 235 PPEGLYFDSVEYS 247
           PP+GLY   V Y 
Sbjct: 239 PPQGLYLHQVFYE 251


>gi|91789465|ref|YP_550417.1| tRNA pseudouridine synthase A [Polaromonas sp. JS666]
 gi|123059533|sp|Q126M3|TRUA_POLSJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91698690|gb|ABE45519.1| tRNA pseudouridine synthase A [Polaromonas sp. JS666]
          Length = 264

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 88/250 (35%), Positives = 124/250 (49%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+GS Y GWQ Q +G+++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRIALGISYSGSAYEGWQSQLSGNTVQDKLESALARFAAQPVRTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD V         +  NA+L     I++     V   FH R SAI R Y Y ++    
Sbjct: 61  VHFDTVLHRDMGSWVRGTNAFL--PSDIAVQWAREVPDTFHCRGSAIARRYAYVVLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   + + LD   MR A  HLVG HDF++FR+  CQA SP++TI+  +++   
Sbjct: 119 RPSVEAGRVGWVYRPLDGAAMRQAITHLVGEHDFSSFRAAQCQAKSPVKTINRIEISERA 178

Query: 182 N----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                       A +FLH  IR+ +G L  +G G      L   + A+ R    P   P 
Sbjct: 179 GTGSKYWHFEFEANAFLHHMIRNIMGCLVAIGQGSHEPGWLLDVMAARSRDAAAPTFSPN 238

Query: 238 GLYFDSVEYS 247
           GLYF    Y 
Sbjct: 239 GLYFLGPVYE 248


>gi|327539206|gb|EGF25829.1| tRNA pseudouridine synthase A [Rhodopirellula baltica WH47]
          Length = 276

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 76/254 (29%), Positives = 118/254 (46%), Gaps = 14/254 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y+G+ Y GWQ Q    SIQ  +E+ I  + G  V V G+GRTD+GVHA+ QVA   
Sbjct: 12  LTVAYDGTEYCGWQVQPEQRSIQSELERVIRPLAGRPVRVLGSGRTDAGVHAIGQVARCV 71

Query: 66  LVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           L       V L +A+N+ L   + I +  +    ++FH    A  + Y Y +    +   
Sbjct: 72  LPAWKANTVALQRAINSKL--PNDIRVKAVRETRERFHPIADATGKQYQYLVQVGGSRDP 129

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS----- 179
                   +   +D   M+ AA   VGRHDF  F+    +  S +RTI            
Sbjct: 130 FANRFVNRVGGPIDHSAMQSAAAKFVGRHDFKAFQGTGAERPSTVRTIHLARWIPRVATG 189

Query: 180 ------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                  G      +    FL+  +R+ +G++  VG GK     +++ L ++DRK  GP 
Sbjct: 190 PTGAELEGEHWCFEIDGEGFLYNMVRNLMGTMLEVGRGKKPLDWIDEVLASRDRKMAGPT 249

Query: 234 APPEGLYFDSVEYS 247
           APP+GL+   V+Y 
Sbjct: 250 APPQGLFLCRVDYP 263


>gi|317126894|ref|YP_004093176.1| tRNA pseudouridine synthase A [Bacillus cellulosilyticus DSM 2522]
 gi|315471842|gb|ADU28445.1| tRNA pseudouridine synthase A [Bacillus cellulosilyticus DSM 2522]
          Length = 260

 Score =  270 bits (691), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV-VVHGAGRTDSGVHALR 59
           M R   I+ Y+G+ Y G+Q Q +  +IQ  +EKA+  +       V  +GRTD+GVH+L 
Sbjct: 1   MKRVKGIVTYDGTKYSGYQVQVDKKTIQAELEKALAKIHKADSWNVVSSGRTDTGVHSLG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           +A N  L   D I + +L  V   FHARF ++ + Y+Y++ T 
Sbjct: 61  QTIHFDTSLSIPEERWPQAFNRLL--PDDIQVRDLQYVHHDFHARFDSVGKKYVYKVNTA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++   +  P  L  E M  AA HL G HDFT+F S        +RTI   ++  
Sbjct: 119 REKDIFKRNFVYHHPYVLSYEKMLEAAMHLEGTHDFTSFSSPRTDVIDKVRTIYAIELEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+      +   FL+  +R   G+L  VG GK    ++ +  + +DR   GP  P  GL
Sbjct: 179 NGDEWTFTYIGNGFLYQMVRVLTGTLLHVGKGKIRPEEIPEIFEGKDRSLAGPSIPGTGL 238

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 239 YLTNVYYD 246


>gi|146302394|ref|YP_001196985.1| tRNA pseudouridine synthase A [Flavobacterium johnsoniae UW101]
 gi|146156812|gb|ABQ07666.1| tRNA pseudouridine synthase A [Flavobacterium johnsoniae UW101]
          Length = 284

 Score =  270 bits (691), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 125/246 (50%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG+ Y GWQ Q N SS+Q ++ KA+ ++    + V GAGRTD+GVHA    
Sbjct: 41  MRYFIHFAYNGTHYHGWQFQPNASSVQETLNKALSVLLNSTINVMGAGRTDTGVHAEEMY 100

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFDL +     +L   LN+YL     I++ NL  V    H RF A +R+Y Y I T + 
Sbjct: 101 GHFDLEKSIDIPVLVHKLNSYL--PKDIAVYNLIPVHDDAHCRFDATKRTYEYHINTVKN 158

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E   +W + + LD E M  AA+ L+   DF  F  ++   ++   TI         
Sbjct: 159 PFLEE--LSWYVTQKLDVELMNEAAKILLKHTDFQCFSKVNTDVNTFDCTIFEAYWKQEN 216

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG+L  +G  K T  D E  + +++R++ G   P  GLY 
Sbjct: 217 NKLVFTISANRFLRNMVRAIVGTLINIGLHKITLADFENIIASKNREKAGFSVPAHGLYL 276

Query: 242 DSVEYS 247
             + Y 
Sbjct: 277 TKIYYD 282


>gi|299144417|ref|ZP_07037497.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298518902|gb|EFI42641.1| tRNA pseudouridine synthase A [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 243

 Score =  270 bits (691), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 82/245 (33%), Positives = 124/245 (50%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   +I+ Y+GS Y G+Q Q   S+++G ++ AI       + ++ AGRTDSGVHA+ Q 
Sbjct: 1   MNIKLIVSYDGSSYHGFQIQPQASTVEGVLKNAIEDTVKHEIKLYTAGRTDSGVHAMGQC 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F          L K +N +L   D IS++  S VD  FHAR+SA  + Y Y I   + 
Sbjct: 61  VNFYSETTINIGNLPKVINFHL--PDDISVVGASYVDDDFHARYSAKGKYYRYMIYRGKY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L + RA   P  L+ + M+    +L+G +D+ TF   H      IR ID  +V   G
Sbjct: 119 RNPLYRNRAMHFPYELNLKKMQSTLNYLIGENDYKTFMGRHAIVKDTIRRIDKIEVVEDG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I    +SFL   +R  VG+   +  G++    ++ AL  + RK  GP AP  GLY 
Sbjct: 179 DFIYIDFYGKSFLKNMVRIIVGTAVEIARGRFEEEYMKYALNKKHRKAAGPTAPSYGLYL 238

Query: 242 DSVEY 246
             + Y
Sbjct: 239 MKIYY 243


>gi|256844460|ref|ZP_05549946.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 125-2-CHN]
 gi|256613538|gb|EEU18741.1| tRNA pseudouridine synthase A [Lactobacillus crispatus 125-2-CHN]
          Length = 262

 Score =  270 bits (691), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 132/250 (52%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V  +GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGQRVIVQVSGRTDAGVHAVGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  A+N+ +     I   +  IVD+ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILAMNSMM--PTDIIFDDCQIVDENFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
                 ++      P  LD E M++AAQ L+G+HDFT+F +   Q    +RTI + ++  
Sbjct: 121 HFVNPFKRFYTGHFPYPLDIEKMQVAAQDLLGKHDFTSFAASGGQIEDKVRTIYYINITK 180

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   
Sbjct: 181 DEKENEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPIHDLQRVIAAKDRQEVRQTAHAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYD 250


>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 =  270 bits (691), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 110/284 (38%), Positives = 148/284 (52%), Gaps = 39/284 (13%)

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  VAHF-------------------------------------DLVREWVPVILCKALNAYL 83
           V HF                                      L   +    L  A+N YL
Sbjct: 61  VVHFDLISPNNSKDLACINKETDNKEVSKQNNTTTTIDSLKMLPCRYNAYKLMSAVN-YL 119

Query: 84  KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
                I + +  I   QFHARFSA  R Y YRII R  P  +E+ R W I   L+  +M 
Sbjct: 120 LKPHRIILTSCEITTLQFHARFSAKARHYKYRIINRAVPSVIEQNRTWWIKTPLNVIDMI 179

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFV 202
            A+QHL+G+HDFT+FRS  CQA SP++T+   +V  +    I+I   A SFLH  +R+ V
Sbjct: 180 DASQHLIGKHDFTSFRSSACQAKSPLKTLTKIEVDTTNYPEIQIYFSAPSFLHHMVRNIV 239

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           G+L  +G  K +   ++  L A++R   GP AP  GLYF  V+Y
Sbjct: 240 GTLVYIGLCKISPAAIKTILFAKNRAMAGPTAPSSGLYFVKVDY 283


>gi|325660678|ref|ZP_08149308.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 4_1_37FAA]
 gi|325473039|gb|EGC76247.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 4_1_37FAA]
          Length = 249

 Score =  270 bits (691), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 90/252 (35%), Positives = 127/252 (50%), Gaps = 10/252 (3%)

Query: 1   MIR-----YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M++     Y M I Y+G GY GWQR  N   +IQG+IE+ +  + G  V + G+GRTD+G
Sbjct: 1   MMKKIKKNYKMTIAYDGGGYKGWQRLTNEPGTIQGTIERVLSEIEGSPVKISGSGRTDAG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  QVAH  L     P +L + LN  L   + I I  +  V + FH+R+SA+ + Y Y
Sbjct: 61  VHAKGQVAHVFLKTNEDPELLRQELNRML--PEDIRICRVESVSQSFHSRYSAVSKVYEY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           RI  R       +   +  P  LD + MR AA HL G HDF +F     + +  +RTI  
Sbjct: 119 RIDQRSRADVFTRKYCYHRPVHLDLDRMRQAADHLTGTHDFGSF--TDNKEADSVRTIFS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            D+      + +      FL+  +R   G+L  VG+G  T   + +A   +DR   G LA
Sbjct: 177 IDMKEENEKLVLAFCGDGFLYHMVRILAGTLLEVGEGIRTPESVLEAFHHRDRSLTGFLA 236

Query: 235 PPEGLYFDSVEY 246
           P  GL    V Y
Sbjct: 237 PAHGLCLREVNY 248


>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 =  270 bits (691), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 128/246 (52%), Gaps = 2/246 (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    +I +     + + FHAR S + R Y Y +I    
Sbjct: 61  IHFDTTKNRPLTAWVKGVNAFL--PSSIKVRWAKNISESFHARHSVLEREYQYLLIKDTN 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 DSVEYS 247
            +++Y 
Sbjct: 239 SNIKYD 244


>gi|302346677|ref|YP_003814975.1| tRNA pseudouridine synthase A [Prevotella melaninogenica ATCC
           25845]
 gi|302150885|gb|ADK97146.1| tRNA pseudouridine synthase A [Prevotella melaninogenica ATCC
           25845]
          Length = 253

 Score =  270 bits (690), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 76/257 (29%), Positives = 117/257 (45%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E A+  +  E + + GAGRTD+GVH    
Sbjct: 1   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLEHALSTILRESIAITGAGRTDAGVHGRMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD    +    L   +N  L     +S+  +  V +  HARFSA  R+Y Y + T +
Sbjct: 61  VAHFDTELSFDCAQLVYKVNRLL--PRDVSVSRIEPVGEDLHARFSATSRTYHYYVHTGK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +  +  SLD + M  AA +L+G  DF  F        + I  +        
Sbjct: 119 QP--FSRQYSCALHYSLDFDKMNEAAAYLIGEKDFKCFCKAGADVKTTICNLTEARWIPT 176

Query: 181 GNL-----------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            +                + A  FL   +R+ VG+L  VG G+ +  + +K +    R +
Sbjct: 177 NDEFALATDDTVTNWCFVITANRFLRNMVRAVVGTLVEVGRGRLSLDEFKKIVDGGTRSD 236

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+   V+Y
Sbjct: 237 AGESMPGNALFLWEVKY 253


>gi|227894551|ref|ZP_04012356.1| tRNA pseudouridine synthase A [Lactobacillus ultunensis DSM 16047]
 gi|227863710|gb|EEJ71131.1| tRNA pseudouridine synthase A [Lactobacillus ultunensis DSM 16047]
          Length = 262

 Score =  270 bits (690), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            RY M + Y+G  + G+Q Q +  ++QG++E A+  +T G+ V+V G+GRTD+GVHA+ Q
Sbjct: 3   TRYKMTMAYDGHLFHGFQLQPDQRTVQGTVEDALKKMTKGKRVIVQGSGRTDAGVHAIGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFD   +      +  A+N+ +     I      IVD+ FHAR+S   + Y YR+   
Sbjct: 63  VIHFDYPGKTIPANRMILAMNSMM--PMDIIFNKCQIVDEDFHARYSIKGKWYRYRVSLD 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
                 ++      P  L+   M+ AA+ L+G+HDFT+F +   Q    +RTI + ++  
Sbjct: 121 HFVNPFKRFYTGHFPYQLNISKMQEAARDLLGKHDFTSFAASGGQIEDKVRTIYYVNIEK 180

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               N +    +   FL+  +R  V +L  +G+G+    DL++ + A+DR+E    A   
Sbjct: 181 DEKENEVIFDFIGSGFLYNMVRIMVAALLEIGNGRRPIHDLKRVISAKDRQEVRQTAQAS 240

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 241 GLYLYHVFYE 250


>gi|332529464|ref|ZP_08405423.1| tRNA pseudouridine synthase A [Hylemonella gracilis ATCC 19624]
 gi|332041110|gb|EGI77477.1| tRNA pseudouridine synthase A [Hylemonella gracilis ATCC 19624]
          Length = 270

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/256 (31%), Positives = 127/256 (49%), Gaps = 12/256 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ Y GWQ Q +G ++Q  +E A+     E +  + AGRTD+GVH L QV
Sbjct: 1   MRVALGLSYDGAAYDGWQSQPSGRTVQDRLEHALGRFANERITTNCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V  +FH+R SA  R Y Y ++    
Sbjct: 61  VHFDTQAQRTPYAWVRGTNTHL--PPDIAVQWAHPVPVEFHSRASATSRRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E  R   + + LD + M+ A  HL+G  DFT+FR+  CQA SPI+ +   +++  G
Sbjct: 119 RPSVEARRVGWVFQPLDLDAMQAALPHLLGERDFTSFRAAACQALSPIKNLMRVEISRRG 178

Query: 182 N----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                             A +FLH  IR+ +G L ++G GK     + + + A+ R    
Sbjct: 179 TRAGAEAPETCYWRFEFEASAFLHHMIRNIMGCLIVIGQGKKPPEWMAEVVAARSRDAAA 238

Query: 232 PLAPPEGLYFDSVEYS 247
           P   P+GLYF    Y 
Sbjct: 239 PTFMPDGLYFLGPRYD 254


>gi|241890020|ref|ZP_04777318.1| tRNA pseudouridine synthase A [Gemella haemolysans ATCC 10379]
 gi|241863642|gb|EER68026.1| tRNA pseudouridine synthase A [Gemella haemolysans ATCC 10379]
          Length = 265

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 125/249 (50%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS Y G+Q Q N ++IQ  IEK++  +  + V ++ +GRTDSGVHA  QV
Sbjct: 1   MRVVLLCRYDGSNYHGFQIQPNNNTIQEEIEKSLKKINKKDVRLYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           KALNA   I   I I+  +   + FH R+++ +++Y Y++   + 
Sbjct: 61  LHFDTDLNIPDEAWVKALNA--TIPKDIRIVGATSASEDFHVRYNSTQKTYYYKLHIGRE 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
                           + E  + A Q+ +G HDF++F S +      +RTI    +    
Sbjct: 119 VDPFLLNYVGKHSFDFNFEKAQEALQYFIGEHDFSSFCSKNSSVEDKVRTIYSLTMEKDL 178

Query: 181 --GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N++   +    FL+  +R  +G+++ V  GK+ +  +++ L+ ++R+  GP A   G
Sbjct: 179 INPNIVNFEITGNGFLYNMVRIIIGTIQNVAAGKYEANYVKEILEKKERQFAGPKADAAG 238

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 239 LYLKEVLYD 247


>gi|296113461|ref|YP_003627399.1| tRNA pseudouridine synthase A [Moraxella catarrhalis RH4]
 gi|295921155|gb|ADG61506.1| tRNA pseudouridine synthase A [Moraxella catarrhalis RH4]
 gi|326559732|gb|EGE10142.1| tRNA pseudouridine synthase A [Moraxella catarrhalis 7169]
 gi|326568129|gb|EGE18213.1| tRNA pseudouridine synthase A [Moraxella catarrhalis BC7]
 gi|326568548|gb|EGE18620.1| tRNA pseudouridine synthase A [Moraxella catarrhalis BC1]
          Length = 268

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 83/243 (34%), Positives = 132/243 (54%), Gaps = 2/243 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IE+ G+ Y GWQRQ+    +Q  IEKA+  +  E + +  AGRTD+GVHA   +AH
Sbjct: 6   LAVGIEFIGTRYRGWQRQEEVIGVQAVIEKALSTIANESIELIAAGRTDAGVHAGNMIAH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F    E       +  N+ L   D I++  +  +   FHARFSAI R Y Y  + +    
Sbjct: 66  FVTHAERSAHSWLRGTNSLL--PDDIALRWVQPMPDDFHARFSAIARRYRYITLNQPYRP 123

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+   +       LD + M IA+Q +VG HDF++FR+  CQ++ P+RT+ H ++   G+ 
Sbjct: 124 AILHHQVTHEYTKLDIDAMIIASQFIVGTHDFSSFRAAACQSNQPVRTVTHANLFQHGSY 183

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A  FLH  +R+ +G+L  VG G+ +     + + A++R    P A  +GLYF +
Sbjct: 184 LILDIQADGFLHHMVRNIMGALFAVGRGEISPETFYELMLAKNRTLAPPTASADGLYFIN 243

Query: 244 VEY 246
             Y
Sbjct: 244 AYY 246


>gi|254467822|ref|ZP_05081228.1| tRNA pseudouridine synthase A [beta proteobacterium KB13]
 gi|207086632|gb|EDZ63915.1| tRNA pseudouridine synthase A [beta proteobacterium KB13]
          Length = 258

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   I+EY G+ Y G+Q Q N ++IQ  I+KA+  +    V +  +GRTD+GVHAL QV
Sbjct: 1   MRIAAIVEYLGTNYAGFQIQPNLNTIQLCIQKALSKIANHDVKIEASGRTDAGVHALGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  N++L     ISI  +S VDK FHARF+ + R Y Y +     
Sbjct: 61  FHFDTESQRPLNSWKRGANSFL--PQDISIKWVSEVDKNFHARFNVMEREYQYLLHCNDT 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P A+   +A      ++ + +    +  +G+HDFT+FRS  CQ+  PIR +         
Sbjct: 119 PSAIWHQKAGHYGYEINFKLLDKVLKEFIGKHDFTSFRSSECQSKKPIRIMHDVSYQKKE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N I  +  A  FLH QIR+ +  +  V  GK     ++   + +DR +      P GLY 
Sbjct: 179 NFILFKFTADGFLHHQIRNMMSVILDVVSGKKPLDYVQYLFEVKDRTKASNTFSPNGLYL 238

Query: 242 DSVEYS 247
            +++Y 
Sbjct: 239 ANIKYE 244


>gi|325955163|ref|YP_004238823.1| tRNA pseudouridine synthase A [Weeksella virosa DSM 16922]
 gi|323437781|gb|ADX68245.1| tRNA pseudouridine synthase A [Weeksella virosa DSM 16922]
          Length = 248

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 131/247 (53%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  YFGWQRQ    S+Q  IE  +  +  E + + GAGRTD+GVHA +  
Sbjct: 1   MRYFLELAYNGQNYFGWQRQPKQLSVQEKIEFCLSTLLREEINIVGAGRTDTGVHAKKMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD         + + LN++L   + IS+ ++  V  + HARF A++R+Y Y I T++ 
Sbjct: 61  AHFDFDGSLTDDFIRR-LNSFL--PEDISVTSIHCVAPEAHARFDAVKRTYHYHIYTQKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-F 180
           P       +W I K LD E M  AA++L+ + DF +F  +H    + I T+   +     
Sbjct: 118 P--FTTTTSWQIRKPLDIEKMNEAAKYLIKKADFGSFAKLHTDVKTNICTVYRAEWIQIE 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +     + A  FL   +R+ VG+L  VG GK T +D    +  +DRK     APP+GL+
Sbjct: 176 KDFFCFEITADRFLRNMVRAIVGTLVEVGLGKITPSDFNNIIDKKDRKFAAASAPPQGLF 235

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 236 LVEVLYP 242


>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 =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 96/279 (34%), Positives = 143/279 (51%), Gaps = 33/279 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + GWQRQ    ++QG++E A     G+ V   G+ RTD+GVHALR V
Sbjct: 7   QRYLVGIEYIGTRFSGWQRQGGVRTVQGTLEDAFSSFMGQSVSTTGSSRTDAGVHALRNV 66

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIR 109
            H DL R              P ++ +A+N +L+  S  + +++   V   FHARF A  
Sbjct: 67  FHVDLARTSKRKPGELLAPHPPDVIVRAVNHFLQRESADVQVVDARFVPPDFHARFRAKE 126

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YRI+         E+ RAW + + L+   M+ A Q L+G HDF++FR+  CQA+SP
Sbjct: 127 RTYYYRILAGSCRASLFERDRAWHVEEPLNLIAMQSACQVLLGTHDFSSFRASGCQAASP 186

Query: 169 IRTIDHFDVNSFGNLIEI--------------------RVVARSFLHTQIRSFVGSLKLV 208
           I+T++   +    +                           A+SFL+ Q+R  VG+LK V
Sbjct: 187 IKTLEELSIRETVSWPHFLTGCSSNAQSSNPDLKSYVVTARAQSFLYHQVRLMVGTLKGV 246

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G GK T  D+ K L+ +      P+AP  GL+   V+Y 
Sbjct: 247 GAGKRTVEDVRKILEGRSISLALPMAPASGLFLADVKYD 285


>gi|27904686|ref|NP_777812.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|29611884|sp|P59508|TRUA_BUCBP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|27904083|gb|AAO26917.1| tRNA pseudouridine synthase A (Pseudouridylate synthase I)
           (Pseudouridine synthase I) (Uracil hydrolyase) (PSU-I)
           [Buchnera aphidicola str. Bp (Baizongia pistaciae)]
          Length = 264

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 92/245 (37%), Positives = 127/245 (51%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEYNGS Y GWQ QK  SS+Q  +E A+ ++    V V  AGRTD+GVH+  QV 
Sbjct: 7   KIALGIEYNGSNYHGWQYQKFASSVQEKVELALSIIANHPVRVTCAGRTDAGVHSTGQVV 66

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF               N YL     IS++    V   FHAR+SA+ R Y Y +      
Sbjct: 67  HFCTSSIRNDQAWILGTNRYL--PKDISVIWKRDVPMHFHARYSALSRRYRYILYNNSCR 124

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            ++         + L+ E M  AAQ+L+G HDFTTFRS HCQ+ +P R I + +V     
Sbjct: 125 SSIFYQGLKFYHRILNVEKMNQAAQYLLGEHDFTTFRSSHCQSKTPFRKILYVNVFCINC 184

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI I +VA SFL+  +R+ VG L  +G  K   T +   L+ ++R     +    GLY  
Sbjct: 185 LIIIDIVANSFLYHMVRNIVGCLIEIGISKKKVTWIRDILKFKNRTSSTKIVESNGLYLV 244

Query: 243 SVEYS 247
            V+YS
Sbjct: 245 QVQYS 249


>gi|298695476|gb|ADI98698.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           ED133]
          Length = 267

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RNPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     A  EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAAAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|282917564|ref|ZP_06325316.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           D139]
 gi|283767311|ref|ZP_06340226.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           H19]
 gi|282318526|gb|EFB48884.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           D139]
 gi|283461190|gb|EFC08274.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           H19]
          Length = 267

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     A  EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEVSDVPKLLESKNRKNVPFTAAAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|238018655|ref|ZP_04599081.1| hypothetical protein VEIDISOL_00490 [Veillonella dispar ATCC 17748]
 gi|237865126|gb|EEP66416.1| hypothetical protein VEIDISOL_00490 [Veillonella dispar ATCC 17748]
          Length = 261

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 72/248 (29%), Positives = 125/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    +I+ Y+G+   G+Q+Q +    ++QG +E  +  +  E + ++GA RTD+GVHA 
Sbjct: 1   MRNIRIIVAYDGTDLAGYQKQPDDKGLTVQGCLEYGLSKICNEPIQIYGASRTDAGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F          + +A+ A+  I   I +L    +   +  R++   + Y+Y I  
Sbjct: 61  FQVCTFQTSGSIPVENIPRAMIAH--IPKDIVVLEALEIPLDWKPRWNIYGKEYVYTIHN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +     L K   W + K L+ + M+ A   L+G HDFTT +  +   + P++TI    V 
Sbjct: 119 QLIANPLTKRYHWHVKKPLNIDLMQAAGNELLGTHDFTTLKGTNSTPADPVKTIIGIHVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + G+ + I VV   FL+  +R+  G L  VG G+    D++  L A+DR+  G  AP +G
Sbjct: 179 AEGSHVTISVVGDGFLYHMVRNIAGLLVDVGLGRRKVEDIKGYLAAKDRRVIGKTAPAQG 238

Query: 239 LYFDSVEY 246
           L  + + +
Sbjct: 239 LCLEEIFF 246


>gi|169830000|ref|YP_001700158.1| tRNA pseudouridine synthase A [Lysinibacillus sphaericus C3-41]
 gi|238688163|sp|B1HMV0|TRUA_LYSSC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|168994488|gb|ACA42028.1| tRNA pseudouridine synthase A [Lysinibacillus sphaericus C3-41]
          Length = 246

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 73/248 (29%), Positives = 115/248 (46%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALR 59
           M R  +II Y+G+ + G+Q Q    ++Q  IE+ + ++  E  V V  +GRTD+ VHA  
Sbjct: 1   MRRLKIIISYDGTHFSGYQVQPGERTVQAEIERVLAIMHKEEKVKVTASGRTDARVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           KALN  L     I +L++  V   FHAR+S   + Y Y     
Sbjct: 61  QTLHFDTPLAIPTDKYRKALNVQL--PRDIRVLSVEEVAHDFHARYSVTGKRYRYIWSCE 118

Query: 120 QAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  +           D   M+ AAQ ++G HDF+ F + +      +RT+      
Sbjct: 119 PIQNPFRRHYTVDTNGVKPDVVAMQKAAQAIIGTHDFSCFCAANTSVQDKVRTVTSLQFE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + + +    FL+  +R   G+L  VG  + T  ++   + ++DR + G  APP+G
Sbjct: 179 WHGEELHMVIEGNGFLYNMVRIIAGTLWEVGIDRRTIENIALVVASEDRDKAGKTAPPQG 238

Query: 239 LYFDSVEY 246
           LY + V Y
Sbjct: 239 LYLEKVFY 246


>gi|262374120|ref|ZP_06067397.1| tRNA pseudouridine synthase A [Acinetobacter junii SH205]
 gi|262311131|gb|EEY92218.1| tRNA pseudouridine synthase A [Acinetobacter junii SH205]
          Length = 265

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 127/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G+ Y GWQ +Q    S+Q +IEK +  +    V++H AGRTD+GVHA  
Sbjct: 1   MQRYAIGIEFCGTQYRGWQTQQAGVVSVQETIEKVLSKIADHPVILHAAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D+ FHARF A+ R Y Y +   
Sbjct: 61  MVAHFDTTAIRPERGWLMGANSQL--PKDISIQWIKCMDENFHARFKAMARRYRYLVYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   + + LD + M  AA    G H+F +FR+  CQ++ P+R + H  +  
Sbjct: 119 PTRPALLHKQVTHLYQELDVQKMIKAAAKFEGTHNFESFRAAACQSNQPVRHVKHCRLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DR+  G  AP +GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRRAAGITAPADGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQSYYP 246


>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 =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 110/285 (38%), Positives = 148/285 (51%), Gaps = 40/285 (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  VAHF--------------------------------------DLVREWVPVILCKALNAY 82
           V HF                                       L   +    L  A+N Y
Sbjct: 61  VVHFDLIAPNNSKDLACINKETDNKEVSKQNNTTTTIDSLKKMLPCRYNAYKLMSAVN-Y 119

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM 142
           L     I + +  I   QFHARFSA  R Y YRII R  P  +E+ R W I   L+  +M
Sbjct: 120 LLKPHRIILTSCEITTLQFHARFSAKARHYKYRIINRTVPSVIEQNRTWWIKPPLNVIDM 179

Query: 143 RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSF 201
             A+QHL+G+HDFT+FRS  CQA SP++T+   +V  +    I+I   A SFLH  +R+ 
Sbjct: 180 IDASQHLIGKHDFTSFRSSACQAKSPLKTLTKIEVDTTNYPEIQIYFSAPSFLHHMVRNI 239

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           VG+L  +G  K +   ++  L A++R   GP AP  GLYF  V+Y
Sbjct: 240 VGTLVYIGLCKISPAAIKTILFAKNRAMAGPTAPSSGLYFVKVDY 284


>gi|317495541|ref|ZP_07953909.1| tRNA pseudouridine synthase A [Gemella moribillum M424]
 gi|316914355|gb|EFV35833.1| tRNA pseudouridine synthase A [Gemella moribillum M424]
          Length = 265

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GSGY G+Q Q N +++Q  IEKA+  +  + + V+ +GRTDSGVHA  QV
Sbjct: 1   MRVVLLCRYDGSGYHGFQIQPNNNTVQEEIEKALKKINKKDIRVYMSGRTDSGVHAYGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           KALNA L     I I  ++  ++ FH R+++ R++Y Y++   Q 
Sbjct: 61  LHFDTELNIPNEAWKKALNANL--PADIRIFGVTTSNEDFHVRYNSTRKTYHYKLYIGQN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV---N 178
                         + + E  + A  + +G HDF++F S +      IR I +F++    
Sbjct: 119 VDPFLLNYVGQHKYNFNFEKAQKALNYFIGEHDFSSFCSKNSSVEDKIREIYYFNMYYDK 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +   +I   V    FL+  +R  +G+++ V  GK+ +  +++ L  ++RK  GP A   G
Sbjct: 179 TNPRVINFDVCGNGFLYNMVRIIIGTIQDVAAGKYGAEYVKEILDKKERKYAGPKADAAG 238

Query: 239 LYFDSVEYS 247
           LY   V Y+
Sbjct: 239 LYLKEVIYN 247


>gi|255321215|ref|ZP_05362381.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SK82]
 gi|262380100|ref|ZP_06073255.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SH164]
 gi|255301769|gb|EET81020.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SK82]
 gi|262298294|gb|EEY86208.1| tRNA pseudouridine synthase A [Acinetobacter radioresistens SH164]
          Length = 265

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 129/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G  Y GWQ +Q    S+Q ++E+ +  +  E +++HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFCGIRYRGWQTQQAGVPSVQETLERVLSKIADEKIILHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     I++  L  + + FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTHAIRTERGWMMGSNSQL--PKDIALQWLQPMGEDFHARFKACARRYRYVIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   + + LD E M+ AA+   G H+F +FR+  CQ++ PIR + H ++  
Sbjct: 119 PYRPALLHKQVTHVYQQLDIEKMKKAAKKFRGVHNFESFRAAACQSNQPIRDVTHCELFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ VG L  VG G +    ++    A+DR+  G  AP +GL
Sbjct: 179 HGRYLVLDIQANGFLHHMVRNIVGCLLEVGQGMYDIGHIDSIFAAEDRRAAGMTAPADGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQAYYP 246


>gi|303230129|ref|ZP_07316898.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-134-V-Col7a]
 gi|302515190|gb|EFL57163.1| tRNA pseudouridine synthase A [Veillonella atypica ACS-134-V-Col7a]
          Length = 261

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 73/248 (29%), Positives = 124/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    +I+ Y+G+   G+Q+Q    G ++QG++EKA+ ++  E + ++GA RTD+GVHA 
Sbjct: 1   MRNIRLIVAYDGTDLAGYQKQPADKGITVQGALEKALSIICAEPIQIYGASRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F          + +A  A+L     I +     +   +  R +   + Y+Y I  
Sbjct: 61  FQVCAFQTSGSIPVKNIPRATIAHL--PKDIVVTEAVEIPLDWKPRHNIFGKEYIYSIYN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R+    + +   W + K LD E MR A + L G HDF+T +  +     P++TI    + 
Sbjct: 119 REIADPMGQRYHWHVKKPLDVEAMRQAGKALEGTHDFSTLKGANTTPVDPVKTIYAIGIK 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                I+I VV   FL+  +R+  G L  +G G+ +   + + L A+DRK  G  AP +G
Sbjct: 179 EKAGRIDISVVGDGFLYHMVRNIAGLLVDIGLGRKSVARIPELLAAKDRKRIGKTAPAQG 238

Query: 239 LYFDSVEY 246
           L  + + +
Sbjct: 239 LVLEEIFF 246


>gi|312898257|ref|ZP_07757648.1| tRNA pseudouridine synthase A [Megasphaera micronuciformis F0359]
 gi|310620754|gb|EFQ04323.1| tRNA pseudouridine synthase A [Megasphaera micronuciformis F0359]
          Length = 266

 Score =  269 bits (689), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/245 (32%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              + + Y+G+ ++G+QRQ +  S+Q  +E A+  + G  + ++GA RTDSGVHA  QV 
Sbjct: 6   NISLRLAYDGTEFYGFQRQSSLPSVQQHVEAALSGIYGRNIRIYGAARTDSGVHARGQVV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F          L  AL   L     I +L+ ++  + F  R     + Y Y ++    P
Sbjct: 66  NFYGDDTIPVERLPYALKGSL--PPAIVVLSATLERENFSVRHDNKGKHYRYTLVNDGVP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                  AW I K L+CE+M+ AA +L G HDF+ F   +    +P++T+    V S  N
Sbjct: 124 DPFMLRYAWYIRKPLNCESMKEAASYLKGTHDFSAFEGANTTPMNPVKTMYGIFVVSKKN 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I I VV   FL+  +R+  G+L  VG G+ +S  +++ L+  DR++ G  AP +GL  +
Sbjct: 184 RIIIDVVGSGFLYHMVRNMAGALVDVGMGRKSSQRIKEILKGGDRRKLGATAPAQGLCLE 243

Query: 243 SVEYS 247
            V YS
Sbjct: 244 EVYYS 248


>gi|163816114|ref|ZP_02207482.1| hypothetical protein COPEUT_02298 [Coprococcus eutactus ATCC 27759]
 gi|158448534|gb|EDP25529.1| hypothetical protein COPEUT_02298 [Coprococcus eutactus ATCC 27759]
          Length = 271

 Score =  269 bits (688), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/273 (29%), Positives = 124/273 (45%), Gaps = 28/273 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------------------- 38
           M  Y     Y+G+ Y GW+ + N  +++G IE  +  +                      
Sbjct: 1   MTNYRFTFSYDGTRYHGWESKTNADTVEGRIEAVLSKMVDGDNGKTADVCRENMSADIRD 60

Query: 39  --TGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSI 96
             T   V +HGAGRTD+GVHA   VA   L     P  +   LN YL     I  L++++
Sbjct: 61  TKTPAKVDIHGAGRTDAGVHARAMVASGRLNTNRTPDEIKDYLNRYL--PADICALDVTV 118

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHD 154
              +FHAR +A  + Y Y +         ++   W +P+   LD + M+ AA +LVG+HD
Sbjct: 119 AGDRFHARLNATGKIYEYTLYVGLEKPVFDRNYVWCVPQGSVLDVDAMKKAASYLVGKHD 178

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           F +F   +    S +RTI   ++   G+ + +R     FL   +R   G+L  +G G   
Sbjct: 179 FRSFCGNNKMKKSTVRTIYDVEIVKEGDYVRMRFHGNGFLQNMVRILTGTLVEIGYGHMD 238

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  + + +   DR+  GP APP GL    VEY 
Sbjct: 239 AEHMPEIIVGMDRQLAGPTAPPHGLCLLKVEYD 271


>gi|294669057|ref|ZP_06734143.1| tRNA pseudouridine synthase A [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291309049|gb|EFE50292.1| tRNA pseudouridine synthase A [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 326

 Score =  269 bits (688), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS +FGWQ+Q +G  S+Q ++E A+  + GE V V  AGRTD+GVHA  QV
Sbjct: 62  RWALTLSYDGSRFFGWQKQADGVVSVQAALESALSQIAGETVNVVAAGRTDTGVHATAQV 121

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       + +N+ L     +++     V   FHARF A  R Y Y + +   
Sbjct: 122 VHFDTAAERGEQSWIRGVNSLL--PQGVAVWQAKRVASHFHARFDAFGRRYRYVLQSSPV 179

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L   R       LD   M+ AA  LVG HDF++FR+  CQA SP++T+    ++   
Sbjct: 180 RSPLLAARVGWTHTPLDFAAMQAAAALLVGEHDFSSFRASQCQAKSPVKTLYSVVLHGTP 239

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ VG+L  VG+G+ +     + L  + R +  P   P+GLY 
Sbjct: 240 QLMALDLHGNAFLHHMVRNIVGALVYVGNGRLSVQGFAELLAEKSRLKAPPTFMPDGLYL 299

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 300 TGVDYP 305


>gi|89893262|ref|YP_516749.1| hypothetical protein DSY0516 [Desulfitobacterium hafniense Y51]
 gi|89332710|dbj|BAE82305.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 271

 Score =  269 bits (688), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/247 (32%), Positives = 118/247 (47%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
              C+ + Y+G+ Y G+QRQ   +G +IQG++E     +  E V ++ AGRTD+GVHA  
Sbjct: 5   RNICLKVAYDGTYYHGFQRQPEFHGPTIQGTLEAVWAKLVEEEVTLNTAGRTDTGVHAAG 64

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          + KA N+ L     I IL      + FHARFSA  + Y YRI   
Sbjct: 65  QVVNFRTGARIPVDKIPKAFNSLL--PRDIRILAAQEAAENFHARFSAKWKRYDYRIDNH 122

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  +   P  LD + M+  AQ+LVGRH+F  F +    + +  RT+    V  
Sbjct: 123 PVADVFTRLYSLHEPVRLDWQRMQQGAQYLVGRHNFKAFSAAGGTSKTFERTLYLCQVAE 182

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + I  +   FL+  +R   G+L  VG  +    ++   L + DRK  G  A P+GL
Sbjct: 183 NQGHLRITCIGDGFLYNMVRIIAGTLVYVGKNRIQPGEIPDILASLDRKRGGVTATPQGL 242

Query: 240 YFDSVEY 246
               V Y
Sbjct: 243 TLSYVHY 249


>gi|160914527|ref|ZP_02076742.1| hypothetical protein EUBDOL_00533 [Eubacterium dolichum DSM 3991]
 gi|158433685|gb|EDP11974.1| hypothetical protein EUBDOL_00533 [Eubacterium dolichum DSM 3991]
          Length = 252

 Score =  269 bits (688), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 118/247 (47%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ+Q N  SIQ  IE A+  +  E V +  +GRTD+ VHAL Q
Sbjct: 1   MDRYKVTVCYDGTNYAGWQKQDNARSIQEEIECALAKINEEAVEIVASGRTDAHVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  +        +A N+ L     I IL +  V   FHARF A+R+ Y Y I    
Sbjct: 61  VFHFDAKKALSDEQWVRACNSLL--PKDIRILKVEKVSDSFHARFDAVRKRYDYYITND- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVNS 179
                 +       KSLD   M+  A   +G HDFT+F S    +  S I+TI   +V  
Sbjct: 118 VLNPFLENYMGKDRKSLDVAYMQECANVFIGTHDFTSFTSSKIDERKSRIKTIYRLEVQQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N + I     +FL   +R     L   G  + T   + + L+A+D+  C   A   GL
Sbjct: 178 EANAVHIIFEGNAFLRYMVRMLAQVLIEAGKHRLTKEAISQMLEAKDKHACRYKASANGL 237

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 238 YLVRVDY 244


>gi|219666536|ref|YP_002456971.1| tRNA pseudouridine synthase A [Desulfitobacterium hafniense DCB-2]
 gi|219536796|gb|ACL18535.1| tRNA pseudouridine synthase A [Desulfitobacterium hafniense DCB-2]
          Length = 271

 Score =  269 bits (688), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 80/247 (32%), Positives = 118/247 (47%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
              C+ + Y+G+ Y G+QRQ   +G +IQG++E     +  E V ++ AGRTD+GVHA  
Sbjct: 5   RNICLKVAYDGTYYHGFQRQPEFHGPTIQGTLETVWAKLVEEQVTLNTAGRTDTGVHAAG 64

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          + KA N+ L     I IL      + FHARFSA  + Y YRI   
Sbjct: 65  QVVNFRTGARIPVDKIPKAFNSLL--PRDIRILAAQEAAEDFHARFSAKWKRYDYRIDNH 122

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  +   P  LD + M+  AQ+LVGRH+F  F +    + +  RT+    V  
Sbjct: 123 PVADVFTRLYSLHEPVRLDWQRMQQGAQYLVGRHNFKAFSAAGGTSKTFERTLYLCQVAE 182

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + I  +   FL+  +R   G+L  VG  +    ++   L + DRK  G  A P+GL
Sbjct: 183 NQGHLRITCIGDGFLYNMVRIIAGTLVYVGKNRIQPGEIPDILASLDRKRGGVTATPQGL 242

Query: 240 YFDSVEY 246
               V Y
Sbjct: 243 TLSYVHY 249


>gi|317154696|ref|YP_004122744.1| tRNA pseudouridine synthase A [Desulfovibrio aespoeensis Aspo-2]
 gi|316944947|gb|ADU63998.1| tRNA pseudouridine synthase A [Desulfovibrio aespoeensis Aspo-2]
          Length = 258

 Score =  269 bits (688), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 120/249 (48%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + + Y+G+ + GWQ Q    ++QG IE A+  + G  V +HGAGRTD+GVHAL Q
Sbjct: 1   MPRFLLTLAYDGTDFSGWQLQARDRTVQGVIETALTEIMGSPVRLHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD       +    ALNA L   + + +L    V   FHAR+ A  ++Y Y +   +
Sbjct: 61  TAHFDCQDIRASIPWQCALNARL--PEDVRVLACRRVADDFHARYQAQAKTYEYTLWHTR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
                ++ R       LD   M  AA+ L G HDF +F++      S IRT+     +  
Sbjct: 119 EFCLPQRRRFAWNCGPLDFTAMEAAARLLTGEHDFASFQNTGTPVRSTIRTVTAISRHPG 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +    R  A  FL   +R+ VG L   G G+    +  + L A DR      APP+G
Sbjct: 179 PTPHESVWRFTANGFLKQMVRNLVGCLAACGRGRLAPDEAGRILLAADRALAPATAPPQG 238

Query: 239 LYFDSVEYS 247
           L   SV Y 
Sbjct: 239 LTLISVAYP 247


>gi|312880338|ref|ZP_07740138.1| tRNA pseudouridine synthase A [Aminomonas paucivorans DSM 12260]
 gi|310783629|gb|EFQ24027.1| tRNA pseudouridine synthase A [Aminomonas paucivorans DSM 12260]
          Length = 260

 Score =  269 bits (688), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 121/246 (49%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY   + Y G+ + G+Q Q N  S+QG +E A+  ++G  V  HGAGRTD+GVHA  Q
Sbjct: 1   MPRYAAEVAYVGASFAGFQAQPNRPSVQGVLEAALEALSGSPVRCHGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFDL R W P  L  A+ A+L    ++ IL ++ V   FHARF A+ R Y + +  + 
Sbjct: 61  VVHFDLPRPWDPFRLRGAMAAHL--PPSVEILQVAQVPDSFHARFDALWREYRFFLWNQA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A +   +   W +   LD   ++     L GRHDF  F     +     RT+ H      
Sbjct: 119 ACVPHLRPFVWWVKSPLDWTLVQHLLPSLRGRHDFGAFCRSVDRPEDSWRTLLHVSCRRR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I  R     FL   +R  VG+L+ V  G          L+   R E G  APP+GL+
Sbjct: 179 GPFIRFRFRGDGFLTNMVRILVGTLEGVARGGMEPEAFLNLLEGGCRSEAGRTAPPQGLF 238

Query: 241 FDSVEY 246
           F  V Y
Sbjct: 239 FWRVGY 244


>gi|302670312|ref|YP_003830272.1| tRNA pseudouridine synthase A TruA2 [Butyrivibrio proteoclasticus
           B316]
 gi|302394785|gb|ADL33690.1| tRNA pseudouridine synthase A TruA2 [Butyrivibrio proteoclasticus
           B316]
          Length = 265

 Score =  269 bits (688), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 122/250 (48%), Gaps = 7/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG----EIVVVHGAGRTDSGVH 56
             Y  II Y+G+ Y GW+++ +   +IQG +E  +  + G      V + GAGRTD+GVH
Sbjct: 18  QNYKFIISYDGTRYHGWEKKPDLEMTIQGKLEGVLNRMIGAEGTGEVNLIGAGRTDAGVH 77

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A    A   L        +   +N YL   + IS+  + +   +FHAR++AI ++Y Y  
Sbjct: 78  ARAMTASAVLDTHLSEAEIQSYMNTYL--PEDISVNEVKVCSDRFHARYNAIGKTYRYTC 135

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                    ++    ++ +  + + MR AA+ L+G HDF +F        S +R +D  +
Sbjct: 136 WYGDGKPVFDRKYVTVLDREPNVDMMRKAAELLIGEHDFRSFCGNSKMKKSTVRVLDTIN 195

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   GN I        FL   +R   G+L  VG G  +   ++  L+A DRK+ GP A P
Sbjct: 196 IEKNGNYIRFYFHGNGFLQNMVRILTGTLLEVGYGNISPEKIQDILKACDRKKAGPTARP 255

Query: 237 EGLYFDSVEY 246
           EGL    V+Y
Sbjct: 256 EGLCMMKVDY 265


>gi|21283867|ref|NP_646955.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49487001|ref|YP_044222.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|297209968|ref|ZP_06926364.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|300910980|ref|ZP_07128430.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|30913392|sp|Q8NVB7|TRUA_STAAW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56749699|sp|Q6G7A2|TRUA_STAAS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21205309|dbj|BAB96003.1| tRNA pseudouridine synthase A [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49245444|emb|CAG43921.1| putative tRNA pseudouridine synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|296885641|gb|EFH24578.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|300887960|gb|EFK83155.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
          Length = 267

 Score =  269 bits (687), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+NG ++Q   EK +  +    V +H + RTD GVHA++Q 
Sbjct: 1   MRILVEIAYQGNNFLGFQIQQNGRTVQQQFEKLLQRMHKRHVRIHPSSRTDRGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD  FH R+  + + Y Y++   Q 
Sbjct: 61  FHFDTELNIPMSQWQYAMNRTL--PDDIYVNNVVTVDDDFHCRYDCVGKRYRYKVYQAQH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    IP++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTFIPETLDLDKMNRAAQQFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  +  V    FL+  +R  V  L  VG G+   +D+ K L++++RK     A  EGLY 
Sbjct: 179 DGFDYIVTGSGFLYNMVRVLVAFLIEVGKGRHEISDVPKLLESKNRKNVPFTATAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|166154677|ref|YP_001654795.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|166155552|ref|YP_001653807.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335947|ref|ZP_07224191.1| tRNA pseudouridine synthase A [Chlamydia trachomatis L2tet1]
 gi|238687386|sp|B0B836|TRUA_CHLT2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238687485|sp|B0BCA1|TRUA_CHLTB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|165930665|emb|CAP04162.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|165931540|emb|CAP07116.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 267

 Score =  269 bits (687), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/251 (34%), Positives = 128/251 (50%), Gaps = 6/251 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M +   + I Y G+ Y GWQ Q N  SIQ  ++  +  + G  + V  +GRTD+GVHA  
Sbjct: 1   MTKKIVLQIAYQGTSYSGWQYQPNALSIQEVLKTILKKIAGFRISVISSGRTDAGVHAQG 60

Query: 60  QVAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           Q+AHF          P  + K LNA L     I I +  + D  FH+RFSAI + Y Y +
Sbjct: 61  QIAHFHCPDHPHFTDPRQIQKMLNALL--PHDIVIRDAVMTDGDFHSRFSAIAKEYRYTL 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                PL   +   +     L+   M+ AAQ+LVG HDF +F ++  + SS IRT+   D
Sbjct: 119 SLLPKPLPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLYTLD 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   +L+ +      FL+  +R+ VG+L  +G GK+    L   L  +DR++  P APP
Sbjct: 179 LSEQEHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKDRRKGPPSAPP 238

Query: 237 EGLYFDSVEYS 247
            GL    V Y 
Sbjct: 239 YGLSLHHVCYP 249


>gi|89898653|ref|YP_515763.1| tRNA pseudouridine synthase A [Chlamydophila felis Fe/C-56]
 gi|123735904|sp|Q253C0|TRUA_CHLFF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|89332025|dbj|BAE81618.1| tRNA pseudouridine synthase A [Chlamydophila felis Fe/C-56]
          Length = 268

 Score =  269 bits (687), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y G+ Y GWQRQ N  SIQ  IE A+  V G+ +VV  +GRTDSGVHA  Q
Sbjct: 1   MKRVVLLLAYQGTAYAGWQRQPNDLSIQEVIESALARVLGKPIVVSSSGRTDSGVHAYGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF      +   P  + K LNA L     I I ++ + D  FHARFSAI + Y Y + 
Sbjct: 61  VAHFSQPDHPLFSQPQSIKKMLNAIL--PKDIVIRDVVLSDVNFHARFSAIAKEYRYSLT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++  A+    S+  + M+  A++L+G HDF +F +     +S  RT+   D+
Sbjct: 119 RSPKPLPWQRYFAYYPRHSIKIDLMQKGAKYLLGTHDFASFANHGRDYTSTERTLFKLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                ++ I      FL+  +R+ VGSL  +   K+    +++ L  + R++  P AP  
Sbjct: 179 IDNEEIVTIICKGNGFLYKMVRNIVGSLLDISKEKYPPEYIQEILAQKSRRKGPPAAPSH 238

Query: 238 GLYFDSVEYS 247
            L    V Y 
Sbjct: 239 ALSLHHVCYP 248


>gi|325856892|ref|ZP_08172390.1| tRNA pseudouridine synthase A [Prevotella denticola CRIS 18C-A]
 gi|325483265|gb|EGC86242.1| tRNA pseudouridine synthase A [Prevotella denticola CRIS 18C-A]
          Length = 255

 Score =  269 bits (687), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 77/257 (29%), Positives = 118/257 (45%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E ++ ++  E + V GAGRTD+GVH    
Sbjct: 3   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLEHSLSILLKETITVTGAGRTDAGVHGRMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  + +    L   +N  L     +S+  +  V    HARFSA+ R+Y Y I T +
Sbjct: 63  VAHFDTAQPFDSEQLVYKMNRLL--PRDVSVSRIEAVSADLHARFSAVSRTYHYYIHTGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +  I   LD + M  AA +L+G  DF  F        +    +       F
Sbjct: 121 QP--FSRRYSCEIHYPLDFDKMNEAASYLIGEKDFKCFCKAGADVKTTFCNLTEARWIPF 178

Query: 181 GN-----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           G+                + A  FL   +R+ VG+L  VG G+ +  D  + +    R +
Sbjct: 179 GDGLSLSSGGTIANWCFVITANRFLRNMVRAVVGTLVDVGRGRLSLADFRQIVDGGTRSD 238

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+   ++Y
Sbjct: 239 AGESMPGNALFLWDIKY 255


>gi|159027087|emb|CAO89272.1| truA [Microcystis aeruginosa PCC 7806]
          Length = 271

 Score =  269 bits (687), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 83/245 (33%), Positives = 117/245 (47%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ +  S+Q  IEKA+  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 8   RIALVIQYVGTNFHGWQRQPHHRSVQEEIEKALADILGHAVTLHGAGRTDSGVHAAAQVA 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF       P    K LNA L   D I I   + V  ++HARFSA+ R Y Y + T   P
Sbjct: 68  HFQQQSPIPPAHWAKVLNARL--DDDIVIRASAQVPDRWHARFSALWRRYRYTLYTDPIP 125

Query: 123 LALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W    + LD + M  A   L+G+H    F   +         +   +    G
Sbjct: 126 NLFVSPFSWHYYHRPLDADLMARALAPLLGKHHLAAFHRANSSRDHSWVEVQGVECYRQG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +++ + A  FL+  +R  VG L  VG G+ +  +       Q R+     AP +GL  
Sbjct: 186 PFVQMEIQANGFLYGMVRLLVGMLVEVGTGERSLENFTDIWVNQRRELVKYAAPAKGLCL 245

Query: 242 DSVEY 246
             V Y
Sbjct: 246 LRVGY 250


>gi|116493132|ref|YP_804867.1| pseudouridylate synthase [Pediococcus pentosaceus ATCC 25745]
 gi|116103282|gb|ABJ68425.1| Pseudouridylate synthase [Pediococcus pentosaceus ATCC 25745]
          Length = 248

 Score =  269 bits (687), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 123/250 (49%), Gaps = 7/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHAL 58
           +RY +I+ Y+G+ + G+Q Q N  +++G +++ +  +       + V+G+GRTD+GVHAL
Sbjct: 1   MRYKIILAYDGTNFAGFQMQPNQRTVEGVLKRIVNKIAKNPTPEISVYGSGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFDL  E     +  ALN+ L     + +  + IVD+ FHARF+   + Y YR+  
Sbjct: 61  GQVVHFDLSIEMSERSMLHALNSQL--PLDMQVKKVEIVDETFHARFTTHGKKYQYRMAL 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            Q     ++         ++   ++ A + L G HDF++F +        +RTI    V 
Sbjct: 119 GQFVDPFKRNYTGHWKFPINIGLIQKAIKDLEGTHDFSSFVASGSTVKDHVRTIYEAKVW 178

Query: 179 SFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                N I        FL+  +R  V  L  +G  +  + D+ +  + +DR +    AP 
Sbjct: 179 EDKKQNEIVFEFYGNGFLYNMVRIMVAVLVEIGSKRRPADDIPRLFEVKDRNQARGTAPA 238

Query: 237 EGLYFDSVEY 246
            GLY   V+Y
Sbjct: 239 SGLYLKEVDY 248


>gi|166367993|ref|YP_001660266.1| tRNA pseudouridine synthase A [Microcystis aeruginosa NIES-843]
 gi|166090366|dbj|BAG05074.1| tRNA pseudouridine synthase 1 [Microcystis aeruginosa NIES-843]
          Length = 276

 Score =  269 bits (687), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 83/245 (33%), Positives = 118/245 (48%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ +  S+Q  IEKA+  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 8   RIALVIQYVGTNFHGWQRQPDHRSVQEEIEKALADILGHDVTLHGAGRTDSGVHAAAQVA 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+      P    K LNA L   D I I     V  ++HARFSA+ R Y Y + T   P
Sbjct: 68  HFEQQSPIPPSHWAKVLNARL--DDDIVIRASGRVPDRWHARFSALWRRYRYTLYTDPIP 125

Query: 123 LALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W    + LD + M  A + L+G+H    F   +         +   +    G
Sbjct: 126 NLFVSPFSWHYYHRPLDADVMARALKPLLGKHHLAAFHRANSSRDHSWVEVQGVECYRQG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +++ + A  FL+  +R  VG L  VG G+ +  +       Q R+     AP +GL  
Sbjct: 186 PFVQMEIQANGFLYGMVRLLVGMLVEVGTGERSLENFTDIWVNQRRELVKYAAPAKGLCL 245

Query: 242 DSVEY 246
             V Y
Sbjct: 246 LRVGY 250


>gi|86141215|ref|ZP_01059761.1| tRNA pseudouridine synthase A [Leeuwenhoekiella blandensis MED217]
 gi|85831774|gb|EAQ50229.1| tRNA pseudouridine synthase A [Leeuwenhoekiella blandensis MED217]
          Length = 263

 Score =  269 bits (687), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 121/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + I Y+G+ Y GWQRQ    ++Q  +E+A+  +    V V GAGRTD+GVHA +  A
Sbjct: 11  RYFIEIAYDGTSYHGWQRQPQSITVQEVLEEALSTLLRSEVPVVGAGRTDAGVHATQLFA 70

Query: 63  HFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HF++   +    L          + + +++  L  V  + HARF A+RRSY Y+I   + 
Sbjct: 71  HFEIEESYSFEALSHLKFRLNRFLPEAVAVNALLPVSAEAHARFDAVRRSYEYKIHMVKN 130

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P      +++   K L+ + M  AA  L+GR DF  F        + I  I     +  G
Sbjct: 131 P--FLVNQSYYFEKPLNVDAMNEAAAFLLGRQDFKCFSRSKTDVKTYICEITEARWDQDG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             ++  + A  FL   +R+ VG+L  +G GK     L+  + ++ R E G  AP  GLY 
Sbjct: 189 AQLKFSISADRFLRNMVRAIVGTLLEIGQGKLKPAALKTIIASRTRSEAGASAPAHGLYL 248

Query: 242 DSVEYS 247
             V Y 
Sbjct: 249 TEVAYP 254


>gi|319763817|ref|YP_004127754.1| tRNA pseudouridine synthase a [Alicycliphilus denitrificans BC]
 gi|330823919|ref|YP_004387222.1| tRNA pseudouridine synthase A [Alicycliphilus denitrificans K601]
 gi|317118378|gb|ADV00867.1| tRNA pseudouridine synthase A [Alicycliphilus denitrificans BC]
 gi|329309291|gb|AEB83706.1| tRNA pseudouridine synthase A [Alicycliphilus denitrificans K601]
          Length = 272

 Score =  268 bits (686), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/257 (31%), Positives = 124/257 (48%), Gaps = 14/257 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGQAYSGWQSQPSGNTVQDHLEAALGRFATQKVATICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FHAR  A+ R Y Y ++    
Sbjct: 61  VHFDTGLQRAPFSWVRGTNTFL--PPDIAVQWAQPVPDAFHARACAVARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +   LD + M+ A QHL+G HDF++FR+  CQA SP++T+    +   G
Sbjct: 119 RPSVEAGRVGWVFHELDGQAMQDAVQHLLGEHDFSSFRASACQAKSPVKTLHRIAITRRG 178

Query: 182 N------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                                 +FLH  IR+ +G +  +G G +    + + L A+ R  
Sbjct: 179 PANGPSLHGCAPCYWRFEFEGNAFLHHMIRNIMGCIVAIGQGLYPPQWMRQVLDARSRDA 238

Query: 230 CGPLAPPEGLYFDSVEY 246
             P   P+GLYF    Y
Sbjct: 239 AAPTFSPDGLYFLGPVY 255


>gi|104773573|ref|YP_618553.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103422654|emb|CAI97262.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
          Length = 263

 Score =  268 bits (686), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 85/253 (33%), Positives = 136/253 (53%), Gaps = 8/253 (3%)

Query: 1   MI--RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHA 57
           M+  RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH+
Sbjct: 1   MMTSRYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKQMTKGQEVRVFGSGRTDAGVHS 60

Query: 58  LRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           + QV HFD   RE     + KALN+ L     +   +  IVDK FH+RFS   + Y YR+
Sbjct: 61  VGQVIHFDYPGREIPAANMIKALNSQL--PMDMVFTDCEIVDKDFHSRFSVKGKWYRYRV 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                    ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +
Sbjct: 119 SLDGFVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVN 178

Query: 177 V--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           V  +   N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A
Sbjct: 179 VALDEENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTA 238

Query: 235 PPEGLYFDSVEYS 247
              GLY   V Y 
Sbjct: 239 QACGLYLYHVFYE 251


>gi|260438877|ref|ZP_05792693.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
 gi|292808716|gb|EFF67921.1| tRNA pseudouridine synthase A [Butyrivibrio crossotus DSM 2876]
          Length = 249

 Score =  268 bits (686), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 73/249 (29%), Positives = 120/249 (48%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHAL 58
             +   I ++G+ YFGW+ Q N   +IQG IE  +  +  + ++  V G GRTD+GVHA 
Sbjct: 3   QNFKFKIMFDGTRYFGWEHQPNTDLTIQGKIETVLQRMVSSEKVPEVIGCGRTDAGVHAK 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             +A+  L  +     +   +N YL   D I +L +    ++FH+R+ A+ ++Y Y   T
Sbjct: 63  AMIANAFLETDMSTDAIRDYMNRYL--PDDICVLEVKEAAERFHSRYKAVGKTYCYTCYT 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  ++   + I ++ D   M  AA+ L+G HD+ +F S      S +R +D   + 
Sbjct: 121 GPLKPVFDRKYVYYIEETPDIGKMEEAAKLLIGIHDYASFCSNPKMKKSTVREVDSIQII 180

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I        FL   +R   G+L  VG GK   + + +  +A+DR   G  AP  G
Sbjct: 181 KKGQYIRFTYHGTGFLQHMVRILTGTLLEVGFGKRDVSSIPELFEAKDRSLAGFTAPASG 240

Query: 239 LYFDSVEYS 247
           L    V+Y+
Sbjct: 241 LCMMQVDYN 249


>gi|160947056|ref|ZP_02094223.1| hypothetical protein PEPMIC_00987 [Parvimonas micra ATCC 33270]
 gi|158446190|gb|EDP23185.1| hypothetical protein PEPMIC_00987 [Parvimonas micra ATCC 33270]
          Length = 247

 Score =  268 bits (686), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 124/247 (50%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I Y+GS +FG+Q+QKN  ++QG IE A+  +T E + +  AGRTD GVH+LR 
Sbjct: 1   MRNIMLTISYDGSLFFGFQKQKNVVTVQGEIEDALKKITEENINIISAGRTDRGVHSLRH 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + +F        +    ALN +L     + +L+   V + FH+RF A  ++Y Y +   +
Sbjct: 61  IINFHTESNVGVLNFKTALNHFL--PIGVRVLDSKEVSENFHSRFDAKMKTYKYILNLDE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +        P  LD E M+ A ++ +GR  F  F        +PIR I+ F++   
Sbjct: 119 VMDPIYYNYKANFPYPLDIEKMKRAKEYFIGRKSFKAFMGPRTGNINPIREINSFEIYKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N +   +  +SF+  Q+R  VG+L  +G G     +LE+ L ++DR   G    P GLY
Sbjct: 179 NNDLIFLIKGQSFIRNQVRIMVGTLVDIGRGLIEEDELERILDSEDRTRAGVTLSPNGLY 238

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 239 LMEILYD 245


>gi|299541963|ref|ZP_07052286.1| tRNA pseudouridine synthase A [Lysinibacillus fusiformis ZC1]
 gi|298725701|gb|EFI66342.1| tRNA pseudouridine synthase A [Lysinibacillus fusiformis ZC1]
          Length = 246

 Score =  268 bits (686), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 115/248 (46%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R  +II Y+G+ + G+Q Q    ++Q  +E+ + ++  GE V V  +GRTD+ VHA  
Sbjct: 1   MRRLKVIISYDGTLFSGYQVQPGERTVQAELERVLAIMHKGEQVKVTASGRTDAKVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           KALN  L     I +L++  V   FHAR+    + Y Y     
Sbjct: 61  QTLHFDTSLAIPAEKYRKALNVQL--PRDIRVLSVEEVAHDFHARYDVAGKRYRYIWSCE 118

Query: 120 QAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  +           + E M+ AA+ + G HDF+ F + +      +RT+      
Sbjct: 119 PIQSPFRRYYTVETNGVKPNVEAMQEAAKAITGTHDFSCFCAANTSVKDKVRTVTLLQFE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + + +    FL+  +R   G+L  VG G+    ++ + + + +R + G  APP+G
Sbjct: 179 WHGEELHMVIEGNGFLYNMVRIIAGTLWEVGIGRRKVDNVSQVVASGNRDKAGKTAPPQG 238

Query: 239 LYFDSVEY 246
           LY + V Y
Sbjct: 239 LYLEKVFY 246


>gi|302388052|ref|YP_003823874.1| tRNA pseudouridine synthase A [Clostridium saccharolyticum WM1]
 gi|302198680|gb|ADL06251.1| tRNA pseudouridine synthase A [Clostridium saccharolyticum WM1]
          Length = 341

 Score =  268 bits (686), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 129/247 (52%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  MI+ Y+G+ Y GWQ Q NG +I+  + K +  +  E + V GA RTDSGVH+   
Sbjct: 1   MKRVKMIVAYDGTNYCGWQIQNNGITIEEVLNKELTSLLKEPITVIGASRTDSGVHSEGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C ALN  L   D I IL    V   +H R     ++Y Y+I+ R+
Sbjct: 61  VAVFDTENRMPADKICFALNQRL--PDDIRILQSQEVRPDYHPRKQNCVKTYEYKIMNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +  ++     LD E MR    +LVG HDF +F +   QA   +RTI   D+   
Sbjct: 119 IEVPTLRLYSYFCYFPLDVERMREGGAYLVGEHDFKSFCTARGQAEETVRTIYSLDIEKS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI IR+    FL+  +R   G+L  VG G +  + +E+ L A+DRK  GP A  +GL 
Sbjct: 179 GDLITIRIKGSGFLYNMVRIIAGTLMKVGMGVYPPSHVEEILDARDRKAAGPKAAAKGLT 238

Query: 241 FDSVEYS 247
             S++Y 
Sbjct: 239 LVSLDYE 245


>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 =  268 bits (686), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQ-RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G+ Y GWQ +Q   +S+Q +IEK +  +    +++HGAGRTD+GVHA  
Sbjct: 1   MQRYAIGIEFCGTQYRGWQTQQAGVASVQETIEKVLSTIADHPIILHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     IS+  +  +D+ FHARF A  R Y Y +   
Sbjct: 61  MVAHFDTTAIRPDRGWLMGTNSQL--PKDISLQWIKRMDESFHARFKARARRYRYIVYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   + ++LD + M  AA    G H+F TFR+  CQ++ P+R + H  +  
Sbjct: 119 PTRPALLYKQVTHLYQTLDVQKMIAAAAKFEGTHNFETFRAAACQSNQPVRHVKHCRLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ +G L  +G G +    ++    AQDRK  G  AP +GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDHMFAAQDRKAAGITAPADGL 238

Query: 240 YFDSVEYS 247
           YF   EY 
Sbjct: 239 YFIQAEYP 246


>gi|326692205|ref|ZP_08229210.1| tRNA pseudouridine synthase A [Leuconostoc argentinum KCTC 3773]
          Length = 261

 Score =  268 bits (686), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 81/257 (31%), Positives = 126/257 (49%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTD 52
           M RY  ++ Y+GS +FG+Q Q     +   ++QG + +A+  +       + V GA RTD
Sbjct: 1   MPRYKAVVAYDGSEFFGFQVQTKNGVERQRTVQGELNRAVNQMAKLPTPAIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL  +  P  + K LN  L     I I  +  V   FHARF+   + Y
Sbjct: 61  TGVHAFGQVVHFDLPFDIQPEGVRKGLNTLL--PRDIMIKQVEKVADDFHARFNTHAKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YR+ T+      ++         LD   ++ A   L+G HDF +F +   Q ++ +RTI
Sbjct: 119 IYRVSTQDFTDPFKRRYTGHFHWRLDVARIQAALPDLLGEHDFASFAASGNQTATTVRTI 178

Query: 173 DHFDVN--SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              DV        +       +FL+ QIR  VG L  +G+G+    D+ + +  +DR++ 
Sbjct: 179 TRADVEVKPDEQELVFTFEGNAFLYNQIRIMVGVLLEIGNGRRDVHDIVRLIAVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
              AP  GLY D + Y 
Sbjct: 239 RFTAPASGLYLDEIYYD 255


>gi|288802284|ref|ZP_06407724.1| tRNA pseudouridine synthase A [Prevotella melaninogenica D18]
 gi|288335251|gb|EFC73686.1| tRNA pseudouridine synthase A [Prevotella melaninogenica D18]
          Length = 253

 Score =  268 bits (686), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 76/257 (29%), Positives = 115/257 (44%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E A+  +  E + + GAGRTD+GVH    
Sbjct: 1   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLEHALSTILRESIAITGAGRTDAGVHGRMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD    +    L   +N  L     +S+  +  V +  HARFSA  R+Y Y + T +
Sbjct: 61  VAHFDTELSFDSAQLVYKVNRLL--PRDVSVSRIEPVGEDLHARFSATSRTYHYYVHTGK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +     +LD + M  AA +L+G  DF  F        + I  +        
Sbjct: 119 QP--FSRQYSCEFRYALDFDKMNEAAAYLIGEKDFKCFCKTGADVKTTICNLTEARWIPA 176

Query: 181 GNL-----------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                             + A  FL   +R+ VG+L  VG G+ +  D +K +    R +
Sbjct: 177 NEEFALTTDNTVTNWCFVITANRFLRNMVRAVVGTLVEVGRGRLSLDDFKKIVDGGTRSD 236

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+   V+Y
Sbjct: 237 AGESMPGNALFLWEVKY 253


>gi|327314538|ref|YP_004329975.1| tRNA pseudouridine synthase A [Prevotella denticola F0289]
 gi|326944120|gb|AEA20005.1| tRNA pseudouridine synthase A [Prevotella denticola F0289]
          Length = 255

 Score =  268 bits (686), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 76/257 (29%), Positives = 118/257 (45%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E+++ ++  E + V GAGRTD+GVH    
Sbjct: 3   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLERSLSILLKETITVTGAGRTDAGVHGRMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  + +    L   +N  L     +S+  +  V    HARFSA+ R+Y Y I T +
Sbjct: 63  VAHFDTAQPFDSEQLVYKMNRLL--PRDVSVSRIKAVSADLHARFSAVSRTYHYYIHTGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +  I   LD + M  AA +L+G  DF  F        +    +        
Sbjct: 121 QP--FSRRYSCEIHYPLDFDKMNEAASYLIGEKDFKCFCKAGADVKTTFCNLTEARWIPS 178

Query: 181 GN-----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           G+                + A  FL   +R+ VG+L  VG G+ +  D  + +    R +
Sbjct: 179 GDGLSLSSGGTIANWCFVITANRFLRNMVRAVVGTLVDVGRGRLSLADFRQIVDGGTRSD 238

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+   ++Y
Sbjct: 239 AGESMPGNALFLWDIKY 255


>gi|291296648|ref|YP_003508046.1| tRNA pseudouridine synthase A [Meiothermus ruber DSM 1279]
 gi|290471607|gb|ADD29026.1| tRNA pseudouridine synthase A [Meiothermus ruber DSM 1279]
          Length = 263

 Score =  268 bits (686), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 92/250 (36%), Positives = 125/250 (50%), Gaps = 9/250 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + +EY+GSG+ G Q Q  G  ++Q  +E A+  + G    +   GRTD+GVHAL  
Sbjct: 13  RRILLTLEYDGSGFAGLQTQAQGERTVQQELEAALSQIPGARPKIWPCGRTDAGVHALAM 72

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             H+D +       +  ALN  L     I  L    V   FHAR S   R Y YRI+ R+
Sbjct: 73  PVHYDTLDNIPTEKIPHALNTLL--PPDIRALAAQEVPADFHARKSCHWREYRYRILQRR 130

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
            P AL++ R W IP SL+   MR A + LVG HDF  F     +  + +R I    +   
Sbjct: 131 MPPALDRHRVWWIPHSLNLIPMRHALECLVGTHDFKAF--AVKEERATVREIYRAHLEVW 188

Query: 179 --SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I I  V   FL  Q+RS VG+L  +G GK  S+ ++  L +  RK+ GP AP 
Sbjct: 189 PTEGGREIWIEFVGSGFLRGQVRSMVGTLVEIGLGKRDSSSIQSLLASGSRKDAGPTAPA 248

Query: 237 EGLYFDSVEY 246
           +GLYF    Y
Sbjct: 249 QGLYFVRAGY 258


>gi|123966948|ref|YP_001012029.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9515]
 gi|166228749|sp|A2BYR1|TRUA_PROM5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123201314|gb|ABM72922.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9515]
          Length = 268

 Score =  268 bits (686), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS + GWQRQKN  S+Q  IE A+F V+ +++    AGRTDSGVHA  Q
Sbjct: 1   MKRVALLVQYDGSYFSGWQRQKNAISVQEMIEDALFKVSNQMIKTFAAGRTDSGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN+ L    TI IL    V K +HA +SA+ R Y Y I   +
Sbjct: 61  VVHFDIDFVIPSDRYANVLNSRL--PSTIRILESVEVKKNWHACYSAVYRHYRYVINNSK 118

Query: 121 APLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    KSLD   M  A   ++G HDF  F+      S+ + TI   ++  
Sbjct: 119 IPNLFLNKWSWHRYQKSLDEFLMSKALNGMIGEHDFYAFQKSGSTRSTSVTTIKSIEIER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI I + A  FL+  +RS VG L LVG+ K +    +     + +++    AP  GL
Sbjct: 179 TEDLILIDIKATGFLYGMVRSIVGQLVLVGEKKISPEIFKDRWVGKKKQDVHESAPANGL 238

Query: 240 YFDSVEY 246
            F +  Y
Sbjct: 239 CFVNSVY 245


>gi|225872353|ref|YP_002753808.1| tRNA pseudouridine synthase A [Acidobacterium capsulatum ATCC
           51196]
 gi|225793375|gb|ACO33465.1| tRNA pseudouridine synthase A [Acidobacterium capsulatum ATCC
           51196]
          Length = 254

 Score =  268 bits (685), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 88/256 (34%), Positives = 123/256 (48%), Gaps = 12/256 (4%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M   + + + Y+G+ Y GWQ Q    +IQG +  A+  +TGE V+  G+GRTD+GVHAL 
Sbjct: 1   MPLNWKLTLAYDGTDYRGWQVQPELPTIQGELAAAVERITGERVLPQGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA F L        L +ALN  L     I +L    + + FHAR SA  + Y YRI   
Sbjct: 61  QVASFVLKAPIPAENLHRALNRTL--PAAIRVLGAESMPEDFHARHSARSKWYEYRIFRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---------SSPIR 170
           +          + +   LD E MR AA   VG HDF +F +               S +R
Sbjct: 119 EVCPPWTARYVYALHWPLDVEAMRRAAAAFVGEHDFRSFAASDPDVAARGSEDAEESHVR 178

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           TI         +L+  RV    FLH  +R+ VG++  VG  ++ + D+   L  +DR   
Sbjct: 179 TIFASGWAEEDDLLIYRVHGNGFLHHMVRNLVGTMIGVGRRQFDAEDMPGLLALRDRSAA 238

Query: 231 GPLAPPEGLYFDSVEY 246
           G  AP  GL+  SV Y
Sbjct: 239 GATAPARGLFLYSVCY 254


>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 =  268 bits (685), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 126/247 (51%), Positives = 159/247 (64%), Gaps = 1/247 (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  TAHADIAKPITPFRLKEALNARLR-PAPVAILACEPVAGDWHARFSCVGRRYVYRIVNRR 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 FDSVEYS 247
           F    Y 
Sbjct: 240 FMEAVYP 246


>gi|303237649|ref|ZP_07324209.1| tRNA pseudouridine synthase A [Prevotella disiens FB035-09AN]
 gi|302482101|gb|EFL45136.1| tRNA pseudouridine synthase A [Prevotella disiens FB035-09AN]
          Length = 255

 Score =  268 bits (685), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 79/258 (30%), Positives = 116/258 (44%), Gaps = 15/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG S+Q  +EKA+  +    + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIKFSYDGTNYHGWQIQPNGISVQEVLEKALSTLLRTKMSVTGAGRTDAGVHARLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         L   LN  L     +S++++  V+ + HARFSA  R+Y Y +   +
Sbjct: 61  VAHFDWEAPIDGQQLAYKLNRML--PRDVSVISVEAVENELHARFSATSRTYHYYM--HR 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
                 +  ++ +P  LD E M  AA++L+G  DF  F        + I  +        
Sbjct: 117 GRNPFSRAYSYEMPYELDFERMNEAAKYLIGERDFKCFCKAGGDNKTTICNLTEARWQHC 176

Query: 179 ---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                             + A  FL   +R+ VG+L  VG G+ T  +  K +    R +
Sbjct: 177 NTEIAIHEAEKAEEWCFVITANRFLRNMVRAVVGTLVEVGRGRITIDEFRKIVDNGTRSD 236

Query: 230 CGPLAPPEGLYFDSVEYS 247
            G   P   L+   V Y 
Sbjct: 237 AGESMPGNALFLWDVTYP 254


>gi|212694471|ref|ZP_03302599.1| hypothetical protein BACDOR_03999 [Bacteroides dorei DSM 17855]
 gi|265750782|ref|ZP_06086845.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_33FAA]
 gi|212662972|gb|EEB23546.1| hypothetical protein BACDOR_03999 [Bacteroides dorei DSM 17855]
 gi|263237678|gb|EEZ23128.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_33FAA]
          Length = 257

 Score =  268 bits (685), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A      + + V GAGRTD+GVHA   V
Sbjct: 1   MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRAFSTFLRQEIEVVGAGRTDAGVHARLMV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +E   V + + LN  L     I++ ++  V    HARF A  R+Y Y +  R+ 
Sbjct: 61  AHFDYDQELDCVQITEKLNRLL--PSDIAVYDVKRVKDDAHARFDATYRTYKYYVTIRK- 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-F 180
                +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I + +     
Sbjct: 118 -DPFNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMYAEWTRVS 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T     K ++ +DR   G   P   L+
Sbjct: 177 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTLDGFRKVIENKDRCSAGSSVPGHALF 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LVDVGYP 243


>gi|153874369|ref|ZP_02002618.1| tRNA pseudouridine synthase A [Beggiatoa sp. PS]
 gi|152069168|gb|EDN67383.1| tRNA pseudouridine synthase A [Beggiatoa sp. PS]
          Length = 272

 Score =  268 bits (685), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 128/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EYNG+ +FGWQ Q +  S+QG +E A+  V    V V  AGRTD+GVHA+ QV
Sbjct: 1   MRIALGVEYNGANFFGWQFQPHARSVQGEVEIALSKVANHPVKVICAGRTDTGVHAIGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D+  +          N+ L     +S+L    VD  FHARFSA  R Y Y I+ R  
Sbjct: 61  IHADVTVQRSTRSWVLGTNSNL--PIDVSMLWAQSVDNNFHARFSAQARHYRYIILNRPT 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL   +     + L+ E M+IA  +L+G HDF        +  +PIRTI    V+   
Sbjct: 119 RPALLTKQVTWERRILEVERMQIAGNYLIGTHDFHLIVPFPVKQKTPIRTISRLMVSRMD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +FLH  +R+  G L  +G G+      +  L+AQDR   G  AP  GLYF
Sbjct: 179 DRVIIDISANAFLHHMVRNIAGVLITIGAGEKRPKWADTVLEAQDRTMGGITAPAAGLYF 238

Query: 242 DSVEYS 247
             ++Y 
Sbjct: 239 CGIDYP 244


>gi|291551097|emb|CBL27359.1| pseudouridylate synthase I [Ruminococcus torques L2-14]
          Length = 244

 Score =  268 bits (685), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 132/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ N  +++QG++E+ I  V G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGTAYQGWQRQANTENTLQGTLERTISSVAGYPVEIDGSGRTDAGVHANG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L          + +N+ L   + I IL+  +V   FHAR SA+ + Y+Y++   
Sbjct: 61  QTATVVLSGRVEDGFFTEKINSRL--PEDIRILDAELVRNGFHARKSAVGKKYIYQLDLA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD + MR AAQ L+G ++F  +     +  S  RTI    +  
Sbjct: 119 EKPDVFTRRYTYHFPQRLDLDAMRKAAQLLIGTYEFAGYTDKKDE-KSTKRTIYAIMICG 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I+     FL+  +R   G+L  VG G  +   +++ L+++DR + G LAP  GL
Sbjct: 178 QGSKVSIQYEGTGFLYHMVRILTGTLLEVGTGARSIESVKEPLKSKDRSQAGFLAPARGL 237

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 238 FLDEVYY 244


>gi|333029910|ref|ZP_08457971.1| tRNA pseudouridine synthase A [Bacteroides coprosuis DSM 18011]
 gi|332740507|gb|EGJ70989.1| tRNA pseudouridine synthase A [Bacteroides coprosuis DSM 18011]
          Length = 260

 Score =  268 bits (685), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 129/246 (52%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+GS Y GWQ Q NGSS+Q  +  A+ +   + + V GAGRTD+GVHA + +A
Sbjct: 13  RYFIYLSYDGSNYHGWQIQPNGSSVQECLMDALKMFLRKEIEVVGAGRTDAGVHAKQMIA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD  R+     +C  LN  L     I+I  +  V+K+ HARF A  R+Y Y I TR+  
Sbjct: 73  HFDFERKLDVDKVCDKLNRIL--PHDIAIHKVIEVNKEAHARFDATARTYQYYITTRK-- 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  A+ + +SLD   M  AAQ L    DFT+F  +H    + + TI   +      
Sbjct: 129 DPFRRNYAYRLYQSLDILKMNEAAQILFEFEDFTSFSKLHSDTRTNLCTIMQAEWTEVDE 188

Query: 183 L-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   + A  FL   +R+ VG+L  VG GK +  +  K ++ QDR   G   P + L+ 
Sbjct: 189 HTLVFTIQANRFLRNMVRAIVGTLIEVGRGKISLEEFRKIIEEQDRGLAGASVPGQALFL 248

Query: 242 DSVEYS 247
            +VEY 
Sbjct: 249 IAVEYP 254


>gi|220906745|ref|YP_002482056.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7425]
 gi|219863356|gb|ACL43695.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7425]
          Length = 282

 Score =  267 bits (684), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 120/246 (48%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ ++GWQRQ +  S+Q  +E+AI +V G  V VHGAGRTD+GVHA  QV
Sbjct: 11  QRIALVIQYLGTHFYGWQRQPHHRSVQEELEQAIAIVVGHPVTVHGAGRTDTGVHAAAQV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD      P    + LN  L     + I   + VD  +H+RFSA+ R Y Y + T   
Sbjct: 71  AHFDTDSVIPPHRWAEILNNRL--PQDVLIRASAGVDSSWHSRFSALWRRYRYTLYTDCR 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    K   W   + LD E M+ A   L+GRH    F             +   +    G
Sbjct: 129 PNLFLKSFTWHYYRPLDTELMQTALNPLLGRHHLAAFHRSKSGRKHSWVEVQVAECVRRG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+EI V A  FL+  +R  VG L  VG G+ +     +  Q Q R +    AP  GL  
Sbjct: 189 SLVEIEVQASGFLYGMMRLLVGMLVQVGTGERSLASFTQIWQKQQRDQVKYAAPARGLCL 248

Query: 242 DSVEYS 247
             V Y 
Sbjct: 249 LRVGYD 254


>gi|302038272|ref|YP_003798594.1| tRNA pseudouridine synthase A [Candidatus Nitrospira defluvii]
 gi|300606336|emb|CBK42669.1| tRNA pseudouridine synthase A [Candidatus Nitrospira defluvii]
          Length = 253

 Score =  267 bits (684), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 94/246 (38%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + +++EY+G+ Y GWQRQ N  +IQ ++E+A+  +    + + GAGRTD+GVHA  Q
Sbjct: 1   MTTFKLVLEYDGTQYAGWQRQPNAPTIQAAVEEALAAIAQTRLTIIGAGRTDAGVHAFGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   R        +ALNA+L     IS L++  V   FHAR+SA  + Y Y ++ R 
Sbjct: 61  VASFRTDRGLSQREWLRALNAHL--PADISALSVKAVPDHFHARYSANGKLYEYHLMNRS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L + RAW++ K LD   M  AA +L G HDF++F +      +P   +   D+   
Sbjct: 119 ERAPLLRERAWMLYKPLDFAAMTEAAAYLTGSHDFSSFETAPTDNENPQCRLQRADLRRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI +   A  FL   +RS VG+L  VG GK T+ D+   L A+ R   G  AP  GLY
Sbjct: 179 GDLIILSFYADRFLKQMVRSMVGTLVEVGQGKRTAADMRTVLAARARAAAGRTAPAHGLY 238

Query: 241 FDSVEY 246
              V+Y
Sbjct: 239 LVRVDY 244


>gi|237711190|ref|ZP_04541671.1| tRNA pseudouridine synthase A [Bacteroides sp. 9_1_42FAA]
 gi|237727555|ref|ZP_04558036.1| tRNA pseudouridine synthase A [Bacteroides sp. D4]
 gi|229434411|gb|EEO44488.1| tRNA pseudouridine synthase A [Bacteroides dorei 5_1_36/D4]
 gi|229455034|gb|EEO60755.1| tRNA pseudouridine synthase A [Bacteroides sp. 9_1_42FAA]
          Length = 267

 Score =  267 bits (684), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ Q NG S+Q ++ +A      + + V GAGRTD+GVHA   V
Sbjct: 11  MRYFIYLAYDGTNYHGWQIQPNGDSVQETLMRAFSTFLRQEIEVVGAGRTDAGVHARLMV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +E   V + + LN  L     I++ ++  V    HARF A  R+Y Y +  R+ 
Sbjct: 71  AHFDYDQELDCVQITEKLNRLL--PSDIAVYDVKRVKDDAHARFDATYRTYKYYVTIRK- 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-F 180
                +  AW +  SLD E M  AA+ L    DFT+F  +H    +    I + +     
Sbjct: 128 -DPFNRHYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMYAEWTRVS 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G      + A  FL   +R+ VG+L  VG GK T     K ++ +DR   G   P   L+
Sbjct: 187 GTEWVFTIKADRFLRNMVRAVVGTLVEVGRGKMTLDGFRKVIENKDRCSAGSSVPGHALF 246

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 247 LVDVGYP 253


>gi|260592560|ref|ZP_05858018.1| tRNA pseudouridine synthase A [Prevotella veroralis F0319]
 gi|260535606|gb|EEX18223.1| tRNA pseudouridine synthase A [Prevotella veroralis F0319]
          Length = 253

 Score =  267 bits (684), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 75/257 (29%), Positives = 114/257 (44%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E+++  +  E V + G GRTD+GVH    
Sbjct: 1   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLERSLSTLLREEVSITGGGRTDAGVHGRMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  +      L   LN  L     +S+  +  V +  HARFSA  R+Y Y + T +
Sbjct: 61  VAHFDTDKTIACQQLVYKLNRLL--PRDVSVSQIVPVSEDLHARFSATSRTYHYYVHTTK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +  I   LD + M  AA +L+G  DF  F        + I  +        
Sbjct: 119 QP--FSRQYSCEIHYPLDFDKMNEAADYLIGEKDFKCFCKTGADVKTTICNLTEARWIPC 176

Query: 181 GNL-----------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                             + A  FL   +RS VG+L  VG G+ +  + +  +    R +
Sbjct: 177 KAEQALVTSDRITNWCFVISANRFLRNMVRSVVGTLVDVGRGRLSLEEFQAIVNNGSRSD 236

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+   ++Y
Sbjct: 237 AGESMPGNALFLWDIKY 253


>gi|320530646|ref|ZP_08031695.1| tRNA pseudouridine synthase A [Selenomonas artemidis F0399]
 gi|320137097|gb|EFW29030.1| tRNA pseudouridine synthase A [Selenomonas artemidis F0399]
          Length = 258

 Score =  267 bits (684), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 123/247 (49%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
               + + Y+G+ Y G+QRQ     ++Q  +EK +  V GE V +  AGRTD+GVHA  Q
Sbjct: 6   RNIALRLSYDGTRYHGFQRQSLPVVAVQNVLEKVLAEVCGEPVELAAAGRTDTGVHAYGQ 65

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F          L +A+N  L     I+++      + F AR S+  ++YLYRI    
Sbjct: 66  VVNFFTDGRIPVAQLPRAVNGLL--PPDIAVMAAWEAGRDFSARHSSTGKAYLYRIERCT 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
            P    +  AW I + LD   MR   + LVG HD+++FR+      SP+RT+D   +   
Sbjct: 124 VPNPFTRNYAWQIFRPLDVAAMRTVLRLLVGTHDYSSFRAAGGAPMSPVRTLDEIRLDEE 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +   +    FL+  +R+ + ++  VG G+ ++    +   A DR+   P AP  GL
Sbjct: 184 EGGQLSCYMHGNGFLYHMVRNIMSTVVHVGLGRISTDRFTEIFAAHDRRLASPTAPACGL 243

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 244 YLLHVDY 250


>gi|67923564|ref|ZP_00517037.1| tRNA pseudouridine synthase [Crocosphaera watsonii WH 8501]
 gi|67854590|gb|EAM49876.1| tRNA pseudouridine synthase [Crocosphaera watsonii WH 8501]
          Length = 285

 Score =  267 bits (684), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 113/246 (45%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y GS + GWQRQ N  ++Q  IE AI  V G    +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYQGSRFHGWQRQPNQRTVQEDIETAIAQVLGYHTPIHGAGRTDAGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD V    P      LN  L   + I I     V   +HARFSA+ R Y Y   T + P
Sbjct: 72  HFDYVSPIPPQRWADILNHRL--PEDILIRGSQGVPATWHARFSALWRRYRYSFYTDKCP 129

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               K  +W      L+ E M+ A   L+G+H    FR            +        G
Sbjct: 130 NLFVKPFSWHYYYEPLNVELMQKALNPLLGKHHLAAFRRAGSHRHHSWVEVQDTQCYRQG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK +  +     Q Q R+     AP +GL  
Sbjct: 190 PFIHLEIQANGFLYGMVRLLVGMLVEVGSGKRSLHNFTDIWQNQRRELVKYSAPAKGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|242277723|ref|YP_002989852.1| tRNA pseudouridine synthase A [Desulfovibrio salexigens DSM 2638]
 gi|259550311|sp|C6BW69|TRUA_DESAD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|242120617|gb|ACS78313.1| tRNA pseudouridine synthase A [Desulfovibrio salexigens DSM 2638]
          Length = 271

 Score =  267 bits (683), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 90/249 (36%), Positives = 132/249 (53%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +II Y+G+ + GWQ Q    ++QG +EKAI  +TG  V VHG+GRTDSGVHAL Q
Sbjct: 1   MQRIKLIIAYDGTNFCGWQLQPKLRTVQGDLEKAITRITGTTVRVHGSGRTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+   +  V   +ALN+ L   D ++IL+  +V  +FH+R+SAIR++Y Y +    
Sbjct: 61  VAHFDVDSCFASVKWQRALNSLL--PDDVTILDAQLVSPEFHSRYSAIRKTYTYTLWLEN 118

Query: 121 APL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +      +   W     LD   +    Q+ +G HDF++F++   +  S +RTI  F    
Sbjct: 119 SFFLPWRRHYVWKC-GPLDFCALDQGMQYFLGEHDFSSFQNTGTEIKSTVRTIHEFKRYP 177

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + + V    FL   +R+ VG L  +G GK     +   LQ +DR      AP +
Sbjct: 178 GQTEQEMILEVCGSGFLKQMVRNMVGCLVRIGRGKAEPETVRSLLQMKDRTAAPATAPAQ 237

Query: 238 GLYFDSVEY 246
           GL    V Y
Sbjct: 238 GLCMAGVYY 246


>gi|313123140|ref|YP_004033399.1| tRNA pseudouridine synthase a [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312279703|gb|ADQ60422.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|325684750|gb|EGD26904.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           lactis DSM 20072]
          Length = 262

 Score =  267 bits (683), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 135/252 (53%), Gaps = 7/252 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHAL 58
           M  RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH++
Sbjct: 1   MTSRYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKRMTKGQEVRVFGSGRTDAGVHSV 60

Query: 59  RQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV HFD   RE     + KALN+ L     +   +  IVDK FH+RFS   + Y YR+ 
Sbjct: 61  GQVIHFDYPGREIPAANMIKALNSQL--PMDMVFTDCEIVDKDFHSRFSVKGKWYRYRVS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                   ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +V
Sbjct: 119 LDGFVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVNV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +   N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A 
Sbjct: 179 ALDEENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTAQ 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ACGLYLYHVFYE 250


>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 =  267 bits (683), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 130/248 (52%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+G G+ GWQ    +G  ++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  QVVHFDSTAERDPRAWT--LGVTGRLPPTVCVRWCMPVDDAFHARFSARARRYRYTLVNR 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 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFLRPLYP 246


>gi|241765867|ref|ZP_04763802.1| tRNA pseudouridine synthase A [Acidovorax delafieldii 2AN]
 gi|241364216|gb|EER59401.1| tRNA pseudouridine synthase A [Acidovorax delafieldii 2AN]
          Length = 289

 Score =  267 bits (683), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 88/257 (34%), Positives = 125/257 (48%), Gaps = 14/257 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + YNG  Y GWQ Q +G+++Q  +E A+   T + V    AGRTD+GVH L QV
Sbjct: 18  TRVALGVSYNGQRYNGWQSQPSGNTVQDHLEAALGRFTTQQVSTLCAGRTDAGVHGLMQV 77

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           +  NA+L     I++     V   FHAR SA+ R Y Y ++    
Sbjct: 78  VHFDTTLVRPDASWVRGTNAFL--PQDIAVQWARAVPSGFHARASAVARRYAYVLLQSPV 135

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +  +L+ + MR AA  L+G HDFT+FR+  CQA SP++T+   D+    
Sbjct: 136 RPSVEAGRVGWVFNALNEDAMRQAALRLLGEHDFTSFRASACQAKSPVKTLQRIDITRTP 195

Query: 182 ------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                               A +FLH  IR+ +GSL  VG G    + + + L A  R  
Sbjct: 196 CPRASAAGEFDACYWRFEFEANAFLHHMIRNIMGSLVAVGKGTKPPSWISEVLDAHSRDA 255

Query: 230 CGPLAPPEGLYFDSVEY 246
             P   P+GLYF    Y
Sbjct: 256 AAPTFSPDGLYFQGPVY 272


>gi|269798518|ref|YP_003312418.1| tRNA pseudouridine synthase A [Veillonella parvula DSM 2008]
 gi|269095147|gb|ACZ25138.1| tRNA pseudouridine synthase A [Veillonella parvula DSM 2008]
          Length = 261

 Score =  267 bits (683), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 73/248 (29%), Positives = 125/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    +I+ Y+G+   G+Q+Q N    ++QG +E  +  +  E + ++GA RTD+GVHA 
Sbjct: 1   MRNIQIIVAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F          + +A+ A+  I   I ++    +   +  R++   + Y+Y I  
Sbjct: 61  FQVCTFQTSGTIPVENIPRAMIAH--IPKDIVVIEAIEIPLDWKPRWNIYGKEYVYTIHN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +     L +   W + K LD + M+ A   LVG HDFTT +  +   + P++TI    V 
Sbjct: 119 QLIADPLTQRYHWHVKKPLDIDRMQAAGNELVGTHDFTTLKGTNSTPADPVKTIMGIRVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + G+ + I VV   FL+  +R+  G L  VG G+    D++  L A+DR+  G  AP +G
Sbjct: 179 ARGSQVTISVVGDGFLYHMVRNIAGLLVDVGLGRRKVEDIKGYLAAKDRRVIGKTAPAQG 238

Query: 239 LYFDSVEY 246
           L  + + +
Sbjct: 239 LCLEEIFF 246


>gi|264677138|ref|YP_003277044.1| tRNA pseudouridine synthase A [Comamonas testosteroni CNB-2]
 gi|299530680|ref|ZP_07044095.1| tRNA pseudouridine synthase A [Comamonas testosteroni S44]
 gi|262207650|gb|ACY31748.1| tRNA pseudouridine synthase A [Comamonas testosteroni CNB-2]
 gi|298721196|gb|EFI62138.1| tRNA pseudouridine synthase A [Comamonas testosteroni S44]
          Length = 276

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/262 (32%), Positives = 130/262 (49%), Gaps = 18/262 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTDSGVH L QV
Sbjct: 1   MRIALGVSYNGQAYRGWQSQPDGNTVQDKLEAALGRFAAQEVSTICAGRTDSGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIV---DKQFHARFSAIRRSYLYRIIT 118
            HFD   +  P    +  N +L     I++   + V      FH+R  A  R Y Y ++ 
Sbjct: 61  VHFDTELQRAPNSWVRGTNTFL--PKDIAVQWAAEVADGPNGFHSRACATARRYAYVLLQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                +++ GR   + ++LD + MR AA  L+G HDF++FR+  CQA SP++T+   D++
Sbjct: 119 SPVRPSVDHGRVGWVFQALDAQRMRAAADLLLGEHDFSSFRAAGCQAKSPVKTLRRIDIH 178

Query: 179 ---------SFGNL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                      G +            +FLH  IR+ +G L  VG G      +++ L+A+
Sbjct: 179 YRPAGQAPMRDGQMECGYWRFEFEGSAFLHHMIRNIMGCLIYVGQGSKPVEWMQQVLEAR 238

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R+   P   P+GLYF    Y 
Sbjct: 239 SREVAAPTFSPDGLYFLGPIYD 260


>gi|116513570|ref|YP_812476.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|122275660|sp|Q04BY4|TRUA_LACDB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116092885|gb|ABJ58038.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|325125205|gb|ADY84535.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 262

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 135/252 (53%), Gaps = 7/252 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHAL 58
           M  RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH++
Sbjct: 1   MTSRYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKQMTKGQEVRVFGSGRTDAGVHSV 60

Query: 59  RQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV HFD   RE     + KALN+ L     +   +  IVDK FH+RFS   + Y YR+ 
Sbjct: 61  GQVIHFDYPGREIPAANMIKALNSQL--PMDMVFTDCEIVDKDFHSRFSVKGKWYRYRVS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                   ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +V
Sbjct: 119 LDGFVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVNV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +   N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A 
Sbjct: 179 ALDEENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTAQ 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 ACGLYLYHVFYE 250


>gi|327438309|dbj|BAK14674.1| pseudouridylate synthase [Solibacillus silvestris StLB046]
          Length = 249

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 121/248 (48%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M+R    I Y+G+G+ G+Q Q    ++Q  IEK +  +  G  V +  +GRTD+ VHA  
Sbjct: 1   MVRLKTTISYDGTGFAGYQVQPGERTVQLEIEKVLTTMQKGTQVKITASGRTDARVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E  P    KALN  L     I +L++  V + FHAR+    + Y Y     
Sbjct: 61  QVIHFDTALEIPPEKFQKALNVQL--PRDIRVLHMEQVKEDFHARYDVSGKRYRYIWDCS 118

Query: 120 QAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  +           + E MR AA+ +VG HDF+ F + +      +RT++  ++ 
Sbjct: 119 TVQSPFRRHYTVETGGVKPNVEAMREAAKAIVGTHDFSCFCAANTSVVDKVRTVETLELV 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + + +    FL+  +R   G+L  VG G+  ++ LEK + + DR + G  AP  G
Sbjct: 179 WQGEELHMTISGNGFLYNMVRIIAGTLWEVGIGRREASSLEKTIASMDRAQAGKTAPAHG 238

Query: 239 LYFDSVEY 246
           LY + V Y
Sbjct: 239 LYLEQVFY 246


>gi|289550174|ref|YP_003471078.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis HKU09-01]
 gi|289179706|gb|ADC86951.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis HKU09-01]
          Length = 267

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 115/244 (47%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q  G ++Q   EK +  +    V +H + RTD GVHAL Q 
Sbjct: 1   MRILVNICYQGSNFLGFQIQNQGRTVQQQFEKILKRMHRHDVRIHPSSRTDRGVHALEQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I +  +  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELKIADSQWQYAMNSAL--PDDIYVKEVKQVDSDFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    +P+ L+ E M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 KNPFESGLKTYVPQQLNIERMNEAAQKFIGTHDFTGFCSQKTEVESKVRTLYQSEIEMTT 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  +  L  VG G  +  ++   L+ ++R      AP EGLY 
Sbjct: 179 YGFDYIVTGSGFLYNMVRVLMAFLIEVGKGNRSPEEVTALLEQKNRDNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|328948028|ref|YP_004365365.1| tRNA pseudouridine synthase A [Treponema succinifaciens DSM 2489]
 gi|328448352|gb|AEB14068.1| tRNA pseudouridine synthase A [Treponema succinifaciens DSM 2489]
          Length = 261

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/257 (31%), Positives = 122/257 (47%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN------GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M    + + Y+G+ + GWQRQ          ++QG IE A+F +    V + G+GRTDSG
Sbjct: 1   MTNILLTVSYDGTDFCGWQRQDKSDNGSPVRTVQGEIENALFKMLKVPVKLSGSGRTDSG 60

Query: 55  VHALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           VHA  Q A+F+            +ALN  L     I IL    V+K F +RF A  R Y 
Sbjct: 61  VHAAGQAANFESPIDTIPCENYVRALNGIL--PQDIRILKARKVEKDFSSRFCATSRLYR 118

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I T+  P A E    W I    + + +      L G  D  +F +    + S  R ID
Sbjct: 119 YFIQTKNPPFASESRYRWFISFRPEIDLLNEMCSCLRGEIDCASFAASGDSSLSTKRYID 178

Query: 174 H---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           +   F      +L+  ++ A +FL   +RS  G+L  +   K +  + +K L+++DR + 
Sbjct: 179 NAFFFWNKENPDLLVFQIEANAFLWKMVRSITGTLIQLAQKKCSPNEFKKILESRDRTKA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           G  APP GL+   V++ 
Sbjct: 239 GITAPPTGLFLWEVKFD 255


>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 =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 120/247 (48%), Positives = 164/247 (66%), Gaps = 1/247 (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+     +++ +  V   F ARFSA++R YLYRI+ R+
Sbjct: 61  VAHIHLARDWRPDQVRDAMTAHLRPHPV-AVVAVERVADDFDARFSAVKRHYLYRIVNRR 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 FDSVEYS 247
             +V Y 
Sbjct: 240 LAAVSYP 246


>gi|325269743|ref|ZP_08136354.1| tRNA pseudouridine synthase A [Prevotella multiformis DSM 16608]
 gi|324987944|gb|EGC19916.1| tRNA pseudouridine synthase A [Prevotella multiformis DSM 16608]
          Length = 255

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 77/257 (29%), Positives = 118/257 (45%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  +E+++ ++  E + V GAGRTD+GVH    
Sbjct: 3   MQRYFITLSYDGTAYHGWQIQPNGISVQEVLERSLSILLKETITVTGAGRTDAGVHGRMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  + +    L   +N  L     +S+  +  V    HARFSA+ R+Y Y I T +
Sbjct: 63  VAHFDTAQPFDSGQLVYKMNRLL--PRDVSVSRIEAVSADLHARFSAVSRTYHYYIHTGK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P       +  I   LD + M  AA +L+G  DF  F        +    +       F
Sbjct: 121 QP--FSHRYSCEIHYPLDFDKMNEAASYLIGEKDFKCFCKAGADVKTTFCNLTEARWIPF 178

Query: 181 GN-----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           G+                + A  FL   +R+ VG+L  VG G+ +  D  + +    R +
Sbjct: 179 GDGLSLSSGSTIANWCFVITANRFLRNMVRAVVGTLVDVGRGRLSLADFRQIVDGGTRSD 238

Query: 230 CGPLAPPEGLYFDSVEY 246
            G   P   L+   ++Y
Sbjct: 239 AGESMPGNALFLWDIKY 255


>gi|221068666|ref|ZP_03544771.1| tRNA pseudouridine synthase A [Comamonas testosteroni KF-1]
 gi|220713689|gb|EED69057.1| tRNA pseudouridine synthase A [Comamonas testosteroni KF-1]
          Length = 276

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/262 (31%), Positives = 129/262 (49%), Gaps = 18/262 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTDSGVH L QV
Sbjct: 1   MRIALGVSYNGQAYRGWQSQPDGNTVQDKLEAALGRFAAQEVSTICAGRTDSGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIV---DKQFHARFSAIRRSYLYRIIT 118
            HFD   +  P    +  N +L     I++   + V      FH+R  A  R Y Y ++ 
Sbjct: 61  VHFDTGLQRTPNSWVRGTNTFL--PKDIAVQWAAEVADGPDGFHSRACATARRYAYVLLQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                ++++GR   + ++LD + MR AA  L+G HDF++FR+  CQA SP++T+   D++
Sbjct: 119 SPVRPSVDQGRVGWVFQTLDAQRMRAAADLLLGEHDFSSFRAAGCQAKSPVKTLRRIDIH 178

Query: 179 SFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                                     +FLH  IR+ +G L  VG G      +++ L+A+
Sbjct: 179 YRPAGQAPMRDTQMQCGYWRFEFEGSAFLHHMIRNIMGCLIYVGQGSKPVEWMQQVLEAR 238

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R+   P   P+GLYF    Y 
Sbjct: 239 SREVAAPTFSPDGLYFLGPIYD 260


>gi|307154816|ref|YP_003890200.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7822]
 gi|306985044|gb|ADN16925.1| tRNA pseudouridine synthase A [Cyanothece sp. PCC 7822]
          Length = 284

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 118/247 (47%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ + GWQRQ N  ++Q  IE AI  V G  + +HGAGRTD+GVHA  QV
Sbjct: 11  QRVALVIQYLGTHFHGWQRQPNRRTVQEEIETAIAQVLGYPITLHGAGRTDAGVHAAAQV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD +    P      LN+ L   D I +     V   +HARFSA+ R Y Y I T + 
Sbjct: 71  AHFDQMSLIPPYRWATILNSRL--PDDIVVRASHKVCDTWHARFSALWRRYRYTIYTDKQ 128

Query: 122 PLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    K  +W      L    M+ A + L+G+H    F   +   +     +        
Sbjct: 129 PNLFVKPFSWHYYQYPLSESLMQAALEPLLGKHHLAAFHRANSARTHSWVEVQAVQCYRS 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A  FL+  +R  +G L  VG+ + + ++     + Q R+E    AP +GL 
Sbjct: 189 GPFIHVEIQANGFLYGMVRLLMGMLIEVGNQQRSLSEFTNIWKNQRREEVKYAAPAKGLC 248

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 249 LLRVGYP 255


>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 =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 100/246 (40%), Positives = 153/246 (62%), 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  VFHFDYEDKLDCKKILLGLNHFLKKKN-ISVLSLDFTNNNFDSRRDAKLRTYTYKILNRI 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|32491058|ref|NP_871312.1| hypothetical protein WGLp309 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|31340463|sp|Q8D2P5|TRUA_WIGBR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|25166265|dbj|BAC24455.1| truA [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 264

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 136/247 (55%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y G+ Y GWQ QKN  SIQ  +E A+F  +GE + ++ AGRTD+ VHAL Q
Sbjct: 1   MKKLAAGISYQGNNYCGWQSQKNIISIQEYVELALFKFSGEKIKIYCAGRTDAKVHALLQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF    +         +N+YL     ISI+ +  V   FHAR+SAI + YLY I    
Sbjct: 61  VVHFYTDIKRSYRQWILGVNSYL--PYDISIMWVIKVHNNFHARYSAIAKKYLYLIHNNI 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +   + +   + +  SL+  +M+ AAQ L+G+HDF++F+   CQ+ +  R I +  +N +
Sbjct: 119 SRSGIFRKYCFNVFISLNINDMKKAAQKLIGKHDFSSFKGSECQSKTTYRVIYYIRINKY 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I + + A SFL+  +R+ +G+L  +G GK +   + + L  ++ K     A P+GLY
Sbjct: 179 KEYIFVEIKANSFLNHMMRNIIGNLIEIGKGKKSKEWMSELLFLKNNKFSIFSADPKGLY 238

Query: 241 FDSVEYS 247
             +V Y 
Sbjct: 239 LSNVYYP 245


>gi|33592579|ref|NP_880223.1| tRNA pseudouridine synthase A [Bordetella pertussis Tohama I]
 gi|42559761|sp|Q7U363|TRUA_BORPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33572225|emb|CAE41775.1| tRNA pseudouridine synthase A [Bordetella pertussis Tohama I]
 gi|332381997|gb|AEE66844.1| tRNA pseudouridine synthase A [Bordetella pertussis CS]
          Length = 270

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 91/249 (36%), Positives = 136/249 (54%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +G ++Q  +E A+      G  V    AGRTD+GVHA 
Sbjct: 1   MSRIALGLAYDGSAWQGWQTQPHGVTVQDQVEAALASFAGGGGPVATVCAGRTDTGVHAA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H D   +       + +NA+L    +I +     V + FHARFSA  R+Y+Y +  
Sbjct: 61  MQVIHLDTDLQRRDESWVRGVNAFL--PPSIVVQWARPVSEAFHARFSARSRTYVYLLWR 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +   AL  GRA    + LD   MR AA+ L+G HDF++FRS  CQA  P+RT+   D++
Sbjct: 119 GRVRPALWAGRAGWAFQPLDVPAMRAAARALLGEHDFSSFRSSQCQARHPVRTLHRLDID 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A +FLH  +R+ +G+L  VG G+     ++  L A+DR+   P   P+G
Sbjct: 179 ERGAFLVFTLRANAFLHHMVRNLIGALLQVGQGREPVAWMDALLCARDRRLGAPTFMPDG 238

Query: 239 LYFDSVEYS 247
           LY  ++EY 
Sbjct: 239 LYLSAIEYP 247


>gi|297587193|ref|ZP_06945838.1| tRNA-pseudouridine synthase I [Finegoldia magna ATCC 53516]
 gi|297575174|gb|EFH93893.1| tRNA-pseudouridine synthase I [Finegoldia magna ATCC 53516]
          Length = 244

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  Q
Sbjct: 1   MKNIKLTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVNQPVKINGAGRTDKGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F +  +         +N +   SD+I I+    VD  FHARFSA  ++Y Y +  + 
Sbjct: 61  VCNFIVDTDISANQFLMGVNHF--TSDSIVIVKSEEVDLDFHARFSAKSKTYKYILCNKY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                           LD + +      L+G+HDFT+F +   + ++PIRTID   +   
Sbjct: 119 YMEPWFNDYKGHRKYYLDFDLLLKCRDMLIGKHDFTSFVNDLEEDTNPIRTIDEITIEKI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +       A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GLY
Sbjct: 179 DDDFVFTFKAESFLRNMVRILVGSMVDVARGRKSIEWLKNALENKDRQSAGITIEPCGLY 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LMDIEY 244


>gi|319642589|ref|ZP_07997236.1| pseudouridylate synthase [Bacteroides sp. 3_1_40A]
 gi|317385823|gb|EFV66755.1| pseudouridylate synthase [Bacteroides sp. 3_1_40A]
          Length = 251

 Score =  267 bits (682), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/241 (34%), Positives = 119/241 (49%), Gaps = 5/241 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y GWQ Q NG S+Q ++ +A+     + + V GAGRTD+GVHA   +AHFD  
Sbjct: 1   MAYDGTNYHGWQIQPNGDSVQETLMRALSTFLRQEIEVVGAGRTDAGVHARLMIAHFDYD 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           RE   V + + LN  L     I++  +  V    HARF A  R+Y Y + TR+      +
Sbjct: 61  RELDCVQITEKLNRLL--PPDIAVYAVKRVKDDAHARFDATYRTYKYYVTTRK--DPFNR 116

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-FGNLIEI 186
             AW +  SLD E M  AA+ L    DFT+F  +H    +    I H +     G     
Sbjct: 117 HYAWRLFNSLDFEKMNEAARVLFDYTDFTSFSKLHTDVKTNNCRIMHAEWTQVSGTEWVF 176

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL   +R+ VG+L  VG GK T  +  K ++ +DR   G   P   L+   V Y
Sbjct: 177 TIKADRFLRNMVRAVVGTLVEVGRGKMTVDEFRKVIEDKDRCSAGSSVPGHALFLVDVGY 236

Query: 247 S 247
            
Sbjct: 237 P 237


>gi|218262724|ref|ZP_03477082.1| hypothetical protein PRABACTJOHN_02761 [Parabacteroides johnsonii
           DSM 18315]
 gi|218223213|gb|EEC95863.1| hypothetical protein PRABACTJOHN_02761 [Parabacteroides johnsonii
           DSM 18315]
          Length = 292

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 119/246 (48%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG  + GWQ Q NG ++Q SIE+A+  +  + V + GAGRTD+GVHA   VA
Sbjct: 46  RYFIYLGYNGKKFCGWQIQPNGITVQQSIEEALATLLRQPVPIVGAGRTDAGVHARLMVA 105

Query: 63  HFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD       ++ L + LN  L     I++  +  V    HARF A  R+Y Y I TR+ 
Sbjct: 106 HFDWKEPIDDLVFLVEKLNRLL--PKDIAVYRIVPVRTDAHARFDATSRTYKYYITTRK- 162

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                    + IP  LD E M  A   L    DFT+F  +H    +    I        G
Sbjct: 163 -DPFNYELVYKIPGKLDFEAMNKACPVLFDYIDFTSFSKLHTDVKTNNCRIYKAGWEKDG 221

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++    + A  FL   +R+ VG+L  VG GK T     + ++A+DR   G  AP   LY 
Sbjct: 222 DVWFFTIQADRFLRNMVRAIVGTLLEVGRGKLTVDGFRQVIEAKDRGRAGTSAPGHALYL 281

Query: 242 DSVEYS 247
             V Y 
Sbjct: 282 VDVTYP 287


>gi|313895792|ref|ZP_07829346.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 137 str.
           F0430]
 gi|312975217|gb|EFR40678.1| tRNA pseudouridine synthase A [Selenomonas sp. oral taxon 137 str.
           F0430]
          Length = 266

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
               + + Y+G+ Y G+QRQ     ++Q  +EK +  V GE V +  AGRTD+GVHA  Q
Sbjct: 14  RNIALRLSYDGTRYHGFQRQSLPVVAVQNVLEKVLAEVCGESVELAAAGRTDTGVHAYGQ 73

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F          L +A+N  L     I+++     ++ F AR S+  ++YLYRI    
Sbjct: 74  VVNFFTDGRIPVAQLPRAVNGLL--PPDIAVMAAWEAERDFSARHSSTGKAYLYRIERCT 131

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
            P    +  AW I + LD   MR   + LVG HD+++FR+      SP+RT+D   +   
Sbjct: 132 VPNPFTRNYAWQIFRPLDVAAMRTVLRLLVGTHDYSSFRAAGGAPMSPVRTLDEIRLDEE 191

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +   +    FL+  +R+ + ++  VG G+ ++    +   A DR+   P AP  GL
Sbjct: 192 EGGQLSCYMHGNGFLYHMVRNIMSTVVHVGLGRISTDRFTEIFAAHDRRLASPTAPACGL 251

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 252 YLLHVDY 258


>gi|154494877|ref|ZP_02033882.1| hypothetical protein PARMER_03921 [Parabacteroides merdae ATCC
           43184]
 gi|154085427|gb|EDN84472.1| hypothetical protein PARMER_03921 [Parabacteroides merdae ATCC
           43184]
          Length = 297

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 119/246 (48%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + YNG  + GWQ Q NG ++Q SIE+A+  +  + V + GAGRTD+GVHA   VA
Sbjct: 46  RYFIYLGYNGKKFCGWQIQPNGITVQQSIEEALATLLRQPVPIVGAGRTDAGVHARLMVA 105

Query: 63  HFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFD       +  L + LN  L     I++  +  V    HARF AI R+Y Y + TR+ 
Sbjct: 106 HFDWQEPIADLAFLAEKLNRLL--PKDIAVYRIVPVRPDAHARFDAISRTYKYYVTTRK- 162

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                    + IP  LD E M  A   L    DFT+F  +H    +    I        G
Sbjct: 163 -DPFNYELVYKIPGKLDFEAMNKACSVLFDYIDFTSFSKLHTDVKTNNCRIYKAGWEREG 221

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++    + A  FL   +R+ VG+L  VG GK T     + ++A+DR   G  AP   LY 
Sbjct: 222 DVWVFTIQADRFLRNMVRAIVGTLLEVGRGKLTVDGFRQVIEAKDRGRAGTSAPGHALYL 281

Query: 242 DSVEYS 247
             V Y 
Sbjct: 282 VDVTYP 287


>gi|220915529|ref|YP_002490833.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219953383|gb|ACL63767.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 245

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +      V  AGRTD+GVHA  Q
Sbjct: 1   MPVVKLVLEYDGTAYVGWQVQPNGPSIQAEVERALATLHKAPRRVTAAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   R          +NA L     +++   S+    F AR SA  + Y Y I    
Sbjct: 61  VVSFPEERPLPVKAYVMGMNALL--PPDVAVRAASLAPDGFDARRSARGKRYRYVIENLP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
               L + +AW     L+  N+R AA HLVGRHDF  F++  C     +R +   DV   
Sbjct: 119 TRAPLTRLQAWQHFHPLELANVREAAAHLVGRHDFAAFQASDCACEHAVREVRRLDVVGE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  IE+ + A +F+   +R+ VG+L  VG G+     +   L   DR E GP APP+GL
Sbjct: 179 GGGRIEVVIEATAFVKHMVRNIVGTLVEVGRGRRAPGSMLDLLARGDRTEAGPTAPPQGL 238

Query: 240 YFDSVEY 246
           + + V Y
Sbjct: 239 FLEEVFY 245


>gi|239908843|ref|YP_002955585.1| tRNA pseudouridine synthase A [Desulfovibrio magneticus RS-1]
 gi|259550383|sp|C4XPZ9|TRUA_DESMR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239798710|dbj|BAH77699.1| tRNA pseudouridine synthase A [Desulfovibrio magneticus RS-1]
          Length = 274

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 86/253 (33%), Positives = 125/253 (49%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+G+ + GWQ Q    G ++QG +E+A+  + G+ V VHGAGRTDSGVHAL
Sbjct: 1   MARLRLTLAYDGTDFAGWQIQAAGGGRTVQGCLEEALATLCGQPVRVHGAGRTDSGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   KAL A L     +++    +V   FH+RF A  + Y Y + T
Sbjct: 61  AQVAHADVPEHRAGLPWGKALTALL--PKDVAVTEARLVAPDFHSRFDATGKEYRYTLWT 118

Query: 119 RQ-APLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           R    L   +   W +    +LD   M   A   VG HDF  F++      S +R +   
Sbjct: 119 RPGHVLPWRRPYVWDVGRYGTLDVAAMEACAGLFVGEHDFAAFQNAGTDVHSTVRRVWDV 178

Query: 176 D--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                +  +    R     FL   +R+ +G+L  VG GK T+ D+   L A DR+     
Sbjct: 179 SRLAGTGPDETVWRFHGEGFLKQMVRNLMGALVAVGRGKATAEDVATLLAAGDRRRAPGT 238

Query: 234 APPEGLYFDSVEY 246
           AP +GL   +VEY
Sbjct: 239 APAQGLCLHAVEY 251


>gi|332522319|ref|ZP_08398571.1| tRNA pseudouridine synthase A [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332313583|gb|EGJ26568.1| tRNA pseudouridine synthase A [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 249

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 126/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           MIRY  +I Y+GS + G+QRQ    +IQ  IEK +  +  G+ + + GAGRTD+GVHA  
Sbjct: 1   MIRYKAVISYDGSQFSGFQRQTKARTIQEEIEKTLMRLNKGKFIAIQGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   +  + I ++++  V   FHAR+S   ++Y + +   
Sbjct: 61  QVIHFDLAERRDLEKLRFALDT--QTPEDIDVISVEEVSNNFHARYSKHLKTYEFIVDVG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +    + +  A   P  LD   + +A + LVG HDFT F +      + +RT+   D + 
Sbjct: 119 RPKNPMMRKYATHYPYPLDFSLIELAIKDLVGTHDFTGFTAAGTSVENKVRTLYQADCSF 178

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S    +        FL+ Q+R+ VG+L  +G+ +     +   L+ ++R+  GP     
Sbjct: 179 DSHRQCLIFTFTGNGFLYKQVRNMVGTLLKIGNQRMPVEQVRIILEQKNRQLAGPTIAGN 238

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 239 GLYLKEIIYE 248


>gi|123969273|ref|YP_001010131.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. AS9601]
 gi|166228750|sp|A2BTB3|TRUA_PROMS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123199383|gb|ABM71024.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. AS9601]
          Length = 268

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS Y GWQ+QKN ++IQ  ++KA+  +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGSHYSGWQKQKNANTIQEILDKALLKITNHTVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN+ L    TI IL    V   +HA +SA  R Y Y I   +
Sbjct: 61  VIHFDIDCVIPGNSYSDVLNSLL--PSTIRILESVEVKDSWHACYSASYRHYRYVINNSK 118

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD   M  A++ + G HDF  F+       + I  I + DV  
Sbjct: 119 FPNLFINNWSWHRYQKVLDEVLMLNASKKMEGEHDFFAFQKSGSNRQNSITKIKNIDVKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +          + + +    AP +GL
Sbjct: 179 VEDLILVDIKATGFLYGMVRLIVGQLVLVGEKKISPEIFTDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEYS 247
            F +  Y 
Sbjct: 239 CFVNAVYE 246


>gi|307719509|ref|YP_003875041.1| hypothetical protein STHERM_c18330 [Spirochaeta thermophila DSM
           6192]
 gi|306533234|gb|ADN02768.1| hypothetical protein STHERM_c18330 [Spirochaeta thermophila DSM
           6192]
          Length = 248

 Score =  266 bits (680), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 121/247 (48%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               +++ Y+G+ + GWQRQ NG S+QG +E A+  +    V VH AGRTDSGVHA+ Q 
Sbjct: 4   RNIKVVLAYDGTDFVGWQRQPNGRSVQGVVEDALARMHKHPVHVHAAGRTDSGVHAVGQC 63

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +F              ALN++L     +  L    V   FHAR+SA+RR Y Y +    
Sbjct: 64  INFITDIDSLPVEKFALALNSFL--PRDVKALQAEEVPPDFHARYSAVRREYRYYVFPSP 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P    +  +  + +  D   +   A  +VG HDF++F S    + S +R I        
Sbjct: 122 SPYPHLRRYSLWVNRLPDVRLLNAYASCIVGEHDFSSFCSPSDPSPSKVRLIHTASWFPE 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +  R+V  +FL   +R+ VG++  +   K     + K L+A+DR      AP  GL+
Sbjct: 182 GSQLVFRIVGNAFLWRMVRALVGTMLDLEKQKADPEMMRKILEARDRSAASDSAPAWGLF 241

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 242 LHEVQYE 248


>gi|282899978|ref|ZP_06307939.1| tRNA pseudouridine synthase [Cylindrospermopsis raciborskii CS-505]
 gi|281195248|gb|EFA70184.1| tRNA pseudouridine synthase [Cylindrospermopsis raciborskii CS-505]
          Length = 292

 Score =  266 bits (680), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 119/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   ++Q  IE AI  V G  V +HGAGRTD+GVHA  QVA
Sbjct: 13  RVALVIQYLGTNFHGWQRQKAQRTVQEEIETAIASVLGYHVTLHGAGRTDAGVHAAAQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             LN+YL     I I   + V + +HARFSA  R Y Y I T   P
Sbjct: 73  HFNATGHIPAHKWATVLNSYL--PPDILIRASAGVKESWHARFSATYRRYRYTIYTEALP 130

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W      L+ + M+ A   LVG+H    F       S     I   +    G
Sbjct: 131 NLFVSPFSWHYYYAPLEEKLMQAALTPLVGKHHLAAFHRAGSARSHSWVEIQAVECGRQG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A  FL+  +R  VG L  VG  + +  D     Q +DR++    APP+GL  
Sbjct: 191 SLVHIEIQANGFLYGMVRLLVGMLVQVGSKQKSLEDFTNIWQTEDREKVKYAAPPQGLCL 250

Query: 242 DSVEYS 247
             V YS
Sbjct: 251 LRVGYS 256


>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 =  266 bits (680), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 160/252 (63%), Gaps = 6/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IEY+G+ + GWQRQ     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 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +AP+  ++GR W +P+ LD   MR  A HL+G+HDFTTFR+  CQA+SP++T+D   +  
Sbjct: 120 RAPVTHDRGRVWQLPQPLDAGLMRQGAAHLIGKHDFTTFRAALCQAASPVKTLDEIAIET 179

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 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|86606117|ref|YP_474880.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-3-3Ab]
 gi|86554659|gb|ABC99617.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-3-3Ab]
          Length = 287

 Score =  266 bits (680), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 120/247 (48%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + I+Y GSG+ GWQRQ    ++QG +E+AI L  G  V ++GAGRTD+GVHA  QV
Sbjct: 4   RRIALKIQYLGSGFRGWQRQAGHRTVQGVLEEAIALRAGHPVALYGAGRTDTGVHASGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD      P    + LN  L   + + +L  + V   +HARFSA  R Y Y I+ R+ 
Sbjct: 64  AHFDTTSGIPPTEWARVLNDCL--PEDVVVLASAQVPDFWHARFSARWRRYRYLILNREL 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +  +W +   L  E M  A   L+G H    FR            +        G
Sbjct: 122 PDVFWRLFSWQVRWPLQVEPMAEALNSLLGEHSLEAFRRRGSDRPHSRVQVQEVLCQRLG 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGL 239
           +LI I V A  FL+  +R  VGSL++VG G+ +        Q  D  R      APP+GL
Sbjct: 182 DLISIEVQASGFLYRMMRLLVGSLEVVGRGEISPQQFVHLWQHNDWSRMRTRYSAPPQGL 241

Query: 240 YFDSVEY 246
               V Y
Sbjct: 242 CLVDVGY 248


>gi|75906940|ref|YP_321236.1| tRNA pseudouridine synthase A [Anabaena variabilis ATCC 29413]
 gi|75700665|gb|ABA20341.1| tRNA pseudouridine synthase [Anabaena variabilis ATCC 29413]
          Length = 282

 Score =  266 bits (680), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 119/247 (48%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++++Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTDSGVHA  QV
Sbjct: 11  QRVALVVQYLGTNFHGWQRQKQHRTVQEEIETAIAKILGHHVTLHGAGRTDSGVHAAAQV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD      P      LN+YL     I I   + V  ++HARFSA  R Y Y I T   
Sbjct: 71  AHFDATGLIPPHKWASVLNSYL--PKDILIKASAAVGDRWHARFSAAYRRYRYTIYTEDR 128

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P       +W      LD   M+ A + L+G+H    F     + S     +   + +  
Sbjct: 129 PNLFVTPFSWHYYYAPLDESLMQAALKPLMGKHHLAAFHRAGSKRSHSWVEVQAVECHRS 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I + A  FL+  +R  VG L  VG G+ T  +  +  + Q R+E    AP +GL 
Sbjct: 189 GPFIHIEIQADGFLYGMVRLLVGMLVQVGSGQRTLANFTELWKEQRREEVKHAAPSQGLC 248

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 249 LLRVGYP 255


>gi|268318033|ref|YP_003291752.1| tRNA pseudouridine synthase A [Rhodothermus marinus DSM 4252]
 gi|262335567|gb|ACY49364.1| tRNA pseudouridine synthase A [Rhodothermus marinus DSM 4252]
          Length = 252

 Score =  266 bits (680), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 96/249 (38%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y ++IEY+G+ + GWQ Q+NG SIQ ++E+A+ +V  E V V G+GRTD+GVHA  Q
Sbjct: 1   MPTYRLLIEYDGTDFSGWQIQRNGPSIQAALEEALAVVLRERVRVVGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF   R   P  L  +LN  L    +I+I ++S+    FHAR+ A  R Y Y + T  
Sbjct: 61  VAHFRTDRPVDPERLQGSLNGLL--PPSIAIRSVSLAPDDFHARYDARWRRYHYYVAT-- 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
            P ALE+   W +  + D E M  AA  L+G HDFTTF        +   T+       +
Sbjct: 117 VPCALERHLRWYLRPAPDFERMNRAACDLLGTHDFTTFCRTQTATRNRTCTVYLARWVPD 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                    +VA  FLH  +R+ VG+L  +G G+     L + L A+DR+  GP AP  G
Sbjct: 177 PRPGDWHFEIVADRFLHGMVRAIVGTLIEIGRGQRDIAALPELLAARDRRLAGPAAPAHG 236

Query: 239 LYFDSVEYS 247
           L  ++V Y 
Sbjct: 237 LVLEAVGYE 245


>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 =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 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|42527777|ref|NP_972875.1| tRNA pseudouridine synthase A [Treponema denticola ATCC 35405]
 gi|51316703|sp|Q73KE3|TRUA_TREDE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|41818605|gb|AAS12794.1| tRNA pseudouridine synthase A [Treponema denticola ATCC 35405]
 gi|325474992|gb|EGC78178.1| tRNA pseudouridine synthase A [Treponema denticola F0402]
          Length = 268

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 124/251 (49%), Gaps = 8/251 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
              + I Y+G+ + GWQ+Q         ++QG +EKA+  +    +  +G+GRTDSGVHA
Sbjct: 9   NILLTISYDGTNFCGWQKQTKEGAETFRTVQGELEKALTKIHKHPIETNGSGRTDSGVHA 68

Query: 58  LRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            RQ  +F    +         ALN+ L     I +++ + V    HARF+A+ R+Y Y+I
Sbjct: 69  ARQAVNFFCDIKSMRASNFLPALNSIL--PKDIRVMDAAEVSPLLHARFNALSRTYRYKI 126

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +   A E+   W I +  D   +   A  L G  D T F +   Q+ S  R I    
Sbjct: 127 KCGKTIFAHEQPYTWHIRRYPDIAALNEMASCLSGELDCTAFSAAGDQSISKSRYIKKAV 186

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                + +   + A +FL   +RS VG+L  + +   +  D +  L+++ R++ GP APP
Sbjct: 187 FFIENDYLIFEICANAFLWKMVRSIVGTLLHLDEIGASKKDFKDILESKMREKAGPTAPP 246

Query: 237 EGLYFDSVEYS 247
           +GL+  S+EY 
Sbjct: 247 QGLFLWSIEYP 257


>gi|121605935|ref|YP_983264.1| tRNA pseudouridine synthase A [Polaromonas naphthalenivorans CJ2]
 gi|166228746|sp|A1VRR5|TRUA_POLNA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120594904|gb|ABM38343.1| tRNA pseudouridine synthase A [Polaromonas naphthalenivorans CJ2]
          Length = 264

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 130/250 (52%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+GS Y GWQ Q +G ++Q  +E A+     + + V  AGRTD+GVHAL QV
Sbjct: 1   MRIALGISYSGSAYEGWQSQLSGKTVQDKLELALSRFAVQPIRVMCAGRTDAGVHALMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L     I++     V  +FH+R SAI R Y Y ++    
Sbjct: 61  VHFDTPLQRETSSWVRGTNAFL--PSDIAVQWAQPVPDEFHSRASAIARRYAYVVLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   + + LD + MR AA HL+G HDF++FR+  CQA SP++T+   +++   
Sbjct: 119 RPSVEAGRVGWVYRPLDGDAMRQAALHLMGEHDFSSFRAAQCQAKSPVKTMSRIEISQRA 178

Query: 182 N----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                       A +FLH  IR+ +G L  +G G      L + + A+ R    P   P+
Sbjct: 179 GPGSRYWRFEFEANAFLHHMIRNIMGCLLAIGQGNHPPEWLAEVVAARRRDAAAPTFSPD 238

Query: 238 GLYFDSVEYS 247
           GLYF    Y 
Sbjct: 239 GLYFLGPVYE 248


>gi|254673733|emb|CBA09384.1| tRNA pseudouridine synthase A [Neisseria meningitidis alpha275]
          Length = 266

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 128/247 (51%), Gaps = 2/247 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  Q
Sbjct: 7   QRWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD           +           + +L+   V  +FHARF A  R Y Y + +  
Sbjct: 67  VVHFDTTAVRPQQAWIRG-RKMPTCPKALPVLHARQVALEFHARFDAYGRHYRYLLESSP 125

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L K RA      LD   MR AA +L+G  DF++FR+  CQA SPI+TI   ++   
Sbjct: 126 VRSPLLKNRAGWTHLKLDIGPMRQAATYLIGEQDFSSFRAAECQAKSPIKTIYRANLTQS 185

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY
Sbjct: 186 AGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLY 245

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 246 LTGVDYP 252


>gi|172038954|ref|YP_001805455.1| tRNA pseudouridine synthase A [Cyanothece sp. ATCC 51142]
 gi|171700408|gb|ACB53389.1| tRNA pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 286

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 114/246 (46%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G  + GWQRQ    ++Q  IE +I  V G  V +HGAGRTD+GVHA  QVA
Sbjct: 12  RVALVIQYQGGRFHGWQRQPTQRTVQEDIETSIAQVLGYHVPIHGAGRTDAGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD V    P      LN  L   D I +   + V   +HARFSA+ R Y Y   T + P
Sbjct: 72  HFDDVSPIPPQRWADILNQRL--PDDILVRGSAEVPLTWHARFSALWRRYRYTFYTDKCP 129

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W      L+ E M  A   L+GRH    FR    +       +        G
Sbjct: 130 NLFVSPFSWHYYYEPLEVELMTKALNPLLGRHHLAAFRRAGSKRHHSWVEVQETQCYRQG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A  FL+  +R  VG L  VG GK +  +  +  Q Q R++    AP +GL  
Sbjct: 190 PFIHLEIQANGFLYGMVRLLVGLLVEVGSGKRSLANFTEIWQHQQREQVKYSAPAKGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|297567108|ref|YP_003686080.1| tRNA pseudouridine synthase A [Meiothermus silvanus DSM 9946]
 gi|296851557|gb|ADH64572.1| tRNA pseudouridine synthase A [Meiothermus silvanus DSM 9946]
          Length = 259

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 93/257 (36%), Positives = 129/257 (50%), Gaps = 15/257 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + +E++G+ + G Q Q K   ++Q ++E+A+  + G I  V  AGRTD+GVHAL 
Sbjct: 1   MRRIKLTVEFDGTHFAGLQTQAKGERTVQNTLEQALAQIPGAIPKVVAAGRTDAGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H+D +    P  +  ALN  L     +  L    V  +FHAR S   R+Y YRI+ R
Sbjct: 61  MPLHYDTLDPIPPEKIPLALNGLL--PPDLRALAAEEVAPEFHARKSCHWRAYRYRILNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           + P AL +  AW IP+ L+   MR A +HLVG HDF  F     +    +R I    +  
Sbjct: 119 KTPSALLRHYAWWIPQQLNLVAMRHALEHLVGEHDFKAF--AVKEKRPTVRRIYRAHLTV 176

Query: 179 ---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                         I +  V   FL  Q+RS VG+L  VG GK  S  L + L+   R +
Sbjct: 177 LTPDIAQDAKNEREIHLEFVGSGFLRGQVRSMVGTLVEVGLGKRDSQSLGELLRTGTRSQ 236

Query: 230 CGPLAPPEGLYFDSVEY 246
            GP APP+GLYF    Y
Sbjct: 237 AGPTAPPQGLYFVGAGY 253


>gi|294792824|ref|ZP_06757971.1| tRNA pseudouridine synthase A [Veillonella sp. 6_1_27]
 gi|294456723|gb|EFG25086.1| tRNA pseudouridine synthase A [Veillonella sp. 6_1_27]
          Length = 261

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 125/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    +I+ Y+G+   G+Q+Q N    ++QG +E  +  +  E + ++GA RTD+GVHA 
Sbjct: 1   MRNIQIIVAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F          + +A+ A+  I   I +L    +   +  R++   + Y+Y I  
Sbjct: 61  FQVCTFQTSGTIPVENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYIYTIHN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +     L +   W + K L+   M+ A   LVG HDFTT +  +  ++ P++TI    V 
Sbjct: 119 QLIADPLTQRYHWHVKKPLNIARMQAAGNELVGTHDFTTLKGTNSTSADPVKTIMGIRVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + G+ + I V+   FL+  +R+  G L  +G G+    D++  L A+DR+  G  AP +G
Sbjct: 179 ARGSQVTISVIGDGFLYHMVRNIAGLLVDIGLGRRKVEDIKGYLAAKDRRAIGKTAPAQG 238

Query: 239 LYFDSVEY 246
           L  + + +
Sbjct: 239 LCLEEIFF 246


>gi|198276843|ref|ZP_03209374.1| hypothetical protein BACPLE_03048 [Bacteroides plebeius DSM 17135]
 gi|198270368|gb|EDY94638.1| hypothetical protein BACPLE_03048 [Bacteroides plebeius DSM 17135]
          Length = 252

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 82/249 (32%), Positives = 120/249 (48%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY + + Y+G+ Y GWQ Q NGSS+Q ++ KA+      E + V GAGRTD+GVHA  
Sbjct: 1   MFRYFIYLAYDGTNYHGWQIQPNGSSVQETLMKALHTFLRDEAIEVVGAGRTDAGVHARL 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD+        +   LN  L     IS+  +  V++  HARF A  R+Y Y + T+
Sbjct: 61  MVAHFDVEWMLDEDTVTDKLNRLL--PPDISVYRVRRVNQDAHARFDATYRTYKYYVTTQ 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   W + + LD   M  AAQ L    DFT+F  +H    +    I H   + 
Sbjct: 119 KNP--FNRAYCWRLFQPLDFTKMNEAAQILFDYTDFTSFSKLHTDVKTNNCKIMHAHWDQ 176

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                    + A  FL   +R+ VG+L  VG GK +     K ++ ++R   G   P   
Sbjct: 177 VSETEWVFTIQADRFLRNMVRAIVGTLVEVGRGKLSVEGFRKVIEEKNRCSAGTSVPGHA 236

Query: 239 LYFDSVEYS 247
           L+   + Y 
Sbjct: 237 LFLVDIGYP 245


>gi|317968841|ref|ZP_07970231.1| tRNA pseudouridine synthase A [Synechococcus sp. CB0205]
          Length = 289

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 119/248 (47%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y+GS Y GWQRQ    S+Q ++E+A+  +       V  AGRTDSGVHA  Q
Sbjct: 11  RRIALCLQYDGSAYCGWQRQPRDPSVQEALERALVQLDPDGPATVVAAGRTDSGVHAAGQ 70

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P     ALN  L    +I + + + V   +HA FSA  R Y Y I   +
Sbjct: 71  VVHFDCAGPIPPHRWPAALNGRL--PASIRVRSAASVPADWHACFSATYRRYRYTIYNAR 128

Query: 121 APLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W      LD + MR A + ++G HDF  F       S    T+    V  
Sbjct: 129 IPNLFLAPWSWHRYQFRLDEDRMREALEGMLGEHDFAAFERAGSARSHSRTTLQEVSVQR 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+E+ + A  FL+  +R  +G L  VG+G+ +     +  + Q R+E    APP+GL
Sbjct: 189 RGDLLEVELQASGFLYGMVRLVMGQLVAVGEGRLSLEAFSRRWRNQAREEVKEAAPPQGL 248

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 249 CLLRVGYP 256


>gi|300812341|ref|ZP_07092776.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496646|gb|EFK31733.1| tRNA pseudouridine synthase A [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 262

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 135/252 (53%), Gaps = 7/252 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHAL 58
           M  RY + + Y+G  + G+Q Q    +IQG++E+ +  +T G+ V V G+GRTD+GVH++
Sbjct: 1   MTSRYKLTLSYDGHDFHGFQSQPGQRTIQGTVEEILKRMTKGQEVRVFGSGRTDAGVHSV 60

Query: 59  RQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QV HFD   RE     + KALN+ L     +   +  IVDK FH+RFS   + Y YR+ 
Sbjct: 61  GQVIHFDYPGREIPAANMIKALNSQL--PMDMVFTDCEIVDKDFHSRFSVKGKWYRYRVS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                   ++      P  +D E M+ AA+ L+GRHDFT+F +   Q    +R + + +V
Sbjct: 119 LDGFVNPFKRFYTGHYPYPVDVEKMQEAAKDLLGRHDFTSFAASGGQIEDKVRDMYYVNV 178

Query: 178 --NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +   N + +  +A  FL+  +R  V +L  +G+G+    DL++ + A++R E    A 
Sbjct: 179 ALDEENNEVIMDFIATGFLYNMVRILVATLLEIGNGRRPVHDLKRVIAAKNRLEVQQTAQ 238

Query: 236 PEGLYFDSVEYS 247
             GLY   V Y 
Sbjct: 239 SCGLYLYHVFYE 250


>gi|121595540|ref|YP_987436.1| tRNA pseudouridine synthase A [Acidovorax sp. JS42]
 gi|166228674|sp|A1WAT5|TRUA_ACISJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120607620|gb|ABM43360.1| tRNA pseudouridine synthase A [Acidovorax sp. JS42]
          Length = 274

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/259 (30%), Positives = 123/259 (47%), Gaps = 16/259 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q + +++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVSYNGQAYNGWQSQPSANTVQDRLEAALGRFATQEVHTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FH+R  A+ R Y Y ++    
Sbjct: 61  VHFDTELQRAPFSWVRGTNTFL--PADIAVQWAQPVPDAFHSRACAVARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             +++ GR   +  +LD + M  A QHL+G HDFT+FR+  CQA SP++T+   D+    
Sbjct: 119 RPSVDAGRVGWVFHALDEQAMHKAVQHLLGEHDFTSFRASACQAKSPVKTLHRIDITRRA 178

Query: 182 N--------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                                   +FLH  IR+ +G +  +G G +    +   L+A+ R
Sbjct: 179 PPAGESTGTHGCVPCYWRFEFEGNAFLHHMIRNIMGCIVAIGQGLYPPEWMRTVLEARSR 238

Query: 228 KECGPLAPPEGLYFDSVEY 246
               P   P+GLYF    Y
Sbjct: 239 DAAAPTFSPDGLYFQGPVY 257


>gi|60680398|ref|YP_210542.1| tRNA pseudouridine synthase A [Bacteroides fragilis NCTC 9343]
 gi|265765551|ref|ZP_06093826.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_16]
 gi|81316532|sp|Q5LGZ6|TRUA_BACFN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|60491832|emb|CAH06590.1| putative tRNA pseudouridine synthase A [Bacteroides fragilis NCTC
           9343]
 gi|263254935|gb|EEZ26369.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_16]
          Length = 252

 Score =  265 bits (679), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 117/248 (47%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ Y GWQ Q NG SIQ  + KA+     +   V GAGRTD+GVHA   V
Sbjct: 4   QRYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRKDTEVIGAGRTDAGVHASLMV 63

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          + + LN  L     IS+  +  V    HARF A  R+Y Y I T +
Sbjct: 64  AHFDYEGEPLDVDKVAEKLNRLL--PQDISVYKVCRVKPDAHARFDATARTYKYYITTVK 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +    
Sbjct: 122 --FPFNRQYRYRIHNPLDFQKMNEAALTLFHYSDFTSFSKLHTDVKTNICKIMHAEWTQE 179

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L  VG GK +  D  K ++ Q+R + G  AP   L
Sbjct: 180 DEYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDDFRKIIEQQNRCKAGTSAPGNAL 239

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 240 FLVNVEYP 247


>gi|239618279|ref|YP_002941601.1| tRNA pseudouridine synthase A [Kosmotoga olearia TBF 19.5.1]
 gi|259550401|sp|C5CGS8|TRUA_KOSOT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239507110|gb|ACR80597.1| tRNA pseudouridine synthase A [Kosmotoga olearia TBF 19.5.1]
          Length = 250

 Score =  265 bits (678), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 89/249 (35%), Positives = 127/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  ++ Y+GS +FG+Q Q N  ++QG  E+A+  +    +   GAGRTD+GVHA  Q
Sbjct: 1   MKRFAAVVVYDGSNFFGYQIQPNKRTVQGVFEEALERIHKAKIPTDGAGRTDTGVHAYGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V  F        P  +  ALNA L   D I +  +  V   F  RF+A +R Y Y I+  
Sbjct: 61  VIAFTSNLDRLTPKHMKDALNANL--PDDIYVRRIHEVPSNFSPRFAAKKRIYHYYILNT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   W  P  +D   MR A+++L+G HDFT+FR+ H    S IRTI    +  
Sbjct: 119 KEPDLFRRKYFWWFPYEVDLNRMRQASRYLIGEHDFTSFRTGHDD-RSTIRTITGIRILR 177

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N+I IRV   SFL   +R+ VG L  VG G       ++ L+A+DR +    AP  G
Sbjct: 178 LQKNIILIRVEGISFLRRMVRNIVGLLMRVGTGGIEPKKTKEILEARDRSKLPSSAPAHG 237

Query: 239 LYFDSVEYS 247
           L    V + 
Sbjct: 238 LVLHKVIFD 246


>gi|320107224|ref|YP_004182814.1| Pseudouridine synthase I, TruA, alpha/beta domain-containing
           protein [Terriglobus saanensis SP1PR4]
 gi|319925745|gb|ADV82820.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Terriglobus saanensis SP1PR4]
          Length = 287

 Score =  265 bits (678), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 89/261 (34%), Positives = 128/261 (49%), Gaps = 20/261 (7%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + + Y+G+ + GWQ Q    +IQGS+  AI  VT E V+  G+GRTD+GVHAL QV  
Sbjct: 17  WRLKLAYDGTDFAGWQVQPGLPTIQGSLASAIRSVTSEEVLPQGSGRTDAGVHALGQVVS 76

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ--- 120
             L     P  L +ALN  L    +I +L   IV  +FHAR   + ++Y Y +   +   
Sbjct: 77  LKLAVPIPPDNLKRALNRIL--PTSIRVLEAGIVAPEFHARRGVLSKTYRYTLFLCRPTK 134

Query: 121 -----APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS-------- 167
                          W  P  LD   M  AA+  VG HDFT+F +   +  +        
Sbjct: 135 DVEEIVCSPERARWVWQYPAPLDVAAMMQAAERFVGTHDFTSFAANDPERKTRLEAESNA 194

Query: 168 --PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
              IRT+        G+ +  +V    FLH  +R+ VG+   VG G+  +T++EK L A+
Sbjct: 195 PDNIRTLYSSAWTLCGDELSYQVRGSGFLHHMVRNLVGTCVDVGAGRILATEMEKILVAK 254

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
           +R   GP APP+GL    VEY
Sbjct: 255 NRGAAGPTAPPQGLSLLEVEY 275


>gi|282898331|ref|ZP_06306322.1| tRNA pseudouridine synthase [Raphidiopsis brookii D9]
 gi|281196862|gb|EFA71767.1| tRNA pseudouridine synthase [Raphidiopsis brookii D9]
          Length = 292

 Score =  265 bits (678), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 121/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   ++Q  IE AI  V G  V +HGAGRTD+GVHA  QVA
Sbjct: 13  RVALVIQYLGTNFHGWQRQKAQRTVQEEIEIAIASVLGYHVTLHGAGRTDAGVHAAAQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             LN+YL     I I   + V + +HARFSA+ R Y Y I T+  P
Sbjct: 73  HFNATGHIPAHKWATVLNSYL--PPDILIRASAGVKESWHARFSAVYRRYRYTIYTQALP 130

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W      L+ E M+ A   LVG+H    F       S     I   +    G
Sbjct: 131 NLFVSPFSWHYYYAPLEEELMQAALTPLVGKHHLAAFHRAGSARSHSWVEIQAVECCRQG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+ I + A  FL+  +R  VG L  VG  + +  D     Q +DR++    APP+GL  
Sbjct: 191 SLVHIEIQANGFLYGMVRLLVGMLVQVGSKQKSLEDFTNIWQTEDREKVKYAAPPQGLCL 250

Query: 242 DSVEYS 247
             V Y+
Sbjct: 251 LRVGYN 256


>gi|227879273|ref|ZP_03997143.1| tRNA pseudouridine synthase A [Lactobacillus crispatus JV-V01]
 gi|227861167|gb|EEJ68816.1| tRNA pseudouridine synthase A [Lactobacillus crispatus JV-V01]
          Length = 256

 Score =  265 bits (678), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 129/246 (52%), Gaps = 6/246 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQVAHF 64
           M + Y+G  + G+Q Q +  ++QG+IE A+  +T G+ V+V G+GRTD+GVHA+ QV HF
Sbjct: 1   MTMAYDGHLFHGFQLQPDQRTVQGTIEDALKKMTKGKRVIVQGSGRTDAGVHAVGQVIHF 60

Query: 65  DLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           D   +      +  A+N+ +     I   N  IV+  FHAR+S   + Y YR+       
Sbjct: 61  DYPGKTIPANRMILAMNSMM--PTDIIFNNCQIVNDDFHARYSIKGKWYRYRVSLDHFVN 118

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF--G 181
             ++      P  LD E M+IAAQ L+G+HDFT+F +   +    +RTI +  +      
Sbjct: 119 PFKRFYTGHFPYPLDIEKMQIAAQDLLGKHDFTSFAASGGRIEDKVRTIYYVKITEDKKD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +    +   FL+  +R  V +L  +G+ +    DL++ + A+DR+E    A   GLY 
Sbjct: 179 NEVIFDFIGSGFLYNMVRIMVAALLEIGNDRRPVHDLQRVIAAKDRQEVRQTAHASGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 YHVFYD 244


>gi|289449823|ref|YP_003475752.1| tRNA pseudouridine synthase A [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
 gi|289184370|gb|ADC90795.1| tRNA pseudouridine synthase A [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
          Length = 274

 Score =  265 bits (677), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 80/252 (31%), Positives = 124/252 (49%), Gaps = 7/252 (2%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   ++ E++G+ Y GWQ Q N  +IQ +++KA+  +  + V+V+G  RTD+GVHA  
Sbjct: 1   MKRNIAILTEWDGTAYGGWQIQANAPTIQENLQKALEKLCHKSVLVNGCSRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            V++F          +  ALNA L   + I++   + +   F+ARF A  + Y Y I   
Sbjct: 61  HVSNFHFDSSIPVANIPLALNAML--PEDIAVQAATEMPLDFNARFDACGKQYSYYICNT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   AL    +    + L    MR AA ++ G HDF  F +   Q  S +RT+   D+ S
Sbjct: 119 KLRHALYSRYSCCEARPLSAAAMREAAGYIEGTHDFACFMASGGQVKSTVRTVYSVDLVS 178

Query: 180 F----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +    G +  I V    FL+  +R   G+L  VG  K    D+ + L++  R E G   P
Sbjct: 179 YPICGGAIWRIIVRGNGFLYNMVRIIAGTLLYVGLNKLNPQDVREVLRSGHRSEAGKTLP 238

Query: 236 PEGLYFDSVEYS 247
             GL+ D V Y 
Sbjct: 239 ACGLFLDRVFYE 250


>gi|301161932|emb|CBW21476.1| putative tRNA pseudouridine synthase A [Bacteroides fragilis 638R]
          Length = 252

 Score =  265 bits (677), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 117/248 (47%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ Y GWQ Q NG SIQ  + KA+     +   V GAGRTD+GVHA   V
Sbjct: 4   QRYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRKDTEVIGAGRTDAGVHASLMV 63

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          + + LN  L     IS+  +  V    HARF A  R+Y Y I T +
Sbjct: 64  AHFDYEGEPLDVDKVAEKLNRLL--PQDISVYKVCRVKPDAHARFDATARTYKYYITTVK 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +    
Sbjct: 122 --FPFNRQYRYRIHNPLDFQKMNEAALTLFHYSDFTSFSKLHTDVKTNICKIMHAEWTQK 179

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L  VG GK +  D  K ++ Q+R + G  AP   L
Sbjct: 180 DEYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDDFRKIIEQQNRCKAGTSAPGNAL 239

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 240 FLVNVEYP 247


>gi|309789641|ref|ZP_07684222.1| tRNA pseudouridine synthase A [Oscillochloris trichoides DG6]
 gi|308228377|gb|EFO82024.1| tRNA pseudouridine synthase A [Oscillochloris trichoides DG6]
          Length = 262

 Score =  265 bits (677), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 127/251 (50%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + + Y+G+ + G Q Q  G S+Q ++E+A   +T E   V+ AGRTD+GVHA+ Q
Sbjct: 1   MRNIALRLAYDGTDFIGSQYQNQGRSVQEALEQAWEGLTQERRRVNLAGRTDAGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+           + + +NA L     ++I  ++ VD  FHAR SA RRSY Y I    
Sbjct: 61  VANIRTETRHSRRTILRGMNAKL--PPDVAIQAVAEVDPDFHARHSANRRSYRYLIDNNA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           A L   +   W + + LD   M  A   L G HDF  F ++  +  S +RT     ++S 
Sbjct: 119 AWLPNLRNYVWFVEQPLDQAAMAEALVRLEGTHDFAAFTALVPEQRSTVRTCYTARLSSV 178

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                +LI I + A +FL   +R  VG++ LVG GK T    +  L+ +DRK  GP A  
Sbjct: 179 TMFDRHLIAIDLAANAFLQHMVRVIVGTVVLVGRGKITPDGFQAILEGRDRKAAGPTAVA 238

Query: 237 EGLYFDSVEYS 247
            GL   SV Y 
Sbjct: 239 HGLTLVSVGYP 249


>gi|116334238|ref|YP_795765.1| pseudouridylate synthase [Lactobacillus brevis ATCC 367]
 gi|122269080|sp|Q03PY8|TRUA_LACBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116099585|gb|ABJ64734.1| Pseudouridylate synthase [Lactobacillus brevis ATCC 367]
          Length = 265

 Score =  265 bits (677), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 70/251 (27%), Positives = 121/251 (48%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHA 57
           M RY + + Y+G+ + G+QRQ N  +++ ++   +  +  +    +V++G+GRTD+GVHA
Sbjct: 1   MQRYKVTLMYDGTNFAGFQRQPNKRTVESTLTDVVNKMAKQPDPAIVIYGSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV HFD         + K LN+ L     + +L +  V   FHAR+    + Y YR+ 
Sbjct: 61  LAQVVHFDFPFLIPADNMRKGLNSML--PMDMEVLKVEEVAPTFHARYDVSGKQYQYRMD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF-- 175
             +     ++         +D   + +A   LVG HD+T+F +   Q  + +RTI     
Sbjct: 119 MGEFRNPFKRNYTGHWKFPVDLAKINVALADLVGEHDYTSFVASGAQTRTFVRTIYEATC 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            ++   + +        F++ Q+R  VG L  +G G     D+ +  + +DRK+     P
Sbjct: 179 HIDEANHELVFEFYGNGFMYNQVRIMVGVLVEIGSGTRPVHDVLRLYEVKDRKQARRTVP 238

Query: 236 PEGLYFDSVEY 246
             GLY   V Y
Sbjct: 239 AAGLYLKHVYY 249


>gi|15618490|ref|NP_224776.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae CWL029]
 gi|33241935|ref|NP_876876.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae TW-183]
 gi|4376873|gb|AAD18719.1| Pseudouridylate Synthase I [Chlamydophila pneumoniae CWL029]
 gi|33236445|gb|AAP98533.1| pseudouridylate synthase I [Chlamydophila pneumoniae TW-183]
          Length = 267

 Score =  265 bits (677), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 125/250 (50%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  ++I Y G+ Y GWQ+Q N  SIQ  IE ++  +T     +  +GRTD+GVHA  Q
Sbjct: 1   MTKVALLIAYQGTAYSGWQQQPNDLSIQEVIESSLKKITKTRTPLIASGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF      +     +  KALNA L     I I ++++ D  FHAR+ AI + Y Y + 
Sbjct: 61  VAHFRAPDHPLFANANLTKKALNAIL--PKDIVIRDVALFDDNFHARYLAIAKEYRYSLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++   +        E M+  A  L+G HDF +F +     +S +RTI   D+
Sbjct: 119 RLAKPLPWQRHFCYTPRHPFSTELMQEGANLLIGTHDFASFANHGRDYNSTVRTIYTLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ + I      FL+  +R+ VG+L  VG G +    L   L+ ++R+E    AP  
Sbjct: 179 VDKGDSLSIICRGNGFLYKMVRNLVGALLDVGKGAYPPEHLLDILEQKNRREGPSAAPAY 238

Query: 238 GLYFDSVEYS 247
           GL    V YS
Sbjct: 239 GLSLHHVCYS 248


>gi|301309451|ref|ZP_07215393.1| tRNA pseudouridine synthase A [Bacteroides sp. 20_3]
 gi|300832540|gb|EFK63168.1| tRNA pseudouridine synthase A [Bacteroides sp. 20_3]
          Length = 252

 Score =  265 bits (677), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 122/248 (49%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++  + V + GAGRTD+GVHA   
Sbjct: 1   MRRYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRKPVPIVGAGRTDAGVHARLM 60

Query: 61  VAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +AHFD       +  L + LN  L     I++  +  V  + HARF A  R+Y Y I TR
Sbjct: 61  IAHFDWEGPIEDLAFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYITTR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +          + +P  LD E M  A + L    DFT+F  +H    +    I H     
Sbjct: 119 K--DPFNYELVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHAGWTQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P   L
Sbjct: 177 EGDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGHAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVTYP 244


>gi|304384407|ref|ZP_07366813.1| tRNA pseudouridine synthase A [Prevotella marshii DSM 16973]
 gi|304334505|gb|EFM00792.1| tRNA pseudouridine synthase A [Prevotella marshii DSM 16973]
          Length = 260

 Score =  265 bits (677), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 123/248 (49%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+GY GWQ Q NG S+Q  +++A+ +V    + V GAGRTD+GVHA R 
Sbjct: 1   MHRYFIHFSYDGTGYHGWQIQPNGISVQEVLQQALSVVLRREMTVTGAGRTDTGVHARRM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD+        L   LN  L     +++ N+  V    HARFSA RR+Y Y I   +
Sbjct: 61  TAHFDIDDATDCTQLTYKLNRLL--PRDVAVENIEEVAPDLHARFSARRRTYHYYIHFAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF-DVNS 179
            P   ++  +  +   LD   M  AA+ L+  +DF  F   H    +    +     +  
Sbjct: 119 NP--FKERYSCELHFPLDFNRMNEAARLLLQTNDFAAFCKSHTDVKTTFCNVTEAVWIRQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +    R+ A  FL   +R+ VG+L  VG G+ ++ D    ++ + R   G   P +GL
Sbjct: 177 TADEWYFRISADRFLRNMVRAVVGTLIDVGRGRLSTDDFRAIIETKRRTAAGESMPAKGL 236

Query: 240 YFDSVEYS 247
           + + +EY 
Sbjct: 237 FLEEIEYE 244


>gi|315659196|ref|ZP_07912060.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis M23590]
 gi|315495621|gb|EFU83952.1| tRNA pseudouridine synthase A [Staphylococcus lugdunensis M23590]
          Length = 264

 Score =  264 bits (676), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 115/244 (47%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q  G ++Q   EK +  +    V +H + RTD GVHAL Q 
Sbjct: 1   MRILVNICYQGSNFLGFQIQNQGRTVQQQFEKILKRMHRHDVRIHPSSRTDRGVHALEQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I +  +  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELKIADGQWQYAMNSAL--PDDIYVKEVKQVDSDFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    +P+ L+ E M  AAQ  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 KNPFESGLKTYVPQQLNIERMNEAAQKFIGTHDFTGFCSQKTEVESKVRTLYQSEIEMTT 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  +  L  VG G  +  ++   L+ ++R      AP EGLY 
Sbjct: 179 YGFDYIVTGSGFLYNMVRVLMAFLIGVGKGNRSPEEVTALLEQKNRDNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|189461835|ref|ZP_03010620.1| hypothetical protein BACCOP_02501 [Bacteroides coprocola DSM 17136]
 gi|189431429|gb|EDV00414.1| hypothetical protein BACCOP_02501 [Bacteroides coprocola DSM 17136]
          Length = 252

 Score =  264 bits (676), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 122/249 (48%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALR 59
           M RY + + Y+G+ Y GWQ Q NG+S+Q ++ +A+     +  + V GAGRTD+GVHA  
Sbjct: 1   MFRYFIYLAYDGANYHGWQIQPNGNSVQETLTRALITFLRDDAIEVTGAGRTDAGVHARL 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD+ R      +   LN  L     IS+  +  V +  H RF A  R+Y Y I TR
Sbjct: 61  MVAHFDIERMLDCDSVTDKLNRLL--PPDISVYQVRRVRQDAHTRFDATYRTYKYYITTR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  AW + +SLD + M  AA+ L    DFT+F  +H    +    I H     
Sbjct: 119 K--DPFNRNYAWRVFQSLDFDKMNEAAKVLFEYTDFTSFSKLHTDVKTNNCRIMHARWEQ 176

Query: 180 FG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            G +     + A  FL   +R+ VG+L  VG GK T     K ++ ++R   G   P   
Sbjct: 177 IGEDEWVFTIQADRFLRNMVRAVVGTLVEVGRGKLTVEGFRKVIEEKNRCSAGTSVPGHA 236

Query: 239 LYFDSVEYS 247
           L+   + Y 
Sbjct: 237 LFLVDIGYP 245


>gi|197303593|ref|ZP_03168631.1| hypothetical protein RUMLAC_02321 [Ruminococcus lactaris ATCC
           29176]
 gi|197297327|gb|EDY31889.1| hypothetical protein RUMLAC_02321 [Ruminococcus lactaris ATCC
           29176]
          Length = 264

 Score =  264 bits (676), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y ++I Y+G+ Y GWQRQ N   +IQG +E  I    G  V V+G+GRTD+GVHA  
Sbjct: 13  MRTYRLVIAYDGTAYQGWQRQANTEMTIQGILESCISKAAGYAVEVNGSGRTDAGVHARG 72

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +       + +N  L     I I    +    FHAR SA+ + Y+Y+I T 
Sbjct: 73  QTASVVLHGKAEDGFFTEKVNKLL--PPDIRIREAGLEKNGFHARKSAVGKRYVYQIDTD 130

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   ++   +  PK LD   M+ AA+ L G H+F  +     + +S  RTI    V  
Sbjct: 131 EKPDVFDRRYTYHFPKKLDIAAMQQAAELLTGTHEFAAYTDKKDE-TSTKRTIYAIMVGG 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I I+     FL+  +R   G+L  VG G      +  AL+A+DR + G LAP  GL
Sbjct: 190 QGGRINIQYEGTGFLYHMVRILTGTLLEVGMGTRRIESVTIALEAKDRTKVGFLAPARGL 249

Query: 240 YFDSVEY 246
           + D V Y
Sbjct: 250 FLDEVYY 256


>gi|160942942|ref|ZP_02090181.1| hypothetical protein FAEPRAM212_00419 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445843|gb|EDP22846.1| hypothetical protein FAEPRAM212_00419 [Faecalibacterium prausnitzii
           M21/2]
          Length = 254

 Score =  264 bits (676), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 122/249 (48%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + + + + Y+G+ Y G+Q Q NG S+  + + A+  V G    + G  RTD+GVHAL   
Sbjct: 1   MNFLLTLAYDGTNYCGFQVQPNGRSVAATFQDALEAVLGSRPDIKGCSRTDAGVHALGFR 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F       P  L  ALN +L     I +L    V + FHAR++A  ++YLYRI     
Sbjct: 61  LNFHADTRIPPQKLPLALNQHL--PPDIRVLAAQTVPEDFHARYAAHTKTYLYRIHNHPI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA---SSPIRTIDHFDVN 178
               +      +P+ LD   M+ AAQ  VG HDF    +    A      +RTI    V 
Sbjct: 119 DSPFDAAYYTRVPRRLDEAAMQAAAQQFVGTHDFLALCAAGSSAAAHGDTVRTITDCHVT 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ ++I V A  +L+  +R   G+L  VG G+  + D+   L ++DR   GP  P +G
Sbjct: 179 RRGDEVDIEVTADGYLYNMVRILAGTLCEVGAGRLRAADIPAILASRDRSRAGPTLPAKG 238

Query: 239 LYFDSVEYS 247
           L+   V+Y 
Sbjct: 239 LFLKCVDYP 247


>gi|166030569|ref|ZP_02233398.1| hypothetical protein DORFOR_00232 [Dorea formicigenerans ATCC
           27755]
 gi|166029571|gb|EDR48328.1| hypothetical protein DORFOR_00232 [Dorea formicigenerans ATCC
           27755]
          Length = 244

 Score =  264 bits (676), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ    ++IQ  +E +I  + G  V V G+GRTD+GVHA  
Sbjct: 1   MRTYKLTISYDGTRYQGWQRQATTDNTIQHILEWSIGKLVGYRVRVDGSGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + +    L  ++N YL   + I I+ + ++   FHAR SA  + Y Y I  R
Sbjct: 61  QVASVQLSKLYDVKELKDSINRYL--PEDIRIMKVELMKNGFHARKSAKGKKYEYYIDCR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P  LD E MR AA +++G  +FT+F +   +   P+R + +  + S
Sbjct: 119 EKPDVFSRRYCYHYPHKLDIEAMREAADYMIGPKNFTSF-TDDSENKDPVRRVTNIKIVS 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I      F++  +R   G+L  VG G+  ++ +   + A+DR   G LAP  GL
Sbjct: 178 NGEKLRITYYGTGFMYHMVRIMTGTLLEVGTGEREASMIPVVIAAEDRSLAGFLAPARGL 237

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 238 FLRKVYY 244


>gi|294673952|ref|YP_003574568.1| tRNA pseudouridine synthase A [Prevotella ruminicola 23]
 gi|294472804|gb|ADE82193.1| tRNA pseudouridine synthase A [Prevotella ruminicola 23]
          Length = 244

 Score =  264 bits (676), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 120/248 (48%), Gaps = 6/248 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+ RY + + Y+G+ Y GWQ Q NG S+QG +++ +  +  + + + GAGRTD+GVHA  
Sbjct: 1   MVKRYFIWLSYDGTNYHGWQVQPNGISVQGELQRVLSTLLRQDISITGAGRTDAGVHARV 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             AHF++  +     L   +N  L     I I  +  V    HARFSA  R+Y Y I TR
Sbjct: 61  MAAHFEIEADIDCKQLAYKMNRML--PQDIVIDRIEEVSLDMHARFSATERTYHYYIHTR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   E+  +  I   LD E M  A + L    DF  F   H    + +  +   +   
Sbjct: 119 KCP--FERHYSCEIHYPLDFEKMNEAGRILCTYEDFGAFCKAHSDVKTTLCNVTRAEWIQ 176

Query: 180 FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            G+      + A  FL   +R+ VG+L  VG G+ +  +    ++ + R + G   P   
Sbjct: 177 TGDTTWYFVITANRFLRNMVRAVVGTLVDVGRGRLSLDEFRSVIEGKRRSDAGESMPGNA 236

Query: 239 LYFDSVEY 246
           L+ + V+Y
Sbjct: 237 LFLEDVKY 244


>gi|197120829|ref|YP_002132780.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
 gi|196170678|gb|ACG71651.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
          Length = 245

 Score =  264 bits (676), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +      V  AGRTD+GVHA  Q
Sbjct: 1   MPVVKLVLEYDGTAYVGWQVQPNGPSIQAEVERALATLHKAPRRVTAAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   R          +NA L     +++   S+    F AR SA  + Y Y I    
Sbjct: 61  VVSFPEDRPLPVKAYVMGMNALL--PPDVAVRAASLEPDGFDARRSARGKRYRYVIENLP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
               L + +AW     L+  ++R AA HLVGRHDF  F++  C     +R +   DV   
Sbjct: 119 TRAPLTRLQAWQHFHPLELASVREAAAHLVGRHDFAAFQASDCACEHAVREVRRLDVLGE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  IE+ + A +F+   +R+ VG+L  VG G+     +   L   DR E GP APP+GL
Sbjct: 179 AGGRIEVVIEATAFVKHMVRNIVGTLVEVGRGRRAPGSMLDLLARGDRTEAGPTAPPQGL 238

Query: 240 YFDSVEY 246
           + + V Y
Sbjct: 239 FLEEVFY 245


>gi|160900673|ref|YP_001566255.1| tRNA pseudouridine synthase A [Delftia acidovorans SPH-1]
 gi|238687164|sp|A9BNH5|TRUA_DELAS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160366257|gb|ABX37870.1| tRNA pseudouridine synthase A [Delftia acidovorans SPH-1]
          Length = 282

 Score =  264 bits (675), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 82/268 (30%), Positives = 127/268 (47%), Gaps = 24/268 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G++IQ  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRVALGVAYNGQRYSGWQSQLSGNTIQDHLEAALGRFAAQEVHTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FH+R  A  R Y Y ++    
Sbjct: 61  VHFDTPLDRAPFSWVRGTNTFL--PPDIAVQWAQPVPDAFHSRACATARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
             ++E GR   +  +LD + M+ AA+HL+G HDF++FR+  CQA SP++T+    +    
Sbjct: 119 RPSVEAGRVGWVFHALDGDAMQAAARHLLGEHDFSSFRASGCQAKSPVKTLHRLSITRRM 178

Query: 181 -GN--------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            G+                             +FLH  +R+ +G L  +G G +    ++
Sbjct: 179 AGDGAQMAAASSMRPGDAAMECCYWRFEFEGSAFLHHMVRNIMGCLIAIGQGTYAPQWMQ 238

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + L A+ R    P   P+GLYF    Y 
Sbjct: 239 QVLDARSRDAAAPTFSPDGLYFLGPVYD 266


>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 =  264 bits (675), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 113/249 (45%), Positives = 155/249 (62%), Gaps = 4/249 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R+ + +EY+G+G  GWQRQK+G S+Q  +E A   + G   V    AGRTDSGVHAL Q
Sbjct: 10  QRWAVKLEYDGTGLVGWQRQKSGLSVQSLLEAAAARLAGNRPVSSITAGRTDSGVHALAQ 69

Query: 61  VAH--FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAH  F     +    + + L+ +LK    + +L+   VD  + ARFSA  RSY YRI+ 
Sbjct: 70  VAHLDFPADVRFSRHSVREGLSYHLK-PHNVVVLDAVQVDTDWSARFSATWRSYQYRILN 128

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R++   L  G  W +  +LD E M+ AA  LVG HDFT+FR++ CQA SP+RT+D  DV+
Sbjct: 129 RRSRPTLLAGNVWHVKSTLDVEKMQEAANILVGPHDFTSFRAVACQAHSPMRTLDQLDVS 188

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + +   ARSFLH Q+R+ VG+LKLVG G W    + +AL+A++R   GP APPEG
Sbjct: 189 RHGDEVLVFAKARSFLHHQVRNMVGTLKLVGIGAWQPERVAEALEARNRCAAGPTAPPEG 248

Query: 239 LYFDSVEYS 247
           LY + V Y 
Sbjct: 249 LYLNGVGYD 257


>gi|254525991|ref|ZP_05138043.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
 gi|221537415|gb|EEE39868.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
          Length = 268

 Score =  264 bits (675), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+G  Y GWQ+QKN +++Q  +E A+F +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGYHYSGWQKQKNATTVQEILESALFKITNHTVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN  L    TI IL    V   +HA +SA+ R Y Y I   +
Sbjct: 61  VVHFDIDSVIPGFSYSNILNNLL--PSTIRILESVEVKNSWHACYSAVYRHYRYVINNGK 118

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD   M  A++ + G HDF  F+       + +  I + D+  
Sbjct: 119 FPNLFINNWSWHRYQKVLDEVLMLRASKTMKGEHDFFAFQKSGSNRRNSVTKIKNIDIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +S         + + +    AP +GL
Sbjct: 179 VEDLIFVDIKATGFLYGMVRLIVGQLVLVGEKKISSDIFIDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEYS 247
            F +  Y 
Sbjct: 239 CFVNAVYE 246


>gi|295132840|ref|YP_003583516.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
 gi|294980855|gb|ADF51320.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
          Length = 250

 Score =  264 bits (675), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 118/246 (47%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ Y GWQ Q    S+Q  +++A+  +  + + V GAGRTD+GVHA +  
Sbjct: 1   MRYFIDLAYLGTAYHGWQIQPEAVSVQQVLQEALSKILQQNIEVVGAGRTDAGVHATQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD         L   LN++L     ISI  L  V  Q HARF A  RSY Y I+  + 
Sbjct: 61  AHFDADLNCDEKTLQFKLNSFL--PKDISIRQLFKVQSQAHARFDACSRSYEYHIVNFKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  ++   A+ + K  D E M  AA  L    +F  F        +    I         
Sbjct: 119 PFKID--LAYYLLKQPDIEKMNHAAAMLKDYTNFKCFSKSRTDVKTYNCNITAAFWEQSK 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +   + A  FL   +R+ VG+L  +G GK +   L++ L+++DR   G   P  GLY 
Sbjct: 177 DELIFHITADRFLRNMVRAIVGTLLDIGLGKNSVEFLKEILKSEDRSMAGTSVPAHGLYL 236

Query: 242 DSVEYS 247
             +EY 
Sbjct: 237 TRIEYP 242


>gi|167759303|ref|ZP_02431430.1| hypothetical protein CLOSCI_01650 [Clostridium scindens ATCC 35704]
 gi|167663177|gb|EDS07307.1| hypothetical protein CLOSCI_01650 [Clostridium scindens ATCC 35704]
          Length = 244

 Score =  264 bits (675), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 130/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+GS Y GWQRQ    ++IQ  +E +I  + G  V V G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGSRYQGWQRQATTDNTIQFVLEWSIGKLVGYRVHVDGSGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + +    L  +LN YL   + I I+ + +V   FHAR SA  + Y Y I  R
Sbjct: 61  QVASVKLSKLYDTKELKDSLNRYL--PEDIRIVKVELVKNGFHARKSAKGKKYEYYIDCR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD E MR A Q+L+G  +FT+F +   +   PIR I +  + S
Sbjct: 119 EKPDVFSRRYCYHYPEKLDIEAMRDAVQYLIGPKNFTSF-TDDKECKDPIRRIINIKIVS 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I      FL+  +R   G+L  +G GK  ++ L   + A+DR   G LAP  GL
Sbjct: 178 TGEKVRITYYGTGFLYHMVRILTGTLLEIGTGKRDASMLPVVIAAEDRCLAGFLAPARGL 237

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 238 FLRKVYY 244


>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 =  264 bits (675), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 91/249 (36%), Positives = 138/249 (55%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + +E++G  + GWQ+Q+N +S+Q  ++ A+  V GE + V  AGRTD+GVHA   +
Sbjct: 10  QRIALALEFDGRPFHGWQQQENATSVQACLQDALQAVEGEPLTVVAAGRTDAGVHAEALL 69

Query: 62  AHFDLV---REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            H D+     +  P       N++L   D I ++ +  V   FHARF+   RSY Y+I  
Sbjct: 70  VHADVSAARWQRSPRAYLHGCNSHL--PDEIRVVGVRAVAADFHARFACRGRSYRYQIWN 127

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R    AL++ R W +P+SL+ E M+ AA H +GRHDF+  R+  CQA+   + I   ++ 
Sbjct: 128 RNTASALQRWRHWWMPRSLNIEAMQGAAVHCLGRHDFSALRAAGCQAAHAEKHIRSLEIV 187

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I I V A +FL+  +R+ VG+L  VG GK +  D    L ++DR+     AP  G
Sbjct: 188 QHGHCIHIHVSADAFLYHMVRNLVGNLVEVGAGKRSPDDFAALLASRDRQLGAATAPAHG 247

Query: 239 LYFDSVEYS 247
           LYF    Y 
Sbjct: 248 LYFTDAWYD 256


>gi|37523138|ref|NP_926515.1| tRNA-pseudouridine synthase A [Gloeobacter violaceus PCC 7421]
 gi|42559743|sp|Q7MBB9|TRUA_GLOVI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|35214141|dbj|BAC91510.1| tRNA-pseudouridine synthase A [Gloeobacter violaceus PCC 7421]
          Length = 304

 Score =  264 bits (675), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 120/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + ++Y G  +FGWQ Q    ++Q  +E+A   +    V  H AGRTD+GVHA  QV 
Sbjct: 16  RLALRVQYLGGHFFGWQWQPGQRTVQQCLEEATERIARHPVRYHAAGRTDTGVHASGQVV 75

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD  ++  P    + LN+ L   D I++   + V   +HARF+A+ R Y Y I     P
Sbjct: 76  HFDTHKKLAPETWVRGLNSLL--PDDIAVRAAAYVSDHWHARFTALWREYRYCIHNSTVP 133

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + ++W  P   LD E +  A   L G HDF  FR         +  +   +    G
Sbjct: 134 DLFVRAQSWYYPYCPLDSEAVAAALATLPGHHDFRAFRRAGSSRPHSLVHVYTAECTREG 193

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I IRV A SFL+  +R  +G+L  VG G+W+        QA +R++    APP+GL  
Sbjct: 194 EQIAIRVRANSFLYGMMRLLIGALAEVGSGRWSVERFAGLWQAGNREQVKYAAPPQGLCL 253

Query: 242 DSVEYS 247
             V Y 
Sbjct: 254 VGVGYP 259


>gi|331085595|ref|ZP_08334679.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330407482|gb|EGG86984.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 239

 Score =  264 bits (675), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 88/242 (36%), Positives = 123/242 (50%), Gaps = 5/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M I Y+G GY GWQR  N   +IQG+IE+ +  + G  V + G+GRTD+GVHA  QVAH 
Sbjct: 1   MTIAYDGGGYKGWQRLTNEPGTIQGTIERVLSKIEGSPVKISGSGRTDAGVHAKGQVAHA 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            L     P +L + LN  L   + I I  +  V + FH+R+SA+ + Y YRI  R     
Sbjct: 61  FLKTNEDPELLRQELNRML--PEDIRICLVESVSQSFHSRYSAVSKVYEYRIDQRSRADV 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +  P  LD + MR AA HL G HDF +F     + +  +RTI   D+      +
Sbjct: 119 FTRKYCYHRPVHLDLDRMRQAADHLTGTHDFGSF--TDNKEADSVRTIFSIDMKEENEKL 176

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R   G+L  VG+G  T   + +A   +DR   G LAP  GL    V
Sbjct: 177 VLAFRGDGFLYHMVRILAGTLLEVGEGIRTPESVLEAFHHRDRSLTGFLAPAHGLCLREV 236

Query: 245 EY 246
            Y
Sbjct: 237 NY 238


>gi|291459136|ref|ZP_06598526.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
 gi|291418390|gb|EFE92109.1| tRNA pseudouridine synthase A [Oribacterium sp. oral taxon 078 str.
           F0262]
          Length = 252

 Score =  264 bits (675), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 124/251 (49%), Gaps = 9/251 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT------GEIVVVHGAGRTDSGV 55
            Y ++I Y+GS Y GW+RQ     +IQG IE  +  +        + V + GAGRTD+GV
Sbjct: 4   NYKLLISYDGSRYLGWERQPGIDRTIQGKIEAVLSRMLLAEGKLQQPVDLIGAGRTDAGV 63

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA    A+  L  +     +   LN YL   D IS+  LSI  K+FHAR+ AI + Y Y 
Sbjct: 64  HARGMCANVFLDSKRSEGEIRAYLNRYL--PDDISVDALSICGKRFHARYHAIGKLYRYS 121

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
               +     E+    ++P+  D E MR+AA+ L+G  D+ +F        S +R ID  
Sbjct: 122 CYFGEKKPVFERKYLLILPEMPDVERMRLAAEALIGEKDYRSFCGNPRMKKSTLRRIDRI 181

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           ++      I        FL  QIR  VG+L  +G GK    D+E+ L A+DR + G  A 
Sbjct: 182 EILERKGCIRFYFHGNGFLQHQIRIMVGTLLEIGLGKREPGDMERILLAKDRSQAGYTAE 241

Query: 236 PEGLYFDSVEY 246
             GL    VEY
Sbjct: 242 AGGLCLMRVEY 252


>gi|288801196|ref|ZP_06406651.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288331807|gb|EFC70290.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 245

 Score =  264 bits (675), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 118/249 (47%), Gaps = 7/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG+++Q  ++KA+ L+    + V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYFAYDGTNYHGWQIQPNGNTVQEELQKALSLILRCNINVVGAGRTDTGVHARSM 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAHFD      +   +L   LN  L     I +  +  V +  HARFSA  R+Y Y +  
Sbjct: 61  VAHFDISTEIVFDAELLSGKLNRLL--PPDIVVFAIKPVAEDMHARFSATWRTYHYYVHK 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P    +  ++   + LD   M  AA++L+   DF  F   H  A + +  +      
Sbjct: 119 GKDPFV--RNYSYSYYRDLDFTLMNEAARYLLEVEDFEAFCKSHSDAKTTLCNVTKAQWI 176

Query: 179 SFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              +      + A  FL   +R+ VG+L  VG  K T  + +  +  + R   G   P  
Sbjct: 177 QDDDTHWHFVIKANRFLRNMVRAVVGTLVEVGQHKITIEEFKNIVDQRKRIGAGESMPAH 236

Query: 238 GLYFDSVEY 246
            L+ + VEY
Sbjct: 237 ALFLEKVEY 245


>gi|186684484|ref|YP_001867680.1| tRNA pseudouridine synthase A [Nostoc punctiforme PCC 73102]
 gi|186466936|gb|ACC82737.1| tRNA pseudouridine synthase A [Nostoc punctiforme PCC 73102]
          Length = 282

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 120/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTDSGVHA  QVA
Sbjct: 12  RVALVIQYLGTHFHGWQRQKQHRTVQEEIETAIATILGHHVTLHGAGRTDSGVHAAAQVA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+      P      LN+YL     I I   + VD ++HARFSA  R Y Y I T    
Sbjct: 72  HFEATGLIPPHKWATILNSYL--PPDILIRASASVDNRWHARFSAAYRRYRYTIYTEDRL 129

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W      LD   ++ A + L+G+H    F     + S     +   +    G
Sbjct: 130 NLFVRPFSWHYYYAPLDESLIQAALKPLLGKHHLAAFHRAGSKRSHSWVEVQAVECRRSG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+  +R  VG L  VG G+ T +   +  + Q R+E    APP+GL  
Sbjct: 190 PFIHIEIQADGFLYGMVRLLVGMLVEVGSGQRTLSSFTELWKEQRREEVKYAAPPQGLCL 249

Query: 242 DSVEYS 247
             V Y 
Sbjct: 250 LRVGYP 255


>gi|71065963|ref|YP_264690.1| tRNA pseudouridine synthase A [Psychrobacter arcticus 273-4]
 gi|71038948|gb|AAZ19256.1| probable tRNA pseudouridine synthase [Psychrobacter arcticus 273-4]
          Length = 276

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 83/244 (34%), Positives = 128/244 (52%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IE+ G+ Y GWQRQ+    +Q ++E AI  V  E V V  AGRTDS VHA   +AH
Sbjct: 14  LAIAIEFLGTHYHGWQRQREVLGVQQALETAISTVANEPVEVIAAGRTDSSVHASNMIAH 73

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F            + +N+ L   D I++  +  +   FHARF+AI R Y Y  + +    
Sbjct: 74  FVTHAYRPTHNWLRGVNSLL--PDDIALRWVQPMPADFHARFAAIARRYRYITLNQTQRP 131

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+   +   I + LD + M++AA  +VG HDF+++R+  CQ++ P+R I H ++ + G  
Sbjct: 132 AILNHQVTHIYEPLDLKAMQLAAADIVGTHDFSSYRAAACQSNQPVRHISHANLFTHGPF 191

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I   + A  FLH  +R+ +G+L  +G  +    D    L  +DR    P A  +GLYF +
Sbjct: 192 IVFDIQADGFLHHMVRNLMGTLYAIGRHELEPADFLNILAKKDRTIAPPTASGDGLYFIN 251

Query: 244 VEYS 247
             Y 
Sbjct: 252 AYYP 255


>gi|304440310|ref|ZP_07400199.1| tRNA pseudouridine synthase A [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304371062|gb|EFM24679.1| tRNA pseudouridine synthase A [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 247

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 78/245 (31%), Positives = 121/245 (49%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   + I Y+G+ ++G+Q+Q  G +I+  + KA+       V +  +GRTDSGVHA  Q 
Sbjct: 1   MNIRIKITYDGTNFYGFQKQDRGRTIEKVLTKAVENTVKHPVKLFYSGRTDSGVHAFGQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A+F          L K +N +L     IS++    VD  FH+R+SA  + Y Y I   + 
Sbjct: 61  ANFYTESTIDIGNLPKVINYHL--PTDISVVEAKYVDDNFHSRYSAKGKFYRYIIYNNKY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL + RAW  P  +D E +  +  +LVG HDF +F   +      IR I   +VN  G
Sbjct: 119 RNALFENRAWQYPHKIDMEILEKSLSYLVGEHDFKSFMGRYATVKDTIRIIHKIEVNKVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           ++I I    +SFL   +R  VG+   +     +    ++AL  ++R   G  AP  GLY 
Sbjct: 179 DVINIDFYGKSFLKNMVRIIVGTSVQISSKNKSPEITKEALVRKERISAGMTAPACGLYL 238

Query: 242 DSVEY 246
             V +
Sbjct: 239 MDVYF 243


>gi|258545708|ref|ZP_05705942.1| tRNA pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
 gi|258519078|gb|EEV87937.1| tRNA pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
          Length = 265

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 99/247 (40%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            RY + +EY+G+ Y GWQRQ    ++IQ  +E A+  V    V    AGRTD+GVHA  Q
Sbjct: 3   TRYAVGLEYDGTHYAGWQRQPFFAATIQEQLECALSQVAAHPVETTCAGRTDAGVHATAQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD              N YL     I +  +  V  +FHAR+SA  R Y Y I  R 
Sbjct: 63  VIHFDTGAARSDFAWLAGANRYL--PADIRLQWIRAVPAEFHARYSARERHYRYLIRHRA 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P AL   R     KSLD   M  AAQ L+G HDF+ FR+  CQA SP R I   DV   
Sbjct: 121 QPSALWARRCHWHKKSLDAAAMHSAAQALIGEHDFSAFRAAECQAKSPWRFIRSIDVRER 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I + +   +FLH  +R+ VG+L  VGDG+  +    + L ++DR+  G  AP +GLY
Sbjct: 181 HGWIAVDICGNAFLHHMVRNIVGTLLAVGDGRRDTAWPGEVLASRDRRCAGVTAPAQGLY 240

Query: 241 FDSVEYS 247
           F  V Y 
Sbjct: 241 FHGVAYP 247


>gi|315186691|gb|EFU20450.1| tRNA pseudouridine synthase A [Spirochaeta thermophila DSM 6578]
          Length = 248

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 121/247 (48%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               +++ Y+G+ + GWQRQ NG S+QG +E A+  +    V VH AGRTDSGVHA+ Q 
Sbjct: 4   RNIKVVLAYDGTDFVGWQRQPNGRSVQGVVEDALARMHKHPVHVHAAGRTDSGVHAVGQC 63

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +F              ALN++L     +  L    V   FHAR+SA+RR Y Y + +  
Sbjct: 64  INFITDIDSLPVEKFALALNSFL--PRDVKALQAEEVPPDFHARYSAVRREYRYYVFSSP 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P    +  +  + +  D   +   A  +VG HDF++F S    + S +R I        
Sbjct: 122 SPYPHLRRYSLWVNRLPDVRLLNAYASCIVGEHDFSSFCSPSDPSPSKVRLIHTASWFPE 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +  R+V  +FL   +R+ VG++  +   K     + K L+A+DR      AP  GL+
Sbjct: 182 GARLVFRIVGNAFLWRMVRALVGTMLDLEKQKADPEMMWKILEARDRSAASDSAPAWGLF 241

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 242 LHEVQYE 248


>gi|225569151|ref|ZP_03778176.1| hypothetical protein CLOHYLEM_05231 [Clostridium hylemonae DSM
           15053]
 gi|225161950|gb|EEG74569.1| hypothetical protein CLOHYLEM_05231 [Clostridium hylemonae DSM
           15053]
          Length = 246

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + + Y+GS Y GWQRQ    ++IQ  +E +I  + G  V V G+GRTD+GVHA  
Sbjct: 3   MRTYKLTVSYDGSRYQGWQRQATTDNTIQFVLEWSIGKLVGYRVHVDGSGRTDAGVHARG 62

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + + P     +LN YL   + I I+   +V   FHAR SA  + Y Y I  R
Sbjct: 63  QVASVKLSKLYDPQEFKDSLNRYL--PEDIRIVKAELVKNGFHARKSAKGKKYEYYIDCR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD E MR A ++LVG  +FT+F +   +   P+R I +  + S
Sbjct: 121 EKPDVFSRRYCYHYPEKLDIEAMRNAVEYLVGVKNFTSF-TDDKECRDPVRRITNIKIVS 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I      FL+  +R   G+L  +G GK  S  L   + A+DR   G LAP  GL
Sbjct: 180 TGDKVRITYYGTGFLYHMVRILTGTLLEIGTGKRDSAMLPVVIAAEDRSLAGFLAPARGL 239

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


>gi|309777173|ref|ZP_07672136.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308915043|gb|EFP60820.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 253

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 120/248 (48%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +I+ Y+GS Y GWQRQ N  SIQ  +E AI  V G  V +  +GRTD+ VHAL Q
Sbjct: 1   MPRYKVILSYDGSAYGGWQRQTNTHSIQQEVEAAIEKVEGRFVSITASGRTDAHVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD V+   P    +ALN+ L     I I  + +VD  FHARF AI + Y Y I T +
Sbjct: 61  VFHFDSVKHLEPENWKRALNSLL--PHDIRIQEVCLVDDAFHARFHAISKRYDYLITT-E 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDVNS 179
                           LD E MR  A   +G HDFT+F S       S I+TI   DV  
Sbjct: 118 VQNPFYYNYMGKDRTRLDVERMRECACIFLGTHDFTSFTSSKVDPRKSKIKTITRLDVVQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + +      FL   +R    +L   G  + +   +++ L  +D+  C   A  EGL
Sbjct: 178 EEHAVRMIFEGNGFLRYMVRMIAQTLIEAGKHRLSVAAVKEMLYGKDKHLCRYKAQAEGL 237

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 238 YLVEVRYP 245


>gi|22297651|ref|NP_680898.1| tRNA pseudouridine synthase A [Thermosynechococcus elongatus BP-1]
 gi|34222849|sp|Q8CWM6|TRUA_THEEB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|22293828|dbj|BAC07660.1| tRNA-pseudouridine synthase I [Thermosynechococcus elongatus BP-1]
          Length = 284

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 108/247 (43%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ + GWQRQ    ++Q  IE+AI  V    V V  AGRTD+GVHA  QV
Sbjct: 12  QRLALLIQYQGTHFHGWQRQVGQRTVQEVIEQAIASVVNHPVSVVAAGRTDTGVHAAGQV 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH  +            LNA L     + I   + V   +HARFSA+ R Y Y + T   
Sbjct: 72  AHVTVNSPIPVHRWPGILNARL--PADVVIRAAAAVPPDWHARFSALWRRYRYTLYTDPC 129

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +   W      LD   M    Q LVGRH  + F       +     +        
Sbjct: 130 PNIFLRPWTWHYYYAPLDVAKMAAVLQPLVGRHHLSAFHRSGSNRAHSWVEVQAVSCQRR 189

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+EI V A  FL+  +R  VG L  VG G+ +     +  Q + R      APP GL 
Sbjct: 190 GALVEIEVQASGFLYGMMRLLVGLLVQVGQGQRSPASFTEIWQQEQRHLVKYAAPPSGLC 249

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 250 LLGVGYP 256


>gi|303234561|ref|ZP_07321198.1| tRNA pseudouridine synthase A [Finegoldia magna BVS033A4]
 gi|302494395|gb|EFL54164.1| tRNA pseudouridine synthase A [Finegoldia magna BVS033A4]
          Length = 244

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 126/246 (51%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  Q
Sbjct: 1   MKNIKLTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVHQPVKINGAGRTDKGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F +  +         +N +   SD+I I+    VD  FHARFSA  ++Y Y +  + 
Sbjct: 61  VCNFIVDTDISANQFLMGVNHF--TSDSIVIVKSEEVDLDFHARFSAKSKTYKYILCNKY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                           LD + +      L+GRHDFT+F +   +  +P+RTID   +   
Sbjct: 119 YMEPWFNDYKGHRKYYLDFDLLLKCRDMLIGRHDFTSFVNDLEEDINPVRTIDEITIEKI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I     A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GLY
Sbjct: 179 DDDIVFTFKAESFLRNMVRILVGSMVDVARGRKSIDWLKNALENKDRQSAGITIEPCGLY 238

Query: 241 FDSVEY 246
             ++EY
Sbjct: 239 LMNIEY 244


>gi|237733260|ref|ZP_04563741.1| tRNA pseudouridine synthase A [Mollicutes bacterium D7]
 gi|229383641|gb|EEO33732.1| tRNA pseudouridine synthase A [Coprobacillus sp. D7]
          Length = 245

 Score =  263 bits (673), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 132/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R    + Y+GS + G+Q Q    ++QG I+KA+  +  E +++HG+GRTD+ VH  +Q
Sbjct: 1   MVRVKCSVSYDGSKFHGFQVQNKLRTVQGEIQKALKNICKEEIIIHGSGRTDAKVHGTKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  RE       +A+N +L   + I IL+   VD+ FH+R+SAI++ Y Y + T +
Sbjct: 61  VFHFDTTREMPEAQWKRAINHFL--PNDIYILDSYFVDENFHSRYSAIKKEYHYLLSTNE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E    +   + LD E MR AA+  +G HDF +F S   Q  + IR +    + + 
Sbjct: 119 Y-SPFETNYIFQYGRPLDLELMREAAKIFIGEHDFASFCSYD-QYGNTIRELYELSITNE 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +I+  +V   F    +R  VG L  VG  + T   L++ L ++  ++C   A P+GLY
Sbjct: 177 KGIIKFILVGNGFRRYMVRHIVGGLIQVGAKRVTKERLQELLDSKGEQKCLFKAKPQGLY 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LHEVFYD 243


>gi|332653968|ref|ZP_08419712.1| tRNA pseudouridine synthase A [Ruminococcaceae bacterium D16]
 gi|332517054|gb|EGJ46659.1| tRNA pseudouridine synthase A [Ruminococcaceae bacterium D16]
          Length = 250

 Score =  263 bits (673), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 127/248 (51%), Gaps = 3/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   + + YNG+ Y GWQ QKN  S+  ++EKA+  V    V   GAGRTD+GVHA  
Sbjct: 1   MERNIALKLMYNGTAYHGWQVQKNAISVAETLEKALSTVVCHPVKCTGAGRTDAGVHAEV 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            +A+F          +  A+N  L     I ++  + V  +F+A  S  R+ Y YRI   
Sbjct: 61  YIANFRTTSTIPCDRIPLAVNTRL--PRDIVVVKATEVPMEFNAIGSCHRKEYTYRIYNS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +        RAW  PK LD + M+ AA   VG HDF   RS+  +  + +RT+ +FDV  
Sbjct: 119 RLGNPFYVDRAWFYPKYLDEKIMQQAADQFVGTHDFRAVRSVGTETRTTVRTVYYFDVTR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              LIE +V A  FL+  +R+  G++    +GK +  D+   L++ +R   GP  PP GL
Sbjct: 179 HDQLIECKVCANGFLYNMVRAMTGTIVYAAEGKLSPQDIPAILESGNRTLAGPTVPPGGL 238

Query: 240 YFDSVEYS 247
           Y   + Y 
Sbjct: 239 YMTKLWYD 246


>gi|322435303|ref|YP_004217515.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX9]
 gi|321163030|gb|ADW68735.1| tRNA pseudouridine synthase A [Acidobacterium sp. MP5ACTX9]
          Length = 258

 Score =  263 bits (673), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 86/260 (33%), Positives = 130/260 (50%), Gaps = 16/260 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + M + Y+G+ Y GWQ Q    ++QG +  A+ L+TGE V+  G+GRTD+GVHAL Q
Sbjct: 1   MRYWKMTLAYDGTAYHGWQVQPGLPTVQGRLAAALKLLTGETVLPQGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           V  F L        L +ALN  L     I +L++  V+ +FHAR  A+R++Y YR+  R 
Sbjct: 61  VVSFGLEAPIPGENLLRALNRAL--PGAIRVLSVEAVEAEFHARRGAVRKTYEYRLFPRV 118

Query: 120 -----QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-------- 166
                +    +     W  P  +D      AA+ ++G HDF++F +     +        
Sbjct: 119 GVRPERICSPMLAAYVWDCPWEIDLGRAEAAARVILGEHDFSSFAASDPDRTERLSGVER 178

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           S +RT+     +    L+  RVV   FLH  +R+ VG       G+   +++   L A+D
Sbjct: 179 SNVRTVYESGWSELDGLMVYRVVGNGFLHHMVRNLVGCFVDAACGRTEVSEVAGILAAKD 238

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R  CG  AP  GL+   VEY
Sbjct: 239 RTACGATAPASGLFLVGVEY 258


>gi|153853827|ref|ZP_01995183.1| hypothetical protein DORLON_01174 [Dorea longicatena DSM 13814]
 gi|149753577|gb|EDM63508.1| hypothetical protein DORLON_01174 [Dorea longicatena DSM 13814]
          Length = 244

 Score =  263 bits (673), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 129/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+GS Y GWQRQ    ++IQ  +E +I  + G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTISYDGSRYQGWQRQATTDNTIQYILEWSIGKLVGYRVHIDGSGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L + +    L  +LN YL   + I I+ + +    FHAR SA  + Y Y I  R
Sbjct: 61  QVASVKLSKLYDTKELKDSLNRYL--PEDIRIVKVELAKNGFHARKSAKGKKYEYYIDCR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +  P+ LD E MR A ++L+G  +FT+F +   +   PIR I +  + S
Sbjct: 119 EKPDVFSRRYCYHYPEKLDIEAMRDATKYLIGPKNFTSF-TDDKECKDPIRKITNIKIVS 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I      FL+  +R   G+L  +G GK  ++ L   + A+DR   G LAP  GL
Sbjct: 178 SGEKVRITYYGTGFLYHMVRILTGTLLEIGAGKRDASMLPVVIAAEDRSLAGFLAPARGL 237

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 238 FLRKVYY 244


>gi|237721333|ref|ZP_04551814.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_2_4]
 gi|229449129|gb|EEO54920.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_2_4]
          Length = 260

 Score =  263 bits (673), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 83/241 (34%), Positives = 117/241 (48%), Gaps = 5/241 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   VAHFD  
Sbjct: 1   MAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLMVAHFDSD 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  +   LN  L     ISI  +  V    HARF A  R+Y Y + T + P    +
Sbjct: 61  ELLDTTSVTDKLNRLL--PPDISIYRVCRVRPDTHARFDATARTYKYYVTTSKYP--FNR 116

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEI 186
              W +   L+ E M  AA+ L   +DFT+F  +H    + I  I H +     +     
Sbjct: 117 QYRWRLYNQLNYERMNEAARILFEYNDFTSFSKLHTDVKTNICHITHAEWTQEEDATWVF 176

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L+  +VEY
Sbjct: 177 TIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQALFLVNVEY 236

Query: 247 S 247
            
Sbjct: 237 P 237


>gi|93006392|ref|YP_580829.1| tRNA pseudouridine synthase A [Psychrobacter cryohalolentis K5]
 gi|92394070|gb|ABE75345.1| tRNA pseudouridine synthase A [Psychrobacter cryohalolentis K5]
          Length = 280

 Score =  263 bits (673), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 83/244 (34%), Positives = 128/244 (52%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + IE+ G+ Y GWQRQ+    +Q ++E AI  V  E V V  AGRTDS VHA   +AH
Sbjct: 18  LAIAIEFLGTHYHGWQRQREVLGVQEALETAISTVANEPVEVIAAGRTDSSVHAGNMIAH 77

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F            + +N+ L   D I++  +  +   FHARF+AI R Y Y  + +    
Sbjct: 78  FVTHAYRPSHNWLRGVNSLL--PDDIALRWVQPMPADFHARFAAIARRYRYITLNQTQRP 135

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+   +   I + LD + M++AA  +VG HDF+++R+  CQ++ P+R I H ++ + G  
Sbjct: 136 AILNHQVTHIHEPLDLKAMQLAAADIVGTHDFSSYRAAACQSNQPVRHISHANLFAHGQF 195

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           I   + A  FLH  +R+ +G+L  +G  +    D    L  +DR    P A  +GLYF +
Sbjct: 196 IVFDIQADGFLHHMVRNLMGTLYAIGRHELEPADFLNILAKKDRTIAPPTASGDGLYFIN 255

Query: 244 VEYS 247
             Y 
Sbjct: 256 AYYP 259


>gi|222111761|ref|YP_002554025.1| tRNA pseudouridine synthase a [Acidovorax ebreus TPSY]
 gi|254789633|sp|B9MDL6|TRUA_ACIET RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221731205|gb|ACM34025.1| tRNA pseudouridine synthase A [Acidovorax ebreus TPSY]
          Length = 274

 Score =  263 bits (673), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 81/259 (31%), Positives = 124/259 (47%), Gaps = 16/259 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + YNG  Y GWQ Q +G+++Q  +E A+     + V    AGRTD+GVH L QV
Sbjct: 1   MRMALGVSYNGQAYNGWQSQPSGNTVQDRLEAALGRFATQEVHTICAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  N +L     I++     V   FH+R  A+ R Y Y ++    
Sbjct: 61  VHFDTQLQRAPFSWVRGTNTFL--PTDIAVQWAQPVPDAFHSRACAVARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             +++ GR   +  +LD + M  A QHL+G HDFT+FR+  CQA SP++T+   D+    
Sbjct: 119 RPSVDAGRVGWVFHALDEQAMHRAVQHLLGEHDFTSFRASACQAKSPVKTLHRIDITRRA 178

Query: 182 N--------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                                   +FLH  IR+ +G +  +G G +    +   L+A+ R
Sbjct: 179 PPAGESTGTHGCIPCYWRFEFEGNAFLHHMIRNIMGCIVAIGQGLYPPEWMRTVLEARSR 238

Query: 228 KECGPLAPPEGLYFDSVEY 246
               P   P+GLYF    Y
Sbjct: 239 DAAAPTFSPDGLYFQGPVY 257


>gi|167755943|ref|ZP_02428070.1| hypothetical protein CLORAM_01463 [Clostridium ramosum DSM 1402]
 gi|167703935|gb|EDS18514.1| hypothetical protein CLORAM_01463 [Clostridium ramosum DSM 1402]
          Length = 245

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 133/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R    + Y+GS + G+Q Q    ++QG I+KA+  +  E +++HG+GRTD+ VH  +Q
Sbjct: 1   MVRVKCSVSYDGSKFHGFQVQNKLRTVQGEIQKALKNICKEEIIIHGSGRTDAKVHGTKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  RE       +A+N +L   + I IL+   VD+ FH+R+SAI++ Y Y + T++
Sbjct: 61  VFHFDTTREMPEAQWKRAINHFL--PNDIYILDSYFVDENFHSRYSAIKKEYHYLLSTKE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E    +   + LD E MR AA+  +G HDF +F S   Q  + IR +    + + 
Sbjct: 119 Y-SPFETNYIFQYGRPLDLELMREAAKIFIGEHDFASFCSYD-QYGNTIRELYELSITNE 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +I+  +V   F    +R  VG L  VG  + T   L++ L ++  ++C   A P+GLY
Sbjct: 177 KGIIKFILVGNGFRRYMVRHIVGGLIQVGAKRVTKERLQELLDSKGEQKCLFKAKPQGLY 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LHEVFYD 243


>gi|225619823|ref|YP_002721080.1| tRNA pseudouridine synthase A [Brachyspira hyodysenteriae WA1]
 gi|254789605|sp|C0QZT8|TRUA_BRAHW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225214642|gb|ACN83376.1| tRNA pseudouridine synthase A [Brachyspira hyodysenteriae WA1]
          Length = 249

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/245 (33%), Positives = 128/245 (52%), Gaps = 4/245 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I+Y+G+ ++GWQ Q N  ++QG I KA+  V GE + ++G GRTD+GVHAL Q
Sbjct: 1   MNNIKITIQYDGTDFYGWQIQPNLRTVQGEIYKAVQKVYGEKITIYGCGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA+F + +  VP+     ALN+YL     + I+    +   F+AR SA  R YLY +   
Sbjct: 61  VANFRVPKMLVPINKVHIALNSYL--DRDLRIIKAEEMPDSFNARASATFREYLYIVHNS 118

Query: 120 QAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  +  AW   K+ +D + +   A++L+G H+FT+F S   +  S  R ++     
Sbjct: 119 STSFPFYERYAWFYRKNVIDEKLINEYARYLIGEHNFTSFCSTEDENDSKFRYLERVKAI 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I   +   +FLH  +R  VG+L      K     +E  L+++DR +    AP  G
Sbjct: 179 RKGDTIYFIIRGNAFLHNMVRIIVGTLVEGQKKKKPINFIEDILKSEDRAKAFVTAPAHG 238

Query: 239 LYFDS 243
           LYF  
Sbjct: 239 LYFRR 243


>gi|110636905|ref|YP_677113.1| tRNA pseudouridine synthase A [Cytophaga hutchinsonii ATCC 33406]
 gi|110279586|gb|ABG57772.1| pseudouridylate synthase I [Cytophaga hutchinsonii ATCC 33406]
          Length = 248

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 131/246 (53%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y G+ Y GWQ Q+N  ++QG ++KA+  V G  + + G+GRTD+GVHA  Q+
Sbjct: 1   MRYFLDISYRGANYHGWQIQENAVTVQGVLQKALSNVLGAKIDILGSGRTDTGVHASSQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D  +E     L   +N YL     I I +  +V    HARF A+ R+Y+YRI   + 
Sbjct: 61  VHLDSPKEIDA-ALIFRINGYL--PKDICIKSARLVQDDAHARFDALSRAYVYRITLVKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E G A+     ++ + M  AA  L+   DF +F  +H   ++   TI H      G
Sbjct: 118 P--FEIGLAYYFYPPIEIDRMNKAAAILLQYEDFESFSKVHTDVTNFNCTIFHAYWERNG 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +++   V A  FL   +R+ VG++  VG G+ +  D  + + A+DRK  G  APPE LY 
Sbjct: 176 DMLYFHVKANRFLRGMVRTLVGTMLEVGKGRMSLDDFVQIILAKDRKRAGISAPPEALYL 235

Query: 242 DSVEYS 247
             VEY 
Sbjct: 236 SEVEYP 241


>gi|256830021|ref|YP_003158749.1| tRNA pseudouridine synthase A [Desulfomicrobium baculatum DSM 4028]
 gi|256579197|gb|ACU90333.1| tRNA pseudouridine synthase A [Desulfomicrobium baculatum DSM 4028]
          Length = 246

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 93/250 (37%), Positives = 125/250 (50%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y G+ Y GWQ Q  G +IQG+IE  +  + GE+V VHG+GRTDSGVHAL Q
Sbjct: 1   MPRIRLTVAYVGTRYQGWQIQGRGETIQGAIEDKLARICGELVRVHGSGRTDSGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+      +   +ALNA L   D ISIL        FHARFS   + Y Y + T  
Sbjct: 61  VAHFDVPESKRHIPWRQALNAML--PDDISILEAREAQDDFHARFSVRSKRYAYTLWTEP 118

Query: 121 -APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
              +       W +   LD E M  AA+ L G HDF  F++   +    +RT++   V +
Sbjct: 119 RFTMPQRAPFVWPVRG-LDFEAMDQAAEVLAGTHDFAAFQNAGTEIKGTVRTLEPI-VRA 176

Query: 180 FGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            G        R  A  FL   +R+ +G L  VG G     D+   L+  DR++    AP 
Sbjct: 177 PGTHSAEWVFRFQADGFLKQMVRNLMGLLVEVGRGGLAPADVRPILEGCDRRKAPATAPA 236

Query: 237 EGLYFDSVEY 246
            GL  + V Y
Sbjct: 237 RGLTLEEVMY 246


>gi|213418519|ref|ZP_03351585.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 239

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 79/223 (35%), Positives = 114/223 (51%), Gaps = 2/223 (0%)

Query: 25  SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLK 84
            S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+             +NA L 
Sbjct: 2   RSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANL- 60

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
               I++  +  V   FHARFSA  R Y Y I   +   A+         + LD E M  
Sbjct: 61  -PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLAKGVTHYYEPLDAERMHR 119

Query: 145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
           AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + + + A +F+H  +R+ VGS
Sbjct: 120 AAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGS 179

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           L  VG      + + + L A+DR      A  EGLY  +V+Y 
Sbjct: 180 LLEVGAHNQPESWIAELLAARDRTLAAATAKAEGLYLVAVDYP 222


>gi|15836112|ref|NP_300636.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae J138]
 gi|16752458|ref|NP_444720.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae AR39]
 gi|12644497|sp|Q9Z7X4|TRUA_CHLPN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|7189101|gb|AAF38045.1| tRNA pseudouridine synthase A [Chlamydophila pneumoniae AR39]
 gi|8978952|dbj|BAA98787.1| pseudouridylate synthase I [Chlamydophila pneumoniae J138]
          Length = 267

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 124/250 (49%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  ++I Y G+ Y GWQ+Q N  SIQ  IE ++  +T     +  +GRTD+GVHA  Q
Sbjct: 1   MTKVALLIAYQGTAYSGWQQQPNDLSIQEVIESSLKKITKTRTPLIASGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF      +     +  KALNA L     I I ++++ D  FHAR+  I + Y Y + 
Sbjct: 61  VAHFRAPDHPLFANANLTKKALNAIL--PKDIVIRDVALFDDNFHARYLTIAKEYRYSLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++   +        E M+  A  L+G HDF +F +     +S +RTI   D+
Sbjct: 119 RLAKPLPWQRHFCYTPRHPFSTELMQEGANLLIGTHDFASFANHGRDYNSTVRTIYTLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ + I      FL+  +R+ VG+L  VG G +    L   L+ ++R+E    AP  
Sbjct: 179 VDKGDSLSIICRGNGFLYKMVRNLVGALLDVGKGAYPPEHLLDILEQKNRREGPSAAPAY 238

Query: 238 GLYFDSVEYS 247
           GL    V YS
Sbjct: 239 GLSLHHVCYS 248


>gi|53712218|ref|YP_098210.1| tRNA pseudouridine synthase A [Bacteroides fragilis YCH46]
 gi|253563743|ref|ZP_04841200.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_2_5]
 gi|62901264|sp|Q64XV0|TRUA_BACFR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52215083|dbj|BAD47676.1| tRNA pseudouridine synthase A [Bacteroides fragilis YCH46]
 gi|251947519|gb|EES87801.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_2_5]
          Length = 252

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 117/248 (47%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ Y GWQ Q NG SIQ  + KA+     +   V GAGRTD+GVHA   V
Sbjct: 4   QRYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRKDTEVIGAGRTDAGVHASLMV 63

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          + + LN  L     IS+  +  V    HARF A  R+Y Y I T +
Sbjct: 64  AHFDYEGEPLDVDKVAEKLNRLL--PQDISVYKVCRVKPDAHARFDATARTYKYYITTVK 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +    
Sbjct: 122 --FPFNRQYRYRIHNPLDFQKMNEAALTLFHYSDFTSFSKLHTDVKTNICKIMHAEWTQE 179

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L  VG GK +  D  K ++ Q+R + G  AP   L
Sbjct: 180 DEYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVVDFRKIIEQQNRCKAGTSAPGNAL 239

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 240 FLVNVEYP 247


>gi|302379698|ref|ZP_07268183.1| tRNA pseudouridine synthase A [Finegoldia magna ACS-171-V-Col3]
 gi|302312605|gb|EFK94601.1| tRNA pseudouridine synthase A [Finegoldia magna ACS-171-V-Col3]
          Length = 244

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  Q
Sbjct: 1   MKNIKLTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVHQPVKINGAGRTDKGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F +  +         +N +   SD+I I+    VD  FHARFSA  ++Y Y +  + 
Sbjct: 61  VCNFIVDTDISANQFLMGVNHF--TSDSIVIVKSEEVDLDFHARFSAKSKTYKYILCNKY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                           LD + +      L+G+HDFT+F +   +  +P+RTID   +   
Sbjct: 119 YMEPWFNDYKGHRKYYLDFDLLLKCRDMLIGKHDFTSFVNDLEEDINPVRTIDEITIEKI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I     A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GLY
Sbjct: 179 DDDIVFSFKAESFLRNMVRILVGSMVDVARGRKSIDWLKNALENKDRQSAGITIEPSGLY 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LMDIEY 244


>gi|210617714|ref|ZP_03291708.1| hypothetical protein CLONEX_03932 [Clostridium nexile DSM 1787]
 gi|210149156|gb|EEA80165.1| hypothetical protein CLONEX_03932 [Clostridium nexile DSM 1787]
          Length = 249

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 127/247 (51%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y MII Y+GS Y GWQRQ     +IQ  +E+ +  + G  V + G+GRTD+GVHA  
Sbjct: 1   MRNYKMIIVYDGSRYKGWQRQNLTNLTIQTILERTVEQIVGYPVEIDGSGRTDAGVHANG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+  +    +       LN  L   + I +  + +V   FH+R+SA  + Y Y I TR
Sbjct: 61  QVANMKV-SGLLDESFVGELNCLL--PEDICVKEMELVPGSFHSRYSAKAKKYKYCIDTR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    +   +   K L  ++M+ AA++L G HDF+ F     +  S +RTI    +  
Sbjct: 118 KKPCVFTRRYTYHFTKELHLDDMKKAAEYLKGTHDFSAFTDNKDE-KSKVRTIYEIKIVK 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +E       FL+  +R   G+L  VG  + +  D++ AL+ ++R+  G LAP  GL
Sbjct: 177 KWTRLEFEFYGTGFLYHMVRILTGTLLEVGCAEKSIEDIKMALEQKERELTGFLAPARGL 236

Query: 240 YFDSVEY 246
           + + V Y
Sbjct: 237 FLEKVYY 243


>gi|218282056|ref|ZP_03488361.1| hypothetical protein EUBIFOR_00932 [Eubacterium biforme DSM 3989]
 gi|218216974|gb|EEC90512.1| hypothetical protein EUBIFOR_00932 [Eubacterium biforme DSM 3989]
          Length = 247

 Score =  262 bits (671), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +    ++ Y+G  Y GWQ+Q+N   IQ  IE+A++ +T E V V  +GRTD+GVHA  QV
Sbjct: 1   MIVKALVSYDGFNYAGWQKQENALGIQQVIEEALYKITKENVDVVASGRTDAGVHAFGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+  +    +   +ALNA L     I IL    +   FHARFSA+ + Y Y       
Sbjct: 61  FHFETNKNIPAIQYERALNALL--PKDIRILKTEEMPDDFHARFSAVGKRYDYYCSYD-I 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNSF 180
                     L+ K LD E M+ A++  +G HDFT+F S       P ++TI + ++   
Sbjct: 118 KNPFNYKYRNLLTKKLDIEAMKNASKVFLGSHDFTSFASSKIDPRKPRVKTISNIEIIEE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +        FL  Q+R   G+L  VG  K    D+++ L A+D+  C   A   GLY
Sbjct: 178 GMDVHFIFEGTGFLRYQVRMMTGTLIAVGQHKIGVDDVQRMLDAKDKSACRYNASSCGLY 237

Query: 241 FDSVEYS 247
              V+Y+
Sbjct: 238 LVEVKYN 244


>gi|296136763|ref|YP_003644005.1| tRNA pseudouridine synthase A [Thiomonas intermedia K12]
 gi|295796885|gb|ADG31675.1| tRNA pseudouridine synthase A [Thiomonas intermedia K12]
          Length = 257

 Score =  262 bits (671), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 87/243 (35%), Positives = 130/243 (53%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M + Y G+ Y GWQ Q  G  +Q  +E+A     G       AGRTD+GVHAL QV H D
Sbjct: 1   MGLSYGGTSYCGWQSQPGGCGVQDFLERAFAQFLGVPTRTICAGRTDAGVHALGQVVHLD 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLS-IVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              +  P    + +NA+L     +++      + + F AR SA +R Y Y +       A
Sbjct: 61  TPLQREPSSWVRGVNAFL--PRDMAVQWARTDLPQTFDARRSAYQRRYRYVLRNHPVRPA 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L+  RA    + LD + +R AAQ L+G HDF+ FRS  CQA SP++T+   ++  +G+ +
Sbjct: 119 LDHARAGWTHRPLDLDLLRAAAQCLLGEHDFSAFRSSECQALSPVKTLHAIEIARYGHTL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
              + A +FLH  +R+ VGSL  VG+G    + L + L ++DR+   P   P+GLYF   
Sbjct: 179 VFDLRANAFLHHMVRNIVGSLLAVGNGSKPVSWLAEVLASRDRRLAAPTFMPDGLYFLGP 238

Query: 245 EYS 247
           +Y 
Sbjct: 239 DYP 241


>gi|282849896|ref|ZP_06259279.1| tRNA pseudouridine synthase A [Veillonella parvula ATCC 17745]
 gi|282580333|gb|EFB85733.1| tRNA pseudouridine synthase A [Veillonella parvula ATCC 17745]
          Length = 261

 Score =  262 bits (671), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 124/248 (50%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    +I+ Y+G+   G+Q+Q N    ++QG +E  +  +  E + ++GA RTD+GVHA 
Sbjct: 1   MRNIRIIVAYDGTDLVGYQKQSNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F          + +A+ A+  I   I +L    +   +  R++   + Y+Y I  
Sbjct: 61  FQVCTFQTSGTIPVENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYVYTIHN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +     L +   W + K L+   M+ A   LVG HDFTT +  +   + P++TI    V 
Sbjct: 119 QLIADPLTQRYHWHVKKPLNIARMQAAGNELVGTHDFTTLKGTNSTPADPVKTIMGIRVE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + G+ + I V+   FL+  +R+  G L  +G G+    D++  L A+DR+  G  AP +G
Sbjct: 179 ARGSQVTISVIGDGFLYHMVRNIAGLLVDIGLGRRKVEDIKGYLAAKDRRAIGKTAPAQG 238

Query: 239 LYFDSVEY 246
           L  + + +
Sbjct: 239 LCLEEIFF 246


>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 =  262 bits (671), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 119/256 (46%), Positives = 160/256 (62%), Gaps = 11/256 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---------NGSSIQGSIEKAIFLVT-GEIVVVHGAGRT 51
            RY + IEY+G+ + GWQRQ             S+Q  +E+A   +  GE V    AGRT
Sbjct: 11  TRYALRIEYDGTPFIGWQRQGTDDSATAQGRAVSVQWVLEQAAARLARGEAVSSIVAGRT 70

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D+GVHA  QVA  DL   + P  + +ALN ++K    ++IL  +     ++ARFSAI RS
Sbjct: 71  DAGVHAQAQVAQIDLPTAFHPERVREALNFHMK-PYPVAILEAAYAPDGWNARFSAIGRS 129

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y Y I+ R+A  AL +GR W + + LD + M  AA+HL+GRHDFT+FR+  CQA SP+RT
Sbjct: 130 YRYLILNRRARPALMEGRVWHVAQPLDADTMDGAAKHLLGRHDFTSFRAAACQAKSPLRT 189

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +D  DV   G+LI I   ARSFLH Q+R+ VG+LKLVGDG+WT+  +  AL A+DR + G
Sbjct: 190 LDRLDVRRDGDLITIIAEARSFLHHQVRNMVGTLKLVGDGRWTAEHVAAALAARDRAKAG 249

Query: 232 PLAPPEGLYFDSVEYS 247
           P APP+GL    V Y 
Sbjct: 250 PTAPPDGLALTGVIYE 265


>gi|296125792|ref|YP_003633044.1| tRNA pseudouridine synthase A [Brachyspira murdochii DSM 12563]
 gi|296017608|gb|ADG70845.1| tRNA pseudouridine synthase A [Brachyspira murdochii DSM 12563]
          Length = 247

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 127/245 (51%), Gaps = 4/245 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I+Y+G+ ++GWQ Q N  ++QG I KA+  + GE + ++G GRTD+GVHAL Q
Sbjct: 1   MNNIKITIQYDGTDFYGWQIQPNLRTVQGEIYKAVQKIYGEKITIYGCGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA+F + +  VP+     ALN+ L     + I+    +D  F+AR SA  R YLY +   
Sbjct: 61  VANFRVPKMLVPINKVHIALNSCL--DRDLRIIKAEEMDDNFNARASATFREYLYVVHNS 118

Query: 120 QAPLALEKGRAWLIPKSL-DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  +  AW   K++ D + +   A++L+G H+FT+F S   +  S  R ++     
Sbjct: 119 STSFPFYERYAWFYRKNIIDEKLINEYAKYLIGEHNFTSFCSTEDENDSKFRYLEKVKAV 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I   +   +FLH  +R  VG+L      K     +E  L+ ++R E    AP  G
Sbjct: 179 RKGDTIYFIIKGNAFLHNMVRIIVGTLVEGQKKKMPVNFIEDILKRENRTEAFVTAPAHG 238

Query: 239 LYFDS 243
           LYF  
Sbjct: 239 LYFRR 243


>gi|256841433|ref|ZP_05546940.1| tRNA pseudouridine synthase A [Parabacteroides sp. D13]
 gi|256737276|gb|EEU50603.1| tRNA pseudouridine synthase A [Parabacteroides sp. D13]
          Length = 265

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++  + V + GAGRTD+GVHA   +
Sbjct: 15  RRYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRKPVPIVGAGRTDAGVHARLMI 74

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD        V L + LN  L     I++  +  V  + HARF A  R+Y Y + T++
Sbjct: 75  AHFDWEEPIGDLVFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYVTTKK 132

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                     + +P  LD E M  A + L    DFT+F  +H    +    I H D    
Sbjct: 133 --DPFNHELVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHADWTQE 190

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P   L+
Sbjct: 191 GDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGHALF 250

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 251 LVDVTYP 257


>gi|332827815|gb|EGK00550.1| tRNA pseudouridine synthase A [Dysgonomonas gadei ATCC BAA-286]
          Length = 254

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 122/248 (49%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  Y GWQ Q NG S+Q +IEKA+  +    V + GAGRTD+GVHA   
Sbjct: 1   MKRYFIYLSYNGEKYCGWQIQPNGVSVQETIEKALSTLLRMPVSIVGAGRTDAGVHARMM 60

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            AHFD  +E    ++L   LN+ L     I+I  +  V    HARF A  R Y Y I T 
Sbjct: 61  TAHFDSEQEITDLLLLANKLNSLL--PKDIAIQKIIEVKPDAHARFDAESRLYRYYITTD 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +          + I  + D E M   A+ L    DFT+F  +H    +   TI       
Sbjct: 119 K--DPFLHHLKYKIYGNPDIEIMNACAKVLFDYEDFTSFSKLHTDVKTNNCTIMLARWEQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN     + A  FL   +RS VG+L   G GK T+ D  + ++A+DR + G   P   L
Sbjct: 177 AGNDYIFTIKANRFLRNMVRSIVGTLLEAGRGKITTDDFRRIIEAKDRCKAGTSVPGHAL 236

Query: 240 YFDSVEYS 247
           + + +EY+
Sbjct: 237 FLEEIEYN 244


>gi|33862089|ref|NP_893650.1| tRNA pseudouridine synthase A [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|42559755|sp|Q7TU31|TRUA_PROMP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33634307|emb|CAE19992.1| tRNA pseudouridine synthase A [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
          Length = 268

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 86/248 (34%), Positives = 125/248 (50%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++I+Y+GS + GWQRQKN  S+Q +IE  +F ++ +I+    +GRTD+GVHA  Q
Sbjct: 1   MKRVALVIQYDGSYFSGWQRQKNAISVQETIENCLFKISNQIIKTFASGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN+ L    TI IL    V   +HA +SA+ R Y Y I   +
Sbjct: 61  VIHFDIDFLIPIDRYADVLNSRL--PHTIRILESVEVKSSWHACYSAVYRHYRYVINNNK 118

Query: 121 APLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    K LD  +M IA   ++G HDF  F+      S+ + TI    +  
Sbjct: 119 IPNLFLNKWSWHRYQKYLDEVSMSIALDGMIGEHDFFAFQKSGSNRSTSVTTIKDIKLER 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI I + A  FL+  +RS VG L LVG+ K T    +     + + +    AP +GL
Sbjct: 179 TEDLILIDIKATGFLYGMVRSIVGQLVLVGEKKITPDIFKDRWVLKKKHDVRESAPAKGL 238

Query: 240 YFDSVEYS 247
            F +  Y 
Sbjct: 239 CFVNSVYE 246


>gi|219684777|ref|ZP_03539719.1| tRNA pseudouridine synthase A [Borrelia garinii PBr]
 gi|219671722|gb|EED28777.1| tRNA pseudouridine synthase A [Borrelia garinii PBr]
          Length = 246

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    +IQG IEKA+  +  + V +H +GRTD GVHA +Q
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTIQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + + I IL L  V   FH RF+A +R Y YRI+   
Sbjct: 61  IITFDININIQLNNLKKALNAIL-LKNGIKILKLKYVKNSFHPRFNAQKRKYSYRILNSN 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESVSTFETILKSKNRNFARTTAPANALF 239

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 240 LDKVYYE 246


>gi|315608004|ref|ZP_07882997.1| tRNA pseudouridine synthase A [Prevotella buccae ATCC 33574]
 gi|315250473|gb|EFU30469.1| tRNA pseudouridine synthase A [Prevotella buccae ATCC 33574]
          Length = 284

 Score =  262 bits (670), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 85/258 (32%), Positives = 123/258 (47%), Gaps = 15/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  +EKA+ L+      + GAGRTD+GVHA   
Sbjct: 24  MQRYFIYLSYDGTNYHGWQIQPNGNSVQEELEKALSLLLRTKTEIVGAGRTDAGVHARLM 83

Query: 61  VAHFDLV----------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           VAHFD            ++     LC  LN  L     ISI  +  V +  HARFSA+ R
Sbjct: 84  VAHFDYEVGTTTEGQEAKDIDCPQLCYKLNRLL--PRDISIRKIIPVAQDMHARFSAVAR 141

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           +Y Y I T + P   E+  ++ +P +LD + MR   + L  + DF  F        S   
Sbjct: 142 TYHYYIHTGKMP--FERHYSYQMPYALDFDAMREGCELLKRQTDFAAFCKAGADNKSTCC 199

Query: 171 TIDHF-DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           T+     V +        + A  FL   +R+ VG+L  +G  K T       ++A  R +
Sbjct: 200 TVTEARWVKTSPETWYFEITANRFLRNMVRAVVGTLVDLGRHKITLDQFRHIVEAGRRSD 259

Query: 230 CGPLAPPEGLYFDSVEYS 247
            G   P   L+ + VEY 
Sbjct: 260 AGESMPGHALFLERVEYP 277


>gi|150008550|ref|YP_001303293.1| tRNA pseudouridine synthase A [Parabacteroides distasonis ATCC
           8503]
 gi|255014350|ref|ZP_05286476.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_7]
 gi|166228743|sp|A6LDA7|TRUA_PARD8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|149936974|gb|ABR43671.1| tRNA pseudouridine synthase A [Parabacteroides distasonis ATCC
           8503]
          Length = 252

 Score =  262 bits (670), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++    V + GAGRTD+GVHA   
Sbjct: 1   MRRYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRTPVPIVGAGRTDAGVHAHLM 60

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +AHFD        V L + LN  L     I++  +  V  + HARF A  R+Y Y + T+
Sbjct: 61  IAHFDWEEPIGDLVFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYVTTK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +          + +P  LD E M  A + L    DFT+F  +H    +    I H     
Sbjct: 119 K--DPFNHELVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHAGWTQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P   L
Sbjct: 177 EGDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGHAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVTYP 244


>gi|163756865|ref|ZP_02163974.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
 gi|161323254|gb|EDP94594.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
          Length = 250

 Score =  262 bits (670), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 123/246 (50%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQ Q N  S+Q  IEKA+ ++    + + GAGRTD+GVHA +  
Sbjct: 1   MRYFIELSYNGEKYHGWQNQPNAISVQEVIEKALSILLRSNIAIVGAGRTDAGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD    +    L   LN++L     ++I  +  V +  HARF A  R+Y Y I++ + 
Sbjct: 61  AHFDTDVVFNRAELTFKLNSFL--PKDVAIQQIHTVKEDAHARFDATGRTYEYWIVSEKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P       A  + K LD + M  AA+ L    DF  F   H    + I  ++       G
Sbjct: 119 P--FYTQSAHTVYKKLDVDLMNKAAKKLFNYQDFKCFSKTHTDVKTYICQLEKAVWEQKG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+   + A  FL   +R+ VG+L  VG GK +    ++ + ++DR + G   P + LY 
Sbjct: 177 ELLVFTIRADRFLRNMVRAIVGTLLEVGLGKLSIEGFKEIIASRDRNKAGTSVPGKALYL 236

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 237 TAVTYP 242


>gi|62184804|ref|YP_219589.1| tRNA pseudouridine synthase A [Chlamydophila abortus S26/3]
 gi|81313017|sp|Q5L6V3|TRUA_CHLAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62147871|emb|CAH63617.1| putative tRNA pseudouridine synthase a [Chlamydophila abortus
           S26/3]
          Length = 268

 Score =  262 bits (670), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 85/250 (34%), Positives = 129/250 (51%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +++ Y G+ Y GWQRQ N  SIQ  IE ++  V G+ + V  +GRTD+ VHA  Q
Sbjct: 1   MTQVVILLAYQGTAYAGWQRQPNDLSIQEVIENSLAQVVGKRIPVTSSGRTDAEVHAFGQ 60

Query: 61  VAHFDLVREWV---PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF             + K LNA L     I I ++ + D +FH+RFSAI + Y Y + 
Sbjct: 61  VAHFSQPDHPQFSQASSIKKMLNALL--PKDIVIRDVVLGDDKFHSRFSAIAKEYRYVLT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  E+  A+     L  + M+  AQ+L+G HDF +F +     +S IRT+ + D+
Sbjct: 119 RSPKPLPWERYFAYYPRHHLKTDLMQEGAQYLLGTHDFASFANHGRDYTSTIRTLFNLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  + I      FL+  +R+ VGSL  +  GK+    +++ L  ++R++  P AP  
Sbjct: 179 VDHGETVTIICRGNGFLYKMVRNIVGSLLDISRGKYPPEYIQEILMQKNRRQGPPAAPSH 238

Query: 238 GLYFDSVEYS 247
            L    V Y 
Sbjct: 239 ALSLYHVCYP 248


>gi|313145437|ref|ZP_07807630.1| tRNA pseudouridine synthase A [Bacteroides fragilis 3_1_12]
 gi|313134204|gb|EFR51564.1| tRNA pseudouridine synthase A [Bacteroides fragilis 3_1_12]
          Length = 255

 Score =  262 bits (670), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 116/248 (46%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ Y GWQ Q NG SIQ  + KA+         V GAGRTD+GVHA   V
Sbjct: 7   QRYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRRDTEVIGAGRTDAGVHASLMV 66

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          + + LN  L     IS+  +  V    HARF A  R+Y Y I T +
Sbjct: 67  AHFDYEGEVLDTDKVTEKLNRLL--PQDISVYKVCRVRPDAHARFDATARTYKYYITTVK 124

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +    
Sbjct: 125 YP--FNRQYRYRIHNPLDFQKMNEAALTLFHYTDFTSFSKLHTDVKTNICKIMHAEWTQE 182

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L  VG GK +     + ++ QDR + G  AP   L
Sbjct: 183 DEYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDGFRRIIEQQDRCKAGTSAPGNAL 242

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 243 FLVNVEYP 250


>gi|298530329|ref|ZP_07017731.1| tRNA pseudouridine synthase A [Desulfonatronospira thiodismutans
           ASO3-1]
 gi|298509703|gb|EFI33607.1| tRNA pseudouridine synthase A [Desulfonatronospira thiodismutans
           ASO3-1]
          Length = 247

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+GY GWQ QK+G +IQG +EKA+  +    + VHG+GRTD+GVHAL QV
Sbjct: 3   MRVRLTLAYDGTGYNGWQIQKDGLTIQGELEKALSRICSASIRVHGSGRTDAGVHALGQV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD   +++ V   +ALNA L     I +L+ +  D++FHARFSA  + Y Y + T+ A
Sbjct: 63  AHFDPPPKFLNVPWNRALNAVL--PPGIRVLDFARTDRKFHARFSARAKQYSYTLWTQGA 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-- 179
               ++         LD E M+ A   L G HDF  F +   + +  IRT+ +  +    
Sbjct: 121 FFYPQRRNFVWNTGPLDLEAMQEATTCLTGSHDFNCFMNKGTEITDTIRTVRNILLAPGF 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                 + + A  FL    R+ V +L  VG  K +  +L+  +Q +DR      AP  GL
Sbjct: 181 TPQETVVWIQADGFLKQMARNIVSALVQVGRKKLSQAELKSIIQGRDRALAPATAPARGL 240

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


>gi|42522098|ref|NP_967478.1| pseudouridylate synthase I [Bdellovibrio bacteriovorus HD100]
 gi|51316639|sp|Q6MQH6|TRUA_BDEBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|39574629|emb|CAE78471.1| pseudouridylate synthase I [Bdellovibrio bacteriovorus HD100]
          Length = 262

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 77/252 (30%), Positives = 128/252 (50%), Gaps = 8/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
            +    + Y+G+G+ GWQ+QK  +  S+   IE+A+  V  E + +  +GRTD+GVHAL 
Sbjct: 3   TKVRFTVAYDGTGFCGWQKQKPEDQISVAQVIEEALSKVFNEKITLFASGRTDAGVHALN 62

Query: 60  QVAHFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HF   R+  P     LC ALN++L    +I      I    FHA  SA  ++Y Y I
Sbjct: 63  QVCHFSTHRKIDPNKKWDLCWALNSHL--PPSIVAKKAWIAPDDFHATLSATHKTYRYLI 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           + +  P A     A  +   +D E+++ ++++L+G  DF +F+S+       +R I   D
Sbjct: 121 VNKPRPSAHLNRYADWVRLPIDIEHLQESSKYLLGNQDFKSFQSVGTPVPDTVREIYKAD 180

Query: 177 VN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  +++  +    FL   +R+ VG+   +       + +++ + AQDR + GP AP
Sbjct: 181 WEWRKPGVMQFTITGSGFLKQMVRNIVGTSLFLERKGLDPSKMQEIIAAQDRMKAGPPAP 240

Query: 236 PEGLYFDSVEYS 247
            +GLY   V Y 
Sbjct: 241 AQGLYLMKVYYP 252


>gi|325297315|ref|YP_004257232.1| tRNA pseudouridine synthase A [Bacteroides salanitronis DSM 18170]
 gi|324316868|gb|ADY34759.1| tRNA pseudouridine synthase A [Bacteroides salanitronis DSM 18170]
          Length = 268

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 117/248 (47%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY M + Y+G+ Y GWQ Q NG+S+Q  ++KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MARYFMYLGYDGTNYHGWQIQPNGASVQEELQKALSTLMRRPVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+       I    LN  L     I++  +  V    HARF A  R Y Y + T +
Sbjct: 61  VAHADIDALADAAIWVGKLNRLL--PPDIAVYRMRRVADDAHARFDATYRKYQYHVTTSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  AW + + LD   M  AA  L    DFT+F  +H    +    I +      
Sbjct: 119 NP--FLRHYAWRVFQPLDFGRMNEAASVLFEYTDFTSFSKLHTDVKTNNCRILYARWEQT 176

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G +     + A  FL   +R+ VG+L  VG GK T     + ++A++R   G   P   L
Sbjct: 177 GADEWVFTIQADRFLRNMVRAVVGTLVEVGRGKLTIEGFRRVIEAKNRCSAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVGYP 244


>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 =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 99/247 (40%), Positives = 147/247 (59%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY +++E++G+ + GWQRQ +G S+Q  +E+A   +  G+      AGRTDSGVHA  
Sbjct: 15  MPRYALLVEFDGAPFVGWQRQPSGLSVQQVLEEAASPLNQGQPAATQAAGRTDSGVHAEG 74

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            V   D+ +   PV L +ALN + +    +++L +++   ++ ARFS I R+Y YRI+ R
Sbjct: 75  MVVQIDIAQALDPVRLREALNYHTR-PHPVAVLGVAVPPAEWSARFSCIGRAYRYRILNR 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|329894995|ref|ZP_08270775.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC3088]
 gi|328922563|gb|EGG29899.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC3088]
          Length = 274

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 85/245 (34%), Positives = 121/245 (49%), Gaps = 3/245 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
             + +EYNGS + GWQRQ     ++Q ++E A+  +    V V  AGRTDSGVHA  QV 
Sbjct: 14  LALAVEYNGSLFHGWQRQGGTDQTVQATLEAALSQIANHDVRVACAGRTDSGVHATSQVV 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F               NA L    T+ +     V  +FHARFSAI+R+Y Y    ++  
Sbjct: 74  SFKAPVSRSLKAWVVGSNAVL--PPTVRVHWACAVPDEFHARFSAIQRTYRYVWCVQEVR 131

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                 +      +L  + M  AAQ L+G  DF+ FR+  CQ+++P R +    V   G 
Sbjct: 132 PTSLLKQVTWSRNALCSQTMNEAAQSLLGEQDFSAFRAASCQSNTPFREVQAVSVVGRGP 191

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +FLH  +R+  GSL LVG G      + + LQ +DR      A P+GLY  
Sbjct: 192 FVVMEIRANAFLHHMVRNIAGSLSLVGRGLKPVDWIAQLLQGKDRTVAADTASPDGLYLT 251

Query: 243 SVEYS 247
           SV Y 
Sbjct: 252 SVAYP 256


>gi|56751899|ref|YP_172600.1| tRNA pseudouridine synthase A [Synechococcus elongatus PCC 6301]
 gi|60416392|sp|O24712|TRUA_SYNP6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56686858|dbj|BAD80080.1| tRNA pseudouridine synthase [Synechococcus elongatus PCC 6301]
          Length = 294

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 108/247 (43%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G G+ GWQRQ    S+QG +E AI  V G  V V  AGRTD+GVHA  QV
Sbjct: 14  QRIALVIQYLGQGFCGWQRQPRQRSVQGELESAIAAVVGHPVSVQSAGRTDTGVHAAAQV 73

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+             LN  L     I     +IV   +HARFSA  R Y Y I T   
Sbjct: 74  AHFETTSPIPAHRWPSVLNGRLTPDLNIR--AAAIVPANWHARFSASYRRYRYTIYTDPC 131

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P        W   +  L    M+ A Q LVG H    F+    +       +    V   
Sbjct: 132 PNLFLNSYVWHYYQAPLCENQMQAALQTLVGYHHLAAFQRSGSKRQHAWVHVQDAWVRRR 191

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LIEI V A  FL+  IR  VG L  VG+G  +          Q R      APP+GL 
Sbjct: 192 DSLIEIEVQASGFLYGMIRLLVGLLVQVGEGSRSLESFTDIWVNQRRDRVRHAAPPQGLC 251

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 252 LLRIGYP 258


>gi|262383400|ref|ZP_06076536.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_33B]
 gi|262294298|gb|EEY82230.1| tRNA pseudouridine synthase A [Bacteroides sp. 2_1_33B]
          Length = 265

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 119/247 (48%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + YNG  + GWQ Q NG ++Q SIE+A+  +  + V + GAGRTD+GVHA   +
Sbjct: 15  RRYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALATLMRKPVPIVGAGRTDAGVHARLMI 74

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD       +  L + LN  L     I++  +  V  + HARF A  R+Y Y I TR+
Sbjct: 75  AHFDWEGPIEDLAFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYITTRK 132

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                     +  P  LD E M  A + L    DFT+F  +H    +    I H      
Sbjct: 133 --DPFNYELVYKFPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHAGWTQE 190

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P   L+
Sbjct: 191 GDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGHALF 250

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 251 LVDVTYP 257


>gi|227871757|ref|ZP_03990163.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
 gi|227842397|gb|EEJ52621.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
          Length = 265

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 127/250 (50%), Gaps = 7/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + + Y G+ Y G+Q+Q+  S+I G++E+ +  L   ++    GA RTD GVHAL  
Sbjct: 10  QRIVLKLAYEGTSYHGFQKQEGLSTIAGTVEEQLRNLFPWKMENFIGASRTDQGVHALGN 69

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD   +     + +ALN+YL   + I ++    V + FH RF+  R++Y Y I   +
Sbjct: 70  LLSFDTEGKVSGEQILRALNSYL--PEDIRVMEAYSVQQDFHPRFTPHRKAYRYSICRSK 127

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA----SSPIRTIDHFD 176
               L +  A+     LDC  +    + L G HDF +F +   Q+     S +R I  F 
Sbjct: 128 VENPLRRRTAYHYTFPLDCGKISEGMELLKGEHDFRSFANPKAQSLLQGGSSVREIYRFS 187

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+ +   V    FL+  IR   G+L  +G G+ + + LE+ L+ +DR   GP AP 
Sbjct: 188 MEEEGDYLHFSVEGNGFLYHMIRILAGTLLELGRGRISLSQLEEILEKKDRTLAGPTAPA 247

Query: 237 EGLYFDSVEY 246
           +GL   +++Y
Sbjct: 248 KGLCLMNLDY 257


>gi|17231681|ref|NP_488229.1| tRNA pseudouridine synthase A [Nostoc sp. PCC 7120]
 gi|42559852|sp|Q8YPK5|TRUA_ANASP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|17133324|dbj|BAB75888.1| tRNA-pseudouridine synthase I [Nostoc sp. PCC 7120]
          Length = 282

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 118/247 (47%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++++Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTDSGVHA  QV
Sbjct: 11  QRVALVVQYLGTHFHGWQRQKQHRTVQEEIETAIAKILGHHVTLHGAGRTDSGVHAAAQV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             +N+YL     I I   + V  ++HARFSA  R Y Y I T   
Sbjct: 71  AHFDATGLIPAHKWASVINSYL--PKDILIKASAAVGDRWHARFSAAYRRYRYTIYTEDR 128

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P       +W      LD   M+ A + L+G+H    F     + S     +   + +  
Sbjct: 129 PNLFVTPFSWHYYYAPLDESLMQAALKPLMGKHHLAAFHRAGSKRSHSWVEVQAVECHRS 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I + A  FL+  +R  VG L  VG G+ T  +  +  + Q R+E    AP +GL 
Sbjct: 189 GPFIHIEIQADGFLYGMVRLLVGMLVQVGSGQRTLANFTELWKEQRREEVKHAAPSQGLC 248

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 249 LLRVGYP 255


>gi|227872273|ref|ZP_03990632.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
 gi|227841885|gb|EEJ52156.1| tRNA-pseudouridine synthase I [Oribacterium sinus F0268]
          Length = 249

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 124/248 (50%), Gaps = 5/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
            Y +I+ Y+GS YFG+++QK+   +IQG +E     + G  E V + GA RTD+GVHA  
Sbjct: 4   NYKLIVAYDGSRYFGFEKQKDQEATIQGKLEGVFSRIPGNEEGVEIIGASRTDAGVHARG 63

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             A+  L  E     +    N YL   + I+I+++  V  +FHAR++A+ + Y Y     
Sbjct: 64  MCANVFLDTELSEEEILDYGNRYL--PEDIAIVSVKKVSPRFHARYNALGKIYRYSCYIG 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++     + +  D E M+ AA+ L+G+ DF +F        S IR+I    +  
Sbjct: 122 RTKPVFDRKILLHLEEEPDLEAMQEAAKFLIGKQDFKSFCGNPKMKKSTIRSISSIRIQK 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             NL+        FL  QIR  VG+L  VG  K  + D+   + A+DR++ G   P +GL
Sbjct: 182 SQNLLRFYFEGSGFLQYQIRIMVGTLLEVGYHKRKAGDIPGIIDAKDRQQAGYTVPAKGL 241

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 242 CLMKVLYD 249


>gi|255007737|ref|ZP_05279863.1| tRNA pseudouridine synthase A [Bacteroides fragilis 3_1_12]
          Length = 252

 Score =  262 bits (669), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 116/248 (46%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ Y GWQ Q NG SIQ  + KA+         V GAGRTD+GVHA   V
Sbjct: 4   QRYFIYLAYDGTHYHGWQIQPNGISIQECLMKALATFLRRDTEVIGAGRTDAGVHASLMV 63

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          + + LN  L     IS+  +  V    HARF A  R+Y Y I T +
Sbjct: 64  AHFDYEGEVLDTDKVTEKLNRLL--PQDISVYKVCRVRPDAHARFDATARTYKYYITTVK 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   + I   LD + M  AA  L    DFT+F  +H    + I  I H +    
Sbjct: 122 YP--FNRQYRYRIHNPLDFQKMNEAALTLFHYTDFTSFSKLHTDVKTNICKIMHAEWTQE 179

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L  VG GK +     + ++ QDR + G  AP   L
Sbjct: 180 DEYTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVDGFRRIIEQQDRCKAGTSAPGNAL 239

Query: 240 YFDSVEYS 247
           +  +VEY 
Sbjct: 240 FLVNVEYP 247


>gi|282859476|ref|ZP_06268581.1| tRNA pseudouridine synthase A [Prevotella bivia JCVIHMP010]
 gi|282587704|gb|EFB92904.1| tRNA pseudouridine synthase A [Prevotella bivia JCVIHMP010]
          Length = 255

 Score =  262 bits (669), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 82/259 (31%), Positives = 119/259 (45%), Gaps = 17/259 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+GS Y GWQ Q NGSS+Q ++EKAI ++  E + + GAGRTD+GVHA   
Sbjct: 1   MQRYFITLSYDGSKYHGWQIQPNGSSVQETLEKAISVLLREPIAIIGAGRTDAGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  +  V    HARFSA RR+Y Y + T++
Sbjct: 61  VAHFDFTGSVDCHQMVYRLNRLL--PHDISVSKIEPVTNDLHARFSASRRTYHYYLHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--- 177
                ++  +  +  +LD + M  AAQ+L+G  DF  F        + I  +        
Sbjct: 119 --NIYQRQYSCYMSYALDFDLMNEAAQYLIGTKDFKCFCKAGADVKTTICELTEARWVPI 176

Query: 178 ----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                               + A  FL   +R+ VG+L  VG GK +    +  +    R
Sbjct: 177 RAELSMPLSSKEQPTDWCFIISANRFLRNMVRAVVGTLVDVGRGKLSLEAFKAIVDGGTR 236

Query: 228 KECGPLAPPEGLYFDSVEY 246
            + G   P   L+   V Y
Sbjct: 237 SDAGESMPGNALFLWEVIY 255


>gi|325287217|ref|YP_004263007.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
 gi|324322671|gb|ADY30136.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
          Length = 251

 Score =  262 bits (669), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 122/246 (49%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G+ Y GWQ Q N  ++Q  +EKA   +  E + + GAGRTD+GVHA +  
Sbjct: 1   MRYFVAFSYFGAAYHGWQIQPNAITVQEELEKAFSTLLKEKISLMGAGRTDAGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+       V L + LN++L   D I+I N+  V +  HARF+A  R+Y Y I T++ 
Sbjct: 61  AHFNTTPISNTVDLMRRLNSFL--PDDIAIQNIYEVPEDAHARFNATERTYEYLITTQKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P ++       I + LD E M  AAQ L+G+ DF  F        +   T+         
Sbjct: 119 PFSIV--TTHYIKQKLDIEKMNKAAQLLLGKQDFECFSKSKTDVKTYYCTVKKAIWEQKE 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +     + A  FL   +R+ VG+L  VG GK T   +   + ++ R E G   P + LY 
Sbjct: 177 DKFVFTITADRFLRNMVRAIVGTLLDVGTGKITIDHIHTIIASKSRAEAGTSVPAKALYL 236

Query: 242 DSVEYS 247
             V Y 
Sbjct: 237 TQVLYP 242


>gi|157414138|ref|YP_001485004.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9215]
 gi|166991165|sp|A8G737|TRUA_PROM2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157388713|gb|ABV51418.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9215]
          Length = 268

 Score =  262 bits (669), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 120/248 (48%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+G  Y GWQ+QKN +++Q  +E A+F +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGYHYSGWQKQKNATTVQEILESALFKITNHTVKTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+            LN  L    TI IL    V   +HA +SA+ R Y Y I   +
Sbjct: 61  VVHFDIDSVIPGFSYSNILNNLL--PSTIRILESVEVKNSWHACYSAVYRHYRYVINNGK 118

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD   M  A++ + G HDF  F+       + +  I + D+  
Sbjct: 119 FPNLFINNWSWHRYQKVLDEVLMLHASKTMEGEHDFFAFQKSGSNRRNSVTLIKNIDIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  VG L LVG+ K +S         + + +    AP +GL
Sbjct: 179 VEDLILVDIKATGFLYGMVRLIVGQLVLVGEKKISSDIFIDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEYS 247
            F +  Y 
Sbjct: 239 CFVNAVYE 246


>gi|284929586|ref|YP_003422108.1| pseudouridylate synthase I [cyanobacterium UCYN-A]
 gi|284810030|gb|ADB95727.1| pseudouridylate synthase I [cyanobacterium UCYN-A]
          Length = 281

 Score =  262 bits (669), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 117/246 (47%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +II+Y+G+ + GWQRQ    ++Q  IE  I    G  V +HGAGRTD+GVHA  QVA
Sbjct: 13  RIALIIQYSGNRFHGWQRQPYRRTVQADIENTITKSLGYKVSIHGAGRTDAGVHATGQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD      P  L + LN YL   + I I N   V   +HARFSA  R Y Y + T    
Sbjct: 73  HFDYAGPIPPKSLARVLNRYL--PEDILIRNSKEVSINWHARFSAQWRRYRYTLYTNNDC 130

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             L K  +W   +  L  ++M  A + L+G H  T FR    Q +     I   +    G
Sbjct: 131 NLLIKSYSWHYYRYPLKVKSMLDALKSLLGTHHLTAFRKKGSQRNHSWVEIQDVECYRKG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+  +R  +G L  VG  K +  +  +  + Q R+     AP  GL  
Sbjct: 191 AFIHIEIQANGFLYGMVRLLMGMLVEVGIDKLSLANFNQIWRDQKREYVRHSAPANGLCL 250

Query: 242 DSVEYS 247
             V Y 
Sbjct: 251 LGVGYP 256


>gi|329942480|ref|ZP_08291290.1| tRNA pseudouridine synthase A [Chlamydophila psittaci Cal10]
 gi|332287117|ref|YP_004422018.1| tRNA pseudouridine synthase A [Chlamydophila psittaci 6BC]
 gi|313847713|emb|CBY16703.1| putative tRNA pseudouridine synthase a [Chlamydophila psittaci RD1]
 gi|325507334|gb|ADZ18972.1| tRNA pseudouridine synthase A [Chlamydophila psittaci 6BC]
 gi|328815390|gb|EGF85378.1| tRNA pseudouridine synthase A [Chlamydophila psittaci Cal10]
 gi|328914357|gb|AEB55190.1| tRNA pseudouridine synthase A [Chlamydophila psittaci 6BC]
          Length = 268

 Score =  262 bits (669), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 130/250 (52%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +++ Y G+ Y GWQRQ N  S+Q  IE ++  V G+ + V  +GRTD+GVHA  Q
Sbjct: 1   MTQVVLLLAYQGTAYAGWQRQPNDLSVQEVIENSLTKVVGKRIHVTSSGRTDAGVHAFGQ 60

Query: 61  VAHFD---LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAHF      R      + K LNA L     I I ++ + D  FH+RFSAI + Y Y + 
Sbjct: 61  VAHFPQPDHPRFSQASGIKKMLNALL--PKDIVIRDVVLGDDTFHSRFSAIAKEYRYLLT 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  E+  ++     L  + M+  A++L+G HDF +F +     +S IRT+ + D+
Sbjct: 119 RSPKPLPWERYFSYYPRHHLRTDLMQEGAKYLIGTHDFASFANHGRDYTSTIRTLFNLDI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  + I      FL+  +R+ VGSL  +  GK+    +++ L  ++R++  P AP  
Sbjct: 179 VDNGETVTIICKGNGFLYKMVRNIVGSLLDISRGKYPPEYIQEILIQKNRRKGPPAAPSY 238

Query: 238 GLYFDSVEYS 247
            L    V Y 
Sbjct: 239 ALSLYHVCYP 248


>gi|149370146|ref|ZP_01889997.1| tRNA pseudouridine synthase A [unidentified eubacterium SCB49]
 gi|149356637|gb|EDM45193.1| tRNA pseudouridine synthase A [unidentified eubacterium SCB49]
          Length = 259

 Score =  262 bits (669), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 118/245 (48%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + I YNG+ Y GWQ+Q +  ++Q  IE  +  V  + V   GAGRTD+GVHA +   
Sbjct: 8   RYFLEIAYNGAKYCGWQKQPDAKTVQQEIEYFLSTVLRQDVTTMGAGRTDTGVHARQMFL 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+ +           N++L     IS+LN   V    HARF+AI R Y Y +   + P
Sbjct: 68  HFDVSKSISIPNFLYKANSFL--PPDISVLNYYEVLDDHHARFNAIAREYEYYVSVVKDP 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            +++   A+ +    D   M  AA  L+   DF +F  +  +  +    +   +    GN
Sbjct: 126 FSIDS--AYYLKNFPDINLMNEAASSLLTYSDFQSFSKVRTEVKTFNCNVTKAEWILNGN 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           ++   + A  FL   +RS VG+L  VG GK T  D    + +++R   G   P  GLY  
Sbjct: 184 MLIFTISADRFLRNMVRSIVGTLLEVGSGKITIEDFHNIIASKNRSNAGISVPAHGLYLT 243

Query: 243 SVEYS 247
            V Y 
Sbjct: 244 KVIYP 248


>gi|319654901|ref|ZP_08008976.1| tRNA pseudouridine synthase A [Bacillus sp. 2_A_57_CT2]
 gi|317393464|gb|EFV74227.1| tRNA pseudouridine synthase A [Bacillus sp. 2_A_57_CT2]
          Length = 269

 Score =  261 bits (668), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 66/226 (29%), Positives = 109/226 (48%), Gaps = 3/226 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R+   I Y+G+ + G+Q Q    ++QG +E+A+  +  GE + V  +GRTD+GVHA  
Sbjct: 1   MQRFKCNITYDGTHFAGYQVQPGKRTVQGELERALKKLHKGEDIKVTASGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN+ L   D ++I+    V   FH RF A  + Y Y +   
Sbjct: 61  QVIHFDSPLNIPIEKWEIALNSLL--PDEVAIVGAETVPDDFHVRFDAKGKEYRYFVHCS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                 ++  A+     L+ + ++ AA  L+G HDFT+F S   +    +R +   +V  
Sbjct: 119 SRRDPFKRHYAYQYSYPLNTDAIKQAAADLIGTHDFTSFCSAKTEVEDKVRELQEIEVQE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
             +++  R     FL+  +R   G+L  VG G+     +   L+ +
Sbjct: 179 KEDMLIFRFRGTGFLYNMVRILAGTLLEVGSGERDPDSMPSVLKEK 224


>gi|126663837|ref|ZP_01734832.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BAL38]
 gi|126624101|gb|EAZ94794.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BAL38]
          Length = 248

 Score =  261 bits (668), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 76/246 (30%), Positives = 118/246 (47%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG  + G+Q Q + SS+Q ++EKA+  +  E + + GAGRTDSGVHA +  
Sbjct: 1   MRYFIEFAYNGKNFHGFQSQPDASSVQETLEKALSTLFREKIAIVGAGRTDSGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+   E         LN++L    +I +  +  V    HARF A  R+Y Y + T   
Sbjct: 61  AHFETELELDSEYWSHKLNSFL--PPSIVVYRIFKVTDNAHARFDASSRTYEYYMHT--F 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A     +W     L+ + M  A   L   +DF  F  +H   ++    I        G
Sbjct: 117 KDAFITDGSWYHSHQLNLDKMNEACAILFEYNDFECFSKVHTDVNTFNCKISEAHWKQVG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG++  +G GK    DL   +++++R + G   P  GLY 
Sbjct: 177 NQLIFTITADRFLRNMVRAIVGTMVNIGLGKIEVADLRTIIESKNRGKAGFSVPAHGLYL 236

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 237 VNVRYP 242


>gi|319938474|ref|ZP_08012868.1| pseudouridylate synthase [Coprobacillus sp. 29_1]
 gi|319806390|gb|EFW03057.1| pseudouridylate synthase [Coprobacillus sp. 29_1]
          Length = 244

 Score =  261 bits (668), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   ++ Y+GS + G+Q Q    ++QG I+KA+  +  E V++H +GRTD+ VHA+ QV
Sbjct: 1   MRVKCVVSYDGSRFHGFQVQDKERTVQGEIQKALKKINEEEVIIHASGRTDAKVHAVHQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  ++  P    +A+N ++   + I IL+ S  D +FH+R+SAI++ Y Y + T++ 
Sbjct: 61  FHFDTKKDLPPQQWKRAINHFM--PNDIYILDASYTDDEFHSRYSAIKKEYRYLLSTKEY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +    +   + LD E MR A+Q  +G H+F +F S   Q  + IRT+  FD+    
Sbjct: 119 -NPFDTNYVFQYGRQLDIELMREASQIFIGEHNFASFCSYD-QYGNTIRTLYTFDIVEED 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I  R++   F    +R  VG +  VG  + +   L + L++   K+C   A P+GLY 
Sbjct: 177 GIITFRLIGNGFRRYMVRHLVGGIIQVGAKRISKEILSEMLESCGTKKCLFKAKPQGLYL 236

Query: 242 DSVEYS 247
             V Y 
Sbjct: 237 QEVYYE 242


>gi|81301016|ref|YP_401224.1| tRNA pseudouridine synthase A [Synechococcus elongatus PCC 7942]
 gi|81169897|gb|ABB58237.1| tRNA pseudouridine synthase A [Synechococcus elongatus PCC 7942]
          Length = 294

 Score =  261 bits (668), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 87/247 (35%), Positives = 108/247 (43%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G G+ GWQRQ    S+QG +E AI  V G  V V  AGRTD+GVHA  QV
Sbjct: 14  QRIALVIQYLGQGFCGWQRQPRQRSVQGELESAIAAVVGHPVSVQSAGRTDTGVHAAAQV 73

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+             LN  L     I     +IV   +HARFSA  R Y Y I T   
Sbjct: 74  AHFETTSPIPAHRWPSVLNGRLTPDLNIR--AAAIVPANWHARFSASYRRYRYTIYTDPC 131

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P        W   +  L    M+ A Q LVG H    F+    +       +    V   
Sbjct: 132 PNLFLNSYVWHYYQAPLCENQMQAALQTLVGYHHLAAFQRSGSKRQHAWVHVQDAWVRRR 191

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LIEI V A  FL+  IR  VG L  VG+G  +          Q R      APP+GL 
Sbjct: 192 DSLIEIEVQASGFLYGMIRLLVGLLVQVGEGSRSLESFTDIWVNQRRDRVRHAAPPQGLC 251

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 252 LLRIGYP 258


>gi|163847952|ref|YP_001635996.1| tRNA pseudouridine synthase ACD [Chloroflexus aurantiacus J-10-fl]
 gi|222525832|ref|YP_002570303.1| tRNA pseudouridine synthase ACD [Chloroflexus sp. Y-400-fl]
 gi|189030130|sp|A9WH95|TRUA_CHLAA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789612|sp|B9LJG1|TRUA_CHLSY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|163669241|gb|ABY35607.1| tRNA pseudouridine synthase A [Chloroflexus aurantiacus J-10-fl]
 gi|222449711|gb|ACM53977.1| tRNA pseudouridine synthase A [Chloroflexus sp. Y-400-fl]
          Length = 278

 Score =  261 bits (668), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 125/251 (49%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++ Y+G+ + G Q Q +  ++QG++E A   +T E   +  AGRTD+GVHA  Q
Sbjct: 1   MRTIALLLAYDGTDFAGSQWQTDIRTVQGALESAWEALTQERRRIVLAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH           + + LNA+L     ++I N+      FHARFSAI+R Y Y I    
Sbjct: 61  VAHVQTTTRHNLQTIWRGLNAHL--PVDLAIQNVGEAVPDFHARFSAIQREYRYLIDCAA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL   + +      +LD   M  A + L G HDF  F +      S +RT+    V  +
Sbjct: 119 APLPQLRHQVLHYAGTLDVAAMTAALKLLEGTHDFAAFTTATPAQRSTVRTMYWTRVGDY 178

Query: 181 G----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 L+ I V A +FL   +R  VG+L LVG G+ T     + L ++DR+  GP AP 
Sbjct: 179 EWFERRLLAIEVAANAFLQHMVRMIVGTLLLVGRGRMTVDQFGEVLASRDRRLAGPTAPA 238

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 239 HGLTLTAVRYP 249


>gi|282890956|ref|ZP_06299470.1| hypothetical protein pah_c032o038 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499171|gb|EFB41476.1| hypothetical protein pah_c032o038 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 254

 Score =  261 bits (668), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 120/249 (48%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +II Y+G  + GWQ+   G SI+ ++E  +  +  E +++  A RTD+GVHA  Q
Sbjct: 1   MKNIRLIISYDGGRFLGWQKTSMGPSIEENLENVLHQILQEPIILQAASRTDAGVHAHEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F   +      +  +LN  L     I +L+  I    FH     + + Y Y I T  
Sbjct: 61  VVNFFTEKPIDLNKITNSLNRLL--PKDIVVLDAQIAPDHFHPTLDCLSKEYRYYISTGP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFDVN 178
                 +  AW  P  LD E ++ AA+ LVG HDF+ F ++    S    +R + +  ++
Sbjct: 119 IQPPNHRFYAWHCPGHLDKELIKKAAEQLVGTHDFSAFCNLKPSESYTHHVREVLNIQIH 178

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               +    +V+ +SFL+  +R+ VG+L  VG GK    D+   L  +DR + G  AP  
Sbjct: 179 ETDAHHFYFQVMGKSFLYKMVRNIVGTLIFVGKGKLRCEDIPLLLSCRDRTKIGMTAPAH 238

Query: 238 GLYFDSVEY 246
           GL    + Y
Sbjct: 239 GLTLYRLNY 247


>gi|255281297|ref|ZP_05345852.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
 gi|255268254|gb|EET61459.1| tRNA pseudouridine synthase A [Bryantella formatexigens DSM 14469]
          Length = 280

 Score =  261 bits (668), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 119/278 (42%), Gaps = 35/278 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT--------------------- 39
             + + + Y+G+ Y GW+ +     +IQG +E  +  +                      
Sbjct: 3   QNFKLTVTYDGTRYHGWEAKPGIEMTIQGKLEAVLTKMLAFPDDVPVQSLIAPAASVVSC 62

Query: 40  -----------GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDT 88
                         V V GAGRTD+GVHA    A+  L    +P  +   LN YL   + 
Sbjct: 63  NPGAADGMPGCPVPVKVIGAGRTDAGVHAREMTANVHLDTAMLPGDIRDYLNRYL--PED 120

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I +  + IV  +FH+R++A  ++Y Y   T       ++   +++ K+ D   M+ AA +
Sbjct: 121 ICVREVCIVSDRFHSRYNATGKTYRYTCFTGPLKPVFDRKYVYVLDKTPDIAAMKKAAGY 180

Query: 149 LVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
           L G HDF +F        S +RTID  ++    + +        FL   +R   G+L   
Sbjct: 181 LCGTHDFASFCGNPKMKKSTVRTIDSIEITQNNSYLYFMYHGNGFLQHMVRILTGTLLET 240

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           G G+ +   + + L A+ R   G LAP +GL    V+Y
Sbjct: 241 GYGRRSPESMPELLAARKRALAGFLAPAQGLCLMKVDY 278


>gi|315919940|ref|ZP_07916180.1| tRNA pseudouridine synthase A [Bacteroides sp. D2]
 gi|313693815|gb|EFS30650.1| tRNA pseudouridine synthase A [Bacteroides sp. D2]
          Length = 260

 Score =  261 bits (668), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 82/241 (34%), Positives = 115/241 (47%), Gaps = 5/241 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ Y GWQ Q NG S+Q  + KA+       + V GAGRTD+GVHA   VAHFD  
Sbjct: 1   MAYDGTNYHGWQIQPNGISVQECLMKALSTFLRREIEVIGAGRTDAGVHASLMVAHFDSD 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                  +   LN  L     ISI  +  V    H RF A  R+Y Y + T + P    +
Sbjct: 61  ELLDTTSVTDKLNRLL--PPDISIYRVCRVRPDAHVRFDATARTYKYYVTTSKYP--FNR 116

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEI 186
              W +   L+ E M  AA  L   +DFT+F  +H    + I  I H +     +     
Sbjct: 117 QYRWRLYNQLNYERMNEAAHILFEYNDFTSFSKLHTDVKTNICHITHAEWTQEEDATWVF 176

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G  AP + L+  +VEY
Sbjct: 177 TIRADRFLRNMVRAIVGTLIEVGRGKLTVEGFRRIIEQQDRCKAGTSAPGQALFLVNVEY 236

Query: 247 S 247
            
Sbjct: 237 P 237


>gi|169350826|ref|ZP_02867764.1| hypothetical protein CLOSPI_01600 [Clostridium spiroforme DSM 1552]
 gi|169292412|gb|EDS74545.1| hypothetical protein CLOSPI_01600 [Clostridium spiroforme DSM 1552]
          Length = 243

 Score =  261 bits (668), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 80/247 (32%), Positives = 130/247 (52%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R   I+ Y+GS ++G+Q Q    ++QG I+KA+  +  E V +H +GRTD+ VH  +Q
Sbjct: 1   MVRVKCIVSYDGSKFYGFQIQNKLRTVQGEIQKALKKICEEEVTIHASGRTDAKVHGNKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD +R+       +A+N +L   + I IL+   V + FH+R+SA ++ Y Y + T++
Sbjct: 61  VFHFDTLRQMPEKQWKRAINHFL--PNDIYILDSLFVSEDFHSRYSATKKEYRYLLSTKE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E    +   + LD E M+ AA   +G HDF +F S   Q  + IR +    +   
Sbjct: 119 Y-SPFETNYIYQYGRPLDLELMKDAANIFIGEHDFASFCSYD-QYGNTIRELYKILIEDN 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +I   +V   F    +R  VG L  VG  + T   L++ L ++ +++C   A P+GLY
Sbjct: 177 NGIITFTIVGNGFRRYMVRHIVGGLIQVGAKRITKKRLQEFLDSKGKEKCLFKAKPQGLY 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LYEVFYD 243


>gi|194477033|ref|YP_002049212.1| tRNA pseudouridine synthase A [Paulinella chromatophora]
 gi|171192040|gb|ACB43002.1| tRNA pseudouridine synthase A [Paulinella chromatophora]
          Length = 252

 Score =  261 bits (668), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 120/249 (48%), Gaps = 4/249 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M R  + ++Y GS Y GWQRQ+N  S+Q  +E+A+  +   + ++   AGRTD+GVHA  
Sbjct: 1   MKRIALCLQYEGSSYCGWQRQRNALSVQEVLEEALLALGCDKPIISFAAGRTDAGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN YL    +I  L  + V   +HA +SA+ R Y Y ++  
Sbjct: 61  QVVHFDTNSPIPTDSWASALNGYL--PSSIRALKATSVPNNWHACYSAVYRRYRYTLLNS 118

Query: 120 QAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           + P       +W    + LD   MR +    +G HDF+ F+       S   TI    + 
Sbjct: 119 REPDLFIAPYSWHRYDTVLDENAMRRSLLTFLGTHDFSAFQRSGSDRISTRTTIQEVSLE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +   I + + A  FL+  +R  V  L  VG+G+ T ++LE+  +   R +    AP +G
Sbjct: 179 RYDEKITLEIQASGFLYGMVRLMVAQLVEVGEGRLTESNLEQRWRQHCRGQIKEAAPAQG 238

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 239 LCLLQVGYP 247


>gi|300870453|ref|YP_003785324.1| tRNA-pseudouridine synthase TrmA [Brachyspira pilosicoli 95/1000]
 gi|300688152|gb|ADK30823.1| tRNA-pseudouridine synthase, TrmA [Brachyspira pilosicoli 95/1000]
          Length = 247

 Score =  261 bits (668), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 126/245 (51%), Gaps = 4/245 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I+Y+G+ +FGWQ Q N  ++QG I KA+  +  +   ++G GRTD+GVHAL Q
Sbjct: 1   MTNIKITIQYDGTDFFGWQIQPNLRTVQGEIYKAVQKIYSKKSTIYGCGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA+F + +  VP   + +ALN+ L     I I+   +VD  F+AR SA  R Y+Y +   
Sbjct: 61  VANFRVEKMLVPIERVTRALNSAL--PKDIRIIKSEVVDDSFNARASATFREYIYVVQNS 118

Query: 120 QAPLALEKGRAWLIPKSL-DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              +   +  +W   K++ + + +   A++LVG H+FT+F S   +  S  R I+     
Sbjct: 119 DISVPFYERYSWFYRKNIINEKLINEYAKYLVGEHNFTSFCSTEDENDSKFRYIERVRAI 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + I   +   +FLH  +R  VG+L            +E+ L+ +DR      AP  G
Sbjct: 179 RKKDTIYFIIRGNAFLHNMVRIIVGTLVEGQRKNMPVNFIEEILKKEDRTLAFVTAPAHG 238

Query: 239 LYFDS 243
           LYF  
Sbjct: 239 LYFRR 243


>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 =  261 bits (667), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 114/249 (45%), Positives = 152/249 (61%), Gaps = 4/249 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQ 60
            R+ + IEY+G  + GWQRQ  G S+Q  +E+A   +  G +V    AGRTD+GVHA  Q
Sbjct: 7   QRWAVRIEYDGRPFVGWQRQITGLSVQQVLEEAASRLASGRVVPSITAGRTDAGVHATGQ 66

Query: 61  VAHFDLVR--EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            AH D           +  ALN ++K    +++L    VD ++ ARFSAIRRSY YRI+ 
Sbjct: 67  AAHLDFPGDVRLNDSTVRDALNFHMK-PYPVAVLRACPVDTEWSARFSAIRRSYRYRILN 125

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R++   L+ GR WL+ ++LD   M  AA+ L+GRHDFT+FR+  CQA SP+RT+D   V 
Sbjct: 126 RRSRPTLDDGRVWLVKRTLDEAAMARAARLLLGRHDFTSFRASACQARSPLRTLDRLGVV 185

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I I   ARSFLH Q+R+ VG+LKLVG+G W    +  AL A DR+  GP APP+G
Sbjct: 186 RQGEEIVIEAEARSFLHHQVRNMVGTLKLVGEGLWAPDRVAAALAACDRRAAGPTAPPDG 245

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 246 LYLTGVGYD 254


>gi|169824810|ref|YP_001692421.1| tRNA pseudouridine synthase A [Finegoldia magna ATCC 29328]
 gi|238687759|sp|B0S2E1|TRUA_FINM2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167831615|dbj|BAG08531.1| tRNA pseudouridine synthase A [Finegoldia magna ATCC 29328]
          Length = 244

 Score =  261 bits (667), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + ++Y+GS ++GWQ+  +  S+Q  IEKA+  +  + V ++GAGRTD GVHA  Q
Sbjct: 1   MKNIKLTVQYDGSKFYGWQKLNDLPSVQLEIEKAVTKMVHQPVKINGAGRTDKGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F +  +         +N +   SD+I I+    +D  FHARFSA  ++Y Y +  + 
Sbjct: 61  VCNFIVDTDISANQFLMGVNHF--TSDSIVIVKSEEMDLDFHARFSAKSKTYKYILCNKY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                           LD + +      L+G+HDFT+F +   +  +P+RTID   +   
Sbjct: 119 YMEPWFNDYKGHRKYYLDFDLLLKCRDMLIGKHDFTSFVNDLEEDINPVRTIDEITIEKI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I     A SFL   +R  VGS+  V  G+ +   L+ AL+ +DR+  G    P GLY
Sbjct: 179 DDDIVFTFKAESFLRNMVRILVGSMVDVARGRKSIDWLKNALENKDRQSAGITIEPSGLY 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LMDIEY 244


>gi|225164227|ref|ZP_03726501.1| tRNA-pseudouridine synthase I [Opitutaceae bacterium TAV2]
 gi|224801166|gb|EEG19488.1| tRNA-pseudouridine synthase I [Opitutaceae bacterium TAV2]
          Length = 354

 Score =  261 bits (667), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 123/250 (49%), Gaps = 6/250 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+   + Y+G+ + GWQ Q +G++IQ  +E+ +  + GE V +HG+GRTD+GVHA  QV 
Sbjct: 100 RWKCTVAYDGTHFSGWQSQPDGNAIQDHLERRLARMLGESVRIHGSGRTDAGVHARAQVF 159

Query: 63  HFDLVREWVPVILCKALNA-----YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD      P  L  A  +        +   I + +  IV   FHARF A  + Y Y + 
Sbjct: 160 HFDAAWRHGPERLLAAFRSGGGEGGGGVPSGIQVTDARIVSAAFHARFDATGKRYTYDLH 219

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFD 176
                    +   W IP+ LD   MR AA  LVGRHDF  F +    +  + +R +   D
Sbjct: 220 HGGFADPFTQDYCWSIPQKLDVVAMRAAAALLVGRHDFCAFSALSGEERETTVRHLTQLD 279

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +++ G  I I   A  FL+  +R  VG+L   G GK T  D+ + L    R      AP 
Sbjct: 280 ISARGARIRITARADGFLYRMVRRLVGALVHAGLGKLTPGDIAQILSEARRTPRIETAPA 339

Query: 237 EGLYFDSVEY 246
            GL+ D V Y
Sbjct: 340 HGLFLDRVFY 349


>gi|298373324|ref|ZP_06983313.1| tRNA pseudouridine synthase A [Bacteroidetes oral taxon 274 str.
           F0058]
 gi|298274376|gb|EFI15928.1| tRNA pseudouridine synthase A [Bacteroidetes oral taxon 274 str.
           F0058]
          Length = 247

 Score =  261 bits (667), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I YNG+ Y GWQ Q N  ++Q ++ +A+ +V G  V + GAGRTD+GVHA    
Sbjct: 1   MRYFIYIAYNGTNYHGWQIQPNAVTVQETVGQAMSVVLGSNVEITGAGRTDTGVHARTMT 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFDL +      L K LN+ L     I++  +  V  + HARFSA+ R+Y Y +   + 
Sbjct: 61  AHFDLTKRIDEANLVKRLNSLL--PADIAVYKIVEVIPEAHARFSAMSRTYEYLLYLDKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +G A+   + LD E M IAA  +    DFT+F  +H    +   T+   + +   
Sbjct: 119 P--FLRGLAYRHYRDLDFEKMNIAANKMRDYTDFTSFAKLHTDTRTNNCTVSKAEWHKQD 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N+    +VA  FL   +R+ VG+L LVG+G+ T  D  + ++A+DR++ G     +GLY 
Sbjct: 177 NIWIFTIVADRFLRDMVRATVGTLILVGEGRITVDDFCRIIEAKDRQKAGQSIDAQGLYL 236

Query: 242 DSVEYS 247
             ++Y 
Sbjct: 237 TDIQYP 242


>gi|218249502|ref|YP_002374546.1| tRNA pseudouridine synthase A [Borrelia burgdorferi ZS7]
 gi|224532546|ref|ZP_03673169.1| tRNA pseudouridine synthase A [Borrelia burgdorferi WI91-23]
 gi|226322073|ref|ZP_03797598.1| tRNA pseudouridine synthase A [Borrelia burgdorferi Bol26]
 gi|226708642|sp|B7J0V1|TRUA_BORBZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1665842|emb|CAA70351.1| pseudouridylate synthase I [Borrelia burgdorferi]
 gi|2911585|emb|CAA11967.1| pseudouridylate synthase I [Borrelia burgdorferi]
 gi|218164690|gb|ACK74751.1| tRNA pseudouridine synthase A [Borrelia burgdorferi ZS7]
 gi|224512489|gb|EEF82867.1| tRNA pseudouridine synthase A [Borrelia burgdorferi WI91-23]
 gi|226232663|gb|EEH31417.1| tRNA pseudouridine synthase A [Borrelia burgdorferi Bol26]
          Length = 246

 Score =  261 bits (667), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDIKINIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIMGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

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


>gi|229829433|ref|ZP_04455502.1| hypothetical protein GCWU000342_01523 [Shuttleworthia satelles DSM
           14600]
 gi|229791864|gb|EEP27978.1| hypothetical protein GCWU000342_01523 [Shuttleworthia satelles DSM
           14600]
          Length = 325

 Score =  261 bits (667), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 81/301 (26%), Positives = 120/301 (39%), Gaps = 56/301 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG------------EIVVVHGA 48
           M  Y + I Y+G+ Y GW+ Q    +IQG +E+A+  + G              V + GA
Sbjct: 27  MQNYRLKIAYDGTRYAGWEHQPGQETIQGKLEQALARMCGLAMDERDFMRPDTPVKLIGA 86

Query: 49  GRTDSGVHALRQVAHF------------------------------------------DL 66
           GRTD+GVHA   VA                                            + 
Sbjct: 87  GRTDAGVHARGMVASIAFEAPAYRPGPWERRESKGRDRGNQPGNMTWQAEPSAQLTRRNQ 146

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
            R      +   LN YL   D IS++       +FHAR+ A+ ++Y Y     +      
Sbjct: 147 PRSMTCQEMQDYLNHYL--PDDISVVAFKEAAARFHARYKAVGKTYQYTAFDGRVKPVFN 204

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +     + + LD   M+ AA  L+G HDF +F        S +R +D  ++      +  
Sbjct: 205 RRYYTPLEEELDVSAMQEAANCLLGEHDFRSFCGNPKMKKSTVRRVDRIEIRRSKGYVYF 264

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                 FL   +R  VG+L  VG  +    D+EK L+A+DRK  GP AP  GL    V+Y
Sbjct: 265 SFHGTGFLQNMVRILVGTLMEVGWHRMRPQDVEKILEARDRKAAGPTAPARGLCLIRVDY 324

Query: 247 S 247
            
Sbjct: 325 D 325


>gi|15594358|ref|NP_212146.1| tRNA pseudouridine synthase A [Borrelia burgdorferi B31]
 gi|3915171|sp|P70830|TRUA_BORBU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2687883|gb|AAC66394.1| pseudouridylate synthase I (hisT) [Borrelia burgdorferi B31]
          Length = 246

 Score =  260 bits (666), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA +Q
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDIKINIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

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


>gi|296121106|ref|YP_003628884.1| tRNA pseudouridine synthase A [Planctomyces limnophilus DSM 3776]
 gi|296013446|gb|ADG66685.1| tRNA pseudouridine synthase A [Planctomyces limnophilus DSM 3776]
          Length = 305

 Score =  260 bits (666), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 79/264 (29%), Positives = 115/264 (43%), Gaps = 23/264 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + I Y+G+ Y GWQ Q NG SIQ ++ +AI   T E  V++ AGRTD+GVHA+ QV  
Sbjct: 8   LKLTIAYDGTAYCGWQTQPNGVSIQSTLMQAIQEFTAETPVLYAAGRTDAGVHAVGQVVS 67

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F             AL  +L   D I I  +  V   FHA+F A  ++Y Y         
Sbjct: 68  FSTTSPVPAANFRPALQRFL--PDDIVIRQVEDVQPGFHAQFHARLKTYRYLFHNAPVWS 125

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS---- 179
              +  A      LD + M  A + +VG  DF +  +      + +RT+    V      
Sbjct: 126 PFYRQYALWHRTRLDEQAMDFAIRQIVGTFDFRSLETQWPNRKTSVRTVIKASVQRIRNW 185

Query: 180 -----------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
                             G  + + + A  FL+  +R+  G+L  +G GKW    L + +
Sbjct: 186 NLLGENGPPSEECQLDPEGEFLCMEITANGFLYNMVRTIAGTLIHIGRGKWGPEKLREIV 245

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
             QDR+  G  AP  GLY   V+Y
Sbjct: 246 DLQDRRRAGETAPAHGLYLWHVDY 269


>gi|119511153|ref|ZP_01630270.1| tRNA pseudouridine synthase A [Nodularia spumigena CCY9414]
 gi|119464141|gb|EAW45061.1| tRNA pseudouridine synthase A [Nodularia spumigena CCY9414]
          Length = 296

 Score =  260 bits (666), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 122/246 (49%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQK   S+Q  IE AI  V G  + +HGAGRTDSGVHA  QVA
Sbjct: 13  RVALVIQYVGTHFHGWQRQKQHRSVQEEIETAIATVLGYHLTLHGAGRTDSGVHAAAQVA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+      P      LN+YL     I I   + VD ++HARFSA  R Y Y I T + P
Sbjct: 73  HFEATGLIPPHRWASILNSYL--PQDILIKASAAVDNRWHARFSAAYRRYRYTIYTEERP 130

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W      LD   ++ A + L+G+H    F     + S     +   + +  G
Sbjct: 131 NLFVRPFSWHYYYAPLDECLIQAALEPLMGKHHLAAFHRAGSKRSHSWVEVQAAECHRSG 190

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A  FL+  +R  VG L  VG GK T     +  Q + R+E    APP+GL  
Sbjct: 191 PFLHIEIQANGFLYGMVRLLVGMLAQVGTGKLTLAGFTELWQEERREEVKYAAPPQGLCL 250

Query: 242 DSVEYS 247
             V Y 
Sbjct: 251 LRVGYP 256


>gi|221217465|ref|ZP_03588936.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 72a]
 gi|223889178|ref|ZP_03623767.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 64b]
 gi|225549711|ref|ZP_03770676.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 118a]
 gi|226321158|ref|ZP_03796699.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 29805]
 gi|221192743|gb|EEE18959.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 72a]
 gi|223885427|gb|EEF56528.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 64b]
 gi|225369671|gb|EEG99119.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 118a]
 gi|226233450|gb|EEH32190.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 29805]
          Length = 246

 Score =  260 bits (666), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDIKINIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

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


>gi|48374280|gb|AAT41969.1| putative t-RNA pseudouridine synthase I [Fremyella diplosiphon
           Fd33]
          Length = 268

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 86/243 (35%), Positives = 122/243 (50%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+I+Y G+ + GWQRQK   ++Q  IE AI  + G  V +HGAGRTD+GVHA  QVAHF+
Sbjct: 1   MVIQYLGTHFHGWQRQKQQRTVQEEIETAIAKILGYHVTLHGAGRTDAGVHAAAQVAHFE 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P      LN+YL   + I I   + V  ++HARFSA  R Y Y I T   P   
Sbjct: 61  ATGLIPPHKWAAVLNSYL--PNDILIRASAGVGNRWHARFSAAYRRYRYTIYTEDQPNLF 118

Query: 126 EKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
            +  +W      LD   ++ A + L+G+H    F     + S     +   + +  G LI
Sbjct: 119 VRPFSWHYYYAPLDESLIKAALKPLLGKHHLAAFHRAGSKRSHSWVEVQAAECHRSGPLI 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG L  VG G+ T  +  +  +A+ R+E    AP +GL    V
Sbjct: 179 HIEIQADGFLYGMVRLLVGMLVQVGTGQRTLANFTELWKAERREEVKYAAPAQGLCLLRV 238

Query: 245 EYS 247
            Y 
Sbjct: 239 GYP 241


>gi|160878286|ref|YP_001557254.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
 gi|160426952|gb|ABX40515.1| tRNA pseudouridine synthase A [Clostridium phytofermentans ISDg]
          Length = 264

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/255 (32%), Positives = 123/255 (48%), Gaps = 11/255 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK----NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
               +II Y+G+ Y GWQR         SIQG +E+ +  V  E + + G+GRTD+GVHA
Sbjct: 9   RNIKLIISYDGTNYSGWQRIPKAANGDHSIQGLLEEFLSKVLLEPIKLIGSGRTDTGVHA 68

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QVA+F         I+ + +N  L   + I IL  + VD  FH+RF A+ + Y Y I 
Sbjct: 69  LGQVANFYSRSNLDVNIIRQKMNQVL--PEDIKILQANEVDLNFHSRFDAVEKIYQYIID 126

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T++      +  ++   K LD E MR AA+ L+G  D+ +F +      S IRTI    +
Sbjct: 127 TKERESVFFRKYSYSCGKDLDIEAMRQAAKLLIGTMDYKSFCTDRKDGKSTIRTISEITI 186

Query: 178 -----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                N     I        FLH  IR   G+L  VG  + +   + +A+  + R+  G 
Sbjct: 187 EELRQNRNQQGIIFTFRGNGFLHHMIRIISGTLLEVGTQERSVESVRQAILGKKREYAGI 246

Query: 233 LAPPEGLYFDSVEYS 247
              P+GL+   V Y 
Sbjct: 247 TLYPQGLFLKQVIYD 261


>gi|300867109|ref|ZP_07111775.1| tRNA pseudouridine synthase A [Oscillatoria sp. PCC 6506]
 gi|300334864|emb|CBN56941.1| tRNA pseudouridine synthase A [Oscillatoria sp. PCC 6506]
          Length = 265

 Score =  260 bits (665), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 109/248 (43%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++I+Y G+   GWQRQ +  ++Q  IE  I  V    V +HGAGRTDSGVHA  Q
Sbjct: 1   MQRIALVIQYIGTDLHGWQRQPHQRTVQEEIETTISTVLQRPVTLHGAGRTDSGVHAAAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD             LN+ L     I I   + V+  +HARFSA  R Y Y + T  
Sbjct: 61  VAHFDAEGPVPAHRWQDILNSRL--PKDILIRASAKVEPTWHARFSATWRRYRYTLYTDP 118

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +  AW      LD   ++ A   L+GR     F             +   +   
Sbjct: 119 VPNLFVRPFAWHYYHAPLDESLIQAALTPLIGRFHLAAFHRAGSSRPHSWVDVQVAECQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG  I I V A  FL+  +R  VG L  VG G+ +  + +     + R+     AP  GL
Sbjct: 179 FGPFIHIEVQASGFLYGMMRLLVGLLVQVGRGERSLENFKDIWVQERREMVKYSAPAHGL 238

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 239 CLLRVGYP 246


>gi|313903119|ref|ZP_07836513.1| tRNA pseudouridine synthase A [Thermaerobacter subterraneus DSM
           13965]
 gi|313466621|gb|EFR62141.1| tRNA pseudouridine synthase A [Thermaerobacter subterraneus DSM
           13965]
          Length = 345

 Score =  260 bits (665), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 79/244 (32%), Positives = 120/244 (49%), Gaps = 2/244 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
              ++ Y+G+ + GWQRQ    ++Q  +E+A+  + G  V V  AGRTD+GVHA  QV H
Sbjct: 85  LRAVLAYDGTDFAGWQRQAGRRTVQQVVEEALSRLLGHPVRVTAAGRTDAGVHARAQVIH 144

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           +   R +    L  AL   L     ++ +        FHAR++A R++Y+Y +       
Sbjct: 145 WQTARPFPAERLVPALRGLL--PLDVAAVAAGEAPAGFHARYAARRKTYVYHLWRAPVAD 202

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
            L +   W +P +LD   M  AA+ L GRHDF  F++      +  RT+    +   G L
Sbjct: 203 PLHRRWQWHLPLALDVAAMAEAARRLEGRHDFAAFKAAGSPVRNTRRTLYRCRLEEHGPL 262

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + I + A  FL    R  VG+L  +G G+W +  ++  L    R+  GP AP  GL    
Sbjct: 263 LRIVLEADGFLMHMARGIVGTLVEIGRGRWPAGHVDMLLATGRRQLAGPTAPAHGLVLWR 322

Query: 244 VEYS 247
           VEY 
Sbjct: 323 VEYD 326


>gi|257452870|ref|ZP_05618169.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|317059412|ref|ZP_07923897.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|313685088|gb|EFS21923.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
          Length = 251

 Score =  260 bits (665), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 88/252 (34%), Positives = 128/252 (50%), Gaps = 11/252 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIFLV---TGEIVVVHGAGRTDSG 54
           +     IEY G+ Y GWQR    Q+   +IQG IE+ +  +     E V V  +GRTD+G
Sbjct: 4   VNLRFSIEYEGTRYLGWQRLGEKQRE-KTIQGKIEQVLARLFALNPEEVSVIASGRTDAG 62

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  Q+A+  L     P  + +  N YL   + I I +   V++ FH+RF A  + Y Y
Sbjct: 63  VHAKEQIANVHLPSGKSPQEIEEYCNQYL--PEDIRIFHAHFVEELFHSRFHAKTKEYHY 120

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I  ++ P    +   W  P  LD E M+ ++Q+ +G HDF  F S+     S IR ID 
Sbjct: 121 EISLQK-PSVFHRNVTWYCPMQLDIEKMKESSQYFLGEHDFIAFSSLKKTKKSTIRRIDR 179

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++    + +  R V   FL   IR  VG+L  VG+GK T  D+    Q++ R++ G LA
Sbjct: 180 IEIQETESGLLFRFVGNGFLQNMIRILVGTLIEVGEGKKTKEDIISIFQSKTRQKAGFLA 239

Query: 235 PPEGLYFDSVEY 246
           P +GL    V Y
Sbjct: 240 PAKGLTLYKVYY 251


>gi|229496121|ref|ZP_04389842.1| tRNA pseudouridine synthase A [Porphyromonas endodontalis ATCC
           35406]
 gi|229316952|gb|EEN82864.1| tRNA pseudouridine synthase A [Porphyromonas endodontalis ATCC
           35406]
          Length = 264

 Score =  260 bits (665), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 87/251 (34%), Positives = 125/251 (49%), Gaps = 8/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + I ++GS Y GWQRQ NG ++Q  IE+A+ L+    + + GAGRTD+GV+A   
Sbjct: 1   MPRYFLDIAFDGSSYCGWQRQPNGLAVQQVIEEALSLLFRTPISIVGAGRTDAGVNAYSL 60

Query: 61  VAHFDLVREW--VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            AH D+       P    K+LN  L     I+I ++  V    HARF AI R YLY I  
Sbjct: 61  PAHVDIPETAKGTPYRWRKSLNGIL--PHNINIRSIRPVQPSAHARFDAISRRYLYFI-- 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +     +    D E M  AAQ+L+G HDFT+F  +H    + I TI     +
Sbjct: 117 AEERDPFNRQWVLPVRPFPDIEKMNQAAQYLLGTHDFTSFSRLHTDTHTNICTIQEAFWS 176

Query: 179 S--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              + +  +  + A  FL   +R+ VG+L  VG       D+ + ++AQDR   G     
Sbjct: 177 PSSYPSTWQFSITANRFLRNMVRAIVGTLLEVGASTLAPEDIIEIIRAQDRNRAGASVRG 236

Query: 237 EGLYFDSVEYS 247
           E L+   VEY 
Sbjct: 237 EALFLAHVEYP 247


>gi|312149333|gb|ADQ29404.1| tRNA pseudouridine synthase A [Borrelia burgdorferi N40]
          Length = 246

 Score =  260 bits (665), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 124/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDIKINIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L   N+   A+ L+G HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLSISNLNQMAKTLIGNHDFTTFSCIKDKSKSKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

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


>gi|313905811|ref|ZP_07839169.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
 gi|313469325|gb|EFR64669.1| tRNA pseudouridine synthase A [Eubacterium cellulosolvens 6]
          Length = 252

 Score =  260 bits (665), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 79/251 (31%), Positives = 122/251 (48%), Gaps = 9/251 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG----EIVVVHGAGRTDSGVHA 57
            Y M I Y+G+ +FGW+ Q     +IQG +E  +  + G    + V V GAGRTD+GVHA
Sbjct: 4   NYKMKISYDGTRFFGWEHQPKQEMTIQGKLETVLSRMVGAPEDQPVTVIGAGRTDAGVHA 63

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              +A+  L        +   +N YL   + IS+  L +   +FH+RF A  ++Y Y   
Sbjct: 64  KEMIANVLLDTRMSEEEIQTYMNRYL--PEDISVNELKVCADRFHSRFKAKGKTYCYSFW 121

Query: 118 --TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                     ++    ++ K  + + MR AA+ +VG  DF +F        S +R +D  
Sbjct: 122 YADGGVRPTFDRKYVTVLDKRPNVDRMRKAAEEIVGMRDFKSFCGNSHMKKSTVRLVDSI 181

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +    G  I I +    FL   +R   G+L  VG GK T   + + ++A+DRK  GP AP
Sbjct: 182 EFKIRGPYIRIYIHGSGFLQNMVRIIAGTLLEVGYGKRTPESIAELIEARDRKLAGPTAP 241

Query: 236 PEGLYFDSVEY 246
            +GL    V+Y
Sbjct: 242 AQGLCLIKVDY 252


>gi|313897268|ref|ZP_07830812.1| tRNA pseudouridine synthase A [Clostridium sp. HGF2]
 gi|312957989|gb|EFR39613.1| tRNA pseudouridine synthase A [Clostridium sp. HGF2]
          Length = 252

 Score =  260 bits (665), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 120/247 (48%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQRQ N  SIQ  IE A+  + G  + +  +GRTD+ VHAL Q
Sbjct: 1   MPRYKVTLSYDGTAYGGWQRQTNTHSIQQEIEAAMEKIEGNFIRITASGRTDAHVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD  ++  P    +ALN+ L     I I ++ +V+  FHARF A+ + Y Y I T  
Sbjct: 61  VFHFDSAKDLAPENWRRALNSLL--PHDIRIQDVCLVEDDFHARFHAVSKRYDYLITTD- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDVNS 179
                         K LD + M   A+  +G HDFT+F S       S ++TI   D+  
Sbjct: 118 VNNPFYYHYMGKDRKVLDVKRMSECARVFLGTHDFTSFTSSKLDPRKSKVKTITRLDIVQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + +      FL   +R    +L   G  +    D+++ L  QD+  C   A  EGL
Sbjct: 178 EEHAVRLVFEGNGFLRYMVRMIAQTLIEAGKHRLDVADVKQMLYGQDKHLCRYKAQAEGL 237

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 238 YLVHVTY 244


>gi|311745793|ref|ZP_07719578.1| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
 gi|126575993|gb|EAZ80271.1| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
          Length = 252

 Score =  260 bits (664), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 88/245 (35%), Positives = 121/245 (49%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y G+ Y GWQ Q N  S+Q  IE A+       + V G+GRTD+GVHA  QV 
Sbjct: 6   RYFLELSYKGTKYHGWQIQNNAFSVQECIESALSTYFRSPITVMGSGRTDTGVHAKMQVC 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFDL  +       KA+N  L     ISI+++  V    HARF A+ RSY+YRII ++ P
Sbjct: 66  HFDLADDIDYGKFLKAINGIL--PIDISIMSIRQVTPNAHARFDAVSRSYVYRIIFQKNP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                G AW      D E M +AA+ L+   DF  F  +H +       I          
Sbjct: 124 --FLDGLAWHSYFIPDLEKMNLAAETLLKHDDFECFSKVHTEVKHFRCDIKSCSWEQKDG 181

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +   + A  FL   +R+ VG+L  VG GK    D+EK + ++DR   G  AP  GL+  
Sbjct: 182 ELLFHITANRFLRGMVRAIVGTLMEVGLGKKAPEDMEKIILSKDRSNAGKSAPARGLFLS 241

Query: 243 SVEYS 247
            + Y 
Sbjct: 242 RIIYP 246


>gi|270294324|ref|ZP_06200526.1| tRNA pseudouridine synthase A [Bacteroides sp. D20]
 gi|270275791|gb|EFA21651.1| tRNA pseudouridine synthase A [Bacteroides sp. D20]
          Length = 250

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 118/248 (47%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDSPLDTVFMTDKLNRLL--PPDISVYRLRAVKPDAHARFDATARMYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P    +     + ++ D E M  AAQ L    DFT+F  +H    +    I H      
Sbjct: 119 SP--FNRQYRCRLFQTPDFERMNEAAQTLFDYTDFTSFSKLHTDVKTNNCKIMHAAWTRV 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            ++     + A  FL   +R+ VG+L  VG GK +     + ++ +DR + G   P   L
Sbjct: 177 DDVTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVEGFRRVIEQKDRCQAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVAYP 244


>gi|332712143|ref|ZP_08432071.1| pseudouridylate synthase I [Lyngbya majuscula 3L]
 gi|332348949|gb|EGJ28561.1| pseudouridylate synthase I [Lyngbya majuscula 3L]
          Length = 277

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 114/247 (46%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ ++GWQRQ    S+Q  IE  +  V    + ++GAGRTD+GVHA  QV
Sbjct: 10  QRIALVIQYLGNNFYGWQRQPQHRSVQSEIETVLSSVQQRAITLYGAGRTDTGVHAAAQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+             LN+ L   + I +   ++V + +HARFSAI R Y Y I T   
Sbjct: 70  AHFNATGPIPAHRWAAILNSRL--PEDILVRASALVSQDWHARFSAIWRRYRYTIYTDAC 127

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +   W   +  LD   ++ A + L+G+H    F   +   S     +   +    
Sbjct: 128 PNLFVQPFCWHYYQAPLDESLIQAALKPLLGKHHLAAFHRSNSGRSHSWVNVQAAECYRN 187

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I + A  FL+  +R  VG L  VG GK T          Q R +    +P +GL 
Sbjct: 188 GPFIHIEIQANGFLYGMVRLLVGMLVQVGIGKLTPEQFTDIWVNQQRDKVKHASPAKGLC 247

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 248 LLRVGYP 254


>gi|160903290|ref|YP_001568871.1| tRNA pseudouridine synthase A [Petrotoga mobilis SJ95]
 gi|189030138|sp|A9BGW7|TRUA_PETMO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160360934|gb|ABX32548.1| tRNA pseudouridine synthase A [Petrotoga mobilis SJ95]
          Length = 245

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 82/243 (33%), Positives = 125/243 (51%), Gaps = 5/243 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      + Y+GS ++G+Q Q    ++Q   EKA+ ++  + +  +  GRTD+GVHA+ Q
Sbjct: 1   MKWVAATVMYDGSNFYGYQSQPTFRTVQDEFEKALKVIFKKEIPSYACGRTDTGVHAVGQ 60

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V  F +         +  ALNA L   + + +  +  V + F+ R  A +R Y Y I   
Sbjct: 61  VISFKVENENMTEKNIKDALNAIL--PEDVYVKEVKEVKEGFNPRAEAKKRIYHYFIYIS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P    + R W IP +L+ E MR AA++  G HDFT+F        +PIRTI    +  
Sbjct: 119 EDPNIFLRDRVWWIPFALNLEKMRQAAKYFEGEHDFTSF-KTGNDERNPIRTIYRVRIIE 177

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +LI IRV  +SFL   +R+ VGSL  VG   W    +++ L+A+ R      AP +G
Sbjct: 178 LRKDLILIRVEGKSFLKRMVRNIVGSLVKVGTDVWEVEKIQEILEAKKRALAPASAPAQG 237

Query: 239 LYF 241
           LYF
Sbjct: 238 LYF 240


>gi|160891004|ref|ZP_02072007.1| hypothetical protein BACUNI_03451 [Bacteroides uniformis ATCC 8492]
 gi|317480950|ref|ZP_07940030.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_1_36]
 gi|156859225|gb|EDO52656.1| hypothetical protein BACUNI_03451 [Bacteroides uniformis ATCC 8492]
 gi|316902843|gb|EFV24717.1| tRNA pseudouridine synthase A [Bacteroides sp. 4_1_36]
          Length = 250

 Score =  259 bits (663), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 117/248 (47%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDSPLDTVFMTDKLNRLL--PPDISVYRLRAVKPDAHARFDATARMYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +     + ++ D E M  AAQ L    DFT+F  +H    +    I H      
Sbjct: 119 MP--FNRQYRCRLFQTPDFERMNEAAQTLFDYTDFTSFSKLHTDVKTNNCKIMHAAWTRV 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            ++     + A  FL   +R+ VG+L  VG GK +     + ++ +DR + G   P   L
Sbjct: 177 DDVTWVFTIQADRFLRNMVRAIVGTLLEVGRGKLSVESFRRVIEQKDRCQAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVAYP 244


>gi|332886051|gb|EGK06295.1| tRNA pseudouridine synthase A [Dysgonomonas mossii DSM 22836]
          Length = 250

 Score =  259 bits (663), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  Y GWQ Q NG S+Q +IEKA+  +    + + GAGRTD+GVHA   
Sbjct: 1   MRRYFIYLAYNGENYCGWQIQPNGVSVQEAIEKALTTLLRTPIAIVGAGRTDAGVHARMM 60

Query: 61  VAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            AHFD         +L K LN+ L     ISI N+  V    HARF A  R Y Y I T 
Sbjct: 61  AAHFDYEAANLDLPLLAKKLNSIL--PKDISIYNIVEVKPDAHARFDATSRLYRYYITTE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +          + +  +LD + M   A  L    DFT+F  +H    +   TI       
Sbjct: 119 K--DPFLYHLKYKVHGNLDIDKMNACADILFEYEDFTSFSKLHTDVKTNNCTILAAQWEK 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN     + A  FL   +RS VG+L   G GK  S ++ + ++A++R E G   P   L
Sbjct: 177 KGNDYIFTIKANRFLRNMVRSIVGTLLEAGKGKIDSGEMRRIIEAKNRGEAGISVPGHAL 236

Query: 240 YFDSVEYS 247
           + + +EY+
Sbjct: 237 FLEEIEYN 244


>gi|332877177|ref|ZP_08444927.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332684920|gb|EGJ57767.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 268

 Score =  259 bits (663), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/254 (31%), Positives = 114/254 (44%), Gaps = 11/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  ++KA+  +  + V + GAGRTD+GVHA   
Sbjct: 1   MQRYFLYLAYDGTNYHGWQIQPNGISVQEVLQKALATLLRQPVSITGAGRTDTGVHARMM 60

Query: 61  VAHFDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAHFD        R      L   LN  L     ISI     V    HARF A+ R+Y Y
Sbjct: 61  VAHFDFEYADDPVRRIDGRWLTDKLNRLL--PPDISIYKTVPVAADAHARFDALSRTYHY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +   ++P    +  +  + + LD E M  AA  L    DFT+F  ++    +    I  
Sbjct: 119 YLHFGKSP--FLRAYSCRLYRMLDFEKMNEAAAALFDYTDFTSFSKVNTDTKTNNCRIMQ 176

Query: 175 FDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                         + A  FL   +R+ VG+L  VG GK T       ++ +DR   G  
Sbjct: 177 ARWTELAPGEWRFEIQADRFLRNMVRAIVGTLVEVGRGKLTPEGFRAVIEGKDRCRAGES 236

Query: 234 APPEGLYFDSVEYS 247
            P   L+   V Y 
Sbjct: 237 MPGNALFLVDVAYP 250


>gi|282879881|ref|ZP_06288608.1| tRNA pseudouridine synthase A [Prevotella timonensis CRIS 5C-B1]
 gi|281306275|gb|EFA98308.1| tRNA pseudouridine synthase A [Prevotella timonensis CRIS 5C-B1]
          Length = 243

 Score =  259 bits (663), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 120/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ+Q N  S+Q  ++KA+  +  E +VV GAGRTD+GVHA + 
Sbjct: 1   MQRYFIYFSYDGTSYHGWQQQPNSHSVQAELQKALSTILREPIVVVGAGRTDTGVHARKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+        L   LN  L     IS+  +  V    HARFSA  R+Y Y + + +
Sbjct: 61  VAHFDIEAVIDGEQLAYKLNRLL--PRDISVAGVKPVQADMHARFSAKWRTYHYYVHSHK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +  +P  LD   M  AA HL+   DF  F   H    + +  +   +    
Sbjct: 119 NP--FLRHYSCQLPFQLDYPLMNQAANHLLSVTDFGAFCKTHTDVKTTLCEVVRAEWVQT 176

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G +     + A  FL   +R+ VG+L  VG  + T    +  +++ +R   G   P   L
Sbjct: 177 GEDSWYFVIKANRFLRNMVRAVVGTLIEVGRHRMTLEQFDAVIRSGNRSNAGESMPAHAL 236

Query: 240 YFDSVEY 246
           + + +EY
Sbjct: 237 FLEEIEY 243


>gi|158334430|ref|YP_001515602.1| tRNA pseudouridine synthase A [Acaryochloris marina MBIC11017]
 gi|158304671|gb|ABW26288.1| tRNA pseudouridine synthase A [Acaryochloris marina MBIC11017]
          Length = 292

 Score =  259 bits (663), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/255 (32%), Positives = 111/255 (43%), Gaps = 11/255 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ + GWQRQ    S+Q  IE  +  +    V +HGAGRTDSGVHA  QV
Sbjct: 9   QRVALVIQYLGTHFHGWQRQPQHRSVQADIEDTLAEIVQHPVTLHGAGRTDSGVHAAAQV 68

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+            LNA L     I I   ++V   +HARFSA  R Y Y + T   
Sbjct: 69  AHFDVESPIPAHRWASVLNARL--PQDILIRGSALVPSDWHARFSATWRRYRYTLYTDPC 126

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +  +W      LD + M+ A   L+GRH    F             +        
Sbjct: 127 PNLFLRPYSWHYYYQPLDVQRMQAALDPLIGRHHLAAFHRAGSSRPHSWVDVHEATCVQR 186

Query: 181 G--------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                     LI+I V A  FL+  +R  VG L  VG G  +     +  QA+ R +   
Sbjct: 187 PTVEAKDSSPLIQIEVQASGFLYGMMRLLVGLLVQVGRGLRSPDSFTELWQAERRDQVKY 246

Query: 233 LAPPEGLYFDSVEYS 247
            AP +GL    V Y 
Sbjct: 247 SAPAKGLCLLRVGYP 261


>gi|325279339|ref|YP_004251881.1| tRNA pseudouridine synthase A [Odoribacter splanchnicus DSM 20712]
 gi|324311148|gb|ADY31701.1| tRNA pseudouridine synthase A [Odoribacter splanchnicus DSM 20712]
          Length = 245

 Score =  259 bits (663), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 119/248 (47%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY + + YNGS Y GWQ Q   SS+Q  I +A+  +  + + V GAGRTD+GVHA   
Sbjct: 1   MVRYFIELAYNGSRYHGWQIQPGASSVQEEINRALSTLLRQDIYVVGAGRTDTGVHASFF 60

Query: 61  VAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAHFD+  E   P  +   LN  L     I+I  +  V    HARFSAI R+Y Y I   
Sbjct: 61  VAHFDIECELPEPQQVVYKLNGLL--DKDIAIYKIYRVPMDKHARFSAISRTYKYYI--D 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +         AW      D + M  A + L    DFT+F  +H    +    I       
Sbjct: 117 KTKDPFTYPFAWKAYPLPDIQTMNEACRVLFDYTDFTSFSKLHTDVKTNNCIIYEAQWEE 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +   V A  FL   +R+ VG+L  VG GK T  D+ K +++++R   G   P + L
Sbjct: 177 TDKQLIFTVKANRFLRNMVRAIVGTLIDVGRGKLTPEDVRKIIESKNRCNAGTSVPAQAL 236

Query: 240 YFDSVEYS 247
           +   +EY 
Sbjct: 237 FLCHIEYP 244


>gi|193214164|ref|YP_001995363.1| tRNA pseudouridine synthase A [Chloroherpeton thalassium ATCC
           35110]
 gi|193087641|gb|ACF12916.1| tRNA pseudouridine synthase A [Chloroherpeton thalassium ATCC
           35110]
          Length = 265

 Score =  259 bits (663), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 122/248 (49%), Gaps = 7/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
               M++EY+G+ + GWQRQ    +  +IQG IE  +  V  E V +  AGRTD+GVHA 
Sbjct: 19  RNLKMLLEYDGTDFAGWQRQPQNLHQKTIQGEIESVLCRVLQEPVELIAAGRTDAGVHAK 78

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVA+F          L  ALN  L     I I+ +    + F+ARF A  R+Y Y ++T
Sbjct: 79  AQVANFLTENSLSISRLKHALNGLL--PSQIKIIEIEDAPENFNARFDAKSRTYRYFLLT 136

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R    AL      +     D   M    Q ++G+HDFT+F     Q  + I TI+     
Sbjct: 137 RY--SALLSRFTGIYRYDFDARAMNACCQEILGQHDFTSFSKAGSQTKTRICTIEKARWY 194

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              N + + + A  FLH+ +R  VG++  VG+G+ +  D +    A+D       A P+G
Sbjct: 195 QRKNGLMLEIRANRFLHSMVRLLVGTMIKVGNGELSVQDFDAIFSAKDVCLAATSAQPQG 254

Query: 239 LYFDSVEY 246
           L+   VEY
Sbjct: 255 LFLWHVEY 262


>gi|228473082|ref|ZP_04057839.1| tRNA pseudouridine synthase A [Capnocytophaga gingivalis ATCC
           33624]
 gi|228275664|gb|EEK14441.1| tRNA pseudouridine synthase A [Capnocytophaga gingivalis ATCC
           33624]
          Length = 240

 Score =  259 bits (662), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/245 (31%), Positives = 125/245 (51%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQRQ +  S+Q  +E+A+ ++  + + + GAGRTD+GVHA    
Sbjct: 1   MRYFIQLSYNGKNYCGWQRQPHSPSVQEELEEAMSMLLKKEIALVGAGRTDTGVHARDYY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD      P  L + LN++L     I+I  +  V    HARF A  R+Y Y I   + 
Sbjct: 61  AHFDSDSSL-PDRLVEKLNSFL--PKEIAIKQIFPVKNDAHARFDACSRTYQYFIALEKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E+  ++ I   LD   M  A + L+   DF  F  ++    +    +        G
Sbjct: 118 PFLYEQ--SYYIHFPLDLSLMNKAGEILLQHTDFQCFSKVNTDVKTYNCQLKEAYWRKEG 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           NL+  R+ A  FL   +R+ VG++  +G G+ +  DL++ L ++DR + G   P   L+ 
Sbjct: 176 NLLIFRITADRFLRNMVRAIVGTMIEIGRGRLSLEDLQQILLSKDRSKAGYSVPGHALFL 235

Query: 242 DSVEY 246
           + + Y
Sbjct: 236 EEIIY 240


>gi|126697063|ref|YP_001091949.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9301]
 gi|166228747|sp|A3PF23|TRUA_PROM0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|126544106|gb|ABO18348.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9301]
          Length = 268

 Score =  259 bits (662), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  ++++Y+GS Y GWQ+QKN +++Q  +++A+  +T   V    AGRTD+GVHA  Q
Sbjct: 1   MKRVALLVQYDGSHYSGWQKQKNATTVQEILDRALLKITNHTVQTFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D+            LN+ L    +I IL    V   +HA +SA+ R Y Y I   +
Sbjct: 61  VVHCDVDCVVPGNSYSDVLNSLL--PSSIRILESIEVKDSWHACYSALYRHYRYVINNSK 118

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD   M  A++ ++G HDF  F+      ++ I  I + D+  
Sbjct: 119 FPNLFIDNWSWHRYQKVLDEVLMLNASRQMIGEHDFFAFQKTGSNRTNSITKIKNIDIKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI + + A  FL+  +R  +G L LVG+ K +          + + +    AP +GL
Sbjct: 179 VEDLIFVDIKATGFLYGMVRLIIGQLVLVGENKISPEIFTDRWVNKKKNDVKESAPAKGL 238

Query: 240 YFDSVEYS 247
            F +  Y 
Sbjct: 239 CFVNAVYE 246


>gi|219849858|ref|YP_002464291.1| tRNA pseudouridine synthase ACD [Chloroflexus aggregans DSM 9485]
 gi|254789611|sp|B8G6P6|TRUA_CHLAD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219544117|gb|ACL25855.1| tRNA pseudouridine synthase A [Chloroflexus aggregans DSM 9485]
          Length = 278

 Score =  259 bits (662), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 123/251 (49%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++ Y+G+ + G Q Q +  ++QG+IE A   +T E   +  AGRTD+GVHA  Q
Sbjct: 1   MRTIALLLAYDGTDFAGSQWQTDIRTVQGAIEAAWEALTQEQRRIVLAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH           + + LNA+L     +++ N+    + FHAR+SAI R Y Y I    
Sbjct: 61  VAHVQTATRHSLATIWRGLNAHL--PTDVTVQNVGEAVRDFHARYSAIEREYRYLIDCAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            PL   + +A     +LD   M  A + L G HDF  F +      S +RT+    +   
Sbjct: 119 VPLPQLRHQALHYAGTLDVTAMATALKLLEGTHDFAAFTTATPSQRSTVRTMYWTRIVER 178

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 L+ I + A +FL   +R  VG+L LVG G+ T     + L  +DR+  GP AP 
Sbjct: 179 VWFDRRLLAIELAANAFLQHMVRMIVGTLLLVGRGRMTVDQFGEVLAGRDRRLAGPTAPA 238

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 239 HGLTLTAVRYP 249


>gi|332664422|ref|YP_004447210.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
 gi|332333236|gb|AEE50337.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
          Length = 256

 Score =  259 bits (662), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 135/248 (54%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M ++ + +EY+GS + GWQ Q++  SIQG + KA  +V   + V V+G+GRTD+GVHAL 
Sbjct: 1   MAKFKLTLEYDGSRFKGWQVQEDARSIQGQLIKAAKIVFETDKVEVYGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH  +  +    ++ + LN  L     I++L++  V  +FHAR  A+ RSY+Y+I  R
Sbjct: 61  QVAHLAVDTKMPVKMIRQKLNDQLT--HDINVLSVDPVSDKFHARHDAVARSYVYQISRR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               A  K   W +   LD E M +AA HL+G HDF +F +      S    + H  V  
Sbjct: 119 --RNAFGKHFMWWVKDPLDVERMNVAAAHLIGMHDFKSFSNEKGTEKSSKVELQHLKVVE 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + + ++A  FL   +R  VGSL  VG G+      ++ L+   ++     APP GL
Sbjct: 177 KGDKVVVHIIASHFLWKMVRRVVGSLVEVGAGRLDPDKFKEWLEKPSQEPAKFTAPPAGL 236

Query: 240 YFDSVEYS 247
           + + V + 
Sbjct: 237 FLERVYFP 244


>gi|254495151|ref|ZP_05108075.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
 gi|85819501|gb|EAQ40658.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
          Length = 241

 Score =  259 bits (662), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/246 (30%), Positives = 122/246 (49%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQ Q +  S+Q  +  A+  +  + + V GAGRTD+GVHA +  
Sbjct: 1   MRYFIELSYNGKNYHGWQIQPDVISVQEKLNSALSTIFQQDIQVVGAGRTDTGVHASQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+ +          LN+ L     I +  + +VD + HARF A+ RSY Y+I   + 
Sbjct: 61  AHFDVDKNLKGD-FAFKLNSIL--PKDIVVYKVFLVDDEKHARFDAVSRSYEYKIWLGRN 117

Query: 122 PLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P  L+   +W I  +  D + M  AA+ L    DF TF  +  +  +    +        
Sbjct: 118 PFLLD--FSWQIHSQKPDLKLMNEAAKLLTEYTDFQTFSKVKTEVYTFNCDVTEAFWEQK 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +   + A  FL   +R+ VG+L  VG GK +  D    +++++R   G   P +GL+
Sbjct: 176 GEELTFHISANRFLRNMVRAIVGTLLDVGFGKISIDDFRNIIESKNRGNAGLSVPAKGLF 235

Query: 241 FDSVEY 246
              ++Y
Sbjct: 236 LTQIKY 241


>gi|281355314|ref|ZP_06241808.1| tRNA pseudouridine synthase A [Victivallis vadensis ATCC BAA-548]
 gi|281318194|gb|EFB02214.1| tRNA pseudouridine synthase A [Victivallis vadensis ATCC BAA-548]
          Length = 272

 Score =  258 bits (661), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 74/247 (29%), Positives = 119/247 (48%), Gaps = 6/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQV 61
           RY + I Y+G+ Y GWQ Q +  ++Q  +++ +  +  G+ + + G+ RTD+GVHA R  
Sbjct: 13  RYLLEIAYDGTNYSGWQIQPHRVAVQQRVQEILTKMYNGQPIHLIGSSRTDAGVHAQRFA 72

Query: 62  AHFDLVRE--WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           A +            + +A+N  L     I +  +  V  +FHAR+ A+ ++Y Y +   
Sbjct: 73  ASYLTPVRPDIPTDKILRAVNRQL--PGDIKLRTVREVPLEFHARYDALGKAYTYVLNLG 130

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P        W     +D E +R A+Q L G HD+++F          +RTI   DV  
Sbjct: 131 D-PSPFTDRYTWRPIHRMDVEKIRAASQVLTGTHDYSSFVVERSLIDEAVRTIYRIDVQE 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG    +  V   FL+  IR  +G+L+  G GK +   + + L+A DR      APP GL
Sbjct: 190 FGQFCCVTFVGNGFLYKMIRCLMGTLEAAGAGKLSPEAVRRILEACDRTVAPETAPPNGL 249

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 250 FLMKVFY 256


>gi|225549204|ref|ZP_03770177.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 94a]
 gi|225370062|gb|EEG99502.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 94a]
 gi|312148421|gb|ADQ31080.1| tRNA pseudouridine synthase A [Borrelia burgdorferi JD1]
          Length = 246

 Score =  258 bits (661), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  +   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDIKINIQLNNLKKALNAIL-LKNSIKILKLRYIKNSFHPRFSAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L   N+   A+ L+G+HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

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


>gi|206901950|ref|YP_002250733.1| tRNA pseudouridine synthase A [Dictyoglomus thermophilum H-6-12]
 gi|238057728|sp|B5YDX5|TRUA_DICT6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|206741053|gb|ACI20111.1| tRNA pseudouridine synthase A [Dictyoglomus thermophilum H-6-12]
          Length = 245

 Score =  258 bits (661), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MI + + + Y G  ++G+Q+Q    ++QG +EK + L+  E + V GAGRTD+GVHAL Q
Sbjct: 1   MINWKVELSYIGKDFWGFQKQPGKRTVQGELEKVLKLLFDEDIKVIGAGRTDAGVHALGQ 60

Query: 61  VAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V +F     + +    L K LN  L     I I  + IVD  FHAR+SA RR Y+Y I  
Sbjct: 61  VVNFKTKESKNFSCDKLYKVLNKLL--PGDIKIKKVEIVDDNFHARYSAKRRWYIYVIYN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +      +   W I K LD + + ++A    G HDF  F  I     +    I      
Sbjct: 119 NEEKNLFLRDYCWWINKPLDKDLLNLSANLFKGIHDFRNFCVIE-NYDNTNVEIYESFWY 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+   V A  FL   +R  VGS+  VG  K    DLEK L+ +  +     AP  G
Sbjct: 178 FKEDLLIYFVSAPFFLRKMVRFIVGSMVEVGLKKKELEDLEKYLKDRKEERFSSPAPASG 237

Query: 239 LYFDSVEY 246
           LY   ++Y
Sbjct: 238 LYLFKIDY 245


>gi|86156809|ref|YP_463594.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773320|gb|ABC80157.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 264

 Score =  258 bits (661), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 87/244 (35%), Positives = 124/244 (50%), Gaps = 3/244 (1%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +      V  AGRTD+GVHA  QVA 
Sbjct: 23  VKLVLEYDGTAYVGWQVQPNGPSIQAEVERALATLHKAPRRVTAAGRTDAGVHARGQVAS 82

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F   R          +NA L     +++   S+    F AR SA  + Y Y I       
Sbjct: 83  FREDRPLPVKAYVMGMNAVL--PPDVAVRAASLEPDGFDARRSARGKRYRYVIENLPTRA 140

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSFGN 182
            L + +AW     L+  N+R AA HLVGRHDF  F++  C     +R +   +V    G 
Sbjct: 141 PLTRLQAWQHFHPLELANVREAAAHLVGRHDFAAFQAADCACEHAVREVRRLEVLGEAGG 200

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            IE+ + A +F+   +R+ VG+L  VG G+     +   L   DR E GP APP+GL+ +
Sbjct: 201 RIEVVIEATAFVKHMVRNIVGTLVEVGRGRRAPGSMLALLARGDRTEAGPTAPPQGLFLE 260

Query: 243 SVEY 246
            V Y
Sbjct: 261 EVFY 264


>gi|121611771|ref|YP_999578.1| tRNA pseudouridine synthase A [Verminephrobacter eiseniae EF01-2]
 gi|166229848|sp|A1WSF3|TRUA_VEREI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|121556411|gb|ABM60560.1| tRNA pseudouridine synthase A [Verminephrobacter eiseniae EF01-2]
          Length = 272

 Score =  258 bits (661), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 86/257 (33%), Positives = 127/257 (49%), Gaps = 14/257 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I YNG  Y GWQ Q +  ++Q ++E A+       V    AGRTD+GVH L QV
Sbjct: 1   MRMALGISYNGQAYCGWQSQPSVRTVQDALEAALGRFATHPVSTLCAGRTDAGVHGLMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  N +L     I++     V   FHAR SA+ R Y Y ++    
Sbjct: 61  VHFDTPLDRPAASWVRGTNGFL--PADIAVQWAQAVPDSFHARASALARRYAYVLLQSPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             ++E GR   +   LD + M+ AA +LVG HDF+ FR+  CQA SP++T+    ++  G
Sbjct: 119 RPSVESGRVGWVCHRLDHDAMQQAADYLVGEHDFSAFRASTCQAPSPVKTLRRIGISCRG 178

Query: 182 N------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                              VA +FLH  IR+ +G L  +G GK +   +++ L+A+ R  
Sbjct: 179 QSPPHPALGWSPCYWRFEFVANAFLHHMIRNIMGCLVAIGQGKQSPQWMQQLLRARSRAA 238

Query: 230 CGPLAPPEGLYFDSVEY 246
             P   P+GLYF    Y
Sbjct: 239 AAPTFAPDGLYFLGPVY 255


>gi|297623065|ref|YP_003704499.1| tRNA pseudouridine synthase A [Truepera radiovictrix DSM 17093]
 gi|297164245|gb|ADI13956.1| tRNA pseudouridine synthase A [Truepera radiovictrix DSM 17093]
          Length = 260

 Score =  258 bits (661), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 89/254 (35%), Positives = 132/254 (51%), Gaps = 11/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R  + +E++G+ +FGWQ Q        ++QG +E A+  + G     H AGRTD+GVH
Sbjct: 1   MRRIKLTLEFDGTDFFGWQVQAGAAHPVRTVQGVLEAALATLPGARPKAHAAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR- 115
           AL  VAH+D         +  ALNA L     + +L+   V + F A+FS   R YLYR 
Sbjct: 61  ALAMVAHYDTDDRIPVAKVPAALNARL--PPDVRVLHAEEVPRSFEAQFSCCYRRYLYRM 118

Query: 116 --IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
             +   +A  ALE+ R   +P +LD E M+ AA    G  DF    +   ++ + +RT+ 
Sbjct: 119 RLLRASRAGSALERRRVLFVPGALDLEAMQRAAPRFEGTRDFAALATQ--ESRTTVRTVY 176

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              + + G  + + + A  FL   +R+ VG+L  VG+GK    D+   L A+DR+  GP 
Sbjct: 177 RCRLGAAGPDLTLDIAADGFLRNMVRAVVGTLLWVGEGKLAPEDVSALLAARDRRRAGPN 236

Query: 234 APPEGLYFDSVEYS 247
           APP GLYF    Y 
Sbjct: 237 APPHGLYFAEAGYE 250


>gi|288924968|ref|ZP_06418904.1| tRNA pseudouridine synthase A [Prevotella buccae D17]
 gi|288338158|gb|EFC76508.1| tRNA pseudouridine synthase A [Prevotella buccae D17]
          Length = 261

 Score =  258 bits (661), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 85/258 (32%), Positives = 123/258 (47%), Gaps = 15/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  +EKA+ L+      + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLNYDGTNYHGWQIQPNGNSVQEELEKALSLLLRTKTEIVGAGRTDAGVHARLM 60

Query: 61  VAHFDLV----------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           VAHFD            ++     LC  LN  L     ISI  +  V +  HARFSA+ R
Sbjct: 61  VAHFDYEVGTTTEGQAAKDIDCPQLCYKLNRLL--PRDISIRKIIPVAQDMHARFSAVAR 118

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           +Y Y I T + P   E+  ++ +P +LD + MR   + L  + DF  F        S   
Sbjct: 119 TYHYYIHTGKMP--FERHYSYQMPYALDFDAMREGCELLKRQTDFAAFCKAGADNKSTCC 176

Query: 171 TIDHF-DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           T+     V +        + A  FL   +R+ VG+L  +G  K T       ++A  R +
Sbjct: 177 TVTEARWVKTSPGTWYFEITANRFLRNMVRAVVGTLVDLGRHKITLEQFRHIVEAGRRSD 236

Query: 230 CGPLAPPEGLYFDSVEYS 247
            G   P   L+ + VEY 
Sbjct: 237 AGESMPGHALFLERVEYP 254


>gi|298376183|ref|ZP_06986139.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_19]
 gi|298267220|gb|EFI08877.1| tRNA pseudouridine synthase A [Bacteroides sp. 3_1_19]
          Length = 265

 Score =  258 bits (660), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 120/247 (48%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + YNG  + GWQ Q NG ++Q SIE+A+ ++    V + GAGRTD+GVHA   +
Sbjct: 15  RRYFIYLGYNGKNFRGWQIQPNGMTVQQSIEEALAILMRTPVPIVGAGRTDAGVHAHLMI 74

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD        V L + LN  L     I++  +  V  + HARF A  R+Y Y + T++
Sbjct: 75  AHFDWEEPIGDLVFLAEKLNRLL--PKDIAVYKIVPVVPEAHARFDATSRTYKYYVTTKK 132

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                     + +P  LD E M  A + L    DFT+F  +H    +    I H      
Sbjct: 133 --DPFNHELVYKLPGRLDFEAMNEACKVLFDYIDFTSFSKLHTDVKTNNCHIQHAGWTQE 190

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++    + A  FL   +R+ VG+L  VG G+ T       ++A+DR + G   P   L+
Sbjct: 191 GDIWVFTIRADRFLRNMVRAIVGTLLEVGRGRLTIDGFRNVIEAKDRCKAGTSVPGHALF 250

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 251 LVDVTYP 257


>gi|293402539|ref|ZP_06646674.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291304053|gb|EFE45307.1| tRNA pseudouridine synthase A [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 251

 Score =  258 bits (660), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  ++ Y+GS Y GWQ+Q N +SIQ  IE+A+  +    V +  +GRTD+GVHA+ Q
Sbjct: 1   MARYKAVVSYDGSSYGGWQKQLNTTSIQEVIEQALAKMHKHDVAIVASGRTDAGVHAIAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       KALN+ L     I I ++  V + FHARF AI + Y Y I    
Sbjct: 61  VFHFDSEMKIQEKHWIKALNSLL--PKDIRIQSVKQVTEAFHARFDAIGKRYDYLISND- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNS 179
                ++         LD   M+  A  L+G HDFT+F S       P ++TI   +V  
Sbjct: 118 ILNPFKENYMAKDAHKLDVAYMQECATVLIGTHDFTSFTSNKIDPRKPRVKTITRLEVLQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + +      FL   +R    +L   G  + T  D++K L+A+D+  C   A P+GL
Sbjct: 178 EKDHVHMIFEGNGFLRYMVRMLSQTLIEAGKHRITKADIKKMLEAKDKHACRYKAVPQGL 237

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 238 YLVRVDY 244


>gi|120434790|ref|YP_860476.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
 gi|117576940|emb|CAL65409.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
          Length = 259

 Score =  258 bits (660), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 121/245 (49%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y G  Y GWQ Q N  S+Q  IEK +  V    + + GAGRTD+GVHA +  A
Sbjct: 13  RYFIELSYFGKAYHGWQIQPNSISVQEVIEKNLSKVLRSTIEIVGAGRTDAGVHAKQMFA 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+ R     +L   LN+ L     I+I ++  V+K  HARF A  RSY Y +I  +  
Sbjct: 73  HFDVDRVLDLELLKYKLNSML--PKDIAISDIFPVNKNVHARFDATSRSYEYHLIQEK-- 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  AW +   +  E M +AA  L G  +F  F        +    ID  +    GN
Sbjct: 129 DPFNRESAWFLKHEVKIEKMNMAAATLRGYTNFKCFSKSKTDVRTYNCRIDEAEWRMEGN 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           L+   + A  FL   +R+ VG+L  +G  K   + + + ++++DR + G   P  GLY  
Sbjct: 189 LMVFHITADRFLRNMVRAVVGTLIEIGQNKHPVSYMHEVIKSEDRGKAGASVPAHGLYLT 248

Query: 243 SVEYS 247
            ++Y 
Sbjct: 249 RIKYP 253


>gi|219685340|ref|ZP_03540159.1| tRNA pseudouridine synthase A [Borrelia garinii Far04]
 gi|219673113|gb|EED30133.1| tRNA pseudouridine synthase A [Borrelia garinii Far04]
          Length = 246

 Score =  258 bits (660), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y GS Y G+Q Q    +IQG IEKA+  +  + V +H +GRTD GVHA +Q
Sbjct: 1   MKKILAEIAYEGSIYHGFQIQPTKPTIQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALN+ L + ++I IL L  V   FH RF+A +R Y YRI+   
Sbjct: 61  IITFDININIQLNNLKKALNSIL-LKNSIKILKLKYVKNSFHPRFNAQKRKYSYRILNSN 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESVSTFETILKSKNRNLARTTAPANALF 239

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 240 LDKVYYE 246


>gi|307565293|ref|ZP_07627786.1| tRNA pseudouridine synthase A [Prevotella amnii CRIS 21A-A]
 gi|307345962|gb|EFN91306.1| tRNA pseudouridine synthase A [Prevotella amnii CRIS 21A-A]
          Length = 257

 Score =  258 bits (660), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 78/259 (30%), Positives = 125/259 (48%), Gaps = 17/259 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NGSS+Q ++EKA+ ++  + + + GAGRTD+GVHA   
Sbjct: 3   MQRYFITLSYDGNNYHGWQIQPNGSSVQETLEKALTILLRQPISIIGAGRTDTGVHARMM 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+  ++  + +   LN  L     IS+ ++  V    HARFSAI+R+Y Y +  ++
Sbjct: 63  VAHFDMKSKFDNMQISYRLNRLL--PHDISVSSIIPVSNDMHARFSAIKRTYHYYLHLQK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  +  +  +L+ + M  AA +L+G+ DF  F        + I  I        
Sbjct: 121 --DIYNRQYSCYVGYNLNFDLMNEAALYLIGKKDFKCFCKTGADVKTTICNITEAYWKPI 178

Query: 181 GNL-------------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                               + A  FL   +R+ VG+L  VG GK + T  +  +    R
Sbjct: 179 YPELSTLSSTDIKPTNWCFIISANRFLRNMVRAIVGTLIAVGRGKMSITKFKTIVDTGSR 238

Query: 228 KECGPLAPPEGLYFDSVEY 246
            + G   P   L+   +EY
Sbjct: 239 SDAGESMPGNALFLWDIEY 257


>gi|119952818|ref|YP_945027.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
 gi|254789604|sp|A1QYG5|TRUA_BORT9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119861589|gb|AAX17357.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
          Length = 245

 Score =  258 bits (659), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 122/247 (49%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y+G+Q Q    +IQG IEK +  ++   + +H AGRTD GVHA  Q
Sbjct: 1   MKKVLAKITYDGSLYYGFQIQPKKPTIQGEIEKVLEKISKTKIKIHSAGRTDKGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  F +        L  A+N+ LK  D I I+ L  V+ +F  RF A RR Y Y I+  +
Sbjct: 61  IISFYIKINIKLKNLKTAINSLLK--DDIRIIKLKYVEDKFQPRFDAKRRKYSYYILNNE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  RA+ + K L+   +   A+ L+G HDFTTF  I  Q +S ++ I +      
Sbjct: 119 NHYPWEGYRAYYVKKKLNINRLNEMAEMLIGIHDFTTFSCIRDQTNSKLKEIYYARFKKK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I   ++  SFL   +RS VG +  +          +K L +++RK     AP + L+
Sbjct: 179 NKFIIFEIIGSSFLWKMVRSIVGVMIDIEIKNEPVDTFKKILNSKNRKLTRKTAPAKALF 238

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 239 LDKVFYE 245


>gi|153007028|ref|YP_001381353.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. Fw109-5]
 gi|152030601|gb|ABS28369.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. Fw109-5]
          Length = 245

 Score =  258 bits (659), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 131/247 (53%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++EY+G+ Y GWQ Q NG SIQ  +E+A+  +  E   V  AGRTD+GVHA  Q
Sbjct: 1   MPVVKLVLEYDGTRYVGWQVQPNGPSIQAEVERALATLHKEPRRVTAAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   R        K +NA L   D +++   S+    F AR SA  + Y Y +   +
Sbjct: 61  VVSFPEARPLPLAAYVKGMNALL--PDEVAVRAASVEPDGFDARRSARGKRYRYVLENLE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
               L + +AW +  +LD   MR A++HL+GR DF  F++  C     +R +   DV   
Sbjct: 119 TRAPLSRLQAWQLFGALDVGAMREASRHLLGRQDFAAFQAADCACDHAVREVHRLDVLGE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +E+ V A +F+   +R+FVG+L  VG G+  + D+   + ++DR   G  APP+GL
Sbjct: 179 PSGRVELVVEATAFVKHMVRNFVGTLVEVGKGRRRAEDMPALVASRDRTRAGRTAPPQGL 238

Query: 240 YFDSVEY 246
           + + V Y
Sbjct: 239 FLEEVFY 245


>gi|171058363|ref|YP_001790712.1| tRNA pseudouridine synthase A [Leptothrix cholodnii SP-6]
 gi|170775808|gb|ACB33947.1| tRNA pseudouridine synthase A [Leptothrix cholodnii SP-6]
          Length = 262

 Score =  258 bits (659), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 122/246 (49%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y GS Y GWQ Q NG+++Q  +E A+       + V  AGRTD+GVHAL QV
Sbjct: 1   MRLALGLSYRGSAYRGWQSQTNGATVQDVLEAALCRFAATPIRVSCAGRTDAGVHALNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D  R+  P    +  N YL     +++     V   FHAR +A  R Y Y ++    
Sbjct: 61  VHLDTDRDREPFSWVRGTNTYL--PPDVAVQWCRPVPDAFHARNAARARRYAYVLLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+E G+   I + LD   M  +A  L+G HDF+ FRS  CQA SP++ +    +   G
Sbjct: 119 RPAMEAGQVGWIFRPLDQARMEASAALLIGEHDFSAFRSADCQALSPVKQMRTIRIGRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FLH  IR+ +G L  VG G      L   L ++DR+   P   P+GLYF
Sbjct: 179 PYWRFDFEASAFLHHMIRNLMGCLIAVGTGARDPAWLAGVLASRDRRLAAPTFSPDGLYF 238

Query: 242 DSVEYS 247
               Y 
Sbjct: 239 LGPRYD 244


>gi|317502836|ref|ZP_07960938.1| tRNA pseudouridine synthase A [Prevotella salivae DSM 15606]
 gi|315666051|gb|EFV05616.1| tRNA pseudouridine synthase A [Prevotella salivae DSM 15606]
          Length = 243

 Score =  258 bits (659), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG S+Q +++ A+  +  + V + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYFCYDGTAYHGWQIQPNGMSVQETLQNALSTILRQRVEIVGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL  E     L   LN  L     IS+ N+  VD   HARFSA  R+Y Y I TR+
Sbjct: 61  VAHLDLAEEIECEQLTYKLNRLL--PRDISVFNIQPVDSNMHARFSAKWRTYRYFIHTRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  ++  P  LD E M   A+ L    DF  F       ++ + TI        
Sbjct: 119 --DPFLRKYSYESPYLLDFELMEQGAELLKQHQDFAAFCKSGADNTTTLCTIKESKWVKT 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L L+G  + T  DLE+ L+  +R + G   P   L
Sbjct: 177 SPYSWYFEITANRFLRNMVRATVGTLILLGRHRITIKDLERILEEGNRSQAGESMPGHAL 236

Query: 240 YFDSVEY 246
           + +++EY
Sbjct: 237 FLENIEY 243


>gi|88801321|ref|ZP_01116849.1| tRNA pseudouridine synthase A [Polaribacter irgensii 23-P]
 gi|88781979|gb|EAR13156.1| tRNA pseudouridine synthase A [Polaribacter irgensii 23-P]
          Length = 241

 Score =  258 bits (659), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 123/246 (50%), Gaps = 6/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG+ Y GWQ Q +  S+Q  +  AI  V    V V GAGRTD+GVHA++  
Sbjct: 1   MRYFIELSYNGTKYHGWQIQPDMVSVQEKLNNAISTVLQSKVEVVGAGRTDTGVHAVQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+     +       LN+ L   + IS+  +  V +  HARF A  RSY YRI   + 
Sbjct: 61  AHFNTE-ILIENNFVHKLNSIL--PNDISVDKVLEVLEDKHARFDAKSRSYEYRIWLGRN 117

Query: 122 PLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P  L+   +W I  +  D   M  AA  L+   +F TF  +  +  +    +        
Sbjct: 118 PFLLD--FSWQIHSQKPDLSKMNAAAILLLEYENFQTFSKVKTEVHTFNCNVTAAFWRQE 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GNL+   + A  FL   +R+ VG+L  VG GK +  +  + +++++R   G   P +GL+
Sbjct: 176 GNLLIFHISANRFLRNMVRAIVGTLVDVGLGKISIAEFRQIIESKNRSNAGLSVPAKGLF 235

Query: 241 FDSVEY 246
              ++Y
Sbjct: 236 LTQIKY 241


>gi|325675475|ref|ZP_08155159.1| tRNA pseudouridine synthase A [Rhodococcus equi ATCC 33707]
 gi|325553446|gb|EGD23124.1| tRNA pseudouridine synthase A [Rhodococcus equi ATCC 33707]
          Length = 296

 Score =  257 bits (658), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 123/248 (49%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ    ++ G IE+ +  +    V++  AGRTD+GVHA  QV
Sbjct: 21  VRLRLDISYDGTDFSGWARQPGRRTVCGEIEEKLSAIVRTPVLLTVAGRTDAGVHASGQV 80

Query: 62  AHFDLVREWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH D+  + +P    + +      +   + +  +S   + F ARFSAIRR Y YR+ T  
Sbjct: 81  AHVDVPADMIPEEPSRLVRRLARFLPRDVRVKAVSFAPEHFDARFSAIRRHYEYRLTTAP 140

Query: 121 APL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L        PK +D + MR A+  L+G HDF  F     + ++ +R +  FD   
Sbjct: 141 YGAEPLRARDTVAWPKDVDVDAMRKASSRLLGLHDFAAFCKRR-EGATTVRELQRFDWEQ 199

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   V A +F  + +RS VG+   VG+G+ T   +   L  ++R     +AP  GL
Sbjct: 200 SGHELTAFVSADAFCWSMVRSLVGAALAVGEGRRTVEWMAGLLAERERASAVAVAPAHGL 259

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 260 SLIRVDYP 267


>gi|86609047|ref|YP_477809.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86557589|gb|ABD02546.1| tRNA pseudouridine synthase A [Synechococcus sp. JA-2-3B'a(2-13)]
          Length = 285

 Score =  257 bits (658), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 119/247 (48%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + I+Y GS ++GWQRQ    ++QG +E+AI    G  V ++GAGRTD+GVHA  QV
Sbjct: 4   RRIALRIQYLGSRFYGWQRQAARRTVQGVLEEAIASRAGHPVTLYGAGRTDTGVHAAGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD       V   + LN  L   + + +L  + V   +HARFSA  R Y Y I+ R+ 
Sbjct: 64  AHFDTTSGIPAVEWSRVLNDCL--PEDVVVLASAQVPDSWHARFSARWRRYRYLILNRER 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +  +W +   L  E M  A   L+G H    FR            +        G
Sbjct: 122 PDVFWRLFSWQVRWPLQVEPMAEALNSLLGEHSLEAFRRRGSDRPHSRVQVQEVLCQRLG 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE--CGPLAPPEGL 239
           +LI I V A  FL+  +R  VGSL++VG G+ +        Q  D  +      APP+GL
Sbjct: 182 DLISIEVQASGFLYRMMRLLVGSLEVVGRGQLSPAQFVHLWQHNDWSQMRTRYSAPPQGL 241

Query: 240 YFDSVEY 246
               V Y
Sbjct: 242 CLTDVGY 248


>gi|297159627|gb|ADI09339.1| tRNA pseudouridine synthase A [Streptomyces bingchenggensis BCW-1]
          Length = 292

 Score =  257 bits (658), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 80/254 (31%), Positives = 120/254 (47%), Gaps = 9/254 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVH 56
           +R  + + Y+G+ + GW +Q+      ++QG +E A+ +V    + V +  AGRTD+GVH
Sbjct: 10  VRVRLNLSYDGTDFSGWAKQRGRDTVRTVQGELESALKVVMRMQDPVELTVAGRTDAGVH 69

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           A  QVAH DL          K L     ++   I + ++      F+ARFSAI R Y+YR
Sbjct: 70  ARGQVAHVDLPEPIWAEHHEKLLRRLAGRLPHDIRVWSVGEAPPGFNARFSAIWRRYVYR 129

Query: 116 IITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           ++        L +G        LD + M  AAQ L+G HDF  +       ++ IRT+  
Sbjct: 130 VVDHPGGVDPLLRGHVLWHDWPLDVDAMNEAAQKLLGEHDFAAYCKKR-DGATTIRTLQR 188

Query: 175 FDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                  + +I   V A +F H  +RS VG+L  VGDG   +    K L A  R     +
Sbjct: 189 LSWERGPDGIITATVRADAFCHNMVRSLVGALLFVGDGHRPADWPAKVLAAGVRDSAVHV 248

Query: 234 APPEGLYFDSVEYS 247
             P GL  + V Y 
Sbjct: 249 VRPHGLTLEQVGYP 262


>gi|223984957|ref|ZP_03635058.1| hypothetical protein HOLDEFILI_02362 [Holdemania filiformis DSM
           12042]
 gi|223963077|gb|EEF67488.1| hypothetical protein HOLDEFILI_02362 [Holdemania filiformis DSM
           12042]
          Length = 268

 Score =  257 bits (658), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 131/249 (52%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R+  ++ Y+G  Y GWQ Q    G++IQ +I+ AI ++  + V + G+GRTD+ VHA 
Sbjct: 2   MQRFKAVVSYDGFDYAGWQIQPAERGATIQQTIQDAISVICQQPVSITGSGRTDAQVHAW 61

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD+          +A+N +L     I I ++  VD +FHARF AI + Y YRI  
Sbjct: 62  GQVFHFDVDFSLNAFQWKRAINGHL--PKDIHIRSVEAVDSRFHARFDAIGKRYEYRIQL 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDV 177
            +A     +  A+  P +L+ + MR  A +L+G HDF++F +    +     RTI   ++
Sbjct: 120 GEA-NVFTRRYAFQSPWTLNVQAMREGAAYLIGEHDFSSFCANSRAEMPDQARTITRLEL 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + + +      FL   +R   G+L  VG G+    D++  LQAQD++ C   A P+
Sbjct: 179 AEENDQLRLIYEGSGFLRYMVRMMTGTLIEVGRGRLAPQDVQWMLQAQDKQICHFNAKPQ 238

Query: 238 GLYFDSVEY 246
           GL    V Y
Sbjct: 239 GLTLVEVYY 247


>gi|257466765|ref|ZP_05631076.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917914|ref|ZP_07914154.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313691789|gb|EFS28624.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 251

 Score =  257 bits (658), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 88/252 (34%), Positives = 127/252 (50%), Gaps = 11/252 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIFLV---TGEIVVVHGAGRTDSG 54
           +     IEY G+ Y GWQR    Q+   +IQG IE+ +  +     E V V  +GRTD+G
Sbjct: 4   VNLRFSIEYEGTRYLGWQRLGEKQRE-KTIQGKIEQVLARLFALNPEEVSVIASGRTDAG 62

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  Q+A+  L     P  + +  N YL   + I I +   V++ FH+RF A  + Y Y
Sbjct: 63  VHAKEQIANVHLPSGKSPQEIEEYCNQYL--PEDIRIFHAHFVEELFHSRFHAKTKEYHY 120

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I  ++ P    +   W  P  LD E M+ ++Q+ +G HDF  F S+     S IR ID 
Sbjct: 121 EISLQK-PSVFHRNVTWYCPIQLDIEKMKESSQYFLGEHDFLAFSSLKKTKKSTIRRIDR 179

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++      +  R V   FL   IR  VG+L  VG+GK T  D+    Q++ R++ G LA
Sbjct: 180 IEIQETEFGLLFRFVGNGFLQNMIRILVGTLIEVGEGKKTKEDIISIFQSKARQKAGFLA 239

Query: 235 PPEGLYFDSVEY 246
           P +GL    V Y
Sbjct: 240 PAKGLTLYKVYY 251


>gi|255556594|ref|XP_002519331.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223541646|gb|EEF43195.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 344

 Score =  257 bits (658), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 132/254 (51%), Gaps = 11/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHALR 59
           ++ ++I Y+G+ Y GWQ Q++  +IQ  +EKA+     +  + +++ GA RTD+GVHA  
Sbjct: 72  KWRLVIAYDGTRYAGWQFQQSPPTIQCYLEKALIQVTKLDRKDLLLVGASRTDTGVHAFG 131

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +     +  ALN  L     I +  +S    +FHARFS I + Y Y+I  
Sbjct: 132 QVAHFVTPFNYPSLDTIHAALNGLL--PPDIRVREISPAVPEFHARFSTISKLYHYKIYN 189

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFD 176
                   +  A+     L+   MR AA++ +G HDF+ F   S   +  +P++TI  FD
Sbjct: 190 DTFMDPFLRHYAYHSTYKLNAAAMRQAAKYFIGSHDFSAFANASRDDRVPNPVKTIFRFD 249

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA-- 234
           V   G L+++ V    FL+ Q+R+ V  L  +G        + K L A+DR+E    A  
Sbjct: 250 VIEMGALLQLEVEGTGFLYRQVRNMVALLLQIGKEAVPPEIVPKILAARDRRELAKYALP 309

Query: 235 -PPEGLYFDSVEYS 247
            PP GL   S++Y+
Sbjct: 310 TPPHGLCLVSIKYN 323


>gi|283853830|ref|ZP_06371050.1| tRNA pseudouridine synthase A [Desulfovibrio sp. FW1012B]
 gi|283570781|gb|EFC18821.1| tRNA pseudouridine synthase A [Desulfovibrio sp. FW1012B]
          Length = 270

 Score =  257 bits (658), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 119/252 (47%), Gaps = 8/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+G+ + GWQ Q    G ++QG +E+A+  + GE V + GAGRTDSGVHA+
Sbjct: 1   MPRLRLTLAYDGTAFAGWQLQAPGRGRTVQGCLEEALATLCGEPVRIFGAGRTDSGVHAM 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   KALNA L     +S+    +V   FHARF A  + Y Y + T
Sbjct: 61  AQVAHVDVPEGRAAIPWQKALNALL--PADMSVAGAELVPDGFHARFCATGKVYHYTLWT 118

Query: 119 RQ-APLALEKGRAWLI--PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                L   +   W +     LD   M   A    G HDF  F++      +  R +   
Sbjct: 119 EPGHVLPWRRPYVWDVGRYGRLDVAAMDACAACFAGFHDFAAFQNAGSDVKTTTRLVHGV 178

Query: 176 -DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             + + G  +  R  A  FL   +R+ +G+L  VG GK +  D+   L    R+     A
Sbjct: 179 TRLATGGPEMVWRFHAEGFLKQMVRNLMGALVAVGRGKVSPEDIRSVLTQGQRRLAPQTA 238

Query: 235 PPEGLYFDSVEY 246
           P  GL    VEY
Sbjct: 239 PASGLCLVVVEY 250


>gi|323342828|ref|ZP_08083060.1| tRNA pseudouridine synthase A [Erysipelothrix rhusiopathiae ATCC
           19414]
 gi|322463940|gb|EFY09134.1| tRNA pseudouridine synthase A [Erysipelothrix rhusiopathiae ATCC
           19414]
          Length = 245

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 128/247 (51%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R+   ++Y+GS + GWQ+Q  G  +Q  IE  +  +  E + + G+GRTD+GVHAL Q
Sbjct: 1   MMRFKATVQYDGSMFKGWQKQPFGRCVQTEIESVLTRINKEPIHISGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD V +     L +ALN  L   + I I ++  V+  FHARF  + ++Y YR+    
Sbjct: 61  VFHFDNVVDMDEKQLFRALNTLL--PNDIVITDIHPVEPNFHARFDVVSKTYEYRLNMGA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVNS 179
                E+   +   K+LD + +R A +  VG HDFT+F +    +  + +RTI +FD+  
Sbjct: 119 Y-NLFERNYVYQYNKALDLQAIRDAMESFVGTHDFTSFNATGLDEIENQVRTITNFDLIV 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +   ++   FL   +R  V +    G GK  + ++ + L+A D+          GL
Sbjct: 178 SDDHLNFVIIGDGFLRYMVRMIVATCVACGSGKCDAHEIAQMLKAADKNSISYNIDACGL 237

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 238 YLKKVNY 244


>gi|195941752|ref|ZP_03087134.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 80a]
 gi|216264809|ref|ZP_03436801.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 156a]
 gi|224533912|ref|ZP_03674497.1| tRNA pseudouridine synthase A [Borrelia burgdorferi CA-11.2a]
 gi|215981282|gb|EEC22089.1| tRNA pseudouridine synthase A [Borrelia burgdorferi 156a]
 gi|224512915|gb|EEF83281.1| tRNA pseudouridine synthase A [Borrelia burgdorferi CA-11.2a]
          Length = 246

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 124/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTVQGEIEKALMKINKKKVKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDIKINIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L   N+   A+ L+G+HDFTTF  I  ++    R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLSISNLNQMAKTLIGKHDFTTFSCIKDKSKFKFRHIYFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

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


>gi|87300888|ref|ZP_01083730.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 5701]
 gi|87284759|gb|EAQ76711.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 5701]
          Length = 316

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 72/248 (29%), Positives = 114/248 (45%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ +  S+Q ++E+A+  +     +    AGRTDSGVHA  Q
Sbjct: 11  QRIALCLQYEGSSFCGWQRQPHQPSVQETLERALATLDPHRPIRAMAAGRTDSGVHAAGQ 70

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+            ALN  L    +I +   + V   +HA FSA  R Y Y +   +
Sbjct: 71  VVHFEASGPIPSERWAAALNGRL--PASIRVRAAAAVPSTWHACFSACYRRYRYTLYNGR 128

Query: 121 APLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W    + L+   M  A + L+G HDF+ F+    +       +    +  
Sbjct: 129 RPNLFLSPWSWHRYRQRLNERAMATALRGLLGFHDFSAFQRAGSRRPHARTKVQAVSLER 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ + + A  FL+  +R  +G L  VG+G+ +    E+  + + R E    AP  GL
Sbjct: 189 HGDLVVVEIQASGFLYGMVRLIMGQLVAVGEGQLSLAGFERRWRQRARSEVKEAAPAHGL 248

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 249 CLLRVGYP 256


>gi|299140694|ref|ZP_07033832.1| tRNA pseudouridine synthase A [Prevotella oris C735]
 gi|298577660|gb|EFI49528.1| tRNA pseudouridine synthase A [Prevotella oris C735]
          Length = 243

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 120/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+GS Y GWQ Q NG S+Q  +++A+  +  + + + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLSYDGSAYHGWQIQPNGISVQEKLQEALSKLLRQKIEIVGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  +      L   LN  L     I+I  +  V+   HARFSA  R+Y Y I T++
Sbjct: 61  VAHFDFPKSIEEEQLRYRLNRLL--PRDITINKVIPVEADMHARFSAKWRTYRYYIHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A  +  ++  P  LD + M   A+ L    DF  F        S + TI        
Sbjct: 119 --DAFLRHYSYESPYKLDYQLMNQGAELLKSHTDFAAFCKTGADNKSTLCTIRESKWVQT 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L L+G    +  DL+  LQ  DR   G   P   L
Sbjct: 177 SAISWYFEITANRFLRNMVRATVGTLFLLGRHHISLDDLDYILQEGDRSNAGESMPGHAL 236

Query: 240 YFDSVEY 246
           + +++EY
Sbjct: 237 FLENIEY 243


>gi|281425834|ref|ZP_06256747.1| tRNA pseudouridine synthase A [Prevotella oris F0302]
 gi|281400095|gb|EFB30926.1| tRNA pseudouridine synthase A [Prevotella oris F0302]
          Length = 243

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 120/247 (48%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+GS Y GWQ Q NG S+Q  +++A+  +  + + + GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLSYDGSAYHGWQIQPNGISVQEKLQEALSKLLRQEIEIVGAGRTDTGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD  +      L   LN  L     I+I  +  V+   HARFSA  R+Y Y I T++
Sbjct: 61  VAHFDFPKSIEEEQLRYRLNRLL--PRDITINKVIPVEADMHARFSAKWRTYRYYIHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A  +  ++  P  LD + M   A+ L    DF  F        S + TI        
Sbjct: 119 --DAFLRHYSYESPYKLDYQLMNQGAELLKSHTDFAAFCKTGADNKSTLCTIRESKWVQT 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L L+G    +  DL+  LQ  DR   G   P   L
Sbjct: 177 SAISWYFEITANRFLRNMVRATVGTLFLLGRHHISLDDLDYILQEGDRSNAGESMPGHAL 236

Query: 240 YFDSVEY 246
           + +++EY
Sbjct: 237 FLENIEY 243


>gi|295099211|emb|CBK88300.1| pseudouridylate synthase I [Eubacterium cylindroides T2-87]
          Length = 243

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 129/246 (52%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y +I+ Y+GS Y GWQ+Q+N   IQ  IEKA+  +  + + +  +GRTD+ VHAL QV
Sbjct: 1   MIYKVILAYDGSNYAGWQKQENALGIQEVIEKALTTIHKKEIFITASGRTDAKVHALGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+  ++  P     ALNA L   + I IL +S+    FHARFSA  + Y Y I T + 
Sbjct: 61  FHFEADKKIGPDRYKMALNALL--PEDIRILKVSMEADDFHARFSAKSKRYDY-ICTYEK 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNSF 180
                     ++  +L+ E MR A+++LVG HDFT+F S       P I+TI   D+   
Sbjct: 118 ENPFVYKYKEILNHTLNIEAMRKASEYLVGTHDFTSFSSSKIDPRKPRIKTITRIDIFEE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I        FL  Q+R    +L +VG  K  + ++++ L  +D+  C   A P GLY
Sbjct: 178 NQDIRFIYEGTGFLRYQVRMMTETLIMVGSNKIDTEEVKRILDKKDKSACRYNASPNGLY 237

Query: 241 FDSVEY 246
              V Y
Sbjct: 238 LVHVNY 243


>gi|302536280|ref|ZP_07288622.1| tRNA pseudouridine synthase A [Streptomyces sp. C]
 gi|302445175|gb|EFL16991.1| tRNA pseudouridine synthase A [Streptomyces sp. C]
          Length = 287

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/251 (32%), Positives = 117/251 (46%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q+   ++QG +E A+  V    E V +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQRTLRTVQGELESALQTVMRLKEPVELTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVA FDL  E       K L     ++   I +   +   + F+ARFSAI R Y YR+  
Sbjct: 70  QVAQFDLAEEVWAEHHDKLLRRLAGRLPHDIRVWKAAEAPEGFNARFSAIWRRYAYRVGD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            +A    L +G        LD + M  AA  LVG HDF  +     + ++ IRT+     
Sbjct: 130 HRAGVDPLRRGHVLWHQWPLDVDAMNEAAAALVGEHDFAAYCKKR-EGATTIRTLQQLSW 188

Query: 178 NSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               + +    V A +F H  +RS VG+L  VGDG        + L A  R     +  P
Sbjct: 189 ERGEDGVVTATVRADAFCHNMVRSLVGALLHVGDGHRPVEWPGQVLAAAVRDSSVHVVKP 248

Query: 237 EGLYFDSVEYS 247
            GL  + V Y 
Sbjct: 249 HGLTLEEVGYP 259


>gi|203283942|ref|YP_002221682.1| pseudouridylate synthase I [Borrelia duttonii Ly]
 gi|203287485|ref|YP_002222500.1| pseudouridylate synthase I [Borrelia recurrentis A1]
 gi|238690561|sp|B5RLM0|TRUA_BORDL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690579|sp|B5RQJ5|TRUA_BORRA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|201083385|gb|ACH92976.1| pseudouridylate synthase I [Borrelia duttonii Ly]
 gi|201084705|gb|ACH94279.1| pseudouridylate synthase I [Borrelia recurrentis A1]
          Length = 245

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 122/247 (49%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    +IQG IEKA+  +    V +  AGRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSLYHGFQIQPTKPTIQGEIEKALEKINKTKVKIQSAGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  F +        L  A+N+ LK  + I I+ L  V  +F  RF A +R Y Y I+  +
Sbjct: 61  IISFYIKININLKNLKTAINSLLK--NDIRIIKLKYVSNEFQPRFHAKKRKYTYYILNNE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E+ +A+ + K L+   +   A+ L+G HDFTTF  I  Q +S ++ I        
Sbjct: 119 NHYPWEEYQAYYVRKKLNINRLNTMAEMLIGLHDFTTFSCIRDQTNSKLKEIYLAKFKKK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I   ++  SFL   +RS VG++  +     +     K L++++RK     AP + L+
Sbjct: 179 NKFIVFEIIGSSFLWKMVRSIVGTMIDIEIKNESVDTFIKILKSKNRKYARTTAPAKALF 238

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 239 LDRVFYE 245


>gi|284992843|ref|YP_003411397.1| tRNA pseudouridine synthase A [Geodermatophilus obscurus DSM 43160]
 gi|284066088|gb|ADB77026.1| tRNA pseudouridine synthase A [Geodermatophilus obscurus DSM 43160]
          Length = 282

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+   GW RQ    ++QG +E+A+  V  + V +  AGRTD+GVHA  QV
Sbjct: 19  VRLRLGIAYDGTALHGWARQPAQRTVQGDLEEALSRVLRQPVSLTVAGRTDAGVHATGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH D+ R        + +      +   I++  +    + F ARF A+RR Y+YR+    
Sbjct: 79  AHGDVPRAVWAEQRPRLVRRLRGVLPPDIAVHTVEEAPRDFDARFGALRRHYVYRLTDAD 138

Query: 121 A-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P  L +      P+ LD + M +AA+ L+G HDF  F     + ++ IRT+    V  
Sbjct: 139 SGPPPLRRADTVGWPRRLDADAMAVAAELLLGLHDFAAFCRRR-EGATTIRTLLTLAVTR 197

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ +R  A +F H+ +RS VG+L  VG+G+         L + +R    P+ PP GL
Sbjct: 198 EGDLVTVRASADAFCHSMVRSLVGALTAVGEGRRPPEWPAALLTSTERSSEVPVVPPGGL 257

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 258 TLVGVDYP 265


>gi|187917895|ref|YP_001883458.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
 gi|238689303|sp|B2S1K1|TRUA_BORHD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119860743|gb|AAX16538.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
          Length = 245

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 123/247 (49%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y+G+Q Q    +IQG IEKA+  ++   V VH AGRTD GVHA  Q
Sbjct: 1   MKKILAEIAYDGSLYYGFQIQPTKPTIQGEIEKALEKISKTKVKVHSAGRTDKGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  F +        L  A+N+ L+    I I+ L  V  +F  RF+A RR Y Y I+  +
Sbjct: 61  IISFYIRINIKLKNLKTAINSLLR--KDIRIIKLKYVADEFQPRFNAKRRKYSYYILNNE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A+ + K L+   +   A+ L+G HDFTTF  I  Q +S ++ I        
Sbjct: 119 NHYPWEGYQAYYVKKKLNINRLNEMAKMLIGIHDFTTFSCIKDQTNSKLKKIYFARFKKK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI   ++  SFL   +RS VG++  +          +K L +++RK     AP + L+
Sbjct: 179 NKLIIFEIIGSSFLWKMVRSIVGTIIDIEIKNEPVYTFKKILNSKNRKFTRTTAPAKALF 238

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 239 LDKVFYE 245


>gi|159904194|ref|YP_001551538.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9211]
 gi|226741290|sp|A9BCM2|TRUA_PROM4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|159889370|gb|ABX09584.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9211]
          Length = 289

 Score =  257 bits (656), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 122/247 (49%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQV 61
           R  ++I+YNGSG+ GWQRQK G+S+Q  +E+A+  +   + + V  AGRTDSGVHA  QV
Sbjct: 17  RIALLIQYNGSGFCGWQRQKEGNSVQSILEEAVSSLDPFQPIKVVAAGRTDSGVHASGQV 76

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD            ALN  L     I +   ++    +HA FSA  R Y Y I     
Sbjct: 77  AHFDCSGFIPANRWAAALNGRL--PKAIRVRYSALRPITWHACFSATYRRYRYTIYNGCK 134

Query: 122 PLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P        W      LD   M +A Q + G HDFT F+       + + T++   +   
Sbjct: 135 PNLFLSPWCWHRYQFRLDENLMNLALQGIKGFHDFTAFQRAGSNRPNALTTVEDVHLFRQ 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ I + A  FL+  +R  VG L  VG+ + +  + E+  + + R+E    APP GL 
Sbjct: 195 GDLVSIDIQATGFLYGMVRLLVGQLVAVGEHRISVAEFERRWKLKLREEVREAAPPNGLS 254

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 255 LIRVGYE 261


>gi|150025482|ref|YP_001296308.1| tRNA pseudouridine synthase A [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772023|emb|CAL43499.1| tRNA-pseudouridine synthase I [Flavobacterium psychrophilum
           JIP02/86]
          Length = 250

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 75/246 (30%), Positives = 115/246 (46%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG+ Y GWQ Q N +S+Q ++ K    +  E + + GAGRTD+GVHA +  
Sbjct: 1   MRYFIEFAYNGTQYHGWQYQPNATSVQETLNKVFSTLLQEKIDIMGAGRTDAGVHAKQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD              N++L     I I N+  V  Q HARF A  R+Y Y I T + 
Sbjct: 61  GHFDTDISIDNAKFIHKANSFL--PKDIVIFNIIPVHNQAHARFDATSRTYNYHISTYK- 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                   AW   K +D   M  AA+ L+   DF  F   +   ++    I     +   
Sbjct: 118 -NVFTNNLAWYSSKKIDVIAMNEAAKVLLKFTDFKCFSKTNTDVNTYNCKITEAFWSIEK 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   + A  FL   +R+ VG+L  +G  K T  +  + +++Q+R+  G   P  GL+ 
Sbjct: 177 EQLIFTITADRFLRNMVRAIVGTLINIGLHKITIENFIQIIESQNRENAGFSVPAHGLFL 236

Query: 242 DSVEYS 247
            ++EY 
Sbjct: 237 TNIEYP 242


>gi|281420165|ref|ZP_06251164.1| tRNA pseudouridine synthase A [Prevotella copri DSM 18205]
 gi|281405965|gb|EFB36645.1| tRNA pseudouridine synthase A [Prevotella copri DSM 18205]
          Length = 247

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 115/248 (46%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y+G+ Y GWQ Q N +S+Q  +++A+ ++  + + V GAGRTD+GVHA    
Sbjct: 1   MRYFIFFGYDGTNYHGWQIQPNANSVQQELQRALSILLRKEMEVVGAGRTDTGVHARHMA 60

Query: 62  AHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD  R    P  L   LN  L     I++  +  V  + HARFSAI R+Y Y I T++
Sbjct: 61  AHFDTDRIPMEPDQLVYRLNRIL--PRDIAVYEVMEVAPEMHARFSAISRTYHYYIHTQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NS 179
                E+  +  +   L+ E M  AAQH +   D+  F        + I  +       +
Sbjct: 119 --DPFERHYSLQMNYPLNFEKMNEAAQHFLHHEDYAAFCKAGGDNKTTICHVTAARWIQT 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   + A  FL   +R+ VG+L  VG  K T       L    R + G   P   L
Sbjct: 177 SPTTWYFEITANRFLRNMVRAVVGTLIDVGREKITMEQFLDILHNGSRSDAGESMPGNAL 236

Query: 240 YFDSVEYS 247
           + + V Y 
Sbjct: 237 FLEDVGYD 244


>gi|327404294|ref|YP_004345132.1| tRNA pseudouridine synthase A [Fluviicola taffensis DSM 16823]
 gi|327319802|gb|AEA44294.1| tRNA pseudouridine synthase A [Fluviicola taffensis DSM 16823]
          Length = 256

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 89/250 (35%), Positives = 126/250 (50%), Gaps = 8/250 (3%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHAL 58
           M  RY + + Y G+ Y GWQ Q N SSIQ  IE+ +  + G   + V G GRTD+GVHA 
Sbjct: 1   MTFRYALELAYRGTNYHGWQIQPNASSIQEEIERRLTQLNGNLPISVVGCGRTDTGVHAT 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             V HFD  +E     L   LN  L   + IS+ +  +V ++FHARFS   R+Y Y I  
Sbjct: 61  YYVLHFDSQKELDTEQLVFKLNKML--PEDISLFSAQLVSEEFHARFSPTTRTYHYFIHQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           ++ P  L+  R   I   +D E M  AA+ L+G  DFT+F  +H    + I T+     N
Sbjct: 119 KKNPFLLDSHR---IVSEIDFEAMNRAARLLLGTQDFTSFSKLHTDVKTNICTVSEAKWN 175

Query: 179 SFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                     + A  FL   +R+ VG+L  VG G     D+ K +  +DR E     P +
Sbjct: 176 QVSESEWYFEIKADRFLRNMVRAVVGTLLEVGYGNLGENDITKIVALKDRGEAKLSVPAK 235

Query: 238 GLYFDSVEYS 247
           GL+  ++EY 
Sbjct: 236 GLFLVNIEYP 245


>gi|313676221|ref|YP_004054217.1| tRNA pseudouridine synthase a [Marivirga tractuosa DSM 4126]
 gi|312942919|gb|ADR22109.1| tRNA pseudouridine synthase A [Marivirga tractuosa DSM 4126]
          Length = 247

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 125/246 (50%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY   I Y G+ Y GWQ+Q N   +Q  IE+    +  +   + G+GRTDSGVHA  QV
Sbjct: 1   MRYFFTIAYKGTQYHGWQKQPNAIGVQQKIEEVFSTILNQKSEIVGSGRTDSGVHATAQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E  P+ L    N  L     +++ +  +V ++ HARF A  R+Y Y I+T + 
Sbjct: 61  FHFDYSGELDPLQLVFKANKML--PKDVALKHAKLVKEEAHARFDAESRAYQYHIVTEKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P A+++  A+   + L  E M +AA+ L+   DF +F  +     +   +I         
Sbjct: 119 PFAIDQ--AYFFTQELAIEKMNLAAEKLLNYQDFESFSKVKTDVFTFNCSIFEAIWKQEV 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +   + A  FL   +R+ VG+L  VG  K +  + E+ ++A++RK  G   P  GLY 
Sbjct: 177 DSLVFHIKANRFLRGMVRAIVGTLLDVGQHKISIENFEEIIKAKNRKSAGRAVPAHGLYL 236

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 237 TEVQYP 242


>gi|188584870|ref|YP_001916415.1| tRNA pseudouridine synthase A [Natranaerobius thermophilus
           JW/NM-WN-LF]
 gi|229557997|sp|B2A4Q5|TRUA_NATTJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|179349557|gb|ACB83827.1| tRNA pseudouridine synthase A [Natranaerobius thermophilus
           JW/NM-WN-LF]
          Length = 253

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 87/255 (34%), Positives = 133/255 (52%), Gaps = 10/255 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M    + I Y+GS Y G+Q Q+N  ++Q  +EKA+  V     +  + A RTDSGVHA  
Sbjct: 1   MDNIKLTIAYDGSNYHGYQLQENAVTVQEKLEKALNTVYYPYKITPYSASRTDSGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F   ++     +  ALN  L   + I+I+N  +V   F AR  AI++ Y Y +   
Sbjct: 61  QVANFFAPKQIPIHKIPLALNTNL--PNDIAIINAEVVGSNFRARRDAIKKEYRYYVYHA 118

Query: 120 QAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS--PIRTIDHFD 176
                  +  A     ++LD   ++ AA   +G+HDF+ FR+I     S  P++ I  FD
Sbjct: 119 PYMDPFWRNYALHYREQNLDYTKLQQAANDFIGKHDFSPFRAIQGSNPSIDPVKEIYEFD 178

Query: 177 VN----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           ++      GNLI  +V+  +FL+  +R  VG+L  +G+GK     ++KALQ  DR   GP
Sbjct: 179 IDVNAGEDGNLIIFKVIGNAFLYKMVRILVGTLLQIGNGKLEINAVKKALQTGDRLFVGP 238

Query: 233 LAPPEGLYFDSVEYS 247
            A P+GL    + Y 
Sbjct: 239 TASPQGLVLQQIWYP 253


>gi|218134082|ref|ZP_03462886.1| hypothetical protein BACPEC_01972 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991457|gb|EEC57463.1| hypothetical protein BACPEC_01972 [Bacteroides pectinophilus ATCC
           43243]
          Length = 272

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 124/249 (49%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M  Y M +EY+G  Y GWQR     N +++   I + +  +TG  V +    RT++GVHA
Sbjct: 27  MYNYRMTLEYDGGRYAGWQRMGRDDNSNTVSAKITEVLKKMTGSDVEIFCGSRTETGVHA 86

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QVA+F L RE+    +   LN YL     I++L L    ++FH++ +A  R+Y+YR+ 
Sbjct: 87  YGQVANFKLDREYRAREIQNYLNRYL--PQDIAVLELEETQERFHSQLNAKSRTYVYRVD 144

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T+      E+   +      D + M  AAQ+ +G HD+  F ++     S +R ++  D+
Sbjct: 145 TKNIANVFERRYMYHTFHKPDVDAMNKAAQYFLGEHDYKVFSTVKKN-KSTVRNVESVDI 203

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ +EI + A  FLH   R  +G L  +G G+    D+ K L      E    A   
Sbjct: 204 YDDGDTLEITIKADDFLHNMARLMIGILLDIGSGERRPEDVRKLLDGVKGVEISKPAESY 263

Query: 238 GLYFDSVEY 246
           GLY   VEY
Sbjct: 264 GLYLLEVEY 272


>gi|307297407|ref|ZP_07577213.1| tRNA pseudouridine synthase A [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916667|gb|EFN47049.1| tRNA pseudouridine synthase A [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 252

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 87/249 (34%), Positives = 125/249 (50%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  I+ Y+G+ +FG+Q Q    ++QG  E+A+  +    +   GAGRTD+GVH   Q
Sbjct: 3   MKRFAAIVSYDGTDFFGFQNQPGLRTVQGKFEEALHRIHKFCISSQGAGRTDTGVHGFGQ 62

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V  FD          +  ALNA L     + +  +  VD+ F  RF+A +R Y Y I T 
Sbjct: 63  VIAFDSNLDRLEATTMRDALNANL--PSDMYVRKVHEVDENFSPRFAAKKRIYHYYIQTS 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P    +   W  P SLD ++MR AA +L+G HDF  FR       +P+RTI    +  
Sbjct: 121 SEPDIFRRRFVWWFPYSLDIKSMRRAAVNLLGEHDFAAFR-TGKDDRNPVRTITAIRIIR 179

Query: 180 FGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +   I  IRV   SFL   +R+ VG+L  VG G  +   + + L + DR      APP+G
Sbjct: 180 YKPYIILIRVEGISFLKRMVRNIVGTLVKVGTGSVSEESVSEFLSSHDRSTLPGTAPPQG 239

Query: 239 LYFDSVEYS 247
           L F  V + 
Sbjct: 240 LVFYKVIFD 248


>gi|72382942|ref|YP_292297.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. NATL2A]
 gi|72002792|gb|AAZ58594.1| tRNA pseudouridine synthase [Prochlorococcus marinus str. NATL2A]
          Length = 276

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 118/250 (47%), Gaps = 5/250 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           M  R  ++I+Y+GSG+ GWQ QK+  ++QG++E+ I  +     V    AGRTDSGVHA 
Sbjct: 1   MTNRIALVIQYDGSGFRGWQNQKDSITVQGTLEEKIAELDPIRPVKAIAAGRTDSGVHAS 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD            ALN  L    +I +L    V K +HA +SA  R Y Y I  
Sbjct: 61  GQVVHFDCSGPIPIHKWASALNGRL--PASIKVLEAVGVPKVWHACYSAKYRRYRYSIFN 118

Query: 119 RQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
              P    +  +W      LD   M+ A   L+G HDF  F+      S+ + T+    +
Sbjct: 119 GSYPNLFLQNISWHKYRFMLDINLMKHALNDLLGLHDFAAFQKAGSNRSNSLTTVQDVSI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           + +G+++ + + A  FL+  +R  +G L  VG+ + +        +   R E    AP  
Sbjct: 179 SRYGDIVTVEIQASGFLYGMVRLLMGQLVAVGEKRLSLEKFRYRWRKGLRSEVKEAAPAH 238

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 239 GLCLIRVGYE 248


>gi|255536203|ref|YP_003096574.1| tRNA pseudouridine synthase A [Flavobacteriaceae bacterium 3519-10]
 gi|255342399|gb|ACU08512.1| tRNA pseudouridine synthase A [Flavobacteriaceae bacterium 3519-10]
          Length = 245

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 122/247 (49%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y+G  YFG+Q Q    +IQ  +EKA+  +    +   GAGRTD+GVHA +  
Sbjct: 1   MRYFIEFSYHGKNYFGYQIQPREITIQQELEKALSTLLRAEIKTTGAGRTDTGVHAKKMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD     V   L   LN++L     I++  +  V    HARF A  R+Y Y I   + 
Sbjct: 61  AHFDTE-IAVEDNLPYRLNSFL--PQDIAVSRIFKVKDDLHARFDATFRTYEYYISLAKN 117

Query: 122 PLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P    +  +W I  ++L+   M  A + L    DFT+F  +H    +    I        
Sbjct: 118 P--FSQDFSWQIRNRTLEIGKMNEACRILFEYEDFTSFSKLHTDNKTNNCKIYKAFWEQN 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN ++  V A  FL   +R+ VG++  +G+GK    DL K ++A+DR   G  AP +GL+
Sbjct: 176 GNELKFTVSADRFLRNMVRAIVGTMVEIGNGKIQPMDLRKIIEAKDRSFAGTSAPAQGLF 235

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 236 LVDVGYD 242


>gi|257457999|ref|ZP_05623158.1| tRNA pseudouridine synthase A [Treponema vincentii ATCC 35580]
 gi|257444712|gb|EEV19796.1| tRNA pseudouridine synthase A [Treponema vincentii ATCC 35580]
          Length = 265

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/252 (30%), Positives = 121/252 (48%), Gaps = 8/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
               + I Y+G+ + GWQ+Q     ++  ++QG +E+A+ L+    V + G+GRTD+GVH
Sbjct: 10  RNILLRISYDGTRFHGWQKQLQHGEESFRTVQGEVERALALLHKHPVELFGSGRTDAGVH 69

Query: 57  ALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           A  Q AHF        P     ALN+ L     + I+  + V    HARFSA  R+Y Y 
Sbjct: 70  ACGQAAHFFTDIARIKPESFVPALNSAL--PKDVRIIEAAHVSDNLHARFSARSRTYRYF 127

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +   +   A +    W I +  D   +   A  L G  D TTF +   Q+ S  R I   
Sbjct: 128 VHCGKTAFAHQLPYCWHIRREPDINLLNRMAGVLSGELDCTTFSAAGDQSKSKSRYIYTA 187

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +  + +   + A +FL   +RS  G+L        T  D E  L+++DR+  G  AP
Sbjct: 188 HFFTDRDFLVFEISANAFLWRMVRSVTGTLLHYEQQNGTKEDFEAVLRSKDRRNAGETAP 247

Query: 236 PEGLYFDSVEYS 247
           P+GL+  S++Y 
Sbjct: 248 PQGLFLWSIDYP 259


>gi|124026684|ref|YP_001015799.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. NATL1A]
 gi|123961752|gb|ABM76535.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. NATL1A]
          Length = 276

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 115/250 (46%), Gaps = 5/250 (2%)

Query: 1   MI-RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           M  R  ++I+Y+G G+ GWQ QK+  ++QG++E+ I  +     V    AGRTDSGVHA 
Sbjct: 1   MTNRIALVIQYDGLGFRGWQNQKDSITVQGTLEEKIAELDPIRPVKAIAAGRTDSGVHAS 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD            ALN  L    +I +L    V   +HA +SA  R Y Y I  
Sbjct: 61  GQVVHFDCSGPIPIHKWASALNGRL--PASIKVLEAVSVPSAWHACYSAKYRRYRYSIFN 118

Query: 119 RQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
              P    +  +W      LD   M+ A   L+G HDF  F+      S+ + T+    +
Sbjct: 119 GSYPNLFLQNISWHKYRFKLDINLMKQALNDLLGLHDFAAFQKAGSNRSNSLTTVQDVSI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G+++ + + A  FL+  +R  +G L  VG+ + +        +   R E    AP  
Sbjct: 179 SRDGDIVTVEIQASGFLYGMVRLLMGQLVAVGEKRLSLEKFRYRWRKGLRSEVKEAAPAH 238

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 239 GLCLIRVGYE 248


>gi|294794578|ref|ZP_06759714.1| tRNA pseudouridine synthase A [Veillonella sp. 3_1_44]
 gi|294454908|gb|EFG23281.1| tRNA pseudouridine synthase A [Veillonella sp. 3_1_44]
          Length = 254

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 120/241 (49%), Gaps = 4/241 (1%)

Query: 8   IEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + Y+G+   G+Q+Q N    ++QG +E  +  +  E + ++GA RTD+GVHA  QV  F 
Sbjct: 1   MAYDGTDLAGYQKQPNDKGLTVQGCLEYGLSRICNEPIQIYGASRTDAGVHAKFQVCTFQ 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    + +A+ A+  I   I +L    +   +  R++   + Y+Y I  +     L
Sbjct: 61  TSGTIPVENIPRAMIAH--IPKDIVVLEAVEIPLDWKPRWNIYGKEYVYTIHNQLIADPL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            K   W + K LD + M+ A   L+G HDFTT +  +   + P++TI    V      + 
Sbjct: 119 TKRYHWHVKKPLDIDRMQAAGNELLGTHDFTTLKGTNSTPADPVKTILGIHVKVKEAHVT 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I VV   FL+  +R+ VG L  VG G+    D++  L A+DR+  G  AP +GL  + + 
Sbjct: 179 ISVVGDGFLYHMVRNIVGLLVDVGLGRRKVEDIKGYLVAKDRRVIGKTAPAQGLCLEEIF 238

Query: 246 Y 246
           +
Sbjct: 239 F 239


>gi|332881976|ref|ZP_08449617.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332680102|gb|EGJ53058.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 250

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 118/246 (47%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   YNG  Y GWQ Q    ++QG ++ A+  +  E + V GAGRTDSGVHAL+  
Sbjct: 1   MRYFIEFSYNGKNYHGWQLQPKAITVQGVLQNALTTILREEISVIGAGRTDSGVHALQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  RE     L + LNA+L     I++ ++  V    HARF A++R+Y Y I   ++
Sbjct: 61  AHFDTERELSDD-LVRKLNAFL--PYDIAVHSICAVKPDAHARFDALKRTYQYHISIEKS 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P       +  +   L+ + M  AAQ L    DF  F   H    +    I        G
Sbjct: 118 P--FRYNYSMPLTLPLNIDVMNEAAQILFDYTDFQCFSKTHTDVKTFNCKIYEAHWAVVG 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   + A  FL   +R+ VG+L  VG  K + T  E  + ++ R + G   P  GL+ 
Sbjct: 176 GELVFTITADRFLRNMVRAIVGTLINVGLQKLSLTGFEDIIISKSRSKAGASVPACGLFL 235

Query: 242 DSVEYS 247
             V Y 
Sbjct: 236 TQVTYP 241


>gi|51598275|ref|YP_072463.1| tRNA pseudouridine synthase A [Borrelia garinii PBi]
 gi|62901275|sp|Q663A0|TRUA_BORGA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|51572846|gb|AAU06871.1| pseudouridylate synthase I [Borrelia garinii PBi]
          Length = 246

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 126/247 (51%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    +IQG IEKA+  +  + V +H +GRTD GVHA +Q
Sbjct: 1   MKKILAEITYDGSIYHGFQIQPTKPTIQGEIEKALMKINKKKVKIHSSGRTDKGVHAKKQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  +   FH RF+A +R Y YRI+   
Sbjct: 61  IITFDININIQLNNLKKALNAIL-LKNSIKILKLKYMKNSFHPRFNAQKRKYSYRILNSN 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIYLAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 240 LDKVYYE 246


>gi|225850198|ref|YP_002730432.1| tRNA pseudouridine synthase A [Persephonella marina EX-H1]
 gi|225645344|gb|ACO03530.1| tRNA pseudouridine synthase A [Persephonella marina EX-H1]
          Length = 244

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/244 (33%), Positives = 127/244 (52%), Gaps = 5/244 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            Y ++I Y G  Y GWQ+Q    ++QG +E+ + ++  E +V+ G+GRTD+GVHAL QVA
Sbjct: 6   NYKLVIMYIGKNYHGWQKQPKHRTVQGVLEEKLKVLFKEDIVLIGSGRTDAGVHALGQVA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F  +    P  + + LNA L     IS+ ++  V   FHARFSA  ++Y+YRI T+  P
Sbjct: 66  NFKTISYRKPEEIYRYLNATL--PRDISVKSVEEVPLSFHARFSAKGKTYIYRIYTK--P 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                G  W I K LD + M  A + +    D  +           +  I    +   G 
Sbjct: 122 DPFLHGFGWYISKKLDLKGMLEALEIVKKSKDLRSLSKKGEYLREDV-EIRELSMTYDGK 180

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +IEI++ A  FL   +R  VG +  +G G  +  + E  ++A+D  +   +APPEGL+  
Sbjct: 181 IIEIQITASHFLRYMVRKIVGHVVQIGLGSLSIQEFENIIEAKDPTKGLFIAPPEGLFLK 240

Query: 243 SVEY 246
            V Y
Sbjct: 241 EVYY 244


>gi|224534868|ref|ZP_03675437.1| tRNA pseudouridine synthase A [Borrelia spielmanii A14S]
 gi|224513808|gb|EEF84133.1| tRNA pseudouridine synthase A [Borrelia spielmanii A14S]
          Length = 246

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    +IQG IEKA+  +  + + +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTIQGEIEKALMKINKKKIKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L +   I IL L  V   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDMNINIQLNNLKKALNAIL-LKSGIKILKLKHVKNSFHPRFSAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A+ + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWESYQAYYVNKKLNISNLNQMAKILIGSHDFTTFSCIKDRSKSKFRHIHFAKFKKK 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS VG++  +     + +  EK LQ+++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIVGTMLDIEIKNESISTFEKILQSKNRNLARTTAPANALF 239

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 240 LDKVYYE 246


>gi|332297806|ref|YP_004439728.1| tRNA pseudouridine synthase A [Treponema brennaborense DSM 12168]
 gi|332180909|gb|AEE16597.1| tRNA pseudouridine synthase A [Treponema brennaborense DSM 12168]
          Length = 257

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/254 (30%), Positives = 119/254 (46%), Gaps = 9/254 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG------SSIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           M    + + Y+G+ + GWQRQ +        ++Q  +E+A+ ++    V + G+GRTDSG
Sbjct: 1   MKNVLLTVSYDGTDFCGWQRQDHADRGEPVRTVQAELERALRIMLKTPVALTGSGRTDSG 60

Query: 55  VHALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           VHA  Q A+F        P     ALN+ L     + +     V   FHARF A  R+Y 
Sbjct: 61  VHAFAQAANFLSPFDSVPPENYVPALNSSL--PPDVRVTAAREVPPGFHARFDARMRTYR 118

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y +     P A E    W I +  D   +   A  L G  D TTF +      S  R ++
Sbjct: 119 YFLYCGATPPAHETRYVWPIRRYPDIARLNRMASCLYGEIDCTTFAAAGDPCESKKRYLE 178

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                + G+ +   + A +FL   +RS VGSL         +    + L+A+DR+  GP 
Sbjct: 179 KAVFYADGDKLVFEIAANAFLWKMVRSVVGSLVYYEQKGKDADFFAEILRARDRRSAGPT 238

Query: 234 APPEGLYFDSVEYS 247
           APP+GL+  +V++ 
Sbjct: 239 APPQGLFLWNVDFE 252


>gi|297620993|ref|YP_003709130.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
 gi|297376294|gb|ADI38124.1| tRNA pseudouridine synthase A [Waddlia chondrophila WSU 86-1044]
          Length = 254

 Score =  256 bits (654), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 127/246 (51%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            + + I Y+G+ + GWQ  K G SI+G ++KA+ ++  E + ++GA RTD+GVHAL Q+A
Sbjct: 6   NFLLTIAYDGTPFLGWQETKEGPSIEGELKKALRIILKEEIKLNGASRTDAGVHALGQLA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F   ++     L K++NA L     I +  +  V+  FHA  +   + Y YR+      
Sbjct: 66  NFHTTKKPHLFTLLKSINALL--PGEIKVTAIEEVEASFHATLNNTGKQYRYRLSFGPVQ 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDVNS- 179
               + R W IP  LD E MR+AA+ L G HDF  F ++    +  S IRT+    +   
Sbjct: 124 FPHVRHREWHIPGKLDIEAMRLAAKSLEGTHDFKAFCNVKKNDTYDSTIRTLSKLSLAEL 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +E+ +    FL+   R+ VG+L  +G  +     L+K +   DR + GP AP  GL
Sbjct: 184 ENDTLEVIMEGNHFLYKMARNIVGTLVYIGKKRIQLNTLKKLVLNGDRTQLGPTAPAHGL 243

Query: 240 YFDSVE 245
               V 
Sbjct: 244 TLFHVF 249


>gi|291567810|dbj|BAI90082.1| tRNA pseudouridine synthase A [Arthrospira platensis NIES-39]
          Length = 278

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 108/248 (43%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  +II+Y+G+ + GWQRQ N  ++Q  IE AI  V   E V +H AGRTDSGVHA  Q
Sbjct: 5   QRIALIIQYDGTHFHGWQRQPNQRTVQEDIETAISKVLKQERVPLHAAGRTDSGVHAAAQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD             LN  L     + I   + V   +HARF A  R Y Y + T  
Sbjct: 65  VAHFDAPAHIPAYRWATILNGRL--PADVLIRASAPVPSDWHARFDAQWRRYRYSLYTDA 122

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +   W      LD   M  A + L+G H  + F+            +   +   
Sbjct: 123 RPNLFIRQFTWHYYHQRLDESLMLAALKPLLGYHHLSAFQRAGSSRPHAWVDVQDVECWR 182

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I V A  FL+  +R  VG L  VG  + +  + +     + R+     APP+GL
Sbjct: 183 SEAFIHIEVQASGFLYGMMRLLVGLLVQVGAKERSLENFQDIWVNERREIVKSAAPPQGL 242

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 243 CLLRVGYP 250


>gi|227494575|ref|ZP_03924891.1| tRNA-pseudouridine synthase I [Actinomyces coleocanis DSM 15436]
 gi|226832309|gb|EEH64692.1| tRNA-pseudouridine synthase I [Actinomyces coleocanis DSM 15436]
          Length = 302

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 86/265 (32%), Positives = 138/265 (52%), Gaps = 20/265 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ +   Y G+ + GW +Q    ++QG++E+A+ LV  E V +  AGRTD+GVHA  Q 
Sbjct: 1   MRFRLECAYRGTFFRGWAKQPGLRTVQGTLEEALALVLREPVELTVAGRTDAGVHASAQT 60

Query: 62  AHFDLVREWVP------------VILCKALNAYLKISD-------TISILNLSIVDKQFH 102
           AHFD+  + +               L + LN  ++ +D        + + ++  V   F 
Sbjct: 61  AHFDVCADRLMQVTKQAEVVHACEALTRRLNRLIRRADSNASGLPDVVVYSIEPVADVFD 120

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           ARF+A+RR Y+YR+        L     W + + L    MR AA+ LVG HDF +F    
Sbjct: 121 ARFAALRRHYVYRVADVAGRNPLYAESVWWVEEPLQIHLMREAARALVGEHDFLSFCKPR 180

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
            + +S IRT++  D+      +E+R+ A +F H+ +RS VG+L  VG G+   T +   +
Sbjct: 181 -EGASTIRTLEAVDLVETDTGLEVRLSADAFCHSMVRSIVGALVEVGRGRKPVTWIADLV 239

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
               R++  PLAPP GL   +V+Y 
Sbjct: 240 AFPSREQAAPLAPPHGLTLRAVDYP 264


>gi|210615874|ref|ZP_03290836.1| hypothetical protein CLONEX_03055 [Clostridium nexile DSM 1787]
 gi|210150077|gb|EEA81086.1| hypothetical protein CLONEX_03055 [Clostridium nexile DSM 1787]
          Length = 247

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 117/249 (46%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + IEY+GS Y GWQR    ++ ++I   I + I  +T E + +    RT+ GVHA
Sbjct: 1   MRNIKLTIEYDGSRYQGWQRLGKDESTNTIANKITEVIKKMTNEDIELFCGSRTEVGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             Q A F    +   + +   LN YL     I+I ++    ++FHA  +A  + Y+YRI 
Sbjct: 61  YGQAASFKTTTDMTLIEIQHYLNRYL--PMDIAITDIEEKPERFHASLNATSKIYMYRIS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P   E+   +   K  D + M+ AA  LVG+HDF  F ++     S ++ I   DV
Sbjct: 119 VSEVPSVFERKYVYHSFKRPDVDLMKQAAILLVGKHDFKKFSTVKKN-KSTVKEIYDIDV 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  ++I +    FLH   R  +G+L  +G G     D+E    +         A P+
Sbjct: 178 YDDGEELQITLHGNDFLHNMARMILGTLLDIGVGNRKKEDIELIFDSNSDVAASAPADPK 237

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 238 GLYLQEVLY 246


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

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 165/211 (78%), Gaps = 1/211 (0%)

Query: 38  VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSI 96
           +TGE V V GAGRTDSGVHA+ QV H DL +EW P  L  ALNA+L+++ + +SIL++  
Sbjct: 16  LTGETVSVRGAGRTDSGVHAMGQVIHVDLSKEWSPYQLQNALNAHLRLAGERVSILDVEA 75

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           V + F ARFSA+RR YLYRI++R+APLALE G+AW +PK+LD E M  AAQ LVGRHDF+
Sbjct: 76  VPEFFDARFSALRRHYLYRIVSRRAPLALEAGKAWWVPKTLDHEVMHAAAQRLVGRHDFS 135

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           TFRS HCQA+SP+RT+D  DV   G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  
Sbjct: 136 TFRSAHCQANSPVRTLDRLDVTRSGALIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPD 195

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           D+E AL+A++RK CGP+APP+GLYF  V+Y 
Sbjct: 196 DVEAALEARNRKACGPVAPPDGLYFLQVDYP 226


>gi|326792524|ref|YP_004310345.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
 gi|326543288|gb|ADZ85147.1| tRNA pseudouridine synthase A [Clostridium lentocellum DSM 5427]
          Length = 245

 Score =  255 bits (653), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 122/247 (49%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  + ++I+Y+GS Y G+Q Q++   ++Q  IE  +  +T E V + G  RTD GVHA  
Sbjct: 1   MRNFKIVIQYDGSRYKGFQLQRDTDLTVQAKIEAVLEKMTEEQVEIIGCDRTDVGVHAEN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VA F          +   L  Y  + + I + ++  VD++FHAR++   ++Y Y I   
Sbjct: 61  YVASFKTECTLSTACMLDYL--YEFLPEDIVVKSIEEVDERFHARYNVKAKTYEYTINCG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +     + ++ D ++M   A    G HDF +F S+     S ++TI+  ++  
Sbjct: 119 AQRNVFNRKYVHHMSENFDLKSMNEVAAVFKGTHDFQSFTSLKPNGKSTMQTINEIEIIQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++++IRV A  FL    R  +G++   G G  T+   ++ +  + R    P+A P+ L
Sbjct: 179 KGDILQIRVTADDFLLHMPRMIIGAIVEAGKGTITAQQTQEVMDKKQRATGYPMAKPKAL 238

Query: 240 YFDSVEY 246
               V+Y
Sbjct: 239 SLVEVKY 245


>gi|209527116|ref|ZP_03275630.1| tRNA pseudouridine synthase A [Arthrospira maxima CS-328]
 gi|209492456|gb|EDZ92797.1| tRNA pseudouridine synthase A [Arthrospira maxima CS-328]
          Length = 278

 Score =  255 bits (653), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 110/248 (44%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  +II+Y+G+ + GWQRQ N  ++Q  IE AI  V   E V +H AGRTDSGVHA  Q
Sbjct: 5   QRIALIIQYDGTHFHGWQRQPNQRTVQEDIETAIGKVLKQERVPLHAAGRTDSGVHAAAQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD             LN+ L     + I   + V K +HARF A  R Y Y + T  
Sbjct: 65  VAHFDAPAHIPAYRWATILNSRL--PADVLIRASAPVAKDWHARFDAQWRRYRYSLYTDA 122

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +   W      LD   M  A + L+G H  + F+            +       
Sbjct: 123 RPNLFIRRFTWHYYHQRLDESLMLAALKPLLGYHHLSAFQRAGSSRPHAWVDVQDVQCWR 182

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I V A  FL+  +R  VG L  VG G+ +  + +     + R+     APP+GL
Sbjct: 183 SEAFIHIEVQASGFLYGMMRLLVGLLVQVGAGERSLENFQDIWVNERREIVKSAAPPQGL 242

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 243 CLLRVGYP 250


>gi|225013075|ref|ZP_03703490.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-2A]
 gi|225002803|gb|EEG40784.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-2A]
          Length = 248

 Score =  255 bits (653), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 115/247 (46%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G+ Y GWQRQ N  S+Q  +E A+  +  E + +  +GRTD+GVHA +  
Sbjct: 1   MRYFLEFSYAGTNYHGWQRQPNAVSVQEVLEHALSTLLKETISLLASGRTDTGVHARQMF 60

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          L   LN +L     I + +L  V  + HARF A+ RSY Y I   +
Sbjct: 61  AHFDGKLSLETFQQLVYQLNQFL--PQDIVVHSLREVKAEAHARFDALSRSYEYHIALGK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P        + I + LD E M  AA  L+   DF  F        + +  I +   +  
Sbjct: 119 TP--FGNSMHYRINQDLDLEAMNEAAAILLEYEDFECFSKSRTDVKTFLCDISYAQWSKT 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N     + A  FL   +R+ VG+L  +G  K    DL   ++++ R + G   P +GL+
Sbjct: 177 KNGYIFTITANRFLRNMVRAIVGTLIEIGLKKKEIEDLRGIIKSKSRSKAGFSVPAQGLF 236

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 237 LTRIEYP 243


>gi|284053328|ref|ZP_06383538.1| tRNA pseudouridine synthase A [Arthrospira platensis str. Paraca]
          Length = 278

 Score =  255 bits (652), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 108/248 (43%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  +II+Y+G+ + GWQRQ N  ++Q  IE AI  V   E V +H AGRTDSGVHA  Q
Sbjct: 5   QRIALIIQYDGTHFHGWQRQPNQRTVQEDIETAISKVLKQERVPLHAAGRTDSGVHAAAQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD             LN  L     + I   + V   +HARF A  R Y Y + T  
Sbjct: 65  VAHFDAPAHIPAYRWATILNGRL--PADVLIRASAPVPSDWHARFDAQWRRYRYSLYTDA 122

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +   W      LD   M  A + L+G H  + F+            +   +   
Sbjct: 123 RPNLFIREFTWHYYHQRLDESLMLAALKPLLGYHHLSAFQRAGSSRPHAWVDVQDVECWR 182

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I V A  FL+  +R  VG L  VG  + +  + +     + R+     APP+GL
Sbjct: 183 SEAFIHIEVQASGFLYGMMRLLVGLLVQVGAKERSLENFQDIWVNERREIVKSAAPPQGL 242

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 243 CLLRVGYP 250


>gi|288817539|ref|YP_003431886.1| pseudouridylate synthase [Hydrogenobacter thermophilus TK-6]
 gi|288786938|dbj|BAI68685.1| pseudouridylate synthase [Hydrogenobacter thermophilus TK-6]
 gi|308751142|gb|ADO44625.1| tRNA pseudouridine synthase A [Hydrogenobacter thermophilus TK-6]
          Length = 241

 Score =  255 bits (652), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/244 (32%), Positives = 131/244 (53%), Gaps = 5/244 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y +++ Y G+ + GWQ Q N  ++QG I++++  V  E + + G  RTD+GVHA   
Sbjct: 1   MPNYVLLLSYVGTNFHGWQVQPNLRTVQGVIKESLEKVFREDIKLVGCCRTDAGVHAKEY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F   +E  P  L KALN+ L   + + I  +  V + F+AR+S   + Y+YR++   
Sbjct: 61  VANFYAKKEMEPYKLLKALNSLL--PEDVGIKRVW-VQEGFNARYSVRGKVYVYRVLNSF 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +  A  +  AW +P+ LD   M+ A + L GR DF+ F     +  + +  ++   ++  
Sbjct: 118 SRDAFIEPFAWRVPQKLDLSKMQKACELLAGRRDFSAFAKKEEEDKNTVIDLEEVRLSKV 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +LIEI   ARSFL   +R  VG +  +G G+   + LE+ L   +RK C   A  +GL 
Sbjct: 178 EDLIEISFRARSFLRYMVRRMVGCMVQIGLGRINLSHLEEYLS--NRKTCPYTAKAKGLT 235

Query: 241 FDSV 244
            + V
Sbjct: 236 LEKV 239


>gi|239994150|ref|ZP_04714674.1| tRNA pseudouridine synthase A [Alteromonas macleodii ATCC 27126]
          Length = 242

 Score =  255 bits (652), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 77/226 (34%), Positives = 112/226 (49%), Gaps = 2/226 (0%)

Query: 22  KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNA 81
           +   S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV HF+             +NA
Sbjct: 1   REVPSVQEHLEKALSTVANEPIEVQCAGRTDAGVHATGQVVHFNCDAPRSERAWTLGVNA 60

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
            L   +++++     V   FHARFSA  R Y Y I   +   A+       I + LD + 
Sbjct: 61  NL--PNSVAVTWAKNVSDDFHARFSATHRRYRYVIHNAKMRPAILHSGVTHIHRELDEKK 118

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
           M +AAQ L+G  DFT+FR+  CQ+ +P R +    V   G  + I + A +FLH  +R+ 
Sbjct: 119 MHVAAQALLGEQDFTSFRAALCQSKTPFRNVTDVSVYRQGRYVIIDIRANAFLHHMVRNI 178

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            G+L  +G G+     +   L  +DR +    A P GLY   V Y 
Sbjct: 179 TGALVEIGAGEQDVNWIAHLLSLKDRSKSAATAKPNGLYLVDVTYP 224


>gi|318042539|ref|ZP_07974495.1| tRNA pseudouridine synthase A [Synechococcus sp. CB0101]
          Length = 294

 Score =  255 bits (652), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 118/248 (47%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y+G+ Y GWQRQ    S+Q ++E+AI  +     + V  AGRTD+GVHA  Q
Sbjct: 22  RRIALCLQYDGAPYCGWQRQPRDPSVQETLERAIAALDPRRPLSVQAAGRTDTGVHAAAQ 81

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L    +I +   + V   +HA FSA  R Y Y +   +
Sbjct: 82  VVHFDAEGPIPAQRWPAALNGRL--PASIRVRAGAEVPADWHACFSASYRRYRYTLYNAR 139

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD + MR A + ++G HDF  F       S    T+    V  
Sbjct: 140 LPNLFLAPWSWHRYQLRLDEQLMRQALEGMLGEHDFAAFERAGSSRSHSRTTLQEVTVER 199

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LIE+ + A  FL+  +R  +G L  VG+ + +    E+  +++ R E    APP GL
Sbjct: 200 RGDLIEVELQASGFLYGMVRLVMGQLVAVGEQRLSLAAFERRWRSRARDEVKEAAPPHGL 259

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 260 TLLRVGYP 267


>gi|326522897|dbj|BAJ88494.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 328

 Score =  255 bits (651), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 87/255 (34%), Positives = 126/255 (49%), Gaps = 11/255 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHAL 58
            ++ M+I Y+G+ + GWQ Q +  +IQ  +EKA+  +T    + + + GAGRTD+GVHA 
Sbjct: 47  RKWRMVIAYDGTKFKGWQYQPSPPTIQCFLEKALMRITKLDRKELCLVGAGRTDTGVHAR 106

Query: 59  RQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAHF              A+N  L     I +  +S    +FHAR S   + Y Y+I 
Sbjct: 107 GQVAHFTTPFAYHCLDSFHSAINGLL--PPDIRVREISAACGEFHARTSTKSKIYHYKIY 164

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHF 175
                       A+     L+   M+ AA H VG HDFT+F +   + +  SPI+ I  F
Sbjct: 165 NEAVMDPFHTNYAYHSAHKLNPHAMQEAANHFVGVHDFTSFANAVHNDRVRSPIKKISRF 224

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL-- 233
           DV     +I++ V    FL+ Q+R+ V  L  VG        + K + A+DRKE   +  
Sbjct: 225 DVTKMDAIIQLEVEGTGFLYRQVRNMVALLIQVGREGLPPEIVPKIIAAKDRKELAKVAL 284

Query: 234 -APPEGLYFDSVEYS 247
            APP GLY  SV Y 
Sbjct: 285 SAPPHGLYLMSVNYD 299


>gi|224531952|ref|ZP_03672584.1| tRNA pseudouridine synthase A [Borrelia valaisiana VS116]
 gi|224511417|gb|EEF81823.1| tRNA pseudouridine synthase A [Borrelia valaisiana VS116]
          Length = 246

 Score =  255 bits (651), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 124/247 (50%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + + +H +GRTD GVHA  Q
Sbjct: 1   MRKILAEIAYDGSIYHGFQIQPKKPTVQGEIEKALMKINKKKIKIHSSGRTDKGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  V   FH RF+A +R Y Y I+   
Sbjct: 61  IITFDININIQLNNLKKALNAIL-LKNSIKILKLKYVKNSFHPRFNAKKRKYRYCILNSN 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLNISNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIHFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISIFETILKSKNRNLARTTAPANALF 239

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 240 LDKVYYE 246


>gi|331092366|ref|ZP_08341192.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401390|gb|EGG80976.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 246

 Score =  255 bits (651), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 83/242 (34%), Positives = 127/242 (52%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MII Y+G+ Y GWQRQ     +IQG IEK I  V G  V + G+GRTD GVHA  QVA+ 
Sbjct: 1   MIIAYDGTKYQGWQRQSGTPMTIQGIIEKTIGEVVGYPVEIDGSGRTDGGVHAGGQVANV 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            L  +    +  + LN  L   + I I ++ +V  +FH+R  A+ ++Y Y +  R+    
Sbjct: 61  RLSGKVEEAVFQEKLNEKL--PEDIRICHVELVLNRFHSRLDAVAKTYEYVVDMREKADV 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   +   K L+ E MR AA  L+G+HDF+ F     +  S +R +    + ++   +
Sbjct: 119 FTRKYCYHYTKPLEPEKMRKAAALLIGKHDFSAFTDKKDE-KSAVRELYDIQIETYRQKL 177

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R     F++ Q+R FVG+L   G G+ +   + +AL+++ R   G LAP   L    V
Sbjct: 178 YFRFYGNGFMYHQVRIFVGTLLEAGAGERSVESVLEALKSKKRVNAGFLAPAHALTLKEV 237

Query: 245 EY 246
           EY
Sbjct: 238 EY 239


>gi|254430842|ref|ZP_05044545.1| tRNA pseudouridine synthase A [Cyanobium sp. PCC 7001]
 gi|197625295|gb|EDY37854.1| tRNA pseudouridine synthase A [Cyanobium sp. PCC 7001]
          Length = 306

 Score =  255 bits (651), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 79/252 (31%), Positives = 116/252 (46%), Gaps = 8/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVH 56
            R  + ++Y+G  + GWQRQ N  S+Q ++E AI ++              AGRTD+GVH
Sbjct: 12  RRIALCLQYDGGAFHGWQRQHNAPSVQAALEDAIAILDPPAARPRPPRTWAAGRTDTGVH 71

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QV HFD           KALN  L    TI ++  S V   +HA +SA  R Y Y I
Sbjct: 72  AAAQVVHFDSCGPIPAGRWPKALNGRL--PPTIRVMAASQVPPDWHACYSATYRRYRYTI 129

Query: 117 ITRQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              +AP       +W      LD   M  A Q ++G HDF+ F+    +      T+   
Sbjct: 130 FNGRAPNLFLAPWSWHRYQYRLDENAMVQALQGMLGEHDFSAFQRTGSRRRHARTTLQDV 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +   G+L+ + + A  FL+  +R  +G L  VG+G+ +     +  + +DR      AP
Sbjct: 190 LLEREGDLLRVELQASGFLYGMVRLVLGQLVAVGEGRLSPEAFARRWRHRDRGAVKEAAP 249

Query: 236 PEGLYFDSVEYS 247
           P GL    V Y 
Sbjct: 250 PHGLCLLRVGYP 261


>gi|330998477|ref|ZP_08322301.1| tRNA pseudouridine synthase A [Paraprevotella xylaniphila YIT
           11841]
 gi|329568583|gb|EGG50388.1| tRNA pseudouridine synthase A [Paraprevotella xylaniphila YIT
           11841]
          Length = 256

 Score =  254 bits (650), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 80/254 (31%), Positives = 113/254 (44%), Gaps = 11/254 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  ++KA+  +  + V + GAGRTD+GVHA   
Sbjct: 1   MQRYFLYLAYDGTSYHGWQIQPNGISVQEVLQKALATLLRQPVSITGAGRTDTGVHARMM 60

Query: 61  VAHFDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAHFD        R      L   LN  L     ISI     V    HARF A+ R+Y Y
Sbjct: 61  VAHFDFEYADDPVRRIDGRWLTDKLNRLL--PPDISIYKTVPVAADAHARFDALSRTYHY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +   ++P    +  +  + + LD   M  AA  L    DFT+F  ++    +    I  
Sbjct: 119 YLHFGKSP--FLRAYSCRLYQMLDFGKMNEAAAALFDYTDFTSFSKVNTDTKTNNCRIMQ 176

Query: 175 FDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                         + A  FL   +R+ VG+L  VG GK T       ++ +DR   G  
Sbjct: 177 ARWTELAPGEWRFEIQADRFLRNMVRAIVGTLVEVGRGKLTPEGFRAVIEGKDRCRAGES 236

Query: 234 APPEGLYFDSVEYS 247
            P   L+   V Y 
Sbjct: 237 MPGNALFLVDVAYP 250


>gi|225432191|ref|XP_002275097.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 336

 Score =  254 bits (650), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 128/254 (50%), Gaps = 11/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ ++I Y G+ Y GWQ Q++  +IQ  +EKA+   T    E + + GA RTD+GVHA  
Sbjct: 56  KWRLVIAYEGTRYSGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTDTGVHAWG 115

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +     +  ALN  L     I +  +S    +FHARFS   + Y Y+I  
Sbjct: 116 QVAHFLTPFNYDGLESIHAALNGLL--PPDIRVREISPAVPEFHARFSVKSKIYHYKIYN 173

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFD 176
                   +   +     L+   MR AA+H  G+HDF+ F +   + ++ +P++ I  FD
Sbjct: 174 DAVMDPFLRHYVYHSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKNIFRFD 233

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---L 233
           VN  G L+++ V    FL+ Q+R+ V  L  +G        +   L  +DRKE       
Sbjct: 234 VNEMGALLQLEVEGSGFLYRQVRNMVALLLQIGREAIPPNIVPWILATRDRKELAKYALS 293

Query: 234 APPEGLYFDSVEYS 247
           APP GL   SV+Y+
Sbjct: 294 APPHGLCLMSVKYN 307


>gi|297736816|emb|CBI26017.3| unnamed protein product [Vitis vinifera]
          Length = 326

 Score =  254 bits (650), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 128/254 (50%), Gaps = 11/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ ++I Y G+ Y GWQ Q++  +IQ  +EKA+   T    E + + GA RTD+GVHA  
Sbjct: 46  KWRLVIAYEGTRYSGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTDTGVHAWG 105

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +     +  ALN  L     I +  +S    +FHARFS   + Y Y+I  
Sbjct: 106 QVAHFLTPFNYDGLESIHAALNGLL--PPDIRVREISPAVPEFHARFSVKSKIYHYKIYN 163

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFD 176
                   +   +     L+   MR AA+H  G+HDF+ F +   + ++ +P++ I  FD
Sbjct: 164 DAVMDPFLRHYVYHSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKNIFRFD 223

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---L 233
           VN  G L+++ V    FL+ Q+R+ V  L  +G        +   L  +DRKE       
Sbjct: 224 VNEMGALLQLEVEGSGFLYRQVRNMVALLLQIGREAIPPNIVPWILATRDRKELAKYALS 283

Query: 234 APPEGLYFDSVEYS 247
           APP GL   SV+Y+
Sbjct: 284 APPHGLCLMSVKYN 297


>gi|329965278|ref|ZP_08302208.1| tRNA pseudouridine synthase A [Bacteroides fluxus YIT 12057]
 gi|328523298|gb|EGF50398.1| tRNA pseudouridine synthase A [Bacteroides fluxus YIT 12057]
          Length = 288

 Score =  254 bits (650), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 115/247 (46%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   V
Sbjct: 30  QRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLMV 89

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD         +   LN  L     IS+ +L  V  + HARF A  R Y Y + T + 
Sbjct: 90  AHFDSETPLDVTFMADKLNRLL--PPDISVYSLRAVKPEAHARFDATARMYKYYVTTAKV 147

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +     + ++ D E M  AA+ L    DFT+F  +H    +    I H       
Sbjct: 148 P--FNRRYRCRLFQTPDFERMNEAAKTLFDYTDFTSFSKLHTDVKTNNCRIMHAAWTQLD 205

Query: 182 NL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +     V A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   L+
Sbjct: 206 EVTWVFTVQADRFLRNMVRAIVGTLLEVGRGKLTVEGFRRVIEQKDRCRAGTSVPGNALF 265

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 266 LVDVAYP 272


>gi|284036658|ref|YP_003386588.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
 gi|283815951|gb|ADB37789.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
          Length = 252

 Score =  254 bits (649), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 123/247 (49%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ Y GWQRQ NG S+Q  +E A+  V  + + + G+GRTD+GVHA +Q 
Sbjct: 1   MRYFLHLAYKGTKYHGWQRQPNGLSVQEVLETALSTVLRQPIAIVGSGRTDAGVHAGQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD      P  L ++LN+   I   I++     V    HARF+A  R Y Y+I  R+ 
Sbjct: 61  AHFDTDVAL-PTQLLRSLNSM--IPPDIAVYECFPVRPDDHARFTAQSRYYQYQISRRK- 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +G  ++    L+ E M  AA  L+   DF +F  +     +    I+        
Sbjct: 117 -DPFREGLVYVFTLPLNVELMNEAASRLLHHIDFESFSKVKTDVKTFNCQIEWAYWAQQP 175

Query: 182 NL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           N  +   + A  FLH  +R+ VG+L  VG  + + TD E+ +   DRK  G  AP EGL 
Sbjct: 176 NGDLVFHIKANRFLHGMVRAIVGTLLAVGQERLSVTDFEQIILDHDRKRAGRAAPAEGLS 235

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 236 LVEVGYP 242


>gi|332521721|ref|ZP_08398172.1| tRNA pseudouridine synthase A [Lacinutrix algicola 5H-3-7-4]
 gi|332042551|gb|EGI78752.1| tRNA pseudouridine synthase A [Lacinutrix algicola 5H-3-7-4]
          Length = 247

 Score =  254 bits (649), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 125/246 (50%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQ Q N  S+Q  +EK +  +  E +   GAGRTD+GVHA++  
Sbjct: 1   MRYFIELSYNGKAYHGWQVQPNAISVQEVLEKGLSTLLKEKISTMGAGRTDAGVHAIQLF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD    +   +L   LN++L   + ISI N+  V    HARF A+ R YLYRI  ++ 
Sbjct: 61  AHFDTEVIFEEHMLQYKLNSFL--PEAISIQNIFKVKADAHARFDAVSRQYLYRIALQKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E+  A+L+   LD + ++ A + L    DF  F   +    +    I        G
Sbjct: 119 PFNTEQ--AFLLKAKLDIDRIKEATKILFNYKDFQCFSKSNTDVKTYNCNIMKAQWEVVG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N ++  + A  FL   +R+ VG+L  VG GK    D+   +++++R E G   P   LY 
Sbjct: 177 NELQFTIKADRFLRNMVRAIVGTLINVGVGKLEVNDMHNIIKSKNRSEAGFSVPAHALYL 236

Query: 242 DSVEYS 247
             V Y 
Sbjct: 237 TEVAYP 242


>gi|297829238|ref|XP_002882501.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297328341|gb|EFH58760.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 323

 Score =  254 bits (649), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 85/254 (33%), Positives = 129/254 (50%), Gaps = 12/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHALR 59
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T    + + + GAGRTD+GVHA  
Sbjct: 42  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELHLIGAGRTDAGVHAWG 101

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +        ALN  L     I +  LS    +FHARFSA  + Y Y+I  
Sbjct: 102 QVAHFVTPFNYTSLDSFHAALNGLL--PKDIRVRELSAAVPEFHARFSAHSKVYRYQIYN 159

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSPIRTIDHFD 176
                  ++  A+     L+   MR AA   VG HDF+ F +   +     P++TI  FD
Sbjct: 160 DTFMDPFQRHWAYHCAYKLNASKMREAANLFVGMHDFSAFANATREDGLPDPLKTISRFD 219

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---- 232
           V   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR+        
Sbjct: 220 VIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTTL 279

Query: 233 LAPPEGLYFDSVEY 246
            APP GL   SV+Y
Sbjct: 280 PAPPHGLCLVSVKY 293


>gi|156743919|ref|YP_001434048.1| tRNA pseudouridine synthase ACD [Roseiflexus castenholzii DSM
           13941]
 gi|189029997|sp|A7NR34|TRUA_ROSCS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|156235247|gb|ABU60030.1| tRNA pseudouridine synthase A [Roseiflexus castenholzii DSM 13941]
          Length = 270

 Score =  254 bits (649), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 88/251 (35%), Positives = 124/251 (49%), Gaps = 8/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ + G Q Q NG S+QG++E A   +TGE   +  AGRTD+GVHA  Q
Sbjct: 1   MRNIALRIEYDGTDFVGSQWQTNGRSVQGALEAAWQQLTGERRRMILAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+           + + LN  L   + I IL    V ++FHAR+SA+RR Y Y I   +
Sbjct: 61  VANVSTNTRHSLATIIRGLNGVL--PEDIGILAAWEVPEEFHARYSAVRREYRYVIDNGR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +  A  +P+ LD   M  A Q ++G HDF    S   Q  S +R          
Sbjct: 119 TPSPLLRRHAAYVPRRLDVAAMDRAIQQVIGTHDFAPL-SDGPQEGSTVRICYDARCTCT 177

Query: 181 G----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 L+ I V A +FL   +R+ VG+L  VG+G+  +      L   +R+    LAP 
Sbjct: 178 EVWGQPLVLIDVAANAFLRHMVRNLVGTLIQVGEGRIDADGFAAVLAGANRR-ARVLAPA 236

Query: 237 EGLYFDSVEYS 247
            GLY  +V Y 
Sbjct: 237 HGLYLMAVRYP 247


>gi|46446316|ref|YP_007681.1| putative tRNA-pseudouridine synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
 gi|51316630|sp|Q6MDE3|TRUA2_PARUW RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|46399957|emb|CAF23406.1| putative tRNA-pseudouridine synthase I [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 262

 Score =  254 bits (649), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 114/250 (45%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + I Y+G  YFGWQ+   G S++ +++ ++  +    + +  A RTD GVHA  Q
Sbjct: 15  MQNIKLKIAYDGQAYFGWQKTPAGPSVEKTLQNSLEQILQHTISLQAASRTDKGVHARGQ 74

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           + +F   +          +LN+ L     + IL+   +   FH   + + + Y Y I   
Sbjct: 75  IVNFLTTKSITDLQKFILSLNSLL--PTDLRILSAEKMPSTFHPTLNCVAKEYCYYICYD 132

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSPIRTIDHFDV 177
              L   +  +W  P  L    M  A   L+G HDF+ F +       +  IR +    +
Sbjct: 133 FVQLPEYRPYSWHCPFPLMLGKMTQAISVLIGEHDFSAFCNFKKNVNYTDYIRRVQAIHL 192

Query: 178 NSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               +  + IR+    FL+  +R+ VG+L  +G GK    D+   LQ+QDRK  G  AP 
Sbjct: 193 EVLNHKRLCIRIKGNHFLYKMVRNIVGTLIYIGKGKLMVEDIPSILQSQDRKMAGVTAPA 252

Query: 237 EGLYFDSVEY 246
            GL+  +V Y
Sbjct: 253 HGLFLQTVLY 262


>gi|320160443|ref|YP_004173667.1| tRNA pseudouridine synthase A [Anaerolinea thermophila UNI-1]
 gi|319994296|dbj|BAJ63067.1| tRNA pseudouridine synthase A [Anaerolinea thermophila UNI-1]
          Length = 259

 Score =  254 bits (649), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +I+ Y+G+ + G+QRQ    ++Q  +EKA+  +      +  +GRTD+GVHA  Q
Sbjct: 1   MARYKVILAYDGTHFQGFQRQAGARTVQAEVEKALRSLGWGEESLLSSGRTDTGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FDL        L  ALNA L   + ++   +  V   FH RF+AI R+YLYRII  +
Sbjct: 61  VIAFDLDWRHSLEALRNALNARL--PEDVAAKQVEEVPGDFHPRFNAIERAYLYRIIVAE 118

Query: 121 APLALEKGRAWLIPKSLDC-ENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               L +  AW +   L+  E ++ AAQ L G HDF+ F +   +  S +R I   +   
Sbjct: 119 TRDPLRERYAWRLWPPLEAPEALQSAAQALCGTHDFSAFGTPPVEGGSTLRHIYQAEWRE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+     V   +FL+  +R  V +   VG  + +  D  +A+Q Q R     LAP  GL
Sbjct: 179 NGDEWLFEVRGNAFLYHMVRRMVWAQVQVGLNRLSLADFLEAVQ-QARPLPPGLAPAHGL 237

Query: 240 YFDSVEY 246
               V Y
Sbjct: 238 VLTGVRY 244


>gi|255036264|ref|YP_003086885.1| tRNA pseudouridine synthase A [Dyadobacter fermentans DSM 18053]
 gi|254949020|gb|ACT93720.1| tRNA pseudouridine synthase A [Dyadobacter fermentans DSM 18053]
          Length = 248

 Score =  254 bits (649), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 124/247 (50%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y G+ Y GWQ+Q N   +Q  +E A+  V    V V G+ RTD+GVHA +Q 
Sbjct: 1   MRYFIEFSYRGTAYNGWQKQNNALGVQEVLEAALAKVLRAPVEVTGSSRTDAGVHAEQQF 60

Query: 62  AHFDLVREWVPVIL-CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFDL      V L    LNA   +   I++  L  V +  H+RF+A  R Y YRI  ++
Sbjct: 61  AHFDLPAAIPDVDLMVYKLNAL--VPKDIAVQRLIPVAEDVHSRFAATHRKYEYRITFQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P       A  + ++LD   M  AA  L+  +DF +F  IH   ++   TI        
Sbjct: 119 NP--FLTDLATQMRRNLDVPRMNEAAALLLAHNDFESFSKIHTNVNNFRCTITESRWVEV 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G ++   V A  FL   +R+ VG++  VG  K T  D E+ + +++RK  G  AP EGL+
Sbjct: 177 GEMLVFHVKANRFLRGMVRALVGTMLEVGRQKITVDDFEQIILSRNRKNAGAQAPAEGLF 236

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 237 LVEVGYP 243


>gi|297180263|gb|ADI16482.1| pseudouridylate synthase [uncultured bacterium HF4000_05M23]
          Length = 273

 Score =  254 bits (649), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 119/250 (47%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ +++EY+G+ + G Q Q N  ++QG IE A+  +  E + VH A RTDSGVHA  QV
Sbjct: 1   MRFGLVVEYDGTNFHGSQLQSNARTVQGEIESALLQIFSEKIRVHFASRTDSGVHARGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIV---DKQFHARFSAIRRSYLYRIIT 118
             FD   +  P  + KALN +      + I    +V      F  R  A  R+Y+Y    
Sbjct: 61  GRFDAETDMPPDQIRKALNFHTTT--DVRIRCAQLVEDGPDGFDPRGDASARTYVYTFND 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDV 177
             +  AL++     + K LD   M  A+Q LVG HDF +F        +  +R ++    
Sbjct: 119 APSEPALDRHYVTHVRKPLDEIAMNDASQALVGLHDFASFAGPKAPHDALTMRNVETAST 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ IE ++ A +FLH QIR   G L  VG G      +   L   +R     + P +
Sbjct: 179 TRIGDSIEFKITANAFLHQQIRRIAGVLCDVGTGGSPVAVVGDLLATAERGAASHVMPAQ 238

Query: 238 GLYFDSVEYS 247
           GL  + + Y 
Sbjct: 239 GLCLEKIAYE 248


>gi|298491424|ref|YP_003721601.1| tRNA pseudouridine synthase A ['Nostoc azollae' 0708]
 gi|298233342|gb|ADI64478.1| tRNA pseudouridine synthase A ['Nostoc azollae' 0708]
          Length = 275

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 119/246 (48%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ    ++Q  IE AI  + G  V +HGAGRTD+GVHA  Q+A
Sbjct: 12  RVALVIQYRGTHFRGWQRQSCQRTVQEEIETAIATILGYHVTLHGAGRTDAGVHAAAQIA 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD             LN+YL     I I   + V+  +HARFSA+ R Y Y I T   P
Sbjct: 72  HFDATGFIPAHKWATVLNSYL--PPDILIRASASVNDFWHARFSAVSRRYRYTIYTEVLP 129

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                  +W      LD   ++ A + L+G+H    F       S     +   + +  G
Sbjct: 130 NLFVNPFSWHYYYAPLDESVIQAALKPLLGKHHLAAFHRAGSARSHSWVEVQVAECHRSG 189

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+  +R  VG L  +G G+ T  +  +  + + R++    APP+GL  
Sbjct: 190 PFIHIEIQANGFLYGMVRLLVGMLVQLGSGQVTLDNFTEIWKEERREKVKYAAPPQGLCL 249

Query: 242 DSVEYS 247
             VEY 
Sbjct: 250 LRVEYP 255


>gi|28377870|ref|NP_784762.1| tRNA pseudouridine synthase A [Lactobacillus plantarum WCFS1]
 gi|254556054|ref|YP_003062471.1| tRNA pseudouridine synthase A [Lactobacillus plantarum JDM1]
 gi|308180048|ref|YP_003924176.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ST-III]
 gi|38258756|sp|Q88XU9|TRUA_LACPL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|28270703|emb|CAD63609.1| pseudouridylate synthase A [Lactobacillus plantarum WCFS1]
 gi|254044981|gb|ACT61774.1| tRNA pseudouridine synthase A [Lactobacillus plantarum JDM1]
 gi|308045539|gb|ADN98082.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ST-III]
          Length = 262

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 123/251 (49%), Gaps = 7/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHAL 58
            RY +++ Y+G+ + G+QRQ +  +++  + KA+  +     E +V++GAGRTD+GVHA 
Sbjct: 3   TRYKVVLAYDGTNFAGFQRQPHQRTVEQVVTKAVNKMAKDPVEPIVIYGAGRTDAGVHAF 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            Q  HFDL  E  P  + + LN+ L       +  +SIV   FHAR+  + + Y YR   
Sbjct: 63  GQTLHFDLPYEINPEGVRRGLNSML--PMDTIVKAVSIVPNDFHARYDTVGKRYWYRAYQ 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +     ++        + D + ++ A   L GRHDF+TF +   QA   +R I      
Sbjct: 121 NEFVDPFKRHYTGHFKFAADIDRIQQAIGDLEGRHDFSTFVASGSQAHDHVREIYSAKAW 180

Query: 179 SFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +  +   I+       FL+ Q+R  V  L  +G G+     +   L A+DR++    AP 
Sbjct: 181 ALPDEREIQFEFCGSGFLYNQVRIMVAVLMEIGQGRRAVDCIPALLAAKDREQARGTAPA 240

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 241 AGLYMKKVYYE 251


>gi|218129428|ref|ZP_03458232.1| hypothetical protein BACEGG_01005 [Bacteroides eggerthii DSM 20697]
 gi|317477530|ref|ZP_07936755.1| tRNA pseudouridine synthase A [Bacteroides eggerthii 1_2_48FAA]
 gi|217988158|gb|EEC54481.1| hypothetical protein BACEGG_01005 [Bacteroides eggerthii DSM 20697]
 gi|316906331|gb|EFV28060.1| tRNA pseudouridine synthase A [Bacteroides eggerthii 1_2_48FAA]
          Length = 251

 Score =  253 bits (648), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 115/248 (46%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDAPLDVDFMADKLNRLL--PPDISVYRLRAVRPDAHARFDATARMYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   ++     + ++ D E M  AAQ L    DFT+F  +H    +    I H      
Sbjct: 119 MP--FDRQYRCRLFQTPDFERMNEAAQTLFEYTDFTSFSKLHTDVKTNNCKIMHAAWTQV 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   L
Sbjct: 177 DEVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTVEGFRRIIEQKDRCRAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVTYP 244


>gi|282601160|ref|ZP_05980960.2| tRNA pseudouridine synthase A [Subdoligranulum variabile DSM 15176]
 gi|282570067|gb|EFB75602.1| tRNA pseudouridine synthase A [Subdoligranulum variabile DSM 15176]
          Length = 249

 Score =  253 bits (648), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 115/249 (46%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y + I Y G+ Y G+Q Q N  ++   ++ A+  V G    V G  RTD+GVHA R  
Sbjct: 1   MTYLLWITYKGTNYAGFQVQPNAPTVCAVLQDAMQAVLGSRPDVKGCSRTDAGVHARRFA 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F          +  ALNA+L     I  L +  V + FHAR++A  ++Y Y I+  + 
Sbjct: 61  LSFCYTGRVPAEKIVPALNAHL--PPDIRALAVQAVPEGFHARYAAHEKTYCYHILNARI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS---SPIRTIDHFDVN 178
                      + + LD   M+ AA   VG HDF    +     +     +RTI    V+
Sbjct: 119 DDPFTLDTCHRVAQPLDLAAMQAAAAQFVGTHDFLALCASGSSVAAHGDTVRTISRCTVS 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+   I V A  +L+  +R   G+L   G  K T   +   LQ++DR++ GP  P +G
Sbjct: 179 RCGDRFVITVTADGYLYNMVRILAGTLVEAGLHKRTPDSIPALLQSRDRRQAGPTLPAKG 238

Query: 239 LYFDSVEYS 247
           L+ + V Y 
Sbjct: 239 LFLEDVAYP 247


>gi|16329915|ref|NP_440643.1| tRNA pseudouridine synthase A [Synechocystis sp. PCC 6803]
 gi|3915173|sp|P73295|TRUA_SYNY3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1652401|dbj|BAA17323.1| pseudouridine synthase 1 [Synechocystis sp. PCC 6803]
          Length = 275

 Score =  253 bits (648), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 120/248 (48%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++++Y G+ + GWQRQ N SSIQ  +E AI  V G+ V +HGAGRTD+GVHA  QV
Sbjct: 10  QRVALVMQYLGTHFHGWQRQPNFSSIQEEVELAIAKVVGQPVTLHGAGRTDAGVHAAAQV 69

Query: 62  AHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD    +  P    K LN +L     I +   + VD  +HARFSA+ R Y Y I T Q
Sbjct: 70  AHFDDPVGQIPPHRWSKILNGHL--PQDIIVRGSAAVDSHWHARFSALWRRYRYSIYTDQ 127

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  L  + ++ A + L+G+H    F             +   +   
Sbjct: 128 WPNLFADQFSWHYYRFPLQEKTIQAAMEPLLGKHHLAAFHRAGSARRHSWVEVQGVECYR 187

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++ + + A  FL+  +R  VG L  VG G+ + TD       Q R      AP +GL
Sbjct: 188 RGPMVYLEIQANGFLYGMVRLLVGMLAEVGSGQRSLTDFNDIWVNQRRDLVKYAAPAKGL 247

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 248 CLLRVGYE 255


>gi|297192674|ref|ZP_06910072.1| tRNA pseudouridine synthase A [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197721671|gb|EDY65579.1| tRNA pseudouridine synthase A [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 286

 Score =  253 bits (648), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 117/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G  + GW +Q  G  ++QG IE A+  VT  G    +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQAGGRRTVQGEIEDALRTVTRSGTTYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL  E       K L     ++S  + I +++   + F+ARFSAI R Y YR+ 
Sbjct: 70  GQVAHVDLPSELWAEHREKLLKRLAGRLSRDVRIWSVAEAPEGFNARFSAIWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD   M  A+  LVG HDF  +       ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWPLDVAAMNEASAGLVGEHDFAAYCKKR-DGATTIRTLQQLS 188

Query: 177 VNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  +I   V A +F H  +RS VG+L  VGDG   +    K L A  R     +  
Sbjct: 189 WERDPSGVITATVKADAFCHNMVRSLVGALLFVGDGHRPAEWPAKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|168028382|ref|XP_001766707.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162682139|gb|EDQ68560.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 331

 Score =  253 bits (647), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 92/306 (30%), Positives = 142/306 (46%), Gaps = 60/306 (19%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G+QRQK   ++QG +E A     G+ V+   + RTD+GVHAL   
Sbjct: 10  QRYLITVEYIGTRFLGFQRQKGKRTVQGCLESAFEKFIGQPVISAVSSRTDTGVHALANT 69

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD---TISILNLSIVDKQFHARFSA 107
            H D+ R              P ++  A+N +L        ++++ +  V   FHAR+ A
Sbjct: 70  CHVDVERKSKRKPGEVMPPHEPRVVQTAINHFLHAQKDAGDMAVVGVQCVSPDFHARYRA 129

Query: 108 IRRSYLYRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
             R+Y YR++T  +     +K +AW + + L+  +M  A + LVG HDF++FR+  CQA+
Sbjct: 130 QERTYHYRVLTGNRQMSVFQKDQAWHVSEELNLTSMMEACKVLVGHHDFSSFRATGCQAN 189

Query: 167 SPIRTIDHFDVNSFG--------------------------------------------- 181
           SPIRT+D   V                                                 
Sbjct: 190 SPIRTLDELHVCEMPAWPCFPSPEERQQSSQNAETKDLESTTSELKDPILTSKLGTSEKL 249

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
               I   ARSFL+ Q+R  VG+LK VG G  T  D+++ L A+   +   +AP  GLY 
Sbjct: 250 RCFVITARARSFLYHQVRLMVGTLKAVGCGDLTVQDVQRILDARTITQAPAMAPACGLYL 309

Query: 242 DSVEYS 247
            +V+Y 
Sbjct: 310 ANVKYD 315


>gi|300173999|ref|YP_003773165.1| tRNA pseudouridine synthase A [Leuconostoc gasicomitatum LMG 18811]
 gi|299888378|emb|CBL92346.1| tRNA pseudouridine synthase A [Leuconostoc gasicomitatum LMG 18811]
          Length = 255

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 86/257 (33%), Positives = 130/257 (50%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTD 52
           M RY  I+ Y+GS +FG+Q Q     +   ++QG + KA+  +       + V GA RTD
Sbjct: 1   MPRYKAIVSYDGSDFFGFQVQTKNGVERQRTVQGELNKAVNQMAKNPTPAIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL  +   + + K LN  L     I I ++  V   FHARF+   + Y
Sbjct: 61  TGVHAFGQVVHFDLPFDINVIGVRKGLNTLL--PKDIIIQSVDQVANDFHARFNTHAKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YR+ T+      ++         LD E ++IA   L+G HDF +F +   Q  + IRTI
Sbjct: 119 VYRVSTQDFTDPFKRFYTGHFQWQLDVERIKIALPDLLGEHDFASFAASGNQTITTIRTI 178

Query: 173 DHFD--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              D  VN+    +       +FL+ QIR  VG L  +G+G+    D+ + +  +DR++ 
Sbjct: 179 TRADLKVNNDEQELVFTFEGNAFLYNQIRIMVGVLLEIGNGRRDVHDIIRLIAVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
              AP  GLY D + Y 
Sbjct: 239 RFTAPASGLYLDEIYYD 255


>gi|110737769|dbj|BAF00823.1| putative tRNA pseudouridine synthase [Arabidopsis thaliana]
          Length = 323

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 129/254 (50%), Gaps = 12/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHALR 59
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T    + + + GAGRTD+GVHA  
Sbjct: 42  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELQLIGAGRTDAGVHAWG 101

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +        ALN  L     I +  LS    +FHARFSA  + Y Y+I  
Sbjct: 102 QVAHFVTPFNYTSLDSFHAALNGLL--PKDIRVRELSAAVPEFHARFSASSKVYRYQIYN 159

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHFD 176
                  ++  A+     L+   MR AA   VG+HDF+ F +   +     P++TI  FD
Sbjct: 160 DTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFANATREDGVPDPLKTISRFD 219

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---- 232
           V   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR+        
Sbjct: 220 VIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTSL 279

Query: 233 LAPPEGLYFDSVEY 246
            A P GL   SV+Y
Sbjct: 280 PASPHGLCLVSVKY 293


>gi|300767857|ref|ZP_07077767.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|300494842|gb|EFK30000.1| tRNA-pseudouridine synthase I [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
          Length = 273

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 123/251 (49%), Gaps = 7/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHAL 58
            RY +++ Y+G+ + G+QRQ +  +++  + KA+  +     E +V++GAGRTD+GVHA 
Sbjct: 14  TRYKVVLAYDGTNFAGFQRQPHQRTVEQVVTKAVNKMAKDPVEPIVIYGAGRTDAGVHAF 73

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            Q  HFDL  E  P  + + LN+ L       +  +SIV   FHAR+  + + Y YR   
Sbjct: 74  GQTLHFDLPYEINPEGVRRGLNSML--PMDTIVKAVSIVPNDFHARYDTVGKRYWYRAYQ 131

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +     ++        + D + ++ A   L GRHDF+TF +   QA   +R I      
Sbjct: 132 NEFVDPFKRHYTGHFKFAADIDRIQQAIGDLEGRHDFSTFVASGSQAHDHVREIYSAKAW 191

Query: 179 SFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +  +   I+       FL+ Q+R  V  L  +G G+     +   L A+DR++    AP 
Sbjct: 192 ALPDEREIQFEFCGSGFLYNQVRIMVAVLMEIGQGRRAVDCIPALLAAKDREQARGTAPA 251

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 252 AGLYMKKVYYE 262


>gi|229489482|ref|ZP_04383345.1| tRNA pseudouridine synthase A [Rhodococcus erythropolis SK121]
 gi|229323579|gb|EEN89337.1| tRNA pseudouridine synthase A [Rhodococcus erythropolis SK121]
          Length = 294

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ +  ++ G IE  +  V    V +  AGRTD+GVHA  QV
Sbjct: 21  VRLRLDISYDGTDFSGWARQTDLRTVCGEIEDKLGTVLRRPVQLTVAGRTDAGVHATGQV 80

Query: 62  AHFDLVREWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH D+  E +P    + +      +   + +  +S+V   F ARFSA+RR Y YR+    
Sbjct: 81  AHVDVPGELLPDDPSRLVRRLARFLPKDVRVKQISVVPGDFDARFSAMRRYYEYRVTNAA 140

Query: 121 APL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             +  L        PK LD   M+ A+  L+G H+F  F     + ++ +R +  FD   
Sbjct: 141 FGVEPLRARDTVSYPKPLDLGAMQEASNRLLGLHNFAAFCKRR-EGATTVRELQRFDWTQ 199

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +    V A +F  + +RS VG++  VG+G+ T+  +   L    R     +AP  GL
Sbjct: 200 VGTVFTAYVNADAFCWSMVRSLVGAVLSVGEGRRTADWVAGLLDETSRSSSILVAPAHGL 259

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 260 SLVRVDYP 267


>gi|30680075|ref|NP_187351.2| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|119360081|gb|ABL66769.1| At3g06950 [Arabidopsis thaliana]
 gi|332640958|gb|AEE74479.1| tRNA pseudouridine synthase A [Arabidopsis thaliana]
          Length = 323

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 129/254 (50%), Gaps = 12/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHALR 59
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T    + + + GAGRTD+GVHA  
Sbjct: 42  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELQLIGAGRTDAGVHAWG 101

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +        ALN  L     I +  LS    +FHARFSA  + Y Y+I  
Sbjct: 102 QVAHFVTPFNYTSLDSFHAALNGLL--PKDIRVRELSAAVPEFHARFSASSKVYRYQIYN 159

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHFD 176
                  ++  A+     L+   MR AA   VG+HDF+ F +   +     P++TI  FD
Sbjct: 160 DTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFANATREDGVPDPLKTISRFD 219

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---- 232
           V   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR+        
Sbjct: 220 VIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTSL 279

Query: 233 LAPPEGLYFDSVEY 246
            A P GL   SV+Y
Sbjct: 280 PASPHGLCLVSVKY 293


>gi|310658388|ref|YP_003936109.1| tRNA pseudouridine synthase a [Clostridium sticklandii DSM 519]
 gi|308825166|emb|CBH21204.1| tRNA pseudouridine synthase A 2 (tRNA-uridine isomerase I 2) (tRNA
           pseudouridylate synthase I 2) [Clostridium sticklandii]
          Length = 245

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 118/247 (47%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + ++Y G+ Y GWQR K+  ++IQG +E  +  +T E V V G  RTD GVHA  
Sbjct: 1   MRNIKIALQYEGTRYLGWQRLKDQDNTIQGKLEDLLNKMTDEEVQVIGCSRTDKGVHAKS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            +A+F    +     +   +N YL   + I +  +   D +FHAR +A  + Y + I   
Sbjct: 61  LIANFHTNSKMTLHEIQTYMNYYL--PEDIRVTYIEEADDKFHARHNAKTKVYRFTIDNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  A   PK LD + M  AA +L+G HD+  F ++  +  S  ++I    +  
Sbjct: 119 SFADVFTRKTAIHQPKQLDIKAMEKAANYLIGTHDYDAFTTMKSKKKSCRKSIKSIAITK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N + +      FLH  IR   G+L  VG G+ +  +L   L ++DR   GP+   +GL
Sbjct: 179 KNNYVYLEFEGEGFLHNMIRIITGTLIRVGTGEISPEELANILASKDRSLSGPMVEGKGL 238

Query: 240 YFDSVEY 246
               V Y
Sbjct: 239 MLMQVNY 245


>gi|282877805|ref|ZP_06286618.1| tRNA pseudouridine synthase A [Prevotella buccalis ATCC 35310]
 gi|281300121|gb|EFA92477.1| tRNA pseudouridine synthase A [Prevotella buccalis ATCC 35310]
          Length = 243

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 123/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG+S+Q  +++A+ ++  E +V  GAGRTD+GVHA + 
Sbjct: 1   MHRYFICFRYDGTAYHGWQVQPNGNSVQAELQQAMSVILREPIVTVGAGRTDAGVHARKM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD   E         LN  L     IS+LN+  + +  HARFSA  R+Y Y I   +
Sbjct: 61  FAHFDFHAEIDTKQFTYKLNRLL--PRDISVLNVFSLSEDMHARFSAKWRTYHYYIHLSK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  +  +P  LD   M  AA HL+   DF  F   +    + +  +   +    
Sbjct: 119 NP--FLRHYSCQLPYQLDFSLMNEAASHLLKVEDFGAFCKSNTDVKTTLCHVVQAEWVEV 176

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G +     + A  FL   +R+ VG+L  VG  + T  + +  +++ +R + G   P   L
Sbjct: 177 GEDAWYFVIKANRFLRNMVRAVVGTLIEVGRHRMTLDEFDAVVRSGNRTKAGESMPANAL 236

Query: 240 YFDSVEY 246
           + + VEY
Sbjct: 237 FLEDVEY 243


>gi|72163015|ref|YP_290672.1| tRNA pseudouridine synthase A [Thermobifida fusca YX]
 gi|71916747|gb|AAZ56649.1| tRNA pseudouridine synthase [Thermobifida fusca YX]
          Length = 296

 Score =  253 bits (646), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 110/250 (44%), Gaps = 5/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALRQ 60
            R  + I Y+G+ + GW  Q    ++QG ++ A+  V       +  AGRTD+GVHA  Q
Sbjct: 25  TRLRLDISYDGTDFSGWAEQPGRRTVQGELQAALARVLRIPTPQLTVAGRTDAGVHARGQ 84

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D+    W              +   + +  ++     F ARFSA+ R Y+YR+   
Sbjct: 85  VAHVDVPASVWEAEGERLLRRLAGVLPPDVRVTAVAPAPPGFDARFSALFRRYVYRVSDA 144

Query: 120 QAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 L +       + LD + M  AA  L+G HDF  +     + +S +R +   +  
Sbjct: 145 PGGVDPLRRHEVLWHRRPLDVDRMNEAAAALLGEHDFAAYCRKR-EGASTVRELQRLEWR 203

Query: 179 SFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                +    V A +F H  +R+ VG+L  VGDG+       + L+A  R     + PP 
Sbjct: 204 RESEHVYAATVQADAFCHNMVRALVGALLAVGDGRRPPEWPAQVLRAGVRDSAVHVVPPH 263

Query: 238 GLYFDSVEYS 247
           GL  + V Y 
Sbjct: 264 GLTLEEVRYP 273


>gi|313205364|ref|YP_004044021.1| tRNA pseudouridine synthase a [Paludibacter propionicigenes WB4]
 gi|312444680|gb|ADQ81036.1| tRNA pseudouridine synthase A [Paludibacter propionicigenes WB4]
          Length = 251

 Score =  253 bits (646), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 117/247 (47%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY +   Y G+ Y GWQ Q NG S+Q  + +A+  +    + + GAGRTD+GVHA   V
Sbjct: 3   RRYFIYFSYKGTAYHGWQMQPNGISVQEVLTRALCTILRTNLEIVGAGRTDAGVHAKLMV 62

Query: 62  AHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          L   LN++L     ISI  ++ V    HARF AI R Y Y I T +
Sbjct: 63  AHFDFETALPSEFDLVAKLNSFL--PGDISIYKIAEVKPDAHARFDAISRRYEYHIFTNK 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +   A      LD E M +AA+ L    DFT+F  +H    +    I H +    
Sbjct: 121 --NVFKNELAVRESDKLDFEAMNLAAKTLTKFKDFTSFSKLHTDVKTNNCQIHHAEWTQQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+     + A  FL   +R+ VG+L  VG  K  + +    + A++R + G   P  GLY
Sbjct: 179 GDEWVFTIEADRFLRNMVRAIVGTLFEVGRRKMNTDEFATVIAAKNRCKAGVSVPAHGLY 238

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 239 LVDIKYP 245


>gi|194366624|ref|YP_002029234.1| tRNA pseudouridine synthase A [Stenotrophomonas maltophilia R551-3]
 gi|238693473|sp|B4SQV6|TRUA_STRM5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|194349428|gb|ACF52551.1| tRNA pseudouridine synthase A [Stenotrophomonas maltophilia R551-3]
          Length = 256

 Score =  253 bits (646), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EY+GS + GWQ   + G S+Q S+E+A+  V    + V  AGRTD+GVH   Q
Sbjct: 1   MRYALGVEYDGSDFRGWQNLGEGGPSVQASLEQALSSVADTPLQVVCAGRTDAGVHGQCQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P      L    ++  +I++     V   FHARFSA  R Y YR++ R+
Sbjct: 61  VVHFDTDVVRDPRAWM--LGTTTRLPRSIAVRWCVPVADDFHARFSARARRYRYRLLNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              ALE+       ++LD   M IA Q L+G +DF  FRS+ CQA    R +    V+  
Sbjct: 119 VRPALERQTLSWERRALDETRMHIAGQALLGENDFNAFRSVQCQALHARRELQSLQVSRH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +IE+ V   +FLH  +R+ VGSL LVG G+     + + L  +DR   GP APP+GL 
Sbjct: 179 GEVIEVSVQGNAFLHHMVRNIVGSLILVGSGEKPVEWIAELLAGRDRTVAGPTAPPQGLV 238

Query: 241 FDSVEYS 247
           F    Y 
Sbjct: 239 FLGPLYP 245


>gi|189467951|ref|ZP_03016736.1| hypothetical protein BACINT_04345 [Bacteroides intestinalis DSM
           17393]
 gi|189436215|gb|EDV05200.1| hypothetical protein BACINT_04345 [Bacteroides intestinalis DSM
           17393]
          Length = 253

 Score =  253 bits (646), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 116/248 (46%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + +A+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGDSVQECLMRALATLMRREVEVIGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       V     LN  L     ISI  +  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSDEPLDTVFFTDKLNRLL--PPDISIYRIRAVKPDAHARFDATARMYKYYVTTVK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P    +     + ++ D E M  AA+ L    DFT+F  +H    +    I H      
Sbjct: 119 SP--FNRQYRCRLFQAPDFERMNEAARILFDYTDFTSFSKLHTDVKTNNCRIMHAAWTQV 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            ++     + A  FL   +R+ VG+L  VG GK T     + ++ +DR + G   P   L
Sbjct: 177 DDVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTVEGFRRVIEQKDRCKAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVTYP 244


>gi|218960843|ref|YP_001740618.1| putative pseudouridylate synthase I [Candidatus Cloacamonas
           acidaminovorans]
 gi|167729500|emb|CAO80411.1| putative pseudouridylate synthase I [Candidatus Cloacamonas
           acidaminovorans]
          Length = 274

 Score =  253 bits (646), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 126/249 (50%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + I Y+G+GY GWQ+QKNG +IQ  +EK + +  G+   +  AGRTD+GVH+L Q
Sbjct: 3   MARYLIKICYDGTGYCGWQKQKNGLAIQEVMEKMLEIFAGKKTSLIAAGRTDAGVHSLGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD         L  A N YL   D+I +L +  V    +AR+ A  RSY YR+   +
Sbjct: 63  YAHFDYSGSMQEKQLFLAFNRYL--PDSIKVLEIMKVSPCLNARYQAYERSYRYRLAKEK 120

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +  +   P   L+ E M+ A Q+L+G+HDF+TF   + +  + I  + H  ++ 
Sbjct: 121 TP--FNRNYSGFFPHLHLNLEKMQSAVQYLLGKHDFSTFGKSNPEVPNRICELKHISISE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEG 238
                     A  FLH  +R  VG+L  +         + + L+ +  R+     AP  G
Sbjct: 179 TERYFVFDFTADRFLHNMVRRIVGTLANISHLHLPPETVLEILENRCPRQNLVITAPASG 238

Query: 239 LYFDSVEYS 247
           LY   V+Y 
Sbjct: 239 LYLMDVKYP 247


>gi|46199569|ref|YP_005236.1| tRNA pseudouridine synthase A [Thermus thermophilus HB27]
 gi|55981600|ref|YP_144897.1| tRNA pseudouridine synthase A [Thermus thermophilus HB8]
 gi|51316686|sp|Q72I65|TRUA_THET2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901217|sp|Q5SHU9|TRUA_THET8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46197195|gb|AAS81609.1| tRNA pseudouridine synthase A [Thermus thermophilus HB27]
 gi|55773013|dbj|BAD71454.1| tRNA pseudouridine synthase A (pseudouridylate synthase I) [Thermus
           thermophilus HB8]
          Length = 253

 Score =  253 bits (646), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 124/252 (49%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ +   ++QG +E+A+  + G +     AGRTD+GVHAL 
Sbjct: 1   MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGI-GALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H D+        + +ALN  L   + + ++    V   FHAR  A+ R+Y YRI+ R
Sbjct: 60  MPFHVDVESAIPVEKVPEALNRLL--PEDLKVVGAREVAPDFHARKDALWRAYRYRILVR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
             P  L + RA  + + LD E M  A   L+GRH+F  F     +     R +    +  
Sbjct: 118 PHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGE--RELLEARLQV 175

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G  + +    +SFL  Q+R  VG+L  VG GK     L+  L+  DR+  GP AP
Sbjct: 176 AEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAP 235

Query: 236 PEGLYFDSVEYS 247
             GLYF    Y 
Sbjct: 236 AHGLYFVEAAYP 247


>gi|226305372|ref|YP_002765330.1| tRNA pseudouridine synthase TruA [Rhodococcus erythropolis PR4]
 gi|226184487|dbj|BAH32591.1| tRNA pseudouridine synthase TruA [Rhodococcus erythropolis PR4]
          Length = 294

 Score =  252 bits (645), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ +  ++ G IE  +  V  + V +  AGRTD+GVHA  QV
Sbjct: 21  VRLRLDISYDGTDFSGWARQTDLRTVCGEIEDKLGTVLRQPVQLTVAGRTDAGVHATGQV 80

Query: 62  AHFDLVREWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH D+  E +P    + +      +   + +  +S+V   F ARFSAIRR Y YR+    
Sbjct: 81  AHVDVPGELLPDDPSRLVRRLARFLPKDVRVKQISVVPGDFDARFSAIRRYYEYRVTNAA 140

Query: 121 APL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             +  L        PK LD   M+ A+  L+G H+F  F     + ++ +R +  FD   
Sbjct: 141 FGVEPLRARDTVSYPKPLDLAAMQEASNRLLGLHNFAAFCKRR-EGATTVRELQRFDWAQ 199

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +    V A +F  + +RS VG++  VG+G+ T+  +   L    R     +AP  GL
Sbjct: 200 EGTVFTAYVNADAFCWSMVRSLVGAVLSVGEGRRTADWVAGLLDETLRSSSILVAPAHGL 259

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 260 SLVRVDYP 267


>gi|85860424|ref|YP_462626.1| tRNA pseudouridine synthase A [Syntrophus aciditrophicus SB]
 gi|85723515|gb|ABC78458.1| tRNA pseudouridine synthase A [Syntrophus aciditrophicus SB]
          Length = 328

 Score =  252 bits (645), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 91/247 (36%), Positives = 133/247 (53%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++Y + +EY+G+GY GWQ QKN  SIQG++ +    + G  V + GAGRTD+GVHAL QV
Sbjct: 65  VKYRLTLEYDGTGYSGWQMQKNAKSIQGTLLRVAEDLLGGPVDIQGAGRTDAGVHALAQV 124

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH +  R   P  L + LN  L    +I+IL +      FHAR SA  RSYLY I   + 
Sbjct: 125 AHLETTRRMPPRKLLEGLNDAL--PSSINILRVEEAPPLFHARHSAQLRSYLYVISGHRT 182

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT-IDHFDVNSF 180
             A  K   W I   L+ + M+ A++   G HDF++F        +P R  ++  ++++ 
Sbjct: 183 --AFGKRYVWWIRDHLELKKMQAASRLFAGFHDFSSFADKRMDKQAPTRVKVEATELHAS 240

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI  RV    FL   +R  VG +  VG  K   +D+ + L++   +     APP GLY
Sbjct: 241 GDLIFFRVTGSHFLWKMVRRMVGVMVEVGREKLDISDVRQMLKSYSPEPARLTAPPSGLY 300

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 301 LERVLYE 307


>gi|89890586|ref|ZP_01202096.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BBFL7]
 gi|89517501|gb|EAS20158.1| tRNA  pseudouridine synthase A [Flavobacteria bacterium BBFL7]
          Length = 251

 Score =  252 bits (645), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 76/245 (31%), Positives = 119/245 (48%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + Y+G+ Y GWQRQ    ++Q  +E+ +  +  E + V GAGRTD+GVHA   VA
Sbjct: 6   RYFIELAYDGTAYHGWQRQPQSITVQEVLEEGLHKMLREQIKVQGAGRTDAGVHAAYMVA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD         L   LN +L     I++  +  V    HARF A +RSY Y  + R  P
Sbjct: 66  HFDYSGAIDLDHLVYRLNRWL--PKDIAVYEVKPVVNNAHARFHAYKRSYEYHFLLR--P 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              +  +A+++ +  D + M+ AA  L    DF  F   +    + +  +         +
Sbjct: 122 DPFQVMQAYVLFRKPDFKLMQEAAAILPEYKDFECFSRSNTDVKTYVCDLTEAYFEFKDH 181

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +   + A  FL   +R+ VG+L  +G GK T  DL + + ++DR   G  AP  GL+  
Sbjct: 182 KVIFHITANRFLRNMVRAVVGTLLDIGYGKKTIEDLREIIASKDRSNAGASAPAGGLFLT 241

Query: 243 SVEYS 247
            + Y 
Sbjct: 242 KIHYP 246


>gi|256820760|ref|YP_003142039.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea DSM 7271]
 gi|256582343|gb|ACU93478.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea DSM 7271]
          Length = 250

 Score =  252 bits (644), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 120/246 (48%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + + G  Y+GWQ Q    S+Q  ++KA+  +    + V GAGRTDSGVHAL+  
Sbjct: 1   MRYFIELSFFGKNYYGWQFQPKAISVQEVLQKALSTLLRTPIEVVGAGRTDSGVHALQMY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+     P  L   LNA+L     I++ ++  V    HARF A++R+Y Y I T++ 
Sbjct: 61  AHFDVTEAL-PANLVHKLNAFL--PKDIAVHHIYEVQPNAHARFDALKRTYQYHISTQK- 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A     A  +   L+   M  AAQ L    DF  F   H    +    I     +   
Sbjct: 117 -DAFAYDYAMALTLPLNVALMNEAAQILFDYTDFQCFSKTHTDVKTYNCKIYEAHWDKVE 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG+L  VG  K + TD E  + ++ R + G   P  GLY 
Sbjct: 176 NQLIFTITADRFLRNMVRAIVGTLIDVGLQKLSLTDFEDIILSKKRSKAGASVPACGLYL 235

Query: 242 DSVEYS 247
             +EY 
Sbjct: 236 THIEYP 241


>gi|329957112|ref|ZP_08297679.1| tRNA pseudouridine synthase A [Bacteroides clarus YIT 12056]
 gi|328523380|gb|EGF50479.1| tRNA pseudouridine synthase A [Bacteroides clarus YIT 12056]
          Length = 251

 Score =  252 bits (644), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 116/248 (46%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  L  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSEVPLDVTFMADKLNRLL--PPDISVYRLRAVRPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   ++     + ++ D E M  AAQ L    DFT+F  +H    +    I H      
Sbjct: 119 MP--FDRRYRCRLFQTPDFERMNEAAQTLFEYTDFTSFSKLHTDVKTNNCKIMHAAWTQV 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   L
Sbjct: 177 DEVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTIEGFRRVIEQKDRCRAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   + Y 
Sbjct: 237 FLVDIAYP 244


>gi|302553571|ref|ZP_07305913.1| tRNA pseudouridine synthase A [Streptomyces viridochromogenes DSM
           40736]
 gi|302471189|gb|EFL34282.1| tRNA pseudouridine synthase A [Streptomyces viridochromogenes DSM
           40736]
          Length = 284

 Score =  252 bits (644), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 117/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSKETYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL RE       K L     ++   + +  L      F+ARFSA+ R Y YR+ 
Sbjct: 70  GQVAHVDLPREVWAEHHQKLLKRLAGRLPRDVRVWALREAPSGFNARFSAVWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +         LD + M  AA+ L+G HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRNHVLWHDWPLDVDAMNEAARRLLGEHDFAAYCKKR-EGATTIRTLQELS 188

Query: 177 -VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V     +I   V A +F H  +RS +G+L  VGDG        K L A  R     +  
Sbjct: 189 LVKGEDGIITATVRADAFCHNMVRSLIGALLFVGDGHRPPDWPGKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|254383143|ref|ZP_04998497.1| tRNA pseudouridine synthase A [Streptomyces sp. Mg1]
 gi|194342042|gb|EDX23008.1| tRNA pseudouridine synthase A [Streptomyces sp. Mg1]
          Length = 283

 Score =  252 bits (644), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 79/251 (31%), Positives = 118/251 (47%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q+   ++QG +E A+  V    + V +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQRVLRTVQGELESALTTVMRLPDPVELTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVA FD+  E       K L     ++   + +  ++   + F+ARFSAI R Y YR+  
Sbjct: 70  QVAQFDVAEEVWAEHHDKLLRRLAGRLPHDVRVWKVAEAPQGFNARFSAIWRRYAYRVGD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            Q     L +G        LD + M  AA  L+G HDF  +     + ++ IRT+     
Sbjct: 130 HQGGVDPLRRGHVLWHQWPLDVDAMNRAAAALLGEHDFAAYCKKR-EGATTIRTLQQLSW 188

Query: 178 NSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              G+ I    V A +F H  +RS VG+L  VGDG        + L A  R     +  P
Sbjct: 189 ERAGDGIVTATVRADAFCHNMVRSLVGALLHVGDGHRPVEWPGQVLAAGVRDSSVHVVKP 248

Query: 237 EGLYFDSVEYS 247
            GL  + V Y 
Sbjct: 249 HGLTLEEVGYP 259


>gi|294506655|ref|YP_003570713.1| tRNA pseudouridine synthase A [Salinibacter ruber M8]
 gi|294342983|emb|CBH23761.1| tRNA pseudouridine synthase A [Salinibacter ruber M8]
          Length = 265

 Score =  252 bits (644), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 88/249 (35%), Positives = 130/249 (52%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  +IEY+G+ + GWQ Q    ++QG++E+A+  V G    V G+GRTD+GVHA  Q
Sbjct: 1   MPRYRFLIEYDGTDFHGWQIQPTVPTVQGALEEAVDTVVGTACRVAGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL     P  L  +LN      D +++  +      FHAR+ A RR Y Y + T+ 
Sbjct: 61  VAHVDLPETRDPYRLRGSLNGL--TPDAVAVRRVERAPDDFHARYDACRRRYHYHLHTQ- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
            P AL +     +    D   +R AA  L+GRH+F++F     +  + + T+ H      
Sbjct: 118 -PCALGRRARTPVRPVPDFGRIRAAAPDLLGRHNFSSFCLTQSETENRVCTLTHLRWVDE 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +      + VV   FLH  +R+ VG+L  +G  K  +  L   L A+DR+  GP  PPEG
Sbjct: 177 ARRGCWRVEVVGTRFLHGMVRALVGTLVEIGHEKRAADALPAVLAARDRRAAGPSMPPEG 236

Query: 239 LYFDSVEYS 247
           L  ++V Y 
Sbjct: 237 LVLEAVRYE 245


>gi|86132219|ref|ZP_01050814.1| Pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85817138|gb|EAQ38321.1| Pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 263

 Score =  252 bits (644), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 118/248 (47%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G  Y GWQRQ N  ++Q +IEKA+  +  + V++ GAGRTD+GVHA +  
Sbjct: 8   VRYFIELSYFGKDYHGWQRQPNAVTVQETIEKALSTILRKPVLIMGAGRTDAGVHATQMY 67

Query: 62  AHFDLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHFD   +       + L   L   +   I+I  +  V  + H RF A  RSYLYRI  R
Sbjct: 68  AHFDWDDDLSLDNKLRNLTYKLNRFLPPDIAIDRIFNVRDEAHTRFDATSRSYLYRIAKR 127

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P + E+  A  I   +D   M  AA  L+   DF  F     + ++ +  I       
Sbjct: 128 KNPFSTEQAHA--IAYDIDLSLMNEAAAALLDYSDFECFSKSKTEVNTYLCDITRAQWLE 185

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  +G GK   + +   ++ + R   G   P  GL
Sbjct: 186 TEDEYHFHITANRFLRNMVRAIVGTLLEIGQGKKPVSWIHDVVKGKSRSRAGSSVPGHGL 245

Query: 240 YFDSVEYS 247
           Y   + Y 
Sbjct: 246 YLTEIIYP 253


>gi|190575294|ref|YP_001973139.1| tRNA pseudouridine synthase A [Stenotrophomonas maltophilia K279a]
 gi|229558000|sp|B2FNZ6|TRUA_STRMK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|190013216|emb|CAQ46850.1| putative tRNA pseudouridine synthase A [Stenotrophomonas
           maltophilia K279a]
          Length = 256

 Score =  252 bits (644), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 93/247 (37%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EY+GS + GWQ   + G S+Q S+E+A+  V    + V  AGRTD+GVH   Q
Sbjct: 1   MRYALGVEYDGSDFRGWQNLGEGGPSVQASLEQALSSVADTPLQVVCAGRTDAGVHGQCQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P      L    ++  +I++     V   FHARFSA  R Y YR++ R+
Sbjct: 61  VVHFDTDVVRDPRAWM--LGTTTRLPRSIAVRWCVPVADDFHARFSARARRYRYRLLNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL++       ++LD   M  A Q L+G +DF+ FRS+ CQA    R +    V+  
Sbjct: 119 VRPALDRQTLSWERRALDETLMHAAGQALIGENDFSAFRSVQCQALHARRELQSLQVSRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +IE+ V   +FLH  +R+ VGSL LVG G+     + + L  +DR   GP APP+GL 
Sbjct: 179 GEVIEVAVQGNAFLHHMVRNIVGSLILVGSGEKPVEWIAELLAGRDRTVAGPTAPPQGLV 238

Query: 241 FDSVEYS 247
           F    Y 
Sbjct: 239 FLGPLYP 245


>gi|289547965|ref|YP_003472953.1| tRNA pseudouridine synthase A [Thermocrinis albus DSM 14484]
 gi|289181582|gb|ADC88826.1| tRNA pseudouridine synthase A [Thermocrinis albus DSM 14484]
          Length = 241

 Score =  252 bits (644), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 123/247 (49%), Gaps = 6/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y +I+ + G+ + GWQ Q +  ++QG +   +  +    +   G  RTD+GVHA   
Sbjct: 1   MFNYGLILSFVGTHFHGWQIQPSLRTVQGELSSCLSKIFDRTIKPIGCCRTDAGVHAKEY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F       P  L KALN+ L     I +  + + ++++++R+S   ++Y+YRI    
Sbjct: 61  AANFKAPTFIEPDKLLKALNSLL--PHDIGVKKVWLAEEKWNSRYSIKGKTYVYRIHMSH 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A     +   W IP +L  + MR  +Q LVG HDF+ F        +PI  ++   +   
Sbjct: 119 ARDPFLEPFVWRIPYTLQVDKMREISQLLVGTHDFSGFSKKEDD-KNPIIDLEELVLLQE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ +   AR FL   +R  VG+L  VG  K    ++E+ L  ++   C   AP +GL 
Sbjct: 178 GDILILSFRARRFLRYMVRRMVGALVQVGLEKIGKEEIERYLSGEN---CPYTAPAKGLT 234

Query: 241 FDSVEYS 247
            + + +S
Sbjct: 235 LEKIHFS 241


>gi|319901295|ref|YP_004161023.1| tRNA pseudouridine synthase A [Bacteroides helcogenes P 36-108]
 gi|319416326|gb|ADV43437.1| tRNA pseudouridine synthase A [Bacteroides helcogenes P 36-108]
          Length = 250

 Score =  252 bits (643), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 115/248 (46%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGESVQECLMKALATLLRCDVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD         +   LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 61  VAHFDSAAPLDAAFMVDKLNRLL--PPDISVYRLRAVKSDAHARFDATTRMYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   ++     + ++ D E M  AAQ L    DFT+F  +H    +    I H      
Sbjct: 119 IP--FDRWYRCRLFQTPDFERMNEAAQTLYDYTDFTSFSKLHTDVKTNNCKIMHAVWTQQ 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  VG GK T     + ++ QDR + G   P   L
Sbjct: 177 DEVTWVFTIKADRFLRNMVRAIVGTLLEVGRGKLTVEGFRRVIEQQDRCQAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVSYP 244


>gi|122919612|pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua
           From Thermus Thermophilus Hb8
 gi|122919613|pdb|1VS3|B Chain B, Crystal Structure Of The Trna Pseudouridine Synthase Trua
           From Thermus Thermophilus Hb8
          Length = 249

 Score =  252 bits (643), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 124/252 (49%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ +   ++QG +E+A+  + G +     AGRTD+GVHAL 
Sbjct: 1   MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGI-GALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H D+        + +ALN  L   + + ++    V   FHAR  A+ R+Y YRI+ R
Sbjct: 60  MPFHVDVESAIPVEKVPEALNRLL--PEDLKVVGAREVAPDFHARKDALWRAYRYRILVR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
             P  L + RA  + + LD E M  A   L+GRH+F  F     +     R +    +  
Sbjct: 118 PHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGE--RELLEARLQV 175

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G  + +    +SFL  Q+R  VG+L  VG GK     L+  L+  DR+  GP AP
Sbjct: 176 AEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAP 235

Query: 236 PEGLYFDSVEYS 247
             GLYF    Y 
Sbjct: 236 AHGLYFVEAAYP 247


>gi|331090989|ref|ZP_08339831.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330405211|gb|EGG84747.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 248

 Score =  252 bits (643), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 121/250 (48%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + +EY+GS Y GWQR    ++ ++I   I + I  +T E V +    RT+ GVHA
Sbjct: 1   MRNIKLTLEYDGSRYQGWQRLGKNESSNTIANKIIEVIKKMTNEDVELFCGARTEVGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             Q+ +F    +     + + LN YL     I++ ++    ++FHA  +A  + Y+YR+ 
Sbjct: 61  YAQIVNFKTTSDMKLGEIKQYLNRYL--PMDIAVTDIEEKPERFHASLNATSKIYMYRMA 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P   E+   + + K  D + M+ AA  LVG+HDF  F ++  ++ S ++ I   D+
Sbjct: 119 IGEVPSVFERKYTYYVFKKPDVDVMKQAALLLVGKHDFKNFSTVK-KSKSTVKEIYDIDI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +    I+I + A  FLH   R  +G+L  +G G     ++E     +   +       +
Sbjct: 178 YTDDEEIQITLHANDFLHNMARMVIGTLIDIGLGNRKKEEIEDIFNPESSVQASSPCDAK 237

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 238 GLYLQEVLYE 247


>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 =  252 bits (643), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 103/247 (41%), Positives = 146/247 (59%), Gaps = 2/247 (0%)

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  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            AHFD  +E      L K++N ++     IS+L +     +FHAR SA +R Y Y I  R
Sbjct: 61  SAHFDCKKEIQNLDKLLKSINHFIN-DKGISVLAIKKRSLKFHARHSAKQRIYKYIIFNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +  +LEK R W I K LD E M+  ++ L+G  DF+TFR+  C A SPI+T+   ++ S
Sbjct: 120 LSKPSLEKERGWHIIKKLDIELMKKGSKKLLGTKDFSTFRASSCNAKSPIKTMKSVNIKS 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               IEI+  ++SFL  Q+RS VGSLK + + KW     E  ++++ R  C P AP EGL
Sbjct: 180 KDGRIEIQFKSQSFLQQQVRSMVGSLKYLAENKWDLKKFEFVIKSKKRILCAPPAPAEGL 239

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


>gi|317051440|ref|YP_004112556.1| tRNA pseudouridine synthase A [Desulfurispirillum indicum S5]
 gi|316946524|gb|ADU66000.1| tRNA pseudouridine synthase A [Desulfurispirillum indicum S5]
          Length = 263

 Score =  252 bits (643), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 115/248 (46%), Gaps = 5/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + + Y+G+ Y GWQ Q+N  ++IQ  +E A   V    + +HG+GRTD+GVHA  Q
Sbjct: 8   RRIALKVAYDGTHYHGWQTQENAANTIQAILEHAAGSVCNHPLYIHGSGRTDTGVHARGQ 67

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + H           +   +N+ L     I + N   VD+ FH+++S   + Y Y I+   
Sbjct: 68  ICHLTTTSTIPLFKIIMGMNSML--PRDIRVRNAFDVDEDFHSQYSTHSKKYSYAILHGC 125

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
            P  L++  +W + +++D   ++    H VG HDF   R+      + +RTI    V   
Sbjct: 126 QPDPLQRLYSWHVRQTIDPARLQEELNHFVGEHDFKACRAKKATTKTTVRTIYSIGVRVE 185

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + I      FL   IR  VG+      G    + + + L ++DR   G  A P GL
Sbjct: 186 SPHKLHIHFHGNGFLKHMIRIMVGTAVDRAIGCLDRS-IPEILLSRDRTRGGRTAAPCGL 244

Query: 240 YFDSVEYS 247
             + V Y 
Sbjct: 245 VMEEVLYE 252


>gi|225849320|ref|YP_002729484.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225643913|gb|ACN98963.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium azorense
           Az-Fu1]
          Length = 244

 Score =  252 bits (643), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 88/244 (36%), Positives = 120/244 (49%), Gaps = 5/244 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            Y + I Y G+ Y GWQRQKN   IQ  IE  +  +  E + + G+GRTD+GVHAL QVA
Sbjct: 6   NYKLTISYIGTRYSGWQRQKNAVGIQQIIEDLLEKLFKEKITLIGSGRTDAGVHALNQVA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F       P  +   LNA L     IS+  +  VD  F+ARFSA  ++YLYRI T+  P
Sbjct: 66  NFKTYSYKDPSTIYSYLNAKL--PRDISVKKVEEVDLNFNARFSAKGKTYLYRIYTK--P 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                GR W   K LD   M    + L    D T+           +  +    +   G 
Sbjct: 122 DPFLYGRGWFFDKDLDIVKMLQGIEILKKYKDLTSLAKEGNYIRKEV-DLREIKLYYDGK 180

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +I+I + A  FL   +R  VG L  +G G  +  + E  ++A+D  +   LAPPEGLY  
Sbjct: 181 IIDIEITASHFLRNLVRRIVGHLVAIGRGSLSLQEFEDIIKAKDSSKGKFLAPPEGLYLK 240

Query: 243 SVEY 246
            V Y
Sbjct: 241 EVYY 244


>gi|317501544|ref|ZP_07959740.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088594|ref|ZP_08337505.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 3_1_46FAA]
 gi|316897055|gb|EFV19130.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407551|gb|EGG87051.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 260

 Score =  252 bits (643), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 85/263 (32%), Positives = 120/263 (45%), Gaps = 19/263 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ +   +IQG +E+ +    G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGTNYQGWQRQSDTDRTIQGILEETLENCIGYQVQIDGSGRTDAGVHASG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +    +  + +N  L     I IL++ +V   FHAR SA+ + Y YRI T 
Sbjct: 61  QTASVVLPGKVDTALFTEKMNGCL--PPDIRILDVELVKNGFHARKSAVGKVYEYRIDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  +   P   D   MR AA +L G H F  +        S  RTI    +  
Sbjct: 119 IKQDVFTRKYSGHFPGEPDLARMREAAGYLTGTHFFAGYTDKK-DNRSVRRTIYSIMIRD 177

Query: 180 F---------------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
                           GN I IR     FL+  +R   G+L  VG  + T+  +++AL  
Sbjct: 178 ERKDFLPCGKSDQIGNGNCIVIRYDGTGFLYHMVRILTGTLLEVGMRERTAESVKEALLT 237

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
            DR + G LAP  GL+   V Y 
Sbjct: 238 GDRSKAGFLAPAGGLFLREVRYE 260


>gi|258647412|ref|ZP_05734881.1| tRNA pseudouridine synthase A [Prevotella tannerae ATCC 51259]
 gi|260852780|gb|EEX72649.1| tRNA pseudouridine synthase A [Prevotella tannerae ATCC 51259]
          Length = 256

 Score =  252 bits (643), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 121/247 (48%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY +   Y+G  Y GWQ+Q N  S+Q  + KAI  +    + + GAGRTD+ V+A R V
Sbjct: 1   MRYFLYFSYDGGNYHGWQQQPNAISVQEVLNKAISTLLQSAISLVGAGRTDTSVNAKRMV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD     +P      LN  L     I++L++  V+K  HARF A+ R+Y Y I   + 
Sbjct: 61  AHFDF-CCTLPDKFTFRLNRLL--PPDIAVLDIKQVNKDAHARFDALSRTYHYYIY--KK 115

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-NSF 180
               ++  A      LD   M  AA+ L+   DFT+F  +H    + I  +   +     
Sbjct: 116 KDPFKRHYATRYLAELDYTAMNQAAKLLLQVEDFTSFSKLHTDTRTKICHVTKAEWIQEK 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +L    + A  FL   +R+ VG+L  VG G+ +  +  K +Q ++R       P E L+
Sbjct: 176 EDLWRFEITADRFLRNMVRAIVGTLIEVGRGRMSIEEFSKVIQQKNRCAAAESVPGEALF 235

Query: 241 FDSVEYS 247
             +++Y 
Sbjct: 236 LVNIKYP 242


>gi|326335636|ref|ZP_08201823.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325692402|gb|EGD34354.1| tRNA pseudouridine synthase A [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 247

 Score =  251 bits (642), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 128/246 (52%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  YFGWQ+Q +  S+Q  +E+AI L+  E + + GAGRTD+GVHA    
Sbjct: 1   MRFFIELSYNGKNYFGWQKQPHSLSVQEELERAISLLLHEEITLVGAGRTDTGVHARDYF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD     +P  L   LN++L    TI+I  +  +    HARF AI R+Y Y I   + 
Sbjct: 61  AHFDF-SLPLPENLVNKLNSFL--PKTIAIKGIFPMKDAAHARFDAISRTYQYFISREKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E+  ++ + + L    M  A + L+  +DF  F   +    + I  +         
Sbjct: 118 PFLYEQ--SYYVYQPLAISQMNRACEILLKHNDFQCFSKTNTDVRTYICHLTEAFWKEED 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+  R+ A  FL   +R+ VG++  VG GK + ++ E+ L +++R + G   P   L+ 
Sbjct: 176 SLLIFRITADRFLRNMVRAIVGTMIEVGIGKISLSNFEQILLSKNRSQAGYSVPGHALFL 235

Query: 242 DSVEYS 247
           + V Y 
Sbjct: 236 EKVVYP 241


>gi|213962633|ref|ZP_03390894.1| tRNA pseudouridine synthase A [Capnocytophaga sputigena Capno]
 gi|213954628|gb|EEB65949.1| tRNA pseudouridine synthase A [Capnocytophaga sputigena Capno]
          Length = 250

 Score =  251 bits (642), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 76/246 (30%), Positives = 116/246 (47%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + + G  Y GWQ Q    S+Q  +E+ +  +    + V GAGRTDSGVHA +  
Sbjct: 1   MRYFIELSFFGKNYHGWQSQPKAISVQEVLEQGLSTILRTPISVVGAGRTDSGVHASQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+     P      LNA+L     I++ N+  +    H RF A++R+Y Y I T++ 
Sbjct: 61  AHFDVTEPL-PTNFVHRLNAFL--PKDIAVHNIYEMKPNAHTRFDALKRTYQYHISTQK- 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                   A     +L+   M  AAQ L+   DF  F   H    + I  I         
Sbjct: 117 -DVFAYDYAMFFTHTLNIAIMNEAAQILLDYSDFQCFSKTHTDVKTFICKIYKAHWEKID 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   ++A  FL   +R+ VG+L  VG  K + TD E  + +++R + G   P  GL+ 
Sbjct: 176 KQLVFTIIADRFLRNMVRAIVGTLIDVGLQKLSLTDFEDIILSKNRSKAGASVPACGLFL 235

Query: 242 DSVEYS 247
             +EY 
Sbjct: 236 THIEYP 241


>gi|315223896|ref|ZP_07865742.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea F0287]
 gi|314946125|gb|EFS98128.1| tRNA pseudouridine synthase A [Capnocytophaga ochracea F0287]
          Length = 262

 Score =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 118/246 (47%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + + G  Y+GWQ Q    S+Q  ++KA+  +    + V GAGRTDSGVHA +  
Sbjct: 13  MRYFIELSFFGKNYYGWQSQPKAISVQEVLQKALSTLLRTPIEVVGAGRTDSGVHASQMY 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+     P  L   LNA+L     I+I ++  V    HARF A++R+Y Y I TR+ 
Sbjct: 73  AHFDVTEAL-PANLVHKLNAFL--PKDIAIHHIYEVQPNAHARFDALKRTYQYHISTRK- 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A     A      L+   M  AA+ L    DF  F   H    +    I     +   
Sbjct: 129 -DAFAYDYAMAFTLPLNVALMNEAAEILFDYTDFQCFSKTHTDVKTYNCKIYEAHWDKVE 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N +   + A  FL   +R+ VG+L  VG  K + TD E  + ++ R + G   P  GLY 
Sbjct: 188 NQLIFTITADRFLRNMVRAIVGTLIDVGLQKLSLTDFEDIIISKKRSKAGASVPACGLYL 247

Query: 242 DSVEYS 247
             +EY 
Sbjct: 248 THIEYP 253


>gi|224538364|ref|ZP_03678903.1| hypothetical protein BACCELL_03255 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224519993|gb|EEF89098.1| hypothetical protein BACCELL_03255 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 279

 Score =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 115/248 (46%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG S+Q  + +A+  +    V V GAGRTD+GVHA   
Sbjct: 29  MQRYFIYLAYDGTAYHGWQIQPNGDSVQECLMRALATLMRREVEVIGAGRTDAGVHASLM 88

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD             LN  L     IS+  L  V    HARF A  R Y Y + T +
Sbjct: 89  VAHFDSDEPLDTAFFTDKLNRLL--PPDISVYRLRAVKPDAHARFDATARMYKYYVTTAK 146

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P    +     + ++ D E M  AA+ L    DFT+F  +H    +    I H      
Sbjct: 147 SP--FNRQYRCRLFQTPDFERMNEAARSLFDYTDFTSFSKLHTDVKTNNCRIMHAAWTQI 204

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            ++     + A  FL   +R+ VG+L  VG GK T     + ++ +DR + G   P   L
Sbjct: 205 DDVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTVDGFRRVIEQKDRCKAGTSVPGNAL 264

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 265 FLVDVTYP 272


>gi|153815016|ref|ZP_01967684.1| hypothetical protein RUMTOR_01233 [Ruminococcus torques ATCC 27756]
 gi|145847584|gb|EDK24502.1| hypothetical protein RUMTOR_01233 [Ruminococcus torques ATCC 27756]
          Length = 260

 Score =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 85/263 (32%), Positives = 120/263 (45%), Gaps = 19/263 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I Y+G+ Y GWQRQ +   +IQG +E+ +    G  V + G+GRTD+GVHA  
Sbjct: 1   MRTYKLTIAYDGTNYQGWQRQSDTDRTIQGILEETLENCIGYQVQIDGSGRTDAGVHASG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A   L  +    +  + +N  L     I IL++ +V   FHAR SA+ + Y YRI T 
Sbjct: 61  QTASVVLPGKVDTALFTEKMNGCL--PPDIRILDVELVKNGFHARKSAVGKVYEYRIDTG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  +   P   D   MR AA +L G H F  +        S  RTI    +  
Sbjct: 119 IKQDVFTRKYSGHFPGEPDLARMREAAGYLTGTHFFAEYTDKK-DNRSVRRTIYSIMIRD 177

Query: 180 F---------------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
                           GN I IR     FL+  +R   G+L  VG  + T+  +++AL  
Sbjct: 178 ERKDFLPCGKSDQIGNGNCIVIRYDGTGFLYHMVRILTGTLLEVGMRERTAESVKEALLT 237

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
            DR + G LAP  GL+   V Y 
Sbjct: 238 GDRSKAGFLAPAGGLFLREVRYE 260


>gi|296111462|ref|YP_003621844.1| tRNA pseudouridine synthase A [Leuconostoc kimchii IMSNU 11154]
 gi|295832994|gb|ADG40875.1| tRNA pseudouridine synthase A [Leuconostoc kimchii IMSNU 11154]
          Length = 256

 Score =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 85/257 (33%), Positives = 129/257 (50%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTD 52
           M RY  I+ Y+GSG+FG+Q Q     +   ++QG + KA+  +     E + V GA RTD
Sbjct: 1   MPRYKAIVSYDGSGFFGFQVQTKNGIERQRTVQGELTKAVNQMAKNPTEPIKVVGASRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QV HFDL  +     + K LN  L     + I  +  V   FHARF+   + Y
Sbjct: 61  TGVHAFGQVVHFDLPFDINENGVRKGLNTLL--PRDMLIKQVDKVTPDFHARFNTHAKRY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YR+ T+      ++         LD E ++ A   L+G HDF +F +   Q ++ IRTI
Sbjct: 119 IYRVSTQDFTDPFKRQYTGHFQWHLDIERIKSALPDLLGEHDFASFAASGNQTATTIRTI 178

Query: 173 DHFDVN--SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
              DV        +       +FL+ QIR  VG L  +G+G+    D+ + +  +DR++ 
Sbjct: 179 TRADVTIKPDDQELVFTFEGNAFLYNQIRIMVGVLLEIGNGRRDVHDILRLITVKDREQA 238

Query: 231 GPLAPPEGLYFDSVEYS 247
              AP  GLY D + Y+
Sbjct: 239 RFTAPASGLYLDQIYYN 255


>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 =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 103/247 (41%), Positives = 144/247 (58%), Gaps = 2/247 (0%)

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  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            AHFD  +E      L K++N ++     IS+L +     +FHAR SA +R Y Y I  R
Sbjct: 61  SAHFDCKKEIQNLDKLLKSINHFIN-DKGISVLAIKKRSLKFHARHSAKQRIYKYIIFNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +  +LEK R W I K LD E M+  A+ L+G  DF+TFR+  C A S I+T+    + S
Sbjct: 120 LSKPSLEKERGWHIIKKLDIELMKKGAKKLLGTKDFSTFRASSCNAKSSIKTMKSVKIKS 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               IEI+  ++SFL  Q+RS VGSLK + + KW     E  ++++ R  C P AP EGL
Sbjct: 180 KDGRIEIQFKSQSFLQQQVRSMVGSLKYLAENKWDLKKFEFVIKSKKRILCAPPAPAEGL 239

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


>gi|315656237|ref|ZP_07909128.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. holmesii
           ATCC 35242]
 gi|315493239|gb|EFU82839.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. holmesii
           ATCC 35242]
          Length = 297

 Score =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 89/273 (32%), Positives = 131/273 (47%), Gaps = 28/273 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++QG++E A+ ++  + V +  AGRTD+GVHA  QV
Sbjct: 1   MRIRLDIRYDGTPFHGWAAQPGLPTVQGALESALTVIYRQTVELTVAGRTDAGVHASGQV 60

Query: 62  AHFDLV----REWVPVILCKALNAYL------------------KISDTI---SILNLSI 96
           AHF +     R   P  L   L A L                     + I    +   ++
Sbjct: 61  AHFTVPEVGDRIVSPDTLAPRLGAVLRAVLSGNLASPLPDSPAAYPPNAIDALVVTAATV 120

Query: 97  VDKQFHARFSAIRRSYLYRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
           V + F ARFSA+ R Y+YRI+    A   L +   W  P  LD   M  +A  L+G HDF
Sbjct: 121 VPETFDARFSALARHYVYRIVDDLAARNPLSRNYCWWYPTQLDAAAMNTSAAVLLGEHDF 180

Query: 156 TTFRSIHCQASSPIRTIDHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             F     + ++ IRT+   +       ++EIRV A +F H+ +RS VG+L  VG  K  
Sbjct: 181 AAFCKPR-EGATTIRTLQQLETLRTAPGMMEIRVRADAFCHSMVRSLVGALTEVGRAKRD 239

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  L  AL A+ R    P+AP  GL    V+Y 
Sbjct: 240 TAWLADALAAKARIPEIPVAPALGLTLTQVDYP 272


>gi|312140887|ref|YP_004008223.1| tRNA pseudouridine synthase a [Rhodococcus equi 103S]
 gi|311890226|emb|CBH49544.1| tRNA pseudouridine synthase A [Rhodococcus equi 103S]
          Length = 274

 Score =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 75/245 (30%), Positives = 121/245 (49%), Gaps = 3/245 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + I Y+G+ + GW RQ    ++ G +E+ +  +    V++  AGRTD+GVHA  QVAH 
Sbjct: 2   RLDISYDGTDFSGWARQPGRRTVCGEVEEKLSAIVRTPVLLTVAGRTDAGVHASGQVAHV 61

Query: 65  DLVREWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           D+  + +P    + +      +   + +  +S   + F ARFSAIRR Y YR+ T     
Sbjct: 62  DVPADMIPEEPSRLVRRLARFLPRDVRVKAVSFAPEHFDARFSAIRRHYEYRLTTAPYGA 121

Query: 124 -ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L        PK +D + MR A+  L+G HDF  F     + ++ +R +  FD    G+
Sbjct: 122 EPLRARDTVAWPKDVDVDAMREASSRLLGLHDFAAFCKRR-EGATTVRELQRFDWEQSGH 180

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +   V A +F  + +RS VG+   VG+G+ T   +   L  ++R     +AP  GL   
Sbjct: 181 ELTAFVSADAFCWSMVRSLVGAALAVGEGRRTVEWMAGLLAERERASAVAVAPAHGLSLI 240

Query: 243 SVEYS 247
            V+Y 
Sbjct: 241 RVDYP 245


>gi|33241136|ref|NP_876078.1| tRNA pseudouridine synthase A [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|42559767|sp|Q7V9Y7|TRUA_PROMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33238666|gb|AAQ00731.1| Pseudouridylate synthase [Prochlorococcus marinus subsp. marinus
           str. CCMP1375]
          Length = 289

 Score =  251 bits (642), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 113/246 (45%), Gaps = 4/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALRQV 61
           R  + I+Y GS + GWQRQK G +IQ  +E AIF + + +   V  AGRTD+GVHA  QV
Sbjct: 17  RIALSIQYQGSNFSGWQRQKVGHTIQAILEDAIFSLDSSKPAKVVAAGRTDAGVHAAGQV 76

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            ALN  L   + I + +       +HA  SA+ R Y Y I     
Sbjct: 77  VHFDSFGPIPVHRWPSALNGRL--PEAIRVRDSVEQSLDWHACHSAVYRRYRYIIYNGCT 134

Query: 122 PLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P        W      LD E M  AA+ L+G HDF+ F+      +    TI    +   
Sbjct: 135 PNLFLNPWTWHKYQYQLDEELMEEAAKGLIGMHDFSAFQRSGSNRTHAFTTIQEVKLVRH 194

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+   + A  FL+  +R  VG L  +G+ + +  D E   + + R E    AP  GL 
Sbjct: 195 GDLLVFDIQASGFLYGMVRLLVGQLVSIGEHRLSINDFETRWKLKLRSEVKEAAPARGLC 254

Query: 241 FDSVEY 246
           F    Y
Sbjct: 255 FIRAGY 260


>gi|262341374|ref|YP_003284229.1| tRNA pseudouridine synthase A [Blattabacterium sp. (Blattella
           germanica) str. Bge]
 gi|262272711|gb|ACY40619.1| tRNA pseudouridine synthase A [Blattabacterium sp. (Blattella
           germanica) str. Bge]
          Length = 247

 Score =  251 bits (641), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 132/247 (53%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  ++GWQ QK  S+++G++E  +  +  E + V GAGRTD GVHA +  
Sbjct: 1   MRFFIELAYNGKYFYGWQVQKKVSTVEGNLEYCLSKLLKESINVIGAGRTDKGVHAKQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD   +     L K LN +L    +I +LN+  V +  HARF+AI+R Y Y ++  + 
Sbjct: 61  AHFDYKGKIS-NNLIKKLNVFL--PKSIKVLNIFPVKENIHARFNAIKRIYKYYLVRDKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSF 180
           P    +  +W     L+ + M IA++ L+G  DF++F      +  + I  ++H   +  
Sbjct: 118 P--FYQDFSWHCFYPLNIQRMNIASKKLMGHKDFSSFCKKKTFETRNNICKVNHVCWSVN 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N+    + A  FL + +RS +G+L  VG  K +  +  + +++++   C  + P  GL+
Sbjct: 176 NNVFCFTIEANRFLRSMVRSIIGTLIDVGRNKISVNEFSEIIESKNSNFCKSIVPACGLF 235

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 236 LTRILYP 242


>gi|218296263|ref|ZP_03497019.1| tRNA pseudouridine synthase A [Thermus aquaticus Y51MC23]
 gi|218243335|gb|EED09865.1| tRNA pseudouridine synthase A [Thermus aquaticus Y51MC23]
          Length = 259

 Score =  251 bits (641), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 125/252 (49%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ+ G  ++QG +EKA+  + G +     AGRTD+GVHAL 
Sbjct: 1   MRRILLLTEYDGTHFAGLQRQRQGLRTVQGELEKALPHI-GALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H DL     P  + +ALN  L   + + ++    V   FHAR  A+ R+Y YR++ R
Sbjct: 60  MPFHIDLQSPIPPEKVPEALNRLL--PEDLKVVAAREVAPDFHARKDALWRAYRYRVLLR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
             P  L + R   + + LD + M  A   L+GRH+F  F     +    +R +    +  
Sbjct: 118 PHPSPLLRHRVLWLRRPLDLKAMEEALPLLLGRHNFLGFAKEETREG--VRELLEARLEV 175

Query: 179 ---SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G  +      RSFL  Q+R  VG+L  VG G+ +   ++  L+  DR+  G  AP
Sbjct: 176 LEGEMGPEVRFYFKGRSFLRGQVRGMVGTLLEVGLGRRSPESVKAILETADRRLAGQSAP 235

Query: 236 PEGLYFDSVEYS 247
             GLYF    Y 
Sbjct: 236 ATGLYFLEAAYP 247


>gi|302543331|ref|ZP_07295673.1| tRNA pseudouridine synthase A [Streptomyces hygroscopicus ATCC
           53653]
 gi|302460949|gb|EFL24042.1| tRNA pseudouridine synthase A [Streptomyces himastatinicus ATCC
           53653]
          Length = 283

 Score =  251 bits (641), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 78/251 (31%), Positives = 115/251 (45%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q+   ++QG +E A+  VT   E   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQRERRTVQGELESALGTVTRSSETPDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL  E       K L     ++   + +  ++     F+ARFSAI R Y YR++ 
Sbjct: 70  QVAHVDLPEELWAEHRDKLLRRLAGRLPHDVRVWRVAAAPPGFNARFSAIWRRYAYRVVD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +G        LD + M  A+  L+G HDF  +       ++ IRT+     
Sbjct: 130 HPGGVDPLLRGHVLWHDWPLDVDAMNAASAPLLGEHDFAAYCKRR-DGATTIRTLQKLSW 188

Query: 178 NSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               + +I   V A +F H  +RS VG+L   GDG        K L A  R     +  P
Sbjct: 189 ERGADGVITATVRADAFCHNMVRSLVGALLFTGDGHRPVDWPGKVLAAGVRDSAVHVVRP 248

Query: 237 EGLYFDSVEYS 247
            GL  + V Y 
Sbjct: 249 HGLTLEEVGYP 259


>gi|261749109|ref|YP_003256794.1| putative tRNA pseudouridine synthase A [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
 gi|261497201|gb|ACX83651.1| putative tRNA pseudouridine synthase A [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
          Length = 247

 Score =  251 bits (641), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 121/247 (48%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + + YNG  Y GWQ Q   +S++G +E  +  +    + + GAGRTD GVHA +  
Sbjct: 1   MRFFIELSYNGKSYHGWQIQSEVNSVEGQLEYCLSKLLNTSINIVGAGRTDRGVHAKQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD   +       K LN  L +  +I + N+  V K  HARF+A+RR+Y Y + + + 
Sbjct: 61  AHFDFEEKIS-NNFVKRLN--LFLPKSIYVSNIFPVKKHIHARFNALRRTYKYYLKSEKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +  +W     LD + M +A+Q L+   DF++F        + I  I H D +   
Sbjct: 118 P--FFQDFSWHCFYPLDIQRMNLASQILMKYKDFSSFCKKRKDKKNNICDIYHADWSRNK 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAPPEGLY 240
                 + A  FL   +RS +G+L  VG GK +     + ++ ++   C  P  P  GL+
Sbjct: 176 IHFCFTIEANRFLRNMVRSIIGTLIDVGRGKISINQFIEIIELKNPNTCSSPSVPACGLF 235

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 236 LTKILYP 242


>gi|6729002|gb|AAF26999.1|AC016827_10 putative tRNA pseudouridine synthase [Arabidopsis thaliana]
          Length = 298

 Score =  250 bits (640), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 129/254 (50%), Gaps = 12/254 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHALR 59
           ++ ++I Y+G+ + GWQ Q++  +IQ  +EKA+  +T    + + + GAGRTD+GVHA  
Sbjct: 17  KWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITELGRKELQLIGAGRTDAGVHAWG 76

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +        ALN  L     I +  LS    +FHARFSA  + Y Y+I  
Sbjct: 77  QVAHFVTPFNYTSLDSFHAALNGLL--PKDIRVRELSAAVPEFHARFSASSKVYRYQIYN 134

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHFD 176
                  ++  A+     L+   MR AA   VG+HDF+ F +   +     P++TI  FD
Sbjct: 135 DTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFANATREDGVPDPLKTISRFD 194

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---- 232
           V   G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR+        
Sbjct: 195 VIQMGSLLQLEVEGSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTSL 254

Query: 233 LAPPEGLYFDSVEY 246
            A P GL   SV+Y
Sbjct: 255 PASPHGLCLVSVKY 268


>gi|258406231|ref|YP_003198973.1| tRNA pseudouridine synthase A [Desulfohalobium retbaense DSM 5692]
 gi|257798458|gb|ACV69395.1| tRNA pseudouridine synthase A [Desulfohalobium retbaense DSM 5692]
          Length = 254

 Score =  250 bits (640), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 121/248 (48%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y G+ + GWQ Q    ++QG +E A   +    + VHGAGRTDSGVHA+ Q
Sbjct: 1   MPRLKLVVAYTGTHFAGWQLQPRDRTVQGCLEDAFATLCQHPLRVHGAGRTDSGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D+  E   +   KALNA L     I++   + V   FHARFSA  + Y Y I T  
Sbjct: 61  VCHCDIPPEKNHIPWQKALNAIL--PKDIAVCEAAYVRDDFHARFSAQAKEYAYTIWTEP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  ++         +D   M +AA+ L G  DF  F++     S  +RT+ H      
Sbjct: 119 RYVLPQRRPLVWSVGRVDEHKMAVAARMLTGTFDFAAFQNTGTPVSHTVRTVYHLAPEPG 178

Query: 181 --GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             GN       A  FL   +R+ +G L  VG  K +  +++  L+ Q R+     APP+G
Sbjct: 179 AAGNESTWLFHADGFLKQMVRNIMGCLVAVGRNKISVDEVKILLEGQKREMAPATAPPQG 238

Query: 239 LYFDSVEY 246
           L    V+Y
Sbjct: 239 LCLRKVKY 246


>gi|297568336|ref|YP_003689680.1| tRNA pseudouridine synthase A [Desulfurivibrio alkaliphilus AHT2]
 gi|296924251|gb|ADH85061.1| tRNA pseudouridine synthase A [Desulfurivibrio alkaliphilus AHT2]
          Length = 252

 Score =  250 bits (640), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 78/255 (30%), Positives = 113/255 (44%), Gaps = 12/255 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  + I Y+G+ + GWQRQ N  +IQ  +E+A+  + GE VV+HGAGRTD+GVHAL  
Sbjct: 1   MVKVKLTIAYDGTDFAGWQRQLNRPTIQAVVEEALARMLGEQVVLHGAGRTDAGVHALGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F+  R          LN+ L     I I+        FHARFSA  + Y Y   T  
Sbjct: 61  VASFNAPRRLPLAAYRLGLNSML--PPAIRIMAADEAADDFHARFSAKGKLYRYCFSTAA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT--------- 171
                 +     +P     E +R     ++G HDF+TF +   +                
Sbjct: 119 VMPPCRRLYRAHLPGPFAAERVRQLLPQMLGEHDFSTFEAAGSRDRDRAGGRGGVRRLNL 178

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +     +  G      +    FL   +R+ VG+L  +G G+    +    L  +DR   G
Sbjct: 179 LQLEQEDPAGQEFCFELGGDGFLRHMVRNIVGTLVAIGQGR-PLAEPVALLVGRDRARAG 237

Query: 232 PLAPPEGLYFDSVEY 246
           P AP  GL    V Y
Sbjct: 238 PTAPACGLTLVKVIY 252


>gi|15606137|ref|NP_213514.1| pseudouridine synthase I [Aquifex aeolicus VF5]
 gi|3929394|sp|O66953|TRUA_AQUAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2983318|gb|AAC06908.1| pseudouridine synthase I [Aquifex aeolicus VF5]
          Length = 241

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 124/244 (50%), Gaps = 5/244 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + + + G+ ++GWQ Q N  ++QG I+KA+  +  E V V G  RTDSGVHAL  
Sbjct: 1   MPNYLLRLAFVGTNFYGWQVQPNLRTVQGEIQKALSQILCEDVKVTGCCRTDSGVHALDY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A+F   +++    L KALN  L     + +  +  V ++F+AR+S   + YLY+I   +
Sbjct: 61  IANFKTQKDFPEEKLLKALNGIL--PKDVGVYAVKKVSEEFNARYSVKGKVYLYKIWNSE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    +W + + ++ E +R   +   G HDF     +  +  + +  ++   +N  
Sbjct: 119 VRNPFLYPFSWQVKREINTEVLRNILKKFEGTHDFRALTKLE-EERNTVINLEEVSLNVE 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LIEIR+ A  FL   +R  VG+   +  G ++   LE+ LQ +        APP+GL+
Sbjct: 178 YPLIEIRLKASHFLRYMVRRIVGTAVKISLGLYSEEVLEELLQGK--GNSPYTAPPQGLH 235

Query: 241 FDSV 244
            + V
Sbjct: 236 LEKV 239


>gi|330444180|ref|YP_004377166.1| tRNA pseudouridine synthase A [Chlamydophila pecorum E58]
 gi|328807290|gb|AEB41463.1| tRNA pseudouridine synthase A [Chlamydophila pecorum E58]
          Length = 267

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  +++ Y G+ Y GWQRQ    +IQ  +E     +    V +  +GRTDSGVHA  Q
Sbjct: 1   MKKIVLLLAYQGTAYAGWQRQPQHLTIQEVLETLFMPILHSRVPMVASGRTDSGVHAYGQ 60

Query: 61  VAHFDLVREW---VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           V HF L        P  L K LNA L     I + ++++ D  FHAR+ AI + Y Y + 
Sbjct: 61  VVHFSLPDHPLTSDPCKLKKLLNARL--PKDIVVRDIALTDASFHARYCAIAKEYHYTLS 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               PL  ++  ++  P  +  + M   AQ+L+G HDF +F ++  + +S IRT+    +
Sbjct: 119 KNIKPLPWQRNFSYSPPHRIRADLMHQGAQYLIGTHDFASFANLGREYTSTIRTLYKVAI 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + + +      FL+  +R+ VG+L  +  G +    +   L+ ++R++  P AP  
Sbjct: 179 EETEHTLTLIFKGNGFLYKMVRNLVGALLDINKGAYPPEHILNMLKEKNRRKGPPSAPAH 238

Query: 238 GLYFDSVEY 246
            L    V Y
Sbjct: 239 ALSLHHVCY 247


>gi|218132910|ref|ZP_03461714.1| hypothetical protein BACPEC_00771 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991783|gb|EEC57787.1| hypothetical protein BACPEC_00771 [Bacteroides pectinophilus ATCC
           43243]
          Length = 256

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 76/257 (29%), Positives = 121/257 (47%), Gaps = 12/257 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+GS Y GWQR  +  ++I+  +  AI   TGE   + G+GRTD+GVHAL 
Sbjct: 1   MNNYRLTIQYDGSRYNGWQRLNDTDNTIEQILTDAIIKSTGEKTKLIGSGRTDAGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A+F   +    +   + LN+ L   + I +     V   FH+R SA  + Y+YRI   
Sbjct: 61  QTANFRCRQRLDEMHFTEELNSML--PEDIRVNLTKRVPPDFHSRHSATGKYYVYRIEIS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +      +  +W      D + M  AAQ ++G HDF  F +        ++T+   ++  
Sbjct: 119 EPANPFRRRYSWKPDGIPDVKLMCEAAQRMIGEHDFKAFCTDAKLMPYTVKTVYDINIHK 178

Query: 178 -------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                       +IE+      FL+  +R   G++   G G+++  D++  L    R   
Sbjct: 179 DYSCLWNREEPGIIELEFHGSGFLYNMVRIMAGTIVDAGLGRFSPADIDAMLNGGTRSMS 238

Query: 231 GPLAPPEGLYFDSVEYS 247
           G LAP  GL+    EYS
Sbjct: 239 GQLAPARGLFLKKAEYS 255


>gi|332702220|ref|ZP_08422308.1| tRNA pseudouridine synthase A [Desulfovibrio africanus str. Walvis
           Bay]
 gi|332552369|gb|EGJ49413.1| tRNA pseudouridine synthase A [Desulfovibrio africanus str. Walvis
           Bay]
          Length = 266

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 119/250 (47%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y G+ + G Q Q    ++QG +E  +  +    V +  A RTDSGVHAL Q
Sbjct: 1   MPRLKLTLAYTGTRFAGLQIQPGCRTVQGEVEAVLARMLNGPVRIDMAARTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           V H D+    + +   KA+NA L   D + +  + +V  +FH+RFSA  + Y Y I +  
Sbjct: 61  VVHLDVPESKMRIPWRKAINALL--PDDVCVTEVEVVPPEFHSRFSATSKVYAYTIWSEL 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  L   K   W +   L+   M  A QH VGRHDF +F+++        RT+  F    
Sbjct: 119 EFILPQRKPFVWRMAG-LNQTAMDKAMQHFVGRHDFKSFQNVGTPIRDTRRTVARFWREP 177

Query: 180 FGNLIE--IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                E   R+ A  FL   +R+ +G L  VG GK    D+   +  +DR    P AP  
Sbjct: 178 GQTQWETVYRIQADGFLKQMVRNIIGCLVAVGRGKLCPNDIPALIAVRDRSLAPPTAPSR 237

Query: 238 GLYFDSVEYS 247
           GL  + + + 
Sbjct: 238 GLCLERIFFD 247


>gi|323345677|ref|ZP_08085900.1| tRNA pseudouridine synthase A [Prevotella oralis ATCC 33269]
 gi|323093791|gb|EFZ36369.1| tRNA pseudouridine synthase A [Prevotella oralis ATCC 33269]
          Length = 243

 Score =  250 bits (639), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +   Y+G+ Y GWQ Q NG+S+Q  ++ A+ ++  + V V GAGRTD+GVHA   
Sbjct: 1   MQRYFVYFAYDGTAYHGWQVQPNGNSVQVELQNALSVLLRQPVEVVGAGRTDAGVHARMM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD       V L   LN  L     IS+  +  VD   HARFSA+ R+Y Y +  R+
Sbjct: 61  AAHFDFDTPVDEVQLAYKLNRLL--PKDISVDRVVAVDSSMHARFSAVSRTYHYYVHCRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH-FDVNS 179
            P   ++  ++ +   LD   M   AQHL+   DF  F   H  + + +  +     V  
Sbjct: 119 NP--FKRAYSYELHYQLDFRAMNEVAQHLLQVEDFGAFCKSHNDSKTTLCRVTRALWVQD 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  VG  + +  +  K ++ ++R   G   P   L
Sbjct: 177 DADSWHFVITANRFLRNMVRAVVGTLIDVGRHRISKEEFIKIVERRNRTGAGESMPAHAL 236

Query: 240 YFDSVEY 246
           + + ++Y
Sbjct: 237 FLEDIKY 243


>gi|307328060|ref|ZP_07607241.1| tRNA pseudouridine synthase A [Streptomyces violaceusniger Tu 4113]
 gi|306886365|gb|EFN17370.1| tRNA pseudouridine synthase A [Streptomyces violaceusniger Tu 4113]
          Length = 288

 Score =  250 bits (639), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 78/251 (31%), Positives = 114/251 (45%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q+   ++QG +E A+  VT   E   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQRERRTVQGELESALRTVTRSSETFELTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL    W             ++   + +  ++     F+ARFSAI R Y YR+  
Sbjct: 70  QVAHVDLPEALWAEHRDRLLRRLAGRLPHDVRVWKVAQAPPGFNARFSAIWRRYAYRVTD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +G        LD   M  A++ L+G HDF  +       ++ IRT+   D 
Sbjct: 130 HPGGVDPLLRGHVLWHDWPLDVAAMNAASERLLGEHDFAAYCKKR-DGATTIRTLQRLDW 188

Query: 178 NSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               + +I   V A +F H  +RS VG+L  VGDG        K L A  R     +  P
Sbjct: 189 VRGADGVITATVRADAFCHNMVRSLVGALLFVGDGHRPWDWPAKVLAAGVRDSAVHVVRP 248

Query: 237 EGLYFDSVEYS 247
            GL  + V Y 
Sbjct: 249 HGLTLEEVGYP 259


>gi|294630922|ref|ZP_06709482.1| tRNA pseudouridine synthase A [Streptomyces sp. e14]
 gi|292834255|gb|EFF92604.1| tRNA pseudouridine synthase A [Streptomyces sp. e14]
          Length = 284

 Score =  250 bits (639), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 82/252 (32%), Positives = 119/252 (47%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGSAFHGWAKQAGGKRTVQGEIEDALRTVTRSQETYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL  +       K L     ++   + +  L      F+ARFSA+ R Y YR+ 
Sbjct: 70  GQVAHVDLPEQVWREHHEKLLKRLAGRLPRDVRVWALRPAPSGFNARFSAVWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWPLDVDAMNEAARRLLGEHDFAAYCKKR-EGATTIRTLQELS 188

Query: 177 VNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +    + +I   V A +F H  +RS +G+L  VGDG  T     K L A  R     +  
Sbjct: 189 LRRGADGIITATVRADAFCHNMVRSLIGALLFVGDGHRTPDWPGKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|312129758|ref|YP_003997098.1| tRNA pseudouridine synthase a [Leadbetterella byssophila DSM 17132]
 gi|311906304|gb|ADQ16745.1| tRNA pseudouridine synthase A [Leadbetterella byssophila DSM 17132]
          Length = 251

 Score =  250 bits (639), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 76/246 (30%), Positives = 120/246 (48%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y G+ + GWQ Q    ++QG +EKA+  V    + + G+ RTD+GVHA +Q 
Sbjct: 1   MRYFIEISYLGTHFHGWQIQPGADTVQGELEKALSTVLNAPISIMGSSRTDTGVHARQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH DL +E     + + LN +L     I+I N   +  + HARF A  R Y+YRI+  + 
Sbjct: 61  AHVDLPQEIHAGYIQR-LNRFL--PKDITIKNFYPLSDEAHARFDATGRKYIYRILHSK- 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             + ++       +  D + M  AA+ L    D+ +F  +    ++   TI         
Sbjct: 117 -DSFQQWICAHYSRRPDVDAMNKAAKILFLHTDYQSFSKVKTDVTTFDCTITEAVWRYVD 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +E  + A  FL   +R+ VG+L  VG GK    + E  + A+DR + G     EGL  
Sbjct: 176 ERLEFHISANRFLRGMVRAVVGTLLEVGYGKIGLQEFENIILAKDRTKAGTAVKAEGLTL 235

Query: 242 DSVEYS 247
           + V Y 
Sbjct: 236 ERVYYP 241


>gi|167765202|ref|ZP_02437315.1| hypothetical protein BACSTE_03590 [Bacteroides stercoris ATCC
           43183]
 gi|167696830|gb|EDS13409.1| hypothetical protein BACSTE_03590 [Bacteroides stercoris ATCC
           43183]
          Length = 251

 Score =  250 bits (639), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 116/248 (46%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q NG+S+Q  + KA+  +    V V GAGRTD+GVHA   
Sbjct: 1   MQRYFIYLAYDGTAYHGWQIQPNGASVQECLMKALSTLLRREVEVVGAGRTDAGVHASLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD       + +   LN  L     IS+  L  V    HARF A  R+Y Y + T +
Sbjct: 61  VAHFDSETPLDVIFMMDKLNRLL--PPDISVYRLRAVRPDAHARFDATARTYKYYVTTAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +     + ++ D E M  AA+ L    DFT+F  +H    +    I H      
Sbjct: 119 MP--FNRQYRCRLFQTPDFERMNEAARTLFEYTDFTSFSKLHTDVKTNNCKIMHAAWTQV 176

Query: 181 GNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +     + A  FL   +R+ VG+L  VG GK T     + ++ +DR   G   P   L
Sbjct: 177 DEVTWVFTIQADRFLRNMVRAVVGTLLEVGRGKLTIGGFRRVIEQKDRCRAGTSVPGNAL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLVDVAYP 244


>gi|256785794|ref|ZP_05524225.1| tRNA pseudouridine synthase A [Streptomyces lividans TK24]
          Length = 275

 Score =  250 bits (639), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 118/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 1   MRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSRETYELTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL RE       K L     ++   + +  L      F+ARFSA+ R Y YR+ 
Sbjct: 61  GQVAHVDLPREVWAEHHVKLLKRLAGRLPRDVRVWALREAPSGFNARFSAVWRRYAYRVT 120

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+    
Sbjct: 121 DNPGGVDPLLRGHVLWHDWPLDVDAMNAAARGLLGEHDFAAYCKKR-EGATTIRTLQELS 179

Query: 177 VNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +    + I    V A +F H  +RS +G+L  VGDG        K L A  R     +  
Sbjct: 180 LVRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRGPEWPAKVLAAGVRDSAVHVVR 239

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 240 PHGLTLEEVGYP 251


>gi|256390175|ref|YP_003111739.1| tRNA pseudouridine synthase A [Catenulispora acidiphila DSM 44928]
 gi|256356401|gb|ACU69898.1| tRNA pseudouridine synthase A [Catenulispora acidiphila DSM 44928]
          Length = 284

 Score =  250 bits (639), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 74/255 (29%), Positives = 118/255 (46%), Gaps = 10/255 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW  Q    ++ G +  A+  V  + V +  AGRTD+GVHA  QV
Sbjct: 10  VRVRLDLAYDGTHFSGWAIQPKRRTVCGELTSALSTVLRQDVTLVVAGRTDAGVHASGQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH D+  E       + L      +   + + +       F ARF+A+ R Y YR+    
Sbjct: 70  AHLDVPLELWAEHEERLLRRLAAVLPGDVRVWSAVPAPVGFDARFAAMGRRYAYRVTDAA 129

Query: 121 A-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L +      P++LD   M  AA  L+G HDF +F     + ++ IR +   +   
Sbjct: 130 YGPHPLRRNDVTWHPRTLDPALMNEAAAALLGEHDFASFCKKR-EGATTIRCLTRLEWTR 188

Query: 180 FG-------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                     L+   V A +F H+ +RS VG+L  VG+G+    D  + L  + R     
Sbjct: 189 EAPTSLTPVGLLVADVRADAFCHSMVRSLVGALLAVGEGRRPVGDPGRILAEEVRSPEVK 248

Query: 233 LAPPEGLYFDSVEYS 247
           +APP+GL  + V Y 
Sbjct: 249 VAPPQGLTLEEVVYP 263


>gi|300088167|ref|YP_003758689.1| tRNA pseudouridine synthase A [Dehalogenimonas lykanthroporepellens
           BL-DC-9]
 gi|299527900|gb|ADJ26368.1| tRNA pseudouridine synthase A [Dehalogenimonas lykanthroporepellens
           BL-DC-9]
          Length = 261

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 82/245 (33%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+G+ Y G Q Q +G+++Q  +E A+  +TGE + +H A RTD+GV A  QVA
Sbjct: 8   KLVLTIEYDGAQYRGSQAQGHGATVQSELETAVARLTGEKIRIHLASRTDAGVSAAEQVA 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F          +  ALN +L     I++  +  V   F  R  A+ R Y YRI+  + P
Sbjct: 68  SFRTSLRLPGRTVADALNHFL--PADIAVKKVFRVPDTFDVRRHAVSREYRYRILNTRIP 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFG 181
             L +  ++ +   LD   +  A   LVG HD   F   +  +  + IR I    + S G
Sbjct: 126 SPLRERHSYRVYGELDIAAIEQAVGKLVGEHDLAAFASKLGRRPGTTIRRILAAGLTSEG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +  R+VA+SFL   +R+ VG L  +G G+ T  + EK L A      GP AP +GL  
Sbjct: 186 EELVFRIVAKSFLPHMVRNIVGVLVKIGTGRLTVAEFEKLLSAAVPGSAGPAAPGKGLCL 245

Query: 242 DSVEY 246
             V Y
Sbjct: 246 IKVNY 250


>gi|329938203|ref|ZP_08287654.1| tRNA pseudouridine synthase A [Streptomyces griseoaurantiacus M045]
 gi|329302692|gb|EGG46582.1| tRNA pseudouridine synthase A [Streptomyces griseoaurantiacus M045]
          Length = 288

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 119/252 (47%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G+G+ GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGTGFSGWAKQAGGRRTVQGEIEDALRTVTRSRETFELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL RE       K L     ++   + +  L      F ARFSA+ R Y YR+ 
Sbjct: 70  GQVAHVDLPREVWAEHHGKLLKRLAGRLPRDVRVWALREAPAGFDARFSAVWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWPLDVDAMNEAARGLLGEHDFAAYCKKR-EGATTIRTLQELS 188

Query: 177 VNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +   G+ I    V A +F H  +RS +G+L  VGDG        K L A  R     +  
Sbjct: 189 LARGGDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRAPDWPAKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|254521233|ref|ZP_05133288.1| tRNA pseudouridine synthase A [Stenotrophomonas sp. SKA14]
 gi|219718824|gb|EED37349.1| tRNA pseudouridine synthase A [Stenotrophomonas sp. SKA14]
          Length = 256

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 93/247 (37%), Positives = 131/247 (53%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EY+GS + GWQ   + G S+Q S+E A+  V    + V  AGRTD+GVH   Q
Sbjct: 1   MRYALGVEYDGSDFRGWQNLGEGGPSVQASLELALSSVADAPLQVVCAGRTDAGVHGQCQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P      L    ++  +I++     V   FHARFSA  R Y YR++ R+
Sbjct: 61  VVHFDTDVVRDPRAWM--LGTTTRLPRSIAVRWCVPVADDFHARFSARARRYRYRLLNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL +       ++LD   M  A Q L+G +DF+ FRS+ CQA    R +    V+  
Sbjct: 119 VRPALGRQTLSWERRTLDEALMHAAGQALLGENDFSAFRSVQCQALHARRELQSLQVSRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +IE+ V   +FLH  +R+ VGSL LVG G+     + + L  +DR   GP APP+GL 
Sbjct: 179 GEVIEVAVQGNAFLHHMVRNIVGSLILVGSGEKPVEWIAELLAGRDRTVAGPTAPPQGLV 238

Query: 241 FDSVEYS 247
           F    Y 
Sbjct: 239 FLGPLYP 245


>gi|295838433|ref|ZP_06825366.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB74]
 gi|197695769|gb|EDY42702.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB74]
          Length = 284

 Score =  249 bits (637), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 77/252 (30%), Positives = 121/252 (48%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G+ + GW RQ     ++Q ++E+A+ +VT   E   +  AGRTD+GVHA 
Sbjct: 1   MRLRLDLSYDGTEFHGWARQPAGRRTVQETLEEALRVVTRAPEPYELTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH ++  E       K L     ++   + +  ++   + F ARFSAI R Y YR+ 
Sbjct: 61  GQVAHVEMADEVWAEHGEKLLKRLAGRLPKDVRVWRVAPAPEGFDARFSAIWRRYAYRVA 120

Query: 118 TRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +      L +G      + LD + M  AA+ L+G HDF  +     + ++ IR +    
Sbjct: 121 DQPGGADPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAYCKKR-EGATTIREMQRLF 179

Query: 177 VNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                + + E  V A +F H  +RS VG+L  VGDG    +   K L A  R     +  
Sbjct: 180 WTRRADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSAVHVVR 239

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 240 PVGLTLEEVGYP 251


>gi|21223110|ref|NP_628889.1| tRNA pseudouridine synthase A [Streptomyces coelicolor A3(2)]
 gi|289769686|ref|ZP_06529064.1| tRNA pseudouridine synthase A [Streptomyces lividans TK24]
 gi|8134769|sp|O86776|TRUA_STRCO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3449243|emb|CAA20387.1| putative pseudouridylate synthase [Streptomyces coelicolor A3(2)]
 gi|289699885|gb|EFD67314.1| tRNA pseudouridine synthase A [Streptomyces lividans TK24]
          Length = 284

 Score =  249 bits (637), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 118/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT   E   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSRETYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL RE       K L     ++   + +  L      F+ARFSA+ R Y YR+ 
Sbjct: 70  GQVAHVDLPREVWAEHHVKLLKRLAGRLPRDVRVWALREAPSGFNARFSAVWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWPLDVDAMNAAARGLLGEHDFAAYCKKR-EGATTIRTLQELS 188

Query: 177 VNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +    + I    V A +F H  +RS +G+L  VGDG        K L A  R     +  
Sbjct: 189 LVRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRGPEWPAKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|113476553|ref|YP_722614.1| tRNA pseudouridine synthase A [Trichodesmium erythraeum IMS101]
 gi|110167601|gb|ABG52141.1| tRNA pseudouridine synthase A [Trichodesmium erythraeum IMS101]
          Length = 272

 Score =  249 bits (636), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 110/247 (44%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  ++I+Y G+ + GWQRQ N  ++Q  IEK I     E V +HGAGRTD+GVHA  QV
Sbjct: 9   QRVALVIQYQGTHFHGWQRQPNQRTVQEEIEKTIASFINEPVTLHGAGRTDAGVHAAAQV 68

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+            LN+ L   + I I   + +D  +H+RF+AI R Y Y I T + 
Sbjct: 69  AHFDVSGPIPAHKWATILNSRLA--NDILIRGSARIDYAWHSRFTAIWRRYRYTIYTDKQ 126

Query: 122 PLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P        W   + SLD + ++ A   L+G H    F+            +        
Sbjct: 127 PNLFVMPFVWHYYQASLDPQLIQAALNPLIGHHHLAAFQRAGSCRPHSWVDVQEVMCERK 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I V A  FL+  +R  VG L  VG  + +          Q R      AP  GL 
Sbjct: 187 GPFIYIEVQASGFLYGMMRLLVGLLIQVGTEELSLESFTDIWVNQRRDIVKHSAPASGLC 246

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 247 LLRVGYP 253


>gi|298345431|ref|YP_003718118.1| tRNA-pseudouridine synthase I [Mobiluncus curtisii ATCC 43063]
 gi|304390987|ref|ZP_07372939.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. curtisii
           ATCC 35241]
 gi|298235492|gb|ADI66624.1| tRNA-pseudouridine synthase I [Mobiluncus curtisii ATCC 43063]
 gi|304325870|gb|EFL93116.1| tRNA pseudouridine synthase A [Mobiluncus curtisii subsp. curtisii
           ATCC 35241]
          Length = 297

 Score =  249 bits (636), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 89/273 (32%), Positives = 131/273 (47%), Gaps = 28/273 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++QG++E A+ ++  + V +  AGRTD+GVHA  QV
Sbjct: 1   MRIRLDIRYDGTPFHGWAAQPGLPTVQGALESALTVIYRQTVELTVAGRTDAGVHASGQV 60

Query: 62  AHFDLV----REWVPVILCKALNAYL------------------KISDTI---SILNLSI 96
           AHF +     R   P  L   L A L                     + I    +   ++
Sbjct: 61  AHFTVPEVGDRIVSPDTLAPRLGAVLRAVLSGNLASPLPDSPAAYPPNAIDALVVTAATV 120

Query: 97  VDKQFHARFSAIRRSYLYRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
           V + F ARFSA+ R Y+YRI+    A   L +   W  P  LD   M  +A  L+G HDF
Sbjct: 121 VPETFDARFSALARHYVYRIVDDLAARNPLSRNCCWWYPTQLDAAAMNTSAAVLLGEHDF 180

Query: 156 TTFRSIHCQASSPIRTIDHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             F     + ++ IRT+   +       ++EIRV A +F H+ +RS VG+L  VG  K  
Sbjct: 181 AAFCKPR-EGATTIRTLQQLETLRTAPGMMEIRVRADAFCHSMVRSLVGALTEVGRAKRD 239

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  L  AL A+ R    P+AP  GL    V+Y 
Sbjct: 240 TAWLADALAAKARIPEIPVAPALGLTLTQVDYP 272


>gi|57234742|ref|YP_181248.1| tRNA pseudouridine synthase A [Dehalococcoides ethenogenes 195]
 gi|57225190|gb|AAW40247.1| tRNA pseudouridine synthase A [Dehalococcoides ethenogenes 195]
          Length = 248

 Score =  249 bits (636), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 79/243 (32%), Positives = 122/243 (50%), Gaps = 3/243 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            ++IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  +
Sbjct: 2   LLVIEYEGTRYSGFQVQDKGATIQGELETAIRKLTSEQTRVSGSGRTDAGVHAAYQVVSY 61

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     +   LN YL     I++  +  V + F  R  AI R Y Y+I+  +    
Sbjct: 62  LSESSLGLDKIKGGLNFYL--PPDIAVKEVHFVAESFDVRRRAISREYSYQILNSKTRSP 119

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNL 183
           L + +AW +P  LD + M  A + L G HDF  F  S+  +    +R ++   +    + 
Sbjct: 120 LARLQAWQVPYKLDIKLMEQAFKMLEGEHDFIAFASSLGPEIKKTVRRVNWTRLGIREDR 179

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   + A SFL  Q+R+ +G+L  +G G  + ++ E   +A+     GP AP  GL    
Sbjct: 180 LIFNIEANSFLTHQVRNTIGTLVELGRGTMSMSEFEALFEAKTPGLAGPAAPACGLSLVR 239

Query: 244 VEY 246
           V Y
Sbjct: 240 VNY 242


>gi|320528746|ref|ZP_08029898.1| tRNA pseudouridine synthase A [Solobacterium moorei F0204]
 gi|320130956|gb|EFW23534.1| tRNA pseudouridine synthase A [Solobacterium moorei F0204]
          Length = 361

 Score =  249 bits (636), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 124/247 (50%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY  ++ Y G  Y GWQ Q+ G SIQ  +E  I  +T E V V G+GRTD+GV+A  Q
Sbjct: 1   MMRYKCVVSYVGRNYSGWQSQRKGDSIQEILETVIERITQEKVNVIGSGRTDAGVNAKAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FD  RE        A+NA+L   + I I+++   D  FHAR++   + Y YRI    
Sbjct: 61  VFMFDTKREMPARKWMGAINAFL--PNDIHIMSVEEEDDCFHARYNVRFKQYNYRINNGP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
                 K  A+  P  LD E M+    +LVG HDFT+   S   +    +RT+    +  
Sbjct: 119 Y-NVFTKDTAFQCPIHLDVEKMKEGIPYLVGTHDFTSLNSSSLEEYPDQVRTVRSITLTE 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              +I +  V + FL   +R     L  +G  K+  + +++ L+A+ +      +P EGL
Sbjct: 178 EDGVITLAFVGKGFLRYMVRMMASVLIEIGKRKYEPSHIQEILEAKRKSFPHKNSPAEGL 237

Query: 240 YFDSVEY 246
             + V+Y
Sbjct: 238 TLEYVDY 244


>gi|124008085|ref|ZP_01692784.1| tRNA pseudouridine synthase A [Microscilla marina ATCC 23134]
 gi|123986499|gb|EAY26305.1| tRNA pseudouridine synthase A [Microscilla marina ATCC 23134]
          Length = 248

 Score =  248 bits (635), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 80/250 (32%), Positives = 128/250 (51%), Gaps = 8/250 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ QKN  S+Q  I+ A+ ++  +   + G+GRTD+GVHA++Q 
Sbjct: 1   MRYFLELAYSGTQYHGWQIQKNAHSVQAEIQNALSVLLRQPTDILGSGRTDAGVHAIQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD  +     +  K +N  L   + ISI  +  V ++ H RF A +R Y+YRI   + 
Sbjct: 61  AHFDTEQTLDGEVFAKKMNGIL--PEDISIKRVINVHEEAHTRFDATQRHYMYRINQEKT 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P    +G ++      D + M  AAQ ++   DF  F  +H   +  +  I         
Sbjct: 119 P--FLRGVSYYNFHRFDIDLMNKAAQIMLKHEDFQCFSKVHTDVNHYLCNIQQAYWQKET 176

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               NL+   + A  FL   +R+  G++  VG GK T  + E+ +  +DRK+ G   P +
Sbjct: 177 SYNVNLLVFYIQANRFLRGMVRAITGTMLNVGSGKITLEEFEQIILNKDRKQAGWSVPAQ 236

Query: 238 GLYFDSVEYS 247
           GL+   VEY 
Sbjct: 237 GLFLAKVEYP 246


>gi|159901453|ref|YP_001547700.1| tRNA pseudouridine synthase ACD [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159894492|gb|ABX07572.1| tRNA pseudouridine synthase A [Herpetosiphon aurantiacus ATCC
           23779]
          Length = 272

 Score =  248 bits (635), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 124/252 (49%), Gaps = 8/252 (3%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   +  EY G+ + G Q Q  G ++Q  +E A   +T E      AGRTD+GVHAL 
Sbjct: 1   MSRTLALCFEYLGTAFCGSQWQPGGRAVQTELETAWQRLTSETGRWIFAGRTDAGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH           + KA+NA       IS+     +   FHARFSA +R+Y Y   + 
Sbjct: 61  QVAHIVSDTPRSLDTIAKAINA--ITPPDISVHEAWEMPTGFHARFSARQRTYRYVFDSA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            AP A   GR   +   LD   M+ A   L+G HDF  F     + S+  RT     +  
Sbjct: 119 PAPSATLSGRVLRLDHQLDWAAMQAALDTLIGTHDFAAFAGAGHEGSTT-RTCMLAQLRP 177

Query: 180 FG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  +  + + A +FL   +R+ VG+L +VGDG+ +    +  + ++DR+  GP AP
Sbjct: 178 AEWLGRPVTVLHLQANAFLKHMVRNIVGTLLMVGDGRLSLEAWQAIIASRDRRNAGPTAP 237

Query: 236 PEGLYFDSVEYS 247
           P+GLY +S+ Y 
Sbjct: 238 PQGLYLESIGYD 249


>gi|320537307|ref|ZP_08037262.1| tRNA pseudouridine synthase A [Treponema phagedenis F0421]
 gi|320145772|gb|EFW37433.1| tRNA pseudouridine synthase A [Treponema phagedenis F0421]
          Length = 261

 Score =  248 bits (635), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 82/252 (32%), Positives = 120/252 (47%), Gaps = 8/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-KNG----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
               + I Y+G+ + GWQ+Q KNG     +IQG IEKA   +  +   + GAGRTD+GVH
Sbjct: 5   RNILLRISYDGTFFSGWQKQVKNGIETFPTIQGEIEKAASKIHKQKKEIIGAGRTDTGVH 64

Query: 57  ALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           A+ Q A+F    +         A N+ L     I +++   V  Q HARFSA  R+Y Y 
Sbjct: 65  AIGQAANFFTEIQTIEAKSFIPAFNSLL--PKQIRVVDAQEVSPQLHARFSAQARTYRYF 122

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I   +   A E+   W I +  D   +   A  L G  D T+F     Q++S  R I   
Sbjct: 123 IQCAKREFAHEQAYCWQIKRYPDISTLNRYAAVLRGELDCTSFSFAKDQSASKSRYIFSA 182

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +   + A +FL   +RS  G+L       +T  D +K L+ +DR   GP AP
Sbjct: 183 HFFIEKDFLVFEISANAFLWRMVRSLTGTLLRCEKEHYTQNDFKKILELKDRGLAGPTAP 242

Query: 236 PEGLYFDSVEYS 247
           P+GL+   + Y 
Sbjct: 243 PQGLFLWHITYP 254


>gi|188994646|ref|YP_001928898.1| tRNA pseudouridine synthase A [Porphyromonas gingivalis ATCC 33277]
 gi|238691471|sp|B2RIV6|TRUA_PORG3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|188594326|dbj|BAG33301.1| putative tRNA pseudouridine synthase A [Porphyromonas gingivalis
           ATCC 33277]
          Length = 252

 Score =  248 bits (635), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 119/251 (47%), Gaps = 8/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + + YNG+ Y GWQ Q N  S+Q ++E+AI  +  + V V GAGRTD+GVHA   
Sbjct: 1   MARFFIYLAYNGTRYSGWQTQPNAPSVQQTVEEAISTIVRQPVGVVGAGRTDAGVHAHEM 60

Query: 61  VAHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           VAH DL  +       L + LN  L     I I  ++ V    HARF AI R+Y Y +  
Sbjct: 61  VAHADLPCDTPAEAATLTERLNKLL--PRDIVIYRMAPVKADAHARFDAISRTYHYYLTE 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           ++      +G      + LD E M  AA  L    DFT+F  +H    +    I      
Sbjct: 119 QK--DPFMEGLMLKTYRKLDFERMNEAAALLPRYIDFTSFSKLHTDVKTNNCRITEARWM 176

Query: 179 SFGNL--IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                      + A  FL   +R+ VG+L  VG GK + TD    +++QDR   G  AP 
Sbjct: 177 PLAQTGQWVFSITADRFLRNMVRAIVGTLFHVGTGKLSITDFRDIIESQDRSRAGSSAPA 236

Query: 237 EGLYFDSVEYS 247
             LY + V Y 
Sbjct: 237 HALYLERVVYP 247


>gi|237756326|ref|ZP_04584878.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237691512|gb|EEP60568.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 243

 Score =  248 bits (635), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 84/244 (34%), Positives = 117/244 (47%), Gaps = 5/244 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            Y + I Y G+ Y GWQRQKNG  IQ  IE  +  +  E + + GAGRTD+GVHALRQVA
Sbjct: 5   NYKLEISYIGTNYNGWQRQKNGIGIQQVIEDLLSELLKEKITLIGAGRTDAGVHALRQVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F   +      +   LNA L     ISIL +  V   F+ARFSA  ++Y+Y+I T+  P
Sbjct: 65  NFKTNKHKNTKTIYTYLNAKL--PRDISILKVEEVPLSFNARFSAKGKTYIYKINTK--P 120

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                  AW   K LD   M      +    D ++           I  +    +   G 
Sbjct: 121 DPFLYKLAWYYDKKLDLIKMVEGINIIKQYKDLSSLAKAGDYIRKEI-DLRELKLYFDGK 179

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +I I + A  FL   +R  VG L  +G G  +  +L+  ++ +        APPEGLY  
Sbjct: 180 IITIEITASHFLRNMVRRIVGHLVALGRGSLSLEELKDIIEKKSPSHGKYTAPPEGLYLK 239

Query: 243 SVEY 246
           +V Y
Sbjct: 240 AVYY 243


>gi|296268583|ref|YP_003651215.1| tRNA pseudouridine synthase A [Thermobispora bispora DSM 43833]
 gi|296091370|gb|ADG87322.1| tRNA pseudouridine synthase A [Thermobispora bispora DSM 43833]
          Length = 294

 Score =  248 bits (635), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 80/269 (29%), Positives = 119/269 (44%), Gaps = 24/269 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
           +R+ + + Y+G+ + GW RQ    ++QG +E A+  +        +  AGRTD+GVHA  
Sbjct: 6   VRFRLDLGYDGTDFQGWARQPGLRTVQGELEAALATLLRLEAPPRLTVAGRTDAGVHARG 65

Query: 60  QVAHFD-----------------LVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQ 100
           QV H D                          LC AL   L   +   + +  +S+    
Sbjct: 66  QVVHVDLPLAALAILEPRGRETATPPAERLPELCSALVRRLAAVLPPDVRVFAVSVPPDG 125

Query: 101 FHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
           F ARFSA+ R Y YR+         L +      PK LD E M  A+  L+G HDF  F 
Sbjct: 126 FDARFSALCRRYCYRVCDAPGGVDPLRRREVLWYPKPLDVELMNAASVRLLGEHDFAAFC 185

Query: 160 SIHCQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               + ++ IR +  F+       +IE  VVA +F H+ +RS VG++  VG+GK      
Sbjct: 186 KKR-EGATTIRELRRFEWARRDDGIIEATVVADAFCHSMVRSLVGAVLAVGEGKRPVEWP 244

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + L    R     +AP  GL  + V Y 
Sbjct: 245 AEVLARAVRDSAVRVAPAHGLTLEEVRYP 273


>gi|298209267|ref|YP_003717446.1| putative tRNA pseudouridine synthase A [Croceibacter atlanticus
           HTCC2559]
 gi|83849194|gb|EAP87063.1| putative tRNA pseudouridine synthase A [Croceibacter atlanticus
           HTCC2559]
          Length = 258

 Score =  248 bits (635), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 122/246 (49%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I YNG  Y G+QRQ    S+Q  +E AI +   + V + GAGRTD+GVH  + +
Sbjct: 1   MRYFLDIAYNGKPYHGFQRQPEDISVQEVLEDAIAVYFQKAVTIFGAGRTDTGVHGKQLI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD             LN  L   D++++ ++ +V+ + HARF A+ R Y Y + TR+ 
Sbjct: 61  AHFDSDTTINESQFLYKLNKLL--PDSVAVRDVYLVNSEAHARFDAMAREYEYVVTTRKD 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E   A  I K LD E M  AA+ L+   DF  F  +     +    I +   +  G
Sbjct: 119 PFLSES--ALYIIKPLDVEAMNTAAKVLLEYTDFECFSKVKTDVKTFNCKITYAHWSQHG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +   + A  FL   +R+ VG+L  VG GK     +   + +++R E G     +GLY 
Sbjct: 177 HKLVFTIRADRFLRNMVRAIVGTLLEVGLGKRLPGSIHDIIASKNRGEAGKSVAAQGLYL 236

Query: 242 DSVEYS 247
             V Y 
Sbjct: 237 TKVLYP 242


>gi|296141060|ref|YP_003648303.1| tRNA pseudouridine synthase A [Tsukamurella paurometabola DSM
           20162]
 gi|296029194|gb|ADG79964.1| tRNA pseudouridine synthase A [Tsukamurella paurometabola DSM
           20162]
          Length = 273

 Score =  248 bits (635), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 118/249 (47%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + I Y+G+ + GW RQ    ++ G +E+AI  V    V +  AGRTD+GVHA  Q
Sbjct: 1   MTRYRLDIAYDGTDFSGWARQPERRTVCGVVEEAIGTVLRTPVQLTVAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D      P  L + L   L     + +  ++    +F ARFSA+RR Y YR+    
Sbjct: 61  VAHVDTDLAL-PEGLVRRLARML--PQDVRVTAIAEAPAEFDARFSALRRHYEYRLTDAP 117

Query: 121 A-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L         + +D E M+ A+  L+G HDF  F     + ++ +R +  F    
Sbjct: 118 YGANPLRARDTAPWRRPVDVERMQAASDALLGLHDFAAFCRRR-EGATTVRELQRFAWRR 176

Query: 180 FGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             + +    V A +F  + +RS VG++  VG+G+ +   +   L  ++R     +A   G
Sbjct: 177 DADGVCTAEVSADAFCWSMVRSLVGAVAAVGEGRRSVEWVAGLLDERERSSAINVAAACG 236

Query: 239 LYFDSVEYS 247
           L    V+Y 
Sbjct: 237 LTLVRVDYP 245


>gi|239636202|ref|ZP_04677206.1| tRNA pseudouridine synthase A [Staphylococcus warneri L37603]
 gi|239598218|gb|EEQ80711.1| tRNA pseudouridine synthase A [Staphylococcus warneri L37603]
          Length = 267

 Score =  248 bits (635), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 120/244 (49%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+ + G+Q Q+ G ++Q   EK +  +    + +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIEYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHISIHPSSRTDRGVHAYQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I + ++  VD+ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELQIENSKWQYAMNSAL--PDDIYVKSVKQVDEDFHCRYDCVGKRYRYKVYQAKH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I  SLD   M  AA+  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTYIADSLDLNQMNEAAKLFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK +  ++ + L+ ++R +    AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLIEVGKGKRSPEEIPQLLEEKNRNKIPFTAPSEGLYL 238

Query: 242 DSVE 245
           + V 
Sbjct: 239 EKVY 242


>gi|73748346|ref|YP_307585.1| tRNA pseudouridine synthase A [Dehalococcoides sp. CBDB1]
 gi|289432394|ref|YP_003462267.1| tRNA pseudouridine synthase A [Dehalococcoides sp. GT]
 gi|73660062|emb|CAI82669.1| tRNA pseudouridine synthase A [Dehalococcoides sp. CBDB1]
 gi|288946114|gb|ADC73811.1| tRNA pseudouridine synthase A [Dehalococcoides sp. GT]
          Length = 246

 Score =  248 bits (635), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  + 
Sbjct: 1   MVIEYEGTRYSGFQIQDKGATIQGELETAIRKLTSEQTRVSGSGRTDAGVHAAYQVVSYL 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +   LN YL     I++  +  V + F  R  AI R Y Y I+  +    L
Sbjct: 61  TESSLGLEKIKGGLNYYL--PPDIAVKEVHFVAENFDVRRRAISREYSYHILNSKTRSPL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
            + +AW +P  LD + M  A + L G HDF  F  S+  +    +R ++   ++   + +
Sbjct: 119 ARLQAWQVPYKLDIKLMEQAFKMLEGEHDFIAFASSLGPEIKKTVRRVNWTRLDIVEDRL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +R+ A SFL  Q+R+ +G L  +G G  +  +     +A+     GP AP  GL    V
Sbjct: 179 ILRIEANSFLTHQVRNTIGVLVELGRGTISMGEFGALFEAKTPGLAGPAAPACGLSLVRV 238

Query: 245 EY 246
            Y
Sbjct: 239 NY 240


>gi|228474552|ref|ZP_04059283.1| tRNA pseudouridine synthase A [Staphylococcus hominis SK119]
 gi|228271215|gb|EEK12583.1| tRNA pseudouridine synthase A [Staphylococcus hominis SK119]
          Length = 267

 Score =  248 bits (634), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 116/244 (47%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G G+ G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA  Q 
Sbjct: 1   MRILVNIAYQGHGFLGFQIQQQGRTVQQQFEKILKRMHRRHVRIHPSSRTDRGVHAYEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   + I + ++  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIEPKQWKYAMNSAL--PEDIYVNSVKQVDDTFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    I   LD + M  AA+H +G HDFT F S   +  S  RT+   +V    
Sbjct: 119 RNPFESGLKTFIKDDLDLDKMNEAAKHFIGTHDFTGFCSQKTEVESKERTLYQSEVVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+A++R      AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLVEVGKGKRQPNEVPELLKAKNRDNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|269792760|ref|YP_003317664.1| tRNA pseudouridine synthase A [Thermanaerovibrio acidaminovorans
           DSM 6589]
 gi|269100395|gb|ACZ19382.1| tRNA pseudouridine synthase A [Thermanaerovibrio acidaminovorans
           DSM 6589]
          Length = 251

 Score =  248 bits (634), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 120/247 (48%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY   + Y GS + G+QRQ N  ++QG++E+++  + GE V   GAGRTD+GVHA  Q
Sbjct: 1   MFRYAAQVSYVGSCFAGFQRQPNLVTVQGALEESLSALAGEGVTCTGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+   W    L  A+ A L     + ++ L+ V   FHARF A  R Y Y +   +
Sbjct: 61  VVHFDMPSRWDLERLRLAIRARL--PRGLEVIRLAEVPGDFHARFDARWREYRYLVWNAR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +   W + + LD   +R  A   +GR DF  F     +    +RT+    V  F
Sbjct: 119 WCYPHMEPYVWPVRRHLDLGVLRELAGMCLGRRDFGAFCRSADRPDDSVRTMMRCSVRRF 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+     A  FL   IR  VG++  V  G+ +       L+   R   G   PP+GL+
Sbjct: 179 GHLLVFTFRADGFLTNMIRILVGTMLEVEAGRMSRERFASLLEGGHRSRAGRTCPPQGLF 238

Query: 241 FDSVEYS 247
           F  V Y 
Sbjct: 239 FWRVGYD 245


>gi|225552068|ref|ZP_03773008.1| tRNA pseudouridine synthase A [Borrelia sp. SV1]
 gi|225371066|gb|EEH00496.1| tRNA pseudouridine synthase A [Borrelia sp. SV1]
          Length = 246

 Score =  248 bits (634), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 126/247 (51%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    ++QG IEKA+  +  + V +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSIYHGFQIQPTKPTVQGEIEKALTKINKKKVKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L + ++I IL L  V   FH RFSA +R Y Y I+   
Sbjct: 61  IITFDIKINIQLNNLKKALNAIL-LKNSIKILKLRYVKNSFHPRFSAQKRKYSYFILNND 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A  + K L+  N+   A+ L+G+HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWEGYQAHYVNKKLNINNLNQMAKTLIGKHDFTTFSCIKDKSKSKFRHIHFAKFKKR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 240 LDRVYYE 246


>gi|320353071|ref|YP_004194410.1| tRNA pseudouridine synthase A [Desulfobulbus propionicus DSM 2032]
 gi|320121573|gb|ADW17119.1| tRNA pseudouridine synthase A [Desulfobulbus propionicus DSM 2032]
          Length = 274

 Score =  248 bits (634), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 84/258 (32%), Positives = 121/258 (46%), Gaps = 13/258 (5%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M+R   ++I Y+G  Y GWQRQ+ G  +IQ  +E+ +  +  E + +HGAGRTD+GVHAL
Sbjct: 1   MLRTIRLLIAYDGGNYCGWQRQRQGEATIQEELEQRLSHLCEEPITLHGAGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             VAHF        V   K LNA L     I IL        FH+RFSA+ ++Y Y   T
Sbjct: 61  GMVAHFHTRAAIPVVAFFKGLNALL--PPDIRILAAEEASATFHSRFSALGKTYRYDFFT 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI------RTI 172
                   +      P   D + +R A   LVGRHDF++F     +  + I      RT+
Sbjct: 119 GAVQCPSTRLHRAHFPGPFDPKRLRTALTQLVGRHDFSSFERSGSRDKTAIDGRGAVRTL 178

Query: 173 DHFDVNSF---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                +      +   + V    FL   +R   G+L  +G GK     +   L A+DR +
Sbjct: 179 YEIRCSPRLGCEDFWSLHVTGDGFLRQMVRILAGTLIEIGHGKRPEEAIAAILAARDRTQ 238

Query: 230 CGPLAPPEGLYFDSVEYS 247
            G  AP  GL+ + + Y 
Sbjct: 239 AGLTAPACGLFLERLYYP 256


>gi|314935862|ref|ZP_07843214.1| tRNA pseudouridine synthase A [Staphylococcus hominis subsp.
           hominis C80]
 gi|313656427|gb|EFS20167.1| tRNA pseudouridine synthase A [Staphylococcus hominis subsp.
           hominis C80]
          Length = 267

 Score =  248 bits (634), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 116/244 (47%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G G+ G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA  Q 
Sbjct: 1   MRILVNIAYQGHGFLGFQIQQQGRTVQQQFEKILKRMHRRHVRIHPSSRTDRGVHAYEQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   + I + ++  VD  FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIEPKQWIYAMNSAL--PEDIYVNSVKQVDDTFHCRYDCVGKRYRYKVYQAEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    I   LD + M  AA+H +G HDFT F S   +  S  RT+   +V    
Sbjct: 119 RNPFESGLKTFIKDDLDLDKMNEAAKHFIGTHDFTGFCSQKTEVESKERTLYQSEVVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+A++R      AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLVEVGKGKRQPNEVPELLKAKNRDNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|254446439|ref|ZP_05059915.1| tRNA pseudouridine synthase A [Verrucomicrobiae bacterium DG1235]
 gi|198260747|gb|EDY85055.1| tRNA pseudouridine synthase A [Verrucomicrobiae bacterium DG1235]
          Length = 243

 Score =  248 bits (633), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 128/246 (52%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+     Y+G+ Y GWQ+Q    S+Q  IE+ +  +  E V +HG+GRTD+GVHAL QV
Sbjct: 1   MRWKCSCSYDGTNYAGWQKQSGQISVQQVIEEVLEQLLKEKVAIHGSGRTDAGVHALEQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD         L KAL++ L     I + + + V ++FHARFSA+ + Y YR+   +A
Sbjct: 61  FHFDYDWRHGGESLVKALHSKL--PKEIRVESATEVGEEFHARFSAVSKRYQYRLALGEA 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSF 180
               +    W + + LD   ++ A    VG HDF  F +    +  S  R +    V+  
Sbjct: 119 -NPFQWAYCWPVSRKLDLNLVKEAMDRFVGTHDFGAFAANRGIEYESTERKMLATGVSQD 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + +   A  F++  +RS VG++  VG G+   +++E+ L++  R      AP +GL+
Sbjct: 178 TEYVGLSFQADGFMYKMVRSLVGAVVNVGLGRMQVSEIERLLESAVRSPMVQAAPAKGLF 237

Query: 241 FDSVEY 246
            + V Y
Sbjct: 238 LEKVFY 243


>gi|261879379|ref|ZP_06005806.1| tRNA pseudouridine synthase A [Prevotella bergensis DSM 17361]
 gi|270333946|gb|EFA44732.1| tRNA pseudouridine synthase A [Prevotella bergensis DSM 17361]
          Length = 244

 Score =  248 bits (633), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 120/247 (48%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I ++G+ Y GWQ Q NG S+Q  +++ +  +  + + V GAGRTD+GVHA R  
Sbjct: 1   MRYFVWISFDGTAYHGWQIQPNGMSVQEKLQQGLTTLLRQPIEVTGAGRTDAGVHARRMA 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+ RE     L   LN  L     IS   +  V+ + HARFSA +R+Y Y I T++ 
Sbjct: 61  AHFDIDRELNCEQLAYRLNRIL--PRDISCEKVVRVNDEMHARFSATKRTYRYFIHTQRN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P   E+  +  +   LD E M  AA  L+   DF  F   H    + +  +        G
Sbjct: 119 P--FERFFSVEMNWQLDFEQMNQAAAILLETDDFKAFCKAHADNKTTLCKVTTARWVQTG 176

Query: 182 N-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
                  + A  FL   +R+ VG+L  VG    T     + ++   R + G   PP GL+
Sbjct: 177 PATYYFEISANRFLRNMVRAVVGTLIDVGRHNITLQQFSEIVEKGSRSDAGQSMPPHGLF 236

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 237 LWDIEYE 243


>gi|328884456|emb|CCA57695.1| tRNA pseudouridine synthase A [Streptomyces venezuelae ATCC 10712]
          Length = 285

 Score =  248 bits (633), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 118/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G  + GW +Q     ++QG IE A+  VT   E   +  AGRTDSGVHA 
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQAQGQRTVQGDIEDALRTVTRSKETYELTVAGRTDSGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL  E       K L     ++S  + + +L+     F+ARFSAI R Y YR+ 
Sbjct: 70  GQVAHVDLPAELWAEHRDKLLRRLAGRLSHDVRVWSLAEAPSGFNARFSAIWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G       +LD + M  AA  LVG HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWALDMDAMNEAAAALVGEHDFAAYCKRR-EGATTIRTLQELR 188

Query: 177 VNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                + + E  V A +F H  +RS VG+L  VGDG        K L A  R     +  
Sbjct: 189 WERRPDGVLEATVKADAFCHNMVRSLVGALLFVGDGHRPVDWPGKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|239929485|ref|ZP_04686438.1| tRNA pseudouridine synthase A [Streptomyces ghanaensis ATCC 14672]
 gi|291437810|ref|ZP_06577200.1| pseudouridylate synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291340705|gb|EFE67661.1| pseudouridylate synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 284

 Score =  248 bits (633), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 80/252 (31%), Positives = 116/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G+G+ GW +Q  G  ++QG +E A+  VT  G    +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGAGFHGWAKQAGGRRTVQGEVEDALRTVTRSGTTYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL          K L     ++   + +  L      F ARFSA+ R Y YR+ 
Sbjct: 70  GQVAHVDLPAGVWAEHKGKLLKRLAGRLPKDVRVWALREAPAGFDARFSAVWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWPLDVDAMNEAARGLLGEHDFAAYCKRR-EGATTIRTLQELS 188

Query: 177 VNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +    + I    V A +F H  +RS +G+L  VGDG        K L A  R     +  
Sbjct: 189 LVRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRPPDWPGKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|269128483|ref|YP_003301853.1| tRNA pseudouridine synthase A [Thermomonospora curvata DSM 43183]
 gi|268313441|gb|ACY99815.1| tRNA pseudouridine synthase A [Thermomonospora curvata DSM 43183]
          Length = 288

 Score =  248 bits (633), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 77/251 (30%), Positives = 125/251 (49%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
           +R  + I Y+G+ + GW RQ +  ++QG IE+A+  V        +  AGRTD+GVHA  
Sbjct: 7   VRLRLDIGYDGTDFSGWARQPDRRTVQGVIEEALGRVLRLDPPPALTVAGRTDAGVHARG 66

Query: 60  QVAHFDLVREWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH D+       +  + ++    +    + +  +++  + F ARFSA+ R Y+YR+  
Sbjct: 67  QVAHVDVPERAYAAVSNRLVHRLAGLLPPDVRVWRIAVAPRGFDARFSALWRRYVYRVCD 126

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           R+A    L +      P+ LD + M  AA  L+G HDF  F     + ++ IR +  ++ 
Sbjct: 127 REAGVDPLRRREVLWHPRPLDLDRMNEAAARLLGEHDFAAFCRRR-EGATTIRRLLRYEW 185

Query: 178 NSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 L    VVA +F H+ +R+ VG+L  VGDG+       + L A  R     +AP 
Sbjct: 186 RREEPALAAATVVADAFCHSMVRALVGALLAVGDGRREVDWPARVLAAGVRDSAVNVAPA 245

Query: 237 EGLYFDSVEYS 247
            GL  + + Y 
Sbjct: 246 HGLSLEEIGYP 256


>gi|302519630|ref|ZP_07271972.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB78]
 gi|318058099|ref|ZP_07976822.1| tRNA pseudouridine synthase A [Streptomyces sp. SA3_actG]
 gi|302428525|gb|EFL00341.1| tRNA pseudouridine synthase A [Streptomyces sp. SPB78]
          Length = 284

 Score =  248 bits (633), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 77/252 (30%), Positives = 120/252 (47%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIV--VVHGAGRTDSGVHAL 58
           +R  + + Y+G+ + GW RQ  G  ++Q ++E+A+ +VT       +  AGRTD+GVHA 
Sbjct: 1   MRLRLDLSYDGTDFHGWARQPGGRRTVQETLEEALRVVTRAPAPYELTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH  +  E       K L     ++   + +  ++   + F ARFSAI R Y YR+ 
Sbjct: 61  GQVAHVGMADEVWAEHGEKLLKRLAGRLPKDVRVWRVAPAPEGFDARFSAIWRRYAYRVA 120

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +      L +G      + LD + M  AA+ L+G HDF  +     + ++ IR +    
Sbjct: 121 DQAGGVDPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAYCKKR-EGATTIREMQQLF 179

Query: 177 VNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                + + E  V A +F H  +RS VG+L  VGDG    +   K L A  R     +  
Sbjct: 180 WTRRADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSAVHVVR 239

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 240 PVGLTLEEVGYP 251


>gi|111023127|ref|YP_706099.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110822657|gb|ABG97941.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 297

 Score =  248 bits (633), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 122/248 (49%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + I Y+G+ + GW RQ    ++ G IE+ +  V    + +  AGRTD+GVHA  QV
Sbjct: 26  RRLRLDIAYDGTDFSGWARQNGLRTVCGEIEEKLGAVLRTPLQLTVAGRTDAGVHATGQV 85

Query: 62  AHFDLVREWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR- 119
           AH D+  + +P    + +      +   + I  ++   + F ARFSA+RR Y YR+ +  
Sbjct: 86  AHVDVPVDALPDDPSRLVRRLARFLPKDVRIKRIAFAPEHFDARFSAMRRHYEYRLTSAV 145

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L        PK LD E MR A+  L+G HDF  F     + ++ +R +  FD   
Sbjct: 146 YGADPLRARDTVSYPKVLDLELMRSASATLLGLHDFAAFCKRR-EGATTVRDLQRFDWER 204

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++    V A +F  + +RS VG++  VG+G+     +E  LQ + R     +AP  GL
Sbjct: 205 DGDVFTAFVSADAFCWSMVRSLVGAVLAVGEGRRDLGWIEGLLQEKSRSSSILVAPAHGL 264

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 265 SLVRVDYP 272


>gi|218186563|gb|EEC68990.1| hypothetical protein OsI_37759 [Oryza sativa Indica Group]
          Length = 391

 Score =  248 bits (633), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 97/318 (30%), Positives = 150/318 (47%), Gaps = 72/318 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V
Sbjct: 71  QRYLVAVEYVGTRFSGSQQQLNQRTVVGVLEEAFHKFIGQPVSIFCSSRTDTGVHALSNV 130

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+ ++  I + ++  V   FHAR+ A+ 
Sbjct: 131 CHVDVERISKRKPGEMLPPHEPGVVKRAVNHFLQKNEGDIMVTDVRCVAPDFHARYKALE 190

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR+++   P    EK  AW IP+ L+ + M+ A   LVG HDF++FR+  CQA+SP
Sbjct: 191 RTYHYRLLSGSEPLSVFEKTSAWHIPEDLNVQAMKKACSILVGHHDFSSFRATGCQANSP 250

Query: 169 IRTIDHFDVNS-------------------FGNLIEIR---------------------- 187
           +RT+D   V                      G+L+  R                      
Sbjct: 251 MRTLDELSVTEVFPSMFFPSSMERSEMESLDGHLVYSRTSVVESSGKGSDASSTSEQSRF 310

Query: 188 ----------------VVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                           V AR+  FL+ Q+R  VG LK VG G  T+ D+E+ L  +    
Sbjct: 311 ENGEEFGKRLRHRCFVVTARARSFLYHQVRLMVGLLKSVGTGDLTTEDVERILNLKAVTA 370

Query: 230 CGPLAPPEGLYFDSVEYS 247
             P+AP  GLY  +V+Y 
Sbjct: 371 APPMAPACGLYLANVKYD 388


>gi|225448126|ref|XP_002263416.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|297739525|emb|CBI29707.3| unnamed protein product [Vitis vinifera]
          Length = 380

 Score =  247 bits (632), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 94/317 (29%), Positives = 148/317 (46%), Gaps = 71/317 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G Q+Q N  ++ G++++A     G+ V +  + RTD+GVHAL  V
Sbjct: 62  QRYLVAVEYIGTRFSGSQQQLNCRTVAGALQEAFHKFIGQPVSIFCSSRTDAGVHALSNV 121

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+ ++  + ++++  V   FHAR+ A  
Sbjct: 122 CHVDVERISKRKPGEVLPPHEPAVVRRAVNHFLQKNEGDVMVIDVRCVPPDFHARYKARE 181

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR+++   P  + EK RAW +P+ LD   M+ A + LVG HDF++FR+  CQA SP
Sbjct: 182 RTYFYRLLSGPEPLSSFEKDRAWHVPEDLDLLAMQKACRVLVGCHDFSSFRAAGCQAKSP 241

Query: 169 IRTIDHFDVNSF------------------------------------------------ 180
           IRT+D   V+                                                  
Sbjct: 242 IRTLDELCVSEVLPTPYFPSITERAQNNFTEENPLACSNNAEVPDSPSTANHDRLDGFNG 301

Query: 181 -GNLIEIRVVARSF---------LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            G    +R   R F         L+ Q+R  VG +K VG G  T +D+E+ L A+     
Sbjct: 302 AGQGFGVRRRHRCFLVTARARSFLYHQVRLLVGVIKCVGTGDLTVSDVERILNAKTVTAA 361

Query: 231 GPLAPPEGLYFDSVEYS 247
            P+AP  GLY  +V Y 
Sbjct: 362 SPMAPACGLYLGNVNYD 378


>gi|333026542|ref|ZP_08454606.1| putative tRNA pseudouridine synthase A [Streptomyces sp. Tu6071]
 gi|332746394|gb|EGJ76835.1| putative tRNA pseudouridine synthase A [Streptomyces sp. Tu6071]
          Length = 284

 Score =  247 bits (632), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 77/252 (30%), Positives = 120/252 (47%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIV--VVHGAGRTDSGVHAL 58
           +R  + + Y+G+ + GW RQ  G  ++Q ++E+A+ +VT       +  AGRTD+GVHA 
Sbjct: 1   MRLRLDLSYDGTDFHGWARQPGGRRTVQETLEEALRVVTRAPAPYELTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH  +  E       K L     ++   + +  ++   + F ARFSAI R Y YR+ 
Sbjct: 61  GQVAHVGMADEVWAEHGEKLLKRLAGRLPKDVRVWRVAPAPEGFEARFSAIWRRYAYRVA 120

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +      L +G      + LD + M  AA+ L+G HDF  +     + ++ IR +    
Sbjct: 121 DQAGGVDPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAYCKKR-EGATTIREMQQLF 179

Query: 177 VNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                + + E  V A +F H  +RS VG+L  VGDG    +   K L A  R     +  
Sbjct: 180 WTRRADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSAVHVVR 239

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 240 PVGLTLEEVGYP 251


>gi|78211903|ref|YP_380682.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9605]
 gi|123743387|sp|Q3AMQ5|TRUA_SYNSC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78196362|gb|ABB34127.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9605]
          Length = 293

 Score =  247 bits (632), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 110/247 (44%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y+GS + GWQRQ+NG S+Q  +E AI  +     V    AGRTD+GVHA  Q
Sbjct: 16  QRIALSLQYDGSSFCGWQRQRNGRSVQAVLEDAIAQLDPHRPVQTFAAGRTDAGVHAAGQ 75

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L    TI +         +HA +SA  R Y Y I   +
Sbjct: 76  VVHFDCSGPIPARKWAPALNGRL--PSTIRVRESVARPLDWHACYSATYRRYRYTIHNGR 133

Query: 121 APLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W      LD   MR A   ++G HDF+ F     + +    T+    V  
Sbjct: 134 RPNLFLSPWSWHCYQHRLDESRMRDALSSMLGLHDFSAFMKAGSRRAHARTTVQEVLVER 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ + + A  FL+  +R  +  L  VG+ + +    E+  + + R E    AP  GL
Sbjct: 194 QGDLLRVEIQASGFLYGMVRLLMAQLVAVGEHRLSVAAFEQRWRERRRHEVKEAAPAAGL 253

Query: 240 YFDSVEY 246
                 Y
Sbjct: 254 CLLRAGY 260


>gi|317484413|ref|ZP_07943328.1| tRNA pseudouridine synthase A [Bilophila wadsworthia 3_1_6]
 gi|316924332|gb|EFV45503.1| tRNA pseudouridine synthase A [Bilophila wadsworthia 3_1_6]
          Length = 269

 Score =  247 bits (632), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 87/259 (33%), Positives = 121/259 (46%), Gaps = 15/259 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + I Y G+ Y GWQ Q         +IQ  IE A+  V GE V VHGAGRTD+GV
Sbjct: 1   MPRLKLTIAYVGTQYHGWQTQARKNASPLPTIQNIIEDAVAHVLGERVHVHGAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+      +    ALN  L     I I +  +V   FHA+ SA+R++Y YR
Sbjct: 61  HAEAQVAHLDVPESRARMDWQLALNTLL--PRDIRIADAVLVPDTFHAQHSAVRKTYEYR 118

Query: 116 II-TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +  +++          W     +D E M   +++L+G+ DF + ++      + +RTI  
Sbjct: 119 LWLSKRYTPPQLFPFVWAC-GPVDVERMDEGSRYLLGKRDFASLKNAGTDLRTTVRTILS 177

Query: 175 FDVNSFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                 G L      +  R  A  FL   +R+ +G L  VG GK    D+   L A DR+
Sbjct: 178 ITRTPEGQLPEDCLELTWRFEADGFLKQMVRNTMGLLVAVGRGKLEPADIPGILDACDRR 237

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                AP  GL    V Y 
Sbjct: 238 IAPLTAPACGLTMKKVWYD 256


>gi|115487730|ref|NP_001066352.1| Os12g0194800 [Oryza sativa Japonica Group]
 gi|108862288|gb|ABA96079.2| tRNA pseudouridine synthase family protein, putative, expressed
           [Oryza sativa Japonica Group]
 gi|113648859|dbj|BAF29371.1| Os12g0194800 [Oryza sativa Japonica Group]
 gi|215678805|dbj|BAG95242.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|222616774|gb|EEE52906.1| hypothetical protein OsJ_35509 [Oryza sativa Japonica Group]
          Length = 391

 Score =  247 bits (632), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 97/318 (30%), Positives = 150/318 (47%), Gaps = 72/318 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V
Sbjct: 71  QRYLVAVEYVGTRFSGSQQQLNQRTVVGVLEEAFHKFIGQPVSIFCSSRTDTGVHALSNV 130

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+ ++  I + ++  V   FHAR+ A+ 
Sbjct: 131 CHVDVERISKRKPGEMLPPHEPGVVKRAVNHFLQKNEGDIMVTDVRCVAPDFHARYKALE 190

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR+++   P    EK  AW IP+ L+ + M+ A   LVG HDF++FR+  CQA+SP
Sbjct: 191 RTYHYRLLSGSEPLSVFEKTSAWHIPEDLNVQAMKKACSILVGHHDFSSFRATGCQANSP 250

Query: 169 IRTIDHFDVNS-------------------FGNLIEIR---------------------- 187
           +RT+D   V                      G+L+  R                      
Sbjct: 251 MRTLDELSVTEVFPSMFFPSSMERSEMESLDGHLVYSRTSVVESSGKGSDASSTSEQSRF 310

Query: 188 ----------------VVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                           V AR+  FL+ Q+R  VG LK VG G  T+ D+E+ L  +    
Sbjct: 311 ENGEEFGKRLRHRCFVVTARARSFLYHQVRLMVGLLKSVGTGDLTTEDVERILNLKAVTA 370

Query: 230 CGPLAPPEGLYFDSVEYS 247
             P+AP  GLY  +V+Y 
Sbjct: 371 APPMAPACGLYLANVKYD 388


>gi|148655308|ref|YP_001275513.1| tRNA pseudouridine synthase ACD [Roseiflexus sp. RS-1]
 gi|166229831|sp|A5USG0|TRUA_ROSS1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148567418|gb|ABQ89563.1| tRNA pseudouridine synthase A [Roseiflexus sp. RS-1]
          Length = 270

 Score =  247 bits (632), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 119/251 (47%), Gaps = 8/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+G+ + G Q Q NG S+QG +E A   +TGE   +  AGRTD+GVHA  Q
Sbjct: 1   MRNIALRIEYDGADFVGSQWQTNGRSVQGVLEAAWQQLTGERRRMTLAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+           + + LN  L   + + +L        FHAR+SA+RR Y Y I   +
Sbjct: 61  VANVRTDTRHTISTIVRGLNGIL--PEDVGVLAAWEAPDDFHARYSAVRREYRYVIDNGR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +  A  +P+ LD   M    + ++G HDF    S   Q  S +R          
Sbjct: 119 TPSPLLRRHAAYVPRRLDTAAMDAVVRQVIGTHDFAPL-SDGPQEGSTVRICYEARCTRT 177

Query: 181 G----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 L+ I + A +FL   +R+ VG+L  VG+G+  +      L   DR+    LAP 
Sbjct: 178 EVWGQPLVLIDIAANAFLRHMVRNLVGTLIQVGEGRIDADRFAAVLAGDDRR-ARVLAPA 236

Query: 237 EGLYFDSVEYS 247
            GLY  +V Y 
Sbjct: 237 HGLYLMAVRYP 247


>gi|33864024|ref|NP_895584.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9313]
 gi|42559756|sp|Q7TUP1|TRUA_PROMM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33635608|emb|CAE21932.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9313]
          Length = 295

 Score =  247 bits (632), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 112/248 (45%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ    S+Q  +E AI  +  +  +    AGRTD+GVHA  Q
Sbjct: 16  RRIGLSVQYEGSNFCGWQRQPQAVSVQQVLEDAISQLDPQRPIQAVAAGRTDAGVHAAGQ 75

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L    TI +         +HA  SAI R Y Y I   +
Sbjct: 76  VVHFDCCGPIPAERWAPALNGRL--PSTIRVREAVARPASWHACHSAIYRRYRYTIYNGR 133

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD   M+IA + L+G  DF+ F+    + +    TI    +  
Sbjct: 134 RPNLFLTPWSWHRYQVRLDETMMQIALEGLLGLQDFSAFQRTGSRRAHARTTIQEVKIER 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LI I + A  FL+  +R  +G L  +G+ +      E+  + + R+E    AP +GL
Sbjct: 194 QGDLIMIEIQASGFLYGMVRLLMGQLVALGEHRLNLETFERRWKEKRRQEVKEAAPAQGL 253

Query: 240 YFDSVEYS 247
                 Y 
Sbjct: 254 CLLRAGYE 261


>gi|331702049|ref|YP_004399008.1| tRNA pseudouridine synthase A [Lactobacillus buchneri NRRL B-30929]
 gi|329129392|gb|AEB73945.1| tRNA pseudouridine synthase A [Lactobacillus buchneri NRRL B-30929]
          Length = 267

 Score =  247 bits (632), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 119/250 (47%), Gaps = 7/250 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHALR 59
           RY + + Y+G+ + G++RQ    +I+G + + + ++       +VV+G+GRTD+GVHAL 
Sbjct: 5   RYKVTLAYDGTLFSGFERQPKRRTIEGVLTQKVNIMAKNPDPPIVVYGSGRTDAGVHALG 64

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +     + + LN+ L     + I     V   FHAR+    + Y+YR+   
Sbjct: 65  QVVHFDFPFDLPTKAIYRGLNSLL--PLDMEIKKAEKVSNTFHARYDVSGKRYVYRLDLG 122

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--V 177
           +     ++         +D E ++ A    VG HDF++F +    A S +RTI   +  +
Sbjct: 123 EFKDPFKRNYTGNWRFPIDIERVQTAMNDFVGEHDFSSFVASGSTARSNVRTIYEANAIL 182

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +   N I +      FL+  +R  VG +  +G       D+ +  + +DR +     P  
Sbjct: 183 DKSANEIRLEFYGNGFLYNMVRIMVGVVVEIGSQMRPEHDILRLYEVKDRDQARRTMPAS 242

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 243 GLYLKKVYYE 252


>gi|147669126|ref|YP_001213944.1| tRNA pseudouridine synthase A [Dehalococcoides sp. BAV1]
 gi|146270074|gb|ABQ17066.1| tRNA pseudouridine synthase A [Dehalococcoides sp. BAV1]
          Length = 246

 Score =  247 bits (632), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  + 
Sbjct: 1   MVIEYEGTRYSGFQIQDKGATIQGELETAIRKLTSEQTRVSGSGRTDAGVHAAYQVVSYL 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +   LN YL     I++  +  V + F  R  AI R Y Y I+  +    L
Sbjct: 61  TESSLGLEKIKGGLNYYL--PPDIAVKEVHFVAENFDVRRRAISREYSYHILNSKTRSPL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFGNLI 184
            + +AW +P  LD + M  A + L G HDF  F S +  +    +R ++   ++   + +
Sbjct: 119 ARLQAWQVPYKLDIKLMEQAFKMLEGEHDFIAFASGLGPEIKKTVRRVNWTRLDIAEDRL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +R+ A SFL  Q+R+ +G L  +G G  +  +     +A+     GP AP  GL    V
Sbjct: 179 ILRIEANSFLTHQVRNTIGVLVELGRGTISMGEFGALFEAKTPGLAGPAAPACGLSLVRV 238

Query: 245 EY 246
            Y
Sbjct: 239 NY 240


>gi|257069454|ref|YP_003155709.1| pseudouridylate synthase I [Brachybacterium faecium DSM 4810]
 gi|256560272|gb|ACU86119.1| pseudouridylate synthase I [Brachybacterium faecium DSM 4810]
          Length = 346

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/268 (30%), Positives = 119/268 (44%), Gaps = 23/268 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ + GW  Q    ++QG +EKA+  +      V  AGRTD+GVHA  QV
Sbjct: 34  TRLRLDLSYDGTDFHGWAAQPGQRTVQGELEKALRRIARIPARVTVAGRTDAGVHARGQV 93

Query: 62  AHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSY 112
            H DL  +         P    +AL + L   + + + +     V   F ARF A  R Y
Sbjct: 94  CHLDLPDDVLATLPGRSPRTPAEALVSRLAGVLPEDVVVHVAREVPDDFDARFGAQWRRY 153

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            YRI  R A     +       + LD E M  A+  L+G HDF ++     + ++ IR +
Sbjct: 154 RYRISDRPAAHDPLRRDVLRHRRPLDVEAMARASAPLLGEHDFLSYCRPR-EGATTIREL 212

Query: 173 DHFDVNSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL---- 222
                   G       LI   VVA +F H  +RS VG+L  VG+G+   +   + L    
Sbjct: 213 RELRWERPGEGRADEGLIVATVVADAFCHHMVRSLVGALLGVGEGRRDESWPAEVLAART 272

Query: 223 ---QAQDRKECGPLAPPEGLYFDSVEYS 247
                +D     PL PP+GL  D V Y 
Sbjct: 273 REAARRDGVGAAPLCPPQGLTLDHVAYP 300


>gi|242083078|ref|XP_002441964.1| hypothetical protein SORBIDRAFT_08g005650 [Sorghum bicolor]
 gi|241942657|gb|EES15802.1| hypothetical protein SORBIDRAFT_08g005650 [Sorghum bicolor]
          Length = 387

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 141/319 (44%), Gaps = 73/319 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V
Sbjct: 66  QRYLVAVEYIGTRFSGSQQQPNQRTVVGVLEEAFHRFIGQPVSIFCSSRTDAGVHALSNV 125

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L  ++  I + ++  V   FHAR+ A+ 
Sbjct: 126 CHVDVERISKRKPGEVLTPHEPGVVKRAVNHFLLKNEGDIMVTDVRCVAPDFHARYKALE 185

Query: 110 RSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR+++   +    E   AW I + LD + M+ A   LVG HDF++FR+  CQA+SP
Sbjct: 186 RTYHYRLLSGPESTSVFETNSAWHISEDLDIQAMKKACSILVGHHDFSSFRAAGCQANSP 245

Query: 169 IRTIDHFDVNSFGNLIEI------------------------------------------ 186
           +RT+D   V      +                                            
Sbjct: 246 MRTLDELSVTEVFPFMFFPSSVERSQLESSNGSLVYSRTPDIESSGKGSDLCCTSSVKSE 305

Query: 187 ---------RVVARSF---------LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                    R   R F         L+ Q+R  VG LK VG G  T+ D+E+ L A+   
Sbjct: 306 LENGEDFGKRSRHRCFVVTARARSFLYHQVRLMVGLLKSVGTGDLTTADVERILDAKTVT 365

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               +AP  GLY  +V+Y 
Sbjct: 366 AAPRMAPAYGLYLANVKYD 384


>gi|288574694|ref|ZP_06393051.1| tRNA pseudouridine synthase A [Dethiosulfovibrio peptidovorans DSM
           11002]
 gi|288570435|gb|EFC91992.1| tRNA pseudouridine synthase A [Dethiosulfovibrio peptidovorans DSM
           11002]
          Length = 247

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 120/247 (48%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++Y + + Y G+ + GWQ Q +  ++Q  +E+A+ ++ G  V V GAGRTDSGVHA  QV
Sbjct: 1   MKYALELSYEGNHFSGWQLQPDSITVQEVLEEALTVLEGAPVKVSGAGRTDSGVHARGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A F+L + W P  L  A+NA L   + +S++  S V   F AR SA+ R Y Y +    +
Sbjct: 61  ASFELSKTWDPYRLTLAVNANL--PEHVSVMRASAVPDDFDARRSALWREYAYFVWHGPS 118

Query: 122 PLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +   W   +   D + +    + LVG HDF  F  +     + +RT+        
Sbjct: 119 CFPHVRDMVWWRKRDDWDMDAVDGCCRALVGEHDFGAFCRLSECPENAVRTLFSVRHIRR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L   R+  + FL   +R  +G++  V  GK      E+ L    R +    AP  GL+
Sbjct: 179 GRLSIFRIRGKGFLTNMVRIILGNIDAVATGKKRLEWFERLLLGGTRVDSATTAPASGLF 238

Query: 241 FDSVEYS 247
           F  V Y 
Sbjct: 239 FWRVGYD 245


>gi|183219967|ref|YP_001837963.1| tRNA pseudouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910091|ref|YP_001961646.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|238687801|sp|B0SJC4|TRUA_LEPBP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238687833|sp|B0SC03|TRUA_LEPBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167774767|gb|ABZ93068.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167778389|gb|ABZ96687.1| tRNA pseudouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 264

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/252 (32%), Positives = 130/252 (51%), Gaps = 7/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV--VVHGAGRTDSGVHAL 58
           M  Y +++EY+G+ + GWQ+QKN  ++Q SIE A+ ++        +  AGRTD+GVHAL
Sbjct: 1   MPNYALLVEYDGTHFNGWQKQKNLPTVQSSIESALGIILRRNPASRLSVAGRTDTGVHAL 60

Query: 59  RQVAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             V +F           L  +LNA       +S+ N+  V   FHARFS   R Y+Y++ 
Sbjct: 61  GMVCNFKTEHPIPNFHKLLVSLNAL--TPTGVSVKNVVEVPSDFHARFSCTGREYIYKLY 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFD 176
             +   +  +GRA+ +   +D E ++   Q LVG  DF +F      A    +R I    
Sbjct: 119 YSKYESSFVEGRAFWVKGHIDWERVKKQLQVLVGEKDFRSFTKAKSMAGKRAVREILAIQ 178

Query: 177 VNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           + +      +IR+ A  F+H  +R  VG+L  +G G+W S  ++  L+ ++R + G   P
Sbjct: 179 LENLSPEWYQIRIRANGFMHNMVRITVGTLLDIGKGRWESRSIDSILEEKNRTQAGVTLP 238

Query: 236 PEGLYFDSVEYS 247
           P+GLYF    Y 
Sbjct: 239 PDGLYFVRAYYE 250


>gi|187734897|ref|YP_001877009.1| tRNA pseudouridine synthase A [Akkermansia muciniphila ATCC
           BAA-835]
 gi|238691867|sp|B2UNB6|TRUA_AKKM8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|187424949|gb|ACD04228.1| tRNA pseudouridine synthase A [Akkermansia muciniphila ATCC
           BAA-835]
          Length = 265

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 83/256 (32%), Positives = 110/256 (42%), Gaps = 11/256 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R      Y+G  Y GWQ Q  G ++Q  +E+A   + G    +HG+GRTD+GVHAL Q
Sbjct: 1   MTRIRFTAAYDGRPYLGWQSQPGGRTVQDVLERAFSGLFGTTCRIHGSGRTDAGVHALGQ 60

Query: 61  VAHFDLV--REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V H D              ALN  L    TI I +   V   FHARFSA  ++Y Y I  
Sbjct: 61  VFHADAPDTHRIPADKWPAALNTRL--PRTIRITHAEYVPPGFHARFSATGKTYRYCISR 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI------RTI 172
                  + G AW  P +   + +  A     G HDFT F ++      PI      RTI
Sbjct: 119 APILNPFDAGLAWHRPLAWSVDILEQAVHLFRGTHDFTAFAALRGNEPRPIPEGYFRRTI 178

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
               V   G  + I      FL+  +R   G+      GK T  +L + + A    +  P
Sbjct: 179 TQTQVAQTGEHVFITFTGTGFLYKMVRLMTGAAHEAARGKITLEELARLINAPLPDDKSP 238

Query: 233 -LAPPEGLYFDSVEYS 247
             APP+GL    V Y 
Sbjct: 239 FCAPPDGLTLMRVHYP 254


>gi|139438880|ref|ZP_01772340.1| Hypothetical protein COLAER_01344 [Collinsella aerofaciens ATCC
           25986]
 gi|133775591|gb|EBA39411.1| Hypothetical protein COLAER_01344 [Collinsella aerofaciens ATCC
           25986]
          Length = 274

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 113/248 (45%), Gaps = 6/248 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
             + Y+GS Y G+  Q   +++ G + +AI  +    + +  AGRTD+GVHA+ Q     
Sbjct: 19  FRVAYDGSSYSGFAEQPGQATVAGELRRAIETLLRRPIDLTCAGRTDAGVHAVAQYISVP 78

Query: 66  LVREWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +    + +   + L A    +   I+I  +    K F ARF A  R+Y YRI  R A   
Sbjct: 79  VTDAELALTRRRWLRAMDALLPKDIAINEVYRARKGFSARFDARSRTYTYRIADRDARPV 138

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFD----VNS 179
           L +G  W     LD E M  A   L+G  DF +F  +         R +   +    V  
Sbjct: 139 LSRGAVWWHRYPLDVEAMSAACPALLGEQDFKSFCKVASAVGKPTHRCVMRAEFGHEVAF 198

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +++   +   +FLH+ +R+ VG+L  +G  +     + + + A DR   GP AP  GL
Sbjct: 199 GEDILTFTIEGNAFLHSMVRTIVGTLVEIGMHRRKPEWMREVIDACDRTAAGPTAPACGL 258

Query: 240 YFDSVEYS 247
            F  V+Y 
Sbjct: 259 TFMGVDYD 266


>gi|255571004|ref|XP_002526453.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223534233|gb|EEF35948.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 372

 Score =  247 bits (630), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 97/317 (30%), Positives = 144/317 (45%), Gaps = 71/317 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G Q+Q NG ++ G +E+A     G+ V V  + RTD+GVHAL  V
Sbjct: 54  QRYLIAVEYIGTKFAGSQKQLNGRTVVGVLEEAFCKFIGQQVSVSLSSRTDAGVHALSNV 113

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+ ++  I + ++  V   FHARF A  
Sbjct: 114 CHVDIERISKRKPGEVLPPHEPAVVRRAVNHFLQKNEGDIMVTDVRCVPSDFHARFKAQE 173

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR ++   P    EK RAW + + LD   M+ A + LVG HDF++FR+  CQA SP
Sbjct: 174 RTYFYRFLSGPEPLSTFEKDRAWHVLEDLDIVAMQEACKVLVGHHDFSSFRASGCQAKSP 233

Query: 169 IRTIDHFDVNSFGNLIEI------------------------------------------ 186
           IRT+    V+   + +                                            
Sbjct: 234 IRTLAEISVSEVASTLYFPSITEREQNCENGENSCCKKFKTDLPMGSHSNTNVAESSFGE 293

Query: 187 -------RVVARSF---------LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                  R   R F         L+ Q+R  VG LK VG G  T++D+E+ L A+     
Sbjct: 294 TDLGFGIRRRHRCFVVTARARSFLYHQVRLLVGVLKSVGIGDLTTSDVERILSAKSVTAA 353

Query: 231 GPLAPPEGLYFDSVEYS 247
            P+AP  GLY   V+Y 
Sbjct: 354 SPMAPARGLYLGHVKYD 370


>gi|302874184|ref|YP_003842817.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|307689556|ref|ZP_07632002.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|302577041|gb|ADL51053.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
          Length = 245

 Score =  247 bits (630), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IE++GS Y GWQ QK+   ++QG IE  +  +TGE + V G  R D+G HA  
Sbjct: 1   MRNLKLTIEFDGSRYKGWQNQKDKEQTVQGKIETVLSKMTGEEIEVIGCERIDTGAHADG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            +A+F    E     +   L  Y  + + I +  +  VD++FHAR++A  + Y Y I   
Sbjct: 61  YIANFKTNCELSCTAISIYL--YEFLPEDILVKFIEEVDERFHARYNAKAKVYEYVINNN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                  +  ++ I   L+ E M  AA+   G+HDF  F ++   A S +RT++   +  
Sbjct: 119 NLRNVFNRKYSYHIDIDLNIEEMLKAAEAFKGKHDFKAFTNLKSSAKSTVRTVEDILIKK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              LI+I ++A  FL    R  VG+L  VG G   +T++ K L+   + E  P+A  + L
Sbjct: 179 DNGLIKIELIADDFLLNMERIIVGTLIEVGKGNVKATNVFKMLKDGKKIETIPMAQAKAL 238

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 239 FLKKVIY 245


>gi|294814496|ref|ZP_06773139.1| Pseudouridylate synthase [Streptomyces clavuligerus ATCC 27064]
 gi|326442885|ref|ZP_08217619.1| tRNA pseudouridine synthase A [Streptomyces clavuligerus ATCC
           27064]
 gi|294327095|gb|EFG08738.1| Pseudouridylate synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 288

 Score =  247 bits (630), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/252 (32%), Positives = 112/252 (44%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G  + GW RQ  G  ++QG IE A+  VT       +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGRDFSGWARQAGGRRTVQGEIEDALRTVTRSARPYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL  E       K L     ++   + I         F+ARFSA+ R Y YR+ 
Sbjct: 70  GQVAHVDLPAEVWAEHREKLLKRLAGRLDRDVRIWRAEEAPAGFNARFSAVWRRYAYRVS 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD   M  A+Q L+G HDF  +     + ++ IRT+    
Sbjct: 130 DHPGGVDPLLRGHVLWHDWPLDVAAMNAASQPLLGEHDFAAYCKKR-EGATTIRTLQRLS 188

Query: 177 VNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  +I   V A +F H  +RS VG+L  VGDG        K L A  R     +  
Sbjct: 189 WERDAAGVITATVRADAFCHNMVRSLVGALLFVGDGHRPVDWPGKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>gi|227509961|ref|ZP_03940010.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227190567|gb|EEI70634.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 255

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 116/243 (47%), Gaps = 7/243 (2%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIE---KAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           Y+G+ + G++RQ N  +I+G +      +  +    ++++G+GRTD+GVHA+ QVAHFD 
Sbjct: 2   YDGTNFSGFERQPNRRTIEGVLTQKVNVMAKMPEPPIIIYGSGRTDAGVHAVAQVAHFDF 61

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
             +     + + LN+ L     + I  +  V   FHAR+    + Y YR+   +     +
Sbjct: 62  PFDLSTEAIYRGLNSML--PLDMEITKVEKVSNDFHARYDVSGKKYFYRMYLGEFQNPFK 119

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--VNSFGNLI 184
           +         +D E +  A   LVG HDF++F +    A S IRTI      ++   N +
Sbjct: 120 RNYTGHWKFPIDMEKVNHALADLVGEHDFSSFVASGSTARSNIRTIYSASAKLDQAENEV 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R  VG +  +G G    +D+ +  + +DR +     P  GLY   V
Sbjct: 180 HLEFYGNGFLYNMVRIMVGVVAEIGSGMRPESDVLRLFEVKDRDQARRTMPASGLYLKRV 239

Query: 245 EYS 247
            Y 
Sbjct: 240 FYE 242


>gi|217967401|ref|YP_002352907.1| tRNA pseudouridine synthase A [Dictyoglomus turgidum DSM 6724]
 gi|226708649|sp|B8E1G5|TRUA_DICTD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217336500|gb|ACK42293.1| tRNA pseudouridine synthase A [Dictyoglomus turgidum DSM 6724]
          Length = 245

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + I Y G  ++G+Q+Q    +IQG +EK +  +  E + V GAGRTD+GVHAL Q
Sbjct: 1   MTNWKLEISYIGKDFYGFQKQPGKRTIQGELEKVLSFLFDEEIRVIGAGRTDTGVHALGQ 60

Query: 61  VAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V +F     + +    L K LN  L   + I I  + IVD  FHAR+SA RR Y+Y +  
Sbjct: 61  VVNFKSRGHKGFSCDKLHKVLNRLL--PEDIKIKKVEIVDDSFHARYSAKRRWYIYVVYN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                   K  +W I + ++ E +  +A    G HDF  F     +    +  +      
Sbjct: 119 NDERDLFLKDYSWWISREINRELLIFSANLFKGVHDFKNFCVTEDEDQ-TVIEVYESFWY 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              +L+   + A  FL   +R  VGS+  +  G+ +  +LE  L+ + ++     APP G
Sbjct: 178 FKKDLLIYFISAPFFLRKMVRFIVGSMVEIALGRKSLIELEDYLKEERKERFSVPAPPWG 237

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 238 LYLFRVDY 245


>gi|302757930|ref|XP_002962388.1| hypothetical protein SELMODRAFT_78854 [Selaginella moellendorffii]
 gi|300169249|gb|EFJ35851.1| hypothetical protein SELMODRAFT_78854 [Selaginella moellendorffii]
          Length = 268

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 77/256 (30%), Positives = 127/256 (49%), Gaps = 13/256 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ +++ Y+G+ + GWQ Q +  ++QG IE A+  +T    E +++  A RTD+GVHAL 
Sbjct: 1   KWRIVVSYDGTRFSGWQYQPDFPTVQGLIEDALTKLTRYTREELLMAAASRTDAGVHALG 60

Query: 60  QVAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF           + + LN  L     I +  +S     FHA+  A  + Y Y++  
Sbjct: 61  QVAHFHSPACIGDLSRIHRGLNGTL--PHEIRVREISPAKSSFHAQACARTKRYQYKLFV 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFD 176
                 L +  A+ +P+ LD   M  A  + VG+HDF+TF +        +P+R I  FD
Sbjct: 119 APVMDPLLRLYAYHVPERLDVAAMAEACGYFVGKHDFSTFSNSSTLRPLQNPVREILRFD 178

Query: 177 V--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP-- 232
           +   + G ++   +    F H QIR+ VG +  +G G+  +  + + L  +DR++     
Sbjct: 179 LLEQASGPVLCFEIEGTGFFHKQIRNMVGLIVAIGKGEHEARVIPELLAMKDRQKLARVS 238

Query: 233 -LAPPEGLYFDSVEYS 247
             AP  GL   SV Y 
Sbjct: 239 ITAPSRGLTLVSVHYD 254


>gi|290958122|ref|YP_003489304.1| tRNA-pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260647648|emb|CBG70753.1| putative tRNA-pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 287

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 118/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT  GE   +  AGRTD+GVHA 
Sbjct: 10  VRVRLDLSYDGSEFSGWAKQAGGRRTVQGEIEDALRTVTRSGETYELTVAGRTDAGVHAR 69

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL          K L     ++   + +  L      F+ARFSAI R Y YR+ 
Sbjct: 70  GQVAHVDLPEAVWREHHEKLLKRLAGRLPRDVRVWALREAPSGFNARFSAIWRRYAYRVT 129

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+    
Sbjct: 130 DNPGGVDPLLRGHVLWHDWPLDVDAMNEAARLLLGEHDFAAYCKRR-EGATTIRTLQELS 188

Query: 177 VNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +    + I    V A +F H  +RS +G+L  VGDG   +    K L A  R     +  
Sbjct: 189 LVRGDDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRGADWPGKVLAAGVRDSAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVGYP 260


>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 =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 124/247 (50%), Positives = 159/247 (64%), Gaps = 1/247 (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  RAHADIAKNIAPFRLMEAINARMR-PAPVAILACETVADDWHARFSCTGRSYVYRIANRR 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 FDSVEYS 247
           F    Y 
Sbjct: 240 FVRATYP 246


>gi|302558965|ref|ZP_07311307.1| tRNA pseudouridine synthase A [Streptomyces griseoflavus Tu4000]
 gi|302476583|gb|EFL39676.1| tRNA pseudouridine synthase A [Streptomyces griseoflavus Tu4000]
          Length = 285

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/253 (32%), Positives = 119/253 (47%), Gaps = 8/253 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHA 57
           +R  + + Y+G+ + GW RQ  G  ++QG IE A+  VT   G +  +  AGRTD+GVHA
Sbjct: 10  VRVRLDLSYDGAEFSGWARQAGGRRTVQGEIEDALRTVTRSGGTVYELTVAGRTDAGVHA 69

Query: 58  LRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             QVAH DL RE       K L     ++   + +  L      F+ARFSA+ R Y YR+
Sbjct: 70  RGQVAHVDLPREVWAEHHTKLLKRLAGRLPRDVRVWALREAPAGFNARFSAVWRRYAYRV 129

Query: 117 ITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                    L +G        LD + M  AA+ L+G HDF  +     + ++ IRT+   
Sbjct: 130 TDNPGGVDPLLRGHVLWHDWPLDVDAMNEAARGLLGEHDFAAYCKRR-EGATTIRTLQEL 188

Query: 176 DVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +    + I    V A +F H  +RS +G+L  VGDG        + L A  R     + 
Sbjct: 189 SLLRGEDGIVTATVRADAFCHNMVRSLIGALLFVGDGHRPPHWPAEVLAAGVRDSAVHVV 248

Query: 235 PPEGLYFDSVEYS 247
            P GL  + V Y 
Sbjct: 249 RPHGLTLEEVGYP 261


>gi|254391364|ref|ZP_05006567.1| tRNA pseudouridine synthase A [Streptomyces clavuligerus ATCC
           27064]
 gi|197705054|gb|EDY50866.1| tRNA pseudouridine synthase A [Streptomyces clavuligerus ATCC
           27064]
          Length = 284

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/252 (32%), Positives = 112/252 (44%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           +R  + + Y+G  + GW RQ  G  ++QG IE A+  VT       +  AGRTD+GVHA 
Sbjct: 6   VRVRLDLSYDGRDFSGWARQAGGRRTVQGEIEDALRTVTRSARPYELTVAGRTDAGVHAR 65

Query: 59  RQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            QVAH DL  E       K L     ++   + I         F+ARFSA+ R Y YR+ 
Sbjct: 66  GQVAHVDLPAEVWAEHREKLLKRLAGRLDRDVRIWRAEEAPAGFNARFSAVWRRYAYRVS 125

Query: 118 TRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L +G        LD   M  A+Q L+G HDF  +     + ++ IRT+    
Sbjct: 126 DHPGGVDPLLRGHVLWHDWPLDVAAMNAASQPLLGEHDFAAYCKKR-EGATTIRTLQRLS 184

Query: 177 VNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  +I   V A +F H  +RS VG+L  VGDG        K L A  R     +  
Sbjct: 185 WERDAAGVITATVRADAFCHNMVRSLVGALLFVGDGHRPVDWPGKVLAAGVRDSAVHVVR 244

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 245 PHGLTLEEVGYP 256


>gi|227512894|ref|ZP_03942943.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227523022|ref|ZP_03953071.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227083894|gb|EEI19206.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227089840|gb|EEI25152.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 255

 Score =  246 bits (628), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 116/243 (47%), Gaps = 7/243 (2%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIE---KAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
           Y+G+ + G++RQ N  +I+G +      +  +    ++++G+GRTD+GVHA+ QVAHFD 
Sbjct: 2   YDGTNFSGFERQPNRRTIEGVLTQKVNVMAKLPEPPIIIYGSGRTDAGVHAVAQVAHFDF 61

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
             +     + + LN+ L     + I  +  V   FHAR+    + Y YR+   +     +
Sbjct: 62  PFDLSAEAIYRGLNSML--PLDMEITKVEKVSNDFHARYDVSGKKYFYRMYLGEFQNPFK 119

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--VNSFGNLI 184
           +         +D E +  A   LVG HDF++F +    A S IRTI      ++   N +
Sbjct: 120 RNYTGHWKFPIDMEKVNHALADLVGEHDFSSFVASGSTARSNIRTIYSASAKLDQAENEV 179

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            +      FL+  +R  VG +  +G G    +D+ +  + +DR +     P  GLY   V
Sbjct: 180 HLEFYGNGFLYNMVRIMVGVVAEIGSGMRPESDVLRLFEVKDRDQARRTMPASGLYLKRV 239

Query: 245 EYS 247
            Y 
Sbjct: 240 FYE 242


>gi|182681198|ref|YP_001829358.1| tRNA pseudouridine synthase A [Xylella fastidiosa M23]
 gi|32130280|sp|Q87DS1|TRUA_XYLFT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238691112|sp|B2I9J0|TRUA_XYLF2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|182631308|gb|ACB92084.1| tRNA pseudouridine synthase A [Xylella fastidiosa M23]
          Length = 257

 Score =  246 bits (628), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M+RY + +EY+GS + GWQ Q    G S+Q ++++A+  V    V V  AGRTD+GVH  
Sbjct: 1   MMRYALGVEYDGSEFLGWQ-QLGEMGPSVQATLQQALASVADSSVRVVCAGRTDAGVHGQ 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD      P      L    ++  ++++       + FHARFSA  R Y YR++ 
Sbjct: 60  CQVVHFDSAVTRPPRAWI--LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRYRLLN 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +    V 
Sbjct: 118 RQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQAISVR 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A   G
Sbjct: 178 RDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTASARG 237

Query: 239 LYFDSVEYS 247
           L F    Y 
Sbjct: 238 LVFVGPLYP 246


>gi|302338166|ref|YP_003803372.1| tRNA pseudouridine synthase A [Spirochaeta smaragdinae DSM 11293]
 gi|301635351|gb|ADK80778.1| tRNA pseudouridine synthase A [Spirochaeta smaragdinae DSM 11293]
          Length = 247

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 79/242 (32%), Positives = 111/242 (45%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           MI+ Y+G  + GWQ Q+   ++QG IE A+  +  + V V  AGRTDSGVHA  QV HFD
Sbjct: 1   MIVAYDGRKFSGWQVQREDRTVQGVIEAALESMEKQKVRVFAAGRTDSGVHARGQVVHFD 60

Query: 66  LV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                        ALNA L     + I+    V   FHAR+SA  RSY Y +        
Sbjct: 61  TSLSSIEADKFAPALNAIL--PADVRIVGSYAVPDDFHARYSAKARSYRYFLYPGVCVSP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L +   +          +  A   L+G HDF++F +    + S +R I          +I
Sbjct: 119 LLRPYCYARRSLPSIGALNRAVSPLLGSHDFSSFSASGDPSPSKVRVIYQAVFLQHRGMI 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           E R+   +FL   +RS VG+   V   +  +  +   L  +DR   G  AP  GL+F  V
Sbjct: 179 EFRITGNAFLWRMVRSIVGTALEVASAEEPARAMRLILDEKDRSLAGTTAPARGLFFWRV 238

Query: 245 EY 246
            Y
Sbjct: 239 HY 240


>gi|140053519|gb|ABE79574.2| tRNA pseudouridine synthase [Medicago truncatula]
          Length = 361

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 97/317 (30%), Positives = 146/317 (46%), Gaps = 71/317 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ +FG+Q+Q    ++ G +E A     G+ V V  + RTD+GVHAL  V
Sbjct: 42  QRYLVAVEYIGTRFFGFQKQLTDRTVAGVLEDAFCKFVGQPVSVVCSSRTDAGVHALSNV 101

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+  +  ++++++  V   FHAR+ A  
Sbjct: 102 CHVDIERISKRKPGEVLQPHEPAVVRRAVNHFLQKENGDLAVIDVRCVPSDFHARYKAQE 161

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR+++        EK RAW IP+ L+   M+ A + LVG HDF++FR+  CQA SP
Sbjct: 162 RTYFYRLLSGPETLSTFEKDRAWHIPEELNLPAMQEACKVLVGHHDFSSFRASGCQAKSP 221

Query: 169 IRTIDHFDVNS-------------------FGNLIEIR---------------------- 187
           IR++D   V                       +L                          
Sbjct: 222 IRSLDELSVVEVTRSPYFPSVMDRENPINVTDDLHCFHSNSETVIPLGSSARIDEVSASK 281

Query: 188 ---------------VVAR--SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                          V AR  +FL+ Q+R  VG LK VG G  T TD+E+ L A+     
Sbjct: 282 EDVGFGKRRYHRCLVVTARARAFLYHQVRLLVGVLKDVGTGNITVTDVERILNAKTVTAT 341

Query: 231 GPLAPPEGLYFDSVEYS 247
            P+AP  GLY   V+Y 
Sbjct: 342 SPMAPACGLYLGEVKYD 358


>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 =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 132/248 (53%), Gaps = 7/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQ 60
            R  + + ++G  Y GWQ Q+N  S+Q +++ A+  + GE  +    AGRTD+GVHA   
Sbjct: 16  TRLRLTVAWDGRDYAGWQEQRNAVSVQETLQTALHALGGEGALRPVSAGRTDAGVHAEAM 75

Query: 61  VAHFDLVREW--VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             H+D+   +    V L +ALNA+L    ++S+L+  +    FHARFS   R Y+YR+  
Sbjct: 76  PLHWDVPTTFRVPLVQLPRALNAWL--PASVSVLSAEVAPAGFHARFSCTERRYVYRLWV 133

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 L  GRA  +P  LD E M  AAQ L+G HDF  F +   +    +R +   +V 
Sbjct: 134 APQRHPLWAGRALHVPGPLDAEAMNRAAQSLIGLHDFAAFATR--EDRQTVRDLLRLEVQ 191

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G L +I V   SFL   +R  VG+L LVG GK  + ++E  L +++R   G   PP G
Sbjct: 192 PQGELWDIHVAGESFLRHMVRGLVGTLLLVGQGKLGAAEVEGILASRERARAGANVPPGG 251

Query: 239 LYFDSVEY 246
           LYF   EY
Sbjct: 252 LYFAGAEY 259


>gi|330685169|gb|EGG96833.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU121]
          Length = 267

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 120/244 (49%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+ + G+Q Q+ G ++Q   EK +  +    + +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIEYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHIRIHPSSRTDRGVHAYQQY 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +        A+N+ L   D I + ++  VD+ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELQIENSKWQYAMNSAL--PDDIYVKSVQHVDEDFHCRYDCVGKRYRYKVYQAKH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I  SLD   M  AA+  +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RDPFQSGLKTYIADSLDLNQMNEAAKRFIGTHDFTGFCSQKTEVESKVRTLYQSEIVKTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK +  ++ + L+ ++R +    AP EGLY 
Sbjct: 179 EGFDYIVTGSGFLYNMVRVLVAFLIEVGKGKRSPEEIPQLLEEKNRNKIPFTAPSEGLYL 238

Query: 242 DSVE 245
           + V 
Sbjct: 239 EKVY 242


>gi|306835272|ref|ZP_07468304.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49726]
 gi|304568865|gb|EFM44398.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49726]
          Length = 293

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 83/261 (31%), Positives = 122/261 (46%), Gaps = 18/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW +QK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 17  VRLRLDLAYDGTNFHGWAKQKGGLRTVQGVLEEQLAMIVRTEVPLTVAGRTDAGVHARGQ 76

Query: 61  VAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+ +E          P  + + L   L   + + +       + F ARFSA+RR Y
Sbjct: 77  VAHVDVPQEMLEQRSVAGDPGTIVRRLAKLL--PEDVRVHGCEFAPEGFDARFSALRRHY 134

Query: 113 LYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           +YRI T     L           K +D + M+ AA  LVG HDF  F      A + IR 
Sbjct: 135 VYRITTSPRGALPTRARDTAEWFKPVDIDAMQDAATALVGLHDFAAFCKAKPNA-TTIRE 193

Query: 172 IDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           +  F            L E RV A +F  + +RS VG    VG+G+         LQ   
Sbjct: 194 LQEFSWQDVSTPEEPQLFEARVTADAFCWSMVRSLVGCCLSVGEGRRDVDFAAALLQETK 253

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R    P+AP +GL    V+Y 
Sbjct: 254 RSSRIPVAPAKGLSLVQVDYP 274


>gi|255530580|ref|YP_003090952.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
 gi|255343564|gb|ACU02890.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
          Length = 261

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 76/262 (29%), Positives = 119/262 (45%), Gaps = 19/262 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + Y+G+ Y GWQ Q N +++Q  ++ A+ +   + V   G GRTD+GVHA + 
Sbjct: 1   MQRYFIELSYDGTPYHGWQIQPNATTVQEYLDSALTVYFRQPVSTLGCGRTDTGVHASQF 60

Query: 61  VAHFDLV--------------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
            AHFDL               +   P+     +NA L     I++  +  V    HARF 
Sbjct: 61  FAHFDLQTEAEQSEATGIPASKCPDPLRSVNGINALL--PYQIAVKRVFEVANTAHARFD 118

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           A  R+Y Y I   + P  L   R+W     LD + M  AA  L+   DF+ F   H Q  
Sbjct: 119 ATARAYHYHIHFHKNPFKL--NRSWFHKGELDMDAMNRAASILLAHSDFSCFSKSHTQTF 176

Query: 167 SPIRTIDHFDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           +    I         +  +   + A  FL   +R+ VG+L  +G  +    + E+ ++++
Sbjct: 177 TNNCKITEAFFEEMEDGALRFTIRADRFLRNMVRAIVGTLIRIGKNELNLAEFEQIIKSK 236

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R   G   P  GLY  +V Y 
Sbjct: 237 NRSNAGQSVPACGLYLVNVIYP 258


>gi|288928084|ref|ZP_06421931.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330918|gb|EFC69502.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 244

 Score =  245 bits (627), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 120/246 (48%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY +   Y+G+ Y GWQ Q N +S+Q  +++A+ L+    V + GAGRTD+GVHA   V
Sbjct: 3   QRYFIYFSYDGTSYHGWQIQPNANSVQAEMQRAMSLLLRHPVELVGAGRTDTGVHARTMV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD+      V L   LN  L     I+I  +  VD   HARFSA +R+Y Y I     
Sbjct: 63  AHFDVDTPIDAVQLTYKLNRVL--PFDITINAIKAVDADMHARFSATKRTYHYYIHLD-- 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  ++ + ++ D + M  AA+ L+   DF  F   H  A + +  +         
Sbjct: 119 RDPFCRAYSYALHQAPDFQLMNEAAEILLSHKDFGAFCKSHSDAKTTLCEVYEARWIKLS 178

Query: 182 NL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           +    +R+ A  FL   +R+ VG+L  VG  K T       L ++ R++ G   P   L+
Sbjct: 179 DTKWHLRISANRFLRNMVRAIVGTLLDVGWHKITLEQFVDILHSKSRQQAGESVPGHALF 238

Query: 241 FDSVEY 246
            + V+Y
Sbjct: 239 LEDVQY 244


>gi|28198519|ref|NP_778833.1| tRNA pseudouridine synthase A [Xylella fastidiosa Temecula1]
 gi|28056603|gb|AAO28482.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
          Length = 258

 Score =  245 bits (627), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M+RY + +EY+GS + GWQ Q    G S+Q ++++A+  V    V V  AGRTD+GVH  
Sbjct: 2   MMRYALGVEYDGSEFLGWQ-QLGEMGPSVQATLQQALASVADSSVRVVCAGRTDAGVHGQ 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD      P      L    ++  ++++       + FHARFSA  R Y YR++ 
Sbjct: 61  CQVVHFDSAVTRPPRAWI--LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRYRLLN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +    V 
Sbjct: 119 RQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQAISVR 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A   G
Sbjct: 179 RDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTASARG 238

Query: 239 LYFDSVEYS 247
           L F    Y 
Sbjct: 239 LVFVGPLYP 247


>gi|269216172|ref|ZP_06160026.1| tRNA pseudouridine synthase A [Slackia exigua ATCC 700122]
 gi|269130431|gb|EEZ61509.1| tRNA pseudouridine synthase A [Slackia exigua ATCC 700122]
          Length = 331

 Score =  245 bits (627), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 87/260 (33%), Positives = 127/260 (48%), Gaps = 19/260 (7%)

Query: 4   YCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
             + + Y+G+ + G+ RQ   + +++QG +E+ + ++    V    AGRTD+GVHAL QV
Sbjct: 74  VALGVAYDGAPFAGFARQAESHVTTVQGELERVLSVLYRRAVDTVCAGRTDAGVHALGQV 133

Query: 62  AHFDLVRE----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             FDL  E         L K++NA   + + I++         F ARF A  R Y Y I 
Sbjct: 134 VSFDLTEEEFASRPLRTLMKSMNAL--VDERITVTCAEERPAGFSARFDATSREYRYFIA 191

Query: 118 TRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHC------QASSPIR 170
           T  A   L     W +    LD + M  AA+ LVG HDF +F           +  S  R
Sbjct: 192 TGNARPVLIARSVWHLRGAPLDVDAMNTAARFLVGEHDFKSFCVASSALHLEGEGRSTCR 251

Query: 171 TIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            +   DV S       ++E+R+V  +FLH+ IR  VG+L  VG G+  ++ +   L A+D
Sbjct: 252 RVIEADVRSTHVMGTPVVEVRIVGNAFLHSMIRIIVGTLVAVGQGRRDASWVADVLAARD 311

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R   G  AP  GL F SV Y
Sbjct: 312 RTAAGETAPACGLTFWSVRY 331


>gi|94987504|ref|YP_595437.1| tRNA pseudouridine synthase A [Lawsonia intracellularis PHE/MN1-00]
 gi|123082124|sp|Q1MPG1|TRUA_LAWIP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|94731753|emb|CAJ55116.1| Pseudouridylate synthase [Lawsonia intracellularis PHE/MN1-00]
          Length = 257

 Score =  245 bits (626), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 83/261 (31%), Positives = 123/261 (47%), Gaps = 18/261 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R    + Y G+ Y GWQ Q         +IQ ++EK I  + G+ V V GAGRTD+GV
Sbjct: 1   MPRLKFTLAYVGTAYHGWQTQRRKSLPELPTIQSTLEKVIASIIGKPVRVCGAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+    + +     LNA L     I +++   V+  FHA+  A+++ Y YR
Sbjct: 61  HAEGQVAHVDIPESKLKLDWQLVLNASL--PKNIRVVHSLYVEDTFHAQHDAVQKLYAYR 118

Query: 116 II-TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI-- 172
           +    +    +     W   + LD E M  A+  L+G H+F + ++   +  S +RTI  
Sbjct: 119 LWLNHRYTPPVLYPFVWSCGR-LDLEAMDKASTFLLGTHNFVSLQNRGTKLLSTVRTISA 177

Query: 173 ------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
                   F +N    +      A  FL   +R+ +G L LVG  K     +   L+A+D
Sbjct: 178 LYREPSQFFSLNESHEVTWF-FKADGFLKQMVRNIMGLLVLVGRRKIQPEKIPYILEAKD 236

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R+   P AP  GL    V YS
Sbjct: 237 RRHSAPTAPAHGLTLKKVFYS 257


>gi|325105198|ref|YP_004274852.1| tRNA pseudouridine synthase A [Pedobacter saltans DSM 12145]
 gi|324974046|gb|ADY53030.1| tRNA pseudouridine synthase A [Pedobacter saltans DSM 12145]
          Length = 258

 Score =  245 bits (626), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 73/249 (29%), Positives = 120/249 (48%), Gaps = 7/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R+ + + Y+G  Y GWQ Q N  ++Q  ++ A+    GE +   G GRTD+GVHA +  
Sbjct: 5   QRFFIELSYHGLQYHGWQYQPNAITVQEKLDNALSTFFGEKIESLGCGRTDTGVHATQFY 64

Query: 62  AHFDLVREWVP---VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           AHFD  +E+     +   K +N+ L     I++ +L  V +  HARF AIRRSY Y I  
Sbjct: 65  AHFDTEKEFSENSEIRFLKGINSLL--PYDIAVKHLHQVHEDAHARFDAIRRSYEYHIHF 122

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   +   +WL  + L+ + M I A +++   DF  F   +    +    +   +  
Sbjct: 123 NKNP--FKTYTSWLHKEPLNVDAMNIGASYILDYEDFGAFCKANAGNFTNNCIVSRAEWE 180

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
              + I   + A  FL   +R+ VG+L  +G GK+    ++  ++++ R   G   P  G
Sbjct: 181 VKNDGIIFHITANRFLRNMVRAIVGTLTDIGKGKYAPEHIKHIIESKKRSSAGASVPACG 240

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 241 LLLTEVCYP 249


>gi|119484807|ref|ZP_01619289.1| tRNA pseudouridine synthase A [Lyngbya sp. PCC 8106]
 gi|119457625|gb|EAW38749.1| tRNA pseudouridine synthase A [Lyngbya sp. PCC 8106]
          Length = 279

 Score =  245 bits (626), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 80/245 (32%), Positives = 113/245 (46%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I+Y G+ + GWQRQ NG ++Q  IE AI  V    V +HGAGRTD+GVHA  QVA
Sbjct: 5   RIALVIQYQGTRFNGWQRQPNGRTVQEEIETAIANVVDSPVTLHGAGRTDTGVHAAAQVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF++            LN  L     I +   + VD  +HARFSA+ R Y Y + T   P
Sbjct: 65  HFEVTGPIPGYRWATILNHRL--PHDILVRASAQVDPSWHARFSAVWRRYRYLLYTDSRP 122

Query: 123 LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               +  +W      LD + M+ A   L+GRH  + F+    +       +        G
Sbjct: 123 NLFVRPWSWHYYHAPLDEKLMQAALIPLLGRHHLSAFQRAGTRRPHAWVDVQDVSCQRQG 182

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I+I V A  FL+  +R  +G L  VG    +  +       + R+     AP  GL  
Sbjct: 183 PFIQIEVQASGFLYGMMRLLLGLLVEVGAQARSLENFTDIWVHERRELVKYSAPARGLCL 242

Query: 242 DSVEY 246
             V Y
Sbjct: 243 LRVGY 247


>gi|116624080|ref|YP_826236.1| tRNA pseudouridine synthase A [Candidatus Solibacter usitatus
           Ellin6076]
 gi|122253167|sp|Q01WL4|TRUA_SOLUE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116227242|gb|ABJ85951.1| tRNA pseudouridine synthase A [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 240

 Score =  245 bits (626), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 82/249 (32%), Positives = 116/249 (46%), Gaps = 12/249 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G  + GWQ Q   ++IQG +E+ +  + G+ V V G+GRTD+GVHAL Q
Sbjct: 1   MRRIRIYLAYDGGPFHGWQVQPGLATIQGILEEIVGGMEGKPVHVAGSGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F +        L +A+N  L     I IL    V   FH RF A+ ++Y YR+   +
Sbjct: 61  VAAFSIENPIPVENLRRAVNRLL--PPAIRILCAEEVQADFHPRFDAVAKTYEYRMFRDE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDV 177
                E    +  P  LD   M   A+   G HDFT F +      +  S +RTI    +
Sbjct: 119 VCSPFEWPYVYHHPYPLDEARMATLARAFEGEHDFTPFAASDARDAEGKSKVRTIFSSTL 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +     +  RV    FL   +R+ VG+L   G G     DL            G  AP +
Sbjct: 179 DRTPQRLVYRVRGSGFLKHMVRNIVGTLIEAGRGNI--ADLNSL-----PARSGATAPAK 231

Query: 238 GLYFDSVEY 246
           GL+  SVEY
Sbjct: 232 GLFQVSVEY 240


>gi|298243939|ref|ZP_06967746.1| tRNA pseudouridine synthase A [Ktedonobacter racemifer DSM 44963]
 gi|297556993|gb|EFH90857.1| tRNA pseudouridine synthase A [Ktedonobacter racemifer DSM 44963]
          Length = 264

 Score =  245 bits (626), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 87/258 (33%), Positives = 125/258 (48%), Gaps = 14/258 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +     IEY+G+ Y G+QRQ   +G ++QG++E A+  ++G  + V GAGRTD GVHA  
Sbjct: 1   MIIACGIEYDGTDYHGFQRQSASHGPTVQGTLEAAVTQISGVQITVMGAGRTDVGVHASG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HF         +  +ALNA L    T+ +     + + FHARFSA  RSY Y I   
Sbjct: 61  QVIHFRTESRLTVEVWRRALNAVL--PSTVVVRWAKEMPEGFHARFSAQSRSYRYTIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-------SPIRTI 172
             P AL    A+   + LD   M  A ++L+GR DF  F      ++         IRT+
Sbjct: 119 CFPTALRARYAYHCSRELDVTLMDDACRYLLGRKDFGAFGHSPNDSNPLKPGPHHCIRTM 178

Query: 173 DHFDV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                   +    LI     A +FL  Q+R  VG+L LVG  + +  +  + +Q  ++  
Sbjct: 179 LEARCLRDHQQAELIYCDFTADAFLTGQVRRMVGTLLLVGQQRLSVAEFAEIVQRAEKTH 238

Query: 230 CGPLAPPEGLYFDSVEYS 247
            G  AP  GL    VEY 
Sbjct: 239 PGSAAPSLGLCLVRVEYP 256


>gi|71899860|ref|ZP_00682009.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
 gi|71730377|gb|EAO32459.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
          Length = 257

 Score =  245 bits (626), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M+RY + +EY+GS + GWQ Q    G S+Q ++++A+  V    V V  AGRTD+GVH  
Sbjct: 1   MMRYALGVEYDGSEFLGWQ-QLGEMGPSVQATLQQALASVADASVRVVCAGRTDAGVHGQ 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD      P      L    ++  ++++       + FHARFSA  R Y YR++ 
Sbjct: 60  CQVVHFDSAVTRPPRAWI--LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRYRLLN 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +    V 
Sbjct: 118 RQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQAISVR 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A   G
Sbjct: 178 RDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTASARG 237

Query: 239 LYFDSVEYS 247
           L F    Y 
Sbjct: 238 LVFVGPLYP 246


>gi|302764370|ref|XP_002965606.1| hypothetical protein SELMODRAFT_84331 [Selaginella moellendorffii]
 gi|300166420|gb|EFJ33026.1| hypothetical protein SELMODRAFT_84331 [Selaginella moellendorffii]
          Length = 269

 Score =  245 bits (625), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 76/257 (29%), Positives = 126/257 (49%), Gaps = 14/257 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ +++ Y+G+ + GWQ Q +  ++QG IE A+  +T    E +++  A RTD+GVHAL 
Sbjct: 1   KWRIVVSYDGTRFSGWQYQPDFPTVQGLIEDALTKLTRYTREELLMAAASRTDAGVHALG 60

Query: 60  QVAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF           + + LN  L     I +  +S     FHA+  A  + Y Y++  
Sbjct: 61  QVAHFHSPACIGDLSRIHRGLNGTL--PHEIRVREISPAKSSFHAQACARTKRYQYKLFV 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFD 176
                 L +  A+ +P+ LD   M  A  + VG+HDF+TF +        +P+R I  F+
Sbjct: 119 APVMDPLLRLYAYHVPERLDVAAMAEACGYFVGKHDFSTFSNSSTLRPLQNPVREILRFE 178

Query: 177 VNSF---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP- 232
           +      G ++   +    F H QIR+ VG +  +G G+  +  + + L  +DR++    
Sbjct: 179 LLEQASLGPVLCFEIEGTGFFHKQIRNMVGLIVAIGKGEHQARVIPELLAMKDRQKLARV 238

Query: 233 --LAPPEGLYFDSVEYS 247
              AP  GL   SV Y 
Sbjct: 239 SITAPSRGLTLVSVHYD 255


>gi|223042638|ref|ZP_03612687.1| tRNA pseudouridine synthase A [Staphylococcus capitis SK14]
 gi|222444301|gb|EEE50397.1| tRNA pseudouridine synthase A [Staphylococcus capitis SK14]
          Length = 267

 Score =  245 bits (625), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 114/244 (46%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H   RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHVRIHPTSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N +L   D I + N+  V++ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIDNQQWQYAMNRFL--PDDIYVKNVQTVEENFHCRYDCVGKRYRYKVYQGEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I   LD   M  AA H +G HDFT F S   +  S +RT+   +V    
Sbjct: 119 RNPFKSGLETFINSDLDLSKMNEAAHHFIGTHDFTGFCSQKTEVESKVRTLYQSEVVQTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+ ++R      AP EGLY 
Sbjct: 179 TGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRQPDEVPQLLEEKNRNNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|71274838|ref|ZP_00651126.1| tRNA pseudouridine synthase [Xylella fastidiosa Dixon]
 gi|71902311|ref|ZP_00684298.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
 gi|170729917|ref|YP_001775350.1| tRNA pseudouridine synthase A [Xylella fastidiosa M12]
 gi|238687976|sp|B0U6K4|TRUA_XYLFM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|71164570|gb|EAO14284.1| tRNA pseudouridine synthase [Xylella fastidiosa Dixon]
 gi|71727947|gb|EAO30171.1| tRNA pseudouridine synthase [Xylella fastidiosa Ann-1]
 gi|167964710|gb|ACA11720.1| Pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 257

 Score =  245 bits (625), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 129/249 (51%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M+RY + +EY+GS + GWQ Q    G S+Q ++++A+  V    V V  AGRTD+GVH  
Sbjct: 1   MMRYALGVEYDGSEFLGWQ-QLGEMGPSVQATLQQALASVADASVRVVCAGRTDAGVHGQ 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD      P      L    ++  ++++       + FHARFSA  R Y YR++ 
Sbjct: 60  CQVVHFDSAVTRPPRAWI--LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRYRLLN 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +    V 
Sbjct: 118 RQVRPALQHQFLSWERYPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQAISVR 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A   G
Sbjct: 178 RDAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTASARG 237

Query: 239 LYFDSVEYS 247
           L F    Y 
Sbjct: 238 LVFVGPLYP 246


>gi|33866624|ref|NP_898183.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8102]
 gi|42559753|sp|Q7TTT1|TRUA_SYNPX RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33633402|emb|CAE08607.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8102]
          Length = 299

 Score =  245 bits (625), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 116/248 (46%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ+NG+S+Q  +E AI  +     +    AGRTD+GVHA  Q
Sbjct: 16  RRIALSLQYEGSAFCGWQRQRNGNSVQAQLEAAIEQLDPYRPIQTFAAGRTDTGVHAAGQ 75

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P     ALN  L    TI +    +  K +HA +SA  R Y Y I   +
Sbjct: 76  VVHFDCGDRIPPAKWAPALNGRL--PFTIRVRESVLRPKDWHACYSATYRRYRYTIHNGR 133

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W   +  LD   MR A   ++G HDF+ F     + +    T+   D+  
Sbjct: 134 RPNLFLAPWSWHRYQLRLDESRMRDALNGMLGLHDFSAFMRAGSRRAHARTTVQEVDLVR 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+++ + + A  FL+  +R  +  L  VG+ + +  D E+  + + R E    AP  GL
Sbjct: 194 QGDMVRVEIQASGFLYGMVRLLIAQLVAVGEHRLSVQDFEQRWRQRRRHEVREAAPGHGL 253

Query: 240 YFDSVEYS 247
                 Y 
Sbjct: 254 CLLRAGYE 261


>gi|285017777|ref|YP_003375488.1| tRNA pseudouridine synthase a (tRNA-uridine isomeraseI (tRNA
           pseudouridylate synthaseI protein [Xanthomonas
           albilineans GPE PC73]
 gi|283472995|emb|CBA15500.1| probable trna pseudouridine synthase a (trna-uridine isomeraseI
           (trna pseudouridylate synthaseI protein [Xanthomonas
           albilineans]
          Length = 257

 Score =  245 bits (625), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 133/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q +++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSAFQGWQQLGESGGPSVQATLQGALSSVADVPVSVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L A  ++  ++ +     V   FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDCAALRPPRGWM--LGATARLPPSVCVRWCVPVADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + L  E M IAAQ L+G  DF+ FRS+ CQA    R +    V  
Sbjct: 119 QVRPALYRQTLSWERRPLQVEAMHIAAQALLGEQDFSAFRSVQCQALHARRELQSIVVTR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L+E ++ A +FLH  +R+ VGSL +VG G+   + + + L  ++R+  GP A P+GL
Sbjct: 179 NGELVEFQLQANAFLHHMVRNIVGSLVMVGTGEKPVSWIGELLSGRNRRIAGPTASPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFVGPLYP 246


>gi|15837974|ref|NP_298662.1| tRNA pseudouridine synthase A [Xylella fastidiosa 9a5c]
 gi|30913418|sp|Q9PDK6|TRUA_XYLFA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|9106376|gb|AAF84182.1|AE003968_13 tRNA pseudouridine synthase A [Xylella fastidiosa 9a5c]
          Length = 257

 Score =  244 bits (624), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 130/249 (52%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M+RY + +EY+GS + GWQ Q    G S+Q ++++A+  V    V V  AGRTD+GVH  
Sbjct: 1   MMRYALGVEYDGSEFLGWQ-QLGEMGPSVQATLQQALASVADASVRVVCAGRTDAGVHGQ 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD      P      L    ++  ++++       + FHARFSA  R Y YR++ 
Sbjct: 60  CQVVHFDSAVTRPPRAWI--LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRYRLLN 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           RQ   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +    V 
Sbjct: 118 RQVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQAISVR 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            +  +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A   G
Sbjct: 178 RYAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTASARG 237

Query: 239 LYFDSVEYS 247
           L F    Y 
Sbjct: 238 LVFVGPLYP 246


>gi|307610015|emb|CBW99548.1| transfer RNA-pseudouridine synthase I [Legionella pneumophila 130b]
          Length = 253

 Score =  244 bits (624), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 75/214 (35%), Positives = 107/214 (50%), Gaps = 2/214 (0%)

Query: 34  AIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILN 93
           A+  V    + V  AGRTD+GVHA  QV HFD  ++          N +L     I +  
Sbjct: 24  ALSKVADSSISVVCAGRTDTGVHATNQVIHFDCEKDRSIRAWIHGANTFL--PKDICVKW 81

Query: 94  LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
              + + FHAR+SA+ R Y Y I        L +G      + LD   M+   Q L+G +
Sbjct: 82  GKEMPENFHARYSAVSRRYRYVIYNGAIRPGLLRGNVTWQYRQLDHRLMQQGGQCLLGEN 141

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           DFT+FRS+ CQ+++P+R I    V   G+L+ + + A +FLH  +R+  G L  VG GK 
Sbjct: 142 DFTSFRSVECQSNTPMRNIHQLQVTRHGDLVVLDITANAFLHHMVRNIAGVLIAVGSGKH 201

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
               ++  L A+DRK     AP  GLY   V Y 
Sbjct: 202 PVGWVKDVLNAKDRKLGAETAPSYGLYLVQVTYP 235


>gi|29831498|ref|NP_826132.1| tRNA pseudouridine synthase A [Streptomyces avermitilis MA-4680]
 gi|38258718|sp|Q82DM1|TRUA_STRAW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|29608614|dbj|BAC72667.1| putative pseudouridine synthase [Streptomyces avermitilis MA-4680]
          Length = 285

 Score =  244 bits (624), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 79/253 (31%), Positives = 116/253 (45%), Gaps = 8/253 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHA 57
           +R  + + Y+G+ + GW +Q     ++QG IE A+  VT        +  AGRTD+GVHA
Sbjct: 10  VRVRLDLSYDGTEFSGWAKQAAGRRTVQGEIEDALRTVTRSGETTYELTVAGRTDAGVHA 69

Query: 58  LRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             QVAH DL  E       K L     ++   + + +L+     F+ARFSAI R Y YR+
Sbjct: 70  RGQVAHVDLPGELWAEHQEKLLKRLAGRLPKDVRVWSLTEAPSGFNARFSAIWRRYAYRV 129

Query: 117 I-TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                    L +         LD + M  AA+ LVG HDF  +     + ++ IRT+   
Sbjct: 130 TDNTGGVDPLLRSHVLWHDWPLDVDAMNEAARRLVGEHDFAAYCKKR-EGATTIRTLQEL 188

Query: 176 DVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +    + +I   V A +F H  +RS +G+L  VGDG        K L    R     + 
Sbjct: 189 SLVRGDDGVITATVCADAFCHNMVRSLIGALLFVGDGHRGPDWPGKVLAVGVRDSAVHVV 248

Query: 235 PPEGLYFDSVEYS 247
            P GL  + V Y 
Sbjct: 249 RPHGLTLEEVGYP 261


>gi|260072704|gb|ACX30601.1| pseudouridylate synthase [uncultured SUP05 cluster bacterium]
          Length = 218

 Score =  244 bits (624), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 76/219 (34%), Positives = 118/219 (53%), Gaps = 3/219 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK+G  ++Q  +E+A+  V    V V  +GRTD+GVHAL Q
Sbjct: 1   MKLALGVEYLGTNFHGWQLQKSGIRTVQQVVEQALSSVADHPVRVFCSGRTDAGVHALEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+   +          N  L     ++      V+  FHARF A  R Y Y+I    
Sbjct: 61  VIHFETTAKREDKAWVLGGNVNL--PFDVNFKWAKQVNDDFHARFDAHARQYHYKIHNTP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A++        ++LD + M  AA+ L+G HDF++FR   CQA SPI+T++   +   
Sbjct: 119 VRSAVKHAYTLWESRTLDIKLMNQAAECLIGEHDFSSFRGSLCQAKSPIKTVEFIRLTQS 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           GN I + + A +FLH  +R+ VG+L  VG G+  S  ++
Sbjct: 179 GNGILLDIKANAFLHHMVRNIVGTLIKVGKGEQDSAWVK 217


>gi|325920196|ref|ZP_08182154.1| pseudouridylate synthase I [Xanthomonas gardneri ATCC 19865]
 gi|325549321|gb|EGD20217.1| pseudouridylate synthase I [Xanthomonas gardneri ATCC 19865]
          Length = 257

 Score =  244 bits (624), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 93/248 (37%), Positives = 131/248 (52%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G ++Q  ++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPTVQARLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++         FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARRDPRSWM--LGTTARLPPSIAVRWCVPAAADFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       +SLD + M  AAQ L+G +DF  FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRSLDADAMHTAAQALLGENDFNAFRSVQCQAPHARRNLQAISVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+     +   L  +DR   GP APP+GL
Sbjct: 179 IGEVVEMQVQANAFLHHMVRNIVGSLILVGTGEQPVDWIATLLAGRDRSVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|282860840|ref|ZP_06269906.1| tRNA pseudouridine synthase A [Streptomyces sp. ACTE]
 gi|282564576|gb|EFB70112.1| tRNA pseudouridine synthase A [Streptomyces sp. ACTE]
          Length = 284

 Score =  244 bits (624), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 77/252 (30%), Positives = 116/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q    ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTGRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL  E       K L     ++   + I         F+ARFSA+ R Y YR+  
Sbjct: 70  QVAHVDLPVEVWAEHREKLLRRMAGRLPLDVRIWRAEEAPAGFNARFSALWRRYAYRVGD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           R      L +G      + LD + M  AA  + G HDF  +     + ++ IRT+     
Sbjct: 130 RPGGVDPLTRGHVLWHDRPLDLDAMNEAAARMTGEHDFAAYCKKR-EGATTIRTLQKLHW 188

Query: 178 NSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              G   ++   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +  
Sbjct: 189 VRDGESGVLTATVQADAFCHNMVRALIGAALFVGDGRRPAGWPAEVLAARVRDPAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVAYP 260


>gi|113954813|ref|YP_729642.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9311]
 gi|113882164|gb|ABI47122.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9311]
          Length = 299

 Score =  244 bits (624), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 111/250 (44%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
            R  + ++Y GS + GWQRQ  G   S+Q  +EKAI  +     +    AGRTDSGVHA 
Sbjct: 18  QRIAICLQYEGSFFCGWQRQTQGRGQSVQAVLEKAIAALDPHRPIKAIAAGRTDSGVHAS 77

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD            ALN  L     I +         +HA +SA  R Y Y I  
Sbjct: 78  GQVVHFDCSGPIPASRWAPALNGRL--PACIRVREAIERPLSWHACYSASYRRYRYTIYN 135

Query: 119 RQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            + P       +W    K LD + M  A   L+G HDF  F+    + S    TI   ++
Sbjct: 136 GRRPNLFLAPWSWHRYHKRLDEQAMAQALAGLMGEHDFAAFQRAGSRRSHSRTTIQDVNI 195

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+L+ + + A  FL+  +R  +G L  VG+ + T    E+  Q + R E    APP 
Sbjct: 196 ERDGDLLSVEIQASGFLYGMVRLLMGQLIAVGEHRLTPQQFEQRWQERRRDEVREAAPPH 255

Query: 238 GLYFDSVEYS 247
           GL      Y 
Sbjct: 256 GLCLLRAGYP 265


>gi|294666793|ref|ZP_06732027.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292603454|gb|EFF46871.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 257

 Score =  244 bits (624), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 95/248 (38%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++         FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRPLDADAMHGAAQALLGENDFSAFRSVQCQALHARRHLQAIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 FGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|317488484|ref|ZP_07947035.1| tRNA pseudouridine synthase A [Eggerthella sp. 1_3_56FAA]
 gi|316912416|gb|EFV33974.1| tRNA pseudouridine synthase A [Eggerthella sp. 1_3_56FAA]
          Length = 280

 Score =  244 bits (624), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 81/252 (32%), Positives = 125/252 (49%), Gaps = 11/252 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + + YNG+ + G+ RQ   +++QG +E A+ ++    V    AGRTD+GVHAL QV  
Sbjct: 31  LALTLSYNGAPFSGFARQPGQTTVQGDLEDALRMLFRRDVETTCAGRTDAGVHALGQVVS 90

Query: 64  FDLVRE----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           FD+            L ++LNA     D I++  +      F ARF A  R Y Y +   
Sbjct: 91  FDVDDRDIAGRSLPSLRRSLNALTH--DAITVREVEPKKLGFSARFDAQAREYHYHLCVD 148

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN 178
                  K  +W +P  LD   M   AQ+L+G HDF +F  +   +     R +     +
Sbjct: 149 STCPIFMKDFSWFVPGGLDITAMEAGAQYLLGEHDFKSFCMAASAEGKPTHRNVREISFH 208

Query: 179 SF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                  NL+ I+VV  +FLH+ +R+ VG+L +VG G+  +  + + L+A DR+  G  A
Sbjct: 209 PETVMGENLMSIKVVGNAFLHSMVRTIVGTLVMVGKGQRDADWVGEVLEACDRRVAGENA 268

Query: 235 PPEGLYFDSVEY 246
           P +GL F  V Y
Sbjct: 269 PAQGLVFWRVIY 280


>gi|254424035|ref|ZP_05037753.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7335]
 gi|196191524|gb|EDX86488.1| tRNA pseudouridine synthase A [Synechococcus sp. PCC 7335]
          Length = 299

 Score =  244 bits (623), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 111/248 (44%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  ++I+Y G+ + GWQRQKN   ++Q  IE  I  V G    + GAGRTD+GVHA  Q
Sbjct: 27  QRVALVIQYKGTHFHGWQRQKNAKRTVQAEIESVIASVLGRKPALVGAGRTDAGVHAAAQ 86

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF              LN  L   D I +   + V   +HA+FSA  R Y Y   T +
Sbjct: 87  VAHFAAPIVIPAERWAIILNDRLG--DDIVVRASTRVASDWHAQFSANWRRYRYTFYTSK 144

Query: 121 APLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P    +   W   +  LD   M  A Q ++G H+   F       +     +       
Sbjct: 145 YPNLFVQPYVWHYYRQRLDENLMLAALQPMMGYHNLLAFHRTGSDRTHSWVELQDVQCTR 204

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + I + A+ FL+  +R  +G +  VG+ + +  +     Q + R      APP+GL
Sbjct: 205 SGDFVRIELQAKGFLYGMVRLIMGLIVQVGERRLSPKEFTAIWQKRRRDLVKYSAPPQGL 264

Query: 240 YFDSVEYS 247
               V YS
Sbjct: 265 CLLRVGYS 272


>gi|227502701|ref|ZP_03932750.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49725]
 gi|227076431|gb|EEI14394.1| tRNA pseudouridine synthase A [Corynebacterium accolens ATCC 49725]
          Length = 293

 Score =  244 bits (623), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 85/261 (32%), Positives = 122/261 (46%), Gaps = 18/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW RQK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 17  VRIRLDLAYDGTDFHGWARQKGGLRTVQGVLEEQLAMIARTEVPLTVAGRTDAGVHARGQ 76

Query: 61  VAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+ +E          P  L + L   L   + + +       + F ARFSA+RR Y
Sbjct: 77  VAHVDVPQEMLEQRSVANDPGKLVRRLAKLL--PEDVRVHGCDFAPEGFDARFSALRRHY 134

Query: 113 LYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           +YRI T        + R      K +D   M+ AA  LVG HDF  F      A + IR 
Sbjct: 135 VYRITTSPRGALPTRARDTAEWFKPVDIGAMQDAANALVGLHDFAAFCKAKPNA-TTIRE 193

Query: 172 IDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           +  F            L E RV A +F  + +RS VG    VG+G+         LQ   
Sbjct: 194 LQEFSWQDVSTPEEPQLFEARVTADAFCWSMVRSLVGCCLSVGEGRRDVDFAAALLQETK 253

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R    P+AP +GL    V+Y 
Sbjct: 254 RSSRIPVAPAKGLSLVQVDYP 274


>gi|168333393|ref|ZP_02691673.1| tRNA pseudouridine synthase A [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 259

 Score =  244 bits (623), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 83/254 (32%), Positives = 116/254 (45%), Gaps = 16/254 (6%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS-------SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
             I+ Y G+ Y G+ RQ           +I   +E AI  +T + V + GAGRTD+GVHA
Sbjct: 10  KFIVAYKGTRYNGFARQAGDKVVGSGIQTISAELELAIEKITQQQVRIVGAGRTDAGVHA 69

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV   ++  +     L  ALN  L     I I ++   ++ FH  FS  R+ Y Y+I+
Sbjct: 70  LAQVCIANIDTQIGNSGLLLALNNKL--PVDIVIKSIEDAEEGFHPTFSGKRKMYRYQIL 127

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA----SSPIRTID 173
                        +  P  LD E M++AA  LVG HDF  F +         SS +RTI 
Sbjct: 128 NTTVSCPFVAEFVYHFPHKLDVEEMKVAAXELVGTHDFRAFCAAKSNVLKKGSSTVRTIF 187

Query: 174 HFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              V    + I  I V    FL+  +R   G+L   G G+     + K L+ ++RK  G 
Sbjct: 188 DIVVARGDDEIIKIDVTGDGFLYNMVRIIAGTLIDKGLGRGMP--IAKILEMRERKNAGK 245

Query: 233 LAPPEGLYFDSVEY 246
            AP  GL    VEY
Sbjct: 246 TAPASGLTMIGVEY 259


>gi|124024021|ref|YP_001018328.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9303]
 gi|166228748|sp|A2CC53|TRUA_PROM3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123964307|gb|ABM79063.1| tRNA pseudouridine synthase A [Prochlorococcus marinus str. MIT
           9303]
          Length = 295

 Score =  244 bits (623), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 72/248 (29%), Positives = 111/248 (44%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ    S+Q  +E+AI  +  +  +    AGRTD+GVHA  Q
Sbjct: 16  RRIGLSVQYEGSNFCGWQRQPQAVSVQQVLEEAISQLDPQRPIQAVAAGRTDAGVHAAGQ 75

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L   +TI +         +HA  SA  R Y Y I   +
Sbjct: 76  VVHFDCCGPIPAERWAPALNGRL--PNTIRVREAVARPASWHACHSATYRRYRYTIYNGR 133

Query: 121 APLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W      LD   M++A + L+G  D + F+    + +    T+    +  
Sbjct: 134 RPNLFLTPWSWHRYHVRLDETVMQVALEGLLGLQDLSAFQRTGSRRAHARTTVQDVKIER 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LI I + A  FL+  +R  +G L  +G+ +      E+  + + R+E    AP +GL
Sbjct: 194 QGDLIMIEIQASGFLYGMVRLLMGQLVALGEHRLNLQTFERRWKEKRRQEVKEAAPAQGL 253

Query: 240 YFDSVEYS 247
                 Y 
Sbjct: 254 CLLRAGYE 261


>gi|325832022|ref|ZP_08165119.1| tRNA pseudouridine synthase A [Eggerthella sp. HGA1]
 gi|325486343|gb|EGC88795.1| tRNA pseudouridine synthase A [Eggerthella sp. HGA1]
          Length = 284

 Score =  244 bits (623), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 81/252 (32%), Positives = 125/252 (49%), Gaps = 11/252 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + + YNG+ + G+ RQ   +++QG +E A+ ++    V    AGRTD+GVHAL QV  
Sbjct: 35  LALTLSYNGAPFSGFARQPGQTTVQGDLEDALRMLFRRDVETTCAGRTDAGVHALGQVVS 94

Query: 64  FDLVRE----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           FD+            L ++LNA     D I++  +      F ARF A  R Y Y +   
Sbjct: 95  FDVDDRDIAGRSLPSLRRSLNALTH--DAITVREVEPKKLGFSARFDAQAREYHYHLCVD 152

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN 178
                  K  +W +P  LD   M   AQ+L+G HDF +F  +   +     R +     +
Sbjct: 153 STCPIFMKDFSWFVPGGLDITAMEAGAQYLLGEHDFKSFCMAASAEGKPTHRNVREISFH 212

Query: 179 SF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                  NL+ I+VV  +FLH+ +R+ VG+L +VG G+  +  + + L+A DR+  G  A
Sbjct: 213 PETVMGENLMSIKVVGNAFLHSMVRTIVGTLVMVGKGQRDADWVGEVLEACDRRVAGENA 272

Query: 235 PPEGLYFDSVEY 246
           P +GL F  V Y
Sbjct: 273 PAQGLVFWRVIY 284


>gi|111114834|ref|YP_709452.1| tRNA pseudouridine synthase A [Borrelia afzelii PKo]
 gi|216264050|ref|ZP_03436044.1| tRNA pseudouridine synthase A [Borrelia afzelii ACA-1]
 gi|122956439|sp|Q0SPF2|TRUA_BORAP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|110890108|gb|ABH01276.1| pseudouridylate synthase I [Borrelia afzelii PKo]
 gi|215980094|gb|EEC20916.1| tRNA pseudouridine synthase A [Borrelia afzelii ACA-1]
          Length = 246

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 123/247 (49%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +    I Y+GS Y G+Q Q    +IQG IEKA+  +  + + +H +GRTD GVHA RQ
Sbjct: 1   MKKILAEIAYDGSMYHGFQIQPTKPTIQGEIEKALMKINKKKIKIHSSGRTDKGVHAKRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD+        L KALNA L     I IL L  V   FH RF+A +R Y Y I+   
Sbjct: 61  IITFDININIQLNNLKKALNAILLKP-GIKILKLKHVKNSFHPRFNAQKRKYSYCILNSD 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E  +A+ + K L+  N+   A+ L+G HDFTTF  I  ++ S  R I        
Sbjct: 120 NYYPWESYQAYYVNKKLNINNLNQMAKILIGNHDFTTFSCIKDKSKSKFRHIHSAKFKKK 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I   ++  SFL   +RS +G++  +     + +  E  L++++R      AP   L+
Sbjct: 180 GKYIIFEIIGSSFLWKMVRSIIGTMLDIEIKNESISTFETILKSKNRNLARTTAPANALF 239

Query: 241 FDSVEYS 247
            D V Y 
Sbjct: 240 LDKVYYE 246


>gi|326777220|ref|ZP_08236485.1| tRNA pseudouridine synthase A [Streptomyces cf. griseus XylebKG-1]
 gi|326657553|gb|EGE42399.1| tRNA pseudouridine synthase A [Streptomyces cf. griseus XylebKG-1]
          Length = 284

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 77/252 (30%), Positives = 117/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL          K L     ++   + I   +     F+ARFSA+ R Y YR+  
Sbjct: 70  QVAHVDLPEAVWAEHEEKLLRRLAGRLPLDVRIWRAAPAPAGFNARFSALWRRYAYRVGD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           R      L +G      + LD + M  AA  +VG HDF  +     + ++ IRT+     
Sbjct: 130 RPGGVDPLTRGHVLWHDRPLDLDAMNEAAALMVGEHDFAAYCKKR-EGATTIRTLQKLRW 188

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  L+   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +  
Sbjct: 189 VRDPATGLLTATVQADAFCHNMVRALIGAALFVGDGRRPAAWPAEVLAAKVRDPGVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVAYP 260


>gi|86739325|ref|YP_479725.1| tRNA pseudouridine synthase A [Frankia sp. CcI3]
 gi|123737799|sp|Q2JFE6|TRUA_FRASC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|86566187|gb|ABD09996.1| tRNA pseudouridine synthase A [Frankia sp. CcI3]
          Length = 274

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 119/249 (47%), Gaps = 6/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA+ Q
Sbjct: 6   VRLRLDLSYDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDSGVHAVGQ 65

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL  +     L + LN  L     + I+ L+     F ARFSA+ R Y+YRI    
Sbjct: 66  VAHVDLPDDVPLGGLARRLNGVL--DRAVRIIGLAPAPPGFDARFSALSRRYVYRITDAP 123

Query: 121 APL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L +      P+ LD   M  AA  LVG HDF  F     + ++ +RT+   DV  
Sbjct: 124 YGAEPLRRFDTLAWPRPLDVPAMAAAALFLVGEHDFAAFCRRR-EGATTVRTLLRLDVLR 182

Query: 180 FGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               + +  V A +F H+ +R+ VG+L  VG+G+         L    R     +AP  G
Sbjct: 183 RPEGVVVADVEADAFCHSMVRALVGALLAVGEGRKPPQWPAAVLHRGVRDPAVTVAPAHG 242

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 243 LTLVDVRYP 251


>gi|314934267|ref|ZP_07841626.1| tRNA pseudouridine synthase A [Staphylococcus caprae C87]
 gi|313652197|gb|EFS15960.1| tRNA pseudouridine synthase A [Staphylococcus caprae C87]
          Length = 267

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 114/244 (46%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H   RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHVRIHPTSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N +L   D I + N+  V++ FH R+  + + Y Y++   + 
Sbjct: 61  FHFDTELNIDNQQWQYAMNRFL--PDDIYVKNVHTVEENFHCRYDCVGKRYRYKVYQGEH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I   LD   M  AA H +G HDFT F S   +  S +RT+   +V    
Sbjct: 119 RNPFKSGLETFINSDLDLSKMNEAAHHFIGTHDFTGFCSQKTEVESKVRTLYQSEVVQTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+ ++R      AP EGLY 
Sbjct: 179 TGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRQPDEVPQLLEEKNRNNVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|294624568|ref|ZP_06703244.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292601141|gb|EFF45202.1| tRNA pseudouridine synthase A [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 257

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 94/248 (37%), Positives = 133/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++         FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q    L +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPTLYRQTLSWERRPLDADAMHGAAQALLGENDFSAFRSVQCQALHARRHLQAIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 FGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|283768478|ref|ZP_06341390.1| tRNA pseudouridine synthase A [Bulleidia extructa W1219]
 gi|283104870|gb|EFC06242.1| tRNA pseudouridine synthase A [Bulleidia extructa W1219]
          Length = 320

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 116/247 (46%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +  I+ Y G+ Y GWQ QK G+SIQ  IE  +  +  E   V  +GRTD+ V+AL Q
Sbjct: 1   MRYFKAIVAYVGANYCGWQSQKKGNSIQEKIEAVLSQINQEKTTVIASGRTDAKVNALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F   +           +++L     I +  +  VD+ FHARF   +++YLYRI    
Sbjct: 61  CFQFQSEKNIDSYRWLGIFHSFL--PKDIYVKQVEEVDETFHARFLVEQKTYLYRIHLGD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
                +K  ++ + + L+ + MR   +   G H F +F  S   +  + +RTI   ++  
Sbjct: 119 Y-DVFQKDDSFQLREDLNLKEMRKCWKLFEGTHSFLSFNTSSLSEYPNQVRTIFRTELRK 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +E+ +    +L   +R  VG+   VG GK T  ++++ L    R      AP +GL
Sbjct: 178 ISDHLELEISGNGYLRHMVRILVGTCLEVGRGKLTIEEVQRMLNDPSRHYATKKAPAQGL 237

Query: 240 YFDSVEY 246
               V Y
Sbjct: 238 CLKEVSY 244


>gi|239943606|ref|ZP_04695543.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 15998]
 gi|239990059|ref|ZP_04710723.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 11379]
 gi|291447073|ref|ZP_06586463.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 15998]
 gi|291350020|gb|EFE76924.1| tRNA pseudouridine synthase A [Streptomyces roseosporus NRRL 15998]
          Length = 284

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 75/252 (29%), Positives = 119/252 (47%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL          K L     ++   + +   +     F+ARFSA+ R Y YR+  
Sbjct: 70  QVAHVDLPEAVWAEHEEKLLRRLAGRLPLDVRVWRAAPAPAGFNARFSALWRRYAYRVGD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           R      L +G      + LD ++M  AA  +VG HDF  +     + ++ IRT+     
Sbjct: 130 RPGGVDPLTRGHVLWHDRPLDLDSMNEAAALMVGEHDFAAYCKKR-EGATTIRTLQKLSW 188

Query: 178 NSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  ++   V A +F H  +R+ +G+   VGDG+  ++   + L A+ R     +  
Sbjct: 189 VRDEESGVLTATVQADAFCHNMVRALIGAALFVGDGRRPASWPAEVLAAKVRDPGVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVAYP 260


>gi|270307870|ref|YP_003329928.1| pseudouridylate synthase [Dehalococcoides sp. VS]
 gi|270153762|gb|ACZ61600.1| pseudouridylate synthase [Dehalococcoides sp. VS]
          Length = 246

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M+IEY G+ Y G+Q Q  G++IQG +E AI  +T E   V G+GRTD+GVHA  QV  + 
Sbjct: 1   MVIEYEGTMYSGFQIQDKGATIQGELETAIQKLTNEKTRVSGSGRTDAGVHAAYQVVSYL 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    +   LN YL     I++  +  V + F  R  AI R Y Y I+  +    L
Sbjct: 61  SESSLGLEKIKGGLNYYL--PTDIAVKEVYFVAENFDVRRRAISREYSYHILNSKTRSPL 118

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGNLI 184
            + +AW +P  LD + M  A + L G HDF  F  S+  +    +R ++   ++   + +
Sbjct: 119 ARLQAWQVPYKLDTKLMEQAFKMLEGEHDFVAFASSLGPEIKKTVRRVNWTRLDIAEDRL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+ A SFL  Q+R+ +G+L  +G G  +  +     +A+     GP AP  GL    V
Sbjct: 179 VFRIEANSFLTHQVRNTIGTLVELGRGILSMREFGALFEAKTPGLAGPAAPACGLSLVRV 238

Query: 245 EY 246
            Y
Sbjct: 239 NY 240


>gi|58582878|ref|YP_201894.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84624740|ref|YP_452112.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188577717|ref|YP_001914646.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|62901158|sp|Q5GXR2|TRUA_XANOR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123766543|sp|Q2P0T9|TRUA_XANOM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238689565|sp|B2SVP0|TRUA_XANOP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|58427472|gb|AAW76509.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84368680|dbj|BAE69838.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188522169|gb|ACD60114.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 257

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 94/248 (37%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++         FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDAHREPRGWM--LGTTARLPPSIAVRWCVPAAADFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M +AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRPLDADAMHVAAQALLGENDFSAFRSVQCQALHARRNLQAIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 IGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|193212885|ref|YP_001998838.1| tRNA pseudouridine synthase A [Chlorobaculum parvum NCIB 8327]
 gi|193086362|gb|ACF11638.1| tRNA pseudouridine synthase A [Chlorobaculum parvum NCIB 8327]
          Length = 238

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 82/242 (33%), Positives = 113/242 (46%), Gaps = 5/242 (2%)

Query: 6   MIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M IEY+G+ Y GWQRQ  +  ++QG IE+ +  +T E V + GAGRTD GVHA  QVA F
Sbjct: 1   MQIEYDGTDYSGWQRQPGDVVTVQGEIERVLGRITQEPVSIDGAGRTDRGVHARGQVASF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            +  E     +  + N+ L    TI I ++  V + FHARFSA  R Y Y ++ R  P A
Sbjct: 61  AVASEMPLGRMMHSANSLL--PSTIRITSMRQVPESFHARFSATSREYRYVLLER--PSA 116

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           ++   A       D   M   A  LVG HDF  F          + T+        G   
Sbjct: 117 IDSRFAGCSHGKPDVVLMNRLAAMLVGTHDFAAFSKETPDQQGTLCTVTEARWYRSGRFH 176

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+ A  FL + +R  V  +  VG G+ +  +  + L    R      A P GL+   V
Sbjct: 177 VFRIEANRFLRSMVRFLVAGMIEVGMGRLSEEEFSRMLVDGGRPASLVPADPAGLFLWKV 236

Query: 245 EY 246
            Y
Sbjct: 237 RY 238


>gi|332290819|ref|YP_004429428.1| tRNA pseudouridine synthase A [Krokinobacter diaphorus 4H-3-7-5]
 gi|332168905|gb|AEE18160.1| tRNA pseudouridine synthase A [Krokinobacter diaphorus 4H-3-7-5]
          Length = 257

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 74/251 (29%), Positives = 113/251 (45%), Gaps = 9/251 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G  Y GWQRQ N  ++Q +IEKA+ ++  + V + GAGRTD+GVHA +  
Sbjct: 1   MRYFIELSYFGKHYHGWQRQPNAVTVQETIEKALSMILRKPVQIMGAGRTDAGVHATQMY 60

Query: 62  AHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AHFD        +     L    N  L     I+   +  V  + H RF A  RSY+YRI
Sbjct: 61  AHFDWDGEQFTTQESIEKLTHKFNRLL--PKDIAFKRIFQVADKAHTRFDATSRSYVYRI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +         A  +   +  E M  AA  L+   DF  F   +   ++ +  I    
Sbjct: 119 --GKEKNPFTSDHAPTVRNEVHIEAMNKAAAILLDYSDFECFSKSNTDVNTYLCDITRAT 176

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                +     + A  FL   +R+ VG+L  +G+GK   T + + +  + R + G   P 
Sbjct: 177 WIETEDEYHFHITANRFLRNMVRAIVGTLLEIGEGKRDITWMHEVITGKSRSQAGKSVPG 236

Query: 237 EGLYFDSVEYS 247
            GLY   + Y 
Sbjct: 237 RGLYLTEILYP 247


>gi|196233677|ref|ZP_03132518.1| tRNA pseudouridine synthase A [Chthoniobacter flavus Ellin428]
 gi|196222347|gb|EDY16876.1| tRNA pseudouridine synthase A [Chthoniobacter flavus Ellin428]
          Length = 251

 Score =  243 bits (622), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 92/248 (37%), Positives = 127/248 (51%), Gaps = 6/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  M+I Y+G  + GWQ Q    ++Q  +E A     G  VVVHG+GRTD+GVHAL Q+A
Sbjct: 6   RLKMLIAYDGRPFRGWQSQATKDAVQDHMEAAFAKTIGGRVVVHGSGRTDAGVHALAQIA 65

Query: 63  HFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           H D+    + V     ALN +L     I +L +S     FHARF A  + Y YR+     
Sbjct: 66  HADVPAARLEVSAWRGALNNFL--PPEIRVLRVSRAAPDFHARFHARGKIYTYRMWNASY 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---RSIHCQASSPIRTIDHFDVN 178
              LE GRAW +P  LD + +R  AQ L G+HDF  F   R+    A   +RTI H  + 
Sbjct: 124 LHPLEIGRAWHMPSKLDLDILRQGAQMLEGKHDFAGFAANRAPGYAAEDTVRTIQHICLT 183

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+L+ +R     FL+  +R   G+L     G+   T +++ L  +  K+    AP EG
Sbjct: 184 RRGDLLNLRFEGNGFLYKMVRLLTGTLVRCAQGRAELTFIKELLAGKGAKKTSFAAPAEG 243

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 244 LYLTRVLY 251


>gi|226365626|ref|YP_002783409.1| tRNA pseudouridine synthase TruA [Rhodococcus opacus B4]
 gi|226244116|dbj|BAH54464.1| tRNA pseudouridine synthase TruA [Rhodococcus opacus B4]
          Length = 270

 Score =  243 bits (621), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 77/245 (31%), Positives = 120/245 (48%), Gaps = 3/245 (1%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + + Y+G+ + GW RQ    ++ G IE+ +  V    + +  AGRTD+GVHA  QVAH 
Sbjct: 2   RLDVAYDGTDFSGWARQNGLRTVCGEIEEKLGAVLRSPLQLTVAGRTDAGVHATGQVAHV 61

Query: 65  DLVREWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-QAP 122
           D+  E +P    + +      +   + I  +S   + F ARFSA+RR Y YR+ +     
Sbjct: 62  DVPVEALPDEPSRLVRRLARFLPKDVRIKQISFAPEHFDARFSAMRRHYEYRLTSAVYGA 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L        PK LD E MR A+  L+G HDF  F     + ++ +R +  FD    G+
Sbjct: 122 DPLRARDTVSYPKILDLELMRSASATLLGLHDFAAFCKRR-EGATTVRDLQRFDWERDGD 180

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +    V A +F  + +RS VG++  VG+G+     +E  L+   R     +AP  GL   
Sbjct: 181 VFTAFVSADAFCWSMVRSLVGAVLAVGEGRRDLDWIEGLLRETSRSSSILVAPAHGLCLV 240

Query: 243 SVEYS 247
            V+Y 
Sbjct: 241 RVDYP 245


>gi|111220576|ref|YP_711370.1| tRNA pseudouridine synthase A [Frankia alni ACN14a]
 gi|111148108|emb|CAJ59776.1| tRNA pseudouridine synthase A (Pseudouridylate synthase I)
           (Pseudouridine synthase I) (Uracil hydrolyase) [Frankia
           alni ACN14a]
          Length = 288

 Score =  243 bits (621), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 120/249 (48%), Gaps = 6/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           +R  + I Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA  Q
Sbjct: 20  VRLRLDIAYDGTPFAGWARQPGQRTVQGDVEDALIRVARLAAVRLTVAGRTDSGVHAAGQ 79

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL  +     L + LN  L    ++ +  L+     F ARFSA+ R Y+YRI    
Sbjct: 80  VAHVDLPTDVPLGGLARRLNGVL--DRSVRVTGLAPAPAGFDARFSALSRRYVYRITDAP 137

Query: 121 APL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L +      P+ LD   M  AA  LVG HDF  F     + ++ +RT+   DV  
Sbjct: 138 FGAEPLRRFDTLAWPRPLDVPAMASAALLLVGEHDFAAFCRRR-EGATTVRTLLRLDVLR 196

Query: 180 FGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             + + +  V A +F H+ +R+ VG+L  VG+G+         L+   R     +AP  G
Sbjct: 197 RPDGVVVADVEADAFCHSMVRALVGALLAVGEGRRPPQWPAAVLRRGLRDPAVTVAPAHG 256

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 257 LTLVEVRYP 265


>gi|242371866|ref|ZP_04817440.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W1]
 gi|242350373|gb|EES41974.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W1]
          Length = 267

 Score =  243 bits (621), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 113/244 (46%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H   RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKRHVRIHPTSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N +L   + I + ++  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNQQWQYAMNRFL--PNDIYVKSVQTVDENFHCRYDCVGKRYRYKVYQGAH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    I   LD   M  AA H +G HDFT F S   +  S +RT+   +V    
Sbjct: 119 RDPFKSGLETFIDNDLDLAKMNEAAHHFIGTHDFTGFCSQKTEVESKVRTLYQSEVVQTE 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    ++ + L+ ++R      AP EGLY 
Sbjct: 179 AGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRNPDEVPQLLEEKNRNNVPFTAPSEGLYL 238

Query: 242 DSVE 245
           + V 
Sbjct: 239 EKVY 242


>gi|21243447|ref|NP_643029.1| tRNA pseudouridine synthase A [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|30913394|sp|Q8PJ25|TRUA_XANAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21109001|gb|AAM37565.1| tRNA pseudouridine synthase A [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 257

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 94/248 (37%), Positives = 133/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++         FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRPLDADAMHGAAQALLGENDFSAFRSVQCQALHARRHLQAIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 IGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|260062032|ref|YP_003195112.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
 gi|88783594|gb|EAR14765.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
          Length = 253

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 73/247 (29%), Positives = 115/247 (46%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQ 60
           +R+ + I Y G+ Y GWQ+Q N  +IQ  +E  +  + G   + + GAGRTD+GVHA + 
Sbjct: 1   MRFFLEISYLGTAYHGWQKQPNALAIQEILEDRMGKLLGNGPIDLVGAGRTDAGVHARQL 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD      P      LNA+L     I++  +  V    HARF A  R+Y Y ++  +
Sbjct: 61  FAHFDRDAAL-PSGFVHRLNAFL--PADIAVKGVYEVAPNAHARFDATGRTYEYHLVREK 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +G A+     LD   M  AA  ++G  +F  F        +    +        
Sbjct: 118 --DPFREGLAYQFQGELDFGAMNRAAASMLGYGNFKAFSRSKSDVKTYNCDLREARWEEG 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +    + A  FL   +R+ VG+L  VG G+  +  ++  +++QDR E G   P +GLY
Sbjct: 176 DGVWVFTISADRFLRNMVRAVVGTLLEVGKGRLDAEGVKTIIKSQDRSEAGVSVPAKGLY 235

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 236 LTRITYP 242


>gi|320451375|ref|YP_004203471.1| tRNA pseudouridine synthase A [Thermus scotoductus SA-01]
 gi|320151544|gb|ADW22922.1| tRNA pseudouridine synthase A [Thermus scotoductus SA-01]
          Length = 254

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 88/252 (34%), Positives = 126/252 (50%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ+    ++QG +E+ +  + G +     AGRTD+GVHAL 
Sbjct: 1   MRRILILTEYDGTHFAGLQRQRTGLRTVQGELERVLPGI-GALPKAVAAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              HFDL        + +ALN  L   + + ++    V   FHAR  A+ R+YLYRI+ R
Sbjct: 60  MPFHFDLGSRIPTEKIPQALNRLL--PEDLKVVAAREVAPDFHARKDALWRAYLYRILLR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L + RA  +   LD   +R A   L GRH+F  F     +A    R +    +  
Sbjct: 118 SHPSPLLRHRALWLRHPLDLAAIREALSFLPGRHNFLGFAKEEVRAGE--RELYEARMEE 175

Query: 180 F----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G  +      +SFL  Q+R  VG+L  VG GK +   +   LQ QDR + GP AP
Sbjct: 176 VEGEAGRELRFYFRGQSFLRGQVRGMVGTLLEVGLGKRSPESIRLILQTQDRGQAGPSAP 235

Query: 236 PEGLYFDSVEYS 247
           P+GLYF    Y 
Sbjct: 236 PQGLYFLEAAYP 247


>gi|311744771|ref|ZP_07718567.1| tRNA pseudouridine synthase A [Aeromicrobium marinum DSM 15272]
 gi|311311888|gb|EFQ81809.1| tRNA pseudouridine synthase A [Aeromicrobium marinum DSM 15272]
          Length = 262

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 118/249 (47%), Gaps = 8/249 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW  Q    ++QG IE A+  +        +  AGRTD+GVHA  
Sbjct: 1   MRLRIDLAYDGTDFRGWAVQPGQRTVQGVIESALGTMLRLDPTPTLTCAGRTDAGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH DL     P +L + L  YL   D I I ++      F ARF+A  R Y+YR+   
Sbjct: 61  QVAHVDLDTH--PGVLERRLRRYL--PDDIRIKSVVEAPPGFDARFAATERRYVYRMTDH 116

Query: 120 QA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            A P  L +      P+ L  + M  AA+HL+G+HDF  F       ++ IRT+      
Sbjct: 117 PAGPDPLARRMIVHHPRPLSVDLMNAAAEHLLGQHDFAAFCKKRA-GATTIRTLLALRTI 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I   V A +F H  +RS +G L  VG+ ++      + L  + R     +  P G
Sbjct: 176 RGGETIATTVRADAFCHAMVRSLMGCLVAVGERRFPPEFAAEVLSGRVRDGRVKVMEPHG 235

Query: 239 LYFDSVEYS 247
           L  + V Y 
Sbjct: 236 LVLEEVSYP 244


>gi|282857331|ref|ZP_06266568.1| tRNA pseudouridine synthase A [Pyramidobacter piscolens W5455]
 gi|282584831|gb|EFB90162.1| tRNA pseudouridine synthase A [Pyramidobacter piscolens W5455]
          Length = 247

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 117/247 (47%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  +I Y+G  + GWQ Q NG+++Q S+E+ + L+ G  V V GAGRTD+GVHA  Q
Sbjct: 1   MPRYSCVISYDGGKFCGWQTQPNGATVQESLERVLSLLNGSPVKVTGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A F L REW P  L  A      + +  ++ ++      F AR  A+ R Y + +    
Sbjct: 61  TASFLLDREWEPRRLLLA--LNANLPEGAAVASVRERPIGFDARRDALWREYAFFVWRGP 118

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               + K   W   K   D + +R     L GRHDF+ F        + +R +       
Sbjct: 119 FCYPMMKPYVWWKKKDDWDHDLIRRGCALLEGRHDFSAFCRAGDLPENAVRRMHFVRYIR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L   R+   +FL   +R  +G+L  V  G+ T + LE  L    R +    APP GL
Sbjct: 179 RGRLSAFRIRGDAFLTNMVRIMIGNLDAVASGRRTLSWLEGLLDGASRGDSAMTAPPNGL 238

Query: 240 YFDSVEY 246
           +F  V Y
Sbjct: 239 FFWKVGY 245


>gi|257790805|ref|YP_003181411.1| tRNA pseudouridine synthase A [Eggerthella lenta DSM 2243]
 gi|257474702|gb|ACV55022.1| tRNA pseudouridine synthase A [Eggerthella lenta DSM 2243]
          Length = 255

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 82/257 (31%), Positives = 127/257 (49%), Gaps = 14/257 (5%)

Query: 2   IR---YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R     + + YNG+ + G+ RQ   +++QG +E A+ ++    V    AGRTD+GVHAL
Sbjct: 1   MRDHTLALTLSYNGAPFSGFARQPGQTTVQGDLEDALRMLFRRDVETTCAGRTDAGVHAL 60

Query: 59  RQVAHFDLVRE----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            QV  FD+            L ++LNA     D I++  +      F ARF A  R Y Y
Sbjct: 61  GQVVSFDVDDRDIAGRSLPSLRRSLNALTH--DAITVREVEPKKLGFSARFDAQAREYHY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTID 173
            +          K  +W +P  LD   M   AQ+L+G HDF +F  +   +     R + 
Sbjct: 119 HLCVDSTCPIFMKDFSWFVPGGLDITAMEAGAQYLLGEHDFKSFCMAASAEGKPTHRNVR 178

Query: 174 HFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
               +       NL+ I+VV  +FLH+ +R+ VG+L +VG G+  +  + + L+A DR+ 
Sbjct: 179 EISFHPETVMGENLMSIKVVGNAFLHSMVRTIVGTLVMVGKGQRDADWVGEVLEACDRRV 238

Query: 230 CGPLAPPEGLYFDSVEY 246
            G  AP +GL F  V Y
Sbjct: 239 AGENAPAQGLVFWRVIY 255


>gi|212550510|ref|YP_002308827.1| tRNA pseudouridine synthase A [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|229557952|sp|B6YQE4|TRUA_AZOPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|212548748|dbj|BAG83416.1| tRNA pseudouridine synthase A [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
          Length = 249

 Score =  243 bits (620), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 118/247 (47%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG  Y GWQ Q NG ++Q  I++ + ++  + V + GAGRTD+GVHA   
Sbjct: 1   MNRYFIYLAYNGRNYCGWQIQPNGITVQQRIQQCLSILLRKSVTIIGAGRTDAGVHANLM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD         L K LN  L     I I  +  V K  HARF AI R Y Y I  ++
Sbjct: 61  TAHFDWEEILSTTSLTKRLNGIL--PCDILIYKIIPVKKNAHARFDAISRKYKYYITYQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P      + + + + L+   M  A+  L    DFT+F  +H    + +  I   + N+ 
Sbjct: 119 NP--FRNEQLFRLKQPLNKHLMNEASNILSEYSDFTSFCKLHSNTRTNVCRISKAEWNTV 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             +    + A  FL   +RS VG++  +G  K + TD  K +++++        P   L+
Sbjct: 177 QGIDIFTIKADRFLRNMVRSIVGTMIDIGKNKLSITDFRKIIESKNHIMLKSSVPAHALF 236

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 237 LTDIEYP 243


>gi|320009073|gb|ADW03923.1| tRNA pseudouridine synthase A [Streptomyces flavogriseus ATCC
           33331]
          Length = 284

 Score =  243 bits (620), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 76/252 (30%), Positives = 117/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL  E       K L     ++   + I   +     F+ARFSA+ R Y YR+  
Sbjct: 70  QVAHVDLPAEVWAEHEEKLLRRMAGRLPLDVRIWRAAEAPAGFNARFSALWRRYAYRVGD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           R      L +G      + LD + M  AA  + G HDF  +     + ++ IRT+     
Sbjct: 130 RPGGVDPLTRGHVLWHDRPLDLDAMNEAAALMTGEHDFAAYCKKR-EGATTIRTLQRLHW 188

Query: 178 NSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  ++   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +  
Sbjct: 189 VRDAESGVLTATVQADAFCHNMVRALIGAALFVGDGRRPAGWPAEVLAAKVRDPAVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVAYP 260


>gi|182436598|ref|YP_001824317.1| tRNA pseudouridine synthase A [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|238689026|sp|B1W3X8|TRUA_STRGG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|178465114|dbj|BAG19634.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 284

 Score =  243 bits (620), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 76/252 (30%), Positives = 117/252 (46%), Gaps = 7/252 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G  + GW +Q +  ++QG IE A+  VT   V   +  AGRTD+GVHA  
Sbjct: 10  VRVRLDLSYDGKDFSGWAKQTSRRTVQGEIEDALRTVTRSSVTYDLTVAGRTDAGVHARG 69

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL          K L     ++   + I   +     F+ARFSA+ R Y YR+  
Sbjct: 70  QVAHVDLPEAVWAEHEEKLLRRLAGRLPLDVRIWRAAPAPAGFNARFSALWRRYAYRVGD 129

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           R      L +G      + LD + M  AA  +VG HDF  +     + ++ IRT+     
Sbjct: 130 RPGGVDPLTRGHVLWHDRPLDLDAMNEAAALMVGEHDFAAYCKKR-EGATTIRTLQKLRW 188

Query: 178 NSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  ++   V A +F H  +R+ +G+   VGDG+  +    + L A+ R     +  
Sbjct: 189 VRDPATGVLTATVQADAFCHNMVRALIGAALFVGDGRRPAAWPAEVLAAKVRDPGVHVVR 248

Query: 236 PEGLYFDSVEYS 247
           P GL  + V Y 
Sbjct: 249 PHGLTLEEVAYP 260


>gi|42559832|sp|Q8NSV0|TRUA_CORGL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21323332|dbj|BAB97960.1| Pseudouridylate synthase (tRNA psi55) [Corynebacterium glutamicum
           ATCC 13032]
          Length = 289

 Score =  243 bits (620), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 128/262 (48%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW +Q   +  ++Q  +E  + +V  E V +  AGRTD+GVHA  
Sbjct: 1   MRIRLDLAYDGTDFHGWAKQGTSDLRTVQKVLEDNLSMVLRETVELTVAGRTDAGVHAAG 60

Query: 60  QVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+             P  L + L   L   D I +  +   +  F ARFSA+RR 
Sbjct: 61  QVAHFDIPAHALEQRSIDGDPSKLVRRLGRLL--PDDIRVHGVRFAEPGFDARFSAMRRH 118

Query: 112 YLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YRI T  A  L   +      PK ++ E M++AA  L+G HDF  F      A + +R
Sbjct: 119 YVYRITTHPAGALPTRRHDTAQWPKPVELERMQLAADALLGLHDFVAFCKAKPHA-TTVR 177

Query: 171 TIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F            + E  VVA +F  + +RS VGS   VG+G+  S    + L A 
Sbjct: 178 ELQKFAWKDVSTDIEPQVYEAHVVADAFCWSMVRSLVGSCMAVGEGRRGSGFTAELLDAS 237

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R    P+AP +GL    V+Y 
Sbjct: 238 ERSPMVPVAPAKGLSLVGVDYP 259


>gi|325282723|ref|YP_004255264.1| tRNA pseudouridine synthase A [Deinococcus proteolyticus MRP]
 gi|324314532|gb|ADY25647.1| tRNA pseudouridine synthase A [Deinococcus proteolyticus MRP]
          Length = 294

 Score =  243 bits (620), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 86/249 (34%), Positives = 126/249 (50%), Gaps = 7/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + ++GS Y GWQ Q N  S+Q ++  A+  +  E      AGRTD+GVHAL   
Sbjct: 31  TRVLLTVAWDGSAYGGWQSQPNAPSVQDTLHAALNRLGLEAARPVAAGRTDAGVHALNMP 90

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH DL    +P     AL    ++  ++++L+       FHARFS  +R YLY+I+   A
Sbjct: 91  AHVDLHAPRIPPE-RLALALARQLPRSVAVLSAQAAPAGFHARFSCTQRRYLYQILNAPA 149

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--- 178
              LE+GR+  +   LD   M  AAQHL+G HDF  F +   +    +R +    V    
Sbjct: 150 RHPLEEGRSLWVRGQLDLSAMNAAAQHLIGLHDFAAFATK--EDRQTVRELQRLAVTASP 207

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             +G  + + VV  SFL   +R  VG+L  VG GK     + + L + DR++ G    P+
Sbjct: 208 LPYGQRVTLAVVGESFLRHMVRGLVGTLIAVGQGKLAPEAVAEILASGDRRQAGINVAPD 267

Query: 238 GLYFDSVEY 246
           GLYF    Y
Sbjct: 268 GLYFAGAGY 276


>gi|318079697|ref|ZP_07987029.1| tRNA pseudouridine synthase A [Streptomyces sp. SA3_actF]
          Length = 282

 Score =  242 bits (619), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 118/249 (47%), Gaps = 7/249 (2%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIV--VVHGAGRTDSGVHALRQV 61
            + + Y+G+ + GW RQ  G  ++Q ++E+A+ +VT       +  AGRTD+GVHA  QV
Sbjct: 2   RLDLSYDGTDFHGWARQPGGRRTVQETLEEALRVVTRAPAPYELTVAGRTDAGVHARGQV 61

Query: 62  AHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH  +  E       K L     ++   + +  ++   + F ARFSAI R Y YR+  + 
Sbjct: 62  AHVGMADEVWAEHGEKLLKRLAGRLPKDVRVWRVAPAPEGFDARFSAIWRRYAYRVADQA 121

Query: 121 AP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L +G      + LD + M  AA+ L+G HDF  +     + ++ IR +       
Sbjct: 122 GGVDPLLRGHVLWHDRPLDIDAMNEAAEGLLGEHDFAAYCKKR-EGATTIREMQQLFWTR 180

Query: 180 FGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             + + E  V A +F H  +RS VG+L  VGDG    +   K L A  R     +  P G
Sbjct: 181 RADGVLEATVRADAFCHNMVRSLVGALLFVGDGHRPPSWPAKVLAAGVRDSAVHVVRPVG 240

Query: 239 LYFDSVEYS 247
           L  + V Y 
Sbjct: 241 LTLEEVGYP 249


>gi|260435918|ref|ZP_05789888.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8109]
 gi|260413792|gb|EEX07088.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 8109]
          Length = 293

 Score =  242 bits (619), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 109/247 (44%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ+NG S+Q  +E AI  +     V    AGRTD+GVHA  Q
Sbjct: 16  QRIALSLQYEGSSFCGWQRQRNGRSVQAVLEDAIAQLDPHRPVQTFAAGRTDAGVHAAGQ 75

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L    TI +         +HA +SA  R Y Y I   +
Sbjct: 76  VVHFDCSGPIPARKWAPALNGRL--PSTIRVRESVARPMDWHACYSATYRRYRYTIHNGR 133

Query: 121 APLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P       +W      LD   MR A   ++G HDF+ F     + +    T+    V  
Sbjct: 134 RPNLFLSPWSWHRYQHRLDASRMRDALSTMLGLHDFSAFMKAGSRRAHARTTVQEVLVER 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ + + A  FL+  +R  +  L  VG+ + +    E+  + + R E    AP  GL
Sbjct: 194 QGDLLRVEIQASGFLYGMVRLLMAQLVAVGEHRLSVAAFEQRWRERRRHEVKEAAPATGL 253

Query: 240 YFDSVEY 246
                 Y
Sbjct: 254 CLLRAGY 260


>gi|260911484|ref|ZP_05918073.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 472 str.
           F0295]
 gi|260634413|gb|EEX52514.1| tRNA pseudouridine synthase A [Prevotella sp. oral taxon 472 str.
           F0295]
          Length = 244

 Score =  242 bits (619), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 77/246 (31%), Positives = 117/246 (47%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY +   Y+G+ Y GWQ Q N +S+Q  +++A+ L+    V + GAGRTD+GVHA   V
Sbjct: 3   QRYFIYFSYDGTAYHGWQIQPNANSVQAEMQRAMSLLLRHPVELVGAGRTDTGVHARTMV 62

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD       V L   LN  L     I+I  +  +D   HARFSA +R+Y Y +     
Sbjct: 63  AHFDEEEPIDTVQLTYKLNRVL--PFDITINQIKPIDGGLHARFSATKRTYHYYVHLD-- 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +  ++ + +  D + M  AAQ L+   DF  F   H  A + +  +         
Sbjct: 119 RDPFCRAYSYALHQVPDFQLMNDAAQILLSHKDFGAFCKSHSDAKTTLCDVYEARWIRLS 178

Query: 182 N-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           N     R+ A  FL   +R+ VG+L  VG  K +       L ++ R++ G   P   L+
Sbjct: 179 NTKWHFRISANRFLRNMVRAIVGTLLDVGWHKVSLEQFVDILHSKSRQQAGESVPGHALF 238

Query: 241 FDSVEY 246
            + V+Y
Sbjct: 239 LEDVQY 244


>gi|220903970|ref|YP_002479282.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219868269|gb|ACL48604.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 259

 Score =  242 bits (619), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 88/260 (33%), Positives = 127/260 (48%), Gaps = 17/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R  ++I Y G+GY GWQ Q+      ++QG++E A+  + G+ V VHG+GRTDSGVHA 
Sbjct: 1   MRLKLLISYVGTGYSGWQIQEKPKPPPTVQGALEAALRTIAGKAVRVHGSGRTDSGVHAH 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
            QVAH D+      +    +LNA L     I +L+ S     FHAR  A+R++Y Y+   
Sbjct: 61  GQVAHCDIPDTRAGLDWRHSLNAVL--PRDIRVLDASPAAPDFHARKDALRKTYAYQFWQ 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R+      +   W     LD + MR A   L+GRHDF   R+      S  RTI    +
Sbjct: 119 DRRFLPPHVRPYVWNC-GMLDLDAMRDALPFLLGRHDFAGLRNAGTDVESTERTIMDARL 177

Query: 178 N---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           +             ++ + + A  FL   +R+  G L   G GK     +   L A+DR+
Sbjct: 178 DALAPCEYYPPHAPMLRLTITADGFLKQMVRNVAGLLAACGQGKIQPAQIPALLAARDRQ 237

Query: 229 ECG-PLAPPEGLYFDSVEYS 247
                 APPEGL   SV+Y 
Sbjct: 238 AVPSVTAPPEGLALVSVKYP 257


>gi|311740028|ref|ZP_07713862.1| tRNA pseudouridine synthase A [Corynebacterium pseudogenitalium
           ATCC 33035]
 gi|311305101|gb|EFQ81170.1| tRNA pseudouridine synthase A [Corynebacterium pseudogenitalium
           ATCC 33035]
          Length = 297

 Score =  242 bits (619), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 125/262 (47%), Gaps = 20/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW +QK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 21  VRLRLDLAYDGTDFHGWAKQKGGLRTVQGVLEEKLAMIARTEVPLTVAGRTDAGVHARGQ 80

Query: 61  VAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+  E          P  L + L   L   + + +         F ARFSA+RR Y
Sbjct: 81  VAHVDVPTEMLAQRSVAGEPGKLVRRLAKLL--PEDVRVHGCEFAPAGFDARFSALRRHY 138

Query: 113 LYRIITRQAPLALEKGR--AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           +YRI T        + R  A  I K +D + M+ AA  LVG HDF  F      A + IR
Sbjct: 139 VYRITTNPRGALPTRARDTAEWI-KPVDIDAMQEAATALVGLHDFAAFCKAKPNA-TTIR 196

Query: 171 TIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F            L E RV A +F  + +RS VG    VG+G+  +      LQ  
Sbjct: 197 ELQEFSWRDASTPEEPELFEARVSADAFCWSMVRSLVGCCLRVGEGRRDADFAAALLQET 256

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    P+AP +GL   +V+Y 
Sbjct: 257 KRSSSIPVAPAKGLSLVAVDYP 278


>gi|255324781|ref|ZP_05365895.1| tRNA pseudouridine synthase A [Corynebacterium tuberculostearicum
           SK141]
 gi|255298256|gb|EET77559.1| tRNA pseudouridine synthase A [Corynebacterium tuberculostearicum
           SK141]
          Length = 297

 Score =  242 bits (618), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 125/262 (47%), Gaps = 20/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW +QK G  ++QG +E+ + ++    V +  AGRTD+GVHA  Q
Sbjct: 21  VRLRLDLAYDGTDFHGWAKQKGGLRTVQGVLEEKLAMIARTEVPLTVAGRTDAGVHARGQ 80

Query: 61  VAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+  E          P  L + L   L   + + +         F ARFSA+RR Y
Sbjct: 81  VAHVDVPTEMLAQRSVAGEPGKLVRRLAKLL--PEDVRVHGCEFAPAGFDARFSALRRHY 138

Query: 113 LYRIITRQAPLALEKGR--AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           +YRI T        + R  A  I K +D + M+ AA  LVG HDF  F      A + IR
Sbjct: 139 VYRITTNPRGALPTRARDTAEWI-KPVDIDAMQEAATALVGLHDFAAFCKAKPNA-TTIR 196

Query: 171 TIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F            L E RV A +F  + +RS VG    VG+G+  +      LQ  
Sbjct: 197 ELQEFSWRDVSTPEEPELYEARVSADAFCWSMVRSLVGCCLRVGEGRRDTDFAAALLQET 256

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    P+AP +GL   +V+Y 
Sbjct: 257 KRSSSIPVAPAKGLSLVAVDYP 278


>gi|312199990|ref|YP_004020051.1| tRNA pseudouridine synthase A [Frankia sp. EuI1c]
 gi|311231326|gb|ADP84181.1| tRNA pseudouridine synthase A [Frankia sp. EuI1c]
          Length = 297

 Score =  242 bits (618), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 82/249 (32%), Positives = 119/249 (47%), Gaps = 6/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQ 60
            R  + + Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTD+GVHA RQ
Sbjct: 29  QRLRIDLAYDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDAGVHAARQ 88

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+  E     L + LN  L     + IL +      F ARFSA+ R Y YRI    
Sbjct: 89  VAHVDIPDEVPLGGLARRLNGVL--DRAVRILGIGPAPVGFDARFSALSRRYNYRISDAP 146

Query: 121 A-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L +      P+ LD   MR+AA  L+G HDF  F     + ++ +RT+   DV  
Sbjct: 147 YGADPLRRHDTLAWPRPLDPAVMRLAALALLGEHDFAAFCRRR-EGATTVRTLLRLDVRR 205

Query: 180 FGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             + +    V A +F H+ +R+ VG+L  VG+G+     + + L    R     + P  G
Sbjct: 206 GPDGVLVADVEADAFCHSMVRALVGALVGVGEGRQPPGWIPQMLARAVRSPGVTVLPAHG 265

Query: 239 LYFDSVEYS 247
           L    V Y 
Sbjct: 266 LTLVEVRYP 274


>gi|42561874|ref|NP_172451.2| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|332190374|gb|AEE28495.1| tRNA pseudouridine synthase A [Arabidopsis thaliana]
          Length = 372

 Score =  242 bits (618), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 90/316 (28%), Positives = 145/316 (45%), Gaps = 70/316 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + G Q+Q    ++ G +++A     G+ V +  + RTD+GVHAL  V
Sbjct: 55  QRYLVAIEYIGTRFSGSQQQAKDRTVVGVLQEAFHKFIGQPVKIFCSSRTDAGVHALSNV 114

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  
Sbjct: 115 CHVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQE 174

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR+++   P   LEK R W +P+ L+   M+ A + LVG HDF++FR+  CQA SP
Sbjct: 175 RTYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEACRVLVGSHDFSSFRAAGCQAKSP 234

Query: 169 IRTIDHFDVNSFG---------------------------------------NLIEIRVV 189
           +R++D  ++                                             +E    
Sbjct: 235 MRSLDELNITEVPSTPYFPSITERTLSNLNNGDPLACSNQPKSETAGVTTNVGEVEGSTE 294

Query: 190 ARSF------------------LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
             SF                  L+ Q+R  VG+LK VG G+ T +D+E+ L+A+      
Sbjct: 295 GDSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAK 354

Query: 232 PLAPPEGLYFDSVEYS 247
           P+AP  GLY   V Y 
Sbjct: 355 PMAPASGLYLARVRYE 370


>gi|226496511|ref|NP_001146958.1| pseudouridylate synthase [Zea mays]
 gi|195605848|gb|ACG24754.1| pseudouridylate synthase [Zea mays]
          Length = 386

 Score =  242 bits (618), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 141/319 (44%), Gaps = 73/319 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G Q+Q N  ++ G +E+A     G+ V +  + RTD+GVHAL  V
Sbjct: 65  QRYLVAVEYIGTRFSGSQKQPNQRTVTGVLEEAFHRFIGQPVSIIFSSRTDAGVHALSNV 124

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L  S+  I + ++  V   FHAR+ ++ 
Sbjct: 125 CHVDVERISKRKPGEVLTPHEPGVVKRAVNHFLLKSEGDIMVTDVCCVAPDFHARYKSLE 184

Query: 110 RSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR++    +    EK   W I + LD ++M+ A   LVG HDF++FR+  CQA+SP
Sbjct: 185 RTYHYRLLAGPESTSVFEKNSVWHISEDLDIQSMKKACSILVGHHDFSSFRAAGCQANSP 244

Query: 169 IRTIDHFDVNSFGNLIEI------------------------------------------ 186
           +RT+D   V      +                                            
Sbjct: 245 VRTLDELSVTEVFPFMFFPSSVERSELELSNVSLVYSRKPDMESSGKGSDGSCTSSVKSD 304

Query: 187 ---------RVVARSF---------LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                    R   R F         L+ Q+R  VG LK VG G  T+ D+E+ L A+   
Sbjct: 305 FENGKDFGKRSRHRCFVVTARARSFLYHQVRLMVGLLKSVGTGDLTTADVERILDAKTVT 364

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               +AP  GLY  +V+Y 
Sbjct: 365 AAPSMAPSCGLYLANVKYD 383


>gi|307579643|gb|ADN63612.1| tRNA pseudouridine synthase A [Xylella fastidiosa subsp. fastidiosa
           GB514]
          Length = 256

 Score =  242 bits (617), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 128/248 (51%), Gaps = 5/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ Q    G S+Q ++++A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFLGWQ-QLGEMGPSVQATLQQALASVADSSVRVVCAGRTDAGVHGQC 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  ++++       + FHARFSA  R Y YR++ R
Sbjct: 60  QVVHFDSAVTRPPRAWI--LGTTTRLPSSVAVRWCVPTSEDFHARFSACARRYRYRLLNR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL+          LD + M +AAQ L+G +DF+ FRS  CQA    R +    V  
Sbjct: 118 QVRPALQHQFLSWERHPLDAQAMHVAAQMLLGENDFSAFRSAQCQALHARRELQAISVRR 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              +IEI V A +FLH  +R+ VGSL +VG G+     + + L  +DR   GP A   GL
Sbjct: 178 DAEVIEICVQANAFLHHMVRNIVGSLLMVGTGERPMEWIAELLAGRDRTMAGPTASARGL 237

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 238 VFVGPLYP 245


>gi|166712630|ref|ZP_02243837.1| tRNA pseudouridine synthase A [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 257

 Score =  242 bits (617), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 94/248 (37%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++         FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSIAVRWCVPTAADFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M +AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRPLDADAMHVAAQALLGENDFSAFRSVQCQALHARRNLQTIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 IGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIAMLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|21231977|ref|NP_637894.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66767896|ref|YP_242658.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|188991012|ref|YP_001903022.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. B100]
 gi|30913393|sp|Q8P7R5|TRUA_XANCP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|81306127|sp|Q4UWD5|TRUA_XANC8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|229470759|sp|B0RR81|TRUA_XANCB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21113710|gb|AAM41818.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66573228|gb|AAY48638.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|167732772|emb|CAP50966.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           campestris]
          Length = 257

 Score =  242 bits (617), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q +++ A+  V    + V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQATLQAALSSVADAPIQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  ++++       + FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSVAVRWCVPAAEDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M  AAQ L+G +DF  FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRPLDAQAMHTAAQALLGENDFGAFRSVQCQALHARRNLQAITVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+     +   L  +DR   GP APP+GL
Sbjct: 179 LGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPIDWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|19551801|ref|NP_599803.1| tRNA pseudouridine synthase A [Corynebacterium glutamicum ATCC
           13032]
 gi|62389456|ref|YP_224858.1| tRNA pseudouridine synthase A [Corynebacterium glutamicum ATCC
           13032]
 gi|41324790|emb|CAF19272.1| PROBABLE TRNA PSEUDOURIDINE SYNTHASE A PROTEIN [Corynebacterium
           glutamicum ATCC 13032]
          Length = 294

 Score =  242 bits (617), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 128/262 (48%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW +Q   +  ++Q  +E  + +V  E V +  AGRTD+GVHA  
Sbjct: 6   VRIRLDLAYDGTDFHGWAKQGTSDLRTVQKVLEDNLSMVLRETVELTVAGRTDAGVHAAG 65

Query: 60  QVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+             P  L + L   L   D I +  +   +  F ARFSA+RR 
Sbjct: 66  QVAHFDIPAHALEQRSIDGDPSKLVRRLGRLL--PDDIRVHGVRFAEPGFDARFSAMRRH 123

Query: 112 YLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YRI T  A  L   +      PK ++ E M++AA  L+G HDF  F      A + +R
Sbjct: 124 YVYRITTHPAGALPTRRHDTAQWPKPVELERMQLAADALLGLHDFVAFCKAKPHA-TTVR 182

Query: 171 TIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F            + E  VVA +F  + +RS VGS   VG+G+  S    + L A 
Sbjct: 183 ELQKFAWKDVSTDIEPQVYEAHVVADAFCWSMVRSLVGSCMAVGEGRRGSGFTAELLDAS 242

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R    P+AP +GL    V+Y 
Sbjct: 243 ERSPMVPVAPAKGLSLVGVDYP 264


>gi|269218953|ref|ZP_06162807.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 848 str.
           F0332]
 gi|269212064|gb|EEZ78404.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 848 str.
           F0332]
          Length = 310

 Score =  242 bits (617), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 79/263 (30%), Positives = 127/263 (48%), Gaps = 19/263 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW  Q    +++G++ +A+ L+TG    +  AGRTD+GVHA  QVA
Sbjct: 8   RLRLRMSYDGTDFHGWAVQPGLRTVEGTVTEALNLITGGSHALTVAGRTDAGVHARGQVA 67

Query: 63  HFDLVREW----------VPVILCKALNAYLKI-------SDTISILNLSIVDKQFHARF 105
           H D+                  + + L+A L         S  +++  +      F ARF
Sbjct: 68  HVDVSENELARAARRAGDPCQAIMRRLSALLARESPGPKGSSDVAVTGVDFAPAGFDARF 127

Query: 106 SAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y YR+    A    L +     + + LD E M  AA+ L G HDF ++     +
Sbjct: 128 SALSRTYSYRVCDDPARFDPLRRRDVLWLREPLDVEAMGAAARKLTGEHDFISYCKPR-E 186

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            ++ IR +    V   G L+E+   A +F H+ +R+ VGSL  VG G+       + L+ 
Sbjct: 187 GATTIRELLELKVERKGGLVEVTARADAFCHSMVRTLVGSLLKVGAGRRDEEWPARRLEE 246

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           + R     +APP  L  +SVEY 
Sbjct: 247 RSRNGEVAVAPPHPLTLESVEYP 269


>gi|331085203|ref|ZP_08334289.1| hypothetical protein HMPREF0987_00592 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330407986|gb|EGG87476.1| hypothetical protein HMPREF0987_00592 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 248

 Score =  242 bits (617), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 115/250 (46%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + +EY+GS Y GWQR   G   +++   I + +  +T E V +    RT+ GVHA
Sbjct: 1   MRNILLTLEYDGSRYQGWQRLGKGESTNTVSNKILEVLKKMTNEDVELFCGARTEVGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV +F    +   + +   +N YL     I++L++    ++FHA  +A  R YLYR+ 
Sbjct: 61  YGQVVNFKTTTDMTLLEIKHYMNRYL--PMDIAVLSVEEKPERFHASLNAKSRIYLYRVA 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P   ++   +   K  D E M+ AA  L G+HDF  F ++     S  + I + D+
Sbjct: 119 IAEVPSVFDRKYTYHSFKKPDTELMKQAALLLAGKHDFKKFSTVKKN-KSTEKEILNIDI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I+I + A  FLH   R  + +L  +G G     ++++               P+
Sbjct: 178 YEDLEEIQITLEATDFLHNMPRMILSTLLDIGLGIRRKEEIDEIFSPTSSTVASAPCDPK 237

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 238 GLYLQEVVYD 247


>gi|284035717|ref|YP_003385647.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
 gi|283815010|gb|ADB36848.1| tRNA pseudouridine synthase A [Spirosoma linguale DSM 74]
          Length = 252

 Score =  242 bits (617), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 120/248 (48%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ Y GWQ Q NG SIQ ++E A+    G+ V + G+GRTD+GVHA +Q 
Sbjct: 1   MRYFIELSYRGTAYHGWQTQANGISIQITLEAALSQRLGKPVYIMGSGRTDAGVHAKQQF 60

Query: 62  AHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD          L  +LN  L   + I+I  +  V  + HARFSAI R Y Y I  ++
Sbjct: 61  AHFDSEEPLDITESLIYSLNCML--PEDIAIHAIFPVSDKTHARFSAISRYYQYHITRQK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
              A +    +     L+ + M  A   L+   +F +F       +     ++      +
Sbjct: 119 --DAFQGTLTYHFRPQLNVDRMNEACTLLLRHTNFQSFSKARANVTHFHCQLEFAYWRYT 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + +   + A  FL   +R+ VG++  +G  + +    EK + A+DRK  G  AP  GL
Sbjct: 177 NVDCLTFHIKANRFLWGMVRTIVGTMLEIGQERMSLEQFEKIILARDRKIAGRAAPANGL 236

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 237 YLVEVGYP 244


>gi|167752124|ref|ZP_02424251.1| hypothetical protein ALIPUT_00366 [Alistipes putredinis DSM 17216]
 gi|167660365|gb|EDS04495.1| hypothetical protein ALIPUT_00366 [Alistipes putredinis DSM 17216]
          Length = 390

 Score =  241 bits (616), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 118/248 (47%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG  Y GWQRQ +  S+Q +IE AI  +  E +++ GAGRTD+GV+A   V
Sbjct: 126 MRYFIELRYNGGAYCGWQRQPDMPSVQQTIEGAISTLLREPILLTGAGRTDTGVNASYYV 185

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD       P  +   LN  L     I++  +  V    HARFSA  R Y Y I  R+
Sbjct: 186 AHFDTSSPVADPEQVVFKLNHML--PGDIAVSRIVPVAADAHARFSAREREYRYYIEPRK 243

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
            P    +  +W     LD   M  AA  L+   DFT+F  ++    + I  +   D    
Sbjct: 244 NP--FTRAASWQYYVPLDVAAMNRAADVLMEYEDFTSFAKLNSDNKTNICHLKRADWTVG 301

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +   + A  FL   +R+ VG+L  VG G++T       + ++D       AP +GL
Sbjct: 302 RDGTLCFTIRADRFLRNMVRAIVGTLVDVGRGRYTVEQFRDIVASRDLSRSSAGAPAQGL 361

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 362 FLSDVLYP 369


>gi|325661070|ref|ZP_08149697.1| hypothetical protein HMPREF0490_00430 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472577|gb|EGC75788.1| hypothetical protein HMPREF0490_00430 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 248

 Score =  241 bits (616), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 115/250 (46%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + +EY+GS Y GWQR   G   +++   I + +  +T E + +    RT+ GVHA
Sbjct: 1   MRNILLTLEYDGSRYQGWQRLGKGESTNTVSNKILEVLKKMTNEDIELFCGARTEVGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV +F    +   + +   +N YL     I++L++    ++FHA  +A  R YLYR+ 
Sbjct: 61  YGQVVNFKTTTDMTLLEIKHYMNRYL--PMDIAVLSVEEKPERFHASLNAKSRIYLYRVA 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P   ++   +   K  D E M+ AA  L G+HDF  F ++     S  + I + D+
Sbjct: 119 IAEVPSVFDRKYTYHSFKKPDTELMKQAALLLAGKHDFKKFSTVKKN-KSTEKEILNIDI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I+I + A  FLH   R  + +L  +G G     ++++               P+
Sbjct: 178 YEDLEEIQITLEATDFLHNMPRMILSTLLDIGLGIRRKEEIDEIFSPTSSTVASAPCDPK 237

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 238 GLYLQEVVYD 247


>gi|145294737|ref|YP_001137558.1| tRNA pseudouridine synthase A [Corynebacterium glutamicum R]
 gi|140844657|dbj|BAF53656.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 294

 Score =  241 bits (616), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 128/262 (48%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW +Q   +  ++Q  +E  + +V  E V +  AGRTD+GVHA  
Sbjct: 6   VRIRLDLAYDGTDFHGWAKQGTSDLRTVQKVLEDNLSMVLRETVELTVAGRTDAGVHAAG 65

Query: 60  QVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+             P  L + L   L   D I +  +   +  F ARFSA+RR 
Sbjct: 66  QVAHFDIPAHALEQRSIDGDPSKLVRRLGRLL--PDDIRVHGVRFAEPGFDARFSAMRRH 123

Query: 112 YLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YRI T  A  L   +      PK ++ E M++AA  L+G HDF  F      A + +R
Sbjct: 124 YVYRITTHPAGALPTRRHDTAQWPKPVELERMQLAADALLGLHDFVAFCKAKPHA-TTVR 182

Query: 171 TIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F            + E  VVA +F  + +RS VGS   VG+G+  S    + L A 
Sbjct: 183 ELQKFAWKDVSTDIEPQVYEAHVVADAFCWSMVRSLVGSCMAVGEGRRGSGFTTELLDAS 242

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R    P+AP +GL    V+Y 
Sbjct: 243 ERSPMVPVAPAKGLSLVGVDYP 264


>gi|300770580|ref|ZP_07080459.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33861]
 gi|300763056|gb|EFK59873.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33861]
          Length = 257

 Score =  241 bits (615), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 116/249 (46%), Gaps = 8/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + I Y G+ Y GWQ Q N  S+Q  +   +  +  + +   GAGRTD+GVHA +   
Sbjct: 7   RFFLEIAYQGTAYHGWQIQHNAVSVQEKLNDVLKTLLRKDIETIGAGRTDTGVHARQLFV 66

Query: 63  HFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           HFD + E     P     +LNA L     I++  L  VD Q HARF A  RSY Y +  +
Sbjct: 67  HFDAIPEGLLLQPDKFVHSLNALL--PHDIAVYRLLPVDDQAHARFDATSRSYEYHLHFK 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-N 178
           + P  +    +WL     D   M  A Q+L+GR DF  F   + Q  +    I   +   
Sbjct: 125 KDPFLINA--SWLTRDIPDVVKMNEACQYLLGRQDFECFSKSNTQVFTNFCDISRAEWLW 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +  + +   + A  FL   +R+ VG+L  +G        +++ + ++ R + G   P  G
Sbjct: 183 NTDDHLVFHISADRFLRNMVRAIVGTLLEIGLKGKEPVYIQEVIASKSRSKAGTSVPAHG 242

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 243 LYLTEVVYP 251


>gi|57867747|ref|YP_189363.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis RP62A]
 gi|293368464|ref|ZP_06615088.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|62901168|sp|Q5HM30|TRUA_STAEQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57638405|gb|AAW55193.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis RP62A]
 gi|291317422|gb|EFE57844.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329737018|gb|EGG73273.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU045]
          Length = 267

 Score =  241 bits (615), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 118/244 (48%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVNETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDKNRNNVPLTAPPDGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|294055498|ref|YP_003549156.1| tRNA pseudouridine synthase A [Coraliomargarita akajimensis DSM
           45221]
 gi|293614831|gb|ADE54986.1| tRNA pseudouridine synthase A [Coraliomargarita akajimensis DSM
           45221]
          Length = 250

 Score =  241 bits (615), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 6/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+  I  Y+G+ + GWQRQ+NG ++Q  +E A+  +    +  HG+GRTD+GVHA  Q 
Sbjct: 1   MRWKCICSYDGTDFEGWQRQRNGLAVQNVLEAALSQIFNLPLKTHGSGRTDAGVHARGQC 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD         L +AL++ L    ++ I  + +VD++FHAR SAI + Y+YR    +A
Sbjct: 61  FHFDGDWPHDTGKLIRALHSIL--PKSLRIERIDLVDERFHARHSAIGKRYVYRYHLGRA 118

Query: 122 PLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDVN 178
              LE+   W    + ++   M+ AA  LVG HDF+ + + H + S  +P++ +   D+ 
Sbjct: 119 -HPLEQRYVWACRDTAINFGAMQEAALRLVGTHDFSAYGATHGKDSDPNPVKNVYRLDLV 177

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I +      +L+  +RSF G+L  VG  + +  D+E+ L+++ R      AP  G
Sbjct: 178 KHGRQIILTTEGSGYLYRMVRSFAGALYSVGRDRLSPDDIEEILRSKIRTHRIVTAPGVG 237

Query: 239 LYFDSVEYS 247
           L  D V Y 
Sbjct: 238 LCLDEVFYP 246


>gi|94968472|ref|YP_590520.1| tRNA pseudouridine synthase A [Candidatus Koribacter versatilis
           Ellin345]
 gi|94550522|gb|ABF40446.1| tRNA pseudouridine synthase A [Candidatus Koribacter versatilis
           Ellin345]
          Length = 257

 Score =  241 bits (615), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 84/259 (32%), Positives = 119/259 (45%), Gaps = 15/259 (5%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R + + + Y+G  + GWQ Q    +IQG++ + I  +TGE  +  G+GRTD+GVHAL 
Sbjct: 1   MPRNFKITLAYDGHEFHGWQIQPGKPTIQGTLAETIERITGEQTLPQGSGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L        L  ALN  L    +I  L +      FHAR SA  ++Y YRI   
Sbjct: 61  QVASVALQTPIPADGLHIALNDKL--PPSIRALTVGEAAPDFHARHSAKGKTYRYRIYRA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS------------S 167
                      W  P  LD   M+ A   + G HDFT+F +     +            S
Sbjct: 119 AICSPFLAHYVWHYPWRLDESVMQSATAFIQGEHDFTSFAASDPDRAQRIRDAEDEDGPS 178

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            +RTI      + G+ +   V    FLH  +R+ VG+    G  +  +  + K L+ + R
Sbjct: 179 NVRTIYDAVWRTEGHELIFEVRGNGFLHHMVRNLVGTFVDFGKWQHPAESMAKILREKSR 238

Query: 228 KECGPLAPPEGLYFDSVEY 246
              GP AP  GLY  +VEY
Sbjct: 239 SAAGPAAPASGLYLVNVEY 257


>gi|210631184|ref|ZP_03296795.1| hypothetical protein COLSTE_00680 [Collinsella stercoris DSM 13279]
 gi|210160151|gb|EEA91122.1| hypothetical protein COLSTE_00680 [Collinsella stercoris DSM 13279]
          Length = 281

 Score =  241 bits (615), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 75/250 (30%), Positives = 111/250 (44%), Gaps = 10/250 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
             + Y+G+G+ G+  Q +  ++ G   +A+       + +  AGRTD+GVHA+ Q     
Sbjct: 26  FRLGYDGAGFSGFAEQPDVRTVAGEARRALETFLRRPIDMTCAGRTDAGVHAISQYVSVP 85

Query: 66  LVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
             RE          +A+ A L   D I++  +      F ARF A  R+Y YRI T  A 
Sbjct: 86  AHREELAIEHRRWMRAMAALL--PDDIALSGVYHAAPGFSARFDARSRTYTYRIATGDAR 143

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSF- 180
             L +   W     LD E M   A HLVG HDF +F  +         R +         
Sbjct: 144 PLLTRNVTWWHRLPLDVEAMEAGAVHLVGEHDFKSFCKMSSAVGKPTCRNVISVSFAREQ 203

Query: 181 ---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + +   +   +FLH+ +R+ VG+L  VG G+     + + L A DR+  GP AP  
Sbjct: 204 ALGEDHLAFTITGNAFLHSMVRTIVGTLVEVGAGRRDPAWVVEVLAACDRRAAGPTAPAR 263

Query: 238 GLYFDSVEYS 247
           GL F  V Y 
Sbjct: 264 GLCFMDVAYD 273


>gi|27468710|ref|NP_765347.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis ATCC
           12228]
 gi|32130291|sp|Q8CML6|TRUA_STAES RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|27316258|gb|AAO05433.1|AE016750_38 tRNA pseudouridine synthase A [Staphylococcus epidermidis ATCC
           12228]
 gi|329731249|gb|EGG67619.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU144]
          Length = 267

 Score =  241 bits (615), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 118/244 (48%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVNETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDKNRNNVPLTAPPDGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|237786326|ref|YP_002907031.1| tRNA pseudouridine synthase A [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237759238|gb|ACR18488.1| tRNA pseudouridine synthase A [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 298

 Score =  241 bits (615), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 88/260 (33%), Positives = 125/260 (48%), Gaps = 17/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ +  S+QG IE+A   V  + V +  AGRTD+GVHA  QV
Sbjct: 23  VRLRLDIAYDGTDFHGWARQNDVRSVQGDIEQAFQTVVRQPVQLVVAGRTDAGVHASGQV 82

Query: 62  AHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           AH D+ R           P  L       L+    + I   S     F ARFSA+RR Y+
Sbjct: 83  AHVDIPRGILNTRSIHNDPSTLVSRFARLLR--PDVRIRGCSFAPDGFDARFSALRRHYV 140

Query: 114 YRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+ T +A  L        +  + ++ ++M  AA+ LVG HDF  F      A + IR +
Sbjct: 141 YRVTTNRAGALPTRARDTAVWDRPVNLDSMNNAAEVLVGLHDFAAFCRARPHA-TTIRDL 199

Query: 173 DHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            HF  +        ++ E RV A +F    +RS VG+   VG+GK     +E  L    R
Sbjct: 200 QHFSWHEVSTAVEPDVYEARVTADAFCWNMVRSIVGASLAVGEGKRPDGFMEDMLAHDSR 259

Query: 228 KECGPLAPPEGLYFDSVEYS 247
               P+AP  GL    V+Y 
Sbjct: 260 HPMVPVAPANGLTLTGVDYP 279


>gi|221632949|ref|YP_002522172.1| tRNA pseudouridine synthase A [Thermomicrobium roseum DSM 5159]
 gi|221155520|gb|ACM04647.1| tRNA pseudouridine synthase A [Thermomicrobium roseum DSM 5159]
          Length = 279

 Score =  241 bits (615), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 87/260 (33%), Positives = 129/260 (49%), Gaps = 16/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY +   Y G+ + G QRQ    ++QG +E+A+  + GE V V  AGRTD+GVHA+ QV
Sbjct: 4   QRYRLDFGYEGTAFSGSQRQPGLRTVQGVLEEALARLAGEPVRVALAGRTDAGVHAVGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A FDL        L +AL A+L   + + +  ++ +   FHAR  A+ R Y YRI   + 
Sbjct: 64  ASFDLCWRHDEATLARALQAWL--PEDVVVYRVARMPAGFHARRGAVDREYRYRIWQGEQ 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI---HCQASSP-IRTIDHFDV 177
           P    +   W     LD   M+ AAQ  +G HDF +F        +A++P +RTI   + 
Sbjct: 122 PPLFLRRFVWRFAGLLDLRAMQEAAQFFLGSHDFRSFAGHGLGGPKATTPRVRTITMAEW 181

Query: 178 N----------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           +          +   ++E RV A  FL   +R+ V +L  VG G    + + + L+  DR
Sbjct: 182 HLLSPVVEPVGTGAQIVEFRVRANGFLPQMVRTMVSALVRVGTGAAEPSWISELLERCDR 241

Query: 228 KECGPLAPPEGLYFDSVEYS 247
           +   P APP GL    V Y 
Sbjct: 242 RAAPPPAPPGGLVLWRVRYP 261


>gi|239980027|ref|ZP_04702551.1| tRNA pseudouridine synthase A [Streptomyces albus J1074]
          Length = 295

 Score =  241 bits (615), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 80/253 (31%), Positives = 112/253 (44%), Gaps = 8/253 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHA 57
           +R  + + Y+G  + GW +Q     ++QG IE A+  VT        +  AGRTDSGVHA
Sbjct: 19  VRVRLDLSYDGRDFSGWAKQAAGRRTVQGEIEDALRTVTRSGERTYELTVAGRTDSGVHA 78

Query: 58  LRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             QVAH DL          K L     ++   + I  ++     F ARFSA+ R Y YR+
Sbjct: 79  RGQVAHVDLPAAVWEEHREKLLRRLAGRLPHDVRIWRVAEAPAGFDARFSAVWRRYAYRV 138

Query: 117 ITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                    L +G       +LD E M  A+  L+G HDF  +     + ++ IRT+   
Sbjct: 139 TDHPGGVDPLLRGHVLWHDWTLDVEAMNAASVALLGEHDFAAYCKRR-EGATTIRTLQEL 197

Query: 176 DVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                 + I    V A +F H  +RS VG+L  VGDG        K L A  R     + 
Sbjct: 198 SWERDRDGIVTATVRADAFCHNMVRSLVGALLFVGDGHRPVEWPGKVLAAGVRDSAVHVV 257

Query: 235 PPEGLYFDSVEYS 247
            P GL  + V Y 
Sbjct: 258 RPHGLTLEEVGYP 270


>gi|70725835|ref|YP_252749.1| tRNA pseudouridine synthase A [Staphylococcus haemolyticus
           JCSC1435]
 gi|123735013|sp|Q4L882|TRUA_STAHJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|68446559|dbj|BAE04143.1| tRNA pseudouridine synthase A [Staphylococcus haemolyticus
           JCSC1435]
          Length = 267

 Score =  241 bits (615), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 114/244 (46%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y GS + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA  Q 
Sbjct: 1   MRILVNISYQGSQFLGFQIQQQGRTVQQQFEKILKRMHRRHVRIHPSSRTDRGVHAYEQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P     A+N+ L   D I +  +  VD  FH R+  + + Y Y++     
Sbjct: 61  FHFDTDLNIEPKQWKYAMNSAL--PDDIYVKEVQQVDDHFHCRYDCLGKRYRYKVYQATH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E G    I + L+   M  AA+H +G HDFT F S   +  S +RT+   ++    
Sbjct: 119 RNPFESGLKTFIKEDLNYSKMNEAAKHFIGTHDFTGFCSQKTEVESKVRTLYQSEIIQTD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK  ++++   L  ++R      AP EGLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKRHASEVSTLLNEKNRDSVPFTAPAEGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|313157719|gb|EFR57130.1| tRNA pseudouridine synthase A [Alistipes sp. HGB5]
          Length = 257

 Score =  241 bits (615), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 124/248 (50%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG+ Y GWQRQ +  S+Q ++E+A+  +  E + V GAGRTD+GV+A   V
Sbjct: 4   MRYFLELRYNGAAYCGWQRQPDMPSVQQTLERALTTLLREKIEVTGAGRTDTGVNASYYV 63

Query: 62  AHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD       P  +   LN  L     I++ +++ V    HARF+A  R Y Y I  R+
Sbjct: 64  AHFDCEEPVPDPAQVVYKLNFLL--PGDIAVGSMTPVGADAHARFAAREREYRYYIEPRK 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   W     LD E M  AA  L+   DFT+F  ++    + I  I H    + 
Sbjct: 122 NP--FTRDATWQYYVPLDMERMNEAAASLLEYDDFTSFAKLNSNNKTNICRIMHAAWTAD 179

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              ++   + A  FL   +RS VG+L  VG G++T     + + ++D       AP +GL
Sbjct: 180 ERGVLCFTIRADRFLRNMVRSLVGTLVDVGRGRYTPDGFREIVGSRDLSRSSGGAPAQGL 239

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 240 FLSDVVYP 247


>gi|294340919|emb|CAZ89314.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) (PSU-I) [Thiomonas sp. 3As]
          Length = 257

 Score =  240 bits (614), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 85/243 (34%), Positives = 131/243 (53%), Gaps = 3/243 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M + Y G+ Y GWQ Q  G  +Q  +E+A+    G       AGRTD+GVHAL QV H D
Sbjct: 1   MGLSYGGTSYCGWQSQPGGCGVQDFLERALAQFLGFPTRTVCAGRTDAGVHALGQVVHLD 60

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLS-IVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              +  P    + +NA+L     +++      + + F AR SA +R Y Y +       A
Sbjct: 61  TPLQREPSSWVRGVNAFL--PRDMAVQWARTDLPQTFDARRSAYQRRYRYVLRNHPVRPA 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L+  +     + LD + +R+AAQ L+G HDF+ FRS  CQA SP++T+   ++   G+ +
Sbjct: 119 LDFAKVGWTHRPLDLDLLRLAAQCLLGEHDFSAFRSSECQALSPVKTLHAIEIARHGHTL 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            + + A +FLH  +R+ VGSL  VG+G    + L + L ++DR+   P   P+GLYF   
Sbjct: 179 VLDLRANAFLHHMVRNIVGSLLAVGNGSKPVSWLAEVLASRDRRLAAPTFMPDGLYFLGP 238

Query: 245 EYS 247
           +Y 
Sbjct: 239 DYP 241


>gi|119718091|ref|YP_925056.1| tRNA pseudouridine synthase A [Nocardioides sp. JS614]
 gi|119538752|gb|ABL83369.1| tRNA pseudouridine synthase A [Nocardioides sp. JS614]
          Length = 268

 Score =  240 bits (614), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 77/251 (30%), Positives = 114/251 (45%), Gaps = 8/251 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW  Q    ++QG +  A+  V     V V  AGRTD+GVHA  Q
Sbjct: 1   MRIRLDLAYDGTDFHGWASQPGLRTVQGELSDALATVLRVPEVAVVCAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVI--LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V H DL       +  L + LN  L     + +         F ARF A+ R Y YRI  
Sbjct: 61  VVHADLDGLEPATVEGLVRRLNGRL--PADVRVRRAVEAPAGFDARFGALWRRYAYRIAD 118

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             A    L +      P++LD + M  A+  LVGRHDF +F     + ++ IRT+     
Sbjct: 119 TPAVVDPLTRSHVLAWPRALDLDAMNAASAFLVGRHDFASFCKQR-EGATTIRTLLELSW 177

Query: 178 NSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                 ++   V A +F H+ +RS VG L  VG+ +      E  L+A+ R     +   
Sbjct: 178 ARDPAGVLVGTVRADAFCHSMVRSLVGCLIAVGEARKPVAWAEDILRAEARDPAVAVVHA 237

Query: 237 EGLYFDSVEYS 247
            GL  + V Y 
Sbjct: 238 HGLTLEEVAYP 248


>gi|289805625|ref|ZP_06536254.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 225

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 73/210 (34%), Positives = 106/210 (50%), Gaps = 2/210 (0%)

Query: 38  VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV 97
           +  E + V  AGRTD+GVH   QV HF+             +NA L     I++  +  V
Sbjct: 1   MANEPINVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANL--PGDIAVRWVKTV 58

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
              FHARFSA  R Y Y I   +   A+         + LD E M  AAQ L+G +DFT+
Sbjct: 59  PDDFHARFSATARRYRYIIYNHRLRPAVLAKGVTHYYEPLDAERMHRAAQCLLGENDFTS 118

Query: 158 FRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           FR++ CQ+ +P R + H +V   G  + + + A +F+H  +R+ VGSL  VG      + 
Sbjct: 119 FRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLLEVGAHNQPESW 178

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + + L A+DR      A  EGLY  +V+Y 
Sbjct: 179 IAELLAARDRTLAAATAKAEGLYLVAVDYP 208


>gi|291451884|ref|ZP_06591274.1| tRNA pseudouridine synthase A [Streptomyces albus J1074]
 gi|291354833|gb|EFE81735.1| tRNA pseudouridine synthase A [Streptomyces albus J1074]
          Length = 287

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 80/253 (31%), Positives = 112/253 (44%), Gaps = 8/253 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHA 57
           +R  + + Y+G  + GW +Q     ++QG IE A+  VT        +  AGRTDSGVHA
Sbjct: 11  VRVRLDLSYDGRDFSGWAKQAAGRRTVQGEIEDALRTVTRSGERTYELTVAGRTDSGVHA 70

Query: 58  LRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             QVAH DL          K L     ++   + I  ++     F ARFSA+ R Y YR+
Sbjct: 71  RGQVAHVDLPAAVWEEHREKLLRRLAGRLPHDVRIWRVAEAPAGFDARFSAVWRRYAYRV 130

Query: 117 ITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                    L +G       +LD E M  A+  L+G HDF  +     + ++ IRT+   
Sbjct: 131 TDHPGGVDPLLRGHVLWHDWTLDVEAMNAASVALLGEHDFAAYCKRR-EGATTIRTLQEL 189

Query: 176 DVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                 + I    V A +F H  +RS VG+L  VGDG        K L A  R     + 
Sbjct: 190 SWERDRDGIVTATVRADAFCHNMVRSLVGALLFVGDGHRPVEWPGKVLAAGVRDSAVHVV 249

Query: 235 PPEGLYFDSVEYS 247
            P GL  + V Y 
Sbjct: 250 RPHGLTLEEVGYP 262


>gi|319400595|gb|EFV88820.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis FRI909]
          Length = 267

 Score =  240 bits (613), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 118/244 (48%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVYETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDRNRNNVPLTAPPDGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|329945764|ref|ZP_08293451.1| putative tRNA pseudouridine synthase A [Actinomyces sp. oral taxon
           170 str. F0386]
 gi|328528212|gb|EGF55190.1| putative tRNA pseudouridine synthase A [Actinomyces sp. oral taxon
           170 str. F0386]
          Length = 308

 Score =  240 bits (613), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 82/276 (29%), Positives = 126/276 (45%), Gaps = 30/276 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GW  Q    +++G +  A+  V  E V +  AGRTD+GVHA  Q
Sbjct: 14  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTSALATVLREPVRLAVAGRTDAGVHAAAQ 73

Query: 61  VAHFDL-VREWVP-----VILCKA-----------------LNAYLKISDTISILNLSIV 97
           V H D+    W         L +A                 L    + +  + +    IV
Sbjct: 74  VVHLDVSPEAWAALPGRSDRLPEAALLTRMAGVLAREAQTSLPRTPRGAGDVVVTGARIV 133

Query: 98  DKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            + F ARF A+ R Y YRI    AP     +     +P  LD E M  +A+ L+G HDF 
Sbjct: 134 PEAFDARFGALSRRYTYRIADADAPRNPARRATVLWLPDRLDVEAMEASAKPLLGEHDFL 193

Query: 157 TFRSIHCQASSPIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           ++     Q ++ IRT+   +           L+ + VVA +F H+ +RS VG+   VG G
Sbjct: 194 SYCKPR-QGATTIRTLRALEWRRVAAGPDAGLVTLSVVADAFCHSMVRSLVGAGLAVGQG 252

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  +   ++ L A+ R    P+APP GL  + V Y 
Sbjct: 253 RRPAAWPDELLAARSRDGAAPVAPPHGLTLEEVVYP 288


>gi|317505831|ref|ZP_07963676.1| tRNA pseudouridine synthase [Segniliparus rugosus ATCC BAA-974]
 gi|316255913|gb|EFV15138.1| tRNA pseudouridine synthase [Segniliparus rugosus ATCC BAA-974]
          Length = 293

 Score =  240 bits (613), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 81/252 (32%), Positives = 114/252 (45%), Gaps = 9/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ    ++ G+IE A+  +      +  AGRTDSGVHA  QV
Sbjct: 21  VRLRLDIAYDGTEFSGWARQPGRRTVAGTIEAALGRLFQAPAQLTVAGRTDSGVHATGQV 80

Query: 62  AHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AH D+          P  L + L   L     + +L    V KQF ARFSA+RR Y Y+I
Sbjct: 81  AHVDVSAELVSGRLPPDKLVRKLARML--PSDVRVLAAREVSKQFDARFSALRRHYRYQI 138

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                    L         + LD   +  A+  LVG HDF  F       S+ IR +  F
Sbjct: 139 TRAPHGADPLRAREVVPWGRPLDLGLLNAASAALVGLHDFAAFCRPRP-GSTTIRELQRF 197

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D    G L+  R+ A +F  +  RS +G++  V +G+         L A  R     +AP
Sbjct: 198 DWTEDGPLLTARISADAFCWSMCRSLIGAVTAVAEGRREPGWAAALLTAPSRSSEIAVAP 257

Query: 236 PEGLYFDSVEYS 247
             GL    V+Y 
Sbjct: 258 GHGLCLTGVDYP 269


>gi|303247874|ref|ZP_07334142.1| tRNA pseudouridine synthase A [Desulfovibrio fructosovorans JJ]
 gi|302490775|gb|EFL50676.1| tRNA pseudouridine synthase A [Desulfovibrio fructosovorans JJ]
          Length = 265

 Score =  240 bits (613), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 125/253 (49%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+G+ + GWQ Q  G   ++QG +E+A+  + GE   VHGAGRTD+GVHA+
Sbjct: 1   MTRVRLTVAYDGTRFAGWQLQAPGMGRTVQGCLEEALARLCGEAARVHGAGRTDAGVHAV 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   +ALNA L   D +S+++ ++V   FHARF A  + Y Y + T
Sbjct: 61  AQVAHVDVPEARAGLPWQRALNALL--PDDVSVVDAAVVPPDFHARFDASGKIYQYTLWT 118

Query: 119 RQ-APLALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           R  + L   +   W + +   LD   M   A    G HDF  F++      +  R +   
Sbjct: 119 RPGSILPWRRPYVWDVGRFSPLDVAAMDACAALFAGYHDFAAFQNAGSSVKTSTRLVHGV 178

Query: 176 DV--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                +  + +  R  A  FL   +R+ +G+L  VG GK    D+   L    R+     
Sbjct: 179 SRLPQANSDEMVWRFHAEGFLKQMVRNLMGALVEVGRGKAAPEDIRSVLTLGQRRHAPRT 238

Query: 234 APPEGLYFDSVEY 246
           AP  GL   +VEY
Sbjct: 239 APAGGLCLMAVEY 251


>gi|251812078|ref|ZP_04826551.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|282875373|ref|ZP_06284246.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis SK135]
 gi|251804412|gb|EES57069.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|281296138|gb|EFA88659.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis SK135]
 gi|329736438|gb|EGG72706.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis VCU028]
          Length = 267

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 118/244 (48%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+   ++ +  
Sbjct: 119 RNPFKSGTETFVYETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 KGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDKNRNNVPLTAPPDGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|291515704|emb|CBK64914.1| pseudouridylate synthase I [Alistipes shahii WAL 8301]
          Length = 259

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 119/248 (47%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + YNG+ Y GWQRQ +  S+Q ++E+A+  +  E V + GAGRTD+GV+A   V
Sbjct: 1   MRYFLELRYNGAAYCGWQRQPDQPSVQQTLERALATLLREPVALTGAGRTDTGVNAAYYV 60

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHFD  R    P      LN  L     I++ +++ V +  HARF A  R Y Y I  R+
Sbjct: 61  AHFDCERPVADPAQTVYKLNFLL--PGDIAVGSMTPVAEDAHARFHAREREYRYFIEPRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-S 179
            P    +   W     LD   M  AA  L    DFT+F  ++    + I  +        
Sbjct: 119 NP--FTRHETWQYYVPLDVGRMNEAAAMLTAYDDFTSFAKLNSNNKTNICRVKEAVWTID 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +   + A  FL   +RS VG+L  VG G++T       ++++D       AP +GL
Sbjct: 177 SRGTMCFTIRADRFLRNMVRSLVGTLVDVGRGRYTPDGFRSIVESRDLSRSSAGAPAQGL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLSDVVYP 244


>gi|297564067|ref|YP_003683040.1| tRNA pseudouridine synthase A [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296848516|gb|ADH70534.1| tRNA pseudouridine synthase A [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
          Length = 279

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 112/250 (44%), Gaps = 5/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW  Q    ++QG +E A+  V     V +  AGRTD+GVHA  Q
Sbjct: 6   VRVRLDVAYDGTDFSGWAAQPGRRTVQGELEAALARVLRLPEVSLTCAGRTDAGVHARGQ 65

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA  D+          + L      +   + +    +    F ARFS + R YLYR+   
Sbjct: 66  VAQADIPARTWESEGERVLRRLAGVLPKDVRVRAARLAPPGFDARFSPLFRRYLYRVSDA 125

Query: 120 QAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 L +         LD + M  AA+ LVG HDF  F     + ++ IR +   +  
Sbjct: 126 PYGVDPLLRRDVLWHRSPLDVDRMNAAAERLVGEHDFAAFCKRR-EGATTIRELLRLEWT 184

Query: 179 S-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               +L+   + A +F H  +R+ VG+L  VGDG+  +    K L A  R     +  P+
Sbjct: 185 RVDEHLLHGTIQADAFCHNMVRALVGALLAVGDGRRDADWPGKVLGAGTRDSSVHVVGPQ 244

Query: 238 GLYFDSVEYS 247
           GL  + V Y 
Sbjct: 245 GLSLEEVRYP 254


>gi|46931324|gb|AAT06466.1| At1g09800 [Arabidopsis thaliana]
          Length = 372

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 90/316 (28%), Positives = 142/316 (44%), Gaps = 70/316 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + G Q+Q    ++ G +++A     G+ V +  + RTD+GVHAL  V
Sbjct: 55  QRYLVAIEYIGTRFSGSQQQAKDRTVVGVLQEAFHKFIGQPVKIFCSSRTDAGVHALSNV 114

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  
Sbjct: 115 CHVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQE 174

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS- 167
           R+Y YR+++   P   LEK R W +P+ L+   M+ A + LVG HDF++FR+  CQA S 
Sbjct: 175 RTYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEACRVLVGSHDFSSFRAAGCQAKSP 234

Query: 168 ---------------------PIRTI---------------------------------- 172
                                  RT+                                  
Sbjct: 235 MRSLDELNITEVPSTPYFPSITERTLSNLNNGDPLACSNQPKSETAGVTTNVGEVEGSTG 294

Query: 173 -DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
            D F          +   +R FL+ Q+R  VG+LK VG G+ T +D+E+ L+A+      
Sbjct: 295 GDSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAK 354

Query: 232 PLAPPEGLYFDSVEYS 247
           P+AP  GLY   V Y 
Sbjct: 355 PMAPASGLYLARVRYE 370


>gi|327398248|ref|YP_004339117.1| tRNA pseudouridine synthase A [Hippea maritima DSM 10411]
 gi|327180877|gb|AEA33058.1| tRNA pseudouridine synthase A [Hippea maritima DSM 10411]
          Length = 241

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 116/245 (47%), Gaps = 4/245 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RYC  I Y+G+ Y G+Q Q +  ++QG IEKA+  +    + ++ AGRTD+GVHA  QV
Sbjct: 1   MRYCACIAYDGTNYSGFQIQPDVKTVQGEIEKALKRIFKTDLRINFAGRTDAGVHAFEQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F ++ +     L KALN+ L   + I I ++ IVD  FH+R+SA  R Y+Y     + 
Sbjct: 61  IDFPVIADIETYSLKKALNSVL--PEDIRIKSVKIVDNSFHSRYSAKFREYVYFAFDGEY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                    W +   LD + MR+A++  VG  DF +F +   +  +  R +    +  + 
Sbjct: 119 LPPFLCRYVWHVKFKLDVDAMRLASRLFVGYKDF-SFVANEPEGKNCTREVYFLRIKRYR 177

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   + A  FL   +R+ VG L                + ++        AP  GL+ 
Sbjct: 178 EFVVFHIRAGGFLRGMVRNIVGLLVGYSANALQIDKSGNIIFSRG-NLKSFKAPACGLFL 236

Query: 242 DSVEY 246
             V Y
Sbjct: 237 RRVAY 241


>gi|257784931|ref|YP_003180148.1| tRNA pseudouridine synthase A [Atopobium parvulum DSM 20469]
 gi|257473438|gb|ACV51557.1| tRNA pseudouridine synthase A [Atopobium parvulum DSM 20469]
          Length = 294

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 113/250 (45%), Gaps = 10/250 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y G+ + G+  Q    S+ G + +A+  V    V +  AGRTD+GVHA  Q     
Sbjct: 40  IKLGYRGAAFCGFAEQPTQRSVAGDLRRALETVLRREVELTCAGRTDAGVHAQVQYVSLP 99

Query: 66  L---VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +      +    L ++L A     D ISI  L    + F ARF A  RSY YRI    A 
Sbjct: 100 VYDADLSFSGEKLVRSLTAL--TDDDISIRQLFRAPQGFSARFDAQARSYRYRICADSAR 157

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSFG 181
             L     W     LD + M  AAQ LVG HDF +F      +     R ++   V    
Sbjct: 158 PILGWDHVWWYNGHLDADLMDKAAQALVGEHDFKSFCKAISAEGKPTHRFVERLSVEEIE 217

Query: 182 N----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                LI + +   +FLH  +R+ VG+L  +G G      +++ L A++R   G  AP +
Sbjct: 218 EAGEKLIAVDITGNAFLHNMVRTIVGTLVEIGRGHRPVEWIDEVLAAKNRIAAGSCAPAQ 277

Query: 238 GLYFDSVEYS 247
           GL F +V Y 
Sbjct: 278 GLTFVNVRYP 287


>gi|94984145|ref|YP_603509.1| tRNA pseudouridine synthase A [Deinococcus geothermalis DSM 11300]
 gi|94554426|gb|ABF44340.1| tRNA pseudouridine synthase A [Deinococcus geothermalis DSM 11300]
          Length = 266

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 124/252 (49%), Gaps = 11/252 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  +++ ++G+ + GWQ Q++  S+Q ++  A+  +T E      AGRTD+GVHA    
Sbjct: 14  RRLRLLLAWDGTDFAGWQAQRDVPSVQDTLYAALLRLTEEAARPVAAGRTDAGVHAEAMP 73

Query: 62  AHFDLVR--EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AH D+ +        L +ALNA+L    ++++L        FHARFS   R Y YR++  
Sbjct: 74  AHVDVPQSFRIPAKKLARALNAHL--PPSVAVLEAEEAPTGFHARFSCTERRYTYRLLNT 131

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
                L +GRA  +P +LD   M  AA  L+G HDF  F +   +    +R +    V+ 
Sbjct: 132 PQRHPLWRGRALHVPGALDVPAMNAAAACLLGTHDFAAFATR--EDRQTVRELRALAVHP 189

Query: 179 ----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                 G + E+RV   SFL   +R  VG+L LVG GK    D+   L  ++R   G   
Sbjct: 190 GPVVPGGRIWEVRVAGESFLRQMVRGLVGTLLLVGQGKLGQEDVTAVLVGRERARAGANV 249

Query: 235 PPEGLYFDSVEY 246
           P  GL F    Y
Sbjct: 250 PGYGLTFTGASY 261


>gi|242243978|ref|ZP_04798421.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis W23144]
 gi|242232611|gb|EES34923.1| tRNA pseudouridine synthase A [Staphylococcus epidermidis W23144]
          Length = 267

 Score =  239 bits (611), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 117/244 (47%), Gaps = 2/244 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y G+ + G+Q Q+ G ++Q   EK +  +    V +H + RTD GVHA +Q 
Sbjct: 1   MRILVEIAYQGNQFLGFQIQQQGRTVQQQFEKILKRMHKHHVRIHPSSRTDRGVHAYQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD            A+N  L   D I + N+  VD+ FH R+  + + Y Y++     
Sbjct: 61  FHFDTELNIDNKQWQYAMNRAL--PDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               + G    + ++LD + M  AAQ  +G HDFT F S   +  S +RT+    + +  
Sbjct: 119 RNPFKSGTETFVYETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSKIVATK 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
              +  V    FL+  +R  V  L  VG GK    D+ K L+ ++R      APP+GLY 
Sbjct: 179 EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDRNRNNVPLTAPPDGLYL 238

Query: 242 DSVE 245
           + + 
Sbjct: 239 EKIY 242


>gi|227539074|ref|ZP_03969123.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33300]
 gi|227241078|gb|EEI91093.1| tRNA-pseudouridine synthase I [Sphingobacterium spiritivorum ATCC
           33300]
          Length = 257

 Score =  239 bits (611), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 115/249 (46%), Gaps = 8/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + I Y G+ Y GWQ Q N  S+Q  +   +  +  + +   GAGRTD+GVHA +   
Sbjct: 7   RFFLEIAYQGTAYHGWQIQHNAVSVQEKLNDVLKTLLRKDIETIGAGRTDTGVHARQLFV 66

Query: 63  HFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           HFD + E     P     +LNA L     I++  L  V  + HARF A  RSY Y +  +
Sbjct: 67  HFDAIPEGLLLQPDKFVHSLNALL--PHDIAVYRLLPVVDEAHARFDATSRSYEYHLHFK 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-N 178
           + P  +    +WL     D   M  A Q+L+GR DF  F   + Q  +    I   +   
Sbjct: 125 KDPFLIHA--SWLTRDIPDVAKMNEACQYLLGRQDFECFSKSNTQVFTNFCDISRAEWLW 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +  + +   + A  FL   +R+ VG+L  +G        +++ + ++ R + G   P  G
Sbjct: 183 NTDDHLVFHISADRFLRNMVRAIVGTLLEIGLKGKEPVYIQEVIASKSRSKAGTSVPAHG 242

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 243 LYLTEVVYP 251


>gi|51971559|dbj|BAD44444.1| unnamed protein product [Arabidopsis thaliana]
 gi|51971573|dbj|BAD44451.1| unnamed protein product [Arabidopsis thaliana]
          Length = 368

 Score =  239 bits (611), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 90/316 (28%), Positives = 142/316 (44%), Gaps = 70/316 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + G Q+Q    ++ G +++A     G+ V +  + RTD+GVHAL  V
Sbjct: 51  QRYLVAIEYIGTRFSGSQQQAKDRTVVGVLQEAFHKFIGQPVKIFCSSRTDAGVHALSNV 110

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  
Sbjct: 111 CHVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQE 170

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS- 167
           R+Y YR+++   P   LEK R W +P+ L+   M+ A + LVG HDF++FR+  CQA S 
Sbjct: 171 RTYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEACRVLVGSHDFSSFRAAGCQAKSP 230

Query: 168 ---------------------PIRTI---------------------------------- 172
                                  RT+                                  
Sbjct: 231 MRSLDELNITEVPSTPYFPSITERTLSNLNNGDPLACSNQPKSETAGVTTNVGEVEGSTG 290

Query: 173 -DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
            D F          +   +R FL+ Q+R  VG+LK VG G+ T +D+E+ L+A+      
Sbjct: 291 GDSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAK 350

Query: 232 PLAPPEGLYFDSVEYS 247
           P+AP  GLY   V Y 
Sbjct: 351 PMAPASGLYLARVRYE 366


>gi|332300500|ref|YP_004442421.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica DSM
           20707]
 gi|332177563|gb|AEE13253.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica DSM
           20707]
          Length = 262

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 80/252 (31%), Positives = 119/252 (47%), Gaps = 10/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ Y GWQ Q  G S+Q  +E+A+ ++  + + V GAGRTD+GVHA   +
Sbjct: 6   QRVFLEVAYDGTNYCGWQVQPRGVSVQSELERALSMLFRQSISVTGAGRTDAGVHAYSMM 65

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH DL     P+  + + L   L+    IS+ +++ V    HARF A  R Y Y I    
Sbjct: 66  AHADLPIPHPPLAQIQRGLCGILR--GGISVRSVTPVIPTAHARFDATSRRYHYYISACS 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P        W      D   M  A +H +G HDFT+F  +H Q      T+        
Sbjct: 124 NP--FWSDYCWERRTLPDMALMNEACRHFIGEHDFTSFSKLHTQTKHNRCTVYTAHWEQV 181

Query: 181 G-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +   V A  FLH  +R+ VG+L  VG G+ T   + + +Q++DR   G  AP
Sbjct: 182 EMPGLWDAMRYEVCANRFLHGMVRTMVGTLLEVGYGQRTPDSIAELIQSEDRSLAGSAAP 241

Query: 236 PEGLYFDSVEYS 247
              L+F    Y 
Sbjct: 242 ARALFFVEATYP 253


>gi|21673806|ref|NP_661871.1| tRNA pseudouridine synthase A [Chlorobium tepidum TLS]
 gi|42559829|sp|Q8KDR7|TRUA_CHLTE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21646936|gb|AAM72213.1| tRNA pseudouridine synthase A [Chlorobium tepidum TLS]
          Length = 247

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 82/251 (32%), Positives = 112/251 (44%), Gaps = 9/251 (3%)

Query: 1   MIR----YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R      M IEY+G+GY GWQRQ  +  ++QG IE+ +  +  E V + GAGRTDSGV
Sbjct: 1   MARSKRTIKMQIEYDGTGYSGWQRQPGDVVTVQGEIERVLERIMQEPVSIDGAGRTDSGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA RQVA F          L  + N+ L    TI I  +    + FHARFSA  R Y Y 
Sbjct: 61  HARRQVASFATCSPMPLGRLIYSANSLL--PSTIRINAMRQAPESFHARFSATSREYRYF 118

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++  + P A++   A       D   M   A  L+G HDF  F          + T+   
Sbjct: 119 LL--EHPSAIDSRFAGCSHGKPDVGAMNRLALMLIGTHDFAAFSKETPDQYGTLCTVTAA 176

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G     R+ A  FL + +R  V  +  VG G+       + L++  R      A 
Sbjct: 177 RWYRSGRFHVFRIEANRFLRSMVRFLVAGMIEVGMGRLEEGAFARMLESGHRPPKLKPAD 236

Query: 236 PEGLYFDSVEY 246
             GL+   V Y
Sbjct: 237 AAGLFLWKVRY 247


>gi|78357749|ref|YP_389198.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|123754841|sp|Q30XU3|TRUA_DESDG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78220154|gb|ABB39503.1| tRNA pseudouridine synthase A [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
          Length = 278

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 87/272 (31%), Positives = 129/272 (47%), Gaps = 27/272 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ------KNG---SSIQGSIEKAIFLVTGEIVVVHGAGRT 51
           M R  +II Y G+ Y GWQ Q       +     ++Q ++E A   + G  V VHGAGRT
Sbjct: 1   MARLKLIIAYAGTRYAGWQIQCLPAGRPHAVQQPTVQQAVEDAAKAILGSAVRVHGAGRT 60

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           DSGVHA  QVAH D+      V   +ALNA L   + IS+L  ++V   FHARF A+++ 
Sbjct: 61  DSGVHAEGQVAHLDIPDAKAAVDWRRALNAKL--PEDISVLQAAVVPDGFHARFDAVKKR 118

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y YRI   +A +  ++     +   LD   M  AA  + G HDF +F++   + ++ +RT
Sbjct: 119 YTYRIWLTRAFVLPQRRPFVHMTGPLDIAAMDAAAAFMTGTHDFASFQNAGTELATTVRT 178

Query: 172 IDHF---------DVNSFGN-------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +            D     +        +     A  FL   +R+ +G L   G G+   
Sbjct: 179 VYSITRTPGLAPDDFPRSHDTTPRAPLELAWHFEADGFLKQMVRNMMGLLLWTGTGRCAP 238

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            D+   + A+DR+   P AP  GL  + V Y 
Sbjct: 239 EDVPAIIAARDRRLSAPTAPACGLTMERVFYP 270


>gi|296168687|ref|ZP_06850436.1| tRNA pseudouridine synthase A [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896596|gb|EFG76237.1| tRNA pseudouridine synthase A [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 302

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 77/259 (29%), Positives = 119/259 (45%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G +++A+  +    + +  AGRTD+GVHA  QV
Sbjct: 27  VRLRLDIAYDGTEFAGWATQAGQRTVAGVLDEALTTLFRAPMRLRAAGRTDTGVHATGQV 86

Query: 62  AHFDLVREWVPVILCKA------------LNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  + +P    +A                  +   + +L ++     F ARFSA+R
Sbjct: 87  AHVDVPPDALPNAYPRAPRVGEPEFLPLVRRLGRFLPTDVRVLGIARAPAGFDARFSALR 146

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR+ T    +           P+ LD + M  A++ LVG HDF  F      A + 
Sbjct: 147 RHYTYRLSTAPYGVEPQRARYVTAWPRPLDVDAMAAASRDLVGLHDFAGFCRHRPNA-TT 205

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   D +  G LI   V A +F  + +RS VG+L  VG+ +   +     L A  R 
Sbjct: 206 IRDLQGLDWSRDGELITAHVTADAFCWSMVRSLVGALLAVGEHRRPVSWCRGLLTATSRS 265

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                APP GL    V+Y 
Sbjct: 266 SDFAAAPPHGLTLVGVDYP 284


>gi|212704912|ref|ZP_03313040.1| hypothetical protein DESPIG_02979 [Desulfovibrio piger ATCC 29098]
 gi|212671683|gb|EEB32166.1| hypothetical protein DESPIG_02979 [Desulfovibrio piger ATCC 29098]
          Length = 264

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 83/260 (31%), Positives = 121/260 (46%), Gaps = 18/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R  +++ Y+GS Y GWQ Q       ++Q ++E A+  + G  V V G+GRTD+GVHA 
Sbjct: 8   MRLRLLLAYDGSRYCGWQIQDIPTPPPTVQAAVEAAVGRIAGRPVRVFGSGRTDAGVHAH 67

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+ R    +    ALNA L     + +L        FHAR SA+R++Y+Y    
Sbjct: 68  GQVAHCDVPR-RPGLDWRHALNALL--PADVRVLYWQEAAPDFHARISALRKTYVYDFWQ 124

Query: 119 RQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            +           W     LD E MR A   L+GRHDF +F++   +  S +R +    +
Sbjct: 125 EKGFVPPRLAPFVWRS-GPLDAEAMRAALPFLLGRHDFASFQNAGTEMESTVRELQAATL 183

Query: 178 NSFG---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                          + + V A  FL   +R+  G L   G  K     +   L+A DR+
Sbjct: 184 TELPPVEFMPPCLPCLRLTVTANGFLKQMVRNMAGLLAAYGRHKLRPDQIPAILEAADRR 243

Query: 229 ECG-PLAPPEGLYFDSVEYS 247
               P APP+GL    VEY 
Sbjct: 244 ALPSPTAPPQGLALAHVEYP 263


>gi|164686559|ref|ZP_02210587.1| hypothetical protein CLOBAR_00126 [Clostridium bartlettii DSM
           16795]
 gi|164604428|gb|EDQ97893.1| hypothetical protein CLOBAR_00126 [Clostridium bartlettii DSM
           16795]
          Length = 201

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 71/203 (34%), Positives = 105/203 (51%), Gaps = 3/203 (1%)

Query: 44  VVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
            V  +GRTD+GVHAL QVA+F    +     L  ALNA L     ISI++   VD  FHA
Sbjct: 2   KVTASGRTDAGVHALGQVANFKTESKIPADRLPDALNAKL--PKDISIISCEEVDIDFHA 59

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           R++A  ++Y Y I  +     L K  ++ +   LD + +R+ A+ L+G HDF  F S   
Sbjct: 60  RYNACGKTYRYLIYNKPYRSPLYKDLSYHVRYDLDLDKIRLEAKSLIGTHDFGGFMSSGS 119

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                +RTI   D+     +I I V    FL+  +R  VG+L  +G G+    ++E+ + 
Sbjct: 120 SVKDTVRTIYDVDIQENDGMISIEVSGNGFLYNMVRIIVGTLVDIGRGRIK-HNMEEIIN 178

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           ++ R  CG  AP  GL+   V Y
Sbjct: 179 SKSRSMCGHTAPAHGLFLKKVNY 201


>gi|297201758|ref|ZP_06919155.1| tRNA pseudouridine synthase A [Streptomyces sviceus ATCC 29083]
 gi|197710867|gb|EDY54901.1| tRNA pseudouridine synthase A [Streptomyces sviceus ATCC 29083]
          Length = 289

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 84/253 (33%), Positives = 120/253 (47%), Gaps = 8/253 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHA 57
           +R  + + Y+GS + GW +Q  G  ++QG IE A+  VT        +  AGRTD+GVHA
Sbjct: 10  VRVRLDLSYDGSDFSGWAKQAGGRRTVQGEIEDALRTVTRSKDVTYELTVAGRTDAGVHA 69

Query: 58  LRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
             QVAH DL          K L     ++   + + +L      F+ARF+A+ R Y+YR+
Sbjct: 70  RGQVAHVDLPEGLWAEHRDKLLKRLAGRLPKDVRVWSLREAPAGFNARFAALWRRYVYRV 129

Query: 117 ITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
             +      L +         LD   M  AA+ LVG HDF  +     + ++ IR I  F
Sbjct: 130 GDQPGGVDPLLRNHVLWHDWELDVAVMDAAAKSLVGEHDFAAYAKRR-EGATTIREILDF 188

Query: 176 DVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            V    + ++EI V A +F H Q+RS VG+L  VGDG        K L A  R     + 
Sbjct: 189 GVRRRADGVVEIEVRADAFCHNQVRSMVGALLFVGDGHRGVEWPRKVLDAGVRDSAVHVV 248

Query: 235 PPEGLYFDSVEYS 247
            P GL  + V Y 
Sbjct: 249 RPHGLTLEEVAYP 261


>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 =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 111/203 (54%), Positives = 141/203 (69%), Gaps = 1/203 (0%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHA 103
           +  AGRTD+GVHA  QVAH DL ++W    +  A+NA+L    + ISILN+      F A
Sbjct: 1   MSAAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDA 60

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           RFSA  R YLYRI  R+APLA++  RAW + K LD + M  AAQ L+G HDFTTFR+  C
Sbjct: 61  RFSARARHYLYRIHNRRAPLAVDYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQC 120

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           QA SP++T+D  DV   G++IE+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+
Sbjct: 121 QAKSPVKTLDRLDVTRNGDMIEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALE 180

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A+DRK CG +APP GLY   V+Y
Sbjct: 181 ARDRKACGQVAPPYGLYLVGVDY 203


>gi|300857811|ref|YP_003782794.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300685265|gb|ADK28187.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302205546|gb|ADL09888.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           C231]
 gi|308275782|gb|ADO25681.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           I19]
          Length = 291

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 80/262 (30%), Positives = 126/262 (48%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ      ++Q  +E ++ L+    + +  AGRTD+GVHA  
Sbjct: 8   VRIRLDLAYDGTHFHGWARQGTSQLRTVQRVLEDSLELILRHPIQLTVAGRTDAGVHAAG 67

Query: 60  QVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+             P  L + L   L   + + +   ++  + F ARFSA+RR 
Sbjct: 68  QVAHFDVPAIALDTRSIDGDPRNLVRRLARLL--PEDVRVHACTLAPEGFDARFSALRRH 125

Query: 112 YLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YR+ T     L          PK +D + M+ AA  L+G HDF  F   H + ++ IR
Sbjct: 126 YVYRLTTHPRGALPTRATDTAHWPKRIDIDAMQAAADVLIGLHDFAAFCK-HREGATTIR 184

Query: 171 TIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F  +         L E  V A +F  + +RS VGS  ++G+GK     ++  L   
Sbjct: 185 DLQEFTWHDVSTSLEPQLYEAHVTADAFCWSMVRSLVGSCLVIGEGKRPEGFVDSLLTET 244

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    P+AP +GL    V+Y 
Sbjct: 245 SRSSQVPVAPAKGLSLVGVDYP 266


>gi|253582682|ref|ZP_04859903.1| tRNA pseudouridine synthase A [Fusobacterium varium ATCC 27725]
 gi|251835552|gb|EES64092.1| tRNA pseudouridine synthase A [Fusobacterium varium ATCC 27725]
          Length = 246

 Score =  239 bits (610), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 115/246 (46%), Gaps = 4/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +   ++GS ++G+QRQ    ++QG IEK + +V  E V +  AGRTD GVHAL Q
Sbjct: 5   MKNIKIRYRFDGSMFYGFQRQPGKRTVQGEIEKLLEVVLREKVNMISAGRTDRGVHALEQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F          L  ALN  L     I I  +  VD  F++RF A  R Y Y I   +
Sbjct: 65  VSNFFTTSPIPVEKLKYALNKGL--PLDIEIFEVEEVDMNFNSRFFAKNRGYKYIISWVK 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E     L+ + +D E      + L+G HDF  FR   C + + IR I    V   
Sbjct: 123 NP--FESRYVTLVREKIDKEIFFKILEPLIGVHDFNNFRLSDCGSKTSIREIYSIVVEEK 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N + + +   SFL +QIR  +G+   +  G +    L   L+   +     +A P GLY
Sbjct: 181 ENKLIVEIKGNSFLKSQIRIIIGTALDIYFGNYDENHLRDMLENPKKDFLKKVADPYGLY 240

Query: 241 FDSVEY 246
              + Y
Sbjct: 241 LSEINY 246


>gi|54022806|ref|YP_117048.1| tRNA pseudouridine synthase A [Nocardia farcinica IFM 10152]
 gi|62901243|sp|Q5Z1K7|TRUA_NOCFA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54014314|dbj|BAD55684.1| putative tRNA pseudouridine synthase [Nocardia farcinica IFM 10152]
          Length = 257

 Score =  238 bits (609), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 77/232 (33%), Positives = 116/232 (50%), Gaps = 4/232 (1%)

Query: 17  GWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILC 76
           GW RQ    ++QG +E A+  V  E + +  AGRTD+GVHA  QVAHFD   E+    L 
Sbjct: 2   GWARQPGLRTVQGVLEDALGKVLREPIQLTVAGRTDAGVHAEGQVAHFDTAAEFDGPQLV 61

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPK 135
             L  +L     + +    +V   F ARFSAIRR Y+YR+ T       L          
Sbjct: 62  HRLARFL--PKDVRVKRADVVPPDFDARFSAIRRHYVYRLTTAPYGAEPLAARSVVPCKS 119

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
           ++D + MR A+  L+G HDF  F     + ++ +R +  FD    G+L+   V A +F  
Sbjct: 120 AVDVDAMRRASGLLLGLHDFAAFCRRR-EGATTVRELQRFDWERQGDLLLAHVSADAFCW 178

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + +RS VG++  VG+G+ +   +   L+   R     +AP  GL   +V+Y 
Sbjct: 179 SMVRSLVGAVLAVGEGRRSPEWVAGLLRETQRSSSVTVAPAHGLSLVAVDYP 230


>gi|259506738|ref|ZP_05749638.1| tRNA pseudouridine synthase A [Corynebacterium efficiens YS-314]
 gi|42559821|sp|Q8FS31|TRUA_COREF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|259165679|gb|EEW50233.1| tRNA pseudouridine synthase A [Corynebacterium efficiens YS-314]
          Length = 282

 Score =  238 bits (609), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 88/262 (33%), Positives = 132/262 (50%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + ++Y+G+ + GW RQ +    ++Q  +E  + +V    V +  AGRTD+GVHA  
Sbjct: 1   MRIRLDLDYDGTDFHGWARQGDSDLRTVQKVLEDNLGMVLRAPVELTVAGRTDAGVHAAG 60

Query: 60  QVAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+ R        +  P  L + L+  L   + I +  ++   + F ARFSA+RR 
Sbjct: 61  QVAHFDIPRESLQQRSIDGDPTKLVRRLSRLL--PEDIRVHGVNYAPEGFDARFSALRRH 118

Query: 112 YLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YRI T  A PL          PK +D + M+ AA  L+G HDF  F      A S +R
Sbjct: 119 YVYRITTHPAGPLPTRVRDTAAWPKPVDIQAMQTAADVLIGLHDFVAFCKAKPNA-STVR 177

Query: 171 TIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F  +     +   L E  VVA +F  + +RS VGS   VG+G+       + L A 
Sbjct: 178 ELQEFTWHDVSTPTEPQLYEAHVVADAFCWSMVRSLVGSCMAVGEGRRAGDFTAQLLTAT 237

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R    P+AP +GL    V+Y 
Sbjct: 238 ERSPDVPVAPAKGLSLVGVDYP 259


>gi|302330101|gb|ADL20295.1| tRNA pseudouridine synthase A [Corynebacterium pseudotuberculosis
           1002]
          Length = 319

 Score =  238 bits (609), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 80/262 (30%), Positives = 126/262 (48%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ      ++Q  +E ++ L+    + +  AGRTD+GVHA  
Sbjct: 36  VRIRLDLAYDGTHFHGWARQGTSQLRTVQRVLEDSLELILRHPIQLTVAGRTDAGVHAAG 95

Query: 60  QVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+             P  L + L   L   + + +   ++  + F ARFSA+RR 
Sbjct: 96  QVAHFDVPAIALDTRSIDGDPRNLVRRLARLL--PEDVRVHACTLAPEGFDARFSALRRH 153

Query: 112 YLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YR+ T     L          PK +D + M+ AA  L+G HDF  F   H + ++ IR
Sbjct: 154 YVYRLTTHPRGALPTRATDTAHWPKRIDIDAMQAAADVLIGLHDFAAFCK-HREGATTIR 212

Query: 171 TIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F  +         L E  V A +F  + +RS VGS  ++G+GK     ++  L   
Sbjct: 213 DLQEFTWHDVSTSLEPQLYEAHVTADAFCWSMVRSLVGSCLVIGEGKRPEGFVDSLLTET 272

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    P+AP +GL    V+Y 
Sbjct: 273 SRSSQVPVAPAKGLSLVGVDYP 294


>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 =  238 bits (609), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 110/203 (54%), Positives = 141/203 (69%), Gaps = 1/203 (0%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHA 103
           +  AGRTD+GVHA  QVAH DL ++W    +  A+NA+L    + ISILN+      F A
Sbjct: 1   MSAAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDA 60

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           RFSA  R YLYRI  R+APLA++  RAW + K LD + M  AAQ L+G HDFTTFR+  C
Sbjct: 61  RFSARARHYLYRIHNRRAPLAVDYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQC 120

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           QA SP++T+D  DV   G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+
Sbjct: 121 QAKSPVKTLDRLDVTRNGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALE 180

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A+DRK CG +APP GLY   V+Y
Sbjct: 181 ARDRKACGQVAPPYGLYLVGVDY 203


>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 =  238 bits (609), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 110/203 (54%), Positives = 140/203 (68%), Gaps = 1/203 (0%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHA 103
           +  AGRTD+GVHA  QVAH DL ++W    +  A+NA+L    + ISILN+      F A
Sbjct: 1   MSAAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDA 60

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           RFSA  R YLYRI  R+APLA+   RAW + K LD + M  AAQ L+G HDFTTFR+  C
Sbjct: 61  RFSARARHYLYRIHNRRAPLAVNYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQC 120

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           QA SP++T+D  DV   G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+
Sbjct: 121 QAKSPVKTLDRLDVTRNGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALE 180

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A+DRK CG +APP GLY   V+Y
Sbjct: 181 ARDRKACGQVAPPYGLYLVGVDY 203


>gi|228470580|ref|ZP_04055437.1| tRNA pseudouridine synthase A [Porphyromonas uenonis 60-3]
 gi|228307707|gb|EEK16683.1| tRNA pseudouridine synthase A [Porphyromonas uenonis 60-3]
          Length = 262

 Score =  238 bits (608), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 81/252 (32%), Positives = 119/252 (47%), Gaps = 10/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ Y GWQ Q  G S+Q  +E+A+ ++  + + V GAGRTD+GVHA   +
Sbjct: 6   QRVFLEVAYDGTNYCGWQVQPRGVSVQSELERALSMLFRQPISVTGAGRTDAGVHAYSMM 65

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH DL     P+  + + L   L+    IS+ +++ V    HARF A  R Y Y I    
Sbjct: 66  AHADLPIPHPPLAQIQRGLCGILR--GGISVRSVTPVIPTAHARFDATSRRYHYYISACS 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P        W      D E M  A +H +G HDFT+F  +H Q      T+        
Sbjct: 124 NP--FWGDYCWERRTLPDMELMNEACRHFIGEHDFTSFSKLHTQTKHNRCTVYTAHWEQV 181

Query: 181 G-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +   V A  FLH  +R+ VG+L  VG G+ T   + + +Q +DR   G  AP
Sbjct: 182 EMPGLWDAMRYEVCANRFLHGMVRTMVGTLLEVGYGQRTPDSIAELIQREDRTLAGSAAP 241

Query: 236 PEGLYFDSVEYS 247
              L+F    Y 
Sbjct: 242 ARALFFVEATYP 253


>gi|256827610|ref|YP_003151569.1| pseudouridylate synthase I [Cryptobacterium curtum DSM 15641]
 gi|256583753|gb|ACU94887.1| pseudouridylate synthase I [Cryptobacterium curtum DSM 15641]
          Length = 273

 Score =  238 bits (608), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 85/258 (32%), Positives = 122/258 (47%), Gaps = 14/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    ++I YNG+ + G+ RQ+    ++QGS+E+A+ L+    V    AGRTD+GVHA  
Sbjct: 1   MATIALLISYNGAPFHGFARQEGDLLTVQGSLEEALSLLYRREVETVCAGRTDTGVHARG 60

Query: 60  QVAHFDLV----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           QV  F++         P  L ++LNA     D I I  L      F ARF A  R Y Y 
Sbjct: 61  QVVTFEVTPEELASHTPHSLIRSLNALTH--DAIGIRQLRRAPDGFSARFDAKSRHYRYF 118

Query: 116 IITRQAPLALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTI 172
           I     P  + +   W +    SLD   M  AA +LVG HDF +F  ++        R +
Sbjct: 119 ISDGSVPPLVMRDFCWQVRGGVSLDANAMTAAAAYLVGEHDFKSFCLAVSAAGKPTRREV 178

Query: 173 DHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
               V         ++ I ++  SFLH+ +R+  G+L  VG G    + + + L A DR 
Sbjct: 179 LSLTVERIEVLGDEVVCIDIIGSSFLHSMVRTIAGTLVAVGRGLRPPSWMAEVLAACDRT 238

Query: 229 ECGPLAPPEGLYFDSVEY 246
             G  AP  GL F  V+Y
Sbjct: 239 AAGEKAPAAGLVFWDVDY 256


>gi|300727110|ref|ZP_07060529.1| tRNA pseudouridine synthase A [Prevotella bryantii B14]
 gi|299775654|gb|EFI72245.1| tRNA pseudouridine synthase A [Prevotella bryantii B14]
          Length = 259

 Score =  238 bits (608), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 79/263 (30%), Positives = 119/263 (45%), Gaps = 21/263 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---------IVVVHGAGRT 51
           M RY +I  Y+G+ Y GWQ Q NG+S+Q  ++ A+ L              + V GAGRT
Sbjct: 1   MHRYFIIFAYDGTNYHGWQIQPNGNSVQAELQHALALSLRSFLLLKSNDFEIEVVGAGRT 60

Query: 52  DSGVHALRQVAHFDLVREWVP-------VILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           D+GVHA +  AHF+L  E  P         +   +N  L     IS+ ++  V+   HAR
Sbjct: 61  DAGVHARQMAAHFELSEEEFPLLDESKCKQIVYRINRIL--PRDISVSDVYPVESDMHAR 118

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           FSA  R+Y Y I T + P    +  +      LD + M    + ++   DF  F      
Sbjct: 119 FSAKWRTYHYYIHTDKNP--FLRFYSLETHYPLDFDLMNEGGKIIMEHQDFAAFCKAGAD 176

Query: 165 ASSPIRTIDHF-DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             + +  +     V +      + + A  FL   +R+ VG+L L+G  K T  DL   L 
Sbjct: 177 NKTTLCDVTECKWVQTSPTSWYLTITANRFLRNMVRAVVGTLFLLGRHKITLDDLRVILH 236

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
             +R + G   P   L+ + VEY
Sbjct: 237 EGNRSKAGESMPGNALFLEKVEY 259


>gi|194336595|ref|YP_002018389.1| tRNA pseudouridine synthase A [Pelodictyon phaeoclathratiforme
           BU-1]
 gi|259550418|sp|B4SA76|TRUA_PELPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|194309072|gb|ACF43772.1| tRNA pseudouridine synthase A [Pelodictyon phaeoclathratiforme
           BU-1]
          Length = 243

 Score =  238 bits (608), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 113/247 (45%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + +EY+G+ + GWQRQ     ++QG IE A+  +  E + +  AGRTD GVHA  
Sbjct: 1   MKNIRVTVEYDGTSFAGWQRQSGAIVTVQGEIEVALGKILQEKISLAAAGRTDKGVHARA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q A+F       P  +  +LN+ L    TI I N   VD  FHAR SA  R Y Y +I  
Sbjct: 61  QTANFFTASSLEPSRIVHSLNSLL--PQTIRISNPEEVDADFHARHSAKERQYRYFLI-- 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P A+    A      LD   M+  A  LVG HDF+ F          I ++       
Sbjct: 117 EEPSAIYGRFAGCSFGKLDVAIMQQMAAILVGTHDFSAFSKEDRDNPGRICSVTACKWYP 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + + +R+ A  FL + +R  V ++   G G+ +  D  + L+          A P GL
Sbjct: 177 CKHYLVLRISADRFLRSMVRYLVDAMIRAGKGRLSVGDFCRMLETGVTTSQLNPALPAGL 236

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 237 FLWDVLY 243


>gi|332159317|ref|YP_004424596.1| tRNA pseudouridine synthase A [Pyrococcus sp. NA2]
 gi|331034780|gb|AEC52592.1| tRNA pseudouridine synthase A [Pyrococcus sp. NA2]
          Length = 263

 Score =  238 bits (608), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 119/247 (48%), Gaps = 24/247 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + G+QRQ N  +++G I KA+     E      A RTD GV AL  V
Sbjct: 1   MRVALKIAYDGTKFHGFQRQPNIRTVEGEIIKALNNSGIEYSDFKSASRTDKGVSALGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                  E     +   LNA L   + + IL+   V   FH RF A  + Y Y + +   
Sbjct: 61  VAITTEDEKALNPMV--LNARL---EDVWILSAIEVPPDFHPRFWAKSKVYRYYLPS--- 112

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                          LD E ++  +Q  +G HDF+ F  +       IR+ID  +V   G
Sbjct: 113 -------------IGLDVERVKECSQLFLGVHDFSAFSKV--DERDTIRSIDRIEVLVLG 157

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEGLY 240
            ++ I + A+SFL   +R  V +L+L G GK ++ D+++ L+ + ++ +  P APPEGL 
Sbjct: 158 PILVIEIEAKSFLWEMVRRIVKALELCGLGKLSAEDVKEMLEGKFNKSKKVPPAPPEGLL 217

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 218 LVDVKYE 224


>gi|324999254|ref|ZP_08120366.1| tRNA pseudouridine synthase a [Pseudonocardia sp. P1]
          Length = 268

 Score =  238 bits (608), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 115/249 (46%), Gaps = 9/249 (3%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + I Y+G+ + GW  Q    ++QG +  A+  V    + +  AGRTD+GVHA  QVAH 
Sbjct: 2   RLDIAYDGTDFSGWATQPTRRTVQGVLTDALSTVLRTPLRLTVAGRTDAGVHASGQVAHV 61

Query: 65  DLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           D+  E  P    L + LN +L     + +   + V + F ARFSA+RR Y YR+ T    
Sbjct: 62  DVPAELDPQLDGLLRRLNRFL--PPDVRVRATTRVPETFDARFSALRRHYRYRVTTASFG 119

Query: 123 L-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-- 179
              L        P  LD   M  A+  +VG HDF  F     + ++ +R +  F+ +   
Sbjct: 120 AEPLRARETVAWPHPLDPALMNAASALMVGEHDFAAFCKRR-EGATTVRALQRFEWDPAP 178

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               ++   V A +F H+ +RS VG++  VG          + L    R     +APP G
Sbjct: 179 GEPGVLVASVSADAFCHSMVRSLVGAVFEVGRVHRPPEWPAELLSRTSRASEVTVAPPHG 238

Query: 239 LYFDSVEYS 247
           L    V+Y 
Sbjct: 239 LSLTGVDYP 247


>gi|163783710|ref|ZP_02178697.1| pseudouridine synthase I [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881035|gb|EDP74552.1| pseudouridine synthase I [Hydrogenivirga sp. 128-5-R1-1]
          Length = 239

 Score =  238 bits (608), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 74/245 (30%), Positives = 127/245 (51%), Gaps = 7/245 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y + + + G+ Y GWQ Q    ++QG++++A+  V GE + V G  RTD+GVHA   
Sbjct: 1   MNNYMLRLAFVGTNYSGWQIQPGVPTVQGTLKEALETVFGEEIRVIGCCRTDAGVHAEDY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F  ++E     L +ALN+ L     I +  + +VD+ F++R+S   ++YLYR+    
Sbjct: 61  VANFRSIKELECEKLLRALNSLL--PKDIGVYEVKLVDENFNSRYSVKGKTYLYRLWNSF 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                    +W + + +D   +  A + + GRHDF  F  +    ++ I       V+  
Sbjct: 119 VRNPFLYPFSWSVTRRVDLNLLSEALEIVSGRHDFRGFAKLEEDKTTVIELETKLAVS-- 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LIE+R  A  FL   +R  VG++    +GK ++ +L + L+ +    C   AP +GL 
Sbjct: 177 GDLIELRFTASHFLRYMVRRLVGAIVKRAEGKVSTGELYEYLKGK---HCPHTAPAKGLT 233

Query: 241 FDSVE 245
            + V 
Sbjct: 234 LERVH 238


>gi|229821589|ref|YP_002883115.1| tRNA pseudouridine synthase A [Beutenbergia cavernae DSM 12333]
 gi|229567502|gb|ACQ81353.1| tRNA pseudouridine synthase A [Beutenbergia cavernae DSM 12333]
          Length = 286

 Score =  238 bits (608), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 78/258 (30%), Positives = 116/258 (44%), Gaps = 14/258 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + GW RQ    ++QG +E+A+  V    E   +  AGRTD+GVHA  Q
Sbjct: 6   RVRLDLAYDGAAFAGWARQPGLRTVQGDLEEALGRVLRLPEPPRLTVAGRTDAGVHARGQ 65

Query: 61  VAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRS 111
           VAH DL RE               AL   L   +   + + +++     F ARFSAI R 
Sbjct: 66  VAHVDLPREAYLAAPGRSERDPGAALRTRLAGVLPPDVVVGHVAPAPPGFDARFSAIWRR 125

Query: 112 YLYRI-ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y YR+         L +G      + LD   M  AA+ L+G HDF  F     + ++ IR
Sbjct: 126 YAYRVADDGALHDPLRRGWTVWHRRPLDVVAMDAAARRLLGEHDFAAFCRPR-EGATTIR 184

Query: 171 TIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           T+           L+   V A +F H+ +R+ VG+   VG+ +         L A  R  
Sbjct: 185 TLQELTWVRDDAGLLVAHVRADAFCHSMVRALVGACLAVGESRREVGWPRAVLDAARRDS 244

Query: 230 CGPLAPPEGLYFDSVEYS 247
              +AP  GL  + + Y 
Sbjct: 245 AVQVAPAHGLVLEEIGYP 262


>gi|189501513|ref|YP_001957230.1| tRNA pseudouridine synthase A [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189496954|gb|ACE05501.1| tRNA pseudouridine synthase A [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 253

 Score =  238 bits (608), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 120/251 (47%), Gaps = 9/251 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y G+ Y GWQ Q+N +S+Q  I+K +  +    + + G+ RTD+GVHA +Q 
Sbjct: 1   MRYFLEIAYQGTHYHGWQIQQNATSVQAVIQKKLTQLLSTNIEIVGSSRTDTGVHAQQQF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH D+        L   LN  L +   I+IL +  V    H+RF A+ R+Y+Y+I   + 
Sbjct: 61  AHVDMPFTIDIDKLKYKLN--LIVPSDIAILGIHPVLPTAHSRFDALSRTYVYKISCTKN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDV 177
           P    +   ++  + LD E M  AA  L    +F +F  +           +  I     
Sbjct: 119 P--FMQATTYVFRRVLDLEKMNEAAAILKIYKNFESFSKVGSITDHTLYPNLCNIIEAHW 176

Query: 178 NS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++   + +  ++ A  FL   +R+ VG+L  VG GK +  D E  L  +DR     L P 
Sbjct: 177 STGSNDQLIFQITANRFLRGMVRAIVGNLLEVGLGKCSVKDFEYTLVQKDRNLAASLVPA 236

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 237 CGLTLVNVTYP 247


>gi|120603116|ref|YP_967516.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris DP4]
 gi|166228695|sp|A1VF73|TRUA_DESVV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120563345|gb|ABM29089.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris DP4]
          Length = 297

 Score =  238 bits (607), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 87/292 (29%), Positives = 121/292 (41%), Gaps = 48/292 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + I Y G+   GWQ Q++       ++QG +E  +  + GE V +H AGRTD+GV
Sbjct: 1   MARLRLTIAYKGTDLHGWQVQEHATRPRPRTVQGVLEPIVSRMAGEQVRLHAAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+    + V   KA+NA L   D I IL++      FHARF A+ + Y YR
Sbjct: 61  HADGQVAHVDIPDHKLDVDWQKAINAQL--PDDICILDVRRAADDFHARFDALGKRYTYR 118

Query: 116 II-TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +  TR+       G+ W     LD   M  AA+HL G HDF  F++     +S +RT+  
Sbjct: 119 LWLTRRFIPPKLHGQVWAT-GPLDVYAMDRAARHLAGTHDFAAFQNQGTDVTSTVRTVHA 177

Query: 175 FDVNSFGNL---------------------------------------IEIRVVARSFLH 195
                 G L                                       +        FL 
Sbjct: 178 IRRCPSGTLPAGALLTYGEPYTSWRCTGTHPDQPPATAGHPLAGIGLELVWSFEGDGFLK 237

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +R+ +G L  VG G   + D+   +   DR      AP  GL    V Y 
Sbjct: 238 QMVRNMMGLLVAVGRGALAADDVPGIMATLDRSRAPATAPACGLTLSEVYYP 289


>gi|46579324|ref|YP_010132.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|51316681|sp|Q72DL8|TRUA_DESVH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|46448738|gb|AAS95391.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|311233151|gb|ADP86005.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris RCH1]
          Length = 297

 Score =  238 bits (607), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 87/292 (29%), Positives = 121/292 (41%), Gaps = 48/292 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + I Y G+   GWQ Q++       ++QG +E  +  + GE V +H AGRTD+GV
Sbjct: 1   MARLRLTIAYKGTDLHGWQVQEHATRPRPRTVQGVLEPIVSRMAGEQVRLHAAGRTDAGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+    + V   KA+NA L   D I IL++      FHARF A+ + Y YR
Sbjct: 61  HADGQVAHVDIPDHKLGVDWQKAINAQL--PDDICILDVRRAADDFHARFDALGKRYTYR 118

Query: 116 II-TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +  TR+       G+ W     LD   M  AA+HL G HDF  F++     +S +RT+  
Sbjct: 119 LWLTRRFIPPKLHGQVWAT-GPLDVYAMDRAARHLAGTHDFAAFQNQGTDVTSTVRTVHA 177

Query: 175 FDVNSFGNL---------------------------------------IEIRVVARSFLH 195
                 G L                                       +        FL 
Sbjct: 178 IRRCPSGTLPAGALLTCSEPYTSWRCTGTHPDQPPATAGHPLAGIGLELVWSFEGDGFLK 237

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +R+ +G L  VG G   + D+   +   DR      AP  GL    V Y 
Sbjct: 238 QMVRNMMGLLVAVGRGALAADDVPGIMATLDRSRAPATAPACGLTLSEVYYP 289


>gi|257064823|ref|YP_003144495.1| pseudouridylate synthase I [Slackia heliotrinireducens DSM 20476]
 gi|256792476|gb|ACV23146.1| pseudouridylate synthase I [Slackia heliotrinireducens DSM 20476]
          Length = 271

 Score =  238 bits (607), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 83/257 (32%), Positives = 123/257 (47%), Gaps = 15/257 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
               + Y+G+ + G+ RQ       ++QG +E A+ ++    V    AGRTD+GVHA+ Q
Sbjct: 17  LACKVAYDGAPFAGFARQAECDRVMTVQGELEHALRVLYRRDVRTTCAGRTDAGVHAIGQ 76

Query: 61  VAHFDLVRE----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           V  FD+  +      P  L ++LNA   + D +S+  +      F ARF A  R Y YRI
Sbjct: 77  VVSFDVTEDEFASRTPRSLLRSLNAL--VDDHMSVSVVEEKPFGFSARFDAKWREYRYRI 134

Query: 117 ITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDH 174
            T  A   L     W +    LD + M  AA HL+G HDF +F            R +  
Sbjct: 135 STAAARPVLIMPLVWHLGGVDLDIDAMNRAAVHLIGEHDFKSFCVAASAVGKPTCRNVME 194

Query: 175 FDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            +V         +  +RVV  +FLH+ +R+ VG+L  VG G+     +   L+A++R   
Sbjct: 195 LEVFEEEILGQQVATVRVVGNAFLHSMVRTIVGTLVEVGRGRRNPEWVCDVLEARNRGAA 254

Query: 231 GPLAPPEGLYFDSVEYS 247
           G  AP +GL F  VEY 
Sbjct: 255 GQNAPAQGLVFWHVEYE 271


>gi|25027130|ref|NP_737184.1| tRNA pseudouridine synthase A [Corynebacterium efficiens YS-314]
 gi|23492410|dbj|BAC17384.1| putative tRNA pseudouridine synthase A [Corynebacterium efficiens
           YS-314]
          Length = 300

 Score =  238 bits (607), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 88/262 (33%), Positives = 132/262 (50%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + ++Y+G+ + GW RQ +    ++Q  +E  + +V    V +  AGRTD+GVHA  
Sbjct: 19  VRIRLDLDYDGTDFHGWARQGDSDLRTVQKVLEDNLGMVLRAPVELTVAGRTDAGVHAAG 78

Query: 60  QVAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+ R        +  P  L + L+  L   + I +  ++   + F ARFSA+RR 
Sbjct: 79  QVAHFDIPRESLQQRSIDGDPTKLVRRLSRLL--PEDIRVHGVNYAPEGFDARFSALRRH 136

Query: 112 YLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YRI T  A PL          PK +D + M+ AA  L+G HDF  F      A S +R
Sbjct: 137 YVYRITTHPAGPLPTRVRDTAAWPKPVDIQAMQTAADVLIGLHDFVAFCKAKPNA-STVR 195

Query: 171 TIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F  +     +   L E  VVA +F  + +RS VGS   VG+G+       + L A 
Sbjct: 196 ELQEFTWHDVSTPTEPQLYEAHVVADAFCWSMVRSLVGSCMAVGEGRRAGDFTAQLLTAT 255

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R    P+AP +GL    V+Y 
Sbjct: 256 ERSPDVPVAPAKGLSLVGVDYP 277


>gi|166032002|ref|ZP_02234831.1| hypothetical protein DORFOR_01704 [Dorea formicigenerans ATCC
           27755]
 gi|166028455|gb|EDR47212.1| hypothetical protein DORFOR_01704 [Dorea formicigenerans ATCC
           27755]
          Length = 310

 Score =  237 bits (606), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 119/250 (47%), Gaps = 9/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVH 56
           M    + IEY+GS Y GW R    ++ ++I   I   +  +TGE  + ++   RT+ GVH
Sbjct: 66  MRNIKITIEYDGSRYQGWTRLGKDESNNTISAKIIDVLGKMTGEKNIELNCGCRTEVGVH 125

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QVA+F          +   LN YL     I+I  +  V  +FHA+ +A+ ++Y+YR+
Sbjct: 126 AYAQVANFKTSSNLSTKDIQHYLNRYL--PMDIAITEVEEVPDRFHAQLNAVSKTYVYRM 183

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P   E+   +   K+ D + M+ AA   +G HDF  F +   ++ +  R +   D
Sbjct: 184 TIMDVPSVFERKHTYHCFKTPDKKAMQQAALLFIGEHDFRNFSTAK-KSKNTTREVYDID 242

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +      ++I + A  FLH   R  +G+L  +G G     D+E     +  K  G    P
Sbjct: 243 IYGDNEEMQILIQADDFLHNMARLMIGTLLDIGFGLRKKEDIEAIFNGE--KAVGNPCDP 300

Query: 237 EGLYFDSVEY 246
           +GLY   VEY
Sbjct: 301 KGLYLQEVEY 310


>gi|227505250|ref|ZP_03935299.1| tRNA pseudouridine synthase A [Corynebacterium striatum ATCC 6940]
 gi|227198149|gb|EEI78197.1| tRNA pseudouridine synthase A [Corynebacterium striatum ATCC 6940]
          Length = 285

 Score =  237 bits (606), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 84/261 (32%), Positives = 123/261 (47%), Gaps = 18/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW RQK    ++QG +E  + ++    V +  AGRTD+GVH+  Q
Sbjct: 4   VRLRLDLAYDGTDFHGWARQKGDLRTVQGVLEDNLSMILRHDVELTVAGRTDAGVHSAGQ 63

Query: 61  VAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAHFD+  E          P  L + L   L   + + +   +   + F ARFSA++R Y
Sbjct: 64  VAHFDVPSEALDQRSIDGDPAKLVRRLAKLL--PEDVRVHACTAAPEGFDARFSALQRHY 121

Query: 113 LYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           +YRI T        + R     PK +D + M+ AA  LVG HDF  F      A + IR 
Sbjct: 122 VYRITTHPRGALPTRARDTAQWPKPVDIDAMQEAATTLVGLHDFAAFCKAKPHA-TTIRD 180

Query: 172 IDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           +  F+       +   L E RV A +F  + +RS VG    VG+G          L    
Sbjct: 181 LHSFEWVDVSTPTEPQLYEARVCADAFCWSMVRSLVGCCLRVGEGARDVDFATAMLAESQ 240

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R    PLAP +GL    V+Y 
Sbjct: 241 RSSQIPLAPAKGLSLVRVDYP 261


>gi|258651414|ref|YP_003200570.1| tRNA pseudouridine synthase A [Nakamurella multipartita DSM 44233]
 gi|258554639|gb|ACV77581.1| tRNA pseudouridine synthase A [Nakamurella multipartita DSM 44233]
          Length = 305

 Score =  237 bits (606), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 78/263 (29%), Positives = 125/263 (47%), Gaps = 18/263 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + I Y+G+ + GW  Q    ++ G +  A+  +    V +  AGRTD+GVHA  QV
Sbjct: 26  RRLRLDISYDGTDFAGWAIQPGLRTVAGELTSALTTIVRTPVRLVVAGRTDAGVHAAGQV 85

Query: 62  AHFDLVREWVPVILCKALNAYLKI----------------SDTISILNLSIVDKQFHARF 105
           AH DL +  +  ++ +    +                      + +  +    + F ARF
Sbjct: 86  AHVDLPQAALLTVIPRDRADHPDPERAGRLGLLRRLGGLLPPDVRVRAVLAAPEGFDARF 145

Query: 106 SAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+RR Y YRI T +  +   ++   +   ++LD E M +AAQ LVG HDF  F     +
Sbjct: 146 SALRRRYRYRIGTAEWGVEPADRRFVYARRRTLDVEAMTLAAQALVGLHDFHAFCRPR-E 204

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            ++ IR +    V   G+ + I VVA +F H+ +R+ VGSL  VG+ +  +    + L A
Sbjct: 205 GATTIRDLQKLTVTRAGDEVRIDVVADAFCHSMVRALVGSLLAVGELRMPTARPAELLAA 264

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
            +R     +AP  GL    V+Y 
Sbjct: 265 GERTSAFAVAPAHGLSLVGVDYP 287


>gi|118473191|ref|YP_885908.1| tRNA pseudouridine synthase A [Mycobacterium smegmatis str. MC2
           155]
 gi|118174478|gb|ABK75374.1| tRNA pseudouridine synthase A [Mycobacterium smegmatis str. MC2
           155]
          Length = 291

 Score =  237 bits (606), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 79/259 (30%), Positives = 118/259 (45%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G I++A+  V    VV   AGRTD+GVHA  QV
Sbjct: 11  VRLRLDIAYDGTDFAGWAVQAGQRTVAGVIDEALTTVFRTPVVTRVAGRTDTGVHATGQV 70

Query: 62  AHFDLVREWVPVILCKA------------LNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  E +P    +                   +   + + ++      F ARFSA+R
Sbjct: 71  AHVDVPAEALPHAYPRHTRPTDAEFTPLVRRLAGFLPADVRVRDIVRAPAGFDARFSALR 130

Query: 110 RSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y+YR+ T    P   E        + LD + M  AAQ L+G +DF  F       ++ 
Sbjct: 131 RHYVYRLTTAPYGPEPHETRFVTPWTRPLDVDAMNAAAQELLGLNDFAAFCRYRA-GATT 189

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   +    G  I   V A +F    +RS VG+L  VG+G+ +     + L A  R 
Sbjct: 190 IRDLQRLEWVRNGFYINAYVTADAFCWNMVRSLVGALLKVGEGRRSPEWTAELLGATSRS 249

Query: 229 ECGPLAPPEGLYFDSVEYS 247
              P AP  GL   +V+Y 
Sbjct: 250 SEFPAAPARGLTLAAVDYP 268


>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 =  237 bits (606), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 92/252 (36%), Positives = 131/252 (51%), Gaps = 8/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  M + Y+G+GY GWQ Q+N  S+Q  IE A++ +TG  V V G+GRTDSGVHAL QV
Sbjct: 20  RRVRMTVAYDGTGYSGWQHQRNAPSVQAEIEDALYRLTGHSVTVVGSGRTDSGVHALGQV 79

Query: 62  AHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            HFDL  E  P V+  +ALNA+L     I I++    +  FHARFSA+ R Y Y I    
Sbjct: 80  CHFDLPDERFPAVVFKRALNAFL--PPAIRIMDSEETNDSFHARFSAMAREYRYLIKREA 137

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDVN 178
                + GR W++ +    E ++  A  + G HDFTTF +         R I    F V 
Sbjct: 138 DMTPFDSGRVWVVKELPSLELLKAHAAEIAGTHDFTTFTAAGDMCERRHRDIYVSDFSVE 197

Query: 179 SF---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  ++   +   +FL+  +RS VG+L  +  G   +T+  + L A+DR + G  A 
Sbjct: 198 KDIHGAEVLVYTICGNAFLYKMVRSIVGTLFFLVLGGVPATETARRLAARDRSQAGRTAS 257

Query: 236 PEGLYFDSVEYS 247
             GLY   + + 
Sbjct: 258 AHGLYLSRISFD 269


>gi|108804942|ref|YP_644879.1| tRNA pseudouridine synthase A [Rubrobacter xylanophilus DSM 9941]
 gi|108766185|gb|ABG05067.1| tRNA pseudouridine synthase A [Rubrobacter xylanophilus DSM 9941]
          Length = 257

 Score =  237 bits (606), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 77/245 (31%), Positives = 115/245 (46%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R   ++EY+G+G+ GW RQ    +++G + +A+  V    V +  AGRTD+GVHA  QV
Sbjct: 1   MRLAGLVEYDGAGFSGWARQPGRRTVEGELSRALETVLRHPVRLTAAGRTDAGVHASGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             FD      P  L    +A L  S+ +++         F AR  A  RSY YRI+    
Sbjct: 61  VSFDARDGTDPGTLAYKASAVL--SEDVALRRCVAAPPGFDARRDAASRSYEYRIVNAPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L + RA  +   LD   +  AA+ ++G HDF  F           R +        G
Sbjct: 119 RSPLRRRRAVHVGYRLDERLLGEAARRVLGVHDFRAFTPAKSHHVRFERAVSESRWERCG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+  R+ A +FL+  +R+ VG++  V  G+      E+ L    R E GP AP  GL  
Sbjct: 179 DLLVYRITADAFLYNMVRALVGTMLEVARGRRDLASFEELLGGARRAEGGPTAPARGLTL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VRVRY 243


>gi|315655839|ref|ZP_07908737.1| tRNA pseudouridine synthase A [Mobiluncus curtisii ATCC 51333]
 gi|315489903|gb|EFU79530.1| tRNA pseudouridine synthase A [Mobiluncus curtisii ATCC 51333]
          Length = 314

 Score =  237 bits (606), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 87/273 (31%), Positives = 129/273 (47%), Gaps = 28/273 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++QG++E A+ ++  + V +  AGRTD+GVHA  QV
Sbjct: 18  MRIRLDIRYDGTPFHGWAAQPGLPTVQGALESALAVIYRQTVELTVAGRTDAGVHASGQV 77

Query: 62  AHFDLV----REWVPVILCKALNAYL------------------KISDTI---SILNLSI 96
           AHF +     R   P  L   L A L                     + +    +    +
Sbjct: 78  AHFTVPEVGDRIVPPDTLAPRLGAVLRAVLSGNLASPLPDSPAAYPPNAVDALVVTTAMV 137

Query: 97  VDKQFHARFSAIRRSYLYRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
           V + F ARFSA+ R Y+YRI+        L +   W  P  LD   M  +A  L+G HDF
Sbjct: 138 VPETFDARFSALARHYVYRIVDDLAVRNPLCRNYCWWYPTPLDAAAMNASAAVLLGEHDF 197

Query: 156 TTFRSIHCQASSPIRTIDHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             F     + ++ IRT+   +       ++EIRV A +F H+ +RS VG+L  VG  K  
Sbjct: 198 AAFCKPR-EGATTIRTLQQLETLRTAPGMMEIRVRADAFCHSMVRSLVGALTEVGRAKRD 256

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  L  AL A+ R    P+AP  GL    V+Y 
Sbjct: 257 TVWLADALAAKARIPEIPVAPALGLTLTQVDYP 289


>gi|293977793|ref|YP_003543223.1| pseudouridylate synthase I [Candidatus Sulcia muelleri DMIN]
 gi|292667724|gb|ADE35359.1| pseudouridylate synthase I [Candidatus Sulcia muelleri DMIN]
          Length = 250

 Score =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/246 (30%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + I Y+G+ ++GWQ QK   S+Q +IE  +  +  + + + GAGRTD+GVHA++  
Sbjct: 1   MRFFLEISYHGASFYGWQIQKKNISVQETIENCLSFLLKKSIKIIGAGRTDTGVHAIQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+   + + +           +   I I+N+  V K+ HARF+AI R Y YRI   + 
Sbjct: 61  AHFEFYEKKILLYRNFLFKLNSFLPLNIKIINIFPVKKKIHARFTAISRVYEYRISLGKN 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P +L     WL  + +  + +   A+ L    D+++F    C   + I  I +   +   
Sbjct: 121 PFSL--SWQWLSKQKIKLKPLNKGAKILKKYKDYSSFCKKKCNYKTYICNIFNAKWHIKN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++   + A  +L   +RS VG+L  +G GK T  D    L A+DR      AP +GL+ 
Sbjct: 179 NILYFNIEANRYLRNMVRSIVGTLIELGIGKITIKDFINILYAKDRNLALISAPAKGLFL 238

Query: 242 DSVEYS 247
             + Y 
Sbjct: 239 TKINYP 244


>gi|229815740|ref|ZP_04446065.1| hypothetical protein COLINT_02789 [Collinsella intestinalis DSM
           13280]
 gi|229808656|gb|EEP44433.1| hypothetical protein COLINT_02789 [Collinsella intestinalis DSM
           13280]
          Length = 292

 Score =  237 bits (604), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 109/251 (43%), Gaps = 11/251 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
             + Y+G+ + G+  Q  G  ++ G + +A+  +    V +  AGRTD+GVHA+ Q    
Sbjct: 36  FRLGYDGAAFSGFAEQPEGLRTVAGEVRRALETILRRPVDLTCAGRTDAGVHAVSQYVSI 95

Query: 65  DLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               +          +A+ A L     I++  +      F ARF A  R+Y YRI+T  A
Sbjct: 96  PAHADELAITHARWMRAMAALL--PSDIALNAVYHARPGFSARFDARSRTYTYRIVTGDA 153

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDVNS- 179
              L +   W     LD + M  AA  LVG HDF +F            R +        
Sbjct: 154 RPLLTRSVTWWHRLPLDMDAMERAAACLVGEHDFKSFCKTSSAIDKPTCRNVIAVSFERA 213

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  I   +   +FLH+ +R+ VGSL  VG G+     L  AL A DR+  GP AP 
Sbjct: 214 SALGEEHIAFTITGNAFLHSMVRTIVGSLVEVGAGRRDERWLSDALAACDRRAAGPTAPA 273

Query: 237 EGLYFDSVEYS 247
            GL F  V Y 
Sbjct: 274 RGLCFMDVAYD 284


>gi|325262993|ref|ZP_08129729.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
 gi|324032087|gb|EGB93366.1| tRNA pseudouridine synthase A [Clostridium sp. D5]
          Length = 244

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 71/249 (28%), Positives = 122/249 (48%), Gaps = 8/249 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    +++EY+G+ Y GWQR   G   +++   + + I  +T E V +    RT+ GVHA
Sbjct: 1   MHNIKLVLEYDGARYQGWQRLGKGESTNTVANKLLEVIHKMTAEDVELFCGARTEVGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV +F    +     + + LN YL     I++L+   + ++FHA  +A  R+Y YRI 
Sbjct: 61  YGQVVNFKTTSDMKTDEIRQYLNRYL--PMDIAVLSAEEMPERFHASLNAKSRTYQYRIA 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P    +   +   ++ D   M+ AA  L GRHDF  F ++  ++ S  + I + D+
Sbjct: 119 IGAVPSVFNRKYTYYAFRTPDIGIMQQAALLLAGRHDFKNFSTVK-KSKSTEKEIYNIDI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + I+I + A  FLH   R  +G+L  +G GK     +E   + ++  E      P+
Sbjct: 178 YGDTDEIQISLRANDFLHNMPRMIIGTLMDIGLGKRKMECIEAIFKGEE--EASAPCDPK 235

Query: 238 GLYFDSVEY 246
           G++  +V Y
Sbjct: 236 GMFLKNVGY 244


>gi|313887179|ref|ZP_07820875.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|312923408|gb|EFR34221.1| tRNA pseudouridine synthase A [Porphyromonas asaccharolytica
           PR426713P-I]
          Length = 262

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 80/252 (31%), Positives = 119/252 (47%), Gaps = 10/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ Y GWQ Q  G S+Q  +E+A+ ++  + + V GAGRTD+GVHA   +
Sbjct: 6   QRVFLEVAYDGTNYCGWQVQSRGVSVQSELERALSILFRQPISVTGAGRTDAGVHAYSMM 65

Query: 62  AHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AH DL     P+  + + L   L+    IS+ +++ V    HARF A  R Y Y I    
Sbjct: 66  AHADLPIPHPPLAQIQRGLCGILR--GGISVRSVTPVIPTAHARFDATSRRYHYYISACS 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P        W      D   M  A +H +G HDFT+F  +H Q      T+        
Sbjct: 124 NP--FWGDYCWERRTLPDMALMNEACRHFIGEHDFTSFSKLHTQTKHNRCTVYTAHWEQV 181

Query: 181 G-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +   V A  FLH  +R+ VG+L  VG G+ T   + + +Q++DR   G  AP
Sbjct: 182 EMPGLWDAMRYEVCANRFLHGMVRTMVGTLLEVGYGQRTPDSIAELIQSEDRSLAGSAAP 241

Query: 236 PEGLYFDSVEYS 247
              L+F    Y 
Sbjct: 242 ARALFFVEATYP 253


>gi|326799821|ref|YP_004317640.1| tRNA pseudouridine synthase A [Sphingobacterium sp. 21]
 gi|326550585|gb|ADZ78970.1| tRNA pseudouridine synthase A [Sphingobacterium sp. 21]
          Length = 255

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 118/249 (47%), Gaps = 8/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + + ++G  Y GWQ Q+N  S+Q  + KA+  +    V   G GRTD+GVHA +  A
Sbjct: 7   RYFVELAFHGGAYHGWQIQENAISVQEVLNKALGTLLRVPVNTVGCGRTDTGVHAKQLFA 66

Query: 63  HFDLVREWVP---VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           HFD     +      +   LNA L     I++  L +V    HARF AI+RSY Y I   
Sbjct: 67  HFDDAVGAIEGNEERIVTGLNALL--PTDIAVKQLFVVAPNAHARFDAIKRSYEYHIHFG 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P     G +W +    D E M  AA+H++   DF+ F   H Q  +    +   +   
Sbjct: 125 KNP--FLHGFSWQLRDRPDVEAMNEAARHMMKYKDFSCFSKSHTQVFTNNCQLTKAEWQW 182

Query: 180 -FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A  FL   +R+ VG+L  +G+GK     + + + +++R   G   P  G
Sbjct: 183 LDGGRLVFYISADRFLRNMVRAIVGTLMEIGNGKRDLNYIHEVINSKNRSMAGVSVPACG 242

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 243 LYLTEVLYP 251


>gi|256544630|ref|ZP_05472002.1| tRNA pseudouridine synthase A [Anaerococcus vaginalis ATCC 51170]
 gi|256399519|gb|EEU13124.1| tRNA pseudouridine synthase A [Anaerococcus vaginalis ATCC 51170]
          Length = 252

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 113/247 (45%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               + I+Y+GS + G+Q QKN  ++Q  +E AI  VTGE   +  +GRTDSGVHA    
Sbjct: 4   QNILLKIQYDGSLFEGFQIQKNKRTVQKELEDAIRKVTGEENRIIASGRTDSGVHANEMY 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F   +          L  YL   D I  L    VDK FHARFS   ++Y Y I   + 
Sbjct: 64  INFLTAKIIRADKFHFHLKKYL--PDDILALESKKVDKNFHARFSVKTKTYKYVISLDKI 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSF 180
              + +     I   LD + ++   + L G HDF  F  S      + IR ID       
Sbjct: 122 LHPIYRNYMEQITYKLDFDKLKQGMEILKGEHDFKAFMLSEKNDIINTIRKIDDCYFVLN 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N + +   A SFLH Q+R   GSL  +  GK +  D +      + +   P     GLY
Sbjct: 182 ENRLYLYFKAESFLHNQVRIMAGSLIELSRGKISLDDFKYYFNKNNTRRANPTLKAGGLY 241

Query: 241 FDSVEYS 247
            DS++YS
Sbjct: 242 LDSIDYS 248


>gi|227876165|ref|ZP_03994281.1| tRNA-pseudouridine synthase I [Mobiluncus mulieris ATCC 35243]
 gi|306819440|ref|ZP_07453147.1| tRNA pseudouridine synthase A [Mobiluncus mulieris ATCC 35239]
 gi|227843126|gb|EEJ53319.1| tRNA-pseudouridine synthase I [Mobiluncus mulieris ATCC 35243]
 gi|304647732|gb|EFM45050.1| tRNA pseudouridine synthase A [Mobiluncus mulieris ATCC 35239]
          Length = 326

 Score =  236 bits (603), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 82/306 (26%), Positives = 118/306 (38%), Gaps = 60/306 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA--- 57
           M R    I Y+G  + GW RQ    ++QG++E A+ ++  + V +  AGRTD+GVHA   
Sbjct: 1   MTRIRFDIRYDGRPFHGWARQPGLPTVQGALETALTVLFRQPVTLTVAGRTDAGVHATGQ 60

Query: 58  --------------------------LRQVAHFDLVREWVPVILCKALNAYL-------- 83
                                     L  +             L   L+  L        
Sbjct: 61  VAHFDLPDQFSGDWLRDAHDTEFAASLGAIVAASNPPGIANFQLSTGLHRRLESVLRLVT 120

Query: 84  -----------------KISDT---ISILNLSIVDKQFHARFSAIRRSYLYRIITRQ-AP 122
                               +    I +     V   F ARFSA+ R Y Y +I    A 
Sbjct: 121 SGNTPTIPGLNLDDQPIYPPEANGAIVVTAARPVPDAFDARFSALARHYEYLVIDEPTAR 180

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-G 181
             L +   W     L+   M  A+  L+G HDF  F     + ++ IRT+    V+    
Sbjct: 181 NPLTRNTCWWYGAPLNVARMHEASAGLLGTHDFAAFCKPR-EGATTIRTLKQLGVSRLAP 239

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I   V A +F H+ +RS VG+L  VG GK  +  LE+AL +  R    PLAP +GL  
Sbjct: 240 GEIRFDVAADAFCHSMVRSLVGALTEVGRGKRDADWLEQALHSAVRIPEIPLAPAQGLTL 299

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 300 VRVDYP 305


>gi|149279607|ref|ZP_01885736.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
 gi|149229643|gb|EDM35033.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
          Length = 283

 Score =  236 bits (603), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 115/250 (46%), Gaps = 8/250 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + YNG+ Y GWQ Q N  ++Q  ++KA+ +   + V   G GRTD+GVHA +  
Sbjct: 35  QRYFIELSYNGTEYHGWQIQPNAVTVQEDLDKALSVFFRQPVATVGCGRTDTGVHATQFF 94

Query: 62  AHFDLV----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            HFDL         P      +N+ L     I+I  +  VD + HARF A  R+Y Y + 
Sbjct: 95  VHFDLPAETASTLDPGRAVTGINSLLSY--QIAIGRIFAVDNEAHARFGATARAYHYHLH 152

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             + P  L   R+WL   SLD E M  AA  ++   DF+ F   + Q  +    +     
Sbjct: 153 FHKDPFKL--NRSWLYKGSLDVEAMNQAAAAILEYTDFSCFSKSNTQTFTNNCKVVEAYF 210

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 ++  + A  FL   +R+ VG+L  VG  +    +  + + +  R   G   P  
Sbjct: 211 TLTDGGLQFTIRADRFLRNMVRAIVGTLIKVGKKEINLNEFREIIASGSRSNAGQSVPAC 270

Query: 238 GLYFDSVEYS 247
           GLY  +V Y 
Sbjct: 271 GLYLVNVVYP 280


>gi|126433747|ref|YP_001069438.1| tRNA pseudouridine synthase A [Mycobacterium sp. JLS]
 gi|126233547|gb|ABN96947.1| tRNA pseudouridine synthase A [Mycobacterium sp. JLS]
          Length = 299

 Score =  236 bits (602), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 77/259 (29%), Positives = 116/259 (44%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ + GW  Q    ++ G I++A+  V    V V  AGRTD+GVHA  QV
Sbjct: 23  TRLRLDVSYDGTDFAGWAPQTGQRTVAGLIDEALTTVFRTPVTVRAAGRTDAGVHATGQV 82

Query: 62  AHFDLVREWVPVILCKA------------LNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  + +P    ++                  +   + I ++      F ARFSA+R
Sbjct: 83  AHVDVPDDALPHAYPRSARPDEPEFLPLVRRLGRFLPADVRIRDIIRAPTGFDARFSALR 142

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR+ T    +           P+ LD E M  A   LVG  DF  F   H + ++ 
Sbjct: 143 RHYTYRLGTAPYGVEPQSARFVTPWPRPLDVEAMNDAGSQLVGLRDFAAFCR-HREGATT 201

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   +    G+L+   V A +F  + +RS VG+L  VG+ +         L A  R 
Sbjct: 202 IRDLQRLEWTRDGDLVTAYVSADAFCWSMVRSLVGALIAVGEHRREPEWCAGLLSATRRS 261

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                APP+GL    V+Y 
Sbjct: 262 SEFAAAPPQGLTLVGVDYP 280


>gi|297849290|ref|XP_002892526.1| hypothetical protein ARALYDRAFT_471082 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297338368|gb|EFH68785.1| hypothetical protein ARALYDRAFT_471082 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 373

 Score =  236 bits (602), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 89/316 (28%), Positives = 142/316 (44%), Gaps = 70/316 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + G Q+Q    ++ G ++ A     G+ V +  + RTD+GVHAL  V
Sbjct: 56  QRYLVAIEYIGTRFSGSQQQAKDRTVVGVLQDAFHKFIGQPVKIFCSSRTDAGVHALSNV 115

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  
Sbjct: 116 CHVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQE 175

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YR++    P   LEK R W +P+ L+  +M+ A + LVG HDF++FR+  CQA SP
Sbjct: 176 RTYFYRLLAGSDPLSILEKDRCWHVPEELNPRSMQEACRVLVGYHDFSSFRAAGCQAKSP 235

Query: 169 IRTIDHFDVNSFG---------------------------------------NLIEIRVV 189
           +R +D  ++                                             +E    
Sbjct: 236 MRYLDELNITEVPSTPYFPSITERAWSNLNNGDPLACSSQPKSETAGVTTNVGEVEGSTD 295

Query: 190 ARSFLH------------------TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
             SF                     Q+R  VG+LK VG G+ T +D+E+ L+A+      
Sbjct: 296 GDSFGRRRRHRCYVVTARSRGFLYHQVRLIVGALKCVGTGELTVSDVERILEAKTVSAAK 355

Query: 232 PLAPPEGLYFDSVEYS 247
           P+AP  GLY   V+Y 
Sbjct: 356 PMAPASGLYLARVKYE 371


>gi|108798087|ref|YP_638284.1| tRNA pseudouridine synthase A [Mycobacterium sp. MCS]
 gi|119867183|ref|YP_937135.1| tRNA pseudouridine synthase A [Mycobacterium sp. KMS]
 gi|108768506|gb|ABG07228.1| tRNA pseudouridine synthase A [Mycobacterium sp. MCS]
 gi|119693272|gb|ABL90345.1| tRNA pseudouridine synthase A [Mycobacterium sp. KMS]
          Length = 299

 Score =  236 bits (602), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 77/259 (29%), Positives = 116/259 (44%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ + GW  Q    ++ G I++A+  V    V V  AGRTD+GVHA  QV
Sbjct: 23  TRLRLDVSYDGTDFAGWAPQTGQRTVAGLIDEALTTVFRTPVTVRAAGRTDAGVHATGQV 82

Query: 62  AHFDLVREWVPVILCKA------------LNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  + +P    ++                  +   + I ++      F ARFSA+R
Sbjct: 83  AHVDVPDDALPHAYPRSARPDEPEFLPLVRRLGRFLPADVRIRDIIRAPTGFDARFSALR 142

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR+ T    +           P+ LD E M  A   LVG  DF  F   H + ++ 
Sbjct: 143 RHYTYRLGTAPYGVEPQSARFVTPWPRPLDVEAMNDAGSQLVGLRDFAAFCR-HREGATT 201

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   +    G+L+   V A +F  + +RS VG+L  VG+ +         L A  R 
Sbjct: 202 IRDLQRLEWTRDGDLVTAYVSADAFCWSMVRSLVGALIAVGEHRREPEWCAGLLSATRRS 261

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                APP+GL    V+Y 
Sbjct: 262 SEFAAAPPQGLTLVGVDYP 280


>gi|145225544|ref|YP_001136222.1| tRNA pseudouridine synthase A [Mycobacterium gilvum PYR-GCK]
 gi|145218030|gb|ABP47434.1| tRNA pseudouridine synthase A [Mycobacterium gilvum PYR-GCK]
          Length = 298

 Score =  236 bits (602), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 80/259 (30%), Positives = 123/259 (47%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G I+ A+  V    V+   AGRTDSGVHA  QV
Sbjct: 20  VRLRLDIAYDGTDFAGWATQAGQRTVAGVIDDALSTVFRTPVLTRAAGRTDSGVHATGQV 79

Query: 62  AHFDLVREWVPVILCKALNAY------------LKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  + +P    + + A               +++ + +  +      F ARFSA+R
Sbjct: 80  AHADIPTDALPHAYPRTVRAGEPEFGPLVRRLGRMLTEDVRVRGIVRAAPGFDARFSALR 139

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y+YR+ T    +   E       P+ LD + M  AAQ+++G HDF  F   H   ++ 
Sbjct: 140 RHYVYRLTTAPYGVEPAEARFVTAWPRPLDVDAMAGAAQNVLGLHDFAAFCR-HRDGATT 198

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   D    G+ I + V A +F    +RS VG+L  VG+ +   T   + L A+ R 
Sbjct: 199 IRELQRLDCVRDGDRISVHVSADAFCWNMVRSLVGALLAVGEHRRDDTWCVQLLHARHRS 258

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                AP  GL    V+Y 
Sbjct: 259 SDFAAAPARGLTLVGVDYP 277


>gi|292557750|gb|ADE30751.1| tRNA pseudouridine synthase [Streptococcus suis GZ1]
          Length = 222

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 71/222 (31%), Positives = 113/222 (50%), Gaps = 5/222 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+G  + G+QRQ +  ++Q  IEK +  + +G+ V VHGAGRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGHDFSGFQRQPHARTVQEEIEKTLVRLNSGQPVTVHGAGRTDAGVHAYG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL        L  AL+   + S+ I ++++  V   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLAGSRDVEKLRFALDT--QTSEDIDVVSVEQVADDFHCRYAKHSKTYEFLVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID--HFDV 177
           +    + +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + 
Sbjct: 119 RPKNPMMRHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTITVASMEY 178

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           +     +        FL+ Q+R+ VG+L  +G+G+     ++
Sbjct: 179 DQQRQFLIFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIK 220


>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 =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 110/203 (54%), Positives = 142/203 (69%), Gaps = 1/203 (0%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISD-TISILNLSIVDKQFHA 103
           +  AGRTD+GVHA  QVAH DL ++W    +  A+NA+L +++  ISILN+      F A
Sbjct: 1   MSAAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMAEERISILNVEKTTDTFDA 60

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           RFSA  R YLYRI  R+APLA+   RAW + K LD + M  AAQ L+G HDFTTFR+  C
Sbjct: 61  RFSARARHYLYRIHNRRAPLAVNYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQC 120

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           QA SP++T+D  DV   G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+
Sbjct: 121 QAKSPVKTLDRLDVTRNGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALE 180

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           A+DRK CG +APP GLY   V+Y
Sbjct: 181 ARDRKACGQVAPPYGLYLIGVDY 203


>gi|308814270|ref|XP_003084440.1| TRUA1_PARUW tRNA pseudouridine synthase A 1 (ISS) [Ostreococcus
           tauri]
 gi|116056325|emb|CAL56708.1| TRUA1_PARUW tRNA pseudouridine synthase A 1 (ISS) [Ostreococcus
           tauri]
          Length = 705

 Score =  235 bits (601), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 81/260 (31%), Positives = 121/260 (46%), Gaps = 18/260 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHALR 59
           Y M I Y+G+ Y G+QRQ  + +S+Q  +E+ +  +TGE    + + G+GRTD GVHA  
Sbjct: 17  YAMTISYDGTNYKGFQRQGADVASVQRELERCLTRLTGEGRDALRLGGSGRTDGGVHARG 76

Query: 60  QVAHFDLVREW----VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           QV HF   ++W          KA+N  L     +           FHARF A R++Y Y 
Sbjct: 77  QVVHFYSEKDWRSAEDFARCVKAMNGML--PRDVRCERFWRPHPAFHARFHATRKTYAYY 134

Query: 116 IITRQAPLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS------P 168
           +  R       +  A     ++ D + +R A Q+ VG  DF  F +      +       
Sbjct: 135 VDARSPHDVFARAYACQCGWRACDVDALRRACQYFVGTRDFRAFANTSRDKPTSDEDLNT 194

Query: 169 IRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            RTI  FDV    + LI +      FL+ Q+R+ VG+  +V  G+     +   L + DR
Sbjct: 195 TRTIFRFDVFEQADGLIRLECEGDGFLYRQVRNMVGAALVVASGREKPEWILDLLASGDR 254

Query: 228 KECGPLAPPEGLYFDSVEYS 247
           +     AP  GL+  SVEY 
Sbjct: 255 RRVPTAAPARGLFLQSVEYP 274


>gi|189346490|ref|YP_001943019.1| tRNA pseudouridine synthase A [Chlorobium limicola DSM 245]
 gi|238692218|sp|B3EIU9|TRUA_CHLL2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189340637|gb|ACD90040.1| tRNA pseudouridine synthase A [Chlorobium limicola DSM 245]
          Length = 243

 Score =  235 bits (601), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 110/247 (44%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M      +EY+G+ + GWQRQ  G  ++QG +E  +  +  E + +  AGRTD GVHA  
Sbjct: 1   MKNIRFDVEYDGTDFCGWQRQPGGIQTLQGELEAQLGRILQENISLTAAGRTDKGVHARL 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          +  ALN+ L   DT+ + N  +V   FHARFSA  R Y Y ++  
Sbjct: 61  QVVNFMTGSAMELSKMAHALNSLL--PDTVRVSNPHVVPLDFHARFSAKEREYRYFLL-- 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P AL          SL    M+ AA  LVG HDF           +P+  I   +   
Sbjct: 117 EEPSALRCRFTGCSKGSLHIGVMQDAAGLLVGEHDFLLLSKEPADKKNPVCLIKECEWQE 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              +   R+ A  FL + +R  VG +  VG G+    DL   L           A P GL
Sbjct: 177 ENGVFVFRIRANRFLRSMVRYLVGVMIAVGRGRAVPEDLGMLLDDGLMTFPLFPAEPNGL 236

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 237 FLWDVSY 243


>gi|171910331|ref|ZP_02925801.1| putative tRNA pseudouridylate synthase I [Verrucomicrobium spinosum
           DSM 4136]
          Length = 258

 Score =  235 bits (601), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 80/256 (31%), Positives = 117/256 (45%), Gaps = 13/256 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + I Y+G  + GWQ Q N  ++Q  +E A+  +TG  V V G+GRTD+GVHAL QV
Sbjct: 4   RRLKLTIAYDGRPWRGWQSQANSVTVQDQVETALRDLTGTQVNVQGSGRTDAGVHALAQV 63

Query: 62  AHFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AH D+            +ALN  L    +I +++      +FHARF A+ + Y YR+   
Sbjct: 64  AHADVPDALKMGREAWVRALNVRL--PQSIRVMDCEDAAGEFHARFDAVGKIYCYRLWRG 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS---------IHCQASSPIR 170
                 E+GRAW +  +LD + +   A  L G H+F    +             A +  R
Sbjct: 122 DVMSPFEQGRAWHVYGALDLDLLHHGAGILTGTHNFARLSANRGGMSEDERREDAEALTR 181

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           T+   D+   G +I I      FL+  +R   GSL  V  G+     L   +      + 
Sbjct: 182 TVRRIDIIPEGEVIRIEFEGDGFLYKMVRLMTGSLVQVARGRERLEWLSDLVGDPSGLKS 241

Query: 231 GPLAPPEGLYFDSVEY 246
              AP +GLY   V Y
Sbjct: 242 NQCAPADGLYLVKVFY 257


>gi|117927545|ref|YP_872096.1| tRNA pseudouridine synthase A [Acidothermus cellulolyticus 11B]
 gi|117648008|gb|ABK52110.1| tRNA pseudouridine synthase A [Acidothermus cellulolyticus 11B]
          Length = 297

 Score =  235 bits (601), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 74/259 (28%), Positives = 119/259 (45%), Gaps = 16/259 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + G+ RQ    ++Q  +E+A+ +V    E   V  AGRTD+GVHA  Q
Sbjct: 20  RLRIDLGYDGTDFAGFARQPGLRTVQAEVERALAVVLRLPEPPPVTAAGRTDAGVHARGQ 79

Query: 61  VAHFDLV-----------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           V H D+                  +   A      + D I++  + +    F ARFSA+ 
Sbjct: 80  VLHVDVPIDALRVVGAAETGAADAVAQLAARLNGVLPDDIAVHAVGLAPPGFDARFSALA 139

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           R Y YR+  R+    L +      P+ LD   M  A   L+G HDF  F     + ++ I
Sbjct: 140 RRYSYRVADRRW-DPLRRRDTLRWPRPLDETAMNAAGAALLGEHDFAAFCRRR-ENATTI 197

Query: 170 RTIDHFDVNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           R +  F+    G+ +   +V A +F H+ +R+ VG++  VG G+       + L A+ R 
Sbjct: 198 RRLLRFEWLRDGDGVLVAQVEADAFCHSMVRALVGAVLAVGAGRRPVGWPAEVLAARARD 257

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               + PP GL  + V Y 
Sbjct: 258 PAVTVVPPHGLTLEEVCYP 276


>gi|256831855|ref|YP_003160582.1| tRNA pseudouridine synthase A [Jonesia denitrificans DSM 20603]
 gi|256685386|gb|ACV08279.1| tRNA pseudouridine synthase A [Jonesia denitrificans DSM 20603]
          Length = 310

 Score =  235 bits (601), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 79/260 (30%), Positives = 113/260 (43%), Gaps = 16/260 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R    + Y G+ + GW RQ    S+QG++E A+  + GE + V  AGRTD+GVHA  QV 
Sbjct: 26  RIRCDVAYRGTDFVGWARQPGLRSVQGTLEDALERLMGERIAVTVAGRTDAGVHARGQVV 85

Query: 63  HFDLVREWVPVILCK-------ALNAYL--KISDTISILNLSIVDKQFHARFSAIRRSYL 113
           H D+  +    +  +       AL A L   +   + +  ++     F ARFSA+ R+Y 
Sbjct: 86  HCDVPGDRWERLPGRSDRTPGEALRAKLGGILPSDVVVRRVAPAPPGFDARFSALSRTYY 145

Query: 114 YRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YRI         L       +   LD E M   A  LVG  DF  F       +S IR +
Sbjct: 146 YRIADDVMMRDPLTAPFVLWVRSPLDVEAMNRGAAPLVGLRDFAAFCKPRP-GASTIREL 204

Query: 173 DHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             F            L+   V A +F H  +R+ VG+   VG G      L +AL ++ R
Sbjct: 205 QDFRWERVEQGPDEGLVRATVRADAFCHNMVRALVGASLDVGRGVRGEEWLVQALTSKSR 264

Query: 228 KECGPLAPPEGLYFDSVEYS 247
                +  P GL  + V Y 
Sbjct: 265 VNSSAVVQPHGLTLEQVAYP 284


>gi|257054500|ref|YP_003132332.1| pseudouridylate synthase I [Saccharomonospora viridis DSM 43017]
 gi|256584372|gb|ACU95505.1| pseudouridylate synthase I [Saccharomonospora viridis DSM 43017]
          Length = 300

 Score =  235 bits (601), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 71/265 (26%), Positives = 116/265 (43%), Gaps = 23/265 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV---VVHGAGRTDSGVHAL 58
           +R  + + Y+G+ + GW RQ    ++QG +E A+            V  AGRTD+GVHA+
Sbjct: 15  VRLRIDLSYDGTDFSGWARQPGRRTVQGVLEDALAKQPPGASIAGPVVVAGRTDAGVHAI 74

Query: 59  RQVAHFDLVR--------------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
            QV H D+ R                  +   +       +   + +L++      F AR
Sbjct: 75  GQVVHVDVTRLAGETRSRMPISSDGLPDLDWARY-RLNRVLPADVRVLSIRRAPAGFDAR 133

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA++R Y Y++         L +      P+ L  + M  AA  L+G HDF  F     
Sbjct: 134 FSAVKRHYRYQVSDAPWGVSPLRRRDTLAWPRPLSVDAMNEAASSLLGLHDFAAFCKRR- 192

Query: 164 QASSPIRTIDHFDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           + ++ IR +            + + V A +F H+ +RS VG+L  VGDG+       + L
Sbjct: 193 EGATTIRELMELRWCRVDEYELHLSVSADAFCHSMVRSLVGALLWVGDGRRDVGWPLEVL 252

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
           +++ R     +AP  GL    V+Y 
Sbjct: 253 RSRQRSSV--VAPAHGLTLVKVDYP 275


>gi|226357340|ref|YP_002787080.1| tRNA-pseudouridine synthase I [Deinococcus deserti VCD115]
 gi|226319330|gb|ACO47326.1| putative tRNA-pseudouridine synthase I (tRNA pseudouridylate
           synthase I) (tRNA-uridine isomerase) [Deinococcus
           deserti VCD115]
          Length = 266

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 115/248 (46%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + ++G  Y GWQ Q N  S+Q ++  A   +         AGRTD+GVHA    
Sbjct: 18  RRLRLTLAWDGGPYAGWQSQPNAPSVQDTLHAAFGRLGSGAFRPVAAGRTDAGVHAEAMP 77

Query: 62  AHFDLVREW--VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            H D+   +      L +ALNA+L    ++S+L        FHARFS   R Y+YR++  
Sbjct: 78  VHVDVPGGFRVPAPKLARALNAWL--PPSVSVLEAFDAPAGFHARFSCTERRYVYRLLVS 135

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GRA  +P +LD   M  AA +L G HDF  F +   +    +R +    V  
Sbjct: 136 SQRHPLWHGRALHLPGALDAGAMNAAATYLTGTHDFAAFATQ--EDRQTVRELRVLRVVP 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G + E++V   SFL   +R  VG+L L G GK     +   L  + R + G   P  GL
Sbjct: 194 EGPVWEVQVTGESFLRHMVRGLVGTLLLCGQGKLEPLAVRDVLAHRQRSQAGANVPAYGL 253

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 254 YFTGASYP 261


>gi|116331308|ref|YP_801026.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116124997|gb|ABJ76268.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 265

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 80/251 (31%), Positives = 128/251 (50%), Gaps = 7/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y +++EY+G  + G+Q QK+  SIQ ++EKAI ++  E + + GAGRTD+GVHA   V
Sbjct: 1   MNYALLVEYDGLCFNGFQTQKDLPSIQENLEKAIKILLKEEISITGAGRTDTGVHARGMV 60

Query: 62  AHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +F  ++          ++NA       +SIL ++ V + F +RFS   R Y Y I+  +
Sbjct: 61  VNFKTIKTVQNFNKFLLSMNA--ITDSGLSILGMTEVGENFDSRFSCNSREYEYLILNTK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS 179
            P  + K RA+     +D   ++   + L G HDF +       +  S IRTI    +  
Sbjct: 119 YPRPIWKNRAFWYQHKIDVPRLKTELELLKGEHDFRSLAKTASMKDRSTIRTILDAKLER 178

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              +  L++I++ A  FLH  IR   G+L  + +GK    ++   L ++DR   G   PP
Sbjct: 179 SSEWEGLLKIKIRANGFLHNMIRILTGTLLEIANGKLKVPNILDILSSKDRTIAGITLPP 238

Query: 237 EGLYFDSVEYS 247
            GLYF    Y 
Sbjct: 239 YGLYFLRAYYD 249


>gi|227501274|ref|ZP_03931323.1| tRNA-pseudouridine synthase I [Anaerococcus tetradius ATCC 35098]
 gi|227216507|gb|EEI81913.1| tRNA-pseudouridine synthase I [Anaerococcus tetradius ATCC 35098]
          Length = 246

 Score =  235 bits (600), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 114/248 (45%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MIR   +   Y+G+ + G+Q QK+  S++  I+KA+  VTGE   +   GRTDSGVHA  
Sbjct: 1   MIRNVLVETAYDGTNFAGFQYQKDQRSVEEEIKKALVKVTGEDNRIVSCGRTDSGVHAKS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              +F    +  P      L  +L     I  L+   VD  FHARFS   + Y Y I   
Sbjct: 61  HFFNFLTASKIDPKAFSYHLQVHL--PADILALSSREVDLSFHARFSCKSKLYKYVIYRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVN 178
           +    + +     I   LD + +    + L G HDF +F       S + +R ID     
Sbjct: 119 KGMHPIYRNYKEEISYKLDLKRLEEGLKLLCGEHDFRSFMREDKDLSINTVRKIDQAYFL 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +EI   A SFLH Q+R  VGSL  +  GK +  D ++      +    P    +G
Sbjct: 179 ENGDDLEIYFKAESFLHNQVRIMVGSLVELSRGKLSLDDYKRFFDEDYKIRANPALGAQG 238

Query: 239 LYFDSVEY 246
           LY   VE+
Sbjct: 239 LYLWRVEF 246


>gi|255083272|ref|XP_002504622.1| predicted protein [Micromonas sp. RCC299]
 gi|226519890|gb|ACO65880.1| predicted protein [Micromonas sp. RCC299]
          Length = 253

 Score =  235 bits (600), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 85/253 (33%), Positives = 123/253 (48%), Gaps = 14/253 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y + + Y+G  Y G+Q Q  G ++QG +E+A+  +TG      G   +GRTD+GVHA  Q
Sbjct: 3   YALKLAYDGEAYLGFQYQPKGKTVQGEVERALTKLTGHDREFLGMQASGRTDTGVHARGQ 62

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           + HF             K+LN  +     +  + +      FHARF A+R++Y Y +  R
Sbjct: 63  ILHFYTKEPVSDLERFHKSLNGIM--PKDVRCVEVMRPHPAFHARFHAVRKTYHYFLDPR 120

Query: 120 QAPLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS---SPIRTIDHF 175
                  +  A     K    E +R AA   VG HDFT+F +     +   SP RTI  F
Sbjct: 121 LVLDPFVRRHALHCGWKPPSVERLREAAAVFVGTHDFTSFSNKSRDKTLVRSPTRTIYRF 180

Query: 176 DVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVG---DGKWTSTDLEKALQAQDRKECG 231
           DV    + LI + V    FL+  +R+ VG+L L     DGK+T+ DL   L+ +DR    
Sbjct: 181 DVVEQPDGLIRLEVEGNGFLYRMVRNMVGALMLAATGEDGKFTAEDLRDMLEGKDRGVAP 240

Query: 232 PLAPPEGLYFDSV 244
             APP GL+   V
Sbjct: 241 MGAPPHGLFLHEV 253


>gi|149196320|ref|ZP_01873375.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
 gi|149140581|gb|EDM28979.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
          Length = 276

 Score =  235 bits (600), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 79/251 (31%), Positives = 123/251 (49%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M  Y + I+++G+ +FGWQ Q +  ++Q  IEKA+  +     + + G+GRTD+GVHA  
Sbjct: 1   MNSYKLSIQFDGTTWFGWQSQNDFEAVQEQIEKALNTLYNCSEIKIDGSGRTDAGVHAFG 60

Query: 60  QVAHFDLVRE--WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             A F   +   +    L K LNA L    +I I +    +  FHARFS I ++Y+Y I 
Sbjct: 61  LCATFTEPKISKFTSDTLRKGLNALL--PVSIRIRSALQCETDFHARFSCIGKTYVYFID 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFD 176
                  +    +W + K L+ E MR + QHL G+HDF+ F           IRT+   +
Sbjct: 119 NSTTSSPILAPYSWHMRKKLNREKMRQSLQHLEGKHDFSAFTVDRKNLQGHAIRTVFKAE 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+++ +      FL+  +RS  G +  VG           AL++  R E G  AP 
Sbjct: 179 LIEIGHIVALLFTGDGFLYRMVRSMAGEVVNVGMEFQNPQHTLDALESHQRSEAGVTAPA 238

Query: 237 EGLYFDSVEYS 247
           +GL+     YS
Sbjct: 239 KGLFLGQCYYS 249


>gi|307701658|ref|ZP_07638674.1| tRNA pseudouridine synthase A [Mobiluncus mulieris FB024-16]
 gi|307613161|gb|EFN92414.1| tRNA pseudouridine synthase A [Mobiluncus mulieris FB024-16]
          Length = 340

 Score =  235 bits (599), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 82/306 (26%), Positives = 117/306 (38%), Gaps = 60/306 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA--- 57
           M R    I Y+G  + GW RQ    ++QG++E A+ ++  + V +  AGRTD+GVHA   
Sbjct: 1   MTRIRFDIRYDGRPFHGWARQPGLPTVQGALETALTVLFRQPVTLTVAGRTDAGVHATGQ 60

Query: 58  --------------------------LRQVAHFDLVREWVPVILCKALNAYL-------- 83
                                     L  +             L    +  L        
Sbjct: 61  VAHFDLPDQFSGDWLRDARDTDFAASLGAIVAASNPPGIANFQLSTGFHRRLDSVLRLVT 120

Query: 84  -----------------KISDT---ISILNLSIVDKQFHARFSAIRRSYLYRIITRQ-AP 122
                               +    I +     V   F ARFSA+ R Y Y +I    A 
Sbjct: 121 SGNTPTIPGINLDDQPIYPPEANGAIVVTAACPVLDAFDARFSALARHYEYLVIDEPTAR 180

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-G 181
             L +   W     LD   M  A+  L+G HDF  F     + ++ IRT+    V+    
Sbjct: 181 NPLTRNTCWWYGAPLDVARMHEASAGLLGTHDFAAFCKPR-EGATTIRTLKQLGVSRLAP 239

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I   V A +F H+ +RS VG+L  VG GK  +  LE+AL +  R    PLAP +GL  
Sbjct: 240 GEIRFDVAADAFCHSMVRSLVGALTEVGRGKRDADWLEQALHSAVRIPEIPLAPAQGLTL 299

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 300 VRVDYP 305


>gi|167758957|ref|ZP_02431084.1| hypothetical protein CLOSCI_01303 [Clostridium scindens ATCC 35704]
 gi|167663364|gb|EDS07494.1| hypothetical protein CLOSCI_01303 [Clostridium scindens ATCC 35704]
          Length = 245

 Score =  235 bits (599), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 121/250 (48%), Gaps = 9/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVH 56
           M    + IEY+GS Y GW R   +++ +++   I + +  ++GE  + ++   RT+ GVH
Sbjct: 1   MRNIKLTIEYDGSRYQGWTRLGKEESNNTVSNKIIEVLRKMSGEYLIELNCGCRTEVGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  Q+A+F    +   + +   LN YL     I+I  +  V ++FHA+ +A  ++Y+YR+
Sbjct: 61  AYAQIANFKTESKMDVLEIKHYLNRYL--PMDIAITEVEEVPERFHAQLNAASKTYVYRM 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P   ++   +   K  D   M+ AA  L+G HDF  F +   ++ S  R I   +
Sbjct: 119 TIDDVPSVFDRKYTYHCFKIPDKRVMQQAAMLLIGTHDFKNFSTAK-KSKSTERQIFEIE 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V      ++I + A  FLH   R  +G+L  +G G     D+E+      R+       P
Sbjct: 178 VYGDTEEMQILIHADDFLHNMARLIIGTLMDIGFGTRRKEDIEEIFAG--RQLASAPCDP 235

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 236 KGLYLQEVAY 245


>gi|325479638|gb|EGC82730.1| tRNA pseudouridine synthase A [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 246

 Score =  235 bits (599), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 117/248 (47%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MI+   +   Y+G+ + G+Q QK+  S++  + KAI  VTGE   +   GRTDSGVHA  
Sbjct: 1   MIKNILLETSYDGALFSGFQYQKDQRSVEEELTKAIRKVTGEENRIVSCGRTDSGVHAKS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              +F    +  P+ +   +  +L   D I  ++   VD  FHARFSA  + Y Y I   
Sbjct: 61  HFVNFLTASDINPIGIKFQIQPHL--PDDILAISSREVDLNFHARFSAKSKLYKYVICRS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVN 178
           +    + +     +   LD + +      LVG HDF  F       S + +RTI+     
Sbjct: 119 KDMHPIYRNYKEHVTYKLDLKKLEEGLNLLVGTHDFRLFMMEDKNLSINTVRTIEEAYFI 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +EI     SFLH Q+R  VGSL  +  G+ +  D EK    ++ K   P    EG
Sbjct: 179 ENGADLEIYFKGESFLHNQVRIMVGSLIELARGRISLDDYEKFFDKENTKRANPALGAEG 238

Query: 239 LYFDSVEY 246
           LY   VE+
Sbjct: 239 LYLWRVEF 246


>gi|296130457|ref|YP_003637707.1| tRNA pseudouridine synthase A [Cellulomonas flavigena DSM 20109]
 gi|296022272|gb|ADG75508.1| tRNA pseudouridine synthase A [Cellulomonas flavigena DSM 20109]
          Length = 306

 Score =  235 bits (599), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 83/267 (31%), Positives = 123/267 (46%), Gaps = 22/267 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-----GEI-VVVHGAGRTDSGV 55
           +R  + + Y+G G+ GW RQ    ++QG +E A+  V      GE    V  AGRTD+GV
Sbjct: 12  VRLRLDLAYDGGGFAGWARQPGLRTVQGELEDALATVLRSGPRGEPRPRVTVAGRTDAGV 71

Query: 56  HALRQVAHFDL-------VREWVPVILCKALNAYL--KISDTISILNLSIVDKQFHARFS 106
           HA  QVAH D+        R          L   L   +   + +  +    + F ARFS
Sbjct: 72  HARGQVAHVDVVPDALAAARGRSDRAAVDVLGTRLAGILPPDVVVHAVRHAPEGFDARFS 131

Query: 107 AIRRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+RR Y YR+   +     L +G      ++LD   M  AA+ LVGRHDF  +      A
Sbjct: 132 ALRRRYAYRVCDSEGTRDPLRRGWVLWHRRALDVAAMDAAARSLVGRHDFAAYCKPRPDA 191

Query: 166 SSPIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            + IRT++ F            L+   V A +F H+ +R+ VG+   VG+G+   T    
Sbjct: 192 -TTIRTLEEFTWTRPVDGPDAGLVVAHVQADAFCHSMVRALVGASLAVGEGRRPVTWPRD 250

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            L A+ R+    +  P+GL  + V Y 
Sbjct: 251 LLDARTRQGGATVVAPQGLTLEDVGYP 277


>gi|269976928|ref|ZP_06183902.1| tRNA pseudouridine synthase A [Mobiluncus mulieris 28-1]
 gi|269934759|gb|EEZ91319.1| tRNA pseudouridine synthase A [Mobiluncus mulieris 28-1]
          Length = 326

 Score =  235 bits (599), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 82/306 (26%), Positives = 118/306 (38%), Gaps = 60/306 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA--- 57
           M R    I Y+G  + GW RQ    ++QG++E A+ ++  + V +  AGRTD+GVHA   
Sbjct: 1   MTRIRFDIRYDGRPFHGWARQPGLPTVQGALETALTVLFRQPVTLTVAGRTDAGVHATGQ 60

Query: 58  --------------------------LRQVAHFDLVREWVPVILCKALNAYL-------- 83
                                     L  +             L   L+  L        
Sbjct: 61  VAHFDLPDQFSGDWLRDAHDTDFAASLGAIVAASNPPGIANFQLSTGLHRRLDSVLRLVT 120

Query: 84  -----------------KISDT---ISILNLSIVDKQFHARFSAIRRSYLYRIITRQ-AP 122
                               +    I +     V   F ARFSA+ R Y Y +I    A 
Sbjct: 121 SGNTPTIPGLNLDDQPIYPPEANGAIVVTTARPVPDAFDARFSALARHYEYLVIDEPTAR 180

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-G 181
             L +   W     L+   M  A+  L+G HDF  F     + ++ IRT+    V+    
Sbjct: 181 NPLTRNTCWWYGAPLNVARMHEASAGLLGTHDFAAFCKPR-EGATTIRTLKQLGVSRLAP 239

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I   V A +F H+ +RS VG+L  VG GK  +  LE+AL +  R    PLAP +GL  
Sbjct: 240 GEIRFDVAADAFCHSMVRSLVGALTEVGRGKRDADWLEQALHSAVRIPEIPLAPAQGLTL 299

Query: 242 DSVEYS 247
             V+Y 
Sbjct: 300 VRVDYP 305


>gi|269122416|ref|YP_003310593.1| tRNA pseudouridine synthase A [Sebaldella termitidis ATCC 33386]
 gi|268616294|gb|ACZ10662.1| tRNA pseudouridine synthase A [Sebaldella termitidis ATCC 33386]
          Length = 244

 Score =  235 bits (599), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 118/246 (47%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    ++ EY+GS + G+QRQ N  ++QGSIE+ I     E V +  +GRTD GVHAL Q
Sbjct: 1   MKNIKIVYEYDGSKFSGFQRQLNKKTVQGSIEEVIKNYFNEEVNLLSSGRTDKGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F + +   P I+   LN  L  S  I + +    D  FHARFSA  R+YLY +  + 
Sbjct: 61  VSNFFMEKSISPDIIKGILNRAL--SGKIRVTDAKEADSDFHARFSAKTRTYLYIMKLKD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E      +   +  E ++   +  +GRH+F +FR       +P R I++      
Sbjct: 119 EITPFESSYVSALDGKIIPEKLQKIMEPFIGRHNFDSFRKKDKDNKNPEREINNIRCYEE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I +  +SFL T IR  +GS   V   K     +   L   D      LAP EGLY
Sbjct: 179 DKRLFIEIEGKSFLKTMIRIMIGSALAVYFEKRNPDYICDKLDNPDSDGEKILAPSEGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LYKVNY 244


>gi|313201346|ref|YP_004040004.1| tRNA pseudouridine synthase a [Methylovorus sp. MP688]
 gi|312440662|gb|ADQ84768.1| tRNA pseudouridine synthase A [Methylovorus sp. MP688]
          Length = 225

 Score =  235 bits (599), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 80/210 (38%), Positives = 112/210 (53%), Gaps = 2/210 (0%)

Query: 38  VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV 97
           +    V V  AGRTD+GVHAL QV HF+   E       + +NA L    ++ +L    V
Sbjct: 1   MACHPVRVIAAGRTDTGVHALAQVVHFETTTERPLNAWVRGVNAGL--PSSVRVLWAQQV 58

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
           D +FHARFSA +R Y Y +  +    A+  G+     + LD + M  AA HL+G HDF+ 
Sbjct: 59  DDEFHARFSARQRYYQYILFDQAVAPAILAGKVGWFHQPLDVDAMAEAAAHLIGEHDFSA 118

Query: 158 FRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           FR+  CQA SP+RT+   +V   G  I       +FLH Q+R+ VG+L  VG G      
Sbjct: 119 FRAAECQAKSPVRTLQQAEVRRAGQAILFEFSGNAFLHHQVRNMVGALVYVGKGSQPPAF 178

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +++ LQ+ DR+   P   P+GLY   V Y 
Sbjct: 179 IQQLLQSHDRRLAPPTFSPDGLYLSGVGYE 208


>gi|116328579|ref|YP_798299.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116121323|gb|ABJ79366.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 265

 Score =  235 bits (599), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 79/251 (31%), Positives = 128/251 (50%), Gaps = 7/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y +++EY+G  + G+Q QK+  SIQ ++EKA+ ++  E + + GAGRTD+GVHA   V
Sbjct: 1   MNYALLVEYDGLCFNGFQTQKDLPSIQENLEKAVKILLKEEISITGAGRTDTGVHARGMV 60

Query: 62  AHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +F  ++          ++NA       +SIL ++ V + F +RFS   R Y Y I+  +
Sbjct: 61  VNFKTIKTVQNFNKFLLSMNA--ITDSGLSILGMTEVGENFDSRFSCNSREYEYLILNTK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS 179
            P  + K RA+     +D   ++   + L G HDF +       +  S IRTI    +  
Sbjct: 119 YPRPIWKNRAFWYQHKIDVPRLKTELELLKGEHDFRSLAKTASMKDRSTIRTILDAKLER 178

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              +  L++I++ A  FLH  IR   G+L  + +GK    ++   L ++DR   G   PP
Sbjct: 179 SSEWEGLLKIKIRANGFLHNMIRILTGTLLEIANGKLKVPNILDILSSKDRTIAGITLPP 238

Query: 237 EGLYFDSVEYS 247
            GLYF    Y 
Sbjct: 239 YGLYFLRAYYD 249


>gi|325847073|ref|ZP_08169899.1| tRNA pseudouridine synthase A [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481045|gb|EGC84090.1| tRNA pseudouridine synthase A [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 252

 Score =  234 bits (598), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 116/246 (47%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               + I+Y+GS + G+Q QK+  ++Q  +E+AI  VTGE   +  +GRTDSGVHA    
Sbjct: 4   QNILLKIQYDGSLFEGFQIQKDKRTVQKELEEAIRKVTGEKNRIIASGRTDSGVHANEMY 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F   ++         L  YL     I  L+   VDK FHARFS   ++Y Y I   + 
Sbjct: 64  INFLTAKDIRADKFHFHLKKYL--PADILALSSKKVDKNFHARFSVKTKTYKYVISLEKI 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSF 180
              + +     I   LD + ++   + L G HDF  F  S      + IR ID       
Sbjct: 122 LHPIYRNYMEQITYKLDFDKLKQGMEILKGEHDFRAFMLSEKNDIINTIRKIDDCYYILD 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N++ +   A SFLH Q+R   GSL  +  GK +  D +      ++K   P     GLY
Sbjct: 182 NNILFLYFKAESFLHNQVRIMAGSLIELSRGKISLDDFKFYFDKNNKKRANPTLKAGGLY 241

Query: 241 FDSVEY 246
            DS++Y
Sbjct: 242 LDSIDY 247


>gi|50955536|ref|YP_062824.1| tRNA pseudouridine synthase A [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|62901288|sp|Q6AD25|TRUA_LEIXX RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|50952018|gb|AAT89719.1| tRNA pseudouridine synthase A [Leifsonia xyli subsp. xyli str.
           CTCB07]
          Length = 288

 Score =  234 bits (598), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 78/266 (29%), Positives = 124/266 (46%), Gaps = 21/266 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---TGEIVVVHGAGRTDSGVHAL 58
            R+ + I Y G+ + GW RQ +  ++QG++E+A+  +   +GE   +  AGRTD+GVHA 
Sbjct: 6   TRFRLDIAYQGTDFAGWARQPDLRTVQGTLEEALATIFRCSGEPPSLTVAGRTDAGVHAT 65

Query: 59  RQVAHFDL---------------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
            QVAH DL                 +     L + +N  L     + +   +     F A
Sbjct: 66  GQVAHVDLSPEQVALLRRPHGKREPQLAHDALKRRVNGVLGPVPDVLVSRATEAPAGFDA 125

Query: 104 RFSAIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R Y YR+  R A    L++ R   +P +LD + M   A  ++G HDF ++    
Sbjct: 126 RFSALWRRYEYRVADRIALRDPLQRHRTAWVPNTLDVDAMDRGAHGMLGLHDFASYCKAR 185

Query: 163 CQASSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            + ++ IRT+  F        + +  V A +F H+ +R+ VG+   VG+GK    DL   
Sbjct: 186 -EGATTIRTLQAFSWRRDAEGVLLGEVAADAFCHSMVRALVGACVEVGEGKLRPGDLVTL 244

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
              + R     + P  GL    V Y 
Sbjct: 245 RDERQRTSAFKVMPARGLTLREVGYP 270


>gi|296394888|ref|YP_003659772.1| tRNA pseudouridine synthase A [Segniliparus rotundus DSM 44985]
 gi|296182035|gb|ADG98941.1| tRNA pseudouridine synthase A [Segniliparus rotundus DSM 44985]
          Length = 278

 Score =  234 bits (598), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 77/251 (30%), Positives = 113/251 (45%), Gaps = 9/251 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW RQ    ++ G IE+A+  +      +  AGRTD+GVHA  QVA
Sbjct: 10  RLRLDVAYDGTEFSGWARQPGRRTVAGVIEEALSTLLQSSAQLTVAGRTDAGVHATGQVA 69

Query: 63  HFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           H D+          P  L + L   L     + +L+   V  QF ARFSA+RR Y Y I 
Sbjct: 70  HVDVRADLVSGRLPPEKLVRKLARML--PTDVRVLSAQKVSAQFDARFSALRRHYRYHIT 127

Query: 118 TR-QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L         + LD + +  A+  LVG HDF  F       ++ IR +  F+
Sbjct: 128 RSVYGADPLRAREVVPWARPLDFDVLNAASSALVGLHDFAAFCRPRP-GATTIRELQRFE 186

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G LI   + A +F  +  RS VG++  V +G+     +   L A  R     +AP 
Sbjct: 187 WAESGVLITASITADAFCWSMCRSLVGAVTAVAEGRRDLAWIRSLLTASSRASEITVAPA 246

Query: 237 EGLYFDSVEYS 247
            GL    V+Y 
Sbjct: 247 HGLCLVGVDYP 257


>gi|289663172|ref|ZP_06484753.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 257

 Score =  234 bits (597), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 95/248 (38%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADGQVQVICAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++     V   FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSIAVRWCVPVADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTVSWERRPLDADAMHAAAQALLGENDFSAFRSVQCQALHARRNLQAIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 IGEVVEVQVQANAFLHHMVRNIVGSLILVGTGERPADWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|161833682|ref|YP_001597878.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri GWSS]
 gi|152206172|gb|ABS30482.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri GWSS]
          Length = 250

 Score =  234 bits (597), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 76/246 (30%), Positives = 125/246 (50%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + I Y+G+ ++GWQ QK   S+Q +IE  +  +  + + + GAGRTD+GVHA++  
Sbjct: 1   MRFFLEISYHGASFYGWQIQKKNISVQETIENCLSFLLKKSIKIIGAGRTDTGVHAIQMF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHF+   + + +           +   I I+N+  V K+ HARF+AI R Y YRI   + 
Sbjct: 61  AHFEFYEKKILLYRNFLFKFNSFLPLNIKIINIFTVKKKIHARFTAISRVYEYRISLGKN 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P +L+    WL  K +    +   A+ L    D+++F    C   + I  I +   +   
Sbjct: 121 PFSLDISWQWLSKKKIKLNPLNKGAKILKKYKDYSSFCKKKCNYKTYICNIFNAKWHIKN 180

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N++   + A  +L   +RS VG+L  +G GK T  D    L A+DR      AP +GL+ 
Sbjct: 181 NILYFNIEANRYLRNMVRSIVGTLIELGIGKITIKDFINILYAKDRNII--SAPAKGLFL 238

Query: 242 DSVEYS 247
             + Y 
Sbjct: 239 TKINYP 244


>gi|311896534|dbj|BAJ28942.1| putative tRNA pseudouridine synthase A [Kitasatospora setae
           KM-6054]
          Length = 302

 Score =  233 bits (596), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 79/259 (30%), Positives = 116/259 (44%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
            R  + + Y+G+ + GW RQ+   ++QG +E A+ +V    E   +  AGRTD+GVHA  
Sbjct: 20  TRIRLDLAYHGAEFSGWARQRERRTVQGELEDALRIVLRSEENFPLTVAGRTDAGVHARG 79

Query: 60  QVAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAH DL          K L     ++   + +  ++     F ARF+AI R Y YR+  
Sbjct: 80  QVAHVDLPDALWAQHGEKLLRRLAGRLPADVRVYRVAEAPHGFDARFAAIWRRYAYRVAD 139

Query: 119 RQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +G      + LD E M  AA+ LVG HDF  +     + ++ IRT+     
Sbjct: 140 HPGGVDPLLRGHVLWHDRPLDLEKMNEAARLLVGEHDFAAYCKKR-EGATTIRTLLELHW 198

Query: 178 NS---------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                       G+L    V A +F H  +R+ VG++ LVGDG        K L    R 
Sbjct: 199 ERVPIDPYAAQEGSLAVATVRADAFCHNMVRALVGAMLLVGDGHRPVEFPGKVLAGGVRD 258

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               +  P GL  + V Y 
Sbjct: 259 SAVNVIRPHGLTLEEVGYP 277


>gi|308371354|ref|ZP_07424662.2| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu003]
 gi|308372553|ref|ZP_07667408.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu004]
 gi|308373747|ref|ZP_07667643.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu005]
 gi|308374881|ref|ZP_07667891.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu006]
 gi|308380705|ref|ZP_07669261.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu011]
 gi|308406162|ref|ZP_07669527.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu012]
 gi|308329092|gb|EFP17943.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu003]
 gi|308332900|gb|EFP21751.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu004]
 gi|308336560|gb|EFP25411.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu005]
 gi|308340435|gb|EFP29286.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu006]
 gi|308360702|gb|EFP49553.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu011]
 gi|308364317|gb|EFP53168.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu012]
 gi|323717939|gb|EGB27128.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           CDC1551A]
          Length = 303

 Score =  233 bits (596), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 77/259 (29%), Positives = 125/259 (48%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G ++ A+  +    V +  AGRTD+GVHA  QV
Sbjct: 28  VRLRLDIAYDGTDFAGWAAQVGQRTVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQV 87

Query: 62  AHFDLVREWVPVILCKA------------LNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  + +P    +A                  +   + IL+++     F ARFSA+R
Sbjct: 88  AHVDVPADALPNAYPRAGHVGDPEFLPLLRRLGRFLPADVRILDITRAPAGFDARFSALR 147

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y+YR+ T    +   +       P+ LD + M  A++ L+G HDF  F   H + ++ 
Sbjct: 148 RHYVYRLSTAPYGVEPQQARYITAWPRELDLDAMTAASRDLMGLHDFAAFCR-HREGATT 206

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   D +  G L+   V A +F  + +RS VG+L  VG+ +  +T   + L A  R 
Sbjct: 207 IRDLQRLDWSRAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRS 266

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               +AP  GL    V+Y 
Sbjct: 267 SDFAVAPAHGLTLIQVDYP 285


>gi|293190229|ref|ZP_06608725.1| tRNA pseudouridine synthase A [Actinomyces odontolyticus F0309]
 gi|292821045|gb|EFF79998.1| tRNA pseudouridine synthase A [Actinomyces odontolyticus F0309]
          Length = 302

 Score =  233 bits (596), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 86/278 (30%), Positives = 126/278 (45%), Gaps = 35/278 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ + GW  Q    ++QG +E A+ + + E VV   AGRTD+GVHA  QV
Sbjct: 4   RRLRLDLGYDGTDFRGWAAQPGLRTVQGEVEAALAMASREDVVTTVAGRTDAGVHARHQV 63

Query: 62  AHFDL---------------VREWVPVILCKALNAYLKISD----------------TIS 90
            H D+                 + V   + + LN  L                     + 
Sbjct: 64  CHADISEAAWARLSPRGGESDEQAVASAIVRRLNKILSGRYGERARGRDLAVARGTCDVR 123

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           I + ++VD  F ARFSA+ RSY YR+  R  P  L +     + + LD   M  A   L+
Sbjct: 124 IYSAAVVDPSFDARFSALGRSYAYRVSDRPEP--LGRWDRLWVEEPLDEAAMNEAGAALL 181

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVG 209
           G HDF  F     + ++ IRT+            +  RV A +F H+ +RS VG+L LVG
Sbjct: 182 GEHDFLGFCRPR-EGATTIRTLRTLLAERDAEGTLVFRVEADAFCHSMVRSLVGALLLVG 240

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            G        + L+A+ R E  P+AP  GL  + VEY 
Sbjct: 241 SGARDVAYPVQILRARSRSEAAPIAPAHGLTLEGVEYP 278


>gi|15843050|ref|NP_338087.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis CDC1551]
 gi|148824665|ref|YP_001289419.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis F11]
 gi|161352460|ref|NP_217972.2| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Rv]
 gi|161511525|ref|NP_857124.2| tRNA pseudouridine synthase A [Mycobacterium bovis AF2122/97]
 gi|253800500|ref|YP_003033501.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           1435]
 gi|254234047|ref|ZP_04927372.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis C]
 gi|254366056|ref|ZP_04982101.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289555726|ref|ZP_06444936.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           605]
 gi|289747288|ref|ZP_06506666.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           02_1987]
 gi|298526939|ref|ZP_07014348.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis
           94_M4241A]
 gi|308377357|ref|ZP_07441941.2| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu008]
 gi|308378330|ref|ZP_07482228.2| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu009]
 gi|308379519|ref|ZP_07668975.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu010]
 gi|54039781|sp|P65847|TRUA_MYCBO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54042086|sp|P65846|TRUA_MYCTU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|13883394|gb|AAK47901.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis CDC1551]
 gi|124599576|gb|EAY58680.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis C]
 gi|134151569|gb|EBA43614.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148723192|gb|ABR07817.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis F11]
 gi|253322003|gb|ACT26606.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           1435]
 gi|289440358|gb|EFD22851.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           605]
 gi|289687816|gb|EFD55304.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           02_1987]
 gi|298496733|gb|EFI32027.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis
           94_M4241A]
 gi|308348190|gb|EFP37041.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu008]
 gi|308352914|gb|EFP41765.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu009]
 gi|308356757|gb|EFP45608.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu010]
 gi|328460231|gb|AEB05654.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis KZN
           4207]
          Length = 297

 Score =  233 bits (595), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 77/259 (29%), Positives = 125/259 (48%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G ++ A+  +    V +  AGRTD+GVHA  QV
Sbjct: 22  VRLRLDIAYDGTDFAGWAAQVGQRTVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQV 81

Query: 62  AHFDLVREWVPVILCKA------------LNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  + +P    +A                  +   + IL+++     F ARFSA+R
Sbjct: 82  AHVDVPADALPNAYPRAGHVGDPEFLPLLRRLGRFLPADVRILDITRAPAGFDARFSALR 141

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y+YR+ T    +   +       P+ LD + M  A++ L+G HDF  F   H + ++ 
Sbjct: 142 RHYVYRLSTAPYGVEPQQARYITAWPRELDLDAMTAASRDLMGLHDFAAFCR-HREGATT 200

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   D +  G L+   V A +F  + +RS VG+L  VG+ +  +T   + L A  R 
Sbjct: 201 IRDLQRLDWSRAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRS 260

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               +AP  GL    V+Y 
Sbjct: 261 SDFAVAPAHGLTLIQVDYP 279


>gi|257066904|ref|YP_003153160.1| tRNA pseudouridine synthase A [Anaerococcus prevotii DSM 20548]
 gi|256798784|gb|ACV29439.1| tRNA pseudouridine synthase A [Anaerococcus prevotii DSM 20548]
          Length = 246

 Score =  233 bits (595), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 75/248 (30%), Positives = 108/248 (43%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MIR   +   Y+G+ + G+Q QK+  S++  +  AI  VTGE   +   GRTDSGVHA  
Sbjct: 1   MIRNVLLETAYDGTNFAGFQYQKDERSVEEELRNAIRKVTGEDNRIVSCGRTDSGVHARS 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              +F       P      +  +L   D I  L+   V   FHARFS   + Y Y I   
Sbjct: 61  HFVNFLTASNISPKAFSFHIQPHL--PDDILALSSKEVSLDFHARFSCKSKLYKYVIYRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVN 178
           +    + +     I   LD + +    + L G HDF  F     +   + +R ID     
Sbjct: 119 RLMYPVFRNYKEEISYPLDLKRLDQGLKILEGEHDFRLFMREDKKLKINTVRKIDEAYFE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + I     SFLH Q+R  VGSL  +  G+ +  D  K     + K   P    +G
Sbjct: 179 EEGDDLAIYFKGESFLHNQVRIMVGSLIELSRGRLSLDDYRKFFDKDNNKRANPALGAQG 238

Query: 239 LYFDSVEY 246
           LY   VE+
Sbjct: 239 LYLRRVEF 246


>gi|221195458|ref|ZP_03568513.1| tRNA pseudouridine synthase A [Atopobium rimae ATCC 49626]
 gi|221184645|gb|EEE17037.1| tRNA pseudouridine synthase A [Atopobium rimae ATCC 49626]
          Length = 281

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 80/248 (32%), Positives = 113/248 (45%), Gaps = 7/248 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y G+ + G+  Q    ++ G +++A+  V    V +  AGRTD+GV AL Q     
Sbjct: 22  IKLGYRGAAFSGFAEQPKQRTVAGDLKQALTTVLRRPVELTCAGRTDAGVSALAQYVSVP 81

Query: 66  LVREWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +      +   + L +   +  D ISI  +      F ARF A+ RSY YRI        
Sbjct: 82  VDAHEEKIPKRQLLRSLTALTDDDISIQEIYKAQSGFSARFDALARSYRYRISAG-LRPV 140

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFGN- 182
           L    AW    +LD   M  AAQ  VG HDF +F            R ++   V      
Sbjct: 141 LAWDHAWWYNGALDVAAMNEAAQIFVGEHDFKSFCKALSAVDKPTHRYVESIQVAEIQEA 200

Query: 183 ---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              LI I +V  +FLHT +R+ VG+L  VG G   +    + L A DRK+ GP AP +GL
Sbjct: 201 GEKLIAIDIVGNAFLHTMVRTMVGTLVEVGRGHRATNWTREVLLACDRKKAGPTAPAKGL 260

Query: 240 YFDSVEYS 247
            F  V Y 
Sbjct: 261 VFTGVLYP 268


>gi|319950123|ref|ZP_08024062.1| tRNA pseudouridine synthase A [Dietzia cinnamea P4]
 gi|319436208|gb|EFV91389.1| tRNA pseudouridine synthase A [Dietzia cinnamea P4]
          Length = 380

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 124/266 (46%), Gaps = 23/266 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ + GW RQ    ++ G +E  +  V    VV+  AGRTD+GVHA  QV
Sbjct: 4   RRIRLDVAYDGTDFSGWARQPGLRTVCGVLEAELSTVLRHPVVLTVAGRTDAGVHARAQV 63

Query: 62  AHFDLVREWV--------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            H D+   W+        P  L + L   L     I++++   V  +F ARFSA+RR Y 
Sbjct: 64  CHLDVDPAWLDQRSLDGRPEALVRRLARLL--PADIAVMDGRWVPDEFDARFSALRRHYE 121

Query: 114 YRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+ T       +         ++ D E +R A++ L+G HDF  F     + ++ IR +
Sbjct: 122 YRLTTAPWGAEPIRARDTAAWTRTADLEAVRAASERLLGLHDFAAFCRRR-EGATTIREL 180

Query: 173 DHFDVNSFGN-----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
             F+  +  +           +    V A +F  + +RS VG++  VG+G+ +   +   
Sbjct: 181 QRFEWRTEPDPRGPDAPGAAEVWTASVSADAFCWSMVRSLVGAVMAVGEGRRSLEWISGL 240

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
           L   +R    P+AP  GL    V+Y 
Sbjct: 241 LAETERSSAVPVAPACGLSLIGVDYP 266


>gi|313819879|gb|EFS57593.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL036PA1]
          Length = 279

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 118/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I  V    +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRGLT--PDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAFCK-HREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|289427598|ref|ZP_06429310.1| tRNA pseudouridine synthase A [Propionibacterium acnes J165]
 gi|289159089|gb|EFD07281.1| tRNA pseudouridine synthase A [Propionibacterium acnes J165]
 gi|313808787|gb|EFS47241.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL087PA2]
 gi|313824843|gb|EFS62557.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL063PA1]
 gi|314979788|gb|EFT23882.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL072PA2]
 gi|315089972|gb|EFT61948.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL072PA1]
 gi|327325121|gb|EGE66927.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL096PA3]
 gi|327449322|gb|EGE95976.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL013PA2]
 gi|332676207|gb|AEE73023.1| tRNA pseudouridine synthase A [Propionibacterium acnes 266]
          Length = 279

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 118/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I  V    +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVLT--PDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAFCK-HREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|282855153|ref|ZP_06264485.1| tRNA pseudouridine synthase A [Propionibacterium acnes J139]
 gi|295131337|ref|YP_003582000.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK137]
 gi|282581741|gb|EFB87126.1| tRNA pseudouridine synthase A [Propionibacterium acnes J139]
 gi|291375873|gb|ADD99727.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK137]
 gi|313773224|gb|EFS39190.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL074PA1]
 gi|313810419|gb|EFS48133.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL083PA1]
 gi|313812247|gb|EFS49961.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL025PA1]
 gi|313817968|gb|EFS55682.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL046PA2]
 gi|313823371|gb|EFS61085.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL036PA2]
 gi|313830085|gb|EFS67799.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL007PA1]
 gi|313832643|gb|EFS70357.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL056PA1]
 gi|314924129|gb|EFS87960.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL001PA1]
 gi|314925807|gb|EFS89638.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL036PA3]
 gi|314960817|gb|EFT04918.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL002PA2]
 gi|314964970|gb|EFT09069.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL082PA2]
 gi|314973066|gb|EFT17162.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL053PA1]
 gi|314975562|gb|EFT19657.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL045PA1]
 gi|314982235|gb|EFT26328.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA3]
 gi|314984846|gb|EFT28938.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA1]
 gi|314986106|gb|EFT30198.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA2]
 gi|314988720|gb|EFT32811.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA3]
 gi|315079903|gb|EFT51879.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL078PA1]
 gi|315083346|gb|EFT55322.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL027PA2]
 gi|315086881|gb|EFT58857.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL002PA3]
 gi|315090495|gb|EFT62471.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA4]
 gi|315093731|gb|EFT65707.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL060PA1]
 gi|315096707|gb|EFT68683.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL038PA1]
 gi|327325250|gb|EGE67055.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL096PA2]
 gi|327325550|gb|EGE67349.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL103PA1]
 gi|327444051|gb|EGE90705.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL043PA1]
 gi|327449450|gb|EGE96104.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL043PA2]
 gi|328756334|gb|EGF69950.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL020PA1]
 gi|328761333|gb|EGF74860.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL099PA1]
          Length = 279

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 118/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I  V    +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVLT--PDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAFCK-HREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|303288620|ref|XP_003063598.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454666|gb|EEH51971.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 261

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 77/256 (30%), Positives = 121/256 (47%), Gaps = 14/256 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHALR 59
           Y + + Y+G  Y G+Q Q  +  ++QG +EKA+  +TGE    + +  +GRTD+GVHA  
Sbjct: 3   YALTLAYDGENYLGFQYQPRDAKTVQGEVEKALTKITGEDRDFLGIQASGRTDAGVHARG 62

Query: 60  QVAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV HF   R         +++N  L     + ++        FHARF A+R++Y Y + T
Sbjct: 63  QVLHFYARRPIEDLARFQRSMNGVL--PRDVRVMKAIRPHPAFHARFHAVRKTYHYYLDT 120

Query: 119 RQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQAS---SPIRTIDH 174
           R       +  A  +     D E +R  A+  VG  DF+ F +     +    P+RTI  
Sbjct: 121 RLTMDPFLRRHALHVGWNPPDVEKLRRGAECFVGTRDFSAFSNKPRDKTLVRDPVRTIYR 180

Query: 175 FDVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVG-DGKWTSTDLEKALQAQDRKECG 231
           FDVN      L+ + V    F++ Q+R+ VG++       K    D+   L+ +DR    
Sbjct: 181 FDVNELKGDGLLRLEVEGNGFMYKQVRNMVGAMITAATSKKMQPADIAAMLEGKDRGVAP 240

Query: 232 PLAPPEGLYFDSVEYS 247
             AP  GL+   V Y 
Sbjct: 241 MGAPAHGLFLHDVVYP 256


>gi|256380565|ref|YP_003104225.1| tRNA-pseudouridine synthase I [Actinosynnema mirum DSM 43827]
 gi|255924868|gb|ACU40379.1| tRNA-pseudouridine synthase I [Actinosynnema mirum DSM 43827]
          Length = 314

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 118/247 (47%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW RQ N  ++ G +E  +  V  E VV+  AGRTD+GVHA  QV
Sbjct: 37  VRVRLDLAYDGTEFSGWARQPNRRTVCGVLEDTMSTVLREDVVLTVAGRTDAGVHAAGQV 96

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH DL        L K L   L     + + +  +V   F ARF+A+RR Y YR+     
Sbjct: 97  AHVDLPEAADVAGLPKRLARAL--PADVRVFSARVVPAAFDARFAALRRHYEYRVTDAPF 154

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +      P+ LD   M  A+  ++G  DF  +     + ++ IR +   +    
Sbjct: 155 GAHPLRRLDTLAWPRQLDVAAMNAASGLMLGERDFCAYCRRR-EGATTIRELQRLEWVRE 213

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+   V A +F H+ +RS VG+L  VG+G+         L    R     +APP GL 
Sbjct: 214 GDLLTAFVSADAFCHSMVRSLVGALLAVGEGRKPVEWPASLLSLHSRSSEVTVAPPHGLS 273

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 274 LVRVDYP 280


>gi|78185547|ref|YP_377981.1| tRNA pseudouridine synthase A [Synechococcus sp. CC9902]
 gi|123743513|sp|Q3AW68|TRUA_SYNS9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78169841|gb|ABB26938.1| tRNA pseudouridine synthase [Synechococcus sp. CC9902]
          Length = 300

 Score =  233 bits (594), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 110/247 (44%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ N  S+Q  +E AI  +     +    AGRTD+GVHA  Q
Sbjct: 16  RRIALSLQYEGSDFCGWQRQNNARSVQAVLETAIAQLDPLRPIQSFAAGRTDAGVHAAAQ 75

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L    +I +       + +HA +SA+ R Y Y I   +
Sbjct: 76  VVHFDCSGPIPAAKWAPALNGRL--PASIRVRESVERPRDWHACYSAVYRRYRYIIHNGR 133

Query: 121 APLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P        W      L+ ENMR+A + ++G HDF  F     +      TI    V  
Sbjct: 134 RPNLFLTPWTWHRYHHRLNEENMRVALEGMIGLHDFAAFMRAGSRRPHSRTTIQDVLVER 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LI + + A  FL+  +R  +  L  VG+ + +    E+  + + R +    AP  GL
Sbjct: 194 EGDLIRVEIQASGFLYGMVRLLMAQLVAVGEHRLSVKAFEQRWRDRRRDQVREAAPARGL 253

Query: 240 YFDSVEY 246
                 Y
Sbjct: 254 CLLRAGY 260


>gi|154507834|ref|ZP_02043476.1| hypothetical protein ACTODO_00316 [Actinomyces odontolyticus ATCC
           17982]
 gi|153797468|gb|EDN79888.1| hypothetical protein ACTODO_00316 [Actinomyces odontolyticus ATCC
           17982]
          Length = 302

 Score =  233 bits (594), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 87/278 (31%), Positives = 127/278 (45%), Gaps = 35/278 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  + + Y+G+ + GW  Q    ++QG +E A+ + + E VV   AGRTD+GVHA  QV
Sbjct: 4   RRLRLDLGYDGTDFRGWAAQPGLRTVQGEVEAALAMASREDVVTTVAGRTDAGVHARHQV 63

Query: 62  AHFDL---------------VREWVPVILCKALNAYLKISD----------------TIS 90
            H D+                 + V   + + LN  L                     + 
Sbjct: 64  CHADISEAAWARLSPRGGESNEQAVASAIVRRLNKILSGRYGERARGRDLAAARGTCDVR 123

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           I + ++VD  F ARFSA+ RSY YR+  R  P  L +     + + LD   M  A   L+
Sbjct: 124 IYSAAVVDPSFDARFSALGRSYAYRVSDRPEP--LGRWDRLWVEEPLDEAAMNEAGAALL 181

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVG 209
           G HDF  F     + ++ IRT+            +  RV A +F H+ +RS VG+L LVG
Sbjct: 182 GEHDFLGFCRPR-EGATTIRTLRTLLAERDAEGTLVFRVEADAFCHSMVRSLVGALLLVG 240

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            G    T   + L+A+ R E  P+AP  GL  + VEY 
Sbjct: 241 SGARDVTYPVQILRARSRSEAAPIAPAHGLTLEGVEYP 278


>gi|315445896|ref|YP_004078775.1| pseudouridylate synthase I [Mycobacterium sp. Spyr1]
 gi|315264199|gb|ADU00941.1| pseudouridylate synthase I [Mycobacterium sp. Spyr1]
          Length = 291

 Score =  233 bits (594), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 79/259 (30%), Positives = 123/259 (47%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G I+ A+  V    ++   AGRTDSGVHA  QV
Sbjct: 13  VRLRLDIAYDGTDFAGWATQAGQRTVAGVIDDALSTVFRTPMLTRAAGRTDSGVHATGQV 72

Query: 62  AHFDLVREWVPVILCKALNAY------------LKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+  + +P    + + A               +++ + +  +      F ARFSA+R
Sbjct: 73  AHVDIPTDALPHAYPRTVRAGEAEFGPLVRRLGRMLTEDVRVRGIVRAAPGFDARFSALR 132

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y+YR+ T    +   E       P+ LD + M  AAQ+++G HDF  F   H   ++ 
Sbjct: 133 RHYVYRLTTAPYGVEPSEARFVTAWPRPLDVDAMAGAAQNVLGLHDFAAFCR-HRDGATT 191

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   D    G+ I + V A +F    +RS VG+L  VG+ +   T   + L A+ R 
Sbjct: 192 IRELQRLDCVRDGDRISVHVSADAFCWNMVRSLVGALLAVGEHRRDDTWCVQLLHARHRS 251

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                AP  GL    V+Y 
Sbjct: 252 SDFAAAPARGLTLVGVDYP 270


>gi|225020488|ref|ZP_03709680.1| hypothetical protein CORMATOL_00495 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224946877|gb|EEG28086.1| hypothetical protein CORMATOL_00495 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 290

 Score =  232 bits (593), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 79/259 (30%), Positives = 117/259 (45%), Gaps = 15/259 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + GW RQ +    ++Q  +E A+ LV  + + +  AGRTD+GVHA+ Q
Sbjct: 5   RIRLDLAYDGTHFHGWARQGHSELRTVQQVLEDALTLVLRQPIALTVAGRTDAGVHAVAQ 64

Query: 61  VAHFDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAHFD+       R                +   + +   +I    F ARFSA+RR Y+Y
Sbjct: 65  VAHFDVPAAALDTRSIAGDPGRLVRRLARLLPTDVRVHAATIAPPDFDARFSALRRHYVY 124

Query: 115 RIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+ T     L          PK +D   M+  A  L+G HDF  F   H   ++ IR + 
Sbjct: 125 RLTTHPRGALPTRVTDTAHHPKPVDLAAMQACAAELIGLHDFAAFCR-HRDGATTIRDLQ 183

Query: 174 HFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            F  N        +  E  V A +F  + +RS VG   +VG+GK  +      L    R 
Sbjct: 184 EFTWNDISTPIEPDTFEAHVTADAFCWSMVRSLVGCCLVVGEGKRPAGFATSLLAETSRS 243

Query: 229 ECGPLAPPEGLYFDSVEYS 247
              P+AP  GL    V+Y 
Sbjct: 244 ALVPVAPAAGLSLVGVDYP 262


>gi|153854831|ref|ZP_01996054.1| hypothetical protein DORLON_02059 [Dorea longicatena DSM 13814]
 gi|149752533|gb|EDM62464.1| hypothetical protein DORLON_02059 [Dorea longicatena DSM 13814]
          Length = 245

 Score =  232 bits (593), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 119/250 (47%), Gaps = 9/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVH 56
           M    + IEY+GS Y GW R    ++G++I   I + +  +T E  + +    RT+ GVH
Sbjct: 1   MRNIKLTIEYDGSRYQGWTRLGKDESGNTISNKITEVLKKMTEEDDLELFCGCRTEVGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  Q+A+F          +   LN YL     I+I+++  V ++FHA+ +A  ++Y+YR+
Sbjct: 61  AYAQIANFKTSSSTTTQNIKHYLNRYL--PMDIAIIDVKEVPERFHAQLNATSKTYVYRM 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P   ++   +   +  D   M+ AA+ L GRHDF  F S   +  S +R I   D
Sbjct: 119 TIDDVPSVFDRKYTYHCYRIPDKRLMQQAAEKLTGRHDFRNFSSAK-KTKSTVREIFDID 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +      ++I + A  FLH   R  VG+L  +G G  +  D++         E      P
Sbjct: 178 IYGDIEEMQILIHADDFLHNMARIIVGTLMDIGLGNRSVQDIDDIFAGI--LEASAPCDP 235

Query: 237 EGLYFDSVEY 246
           +GLY   + Y
Sbjct: 236 KGLYLQEITY 245


>gi|307128564|ref|YP_003880594.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri CARI]
 gi|306483026|gb|ADM89896.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri CARI]
          Length = 252

 Score =  232 bits (593), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 74/248 (29%), Positives = 123/248 (49%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + I Y+G+ ++GWQ Q    S+Q +IEK +  +  + + + GAGRTD+GVHA++  
Sbjct: 1   MRFFLEISYHGALFYGWQIQNKNISVQETIEKCLSFLLKKNIKIIGAGRTDAGVHAIQMF 60

Query: 62  AHFDLVRE--WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AHFD  +    +   +   LN +L     I I N+  V  + HARF+ + R Y YRI   
Sbjct: 61  AHFDFNQNLLLIDKNIKFKLNYFL--PLNIKIKNIFSVKNKIHARFNVLSRVYEYRIFLE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P  L+    WL  K +  + +   A+ L    D+++F        + I  I +     
Sbjct: 119 KNPFYLDTSWQWLYKKKIKIKILNKGAKLLKKYKDYSSFCKKKSNNKTYICHIFYAKWIL 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +   + A  FL   +RS VG+L  +G  K T  D  + ++A++R   G  AP +GL
Sbjct: 179 KKKKLFFYIEANRFLRNMVRSIVGTLIELGIKKITLKDFIQIIEAKNRHLAGISAPAKGL 238

Query: 240 YFDSVEYS 247
           +   + Y 
Sbjct: 239 FLIKINYP 246


>gi|305680135|ref|ZP_07402945.1| tRNA pseudouridine synthase A [Corynebacterium matruchotii ATCC
           14266]
 gi|305660755|gb|EFM50252.1| tRNA pseudouridine synthase A [Corynebacterium matruchotii ATCC
           14266]
          Length = 290

 Score =  232 bits (593), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 79/259 (30%), Positives = 116/259 (44%), Gaps = 15/259 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + GW RQ +    ++Q  +E A+ LV  + + +  AGRTD+GVHA  Q
Sbjct: 5   RIRLDLAYDGTHFHGWARQGHSELRTVQQVLEDALTLVLRQPIALTVAGRTDAGVHAAAQ 64

Query: 61  VAHFDLV------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VAHFD+       R                +   + +   +I    F ARFSA+RR Y+Y
Sbjct: 65  VAHFDVPAAALDTRSIAGDPGRLVRRLARLLPTDVRVHAATIAPPDFDARFSALRRHYVY 124

Query: 115 RIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+ T     L          PK +D   M+  A  L+G HDF  F   H   ++ IR + 
Sbjct: 125 RLTTHPRGALPTRVTDTAHHPKPVDLAAMQACAAELIGLHDFAAFCR-HRDGATTIRDLQ 183

Query: 174 HFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            F  N        +  E  V A +F  + +RS VG   +VG+GK  +      L    R 
Sbjct: 184 EFTWNDISTPIEPDTFEAHVTADAFCWSMVRSLVGCCLVVGEGKRPAGFATSLLAETSRS 243

Query: 229 ECGPLAPPEGLYFDSVEYS 247
              P+AP  GL    V+Y 
Sbjct: 244 ALVPVAPAAGLSLVGVDYP 262


>gi|227832275|ref|YP_002833982.1| tRNA pseudouridine synthase A [Corynebacterium aurimucosum ATCC
           700975]
 gi|262183869|ref|ZP_06043290.1| tRNA pseudouridine synthase A [Corynebacterium aurimucosum ATCC
           700975]
 gi|227453291|gb|ACP32044.1| tRNA pseudouridine synthase A [Corynebacterium aurimucosum ATCC
           700975]
          Length = 286

 Score =  232 bits (593), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 85/262 (32%), Positives = 123/262 (46%), Gaps = 20/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW RQK G  ++Q ++E+ + +V    V +  AGRTD+GVHA  Q
Sbjct: 5   VRLRLDLAYDGTDFHGWARQKGGLRTVQQTVEEKLSMVLRHPVELTVAGRTDAGVHASGQ 64

Query: 61  VAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAHFD  R        +  P  L + L   L     + +   + V   F ARFSA+RR Y
Sbjct: 65  VAHFDTTRAALSQRSIDGEPHKLVRRLAKLL--PVDVRVHACTEVSPDFDARFSALRRHY 122

Query: 113 LYRIITRQAPLALEKGR--AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           +YRI T        + R  A  + K +D + M+ AA  LVG +DF  F      A + IR
Sbjct: 123 VYRITTHPRGALPTRARDTATWL-KPVDLDLMQAAADRLVGLNDFVAFCKAKPHA-TTIR 180

Query: 171 TIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F+       +   L E  V A +F  + +R  VG    VG+G        + L   
Sbjct: 181 ELLAFEWKDVSTPAEPQLYEAHVSADAFCWSMVRCLVGCCLRVGEGSRDVEFAGQMLNET 240

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    PLAP  GL    V+Y 
Sbjct: 241 SRSSQIPLAPAAGLSLVGVDYP 262


>gi|168009447|ref|XP_001757417.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691540|gb|EDQ77902.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 299

 Score =  232 bits (593), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 84/239 (35%), Positives = 119/239 (49%), Gaps = 11/239 (4%)

Query: 18  WQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQVAHFDLVREW-VPV 73
           WQ QKN  SIQ  +E A+   T    + + + GAGRTD+GVHA  QVAHF     +    
Sbjct: 36  WQIQKNYVSIQEKVEDALSKFTRLPRDELKLVGAGRTDAGVHAWGQVAHFTTPTCFCDLE 95

Query: 74  ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
            L  +LN  L     I IL +S V   FHAR+SA R++Y Y+          +   A+ I
Sbjct: 96  PLHTSLNGIL--PPDIRILEVSSVQPDFHARYSACRKTYQYKAYVSPVMDPFQHAYAYHI 153

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVAR 191
             S++   M  AA + VG H+F+ F   S    +   +R +  F V+S G  +   V  +
Sbjct: 154 KNSVNIAAMEEAASYFVGTHNFSAFANHSADTASRDTLRDLLSFTVSSIGPQLLFEVEGK 213

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG---PLAPPEGLYFDSVEYS 247
           SF++ Q+R+ VG L  VG      + +   L  +DR+E     P+AP  GLY  SV Y 
Sbjct: 214 SFMYKQVRNMVGLLVQVGKELVPPSMVRTILLTEDRRELAKISPVAPAHGLYLMSVGYD 272


>gi|326383234|ref|ZP_08204922.1| tRNA pseudouridine synthase A [Gordonia neofelifaecis NRRL B-59395]
 gi|326197984|gb|EGD55170.1| tRNA pseudouridine synthase A [Gordonia neofelifaecis NRRL B-59395]
          Length = 296

 Score =  232 bits (592), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 123/255 (48%), Gaps = 14/255 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  ++I Y+G+ + GW  Q    ++  +IE+A+  V    + +  AGRTD+GVHA  QVA
Sbjct: 16  RLRLLIGYDGTDFSGWATQPGRRTVCETIEQALGTVLRAPIRLTVAGRTDAGVHAAGQVA 75

Query: 63  HFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           H D+          +  P  L + L   L   D + +  +  V + F ARFSA+ R+Y Y
Sbjct: 76  HCDVPAASLRTRSIDGDPARLVRRLAKML--PDDVRVKRIEAVSEDFDARFSALARTYEY 133

Query: 115 RIITRQ--APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           R+      A   L +  A    + LD E M  A+  LVG +DF  F     + S+ IR +
Sbjct: 134 RLTDAPWGAEPTLARITADWT-RPLDVEAMNTASAGLVGLNDFAAFCRYR-EGSTTIREL 191

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
             FD    G ++   V+A +F  + +RS VG++  VGDG+ +       L  + R    P
Sbjct: 192 QRFDWRREGPVVVGTVIADAFCWSMVRSLVGAVASVGDGRRSLGWCTDLLDQRARSAQVP 251

Query: 233 LAPPEGLYFDSVEYS 247
           +A   GL    V+Y 
Sbjct: 252 VAQARGLSLIGVDYP 266


>gi|148238745|ref|YP_001224132.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7803]
 gi|147847284|emb|CAK22835.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7803]
          Length = 297

 Score =  232 bits (592), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 116/248 (46%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ+ G+S+QG +E+AI  +     V    AGRTD+GVHA  Q
Sbjct: 22  QRIAISLQYAGSFFCGWQRQRQGTSVQGVLEQAIADLDPHRPVHAVAAGRTDAGVHAAGQ 81

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L    +I +         +HA +SA  R Y Y +   +
Sbjct: 82  VVHFDSSGPIPASRWAPALNGRL--PASIRVREAVERPLSWHACYSATYRRYRYTLYNGR 139

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P        W   +  LD + M  A + ++G HDF  F+    + +    TI    V  
Sbjct: 140 RPNLFLAPWTWHRYQARLDEQAMAAALEGMLGSHDFAAFQRAGSRRAHSRTTIQDVSVQR 199

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LI++ V A  FL+  +R  +G L  VG+ + T    E+  + + R E    APP+GL
Sbjct: 200 RGDLIDLEVQASGFLYGMVRLMMGQLVAVGEHRLTPDQFERRWRERRRDEVKDGAPPQGL 259

Query: 240 YFDSVEYS 247
                 Y 
Sbjct: 260 CLLRAGYE 267


>gi|294783832|ref|ZP_06749154.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
 gi|294479644|gb|EFG27423.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
          Length = 246

 Score =  232 bits (591), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 119/250 (47%), Gaps = 7/250 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MERKNIKIEFRYDGSRYYGFQRQPDKVTVQGEIEKILKIVTKEDINLISAGRTDRGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           +QV++F              L   L     I IL++  VDK F+AR  A  R Y+Y I  
Sbjct: 61  QQVSNFYTSSNIPVEKYKYLLTRAL--PKDIDILSVEEVDKNFNARHDAKMREYIYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      +   +D E ++      +G HDF  FR   C +   IR I   D+N
Sbjct: 119 EKNP--FEARYCKFVKNKIDVEKLKKIFSSFLGIHDFRNFRLSDCVSKITIREIYSIDIN 176

Query: 179 SF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            F  N ++I +   +FL +Q+R  VG+   V  G      +E  L    +     L   E
Sbjct: 177 YFSENKLKIYIRGSAFLKSQVRIMVGTALEVYYGNLPENHIELMLNDFSKDYKKNLVEAE 236

Query: 238 GLYFDSVEYS 247
           GLY + + YS
Sbjct: 237 GLYLNKIYYS 246


>gi|116075742|ref|ZP_01473001.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9916]
 gi|116067057|gb|EAU72812.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9916]
          Length = 278

 Score =  232 bits (591), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 113/247 (45%), Gaps = 4/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
            R  + ++Y GS + GWQRQ+ G+S+Q ++++AI  +     V    AGRTD+GVHA  Q
Sbjct: 3   RRIALSLQYEGSAFCGWQRQRQGNSVQAALDEAISQLDPIRPVHTVAAGRTDAGVHAAGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD            ALN  L    TI +         +HA +SA  R Y Y I   +
Sbjct: 63  VVHFDCCGPIPAWRWAPALNGRL--PGTIRVREAVERPLDWHACYSATYRRYRYTIYNGR 120

Query: 121 APLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P        W   +  LD   M  A Q L+G HDF  F     + +    TI    +  
Sbjct: 121 RPNLFLTPWTWHRYQARLDDSLMGEALQGLLGLHDFGAFMRAGSRRAHSRTTIQDVSLER 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+L+ + + A  FL+  +R  +G L  VG+ + +    E+  + + R E    APP+GL
Sbjct: 181 EGDLVTVEIQASGFLYGMVRLLMGQLVAVGEHRLSLEAFERRWRERRRSEVKDAAPPQGL 240

Query: 240 YFDSVEY 246
                 Y
Sbjct: 241 CLLRAGY 247


>gi|300742028|ref|ZP_07072049.1| tRNA pseudouridine synthase A [Rothia dentocariosa M567]
 gi|300381213|gb|EFJ77775.1| tRNA pseudouridine synthase A [Rothia dentocariosa M567]
          Length = 316

 Score =  232 bits (591), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 88/280 (31%), Positives = 127/280 (45%), Gaps = 35/280 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  +   Y+G+ + GW RQ N  ++QG +E A+ LV      V  AGRTD+GVHA  Q 
Sbjct: 4   QRVRIDCAYDGTWFSGWARQPNLVTVQGVLEDALELVLRTHHRVTVAGRTDAGVHAQAQT 63

Query: 62  AHFDL-VREWVPVILCKALN----------------------AYLKISDTIS-------- 90
            H D+    W  +     L                         L I + +         
Sbjct: 64  IHLDIATETWQKLTGRDGLADPAESLKRKVSGALKRTLAQAEHTLGIPERMRGLLQGSLV 123

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQ--APLALEKGRAWLIPKSLDCENMRIAAQH 148
           +  +  V + F ARFSA  R Y YRI+  Q  +P  L +  AW IP+SLD E++  AA  
Sbjct: 124 LHQVQPVPQDFDARFSATGRRYTYRILDGQGSSPDPLHRAYAWCIPESLDLEDLNKAAHE 183

Query: 149 LVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKL 207
           L G HDF +F     + ++ IR +    +    + +IE  V A +F H  +RS +G+L L
Sbjct: 184 LTGLHDFLSFCKPR-EGATTIRELRRIYLTRHDDGVIEATVEADAFCHHMVRSLIGALVL 242

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            G GK T   L + L+   R     +APP GL    ++Y 
Sbjct: 243 YGTGKRTQAWLRERLENPQRDASLIMAPPHGLALAHIDYP 282


>gi|300779794|ref|ZP_07089650.1| tRNA-pseudouridine synthase I [Corynebacterium genitalium ATCC
           33030]
 gi|300533904|gb|EFK54963.1| tRNA-pseudouridine synthase I [Corynebacterium genitalium ATCC
           33030]
          Length = 303

 Score =  232 bits (591), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 78/267 (29%), Positives = 118/267 (44%), Gaps = 24/267 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-------SSIQGSIEKAIFLVTGEIVVVHGAGRTDSG 54
           +R  + I Y+G+ + GW RQ           ++QG +E A+ L+    V +  AGRTD+G
Sbjct: 18  VRLRLDIAYDGTRFHGWARQAAAPGEETPVRTVQGELEDALSLILRHPVELTVAGRTDAG 77

Query: 55  VHALRQVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           VHA  QVAH D+ +           P  L + L   L+    + +  ++   + F ARFS
Sbjct: 78  VHATGQVAHADVPKHALDQRSIVGEPEKLTRRLARLLE--PDLRVTAVTEAPRDFDARFS 135

Query: 107 AIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R+Y YR+ T  A P  L +       K +D   ++  A  LVG +D+  F      A
Sbjct: 136 ALTRTYRYRVTTNTAGPNPLRRTDTAAWTKKIDLHAVQETATALVGLNDYAAFCKPRPHA 195

Query: 166 SSPIRTIDHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            + IR I  F            L E  + A +F    +R+ V +   VG G    +  + 
Sbjct: 196 -TTIRDIHSFTWADVSTPEEPELYEATITADAFCWHMVRALVATCLDVGSGARDVSWAKT 254

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            L A +R     LAP  GL    V+Y 
Sbjct: 255 LLAAHERDPLVKLAPANGLTLIRVDYP 281


>gi|315104023|gb|EFT75999.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL050PA2]
          Length = 279

 Score =  232 bits (591), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 117/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I  V    +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     I + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVLT--PDIVVTSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +   LD + +  A   L+G  DF  F   H + ++ IR +     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDCLNTAGTSLLGLRDFAAFCK-HREGATTIRPLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|237736308|ref|ZP_04566789.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
 gi|229421656|gb|EEO36703.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
          Length = 243

 Score =  232 bits (591), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 123/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +   Y+GS ++G+QRQ N  ++QG IEK + +V  + + +  +GRTD GVHAL Q
Sbjct: 1   MRNIKISYRYDGSMFYGFQRQPNKRTVQGEIEKLLNVVLKDEIDMVSSGRTDRGVHALIQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F          L   L     +   I +L++  VD +F++RF A +R Y Y I    
Sbjct: 61  VSNFYTTSTIPLDRLKYVL--MRGLPLDIELLDIEEVDIEFNSRFDAQKRGYTYIISWE- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +      + K ++ E  +     LVG HDF  FR   C + + IR I   +V   
Sbjct: 118 -RDPFKNRYETYVNKEIEAERFQKILDILVGVHDFNNFRMSDCGSKTSIREIYSIEVKKI 176

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G N I + ++  SFL +QIR  +G+   +  G   S  +E+ L+  D+K    +A P GL
Sbjct: 177 GSNRISVEILGSSFLKSQIRIIIGTALNIYFGNLPSNYMEEMLKNPDKKYLKKVAEPNGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YLSKVDY 243


>gi|226227135|ref|YP_002761241.1| tRNA pseudouridine synthase A [Gemmatimonas aurantiaca T-27]
 gi|226090326|dbj|BAH38771.1| tRNA pseudouridine synthase A [Gemmatimonas aurantiaca T-27]
          Length = 259

 Score =  231 bits (590), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 74/248 (29%), Positives = 110/248 (44%), Gaps = 6/248 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
             ++ +Y+G  + GWQRQ +  ++QG +E+ +  ++G   V   GAGRTD+GVHA  Q  
Sbjct: 6   ILLVTQYDGGRFAGWQRQPDVRTVQGDMERVLGRLSGGLYVPAVGAGRTDAGVHAHGQGV 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ-A 121
              +  +W    L +A+NA L   D I +     ++ +FH R+SA  R Y Y I T + A
Sbjct: 66  GVRMPPQWTAPRLRRAMNALL--PDDIWVAAAYQMEPEFHPRYSATARRYGYLIGTDELA 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSPIRTIDHFDVNS 179
                +   W + + LD E +   A  L+G H F  F   H           I H     
Sbjct: 124 SSPFRRRHEWALHRPLDVEALHGEAAELLGEHTFRAFAIAHTAPVDDHHRCIIHHAAWVP 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                   V A  FLH  +R  VG++  V  G+     + + L   D  +  P AP  GL
Sbjct: 184 REGGWVFEVSANRFLHHMVRFLVGTMVDVALGRRPRGTIARLLVTPDNADTSPPAPAHGL 243

Query: 240 YFDSVEYS 247
               V Y 
Sbjct: 244 SLREVTYP 251


>gi|289523335|ref|ZP_06440189.1| tRNA pseudouridine synthase A [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289503027|gb|EFD24191.1| tRNA pseudouridine synthase A [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 268

 Score =  231 bits (590), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 125/247 (50%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQ 60
           R+  ++ Y+GS + G+QRQK+  +++ ++E+A+ L+   G  V V GAGRTD GVHAL Q
Sbjct: 6   RFAALLSYDGSAFHGFQRQKDLPTVELALEEALNLLDKKGRRVKVTGAGRTDRGVHALGQ 65

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD+     P  L KAL A L    +I +  +  VD  FHAR SA+ R Y Y I    
Sbjct: 66  VVHFDISWPHGPTALRKALEANL--PSSIGVYEVVPVDFAFHARRSALWRKYAYFIWKGD 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             L       W   +  D +  +     + G HDF  F     + S   RTI    +   
Sbjct: 124 CRLPHLGRYVWWNRRGWDMDLAKKFLTMIEGFHDFGAFCRKADRPSDARRTIMEARIEEK 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+++ V  RSFL   +R  VG++  +  G+ +  ++ + L    R E GP AP +GL+
Sbjct: 184 GPLLKVSVTGRSFLTNMVRIIVGTMDEIATGRKSLEEVCRLLDGGSRGEAGPTAPAKGLF 243

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 244 LWEVRYD 250


>gi|289669396|ref|ZP_06490471.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 257

 Score =  231 bits (589), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 94/248 (37%), Positives = 133/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADGQVQVICAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++     V   FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSIAVRWCVPVADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTVSWERRPLDADAMHAAAQALLGENDFSAFRSVQCQALHARRNLQAIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   G  APP+GL
Sbjct: 179 IGEVVEVQVQANAFLHHMVRNIVGSLILVGTGERPADWIATLLAGRDRTVAGQTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|50843266|ref|YP_056493.1| tRNA pseudouridine synthase A [Propionibacterium acnes KPA171202]
 gi|289424889|ref|ZP_06426668.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK187]
 gi|62901286|sp|Q6A6S8|TRUA_PROAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|50840868|gb|AAT83535.1| tRNA pseudouridine synthase A [Propionibacterium acnes KPA171202]
 gi|289154588|gb|EFD03274.1| tRNA pseudouridine synthase A [Propionibacterium acnes SK187]
 gi|313763186|gb|EFS34550.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL013PA1]
 gi|313793310|gb|EFS41368.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA1]
 gi|313801047|gb|EFS42315.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL110PA2]
 gi|313828418|gb|EFS66132.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL063PA2]
 gi|313838001|gb|EFS75715.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL086PA1]
 gi|314914385|gb|EFS78216.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL005PA4]
 gi|314917708|gb|EFS81539.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL050PA1]
 gi|314919564|gb|EFS83395.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL050PA3]
 gi|314930155|gb|EFS93986.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL067PA1]
 gi|314957174|gb|EFT01278.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL027PA1]
 gi|314957815|gb|EFT01918.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL002PA1]
 gi|314963491|gb|EFT07591.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL082PA1]
 gi|314969927|gb|EFT14025.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL037PA1]
 gi|315077220|gb|EFT49285.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL053PA2]
 gi|315097933|gb|EFT69909.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL059PA2]
 gi|315100698|gb|EFT72674.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL046PA1]
 gi|315106086|gb|EFT78062.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL030PA1]
 gi|315109179|gb|EFT81155.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL030PA2]
 gi|327451475|gb|EGE98129.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL087PA3]
 gi|327451552|gb|EGE98206.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL092PA1]
 gi|327451838|gb|EGE98492.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL083PA2]
 gi|328752053|gb|EGF65669.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL087PA1]
 gi|328755550|gb|EGF69166.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL025PA2]
          Length = 279

 Score =  231 bits (589), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 118/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I  V    +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     + + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVLT--PDVVVKSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDRLNTAGTSLLGLRDFAAFCK-HREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 KRLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|331699143|ref|YP_004335382.1| tRNA pseudouridine synthase A [Pseudonocardia dioxanivorans CB1190]
 gi|326953832|gb|AEA27529.1| tRNA pseudouridine synthase A [Pseudonocardia dioxanivorans CB1190]
          Length = 263

 Score =  231 bits (589), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 73/248 (29%), Positives = 118/248 (47%), Gaps = 5/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y+G+ + GW  Q    ++ G +  A+  +    V +  AGRTD+GVHA  QV
Sbjct: 1   MRYRLDIAYDGTDFSGWAPQPGRRTVHGVLTDALQRLVRAPVALTVAGRTDAGVHASGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH DL  E  P  L +       +   + +  ++ V  +F ARFSA+RR Y+YR+ T   
Sbjct: 61  AHVDLSGELEPDRLVRR--LARLLPPDVRVRAVTAVPPEFDARFSALRRHYVYRVTTAPW 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L        P  +D + +  A+  L+G HDF  F     + ++ IR +  F  +  
Sbjct: 119 GADPLRARDTLAWPHPIDLDAVARASTALLGEHDFAAFCRRR-EGATTIRELLRFAWSVD 177

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            + ++   + A +F H+ +RS VG++  VG G+         L   +R     +AP  GL
Sbjct: 178 ADGVVRAELSADAFCHSMVRSLVGAMLDVGRGRRAVEWPAGLLDRAERASDVAVAPAHGL 237

Query: 240 YFDSVEYS 247
               V+Y 
Sbjct: 238 TLVGVDYP 245


>gi|327332268|gb|EGE74004.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL097PA1]
          Length = 279

 Score =  231 bits (589), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 118/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I  V    +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     + + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVLT--PDVVVKSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDRLNTAGTSLLGLRDFAAFCK-HREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 KRLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|238916468|ref|YP_002929985.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
 gi|238871828|gb|ACR71538.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
          Length = 245

 Score =  231 bits (589), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 126/249 (50%), Gaps = 7/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M  Y + IEY+G  Y GWQR     + ++I+  + + I  +TGE V ++   RT+ GVHA
Sbjct: 1   MYNYRIEIEYDGGRYDGWQRLGKDASTNTIESRLCEIIARMTGETVDMYAGSRTEKGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L Q A+F L +E   + +   LN YL     I++++++  D++FH++ +A  + Y YR+ 
Sbjct: 61  LCQTANFKLEKEVKAIEIKNYLNRYL--PRDIAVMSVTEADERFHSQLNAKSKIYEYRLD 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T        +  A+      D + MR AA +  G+HDF  F +   ++ S  +TI    V
Sbjct: 119 TGNVANVFRRKYAYHTFDKPDFDAMRKAAGYFEGKHDFKAFTTAK-KSKSTEKTIKKISV 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G    IR+ A  FLH   R  +G +  VG+G     D+++ L  ++ +   P A   
Sbjct: 178 EYEGARAYIRIEADDFLHNMARYIIGMMLDVGNGIKKPEDVKRCLDGENIQMSLP-AESY 236

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 237 GLFLVKVVY 245


>gi|325915522|ref|ZP_08177833.1| pseudouridylate synthase I [Xanthomonas vesicatoria ATCC 35937]
 gi|325538238|gb|EGD09923.1| pseudouridylate synthase I [Xanthomonas vesicatoria ATCC 35937]
          Length = 257

 Score =  231 bits (589), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 95/248 (38%), Positives = 134/248 (54%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    + V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASVQAALSSVADAPIQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++     V   FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDALRQPRGWM--LGTTARLPPSIAVRWCVPVADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD E M  AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRPLDAEAMHAAAQALLGENDFSAFRSVQCQALHARRNLQAITVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E+RV A +FLH  +R+ VGSL L+G G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 IGEVVEVRVQANAFLHHMVRNIVGSLILIGTGEQPTDWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|257463955|ref|ZP_05628340.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
 gi|317061478|ref|ZP_07925963.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
 gi|313687154|gb|EFS23989.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
          Length = 242

 Score =  231 bits (589), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 126/246 (51%), Gaps = 4/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +  +Y+GS + G+QRQ N  ++QG IEK++F +  E + +  +GRTD GVHA++Q
Sbjct: 1   MRNIKISYQYDGSSFMGFQRQPNQRTVQGEIEKSLFHILREKIDLTSSGRTDRGVHAIQQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F          L  AL+  L   + I +L +  VD +FHARFSA  RSY Y I  ++
Sbjct: 61  VSNFFTAVNIPSDRLFYALSRNL--PEDILLLQVEEVDSEFHARFSAKTRSYRYCITWKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E      + + ++        Q  +GRH+F  FR      ++P+R I    V   
Sbjct: 119 NP--FEHRYKAYVKEKIESTEFLKILQVFIGRHNFQNFRLQDSSFANPMREIYSISVEEV 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N + I +VA +FL +QIR  +G+   V  GK     + + L+  + +    LA   GLY
Sbjct: 177 ENGMNIDIVANAFLKSQIRIMIGTALQVYFGKVEGDRITRMLEELETEFPKYLADSSGLY 236

Query: 241 FDSVEY 246
              +EY
Sbjct: 237 LYRIEY 242


>gi|145356339|ref|XP_001422390.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582632|gb|ABP00707.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 286

 Score =  231 bits (589), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 82/260 (31%), Positives = 120/260 (46%), Gaps = 16/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHA 57
           + Y + I Y+G  Y G+Q Q ++  +IQ  +E+A+  +TG   E + +  AGRTD+GVHA
Sbjct: 16  VTYALKISYDGERYNGFQYQGEDVPTIQRELERALAKLTGIDRERLRLGAAGRTDAGVHA 75

Query: 58  LRQVAHFDLVREW--VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
             QVAHF   +          KA+N  L     I +         FH+RF A  ++Y Y 
Sbjct: 76  RGQVAHFYCEKSLGEDLTRCQKAMNGML--PKDIRVDAFWEPHPLFHSRFHASGKTYHYY 133

Query: 116 IITRQAPLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS----PIR 170
           +  R       +  A  +  +  D E +R AAQ  VG  D+  F +     S+      R
Sbjct: 134 VDARATSSPFTRKYAHQVGWRPCDVELLRQAAQLFVGTMDYKGFCNTSRDKSNEDRNTTR 193

Query: 171 TIDHFDVNSF---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           TI  FDV        LI + V    FL+ Q+R+ VG+L +V  GK     L   ++ +DR
Sbjct: 194 TIRRFDVFEDAADDGLIRLEVEGDGFLYRQVRNMVGALLVVASGKHDLAYLRTLIETKDR 253

Query: 228 KECGPLAPPEGLYFDSVEYS 247
                 AP  GL+   V Y 
Sbjct: 254 SRAPMGAPARGLFLHEVFYP 273


>gi|89953446|gb|ABD83318.1| Fgenesh protein 88 [Beta vulgaris]
          Length = 278

 Score =  231 bits (589), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 79/239 (33%), Positives = 117/239 (48%), Gaps = 11/239 (4%)

Query: 18  WQRQKNGSSIQGSIEKAIFLVT---GEIVVVHGAGRTDSGVHALRQVAHFDLVREWV-PV 73
           WQ Q +  ++Q +IEKA+  +T    + + V GAGRTD+GVHA  QVAHF     +    
Sbjct: 26  WQYQASPPTVQCAIEKALTKITHLDRKELSVVGAGRTDTGVHAWGQVAHFFTPFNYDSLD 85

Query: 74  ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
            +  A N  L     I +  +S    QFHARFSA  + Y Y I          +   +  
Sbjct: 86  EVHAAFNGLL--PSDIRVREVSPASPQFHARFSAKGKIYRYSIYNSSFMDPFLRYHVYHS 143

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNSFGNLIEIRVVAR 191
              L+   M  AA++  G+HDFT F +   + +   PI+TI  FDV   G L+E+ V   
Sbjct: 144 TYKLNAAVMAEAARYFTGKHDFTAFANAIRNDRVRDPIKTISRFDVTERGPLLELEVEGS 203

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE-CGPLA--PPEGLYFDSVEYS 247
            FL+ Q+R+ V  L  +G        + + L+ ++R+E        PP GL   SV+Y+
Sbjct: 204 GFLYRQVRNMVALLLQIGREAIPPDIVPEILETKNRRELAKYTKSTPPHGLSLVSVKYN 262


>gi|260579203|ref|ZP_05847093.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium ATCC 43734]
 gi|258602689|gb|EEW15976.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium ATCC 43734]
          Length = 328

 Score =  231 bits (589), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 75/260 (28%), Positives = 120/260 (46%), Gaps = 17/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW  Q  G  ++ G +++ + LVT   + +  AGRTD+GVHA  Q
Sbjct: 29  VRVRLEVAYDGTDFHGWATQSGGLRTVAGVLQEKLSLVTRHPIELVVAGRTDAGVHASGQ 88

Query: 61  VAHFDLV-------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           V H D+            P  L + L+  L     + +   S+  + F ARFSA+RR Y+
Sbjct: 89  VCHADIPADAFEQRSLTRPEDLVRRLSRML--PSDVRLHGASVAPQGFDARFSALRRHYI 146

Query: 114 YRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+ T  A P+ +           +D E  + A+  L+G +DF  F     + ++ +R +
Sbjct: 147 YRVTTHPAGPVPVRARDTAAWRHPIDLEKTQAASDALIGLNDFAAFCKAR-EGATTVREL 205

Query: 173 DHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             F        +     E  V A +F  + +RS VG+   VG GK         L+   R
Sbjct: 206 QEFRWVDVSTEAEPQTYEAHVTADAFCWSMVRSLVGAALTVGSGKRPDDFTPGLLKETKR 265

Query: 228 KECGPLAPPEGLYFDSVEYS 247
               P+AP EGL    V+Y 
Sbjct: 266 SSAVPVAPAEGLNLVRVDYP 285


>gi|282890286|ref|ZP_06298816.1| hypothetical protein pah_c014o179 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499943|gb|EFB42232.1| hypothetical protein pah_c014o179 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 231

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 72/223 (32%), Positives = 106/223 (47%), Gaps = 4/223 (1%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS 86
           IQ  +EK I  +  + V V  +GRTD+GVHA  QVAHF    E        ++N  L   
Sbjct: 3   IQEIVEKEIGKIVRQPVRVVASGRTDAGVHARGQVAHFSTNAEIDLRRFLVSINGLL--P 60

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAA 146
             I + ++  V   FHA++S   ++Y Y +   +      +  AW I + LD   +++AA
Sbjct: 61  KDIRVKDICQVPPDFHAQYSVSGKAYHYHLTLSRVQSPFSRFYAWHIRQKLDLSQLQVAA 120

Query: 147 QHLVGRHDFTTFR--SIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
           Q  VG HDFT+F   +      + +RTI   DV        +      FL+  +R+ VG 
Sbjct: 121 QLFVGTHDFTSFANEAHREHPQNAVRTIKRVDVIMEDEGCRLEFEGDGFLYKMVRNMVGI 180

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           L  V  G    TD+     A+DRK+ G  APP GL+   V + 
Sbjct: 181 LIEVATGYRPITDIPAIFAAKDRKKAGKAAPPHGLFLHQVNFP 223


>gi|291298744|ref|YP_003510022.1| tRNA pseudouridine synthase A [Stackebrandtia nassauensis DSM
           44728]
 gi|290567964|gb|ADD40929.1| tRNA pseudouridine synthase A [Stackebrandtia nassauensis DSM
           44728]
          Length = 300

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 120/249 (48%), Gaps = 4/249 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G +  A+  + G+   +  AGRTD+GVHA  QV
Sbjct: 22  VRLRLDICYDGTDFAGWAFQPGQRTVAGEVFTALSALFGQPEGLTVAGRTDAGVHATGQV 81

Query: 62  AHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRI-ITR 119
           AH D+          + L      +   + I  ++ V  +F+ARFSA+ R Y+YR+  T 
Sbjct: 82  AHVDVPAAAWARYRDRPLWRLRGILPPDVRITAITEVSSEFNARFSALSRRYVYRVADTV 141

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L +      P+ +D + M  AA  LVG HDF  F     + ++ +R +     + 
Sbjct: 142 WGVNPLRRLDTVAWPRPVDLDVMNAAATVLVGEHDFAAFCKRR-EGATTVRALRTVRWDR 200

Query: 180 FGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             + I    VVA +F H+ +RS VG++  VG+G+  +  L   L   +R     +AP  G
Sbjct: 201 DADGIARATVVADAFCHSMVRSLVGAMLAVGEGRRDAAWLAALLTRGERSGEVLVAPANG 260

Query: 239 LYFDSVEYS 247
           L    VE+ 
Sbjct: 261 LTLVEVEFP 269


>gi|225568181|ref|ZP_03777206.1| hypothetical protein CLOHYLEM_04255 [Clostridium hylemonae DSM
           15053]
 gi|225162900|gb|EEG75519.1| hypothetical protein CLOHYLEM_04255 [Clostridium hylemonae DSM
           15053]
          Length = 245

 Score =  230 bits (587), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 123/250 (49%), Gaps = 9/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVH 56
           M    + IEY+GS Y GW R   +++ +++   I + +  +TGE I+ ++   RT+ GVH
Sbjct: 1   MRNIRLTIEYDGSRYQGWCRLGKEESNNTVSNKIIEVLRKMTGEYIIELNCGCRTEVGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QVA+F    +   + +   LN YL     I+I N+  V  +FHA+ +A  ++Y+YR+
Sbjct: 61  AYAQVANFKTDSDMDILEIKHYLNRYL--PMDIAITNVEDVPDRFHAQLNATSKTYVYRM 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P   ++   +   K  D + M+ A+   +G+HDF  F ++     + ++ I   +
Sbjct: 119 TIDDVPSVFDRKYTYHCFKIPDKKLMQQASLLFIGKHDFKNFSTVKKN-KTTVKEIFEIE 177

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V      ++I + A  FLH   R  VG+L  +G G     D+E+   A  +    P    
Sbjct: 178 VYGDTEEMQILIHADDFLHNMARLVVGTLLEIGFGTRKKEDIEEIF-AGTKTPSSP-CDA 235

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 236 KGLYLQEVSY 245


>gi|120402449|ref|YP_952278.1| tRNA pseudouridine synthase A [Mycobacterium vanbaalenii PYR-1]
 gi|119955267|gb|ABM12272.1| tRNA pseudouridine synthase A [Mycobacterium vanbaalenii PYR-1]
          Length = 299

 Score =  230 bits (587), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 84/261 (32%), Positives = 121/261 (46%), Gaps = 18/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G+I+ A+  V    VV   AGRTDSGVHA  QV
Sbjct: 21  VRLRLDIAYDGTDFAGWATQAGQRTVAGAIDDALSTVFRTPVVTRAAGRTDSGVHATGQV 80

Query: 62  AHFDLVREWVPVI--------------LCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           AH D+  + +P                L + L   L   + + +  ++     F ARFSA
Sbjct: 81  AHVDVPADALPYAYPRTTRPGEAEFGPLVRRLGRML--PEDVRVREITRAAPGFDARFSA 138

Query: 108 IRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           +RR YLYR+ T    +   E       P+ LD   M  AA+ LVG HDF  F   H   +
Sbjct: 139 LRRHYLYRLSTAPYGVEPAEARFVTPWPRPLDVAAMAAAARELVGLHDFAAFCR-HRDGA 197

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           + IR +   D    G+ +E+ V A +F    +RS VG+L  VG+ +  +      L A  
Sbjct: 198 TTIRELQRLDCVRDGDRVEVHVSADAFCWNMVRSLVGALLAVGEHRRDAAWCAALLDATG 257

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R      AP  GL    V+Y 
Sbjct: 258 RSSDFAAAPARGLTLVGVDYP 278


>gi|68536845|ref|YP_251550.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium K411]
 gi|68264444|emb|CAI37932.1| tRNA pseudouridine synthase A [Corynebacterium jeikeium K411]
          Length = 328

 Score =  230 bits (587), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 75/260 (28%), Positives = 120/260 (46%), Gaps = 17/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + Y+G+ + GW  Q  G  ++ G +++ + LVT   + +  AGRTD+GVHA  Q
Sbjct: 29  VRVRLEVAYDGTDFHGWATQSGGLRTVAGVLQEKLSLVTRHPIELVVAGRTDAGVHASGQ 88

Query: 61  VAHFDLV-------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           V H D+            P  L + L+  L     + +   S+  + F ARFSA+RR Y+
Sbjct: 89  VCHADIPVDAFEQRSLTRPEDLVRRLSRML--PADVRLHGASVAPQGFDARFSALRRHYI 146

Query: 114 YRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+ T  A P+ +           +D E  + A+  L+G +DF  F     + ++ +R +
Sbjct: 147 YRVTTHPAGPVPVRARDTAAWRHPIDLEKTQAASDALIGLNDFAAFCKAR-EGATTVREL 205

Query: 173 DHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             F        +     E  V A +F  + +RS VG+   VG GK         L+   R
Sbjct: 206 QEFRWVDVSTEAEPQTYEAHVTADAFCWSMVRSLVGAALTVGSGKRPDDFTPGLLKETKR 265

Query: 228 KECGPLAPPEGLYFDSVEYS 247
               P+AP EGL    V+Y 
Sbjct: 266 SSAVPVAPAEGLNLVRVDYP 285


>gi|296119322|ref|ZP_06837890.1| tRNA pseudouridine synthase A [Corynebacterium ammoniagenes DSM
           20306]
 gi|295967714|gb|EFG80971.1| tRNA pseudouridine synthase A [Corynebacterium ammoniagenes DSM
           20306]
          Length = 297

 Score =  230 bits (587), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 85/261 (32%), Positives = 126/261 (48%), Gaps = 18/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R    I Y+G+ + GW  QK    ++QG +E+ + ++    + +  AGRTD+GVHA  Q
Sbjct: 15  VRLRFDIAYDGTDFHGWASQKGQLRTVQGVLEQCLTMILRHPIELTVAGRTDAGVHAAGQ 74

Query: 61  VAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VAH D+          +  P  L + L     + D I I ++S   + F ARFSA+RR Y
Sbjct: 75  VAHADVPVESLQQRSIDGEPAKLVRRLAKL--VDDDIRIHSVSFAPEGFDARFSALRRHY 132

Query: 113 LYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           +YRI T +A     + R      + +D + M+ AA  LVG HDF  F      A + IR 
Sbjct: 133 VYRITTEEAGALPTRLRDTATWTRPVDIDLMQQAATTLVGLHDFAAFCKAKPHA-TTIRD 191

Query: 172 IDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           +  F        S  NL E  V A +F  + +RS VG    VG+G+     +E  L   +
Sbjct: 192 LQEFYWVDASTPSEPNLYEAHVSADAFCWSMVRSLVGCCLAVGEGRRDINFVEAMLGESE 251

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R    P+A  +GL    V+Y 
Sbjct: 252 RSSSIPVAAAKGLSLVGVDYP 272


>gi|254302141|ref|ZP_04969499.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148322333|gb|EDK87583.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 247

 Score =  230 bits (587), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 122/249 (48%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 3   MGRKNIKIEFRYDGSRYYGFQRQPNKITVQGEIEKVLRIVTKEEINLISAGRTDRGVHAN 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 63  HQVSNFYTSSNIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKMREYVYIISW 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +  E +       +G HDF  FR   C +   IR I   +V 
Sbjct: 121 EKNP--FEARHCKFVKEKIVAEKLEKIFSDFIGVHDFKNFRLSDCVSKVTIREIYQIEVK 178

Query: 179 SFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG+  I+I +   +FL +Q+R  VG++  +  G+     ++  L    R+    L   E
Sbjct: 179 YFGDSKIKIYIKGSAFLKSQVRIMVGTVLEIYYGRLPENHIKLMLNDFTREYKKNLVEAE 238

Query: 238 GLYFDSVEY 246
           GLY + ++Y
Sbjct: 239 GLYLNKIKY 247


>gi|162446996|ref|YP_001620128.1| tRNA pseudouridine synthase A [Acholeplasma laidlawii PG-8A]
 gi|161985103|gb|ABX80752.1| pseudouridylate synthase [Acholeplasma laidlawii PG-8A]
          Length = 240

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 82/245 (33%), Positives = 118/245 (48%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY  I  Y+G+ Y G+Q+Q N   IQ  IEKA  L+T   +    A RTD GVHAL QV
Sbjct: 1   MRYKAIFSYDGTNYSGYQKQINQLGIQTVIEKAFRLMTQIDIETFAASRTDKGVHALHQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E        ALN  L     I ++ ++ V   FHAR SA  + Y+Y+I   + 
Sbjct: 61  LHFDSDIELTSDQWVDALNKRL--PTDIRLMKVTPVKDNFHARHSAKSKRYIYKI--AKQ 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  + +G   L  K  D + ++     +VG HDF+ F S + +   PI+TI  FD     
Sbjct: 117 PSTVFRGNHELYVKHFDIDLVKDHLHTIVGTHDFSGF-SPNKEHKPPIKTIYSFDYKETK 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                 +   SFL   +R  +G++  V   K     LE  L+ ++R+     A  +GLY 
Sbjct: 176 THYIFSIHGNSFLRYMVRIIMGNVIAVATNKKPQNQLEILLETKNRELSAKTADAKGLYL 235

Query: 242 DSVEY 246
             + Y
Sbjct: 236 KHIYY 240


>gi|257470657|ref|ZP_05634747.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|317064863|ref|ZP_07929348.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|313690539|gb|EFS27374.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
          Length = 242

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 115/246 (46%), Gaps = 4/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +   ++GS ++G+QRQ    ++QG IEK + +V  E V +  AGRTD GVHAL Q
Sbjct: 1   MRNIKIRYRFDGSMFYGFQRQPGKRTVQGEIEKLLDIVLREKVNMISAGRTDRGVHALEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F          L  ALN  L     I I  +   D  F++RF A  R+Y Y I   +
Sbjct: 61  VSNFLTSSPIPVEKLKHALNKGL--PLDIEIFEVEDADIDFNSRFMAKDRAYRYVISWIK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E     L+ + +D  N     + LVG +DF  FR   C + + IR I        
Sbjct: 119 NP--FESRYVTLVNEKIDKNNFVKILEPLVGVNDFNNFRLSDCGSKTSIREIYSITAEEK 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N + I +   SFL +QIR  +G+   V  G      L+  L+  ++     +A P GLY
Sbjct: 177 ENKLIINIKGNSFLKSQIRIMMGTALDVYFGNRDENYLKNMLKNPNKDFIKKVADPYGLY 236

Query: 241 FDSVEY 246
              V Y
Sbjct: 237 LSEVNY 242


>gi|158317762|ref|YP_001510270.1| tRNA pseudouridine synthase A [Frankia sp. EAN1pec]
 gi|158113167|gb|ABW15364.1| tRNA pseudouridine synthase A [Frankia sp. EAN1pec]
          Length = 275

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 117/247 (47%), Gaps = 5/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQV 61
           R  + + Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA  QV
Sbjct: 9   RLRLDLAYDGTAFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDSGVHAAGQV 68

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AH D+  +     L + LN  L     + +  L+     F ARFSA+ R Y+YRI     
Sbjct: 69  AHVDIPDDTPVGGLARRLNGVL--DRAVRVKGLAPAPDGFDARFSALSRRYVYRITDAPY 126

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +      P+ LD   M  AA  L+G HDF  F     + ++ +RT+   DV+  
Sbjct: 127 GADPLRRFDTLASPRPLDVPAMAEAALLLLGEHDFAAFCRRR-EGATTVRTLLRLDVSRS 185

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++I   V A +F H+ +R+  G+L  VG+G+     +   L    R     + P  GL 
Sbjct: 186 RDVILADVEADAFCHSMVRALAGALVAVGEGRRRPEWVAAVLGRGMRDPAVTVLPAHGLT 245

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 246 LVEVRYP 252


>gi|213582886|ref|ZP_03364712.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 214

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/199 (35%), Positives = 101/199 (50%), Gaps = 2/199 (1%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           GRTD+GVH   QV HF+             +NA L     I++  +  V   FHARFSA 
Sbjct: 1   GRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSAT 58

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
            R Y Y I   +   A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P
Sbjct: 59  ARRYRYIIYNHRLRPAVLAKGVTHYYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTP 118

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            R + H +V   G  + + + A +F+H  +R+ VGSL  VG      + + + L A+DR 
Sbjct: 119 WRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAARDRT 178

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                A  EGLY  +V+Y 
Sbjct: 179 LAAATAKAEGLYLVAVDYP 197


>gi|78048428|ref|YP_364603.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325924659|ref|ZP_08186097.1| pseudouridylate synthase I [Xanthomonas perforans 91-118]
 gi|123743895|sp|Q3BRL0|TRUA_XANC5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78036858|emb|CAJ24551.1| tRNA pseudouridine synthase A [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325544865|gb|EGD16210.1| pseudouridylate synthase I [Xanthomonas perforans 91-118]
          Length = 257

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 94/248 (37%), Positives = 133/248 (53%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+GS + GWQ+  +  G S+Q S++ A+  V    V V  AGRTD+GVH   
Sbjct: 1   MRYALGVEYDGSEFQGWQQLGEHGGPSVQASLQAALSSVADAPVQVVCAGRTDAGVHGEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P      L    ++  +I++         FHARFSA  R Y YR++ R
Sbjct: 61  QVVHFDSDARREPRGWM--LGTTARLPPSIAVRWCVPAADDFHARFSARARRYRYRLLNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   AL +       + LD + M  AAQ L+G +DF+ FRS+ CQA    R +    V  
Sbjct: 119 QIRPALYRQTLSWERRPLDADAMHAAAQALLGENDFSAFRSVQCQALHARRHLQAIHVQR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G ++E++V A +FLH  +R+ VGSL LVG G+  +  +   L  +DR   GP APP+GL
Sbjct: 179 IGEVVEVQVQANAFLHHMVRNIVGSLILVGTGEQPADWIATLLAGRDRTVAGPTAPPQGL 238

Query: 240 YFDSVEYS 247
            F    Y 
Sbjct: 239 VFIGPLYP 246


>gi|256028207|ref|ZP_05442041.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289766139|ref|ZP_06525517.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289717694|gb|EFD81706.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
          Length = 245

 Score =  229 bits (585), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 119/249 (47%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MGRKNIKIEFRYDGSRYYGFQRQPNKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L  S  I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSTIPIEKYKYLLTRAL--SKDIDILSVEEVDENFNARHNAKMREYIYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +D   +       VG HDF  FR   C +   IR I   +V 
Sbjct: 119 EKNP--FEARYCKFVKEKIDVRKLEKIFSDFVGVHDFKNFRLNDCVSKVTIREIYQIEVK 176

Query: 179 SFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG   I+I +   +FL +Q+R  VG+   +  G+     ++  L    R+    L   E
Sbjct: 177 YFGESKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIKLMLNDFTREYKKNLVEAE 236

Query: 238 GLYFDSVEY 246
           GLY + + Y
Sbjct: 237 GLYLNKINY 245


>gi|169630847|ref|YP_001704496.1| tRNA pseudouridine synthase A [Mycobacterium abscessus ATCC 19977]
 gi|169242814|emb|CAM63842.1| tRNA pseudouridine synthase A [Mycobacterium abscessus]
          Length = 294

 Score =  229 bits (585), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 79/261 (30%), Positives = 125/261 (47%), Gaps = 18/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q N  ++ G + +A   + G+ V ++ AGRTD+GVHA  QV
Sbjct: 16  VRLRLDIAYDGTDFAGWATQVNQRTVAGVLGEAFTTIVGDSVQLYAAGRTDAGVHATGQV 75

Query: 62  AHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           AH D+    +P                L + L+ +L     + +L++S     F ARFSA
Sbjct: 76  AHLDVPVACLPGLRGRYRPAGAPEFDRLVRRLSRFL--PSDVRVLDISRAPAHFDARFSA 133

Query: 108 IRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           +RR Y YR+ T     L L +       + LD + M  A+++L+G  DF  F   H + +
Sbjct: 134 LRRHYEYRLSTASFGVLPLARHDVVGWHRPLDVDAMNEASRNLLGLRDFAAFCR-HREGA 192

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           + IR +  FD    G  +   V A +F  + +RS VG++  VG+G+         L  + 
Sbjct: 193 TTIRELQRFDWGVDGQRLTAYVSADAFCWSMVRSLVGAVLAVGEGRRPVQWCVDLLNKER 252

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R      AP  GL    V+Y 
Sbjct: 253 RSSDFAAAPARGLTLVGVDYP 273


>gi|315605929|ref|ZP_07880960.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 180 str.
           F0310]
 gi|315312211|gb|EFU60297.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 180 str.
           F0310]
          Length = 299

 Score =  229 bits (585), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 123/278 (44%), Gaps = 34/278 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GW  Q    ++QG IE A+ + + E V    AGRTD+GVHA  Q
Sbjct: 1   MRRLRLDLGYDGTDFRGWAAQPGLRTVQGEIEAALAMASREEVTTTVAGRTDAGVHARHQ 60

Query: 61  VAHFDL--------------VREWVPVILCKALNAYLKISD----------------TIS 90
           V H DL                +     + + LN  L                     + 
Sbjct: 61  VCHVDLSDEAWARLAPRGERSEDDAATSIVRRLNKILSGRYGERSRTRGMGVARGTCDVR 120

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           I    +VD  F ARFSA+ R Y YR+    AP  L +     + + LD + M  AA  L+
Sbjct: 121 IFAARVVDASFDARFSALARRYTYRVSD--APDPLARWDRLWVDEPLDDQAMNDAAAPLL 178

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           G+HDF  +     + ++ IR +     V      +  RV A +F H+ +RS VG+L LVG
Sbjct: 179 GQHDFLGYCRPR-EGATTIRALRTLRAVREADGTLAFRVEADAFCHSMVRSLVGALLLVG 237

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            G        + L A+ R    P+AP  GL  + V+Y 
Sbjct: 238 SGARNIDYPARVLGARSRASAAPIAPAHGLTLEGVDYP 275


>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 =  229 bits (585), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 93/202 (46%), Positives = 123/202 (60%), Gaps = 1/202 (0%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           ++  GRTD+GVHAL QVAHFD+ +E     +  A+N +LK S  I +LN  +VD  FHAR
Sbjct: 1   MYCGGRTDAGVHALGQVAHFDMEKECELYRIRNAINYHLK-SIPIVVLNAEVVDDAFHAR 59

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           FSA +R Y YRI+ R AP ALE G  W +   LD   MR AA+HL+G+HD ++FRS  C 
Sbjct: 60  FSAKKRYYEYRIVNRYAPAALETGYVWQVFSPLDVNIMREAAKHLLGKHDLSSFRSKDCH 119

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           A++PIRTID  D+   GN I I++ A SFLH Q+R   G+L   G  +    ++   L  
Sbjct: 120 AANPIRTIDDIDIVQNGNHIHIKISAISFLHNQVRIIAGTLVEFGKNRTNPQEMLHILSQ 179

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
             R   G  APP GLY   ++Y
Sbjct: 180 CKRSAAGVTAPPFGLYLVKIDY 201


>gi|300932964|ref|ZP_07148220.1| tRNA pseudouridine synthase A [Corynebacterium resistens DSM 45100]
          Length = 324

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 82/260 (31%), Positives = 128/260 (49%), Gaps = 16/260 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + + Y+G+ + GW  Q    ++QG +E+ + LVT   V +  AGRTD+GVHA  Q
Sbjct: 40  MVRVRLDVAYDGTDFHGWAAQFGLRTVQGVLEEKLSLVTRHAVQLTVAGRTDAGVHADGQ 99

Query: 61  VAHFDLV-------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           VAHFD+            P  L + L+  L     + +   S     F ARFSA+RR Y+
Sbjct: 100 VAHFDVPATTFTQRSLQRPGDLVRRLSRML--PADVRVHGASEAPVGFDARFSALRRHYV 157

Query: 114 YRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+ T  A P  +         + +D + ++ A++ LVG +DF  F     + ++ IR +
Sbjct: 158 YRVTTATAGPRPVRVRDTARWRRPIDLDKVKAASEVLVGLNDFAAFCKAR-EGATTIREL 216

Query: 173 DHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             F        +     E RV A +F  + +RS VG++  VG+GK       + L+  +R
Sbjct: 217 QQFQWFDVSTPAEPETYEARVAADAFCWSMVRSLVGAVLTVGEGKRDGDFTAELLKQNER 276

Query: 228 KECGPLAPPEGLYFDSVEYS 247
               P+AP EGL    V+Y 
Sbjct: 277 SSKVPVAPAEGLNLVQVDYP 296


>gi|315230173|ref|YP_004070609.1| tRNA pseudouridine synthase A [Thermococcus barophilus MP]
 gi|315183201|gb|ADT83386.1| tRNA pseudouridine synthase A [Thermococcus barophilus MP]
          Length = 266

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 119/250 (47%), Gaps = 27/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R  + I Y+GS ++G+QRQ    +++G I + +  +    + E     GA RTD GV A
Sbjct: 1   MRIALKIAYDGSKFYGFQRQPGLRTVEGEIIRVLQKLDVIESPENANFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L  V  F+       +   + LN +L+    I +L ++ V   FH RF A  + Y Y   
Sbjct: 61  LGNVIAFNTEN--PKLAQPRVLNHHLR---DIWVLGVAQVSDDFHPRFWAKSKIYRY--- 112

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +L+ +  D   M+  A+  VG HDF+ F  +  +   PIR ++  ++
Sbjct: 113 -------------YLVDEGFDVNAMKECARLFVGTHDFSAFARVE-KFKDPIREVNRLEI 158

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+LI I +  +SFL   +R  V +LKL G G   + D+ K L+ +  K+  P  PPE
Sbjct: 159 IPRGDLIIIEIEGKSFLWEMVRRIVTALKLCGFGIVETEDIRKMLEGRTDKKLPPS-PPE 217

Query: 238 GLYFDSVEYS 247
            L    ++Y 
Sbjct: 218 NLVLWEIKYE 227


>gi|301165600|emb|CBW25171.1| tRNA pseudouridine synthase A [Bacteriovorax marinus SJ]
          Length = 256

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 81/258 (31%), Positives = 122/258 (47%), Gaps = 14/258 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           M  Y +I+ Y G+ Y GWQ+Q + S +IQG +EKA+  ++  + +   G+GRTDSGVHAL
Sbjct: 1   MSFYKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV    +  E  P+ L KALN++L   + I  ++     + F+  F A  ++Y Y    
Sbjct: 61  GQVVRVQIPLELEPLSLLKALNSHL--PNDIECIHSENSSELFNPVFDAKDKTYKYLFSL 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
                AL       + + +D E MR A +  +G HDF  F ++    SS +R I    + 
Sbjct: 119 NGRRNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLH 178

Query: 178 ---------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                      +       V    FL   +R  VG+L  +G GK    DL+ AL +    
Sbjct: 179 LEKQQGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGA 238

Query: 229 ECGPLAPPEGLYFDSVEY 246
           +   +AP  GLY   V Y
Sbjct: 239 KLAAVAPSNGLYLCEVNY 256


>gi|78189343|ref|YP_379681.1| tRNA pseudouridine synthase A [Chlorobium chlorochromatii CaD3]
 gi|123757011|sp|Q3AQT7|TRUA_CHLCH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78171542|gb|ABB28638.1| tRNA pseudouridine synthase [Chlorobium chlorochromatii CaD3]
          Length = 243

 Score =  229 bits (584), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 117/247 (47%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G+ + GWQRQ     ++QG+IEK +  +T E V+++GAGRTD GVHA +
Sbjct: 1   MRTIRLDIEYDGTDFAGWQRQSGTIPTVQGTIEKLLSQITQEEVLLNGAGRTDKGVHARQ 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA   L        L  +LN  L    TI I N   V   FHARFSA  R+Y Y +   
Sbjct: 61  QVASCALHSSMELSRLAHSLNCLL--PPTIRICNAVHVTDDFHARFSATERTYRYFVS-- 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P AL           LD   M+  A  +VG HDFT F      + +    +     + 
Sbjct: 117 ETPSALCNRFTGCANALLDVGVMQQMAAMVVGEHDFTAFSREERDSPAKRCKVTSCRWHR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              ++ +++ A  FL + +R  V ++   G G+   T  +  +++         AP  GL
Sbjct: 177 LHGMVVLQISANRFLRSMVRYLVHAMLQGGKGRLAPTLFQDMVESGTSSYRMVAAPASGL 236

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 237 FLWRIGY 243


>gi|119356907|ref|YP_911551.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides DSM 266]
 gi|166228693|sp|A1BFF0|TRUA_CHLPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119354256|gb|ABL65127.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides DSM 266]
          Length = 258

 Score =  229 bits (584), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 115/247 (46%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + IEY+G+GY GWQRQ     ++QG IE+ +  +  E + + GAGRTD GVHA  
Sbjct: 9   MKNIRITIEYDGTGYAGWQRQAGSFCTVQGEIERILSQILQEDIRLAGAGRTDKGVHARA 68

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+A F       P  +  ++NA L   +TI I +  +V + FHAR SA  R Y Y +  R
Sbjct: 69  QIATFKSRSSLGPDRMVHSMNALL--PNTIRISDPLVVPEGFHARHSAKEREYRYFV--R 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P A+    +     SLD  +M   A +++G HDF+ F       +  +  +       
Sbjct: 125 EEPSAVLGRFSGCSYGSLDLMSMNRVASYVLGEHDFSVFSKETRDRTGCLCRVISCKWFR 184

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
                 +R+ A  FL + +R     +   G G  +  +  + +++         A P GL
Sbjct: 185 QREFFVLRISANRFLRSMVRYLAALMIDSGKGLLSPEEAREMIESGILTRQLVPAAPNGL 244

Query: 240 YFDSVEY 246
           +   + Y
Sbjct: 245 FLWKITY 251


>gi|237743728|ref|ZP_04574209.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
 gi|229432759|gb|EEO42971.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
          Length = 245

 Score =  229 bits (584), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 118/249 (47%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GSGY+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MGRKNIKIEFRYDGSGYYGFQRQPNKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSTIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKMREYVYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +D   +       VG HDF  FR   C +   IR I   +V 
Sbjct: 119 EKNP--FEARYCKFVKEKIDVRKLEKIFSDFVGVHDFKNFRLNDCVSKVTIREIYQIEVK 176

Query: 179 SFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG   I+I +   +FL +Q+R  VG    +  G+     +   L    R+    L   E
Sbjct: 177 YFGESKIKIYIKGSAFLKSQVRIMVGIALEIYYGRLPENHIRLMLNDFTREYKKNLVEAE 236

Query: 238 GLYFDSVEY 246
           GLY + + Y
Sbjct: 237 GLYLNKINY 245


>gi|78187037|ref|YP_375080.1| tRNA pseudouridine synthase A [Chlorobium luteolum DSM 273]
 gi|123730052|sp|Q3B3P4|TRUA_PELLD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78166939|gb|ABB24037.1| tRNA pseudouridine synthase [Chlorobium luteolum DSM 273]
          Length = 253

 Score =  229 bits (584), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 75/248 (30%), Positives = 110/248 (44%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + +EY+G+ Y GWQRQ  G  ++QG +E  +  +  E V +  AGRTD GVHAL 
Sbjct: 1   MRNIRLRVEYDGTPYAGWQRQPGGIVTVQGELEACLSRILQERVNLAAAGRTDRGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          +  +LN  L   DTI +     VD +FHARFSA  R Y Y ++  
Sbjct: 61  QVVNFQTASSLELQRIAHSLNCLL--PDTIRVDCPQEVDMEFHARFSAAERQYRYFLM-- 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P A+    A    + LD   M   A  L G HDF+ F       +  + ++       
Sbjct: 117 EEPSAVFGRFAGCSSRPLDLPLMHSLAVTLKGIHDFSAFSREDRDGTGSLCSVRMAGWYR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +   + A  FL + +R  VG++  +G G+      +  L A         A   GL
Sbjct: 177 HRGFLVFHIAANRFLRSMVRGLVGAMMDIGAGRLDPCSFKAMLDADAHARRVRPAAASGL 236

Query: 240 YFDSVEYS 247
           +   V Y 
Sbjct: 237 FLSRVVYP 244


>gi|83816613|ref|YP_444802.1| tRNA pseudouridine synthase A [Salinibacter ruber DSM 13855]
 gi|123726203|sp|Q2S4S9|TRUA_SALRD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83758007|gb|ABC46120.1| tRNA pseudouridine synthase A [Salinibacter ruber DSM 13855]
          Length = 265

 Score =  229 bits (584), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 86/249 (34%), Positives = 130/249 (52%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G+ + GWQ Q    ++QG++E+A+  V G    V G+GRTD+GVHA  Q
Sbjct: 1   MPRYRLLVEYDGTDFHGWQIQPTVPTVQGALEEAVDTVVGTACRVTGSGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL     P  L  +LN      D +++  +      FHAR+ A RR Y Y + T+ 
Sbjct: 61  VAHVDLPETRDPYRLRGSLNGL--TPDAVAVRRVERAPDDFHARYDARRRRYHYHLHTQ- 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
            P AL +     +    D   +R A   L+GRH+F++F     +  + + T+ H      
Sbjct: 118 -PCALGRRARTPVRPVPDFGRIRAATPDLLGRHNFSSFCLTQSETENRVCTLTHLRWVDE 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +      + VV   FLH  +R+ VG+L  +G  K  +  L   L A+DR+  GP  PPEG
Sbjct: 177 ARRGCWRVEVVGTRFLHGMVRALVGTLVEIGHEKRAADALPAVLAARDRRAAGPSMPPEG 236

Query: 239 LYFDSVEYS 247
           L  ++V Y 
Sbjct: 237 LVLEAVRYE 245


>gi|188997613|ref|YP_001931864.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932680|gb|ACD67310.1| tRNA pseudouridine synthase A [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 243

 Score =  228 bits (583), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 84/244 (34%), Positives = 116/244 (47%), Gaps = 5/244 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
            Y + I Y G+ Y GWQRQKNG  IQ  IE  +  +  E + + GAGRTD+GVHALRQVA
Sbjct: 5   NYKLEISYIGTNYNGWQRQKNGIGIQQVIEDLLSELLEEKITLIGAGRTDAGVHALRQVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F   +      +   LNA L     ISIL +  V   F+ARFSA  ++YLY+I T+  P
Sbjct: 65  NFKTKKHKNTKTIYTYLNAKL--PRDISILKVEEVPLSFNARFSAKGKTYLYKINTKPDP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                  AW   K LD   M      +    D ++           I  +    +   G 
Sbjct: 123 FLF--KLAWYYDKKLDLIKMVEGINLIKQYKDLSSLAKAGDYIRKEI-DLRELKLYFDGK 179

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +I I + A  FL   +R   G L  +G G  +  +L+  ++ +        APPEGLY  
Sbjct: 180 IITIEITASHFLRNMVRRIAGHLVALGRGSLSLEELKDIIEKKSPSHGKFTAPPEGLYLK 239

Query: 243 SVEY 246
           +V Y
Sbjct: 240 AVYY 243


>gi|311111942|ref|YP_003983164.1| tRNA pseudouridine synthase A [Rothia dentocariosa ATCC 17931]
 gi|310943436|gb|ADP39730.1| tRNA pseudouridine synthase A [Rothia dentocariosa ATCC 17931]
          Length = 327

 Score =  228 bits (583), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 89/280 (31%), Positives = 129/280 (46%), Gaps = 35/280 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  +   Y G+ + GW RQ N  ++QG +E A+ LV      V  AGRTD+GVHA  Q 
Sbjct: 33  QRVRIDCAYEGTWFSGWARQPNLVTVQGVLEDALELVLRAHHRVTVAGRTDAGVHAQAQT 92

Query: 62  AHFDLVREW------------VPVILCKALN-----------AYLKISDTIS-------- 90
            H D+  E                 L + ++             L I + +         
Sbjct: 93  IHLDIAAETWQKLTGRDGLADPAESLKRKVSGALKRTLAQAEHTLGIPERMRGLLQGSLV 152

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQ--APLALEKGRAWLIPKSLDCENMRIAAQH 148
           +  +  V + F ARFSA  R Y YRI+  Q  +P  L +  AW IP+SLD E++  AA  
Sbjct: 153 LHQVQPVPQDFDARFSATGRRYTYRILDGQGSSPDPLRRAYAWCIPESLDLEDLNKAAHE 212

Query: 149 LVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKL 207
           L G HDF +F     + ++ IR +    +    + +IE  V A +F H  +RS +G+L L
Sbjct: 213 LTGLHDFLSFCKPR-EGATTIRELRRIYLTRHDDGVIEATVEADAFCHHMVRSLIGALVL 271

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            G GK T T L + L+   R     +APP GL    ++Y 
Sbjct: 272 YGTGKRTQTWLRERLENPQRDASLIMAPPHGLALAHIDYP 311


>gi|257453277|ref|ZP_05618576.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|317059811|ref|ZP_07924296.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|313685487|gb|EFS22322.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
          Length = 245

 Score =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 127/247 (51%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +  +Y+GS + G+QRQ    ++QG IEK +F +  E + +  +GRTD GVHA+ Q
Sbjct: 1   MKNIKISYQYDGSSFMGFQRQPEKRTVQGEIEKCLFRILKEKIDLTSSGRTDRGVHAMHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F          L  AL+  L   + I +L L    K FHARFSA  RSY YRI   +
Sbjct: 61  VSNFFTAVNIPLDKLFYALSRCL--PEDILLLELEEARKDFHARFSAKTRSYCYRITWEK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P   E+     + K +D ++     +  +G+H+F  FR      ++PIR I    V   
Sbjct: 119 SP--FERRYKTYVKKKIDSQSFFKILEIFMGKHNFQNFRLQDDAFANPIREIYSIQVKEV 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              ++I + A +FL +QIR  +G+   V   K  S  +EK L+  D++    LA P GLY
Sbjct: 177 DEGMDIYIEANAFLKSQIRIMLGTAFQVYFQKVESNRIEKMLKEPDKEFPKYLADPNGLY 236

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 237 LYHIKYD 243


>gi|14521207|ref|NP_126682.1| tRNA pseudouridine synthase A [Pyrococcus abyssi GE5]
 gi|14548295|sp|Q9UZZ3|TRUA_PYRAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|5458425|emb|CAB49913.1| truA pseudouridylate synthase I [Pyrococcus abyssi GE5]
          Length = 263

 Score =  228 bits (582), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 118/247 (47%), Gaps = 24/247 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R    I Y+G+ + G+QRQ N  +++G I KA+            A RTD GV AL  V
Sbjct: 1   MRVAFKIAYDGTRFHGFQRQPNLRTVEGEIIKALNNSGIMYSDFKSASRTDRGVSALGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                  E     +   LNA L   + + IL+   V + FH RF A  + Y Y + +   
Sbjct: 61  VAITTEDEKALNPMV--LNARL---EDVWILSAIEVPQDFHPRFWAKSKVYRYYLPS--- 112

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                          L+ E ++  +Q  +G HDF+ F  +       +R+ID  +V + G
Sbjct: 113 -------------IGLEVEKVKECSQLFLGVHDFSAFSRV--DGRDTVRSIDRIEVFTLG 157

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEGLY 240
            ++ I + A+SFL   +R  V +L+L G G+ +  ++++ L+ + ++ +  P APPEGL 
Sbjct: 158 PILIIEIEAKSFLWEMVRRIVKALELCGLGRLSCEEIKEMLEGKFEKSKKVPPAPPEGLL 217

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 218 LVDIKYE 224


>gi|257467128|ref|ZP_05631439.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315918259|ref|ZP_07914499.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313692134|gb|EFS28969.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 245

 Score =  228 bits (582), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 128/247 (51%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +  +Y+GS + G+QRQ    ++QG IEK +F +  E + +  +GRTD GVHA+ Q
Sbjct: 1   MKNIKISYQYDGSSFMGFQRQPEKRTVQGEIEKCLFRILKEKIDLTSSGRTDRGVHAMHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F          L  AL+  L   + I +L L    K FHARFSA  RSY YRI  ++
Sbjct: 61  VSNFFTAVNIPLDKLFYALSHCL--PEDILLLELEEARKDFHARFSAKTRSYCYRITWKK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P   E+     + K +D ++     +  +G+H+F  FR      ++PIR I    V   
Sbjct: 119 SP--FERRYKTYVKKKIDSQSFFKILEIFMGKHNFQNFRLQDDAFANPIREIYSIQVKEV 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              ++I + A +FL +QIR  +G+   V   K  S  +EK L+  D++    LA P GLY
Sbjct: 177 DEGMDIYIEANAFLKSQIRIMLGTAFQVYFQKVESNRIEKMLKEPDKEFPKYLADPNGLY 236

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 237 LYHIKYD 243


>gi|134103229|ref|YP_001108890.1| tRNA pseudouridine synthase A [Saccharopolyspora erythraea NRRL
           2338]
 gi|291007979|ref|ZP_06565952.1| tRNA pseudouridine synthase A [Saccharopolyspora erythraea NRRL
           2338]
 gi|133915852|emb|CAM05965.1| tRNA pseudouridine synthase A [Saccharopolyspora erythraea NRRL
           2338]
          Length = 296

 Score =  228 bits (582), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 74/264 (28%), Positives = 123/264 (46%), Gaps = 21/264 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHAL 58
           +R  + + Y+G+ +FGW +Q +  ++QG +E A+            V  AGRTD+GVHA 
Sbjct: 14  VRLRLEVSYDGTDFFGWAKQPDRRTVQGLLEDALRKQPPGRSVPRSVVVAGRTDTGVHAT 73

Query: 59  RQVAHF-------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
            QV H               L    +P +          +   + +L   +    F ARF
Sbjct: 74  GQVVHVDVVPSAPDEGGRLPLDEHGIPDLDRMRHRWNRILPGDVRVLGARVAPAGFDARF 133

Query: 106 SAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+RR Y Y++         L +       + LD + +  A++ L+G +DF  F     +
Sbjct: 134 SAMRRHYRYQVSDAPWGVDPLRRRDTLSWNRPLDVDALNAASEDLLGLNDFAAFCKQR-E 192

Query: 165 ASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            ++ +R +  F       +L+  RV A +F H+ +RS VG+L +VGDG+ + T   +AL+
Sbjct: 193 GATTVRELQRFSWERAEPHLLVARVSADAFCHSMVRSLVGALLMVGDGRRSRTWPAEALR 252

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           A +R     +AP  GL    V+Y 
Sbjct: 253 AAERTS--TVAPAHGLTLVGVDYP 274


>gi|326332230|ref|ZP_08198510.1| tRNA pseudouridine synthase A [Nocardioidaceae bacterium Broad-1]
 gi|325949936|gb|EGD41996.1| tRNA pseudouridine synthase A [Nocardioidaceae bacterium Broad-1]
          Length = 287

 Score =  228 bits (582), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 81/266 (30%), Positives = 129/266 (48%), Gaps = 23/266 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-------VVVHGAGRTDSG 54
           +R  + + Y+G+ + GW  Q    ++QG ++ A+              V V  AGRTDSG
Sbjct: 1   MRIRIDLAYDGTMFHGWATQPGLRTVQGELQAALATALRVPSTGERSQVWVTVAGRTDSG 60

Query: 55  VHALRQVAHFDLV-----------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           VHA  QVAHFD+             +     L + LN  L     + +       + F+A
Sbjct: 61  VHARGQVAHFDIDADVLESSRGRSEQSPLDSLVRRLNGIL--PADLRVHRAVEAPEGFNA 118

Query: 104 RFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R Y+YRI+   A    L +G      + LD   M +A+  LVG +DF +F    
Sbjct: 119 RFSALSRRYVYRIVDDPAFVDPLLRGHVLYRTRPLDLSLMNVASADLVGLNDFASFCKPR 178

Query: 163 CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            + ++ IR +     +   + +IE  V+A +F H+ +RS VG L ++G+G+   T  +++
Sbjct: 179 -EGATTIRDLRQLTWDRRPDGIIEATVLADAFCHSMVRSLVGCLMVIGEGRKDVTWAKES 237

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
           L A+ R    P+AP  GL  + V Y 
Sbjct: 238 LAARSRSSSIPIAPANGLTLEEVAYP 263


>gi|87124988|ref|ZP_01080835.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9917]
 gi|86167308|gb|EAQ68568.1| tRNA pseudouridine synthase A [Synechococcus sp. RS9917]
          Length = 274

 Score =  228 bits (582), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 110/242 (45%), Gaps = 4/242 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDL 66
           ++Y GS + GWQRQ+ G+S+QG +EKAI  +     V    AGRTD+GVHA  QV HFD 
Sbjct: 1   MQYEGSSFCGWQRQRQGTSVQGELEKAIAALDPHRPVQAVAAGRTDAGVHAAGQVVHFDC 60

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
                      ALN  L    TI +         +HA  SA  R Y Y I   + P    
Sbjct: 61  CGPIPAQRWAPALNGRL--PGTIRVREAVERPLHWHACHSASYRRYRYTIYNGRRPNLFL 118

Query: 127 KGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
              +W      LD + MR     L+G HDF+ F     + +    T+    +   G+++ 
Sbjct: 119 APWSWHRYHCRLDEDAMRRGLDGLIGSHDFSAFMRAGSRRAHARTTVQDVSLERQGDVLI 178

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + + A  FL+  +R   G L  VG+ +      E+  + + R+E    APP+GL      
Sbjct: 179 LEIQASGFLYGMVRLLTGQLVAVGEHRLHPQAFEQRWRQRRRQEVKEAAPPQGLCLLRAG 238

Query: 246 YS 247
           Y 
Sbjct: 239 YP 240


>gi|319442992|ref|ZP_07992148.1| tRNA pseudouridine synthase A [Corynebacterium variabile DSM 44702]
          Length = 283

 Score =  228 bits (582), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 84/264 (31%), Positives = 127/264 (48%), Gaps = 20/264 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M+R  + + Y+G+ + GW RQK       ++QG +E+ + LV    V +  AGRTD+GVH
Sbjct: 4   MVRVRLDVAYDGTDFHGWARQKGPQEALRTVQGVLEEKLSLVFRTPVELTVAGRTDAGVH 63

Query: 57  ALRQVAHFDLV-------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           A  QVAH D+            P  L + L+  L     + +   S     F ARFSA+R
Sbjct: 64  ATGQVAHVDVPASAFGQRSLEQPSDLVRRLSRML--PADVRLHGASAAAPGFDARFSALR 121

Query: 110 RSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y+YR+ T  A P  L          S+D   +++A+  LVG HDF  F     + S+ 
Sbjct: 122 RHYVYRVTTSMAGPSPLRVRDTAQWRHSVDLSAVQLASDVLVGLHDFAAFCKYR-EGSTT 180

Query: 169 IRTIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R +  F+       +     E  VVA +F  + +RS VG++  VG+G+         LQ
Sbjct: 181 VRELQSFEWRDISTPTEPETYEASVVADAFCWSMVRSLVGAVLTVGEGRRDEGFASCLLQ 240

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
            + R    P+AP  GL   +V+Y 
Sbjct: 241 ERSRSSKVPVAPACGLNLVAVDYP 264


>gi|255637177|gb|ACU18919.1| unknown [Glycine max]
          Length = 370

 Score =  228 bits (581), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 94/317 (29%), Positives = 136/317 (42%), Gaps = 71/317 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + G Q+Q N  ++ G +E+A     G+ V V  + RT +GVHAL  V
Sbjct: 50  QRYLVAIEYIGTRFSGSQKQLNVRTVVGVLEEAFSKFVGQPVSVSCSSRTVAGVHALSNV 109

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+  D  + ++++  V   FHARF A  
Sbjct: 110 CHVDIQRISKRRPGEVLTPHEPAVVGRAVNHFLQKQDSDLMVIDVRCVPSDFHARFKAQE 169

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR+++   P    EK RAW +P+ L    M+ A + LVG HDF++FR+  CQA SP
Sbjct: 170 RIYFYRLLSGPEPLSTFEKDRAWHVPEELSLPAMQEACRVLVGFHDFSSFRAAGCQAKSP 229

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQI------------------------------ 198
           IRT+D   VN          +     H ++                              
Sbjct: 230 IRTLDELSVNEVIESPYFPSLMDREQHNKVSGDLRSCPNNSETDIPPTSNPSIDKVMASS 289

Query: 199 -----------RSFV-----------------GSLKLVGDGKWTSTDLEKALQAQDRKEC 230
                      R  V                 G LK VG G  T  D+E+ L A+     
Sbjct: 290 QDVGFGKRRRHRCLVVTARARAFLYHQVRLLVGVLKAVGTGNLTIPDVERILNARTVTAA 349

Query: 231 GPLAPPEGLYFDSVEYS 247
            P+AP  GLY   V+Y 
Sbjct: 350 SPMAPACGLYLGEVKYD 366


>gi|260495597|ref|ZP_05815722.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_33]
 gi|260196939|gb|EEW94461.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_33]
          Length = 245

 Score =  228 bits (581), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 118/249 (47%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MGRKNIKIEFRYDGSRYYGFQRQPNKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VDK F+AR +A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSTIPIEKYKYLLTRAL--PNDIDILSVEEVDKNFNARHNAKMREYVYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +D   +       VG HDF  FR   C +   IR I   +V 
Sbjct: 119 EKNP--FEARYYKFVKEKIDVRKLEKIFSDFVGVHDFKNFRLNDCVSKVTIRKIYQIEVK 176

Query: 179 SFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG   I+I +   +FL +Q+R  VG+   +  G+     +   L    R+    L   E
Sbjct: 177 YFGESKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLNDFTREYKKNLVEAE 236

Query: 238 GLYFDSVEY 246
           GLY + + Y
Sbjct: 237 GLYLNKINY 245


>gi|289641136|ref|ZP_06473304.1| tRNA pseudouridine synthase A [Frankia symbiont of Datisca
           glomerata]
 gi|289509077|gb|EFD30008.1| tRNA pseudouridine synthase A [Frankia symbiont of Datisca
           glomerata]
          Length = 279

 Score =  228 bits (581), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 80/245 (32%), Positives = 114/245 (46%), Gaps = 9/245 (3%)

Query: 9   EYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVAHFDLV 67
            Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTD+GVHA  QVAH D+ 
Sbjct: 15  AYDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDAGVHARGQVAHVDIP 74

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALE 126
            +     L + LN  L     + I  L+     F ARFSA+ R Y+YRI         L 
Sbjct: 75  DDVPLGGLARRLNGVL--DRAVRITALAPAPPGFDARFSALSRRYVYRIGDAPYGVDPLR 132

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN---- 182
           +      P+ LD E M  AA  LVG  DF  F     + ++ +RT+   DV    +    
Sbjct: 133 RHDTLAWPRPLDAERMADAALALVGERDFAAFCRRR-EGATTVRTLLRLDVARVPDGHDG 191

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           ++   V A +F H+ +R+ VG+L  VG+G+         L    R     +A P GL   
Sbjct: 192 VVVADVEADAFCHSMVRALVGALLAVGEGRRPHHWPADVLARGVRDPAVTVAAPHGLTLV 251

Query: 243 SVEYS 247
            V Y 
Sbjct: 252 EVRYP 256


>gi|172040043|ref|YP_001799757.1| tRNA pseudouridine synthase A [Corynebacterium urealyticum DSM
           7109]
 gi|171851347|emb|CAQ04323.1| tRNA pseudouridine synthase A [Corynebacterium urealyticum DSM
           7109]
          Length = 324

 Score =  227 bits (580), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 82/260 (31%), Positives = 125/260 (48%), Gaps = 17/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  M + Y+G+ + GW  QK G  ++QG +E+ + LV    V +  AGRTD+GVHA  Q
Sbjct: 50  VRVRMDVSYDGTDFHGWAAQKGGLRTVQGVLEEKLTLVCRTPVELTVAGRTDAGVHADGQ 109

Query: 61  VAHFDLV-------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           V H D+            P  L + L+  L   + I +       + F ARFSA+RR Y+
Sbjct: 110 VCHADIPAEAFTHRSLARPEDLVRRLSRML--PEDIRLNAAVAAPEGFDARFSALRRHYV 167

Query: 114 YRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YR+ T    PL           + +D E ++IAA  LVG ++F  +     + ++ IR +
Sbjct: 168 YRVCTAPGGPLPRRVRDTARWRRPVDLEKVQIAADALVGLNNFAAYCKAR-EGATTIREL 226

Query: 173 DHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             F        +     E  VVA +F  + +RS VG+   VG+GK       + L+  +R
Sbjct: 227 QEFTWKDVSTPAEPQTYEAHVVADAFCWSMVRSIVGACLTVGEGKRPEGFTAELLELDER 286

Query: 228 KECGPLAPPEGLYFDSVEYS 247
               P+AP EGL    V+Y 
Sbjct: 287 SSQVPVAPAEGLNLVGVDYP 306


>gi|302336349|ref|YP_003801556.1| tRNA pseudouridine synthase A [Olsenella uli DSM 7084]
 gi|301320189|gb|ADK68676.1| tRNA pseudouridine synthase A [Olsenella uli DSM 7084]
          Length = 284

 Score =  227 bits (580), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 115/255 (45%), Gaps = 13/255 (5%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y G+G+ G+  Q    ++ G +  A+  +    V +  AGRTD+GV+AL Q     
Sbjct: 22  VRLGYRGAGFAGFAEQPGQRTVAGELRTALETLLHRPVDLTCAGRTDAGVNALAQYVSLP 81

Query: 66  LVREWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           + R  +     + +++ + +  D +S+  L   D  F ARF A+ R Y YR+    A   
Sbjct: 82  VTRGELEREGRRLVSSLVALTPDDLSVRGLYKADVSFSARFDALERGYRYRVACGSARPV 141

Query: 125 LEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHC------QASSPIRTIDHFD 176
           L  G  W +     LD + M  AA  L+G HDF +F              S  R +    
Sbjct: 142 LSWGHTWWLRSVADLDVDAMGEAASALLGEHDFRSFCKASSAGLLEADGRSTCRRLSAVS 201

Query: 177 VNS----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           V         L+ I V   +FLH  +R   G+L  VG G   ++ + +AL A DR   GP
Sbjct: 202 VVRAREAGEELVAIDVRGNAFLHNMVRVIAGTLVEVGRGHRDASWVARALAAHDRSAAGP 261

Query: 233 LAPPEGLYFDSVEYS 247
            AP  GL F+ V Y 
Sbjct: 262 TAPAHGLTFEWVGYP 276


>gi|42559717|sp|P60349|TRUA_CORDI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 288

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 125/262 (47%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ +    ++Q  IE  + LV    + +  AGRTD+GVHA  
Sbjct: 6   VRIRLDLAYDGTDFHGWARQGDSDLRTVQKIIEDTLTLVLQRPIDLTVAGRTDAGVHATG 65

Query: 60  QVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+             P  L + L   +   D + I N+S V  +F ARFSA+RR 
Sbjct: 66  QVAHFDVDPAALETRSIAGDPARLIRRLARLM--PDDVRIHNMSFVPAEFDARFSALRRH 123

Query: 112 YLYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YR+ T        + R     P+S+D   M+ AA  L+G HDF  F     + +S IR
Sbjct: 124 YVYRVTTHPRGALPTRARDTAHWPRSVDISAMQAAADALIGMHDFAAFCKYR-EGASTIR 182

Query: 171 TIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F  +         L E  V A +F  + +RS VG+  +VG+GK      E  L   
Sbjct: 183 DLQEFTWHDVSTPQEPQLYEAHVTADAFCWSMVRSLVGACLVVGEGKRADGFTEHLLGET 242

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    P+A   GL    V+Y 
Sbjct: 243 KRSSSIPVAAACGLSLVGVDYP 264


>gi|38233160|ref|NP_938927.1| tRNA pseudouridine synthase A [Corynebacterium diphtheriae NCTC
           13129]
 gi|38199419|emb|CAE49063.1| tRNA pseudouridine synthase A [Corynebacterium diphtheriae]
          Length = 295

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 125/262 (47%), Gaps = 19/262 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW RQ +    ++Q  IE  + LV    + +  AGRTD+GVHA  
Sbjct: 13  VRIRLDLAYDGTDFHGWARQGDSDLRTVQKIIEDTLTLVLQRPIDLTVAGRTDAGVHATG 72

Query: 60  QVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           QVAHFD+             P  L + L   +   D + I N+S V  +F ARFSA+RR 
Sbjct: 73  QVAHFDVDPAALETRSIAGDPARLIRRLARLM--PDDVRIHNMSFVPAEFDARFSALRRH 130

Query: 112 YLYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           Y+YR+ T        + R     P+S+D   M+ AA  L+G HDF  F     + +S IR
Sbjct: 131 YVYRVTTHPRGALPTRARDTAHWPRSVDISAMQAAADALIGMHDFAAFCKYR-EGASTIR 189

Query: 171 TIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +  F  +         L E  V A +F  + +RS VG+  +VG+GK      E  L   
Sbjct: 190 DLQEFTWHDVSTPQEPQLYEAHVTADAFCWSMVRSLVGACLVVGEGKRADGFTEHLLGET 249

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R    P+A   GL    V+Y 
Sbjct: 250 KRSSSIPVAAACGLSLVGVDYP 271


>gi|327401434|ref|YP_004342273.1| tRNA pseudouridine synthase A [Archaeoglobus veneficus SNP6]
 gi|327316942|gb|AEA47558.1| tRNA pseudouridine synthase A [Archaeoglobus veneficus SNP6]
          Length = 290

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/248 (26%), Positives = 114/248 (45%), Gaps = 23/248 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALR 59
           +R  + + Y G+ + G+Q Q +  +++G + KA     +  +      AGRTD+GVHA  
Sbjct: 25  MRVALKLAYIGTDFAGFQYQPDERTVEGELFKAFESLGINVKASNYKCAGRTDAGVHAFS 84

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV   D+       +L + +NA L   D I +   + V   F+ R+ A  R+Y+Y + +R
Sbjct: 85  QVVALDVSD--AKKVLPRVINANL--PDDIVVWAWAKVPDDFNPRY-ATSRTYIYVLYSR 139

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +                 D   MR AA+ L+G HDFT F     +  S +RTI + ++  
Sbjct: 140 EY----------------DISAMRKAAKLLLGTHDFTNFTKKFGEGQSCVRTIYNVELRV 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +   +   +F    +R  + +L+ VG    +    E+ L  +  +E    AP  GL
Sbjct: 184 NGDFLIFEIEGNAFTWNMVRCIIAALEAVGSRHRSVEWFEEMLNPEKHRERIEPAPAYGL 243

Query: 240 YFDSVEYS 247
               ++YS
Sbjct: 244 ILKDIKYS 251


>gi|302524024|ref|ZP_07276366.1| tRNA pseudouridine synthase A [Streptomyces sp. AA4]
 gi|302432919|gb|EFL04735.1| tRNA pseudouridine synthase A [Streptomyces sp. AA4]
          Length = 298

 Score =  227 bits (579), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 80/265 (30%), Positives = 120/265 (45%), Gaps = 23/265 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL-VTGEIV--VVHGAGRTDSGVHAL 58
           +R  + + Y+G+ + GW RQ    ++Q  +E+A+     GE V   V  AGRTD+GVHA 
Sbjct: 17  VRLRLDVSYDGTDFSGWARQPGRRTVQAELEQALQRQPPGEAVPKSVVVAGRTDAGVHAT 76

Query: 59  RQVAHFDL--------------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
            QV H D+               R    +   +     L +   + +LN  +    F AR
Sbjct: 77  GQVVHVDVVPFAPGAPGRIPVDERGIPDLTRMRGRWNKL-LPADVRVLNARVAPDGFDAR 135

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSAIRR Y YR+         L +       + L  E M  AA  L+G  DF  +     
Sbjct: 136 FSAIRRHYRYRVSDAPWGVDPLRRNDTLAWGRPLSTERMNAAAAELLGLQDFAAYCKQR- 194

Query: 164 QASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           +  + IR +   +       L+E+RV A +F H+ +RS VG L LVGDG+  +    + L
Sbjct: 195 EGGTTIRELQRLEWTRIDEHLLEVRVSADAFCHSMVRSLVGVLLLVGDGRRGTGWPGEVL 254

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
            +  R     +AP  GL   +V+Y 
Sbjct: 255 ASGTRDSA--VAPAHGLTLTAVDYP 277


>gi|262066902|ref|ZP_06026514.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
 gi|291379371|gb|EFE86889.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
          Length = 248

 Score =  227 bits (579), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 117/250 (46%), Gaps = 7/250 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 3   MGRKNIKIEFRYDGSRYYGFQRQPNKITVQGEIEKILKIVTKEDINLISAGRTDRGVHAN 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L     I IL++  V++ F+AR  A  R Y+Y I  
Sbjct: 63  HQVSNFYTSSSIPVGKYKYLLTRAL--PKDIDILSVEEVNEDFNARHDAKMREYVYIISW 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      +   +D E +       +G HDF  FR   C +   +R I   DV 
Sbjct: 121 DKNP--FETRYCKFVKDKIDAEKLERIFSSFLGVHDFKNFRLSDCVSKVTVREIYSIDVK 178

Query: 179 SF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            F  N ++I +   +FL +Q+R  VG+   V     +   +E  L    ++    L   E
Sbjct: 179 YFSENKLKIFIRGSAFLKSQVRIMVGTALEVYYKNLSENHIELMLNNFSKEYKKYLVEAE 238

Query: 238 GLYFDSVEYS 247
           GLY + + YS
Sbjct: 239 GLYLNKINYS 248


>gi|308809101|ref|XP_003081860.1| COG0101: Pseudouridylate synthase (ISS) [Ostreococcus tauri]
 gi|116060327|emb|CAL55663.1| COG0101: Pseudouridylate synthase (ISS) [Ostreococcus tauri]
          Length = 338

 Score =  227 bits (579), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 97/300 (32%), Positives = 141/300 (47%), Gaps = 55/300 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ----KNGSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGV 55
            RY   +EY+G+ + G+QRQ    +  +++Q ++++A+   TG    V   G+ RTD GV
Sbjct: 12  PRYLAFLEYDGAKFRGFQRQNLGERATTTVQDALDEALETFTGNRGAVASVGSSRTDVGV 71

Query: 56  HALRQVAHFDLVRE--------WVPVILCKALNAYLKISD-TISILNLSIVD---KQFHA 103
           HA R  AHFD  R         +    + + LN +LK  +  + +     VD     FHA
Sbjct: 72  HATRNSAHFDCGRVGKDGSMDAYDSESVRRGLNYHLKSRERAMRVTECVRVDTLNPTFHA 131

Query: 104 RFSAIRRSYLYRIITRQAPL---ALEKGRAWLIPK----------------------SLD 138
           R  A+ R Y Y I+           ++  AW +                         LD
Sbjct: 132 RHDAVSRRYRYEILVGDRDDGGSVFDRDGAWYLRAVVASDRGAKQTSSRRYTTCEATGLD 191

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF------------GNLIEI 186
            + MR AA  L+G+HDF++FR+  CQA SPIRTI   DV S                + +
Sbjct: 192 VDAMRRAASVLIGKHDFSSFRASGCQAKSPIRTITSLDVVSRTTEWPSPEARGTRQEVSV 251

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           RV A SFL+ Q+R  VG+LK VG G  T  D+ + L+A+D  +   +AP  GLY   V Y
Sbjct: 252 RVEAPSFLYHQVRLLVGALKSVGAGDLTVDDVRELLEAKDVSQAPQMAPAHGLYLMDVGY 311


>gi|313816522|gb|EFS54236.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL059PA1]
          Length = 279

 Score =  227 bits (578), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 118/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E  I  V    +   +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWATQPDRRTVQGELETWIPRVLRLDQPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     + + ++  V   F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDNVDTSAMLRRLSRVLT--PDVVVKSVRPVPSTFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +   LD + +  A   L+G  DF  F   H + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVAPVRGHLDLDRLNTAGTSLLGLRDFAAFCK-HREGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+ +   L+    +  R     + 
Sbjct: 178 KRLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGRRSQDWLDNVAASTSRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLPLEEVGYP 250


>gi|305664970|ref|YP_003861257.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
 gi|88707800|gb|EAR00040.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
          Length = 224

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/220 (31%), Positives = 110/220 (50%), Gaps = 4/220 (1%)

Query: 28  QGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISD 87
           Q  +E AI  +    + V GAGRTD+GVHA    AHFD         L   +NA+L    
Sbjct: 2   QEVLENAISKLLRSPISVVGAGRTDAGVHAREMFAHFDFKDSIDSKDLVYRMNAFL--PA 59

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQ 147
            I++  + +V+ + HARF A  R+Y Y I  ++ P   ++  A  +  +LD + M  AA 
Sbjct: 60  DIAVSQIYLVNGEAHARFDATERTYEYWITQKKNPFYFDR--AHFVKNTLDVKAMNDAAN 117

Query: 148 HLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
             +GR DF  F   +    + +  +         + +   +VA  FL   +R+ VG+L  
Sbjct: 118 LFLGRKDFECFSKSNTDVHTYLCDVRKTIWTEEEDKLVFTIVADRFLRNMVRAVVGTLID 177

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           VG GK +  D+++ L+++DR + G   P +GLY   +EY 
Sbjct: 178 VGTGKTSLADIQRILESKDRTKAGASVPAKGLYLTKIEYP 217


>gi|149916968|ref|ZP_01905469.1| tRNA pseudouridine synthase A [Plesiocystis pacifica SIR-1]
 gi|149822246|gb|EDM81637.1| tRNA pseudouridine synthase A [Plesiocystis pacifica SIR-1]
          Length = 285

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/271 (26%), Positives = 112/271 (41%), Gaps = 30/271 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNG----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            + + Y+G+ + G+ RQ NG     +IQG +E+A+  +  + +   GA RTD+GVHA  Q
Sbjct: 4   LLRVAYDGTDFHGFARQDNGGQPLRTIQGCLEQALSTLYKQPIRTRGASRTDAGVHARGQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDK----QFHARFSAIRRSYLYRI 116
           +  FD         L         +   I      + +       + RF    + Y YR+
Sbjct: 64  LVAFDPPFAIPARGLLLG--LAANLPADIIASAAWLAEDVEGEPLNPRFHTRGKLYRYRL 121

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   L     W +P+ +D   M+ AA    G HDF  FR+  CQA S  R +    
Sbjct: 122 RPVSLRDPLSARYEWHLPRPIDVAAMQAAAPRFAGTHDFAGFRASDCQAKSTTRRVRSVI 181

Query: 177 VN------------SFGNL--------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           VN              G +        + I V   +FL   +R  VG+L  VG G++ + 
Sbjct: 182 VNVETLAELDPLAGQRGRIEGPAAPARVTIDVRGDAFLKNMVRIMVGTLVGVGRGQFGAE 241

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +++ L + DR   G  AP  GL    V + 
Sbjct: 242 RIDEVLASGDRTRAGVTAPACGLTLVEVLWP 272


>gi|323357344|ref|YP_004223740.1| pseudouridylate synthase [Microbacterium testaceum StLB037]
 gi|323273715|dbj|BAJ73860.1| pseudouridylate synthase [Microbacterium testaceum StLB037]
          Length = 285

 Score =  226 bits (577), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 83/263 (31%), Positives = 121/263 (46%), Gaps = 18/263 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW RQ    ++QG +E+A+  + G    +  AGRTD+GVHA  QV
Sbjct: 1   MRLRLDISYDGTHFRGWARQPGLRTVQGVLEEALARILGGDPRLVVAGRTDAGVHASGQV 60

Query: 62  AHFDLVREWVP---------------VILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           AH DL                       L   +   L     +++   S   + F ARFS
Sbjct: 61  AHLDLDDAQQARLPRRRREGDEGDAVAALAGRVRGVLGAYPDVTVHRSSCAPEGFDARFS 120

Query: 107 AIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R Y YRI   QA    LE+ R   +  SLD + M  AAQ L+G HDF  +     +A
Sbjct: 121 AVWRRYSYRIADAQAGYEPLERLRTTSVRASLDVDAMHAAAQRLIGLHDFAAYCKAREEA 180

Query: 166 SSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            + IRT+  +D     + I I  V A +F H+ +R+ VG+   VG+G+    D+ K    
Sbjct: 181 -TTIRTLLEYDWRRGDDGILIANVRADAFCHSMVRALVGACVAVGEGRLEVDDVIKIRDE 239

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
             R     +    GL    V Y 
Sbjct: 240 GRRTADSKVLAARGLVLAEVGYP 262


>gi|19704921|ref|NP_602416.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|42559836|sp|Q8R601|TRUA_FUSNN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|19712818|gb|AAL93715.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 247

 Score =  226 bits (576), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 120/249 (48%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 3   MRRKNIKIEFRYDGSSYYGFQRQPNKITVQGEIEKVLRIVTKEEINLISAGRTDRGVHAN 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 63  HQVSNFYTSSNIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKMREYIYIISW 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +  E +       +G HDF  FR   C +   +R I   +V 
Sbjct: 121 EKNP--FEARYCKFVKEKIVAEKLEKIFSDFIGVHDFKNFRLSDCVSKVTVREIYQIEVK 178

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG N I+I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   E
Sbjct: 179 YFGENKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLLENHIRLMLNDFTKEYKKNLVEAE 238

Query: 238 GLYFDSVEY 246
           GLY + +EY
Sbjct: 239 GLYLNKIEY 247


>gi|14591061|ref|NP_143136.1| tRNA pseudouridine synthase A [Pyrococcus horikoshii OT3]
 gi|3915167|sp|O58941|TRUA_PYRHO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3257659|dbj|BAA30342.1| 262aa long hypothetical pseudouridylate synthase [Pyrococcus
           horikoshii OT3]
          Length = 262

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 116/246 (47%), Gaps = 24/246 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + I Y+G+ + G+QRQ N  +++G I KA+         +  A RTD GV AL  V
Sbjct: 1   MKVALKIAYDGTKFHGFQRQPNVRTVEGEIIKALNNSGIMFNELKSASRTDKGVSALGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                  E +   +   LNA L     + +L+   V   FH RF A  + Y Y + +   
Sbjct: 61  VAITTEDERITNPMI--LNAKL---KDVWVLSAVKVPSDFHPRFWARSKVYRYYLPS--- 112

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                          LD E ++  ++  +G HDF+ F  +       +R+ID  +V   G
Sbjct: 113 -------------FDLDVEKVKECSKLFLGVHDFSAFSRV--DGRETVRSIDRIEVLDLG 157

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEGLY 240
            ++ I V A+SFL   +R  V +L+L G GK +S ++ K L+ + ++    P AP EGL 
Sbjct: 158 PVLAIEVEAKSFLWEMVRRIVKTLELCGLGKLSSEEVRKMLRGKFEKSRKVPPAPAEGLL 217

Query: 241 FDSVEY 246
              V+Y
Sbjct: 218 LVEVKY 223


>gi|269955466|ref|YP_003325255.1| tRNA pseudouridine synthase A [Xylanimonas cellulosilytica DSM
           15894]
 gi|269304147|gb|ACZ29697.1| tRNA pseudouridine synthase A [Xylanimonas cellulosilytica DSM
           15894]
          Length = 293

 Score =  225 bits (575), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 73/268 (27%), Positives = 116/268 (43%), Gaps = 22/268 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG------EIVVVHGAGRTDSG 54
           M+R  + + Y+G+ + GW RQ    ++QG +E  +  +            +  AGRTD+G
Sbjct: 1   MVRVRLDLAYDGTQFAGWARQPALRTVQGVLEDGLEQIVRTAPRGLPAPRLTVAGRTDAG 60

Query: 55  VHALRQVAHFDLVREWV-------PVILCKALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QVAH DL  E              ++L   L   +   + +   ++    F ARF
Sbjct: 61  VHARGQVAHVDLPVERWVALPGRSDREPGESLVTRLTGVLPPDVVVHRAALAPAGFDARF 120

Query: 106 SAIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R Y +RI    A    L +       + LD   M  A Q L G  DF  +      
Sbjct: 121 SALYRRYAFRIADDAAARDPLHRAHVLWHRRPLDVAAMHDAVQPLRGVRDFAAYCKPRP- 179

Query: 165 ASSPIRTIDHFDVNSFGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            ++ IR +         +     L+  RVVA +F H  +R+ VG+   VG+G+   +   
Sbjct: 180 GATTIRELKELSWTRPADGPDAGLVVARVVADAFCHNMVRALVGASIAVGEGRKPVSWPA 239

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + L ++ R+    + PP GL  + V Y 
Sbjct: 240 EVLASKQRERAAAVVPPRGLTLEEVVYP 267


>gi|332665403|ref|YP_004448191.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
 gi|332334217|gb|AEE51318.1| tRNA pseudouridine synthase A [Haliscomenobacter hydrossis DSM
           1100]
          Length = 249

 Score =  225 bits (575), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + + YNG+ YFGWQRQ    S+Q ++E +I  + G  + + G GRTD+GVHA + 
Sbjct: 1   MQRYFIELAYNGTQYFGWQRQPGKISVQQTLEDSINTILGTELEITGCGRTDTGVHARQY 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AHFD   E+ P    + LN +L     I++  +  V+ + HARF A  RSY Y +  R+
Sbjct: 61  FAHFDFEGEF-PAEFVRRLNKFL--PKDIAVYQIIAVEPEAHARFDAYERSYEYHLSFRK 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P        +   +  D   M+ AA  L+   +F  F   +  A + +  +   +    
Sbjct: 118 NPFTEHLAYFYPYVQQPDPVLMQDAAAFLLQYQEFEPFCKSNHDAKTMVCKLTRSEWIFD 177

Query: 181 --GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                    + +  FL   +R  VG    VG G+ +  +L+ A++ Q R +    APPEG
Sbjct: 178 LKEQRAVFHITSNRFLRGMVRLIVGMCIGVGTGQISMEELKTAMEQQSRLKKATSAPPEG 237

Query: 239 LYFDSVEY 246
           LY   ++Y
Sbjct: 238 LYLGGIKY 245


>gi|256825854|ref|YP_003149814.1| pseudouridylate synthase I [Kytococcus sedentarius DSM 20547]
 gi|256689247|gb|ACV07049.1| pseudouridylate synthase I [Kytococcus sedentarius DSM 20547]
          Length = 297

 Score =  225 bits (575), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 72/259 (27%), Positives = 117/259 (45%), Gaps = 13/259 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALR 59
           M R  +   Y+G  + GW  Q    ++Q ++E+ +  V   + V +  AGRTD+GVHA  
Sbjct: 20  MPRLRLDFAYDGRDFHGWATQPGLRTVQETLERGLATVLRAQDVSLTVAGRTDAGVHATG 79

Query: 60  QVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRR 110
            V H D+                 +AL   L   +   + +   + V   F ARFSA+RR
Sbjct: 80  AVCHLDVAHAAWAAVPGRSDRAPAEALVTRLAGVLPADLVVHRATEVPDAFDARFSALRR 139

Query: 111 SYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            Y Y +  R+       +G      K LD E M  AAQ LVG  DF  F     + ++ +
Sbjct: 140 HYRYLLCDRRETLDPRRRGMVVAWRKPLDAEAMHAAAQQLVGLGDFAAFCKPR-EGATTV 198

Query: 170 RTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           RT++ F  +       +  V A +F H+ +R+ VG++  VG+G+       +  + ++R 
Sbjct: 199 RTLERFTWHRDEQGWVVGEVSADAFCHSMVRALVGAVVPVGEGRQPVDWPRQVQEGRERL 258

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               + P  GL   +V+Y 
Sbjct: 259 GAVQVMPAHGLTLVAVDYP 277


>gi|284042832|ref|YP_003393172.1| tRNA pseudouridine synthase A [Conexibacter woesei DSM 14684]
 gi|283947053|gb|ADB49797.1| tRNA pseudouridine synthase A [Conexibacter woesei DSM 14684]
          Length = 261

 Score =  225 bits (575), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 112/244 (45%), Gaps = 8/244 (3%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVAH 63
            + +EY+G  + GW RQ    +++ ++E+A+  V     V +  AGRTD+GVHA  Q A 
Sbjct: 9   RLTLEYDGRDFAGWARQPGRRTVEDALERALATVLRRDAVGLTVAGRTDAGVHAWAQEA- 67

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
                   P      LNA L   D +++++       F AR  A  R+Y YR++ R++  
Sbjct: 68  ----SYEGPPAAPHRLNALL--PDDVAVIDARPAPPGFSARHDATSRAYRYRVLVRRSRS 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A E+GRA   P  LD + +   A  L G HDFT F           R + H    + G++
Sbjct: 122 AHERGRALWWPHRLDRDALDACAAALAGTHDFTAFTPTETDHVRFQREVMHASWRADGDM 181

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           ++  + A +F+    R  VG++  V   + +       L    R   G  APP GLY   
Sbjct: 182 LQFSIEADAFMRNMNRVLVGTMLEVAGERRSVEQFTALLDGAPRDRAGVTAPPHGLYLAG 241

Query: 244 VEYS 247
           V Y 
Sbjct: 242 VGYD 245


>gi|302342258|ref|YP_003806787.1| tRNA pseudouridine synthase A [Desulfarculus baarsii DSM 2075]
 gi|301638871|gb|ADK84193.1| tRNA pseudouridine synthase A [Desulfarculus baarsii DSM 2075]
          Length = 279

 Score =  225 bits (574), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 80/239 (33%), Positives = 113/239 (47%), Gaps = 4/239 (1%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           YNG+G+ GWQ Q  G +IQG +E+ +  + G  V +  AGRTD+GVHA  QVA F     
Sbjct: 43  YNGAGFAGWQIQARGRTIQGQVERELSRLCGHAVRLWAAGRTDAGVHAFGQVASFQTDSR 102

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
                + +AL A L     I +  L    + FHARF A  ++Y Y +  +  P     G 
Sbjct: 103 LEEGRMAQALAAML--PPDIWLRRLGRAPEGFHARFDAAGKTYEYYLWPKARPGVFLDGL 160

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNS-FGNLIEIR 187
            W +   LD E M   A  L+G  D   F +   +   P +R I    V    G +I +R
Sbjct: 161 CWPLACDLDMEAMARGAAFLLGEVDLAAFAAHSSEVEGPTVRRISEATVTPAEGGMILVR 220

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +    FL   +R+ VG+L  +G  +     + + L A  R   GP APP GLY   + Y
Sbjct: 221 LSGSGFLRHVVRNVVGTLTQIGQHRLEPEAVGRMLAAGRRIYPGPKAPPGGLYLGQIYY 279


>gi|237739188|ref|ZP_04569669.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
 gi|229423788|gb|EEO38835.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
          Length = 246

 Score =  225 bits (574), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 79/250 (31%), Positives = 117/250 (46%), Gaps = 7/250 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MERKNIKIEFRYDGSRYYGFQRQPNKETVQGEIEKILKIVTKEDINLISAGRTDRGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L     I IL++  VD++F+AR  A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSTIPVEKYKYLLTRAL--PKDIDILSVEEVDEKFNARHDAKMREYVYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      +   +D E +       +G HDF  FR   C +   +R I   DV 
Sbjct: 119 EKNP--FEARYCKFVKDKIDAERLEKIFSSFLGIHDFRNFRLSDCMSKVTVREIYSIDVK 176

Query: 179 SF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            F  N ++I +   +FL +Q+R  VG+   V         ++  L    ++    L   E
Sbjct: 177 YFSENKLKICIRGSAFLKSQVRIMVGTALEVYYKNLPKNHIDLMLNDFSKEYKKSLVEAE 236

Query: 238 GLYFDSVEYS 247
           GLY + + YS
Sbjct: 237 GLYLNRINYS 246


>gi|269796221|ref|YP_003315676.1| pseudouridylate synthase I [Sanguibacter keddieii DSM 10542]
 gi|269098406|gb|ACZ22842.1| pseudouridylate synthase I [Sanguibacter keddieii DSM 10542]
          Length = 287

 Score =  225 bits (574), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 113/260 (43%), Gaps = 16/260 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y G+ + GW  Q    ++QG++E+ +  V      +  AGRTD+GVH+  QV 
Sbjct: 6   RIRLDVSYRGTDFAGWAVQPGLRTVQGTLEEGLARVLRADTRLTVAGRTDAGVHSRGQVT 65

Query: 63  HFDLVREWVPVILCKALNAYLK---------ISDTISILNLSIVDKQFHARFSAIRRSYL 113
           H D+ RE    +  +      +         +   + +  +S+    F ARFSA+ R Y 
Sbjct: 66  HLDVPREVWDTVSGRGHRTGEQALLSRMTGVLPTDVVVRAVSVAPPGFDARFSALSRRYR 125

Query: 114 YRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           YRI+ R A    L         + LD + M+ A Q LVG  DF  F       ++ IR +
Sbjct: 126 YRIVDRHALRDPLRADWVLWSKRPLDVDAMQAAVQPLVGVRDFKAFCRPRP-GATTIRHL 184

Query: 173 DHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                          L+   V + +F H  +R+ VG+   VG G+       + L+  +R
Sbjct: 185 QELTWERVDGGPDDGLVVASVRSDAFCHNMVRALVGASMAVGHGQRPVGWPAEVLRRGER 244

Query: 228 KECGPLAPPEGLYFDSVEYS 247
                + PP GL  + VEY 
Sbjct: 245 DPLAGVVPPHGLTLEEVEYP 264


>gi|262039471|ref|ZP_06012775.1| tRNA pseudouridine synthase A [Leptotrichia goodfellowii F0264]
 gi|261746538|gb|EEY34073.1| tRNA pseudouridine synthase A [Leptotrichia goodfellowii F0264]
          Length = 249

 Score =  225 bits (574), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 121/246 (49%), Gaps = 4/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              M+ +Y+GS ++G+QRQKN  ++QG IEK I     + + +  +GRTD GVHAL QV+
Sbjct: 6   NIKMVYQYDGSKFYGFQRQKNKKTVQGEIEKVILKNFSQKINMISSGRTDKGVHALGQVS 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F +  +     + + +N  L     I IL++  + ++F++RF A  R+YLY +   +  
Sbjct: 66  NFFIDEKIPLEAIKRQINKNLY--GEIKILSVEEIKREFNSRFDAKSRTYLYIMKKEEEI 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--NSF 180
              E      I   ++ E  +   +   G++DF++F        + +R I +        
Sbjct: 124 TPFESNYITGIKNDINIEQFQKIMEIFKGKYDFSSFMKKDKAIRNTMREIYNIKCEYEER 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I + +   SFL T IR  +GS   +  GK     ++  L+  D  +   LAP EGLY
Sbjct: 184 EKKIYVEICGSSFLKTMIRIMIGSAMAIYFGKEREDYIKMRLENPDADKPKILAPSEGLY 243

Query: 241 FDSVEY 246
              V+Y
Sbjct: 244 LYRVDY 249


>gi|296329175|ref|ZP_06871676.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
 gi|296153531|gb|EFG94348.1| tRNA-pseudouridine synthase I [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
          Length = 247

 Score =  225 bits (573), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 120/249 (48%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ N  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 3   MGRKNIKIEFRYDGSSYYGFQRQPNKITVQGEIEKVLRIVTKEEINLISAGRTDRGVHAN 62

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 63  HQVSNFYTSSNIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKMREYIYIISW 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +  E +       +G HDF  FR   C +   +R I   +V 
Sbjct: 121 EKNP--FEARYCKFVKEKIVAEKLEKIFSDFIGVHDFKNFRLSDCVSKVTVREIYQIEVK 178

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG N I+I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   E
Sbjct: 179 YFGENKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLLENHIRLMLNDFTKEYKKNLVEAE 238

Query: 238 GLYFDSVEY 246
           GLY + +EY
Sbjct: 239 GLYLNKIEY 247


>gi|309812385|ref|ZP_07706140.1| tRNA pseudouridine synthase A [Dermacoccus sp. Ellin185]
 gi|308433690|gb|EFP57567.1| tRNA pseudouridine synthase A [Dermacoccus sp. Ellin185]
          Length = 282

 Score =  225 bits (573), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 70/260 (26%), Positives = 118/260 (45%), Gaps = 17/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           +R+ +   Y+G+ + GW RQ    +++  +  A+  V   E V +  AGRTD+GVHA   
Sbjct: 1   MRFRIDFAYDGTDFSGWARQPGRRTVEEELTGALTRVLRREDVRLTVAGRTDAGVHARGG 60

Query: 61  VAHFDLV-----------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           V H D+                   L   LN  L     + +   S     F ARFSA++
Sbjct: 61  VCHGDIDADAWAALPGRSERAPAQALVTRLNGVLA--GDVVVKAASEQPASFDARFSALK 118

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR++   A    L +    ++ ++LD + M  A+  L+G HDF  +     + ++ 
Sbjct: 119 RRYSYRLLDDAARLDPLRRRDTVVVKRTLDVDAMNAASALLIGLHDFAAYCKPR-EGATT 177

Query: 169 IRTIDHFDVNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           IRT+  +      + +   R+ A +F H+ +R+ +G +  VG+G+       + L A  R
Sbjct: 178 IRTLLDYAWTREADGVLTARLEADAFCHSMVRALIGGVVPVGEGRRPIDWPAQVLTAGRR 237

Query: 228 KECGPLAPPEGLYFDSVEYS 247
                + PP GL  + V Y 
Sbjct: 238 DPGVVVMPPHGLCLEEVSYP 257


>gi|182415339|ref|YP_001820405.1| tRNA pseudouridine synthase A [Opitutus terrae PB90-1]
 gi|177842553|gb|ACB76805.1| tRNA pseudouridine synthase A [Opitutus terrae PB90-1]
          Length = 268

 Score =  225 bits (573), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 92/246 (37%), Positives = 127/246 (51%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R+  +  Y+G  + GWQ Q +G+S+Q +IE  +  + G  V +HG+GRTD+GVHAL QV
Sbjct: 9   PRWKCVCAYDGGHFAGWQSQVSGASVQDAIEARLREMFGREVRIHGSGRTDAGVHALGQV 68

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P  L  AL A L     I I  +  V  +FHARF A  + Y YR+    A
Sbjct: 69  FHFDAHWRHGPEKLLAALRARL--PSAIQIKTVCAVTPEFHARFQASGKRYTYRLHLGDA 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVNSF 180
                +  +W + + LD   M  AA  L GRHDF  F +++  A    +R +   DV   
Sbjct: 127 -DPFTRPYSWPVFRPLDLAAMNAAAAVLRGRHDFRAFTALNGPARVDTVRDLRRLDVRRR 185

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I I   A  FL+  +RS VG L  VG+GK T  D+   L ++ R      APP+GL+
Sbjct: 186 GRVIRIIAEADGFLYKMVRSLVGVLVAVGEGKLTVHDVRAILASRQRTAVVQTAPPQGLF 245

Query: 241 FDSVEY 246
              V Y
Sbjct: 246 LVRVFY 251


>gi|310777852|ref|YP_003966185.1| tRNA pseudouridine synthase A [Ilyobacter polytropus DSM 2926]
 gi|309747175|gb|ADO81837.1| tRNA pseudouridine synthase A [Ilyobacter polytropus DSM 2926]
          Length = 243

 Score =  225 bits (573), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 122/247 (49%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +  EY+GSG+FG+QRQ +  ++QG IE A+ +V  E + +  +GRTD GVHA  Q
Sbjct: 1   MKNIKIEYEYDGSGFFGFQRQPSARTVQGEIESALKVVLKEEINLASSGRTDRGVHAYMQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F    +     L  A+     I + I I ++  V ++FHARFSA  R+Y Y +    
Sbjct: 61  VSNFFTSSKIPLDRLEFAV--KNLIPEDIKIHSMKNVSEEFHARFSAKSRAYEYIM--GW 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A E      I   +D E +    + +VGRH+F  FR   C   +P+R I        
Sbjct: 117 DRTAFETKYVSGIKGKVDPEKLYKILEPIVGRHNFEGFRLTDCSGKNPVRDISEIRCYPK 176

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           G N + + +   +FL +QIR  +G+   V   K     L   L+  D K+   +A   GL
Sbjct: 177 GENKLAVYIKGNAFLKSQIRIIMGTALAVYFEKRPKNYLINKLKNPDSKDEKIVADGSGL 236

Query: 240 YFDSVEY 246
           Y   +EY
Sbjct: 237 YLCDIEY 243


>gi|195953438|ref|YP_002121728.1| tRNA pseudouridine synthase A [Hydrogenobaculum sp. Y04AAS1]
 gi|229470758|sp|B4U9D9|TRUA_HYDS0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|195933050|gb|ACG57750.1| tRNA pseudouridine synthase A [Hydrogenobaculum sp. Y04AAS1]
          Length = 247

 Score =  225 bits (573), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 67/252 (26%), Positives = 114/252 (45%), Gaps = 11/252 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG------EIVVVHGAGRTDSG 54
           M  Y   I + G+ Y GWQ Q N  +IQ  +E+ ++ +        + +   G  RTD G
Sbjct: 1   MKNYKFTISFVGTNYSGWQYQPNVPTIQNEVEEKLYYIVNKKKPIKQKIRAIGCSRTDKG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA+  V +  +  +     L KALN+ L     I I N+  V  +F++RF A++++Y+Y
Sbjct: 61  VHAIEFVFNVKMEFDKDLNFLRKALNSAL--PKDIKIHNIEEVPLEFNSRFDALKKTYIY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           ++   +      + RA L+ K  D   M   +   +G  DF  F     +  +   ++++
Sbjct: 119 KLFFDEKNSPFFQDRAMLVYKPTDLGKMMEISHLFLGYKDFRGFTK-ELEDENGYCSVEN 177

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                   L+EI + A  FL   +R  VG++     G  +  D+   L+A+  +     A
Sbjct: 178 ITFKVDYPLVEISITANRFLRYMVRRMVGTMLSYAQGLISIDDVNDFLKAK--RVSNHTA 235

Query: 235 PPEGLYFDSVEY 246
              GLY   V Y
Sbjct: 236 KAHGLYLKKVYY 247


>gi|147865780|emb|CAN81146.1| hypothetical protein VITISV_020811 [Vitis vinifera]
          Length = 403

 Score =  224 bits (572), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 80/254 (31%), Positives = 119/254 (46%), Gaps = 24/254 (9%)

Query: 16  FGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQVAHFDLVREWV- 71
            GWQ Q++  +IQ  +EKA+   T    E + + GA RTD+GVHA  QVAHF     +  
Sbjct: 123 RGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTDTGVHAWGQVAHFLTPFNYDG 182

Query: 72  PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
              +  ALN  L     I +  +S    +FHARFS   + Y Y+I          +   +
Sbjct: 183 LESIHAALNGLL--PPDIRVREISPAVPEFHARFSXKSKIYHYKIYNDAVMDPFLRHYVY 240

Query: 132 LIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNS---------- 179
                L+   MR AA+H  G+HDF+ F +   + ++ +P++ I  FDVN           
Sbjct: 241 HSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKNIFRFDVNEMMFLELIVNC 300

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---L 233
               G L+++ V    FL+ Q+R+ V  L  +G        +   L  +DRKE       
Sbjct: 301 IIAQGALLQLEVEGSGFLYRQVRNMVALLLQIGREAIPPNIVPWILATRDRKELAKYALS 360

Query: 234 APPEGLYFDSVEYS 247
           APP GL   SV+Y+
Sbjct: 361 APPHGLCLMSVKYN 374


>gi|189500072|ref|YP_001959542.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides BS1]
 gi|189495513|gb|ACE04061.1| tRNA pseudouridine synthase A [Chlorobium phaeobacteroides BS1]
          Length = 233

 Score =  224 bits (572), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 81/242 (33%), Positives = 116/242 (47%), Gaps = 10/242 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           M IEY+G+ + GWQ+Q  G  ++QG +E  +  +  E VV+  AGRTD GVHA  QVA+F
Sbjct: 1   MTIEYDGTDFSGWQKQPEGVVTVQGVLETTLSRIVQEEVVMTAAGRTDRGVHARGQVANF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     L  +LNA L    T+ I ++  V   FHAR+SA+ R Y Y  +  + P A
Sbjct: 61  RTASCLSTGRLLHSLNALL--PSTVCIRDMQEVPDSFHARYSALFREYRYFFL--EKPSA 116

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L K  A +    LD + +   A  LVGRHDF+ +     Q  S   T+           +
Sbjct: 117 LGKRYAGVYGGRLDVDRLNRCAGELVGRHDFSAYAKEDAQNGSTFCTVFGASWGRQDEKV 176

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             R+ A  FL T +R  V +    G G+ T     + L+  +  +    A P GL+   V
Sbjct: 177 VFRIAANRFLRTMVRFLVSAQLEAGPGELT-----ERLRRGNVLKNIVPADPAGLFLWKV 231

Query: 245 EY 246
            Y
Sbjct: 232 LY 233


>gi|311115139|ref|YP_003986360.1| tRNA-pseudouridine synthase I [Gardnerella vaginalis ATCC 14019]
 gi|310946633|gb|ADP39337.1| tRNA-pseudouridine synthase I [Gardnerella vaginalis ATCC 14019]
          Length = 310

 Score =  224 bits (572), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 87/290 (30%), Positives = 131/290 (45%), Gaps = 46/290 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-------IVVVHGAGRTDSG 54
           +R  + + Y+G  ++GW RQ N  ++QG++E A++ V           + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGDFYGWARQPNLRTVQGTLEDALYKVLRVHDGDSCFPLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREW-------VPVILCKALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  +          +   KAL   L+  +   ISI ++SI    F ARF
Sbjct: 61  VHASYQVCHLDVEDDILQNCVGHTNLTPVKALEYRLRGVLPKDISIHSVSIAPSGFDARF 120

Query: 106 SAIRRSYLYRII---TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           SA+ R+Y+YRI     R+      +G    I   LD  +M  AAQ +VG HDF +F   +
Sbjct: 121 SALDRTYVYRISDAANRENLDPRMRGFVLQIDYDLDVNSMNQAAQMIVGLHDFGSFARPN 180

Query: 163 CQASSPIRTIDHFDVNS------------------------FGNLIEIRVVARSFLHTQI 198
               + IR +     N                            LIE  +VA +F H  +
Sbjct: 181 P-GGTTIRCVKKAVWNRVCLDGCAPVGSSIASRSTGNIPPIEHGLIEFTIVADAFAHNMV 239

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           RS V +   VG GK +    +  ++   R+   GP+A   GL  + VEY 
Sbjct: 240 RSLVQACVQVGCGKRSVDWFKDKIENPIREGSTGPIA-SNGLTLEYVEYP 288


>gi|220913398|ref|YP_002488707.1| tRNA pseudouridine synthase A [Arthrobacter chlorophenolicus A6]
 gi|219860276|gb|ACL40618.1| tRNA pseudouridine synthase A [Arthrobacter chlorophenolicus A6]
          Length = 297

 Score =  223 bits (570), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 79/263 (30%), Positives = 118/263 (44%), Gaps = 19/263 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G  + GW  Q    ++QG++E+A+ L+    + V  AGRTD+GVHA  QV 
Sbjct: 18  RIRLDLSYDGGPFSGWAVQPGRRTVQGTLEEALELLVRRPLRVTVAGRTDAGVHARGQVV 77

Query: 63  HFDL---------------VREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFS 106
           H DL                   +   L  ALN  L  ++  + +  ++     F ARFS
Sbjct: 78  HLDLAESEWLGMARGHELDPATAMTRRLRGALNRVLGDLTGAVQVRGIAPAPDGFDARFS 137

Query: 107 AIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R Y YRI    A    LE+         LD E +   A  L+G  +F +F     + 
Sbjct: 138 ALWRRYSYRIADGPALWDPLERAFTLWHKNPLDVELLNQGAARLLGLQNFLSFCKPR-EG 196

Query: 166 SSPIRTIDHFDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           ++ IR +  F+     +  I   V A +F H  +R+ +GS   VG+G      L + L A
Sbjct: 197 ATTIRELQRFEFARAEDGAIVATVQADAFCHNMVRALIGSALYVGEGTVEPGWLYERLLA 256

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           Q R     LA P  L F+ V Y 
Sbjct: 257 QKRDAKSVLAAPHPLVFEEVAYP 279


>gi|161723265|ref|NP_302320.2| tRNA pseudouridine synthase A [Mycobacterium leprae TN]
          Length = 320

 Score =  223 bits (570), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 75/259 (28%), Positives = 118/259 (45%), Gaps = 14/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G +++A   V    V +  AGRTD+GVHA  QV
Sbjct: 44  VRLRLDIAYDGTDFAGWAVQAGQRTVAGVLDEAFTTVFRTPVRLRAAGRTDTGVHATGQV 103

Query: 62  AHFDLV------------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+                 P  L         +   + +L+++     F ARFSA+R
Sbjct: 104 AHVDIPGTALSKANPRSPHTGDPEFLPLLRRLSRLLPVDVRVLDIACAPVGFDARFSALR 163

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR+ T    +   +       P+ LD ++M  A++ L+G  DF  F   H   ++ 
Sbjct: 164 RHYRYRLSTAPYGVQPNQARYVTAWPRELDLDSMSAASRDLLGLRDFAVFCR-HRHGATT 222

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   + +  G LI   + A +F  + +RS +G+L  VGD + T     + L    R 
Sbjct: 223 IRELQRLEWSREGYLITAHITADAFCWSMVRSLIGALLAVGDHRRTIGWCGELLTKASRS 282

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                AP  GL F  V+Y 
Sbjct: 283 SDFTTAPAHGLTFIRVDYP 301


>gi|320333111|ref|YP_004169822.1| tRNA pseudouridine synthase A [Deinococcus maricopensis DSM 21211]
 gi|319754400|gb|ADV66157.1| tRNA pseudouridine synthase A [Deinococcus maricopensis DSM 21211]
          Length = 266

 Score =  223 bits (569), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 121/247 (48%), Gaps = 5/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + ++++G+ + GWQ Q N  S+Q  +  A   +  +      AGRTD+GVHA    
Sbjct: 13  VRYRLTVQWDGTHFAGWQSQPNARSVQDDLHAAFKALGMQAFRPVAAGRTDAGVHAEAMP 72

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            H D       +P            +   +++L+ +     FHARFS   R+Y YR++  
Sbjct: 73  VHVDALSASARIPAARLARA-LNAHLPTDVAVLDAAPAPAHFHARFSCTERAYSYRVLNA 131

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GRA L+   LD   M++AA  L+G HDF  F +   +    +R +   +V  
Sbjct: 132 PQRQPLWAGRALLVHAPLDVAAMQVAATQLLGEHDFAAFATR--EERQTVRRLHALEVRP 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L+E+ V   SFL   +R  VG+L +VG+G+  ++D+   L  + R   GP  PP GL
Sbjct: 190 VGPLLEVHVRGESFLRHMVRGIVGTLLMVGEGRLGASDVAGILVGRARSGAGPNVPPHGL 249

Query: 240 YFDSVEY 246
           YF    Y
Sbjct: 250 YFTDASY 256


>gi|297625831|ref|YP_003687594.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296921596|emb|CBL56150.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 292

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 74/251 (29%), Positives = 115/251 (45%), Gaps = 9/251 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
            R+ + + Y+G+ + GW  Q    +++G +   +  + G  + V +  AGRTD+GVHA  
Sbjct: 4   RRFRLDLSYDGTHFHGWAMQPGQRTVEGELATWLTRIAGTAQPVRLVVAGRTDAGVHARG 63

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT- 118
           QVAH DL        L + L     +   I +  L++    F ARF+AI R Y+YR+   
Sbjct: 64  QVAHADLPATMDAAELKRRL--LRALPPDIVVRRLTVAPPGFDARFAAIWRRYVYRLWDL 121

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P  L +G        LD E M  A   L+G  DF  F     + ++ IRT+   +  
Sbjct: 122 SSHPDPLLRGMVTTKSLDLDPELMTAAGSRLLGLRDFAPFCRRR-EGATTIRTLLQCEAR 180

Query: 179 SFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +    IE+ V A +F H+ +RS  G+L  VG G  +   L++      R     + P
Sbjct: 181 RVADGCGTIELTVRADAFCHSMVRSLTGALVAVGSGTQSMDWLDEVAAGPTRAGSVTVMP 240

Query: 236 PEGLYFDSVEY 246
             GL  + V Y
Sbjct: 241 ARGLCLEQVAY 251


>gi|332669550|ref|YP_004452558.1| tRNA pseudouridine synthase A [Cellulomonas fimi ATCC 484]
 gi|332338588|gb|AEE45171.1| tRNA pseudouridine synthase A [Cellulomonas fimi ATCC 484]
          Length = 316

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 82/267 (30%), Positives = 121/267 (45%), Gaps = 22/267 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-----GEIVV-VHGAGRTDSGV 55
           +R  + + Y+G+ + GW RQ    ++QG +E A+  V      GE    V  AGRTD+GV
Sbjct: 17  VRLRLDLAYDGTSFSGWARQPALRTVQGVLEDALATVLRTAAHGEPAPHVTVAGRTDAGV 76

Query: 56  HALRQVAHFDLV-------REWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFS 106
           HA  QVAH D+        R         AL A L   +   + +  +++    F ARFS
Sbjct: 77  HARGQVAHMDVAPHVLDAVRGRSDRTPTDALVARLAGVLPADVVVHRVAVAPLGFDARFS 136

Query: 107 AIRRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+RR Y YRI     A   L +       + LD   M  AA+ LVGRHDF  +     + 
Sbjct: 137 ALRRRYAYRICDDSGARDPLSRAHVLWHRRPLDVAAMDAAARTLVGRHDFAAYCKPR-EG 195

Query: 166 SSPIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           ++ IRT++ F            L+  RV A +F H+ +R+ VG+   VG+G+       +
Sbjct: 196 ATTIRTLEEFVWERASGGAEAGLVVARVQADAFCHSMVRALVGASVAVGEGRRPVAWPAQ 255

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            L    R     +    GL  + V Y 
Sbjct: 256 LLAGGRRDAAAHVVAAHGLTLEEVGYP 282


>gi|297571891|ref|YP_003697665.1| tRNA pseudouridine synthase A [Arcanobacterium haemolyticum DSM
           20595]
 gi|296932238|gb|ADH93046.1| tRNA pseudouridine synthase A [Arcanobacterium haemolyticum DSM
           20595]
          Length = 293

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 78/268 (29%), Positives = 120/268 (44%), Gaps = 24/268 (8%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW  Q    ++Q  +EKA+ +V  E VV+  AGRTD+GVHA  QVA
Sbjct: 10  RVRLDLGYDGNHFHGWAAQPGLRTVQDELEKALSVVFREPVVLTVAGRTDAGVHARHQVA 69

Query: 63  HFDLVR-----------EWVPVILCKALNAYLKIS------------DTISILNLSIVDK 99
           H D+ R                 L   LN+ L  S              + + +   V  
Sbjct: 70  HCDVSRAAWDALPGRSSRTPGESLVLRLNSLLARSAGGVVAGAPRGYSDVVVHSALEVPA 129

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFSA+ R+Y YRI    A    ++     +   LD + M  A+  L+G HDF ++ 
Sbjct: 130 DFDARFSALWRAYTYRIADSVAEWDPQRHDVLWLSDRLDLDAMNRASVALLGEHDFLSYC 189

Query: 160 SIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
               + +S IRT+          ++  R  A +F H+Q+R+ +G+L  VG G        
Sbjct: 190 KPR-EGASTIRTLLDLGFERVEGIVVGRAKADAFCHSQVRTLMGTLIEVGRGAREERWPL 248

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
             L+   R     +APP  L  + + Y 
Sbjct: 249 LRLEECSRDGQVVVAPPHPLTLEEIGYP 276


>gi|145219589|ref|YP_001130298.1| tRNA pseudouridine synthase A [Prosthecochloris vibrioformis DSM
           265]
 gi|238685549|sp|A4SE87|TRUA_PROVI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145205753|gb|ABP36796.1| tRNA pseudouridine synthase A [Chlorobium phaeovibrioides DSM 265]
          Length = 243

 Score =  223 bits (568), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 105/247 (42%), Gaps = 5/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + +EY+G+ + GWQRQ NG  ++QG IE  +  +  E + +  AGRTD GVHA  
Sbjct: 1   MPNIRLDVEYDGTSFAGWQRQPNGIVTVQGEIEAVLSEILQEKINLAAAGRTDRGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          +  +LN  L    +I I +  +V   FHARFSA+ R Y Y  I  
Sbjct: 61  QVVNFSTRSPLEHSRIRHSLNCLL--PSSICIPSSQLVPDDFHARFSALERQYRYFAI-- 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P AL           +D   M+  +  L G HDF+ F       +  + T+       
Sbjct: 117 PEPSALMGRYTGCSHGDVDFALMQHLSSGLRGTHDFSLFSREDRDGNGSLCTVREAGWYR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              ++   + A  FL + +R  VG +   G G+    +    L           A   GL
Sbjct: 177 HKGVMVFHIAANRFLRSMVRGIVGGMLSAGRGELDPEEYLGMLGGGGGGMRVKPAVASGL 236

Query: 240 YFDSVEY 246
           +   V Y
Sbjct: 237 FLWRVRY 243


>gi|110598437|ref|ZP_01386709.1| tRNA pseudouridine synthase A [Chlorobium ferrooxidans DSM 13031]
 gi|110339971|gb|EAT58474.1| tRNA pseudouridine synthase A [Chlorobium ferrooxidans DSM 13031]
          Length = 244

 Score =  223 bits (568), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 73/249 (29%), Positives = 119/249 (47%), Gaps = 8/249 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M    + +EY+G+ Y GWQRQ  K   ++QG IE A+ ++  E + +  AGRTD GVHA 
Sbjct: 1   MKNIRITVEYDGTPYSGWQRQNRKGCVTVQGEIESALGMILQEKISLAAAGRTDKGVHAK 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            Q+A+F          +  +LNA L   DTI I +   + K+FH+R SA  R Y Y +I 
Sbjct: 61  AQIANFSTASPMDLSRMVHSLNALL--PDTIRITDPLEMPKEFHSRHSARERHYRYFLI- 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P A+    +     + D   M+  A  + G HDF+ F      +   + T+      
Sbjct: 118 -AEPSAIYGRFSGCSFGTPDLAVMQQVAGSVRGVHDFSAFSREDRDSPGRLCTVTACQWY 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPE 237
            + + + + + A  FL + +R  V  +   G G  ++ + ++ L+      +  P+AP  
Sbjct: 177 RYQHFLVLSISANRFLRSMVRYLVDGMLRAGKGTLSAEEFKRMLETGVMTTQLNPVAP-S 235

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 236 GLFLWRVTY 244


>gi|284033969|ref|YP_003383900.1| tRNA pseudouridine synthase A [Kribbella flavida DSM 17836]
 gi|283813262|gb|ADB35101.1| tRNA pseudouridine synthase A [Kribbella flavida DSM 17836]
          Length = 270

 Score =  223 bits (568), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 123/250 (49%), Gaps = 7/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
           +R+ + + Y+G+ + GW RQ    ++QG++E+A+  V    +   V  AGRTD+GVHA  
Sbjct: 1   MRWRIDLRYDGTEFHGWARQDGLRTVQGALEEALGTVLRLPDRPAVTCAGRTDTGVHARG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV H DL        L + LN  L   D +++  ++     F ARFSA+ R Y+YR+   
Sbjct: 61  QVTHVDLDVPVTGRDLLRRLNGVL--PDDVAVTAVAEAADGFDARFSALARRYVYRLCDD 118

Query: 120 QA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 L +     + + LD + M  AA  L+G HDF  F     + +S +R +  +   
Sbjct: 119 AVGWDPLRRREVLRVVRPLDVDRMNAAAAQLLGEHDFAAFCKKR-EGASTVRALLEYSWV 177

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             G  L++  V+A +F H+ +R+ VG+L  VGDG+         L  + R     + P  
Sbjct: 178 RVGPGLLDGTVIADAFCHSMVRALVGALIPVGDGRRDVDWPAAVLAGKMRDSAVAVLPAH 237

Query: 238 GLYFDSVEYS 247
           GL  + V Y 
Sbjct: 238 GLTLEEVRYP 247


>gi|237741391|ref|ZP_04571872.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
 gi|229430923|gb|EEO41135.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
          Length = 245

 Score =  223 bits (568), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 120/249 (48%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MGRKNIKIEFRYDGSRYYGFQRQPDKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSNIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKMREYIYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           ++ P   E      + + +  + +       VG HDF  FR   C +   IR I   +V 
Sbjct: 119 KKNP--FEARYCKFVKEKIIAKKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVK 176

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG N I+I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   E
Sbjct: 177 YFGENKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLTDFTKEYKKNLVEAE 236

Query: 238 GLYFDSVEY 246
           GLY + + Y
Sbjct: 237 GLYLNKISY 245


>gi|88854648|ref|ZP_01129314.1| tRNA pseudouridine synthase A [marine actinobacterium PHSC20C1]
 gi|88815809|gb|EAR25665.1| tRNA pseudouridine synthase A [marine actinobacterium PHSC20C1]
          Length = 315

 Score =  223 bits (568), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 75/269 (27%), Positives = 122/269 (45%), Gaps = 24/269 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHAL 58
            R  + I Y+G+ + GW +Q +  ++QG+IE A+   F   G +  +  AGRTD+GVHA 
Sbjct: 28  TRMRLDIAYDGTDFAGWGKQPSLRTVQGTIEDALGVIFRRFGAVPSLVVAGRTDAGVHAS 87

Query: 59  RQVAHFDLV------------------REWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
            QVAH DL                   R   P  L + +N    +   I +   +I    
Sbjct: 88  GQVAHLDLTDAQLISLDRPRRGNLRGKRYDGPASLARRINGIAGLEADIFLSRSAIAADG 147

Query: 101 FHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
           F ARFS + R Y YRI    +P    ++      P +LD + M IA+  L+G HD+  + 
Sbjct: 148 FDARFSPLWRRYEYRIADNASPRDPRQRNHTVWYPATLDVDAMNIASDELLGLHDWAAYC 207

Query: 160 SIHCQASSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               + ++ +R+++ F+       I +  + A +F H+ +RS VG+   VG GK      
Sbjct: 208 KPR-EGATTVRSLERFNWVRNEEGIIVAELRADAFCHSMVRSLVGAGVFVGQGKLEVDRP 266

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +    + +     + P +GL    V Y 
Sbjct: 267 VEIRDERSKGSEYKVMPAKGLTLVEVGYP 295


>gi|34762680|ref|ZP_00143671.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|27887637|gb|EAA24715.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
          Length = 245

 Score =  223 bits (568), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 119/249 (47%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MGRKNIKIEFRYDGSRYYGFQRQPDKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAN 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSNIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKMREYVYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +  + +       VG HDF  FR   C +   IR I   +V 
Sbjct: 119 EKNP--FEARYCKFVKEKIIAKKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVK 176

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG N I+I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   E
Sbjct: 177 YFGENKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLNDFTKEYKKNLVEAE 236

Query: 238 GLYFDSVEY 246
           GLY + + Y
Sbjct: 237 GLYLNKISY 245


>gi|145352156|ref|XP_001420422.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580656|gb|ABO98715.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 308

 Score =  222 bits (567), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 93/280 (33%), Positives = 139/280 (49%), Gaps = 35/280 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVHAL 58
            RY   +EY+G+ + G+QRQ    +++QG++++A+   TG    +   G+ RTD GVHAL
Sbjct: 12  PRYLAFLEYDGARFRGFQRQCGVAATVQGALDEALTAFTGARGAIECVGSSRTDVGVHAL 71

Query: 59  RQVAHFD---------LVREWVPVILCKALNAYLK-ISDTISILNLSIVDK---QFHARF 105
           R  AHFD          V       + + +N +L+ +   + +     VD+   +FHAR 
Sbjct: 72  RNSAHFDFARTTKDGTTVEPHDGASVRRGVNYHLRKLGAAVRVTECVRVDEMNPKFHARH 131

Query: 106 SAIRRSYLYRIITRQAPL---ALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTF 158
            A+ R Y Y I+  +        +  RAW +       L+ + MR AA  L G HDF++F
Sbjct: 132 DAVARRYRYDILVGERDDGGSLFDAERAWYVRATCDGRLNVDAMRDAAAALTGTHDFSSF 191

Query: 159 RSIHCQASSPIRTIDHFDVNSF------------GNLIEIRVVARSFLHTQIRSFVGSLK 206
           R+  CQASSP+RT+   DV                  I I V A SFL+ Q+R   G+LK
Sbjct: 192 RANGCQASSPVRTLTSIDVKEELTEWPAAEARGTKQKISIAVAAPSFLYHQVRLLAGALK 251

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            VG    T  D+++ L+A+D      +AP  GLY   V Y
Sbjct: 252 AVGANDLTVKDVQELLEAKDVARAPQMAPAHGLYLADVAY 291


>gi|227485306|ref|ZP_03915622.1| tRNA-pseudouridine synthase I [Anaerococcus lactolyticus ATCC
           51172]
 gi|227236766|gb|EEI86781.1| tRNA-pseudouridine synthase I [Anaerococcus lactolyticus ATCC
           51172]
          Length = 246

 Score =  222 bits (567), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 105/245 (42%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              + + ++G  + G+Q Q +  S++  + KAI  VTGE   +   GRTD+GVHA     
Sbjct: 4   NVLLKLAFDGRDFKGYQYQIDQRSVEEELRKAIKEVTGEDNRIIACGRTDAGVHARSFYI 63

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F    +  P      +  +L   D I  L+   V   FHARFS   ++Y Y I   + P
Sbjct: 64  NFLTACDVNPKGFAYHIQPHL--PDDILALSSKEVGLDFHARFSCKSKTYKYIINQEKNP 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVNSFG 181
             + +     I   LD + +    + L G HDF  F         +  R ID        
Sbjct: 122 HPIYRSYMENITYRLDYDKLDEGLEILKGDHDFRLFMKEDKNIDINTNRRIDDCYFKRGE 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +E+   A SFLH Q+R   GSL  +  GK +  D +       +K   P   P GLY 
Sbjct: 182 TRLELYFKAESFLHNQVRIMTGSLIELARGKLSLDDFKAYFDPATKKRANPALSPVGLYL 241

Query: 242 DSVEY 246
             VEY
Sbjct: 242 WEVEY 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 =  222 bits (567), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 113/220 (51%), Positives = 144/220 (65%), Gaps = 1/220 (0%)

Query: 28  QGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISD 87
           Q ++E AI  VTGE   VH AGRTD+GVH L   AH D+ +   P  L +A+NA ++   
Sbjct: 2   QQALEDAIHAVTGERTAVHAAGRTDAGVHGLAMRAHVDIAKVIAPFRLMEAINARIR-PA 60

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQ 147
            +++L+   V   +HARFS IRRSY YRI+ R+APL  E G AW +P++LD   M  AA 
Sbjct: 61  PVAVLDCVEVASDWHARFSCIRRSYEYRIVNRRAPLTHELGLAWQVPQALDEAAMAEAAA 120

Query: 148 HLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
            LVGRHDFTTFRS+HCQA SP+RT+D   V   G  + IR  ARSFLH Q+RS VG L L
Sbjct: 121 RLVGRHDFTTFRSVHCQADSPVRTLDLLSVERDGARLFIRAAARSFLHHQVRSMVGCLAL 180

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           VG G+WT  D+E AL A+DR + G  AP +GL+F   +Y 
Sbjct: 181 VGMGRWTPDDVEAALVARDRAQLGLNAPSDGLFFVRADYP 220


>gi|256846563|ref|ZP_05552020.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
 gi|256718332|gb|EEU31888.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
          Length = 245

 Score =  222 bits (567), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 118/249 (47%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ    ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MGRKNIKIEFRYDGSRYYGFQRQPKKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAY 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSNIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKMREYIYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +  E +       VG HDF  FR   C +   IR I   +V 
Sbjct: 119 EKNP--FEARYCKFVKEKIVVEKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVK 176

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG N I+I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   E
Sbjct: 177 YFGENKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLTDFTKEYKKNLVEAE 236

Query: 238 GLYFDSVEY 246
           GLY + + Y
Sbjct: 237 GLYLNKISY 245


>gi|261415083|ref|YP_003248766.1| tRNA pseudouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371539|gb|ACX74284.1| tRNA pseudouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302325886|gb|ADL25087.1| tRNA pseudouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 250

 Score =  222 bits (567), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 83/252 (32%), Positives = 125/252 (49%), Gaps = 12/252 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           +RY    EY GS ++GWQ Q  G      ++Q ++E+A+       + V G+GRTD+GVH
Sbjct: 1   MRYRFRCEYLGSAFYGWQEQNCGGKLRFVTVQSTLEEALSTALRAPIRVVGSGRTDTGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  Q  HFD   E  P  + +++N   K    I I +L      F+AR+ A+ R Y Y I
Sbjct: 61  ARGQCVHFDFDGELDPQKVVRSVNGLTKR--LIRIRDLEPCASDFNARYDAVLRYYQYTI 118

Query: 117 ITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
            TR  P+AL +   W     +LD E M   AQ  +G HDF  F        S + T+  F
Sbjct: 119 FTR--PVALMRDFGWECGSLNLDIEAMGREAQSFLGEHDFIDFCIPRNDGKSTLCTLSEF 176

Query: 176 DVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +    +      +    FLH Q+R+ VG+L  VG G++    + +  + ++ K     A
Sbjct: 177 RLERLNDWSCMFHIKGNRFLHRQVRAMVGTLFDVGRGRYPEGTVNQIFE-KNFKGERTWA 235

Query: 235 PPEGLYFDSVEY 246
           PP+GL  ++VEY
Sbjct: 236 PPQGLVLENVEY 247


>gi|126654438|ref|ZP_01726177.1| pseudouridylate synthase I [Bacillus sp. B14905]
 gi|126589112|gb|EAZ83311.1| pseudouridylate synthase I [Bacillus sp. B14905]
          Length = 214

 Score =  222 bits (566), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 61/216 (28%), Positives = 97/216 (44%), Gaps = 4/216 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALR 59
           M R  +II Y+G+ + G+Q Q    ++Q  IE+ + ++  E  V V  +GRTD+ VHA  
Sbjct: 1   MRRLKVIISYDGTLFSGYQVQPGERTVQAEIERVLAIMHKEEKVKVTASGRTDARVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q  HFD           KALN  L     I ++++  V+  FHAR+S   + Y Y     
Sbjct: 61  QTLHFDTPLAIPADKYRKALNVQL--PRDIRVMSVEEVEHDFHARYSVTGKRYRYIWSCE 118

Query: 120 QAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                  +           D   M+ AAQ ++G HDF+ F + +      +RT+      
Sbjct: 119 PIQNPFRRHYTVETNGVKPDVVAMQKAAQAIIGTHDFSCFCASNTSVQDKVRTVTSLQFE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             G  + + +    FL+  +R   G+L  VG  + T
Sbjct: 179 WHGEELHMVIEGSGFLYNMVRIIAGTLWEVGIDRRT 214


>gi|151554108|gb|AAI49177.1| PUSL1 protein [Bos taurus]
          Length = 312

 Score =  222 bits (566), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 88/277 (31%), Positives = 128/277 (46%), Gaps = 36/277 (12%)

Query: 3   RYCMIIEYNGSGY------FGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGV 55
           RY +  +Y G+ +       G QR      +Q  +E+A   +     V    + RTD+GV
Sbjct: 34  RYLVYFQYLGTDFNGVAAVRGVQR---AVGVQNYLEEAAERLNSVMPVKFTISSRTDAGV 90

Query: 56  HALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           HAL   AH D+ R      + P +L +ALN +LK    I +L    V   FHAR +AI R
Sbjct: 91  HALSNAAHLDIQRRSDLPPFSPEVLTEALNTHLKHP-AIRVLQAFRVPSHFHARHAAISR 149

Query: 111 SYLYRIITRQAPL----ALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           +YLYR+ T           E+ R W +    LD   M+ AAQHL+G HDF+ F+S    A
Sbjct: 150 TYLYRLATGCPRPDRLPVFERNRCWALQADCLDVAAMQEAAQHLLGTHDFSAFQSAGSPA 209

Query: 166 SSPIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           SSP+RT+    V+                    +   ++SFL+ Q+R     L  VG G 
Sbjct: 210 SSPVRTLRRASVSPDPASPFVLPEESRQLQFWSMEFESQSFLYKQVRRMTAVLVAVGLGA 269

Query: 213 WTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEYS 247
                ++  L+++D   K    +AP  GL+  SV Y 
Sbjct: 270 LMPAQVKAILESRDPLGKHQSRVAPAHGLFLKSVLYE 306


>gi|84494739|ref|ZP_00993858.1| tRNA pseudouridine synthase [Janibacter sp. HTCC2649]
 gi|84384232|gb|EAQ00112.1| tRNA pseudouridine synthase [Janibacter sp. HTCC2649]
          Length = 283

 Score =  222 bits (566), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 75/258 (29%), Positives = 116/258 (44%), Gaps = 14/258 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALRQ 60
           R  + + Y+G+ + GW  Q    +++G +  A+  +    E V +  AGRTD+GVHA  Q
Sbjct: 5   RVRIDLAYDGTDFSGWAAQPGRRTVEGELSAALTTLLRAPEPVRLTVAGRTDAGVHARGQ 64

Query: 61  VAHFDLVREWVPVILCK-------ALNAYL--KISDTISILNLSIVDKQFHARFSAIRRS 111
           V H D+       +  +       A    L   +   + +  +S     F ARF+A+RR 
Sbjct: 65  VVHADVDDTLYAALPGRSSRSPEEAARTRLAGILPSDVVVRAVSRAPDGFDARFAALRRR 124

Query: 112 YLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
           YLYRI     A   L +G   ++   LD   M  AA  LVG HDF  F       ++ +R
Sbjct: 125 YLYRICDDPGALDPLRRGDTVVLKDPLDVAAMNEAAGRLVGLHDFAAFCKKR-DGATTVR 183

Query: 171 TIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           T+  +      +  +E  VVA +F H+ +R+ VGS+  VG G+       + L    R  
Sbjct: 184 TLLDYSWVRAPDGTVEATVVADAFCHSMVRALVGSVVPVGMGRAEVDFPREVLTGGARDP 243

Query: 230 CGPLAPPEGLYFDSVEYS 247
              + P  GL  + V Y 
Sbjct: 244 RVKVMPAHGLSLEEVTYP 261


>gi|18977290|ref|NP_578647.1| tRNA pseudouridine synthase A [Pyrococcus furiosus DSM 3638]
 gi|24638312|sp|Q8U2C1|TRUA_PYRFU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|18892961|gb|AAL81042.1| putative tRNA pseudouridine synthase a [Pyrococcus furiosus DSM
           3638]
          Length = 266

 Score =  222 bits (566), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 108/247 (43%), Gaps = 24/247 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + G+QRQ N  +I+G I +A+     E      A RTD GV A   V
Sbjct: 1   MRVALKIAYDGTKFHGFQRQPNVRTIEGEILRALKDAGIEFENFKSASRTDRGVSARGNV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                  + +   +   LN+ +     + I  ++ V + FH RF A  + Y Y + +   
Sbjct: 61  IALSTEDDRIKNPMV--LNSRMS---DVWIWGIAEVPEDFHPRFWANTKVYRYYLPSL-- 113

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                          ++ + M+  +   +G HDF+ F  +       IR+ID  ++    
Sbjct: 114 --------------GMNIKKMKECSLLFLGTHDFSAFSRV--DGRDTIRSIDRIEIWEKC 157

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEGLY 240
           N++ + +  +SFL   +R  V +L L   G      + + L  + ++    P APPEGL 
Sbjct: 158 NVVVVEIEGKSFLWEMVRRIVSALVLCSQGVLAEERIVEMLNGKFEKSRKVPPAPPEGLL 217

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 218 LWDIKYE 224


>gi|325972112|ref|YP_004248303.1| tRNA pseudouridine synthase A [Spirochaeta sp. Buddy]
 gi|324027350|gb|ADY14109.1| tRNA pseudouridine synthase A [Spirochaeta sp. Buddy]
          Length = 281

 Score =  222 bits (565), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 79/252 (31%), Positives = 113/252 (44%), Gaps = 8/252 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  M + Y+GS Y GWQ+Q N  S+   IE+ +  +  E V V G+GRTDSGVHAL QV
Sbjct: 19  RRIRMTVSYHGSHYSGWQKQSNAKSVAEIIEQTLKQILDEEVQVVGSGRTDSGVHALAQV 78

Query: 62  AHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            H D+    +       ALN  L     I IL+    D  FHAR++ + R+Y Y      
Sbjct: 79  CHMDIANTRIKGEKFALALNRLL--PADIRILDSCETDGTFHARYTTMARTYRYYYKREC 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID----HFD 176
              A +      + +    E +   A  + G HDFTTF +      S  R I       +
Sbjct: 137 DMTAFDDKLVAKVKQFPSLELLNEYACSIRGTHDFTTFTASGDLCPSRFRDIYESYWRLE 196

Query: 177 VNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           ++ FG  L+   +   +FL+  +RS VGS+           +    L ++DR   G  A 
Sbjct: 197 IDRFGKELLSYTICGNAFLYKMVRSLVGSMMEFATKDLPVEEFRHILASKDRSRSGRTAS 256

Query: 236 PEGLYFDSVEYS 247
             GLY   + Y 
Sbjct: 257 ACGLYLYRISYD 268


>gi|163840856|ref|YP_001625261.1| tRNA pseudouridine synthase A [Renibacterium salmoninarum ATCC
           33209]
 gi|162954332|gb|ABY23847.1| tRNA pseudouridine synthase A [Renibacterium salmoninarum ATCC
           33209]
          Length = 297

 Score =  222 bits (565), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 72/263 (27%), Positives = 120/263 (45%), Gaps = 19/263 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G+ + GW  Q    ++QG +E ++ ++   +V V  AGRTD+GVHA  QV 
Sbjct: 18  RLRLDLAYDGAPFSGWALQPERLTVQGVLEDSLAMILRRLVRVTVAGRTDAGVHARGQVV 77

Query: 63  HF-DLVREW----------VPVILCKALNAYL-----KISDTISILNLSIVDKQFHARFS 106
           H      EW              + + L   L     + +  + + ++   +  F ARFS
Sbjct: 78  HAEFYPHEWEQIARRSTASPEEAVLRRLRGALSRVLGEQTGAVVVHSVRPAEPGFDARFS 137

Query: 107 AIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R Y Y I  R A    +++   W     LD E + +A Q L+G  DF  F       
Sbjct: 138 ALWRRYSYHIADRPAQWDPVQRQMTWWHKTELDVELLNLAVQPLLGLQDFRAFCKPRP-G 196

Query: 166 SSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           ++ +R +   + +   +  I++ V A +F H  +R+ +GS   VG G+ +   L + L  
Sbjct: 197 ATTVRELQRLEFSRQPDGTIKVAVQADAFCHNMVRALIGSAVQVGSGEQSPDWLAERLAI 256

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           + R     LAPP  L  + V Y 
Sbjct: 257 KVRDAKSGLAPPHPLVLEEVHYP 279


>gi|159469598|ref|XP_001692950.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158277752|gb|EDP03519.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 239

 Score =  222 bits (565), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 78/237 (32%), Positives = 108/237 (45%), Gaps = 16/237 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y +I+ Y+G+ Y GWQ Q    ++Q  +E A+  V  E   V G   AGRTDSGVHA  Q
Sbjct: 5   YRLILAYDGTDYCGWQLQPAAPTVQAKLEAALGTVLREDRGVLGVRAAGRTDSGVHARGQ 64

Query: 61  VAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V      R  +P   L   LNA L     I ++ +      F    S I ++Y Y I   
Sbjct: 65  VRTGLTGRGGLPVDKLAYKLNAVL--PPDIRVMGVRRTAPDFSVTCSPIGKTYHYNITNS 122

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-----CQASSPIRTIDH 174
           +A   L    A+ + K LD   MR AA  LVG HDFT F +I       +  +P++T+  
Sbjct: 123 EAHDPLRHRYAYHVRKPLDLAGMRAAAALLVGTHDFTQFSNIGEEGGRPRKRNPVKTLRR 182

Query: 175 FDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            DV       F   + I V    FL+  +R   G L  VG+ K     + + L+  D
Sbjct: 183 MDVVELDPAAFPGGVRIEVEGNGFLYKMVRHISGVLVAVGERKLPPGIVSEMLEVGD 239


>gi|294784150|ref|ZP_06749451.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
 gi|294488220|gb|EFG35565.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
          Length = 245

 Score =  222 bits (565), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 119/249 (47%), Gaps = 7/249 (2%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R    +   Y+GS Y+G+QRQ +  ++QG IEK + +VT E + +  AGRTD GVHA 
Sbjct: 1   MGRKNIKIEFRYDGSRYYGFQRQPDKITVQGEIEKILRIVTKEEINLISAGRTDRGVHAY 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV++F              L   L   + I IL++  VD+ F+AR +A  R Y+Y I  
Sbjct: 61  HQVSNFYTSSNIPIEKYKYLLTRAL--PNDIDILSVEEVDENFNARHNAKIREYIYIISW 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            + P   E      + + +  + +       VG HDF  FR   C +   IR I   +V 
Sbjct: 119 EKNP--FEARYCKFVKEKIIAKKLEKIFSDFVGVHDFKNFRLNDCVSKITIREIYQIEVK 176

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            FG N I+I +   +FL +Q+R  VG+   +  G+     +   L    ++    L   E
Sbjct: 177 YFGENKIKIYIKGSAFLKSQVRIMVGTALEIYYGRLPENHIRLMLTDFTKEYKKNLVEAE 236

Query: 238 GLYFDSVEY 246
           GLY + + Y
Sbjct: 237 GLYLNKISY 245


>gi|148243240|ref|YP_001228397.1| tRNA pseudouridine synthase A [Synechococcus sp. RCC307]
 gi|147851550|emb|CAK29044.1| tRNA pseudouridine synthase A [Synechococcus sp. RCC307]
          Length = 291

 Score =  221 bits (564), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 75/254 (29%), Positives = 114/254 (44%), Gaps = 10/254 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL-------VTGEIVVVHGAGRTDSG 54
            R  + ++Y+G  + GWQRQ    S+Q S+++AI         +  ++     AGRTD+G
Sbjct: 4   QRIALCLQYDGGPFCGWQRQPQHRSVQQSLDEAIEALDPLPAGIAAKLSRTIAAGRTDTG 63

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  QV HFD            ALN  L    +I +   + V   +HA FSA  R Y Y
Sbjct: 64  VHAAAQVVHFDCHGPIPAARWAPALNGRL--PGSIRVRASAAVAANWHACFSATYRRYRY 121

Query: 115 RIITRQAPLALEKGRAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
            I   + P       +W      L    M+   Q L+G HDF+ F+    Q +    T+ 
Sbjct: 122 CIYNARRPNLFLSPFSWHRYQWRLQDHLMQELLQELLGHHDFSAFQRAGSQRAHARTTVQ 181

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              +   G+++ + + A  FL+  +R  VG L   G+G+ +     +  + Q R E    
Sbjct: 182 EVSLQREGDILTLEIQASGFLYGMVRLLVGQLVAAGEGRISPEQFRQRWREQRRDEVKEA 241

Query: 234 APPEGLYFDSVEYS 247
           APP+GL    V Y 
Sbjct: 242 APPQGLCLLRVGYP 255


>gi|57640862|ref|YP_183340.1| tRNA pseudouridine synthase A [Thermococcus kodakarensis KOD1]
 gi|62901178|sp|Q5JI92|TRUA_PYRKO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57159186|dbj|BAD85116.1| tRNA pseudouridine synthase A [Thermococcus kodakarensis KOD1]
          Length = 267

 Score =  221 bits (564), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 115/250 (46%), Gaps = 26/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           ++  + + Y+GS ++G+QRQ    +++G I K +  +    + E     GA RTD GV A
Sbjct: 1   MKLALRVAYDGSAFYGFQRQPGVRTVEGEIIKVLQKLGIIESPEKNDFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              V  F +  E   +   + LN +L     + +L ++ V   FH RF A  ++Y Y ++
Sbjct: 61  FFNVVSF-VPSERPDLARPEVLNHHLS---DVWVLGIAEVPDDFHPRFWAKFKTYRYYLV 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                            +  D   MR  A   VGRHDF+ F  +      PIR ++  +V
Sbjct: 117 N----------------EGFDLSAMRECASLFVGRHDFSAFAKLEP-GRDPIREVERVEV 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + I V  +SFL   +R  V +L+  G G   + ++E+ L + +  +  P APPE
Sbjct: 160 IERQGYLVIEVQGKSFLWEMVRRIVNALRFCGLGLLEAEEVERML-SGEYGKKIPPAPPE 218

Query: 238 GLYFDSVEYS 247
           GL    +EY 
Sbjct: 219 GLVLWHIEYP 228


>gi|313836079|gb|EFS73793.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL037PA2]
 gi|314929615|gb|EFS93446.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL044PA1]
 gi|314970609|gb|EFT14707.1| tRNA pseudouridine synthase A [Propionibacterium acnes HL037PA3]
          Length = 279

 Score =  221 bits (564), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 121/253 (47%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E+ I  V   G    +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWAVQPDRRTVQGDLERWIPRVLRLGVPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     + + ++  V  +F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDGVDTSSMLRRLSRVL--DPDVVVKSIRSVPDEFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +P+ LD + +  A   L+G  DF  F     + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVASVPRHLDLDRLNAAGASLLGLRDFAAFCKYR-EGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+     L++   +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGQRNQGWLDEVAASASRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|227549870|ref|ZP_03979919.1| tRNA-pseudouridine synthase I [Corynebacterium lipophiloflavum DSM
           44291]
 gi|227078125|gb|EEI16088.1| tRNA-pseudouridine synthase I [Corynebacterium lipophiloflavum DSM
           44291]
          Length = 285

 Score =  221 bits (564), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 82/264 (31%), Positives = 119/264 (45%), Gaps = 21/264 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG------SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           R  + I Y+G+ + GW RQ+         ++Q +I+ A+  V    V +  AGRTD+GVH
Sbjct: 7   RLRLDIAYDGTDFHGWARQREQPDGTPTRTVQQTIQSALSTVLRTPVELTVAGRTDAGVH 66

Query: 57  ALRQVAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           A  QVAH D+          +  P  L + L   L     + +  +S V   F ARFSA+
Sbjct: 67  ASGQVAHADIPAASLDQRSIDGDPARLVRRLAKLL--PADVRVYGVSAVSPLFDARFSAL 124

Query: 109 RRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            RSY+YR+ T  A  L        +  + +D   M++AA   VG HDF  F      A++
Sbjct: 125 TRSYVYRVTTHPAGALPTRARDTAVWRRPVDIGAMQVAADAFVGLHDFAAFCRAKPHATT 184

Query: 168 PIRTIDHFDVN----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             + ++   V        NL E  V A +F    +RS V +   VG+G    T +E  L 
Sbjct: 185 VRKVVEMRWVEASTGEEPNLYEAHVTADAFCWNMVRSLVAACLQVGEGSKDPTWVEPLLG 244

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
              R     LAP +GL    V Y 
Sbjct: 245 ETTRHPHVLLAPAKGLTLVDVSYP 268


>gi|262203538|ref|YP_003274746.1| tRNA pseudouridine synthase A [Gordonia bronchialis DSM 43247]
 gi|262086885|gb|ACY22853.1| tRNA pseudouridine synthase A [Gordonia bronchialis DSM 43247]
          Length = 291

 Score =  221 bits (564), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 113/255 (44%), Gaps = 13/255 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y G+ + GW RQ +  ++   +E  +  V    V +  AGRTD+GVHA  QV 
Sbjct: 16  RLRLDVGYEGTDFAGWARQTDQRTVGAVLEDTLATVLRIPVRLTVAGRTDAGVHATGQVC 75

Query: 63  HFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           H D+             P +L   L   L   D + +  ++ V   F ARFSA+RR Y Y
Sbjct: 76  HTDIPVSALQTRSIGGDPSLLVGRLAKML--PDDVRVKEIASVSGDFDARFSALRRHYEY 133

Query: 115 RIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           R+   +     +         + LD + M  A+  L+G +DF  F     + ++ IR + 
Sbjct: 134 RLTDARWGAEPIHARTTATWRRPLDVDAMNAASASLLGLNDFAAFCRRR-EGATTIRDLQ 192

Query: 174 HFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            F      G ++  +V A +F  + +RS VG++  VGDG+         L    R    P
Sbjct: 193 QFSWTRHAGGVLVGQVSADAFCWSMVRSLVGAVASVGDGRRDIDWCRGLLAETQRSSQVP 252

Query: 233 LAPPEGLYFDSVEYS 247
           +A   GL    V+Y 
Sbjct: 253 VADACGLCLVRVDYP 267


>gi|115375174|ref|ZP_01462441.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
 gi|115367825|gb|EAU66793.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 221

 Score =  221 bits (563), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 68/203 (33%), Positives = 99/203 (48%), Gaps = 3/203 (1%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           +  AGRTDSGVHA  QV  FD  R+       + LN  L   + I+++    V   F  R
Sbjct: 1   MVAAGRTDSGVHATGQVVCFDTERQLPLKAYHRGLNGLL--PEDIAVVRAEEVSAAFDPR 58

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
             +  + Y YR+    +   L +   W I   L  E M  AA  L+GRHD++ FR+  CQ
Sbjct: 59  RWSRGKRYRYRVSNLPSRSPLRRHTHWEIYAPLQVEAMARAATSLLGRHDYSAFRASDCQ 118

Query: 165 ASSPIRTIDHFDVN-SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           A+  +R +    V  + G+ +   V   +FL   +R+ VG+L  VG G+     + + L 
Sbjct: 119 AAHAVREVRRLSVEGTPGDAVAFVVEGTAFLKHMVRNLVGTLVEVGKGRRPEAWVAEVLA 178

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           + DR   GP APP GL  + V Y
Sbjct: 179 SGDRTLAGPTAPPHGLVLEEVFY 201


>gi|256370635|ref|YP_003108460.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri SMDSEM]
 gi|256009427|gb|ACU52787.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri SMDSEM]
          Length = 270

 Score =  221 bits (563), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 126/270 (46%), Gaps = 28/270 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R+ + I Y GS  FGWQ QK   SIQ +IE  +  +  + + + GAGRTD+GVHA++  
Sbjct: 1   MRFFIEISYKGSSLFGWQIQKKNLSIQETIETCLSFLLKKKIKIIGAGRTDTGVHAIQMF 60

Query: 62  AHFDLV------------------------REWVPVILCKALNAYLKISDTISILNLSIV 97
           AHFDL                         +  +       LN++L     I I+N+  V
Sbjct: 61  AHFDLTFDLTFDLTFDLTFDLTFDLTFDLTKNHINNHFKSKLNSFL--PLNIKIINIFSV 118

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
            K  HARF+AI R Y YRI   + P   +    WL    ++ + ++  A  L    DF++
Sbjct: 119 KKNIHARFNAISRVYEYRISLSKDPFLFQTSWQWLSKNQIELKILKKGANILKKYKDFSS 178

Query: 158 FRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           F     + +  +  I         N++  R+ A  FL   +RS VG+L  +G  K T  D
Sbjct: 179 FCKEKSKKN--LCEISTAKWILKKNILYFRIEANRFLRNMVRSLVGTLIELGIKKITIKD 236

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             K ++A++R   G  AP +GL+   + Y 
Sbjct: 237 FIKIIEAKNRNLAGITAPAKGLFLIKINYP 266


>gi|328955882|ref|YP_004373215.1| tRNA pseudouridine synthase A [Coriobacterium glomerans PW2]
 gi|328456206|gb|AEB07400.1| tRNA pseudouridine synthase A [Coriobacterium glomerans PW2]
          Length = 299

 Score =  221 bits (563), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 81/250 (32%), Positives = 117/250 (46%), Gaps = 10/250 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ---VA 62
           + + Y+G+ Y G+  Q +  ++ G + +A+       + +  AGRTD+GVHA+ Q   VA
Sbjct: 44  LKLGYDGTRYSGFAEQPDRCTVAGEVRQAMETFLRRPIELICAGRTDAGVHAIGQHVSVA 103

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                 E       +A++A L     IS+  +    + F ARF A  R+Y YRI      
Sbjct: 104 VLPAECEIPRARWLRAMDALL--PPDISVAGVFRARRGFSARFDARDRTYTYRIAAGSVR 161

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVN 178
            AL +   W     LD   MR AA  LVG HDF +F      A  P    +  +D    +
Sbjct: 162 PALIRPYVWWHRLELDEGAMRDAATCLVGEHDFKSFCRASSAAGRPTSRRVLDVDFAHES 221

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             G N++   +   +FLH+ +R+ VGSL  VG  +     L  AL A+DR   GP AP  
Sbjct: 222 ELGENVLAFTIRGNAFLHSMVRTIVGSLAEVGTHRRDPAWLADALAARDRAAAGPTAPAC 281

Query: 238 GLYFDSVEYS 247
           GL F  V Y 
Sbjct: 282 GLCFMDVSYD 291


>gi|85057773|ref|YP_456689.1| tRNA pseudouridine synthase A [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|123738898|sp|Q2NIY3|TRUA_AYWBP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|84789878|gb|ABC65610.1| tRNA pseudouridine synthase A [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 243

 Score =  220 bits (561), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 102/243 (41%), Gaps = 5/243 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +I+ Y+G+ Y G+Q+Q    ++Q + EKA+  +T + +    A RTD GVH+  Q  H
Sbjct: 6   YKLILSYDGTFYCGYQKQPQKKTVQQTFEKALKKMTHQNIPTFAASRTDKGVHSQGQTLH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P    K LN  L     I +  +      FHAR+SA  + Y Y     + PL
Sbjct: 66  FQTTFSLKPKHFQKTLNYLL--PPDIRVRQMHFATPNFHARYSAKSKIYQYVFS--KKPL 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                   +     D   +  A + + G H+F  F S   Q  +  +TI    +    + 
Sbjct: 122 NAFNHHFQIFADKFDFVKITKALKFIEGTHNFFAFTS-ETQPKNFSKTIFQASLKETVHK 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             +      FL   IR  VGSL  +G  K++    +  L     K+   LAP + L    
Sbjct: 181 YILVFHGNGFLKYMIRFLVGSLIEIGKNKFSLEQFQAMLLGNKTKKATLLAPAKALVLKK 240

Query: 244 VEY 246
           + Y
Sbjct: 241 IFY 243


>gi|328906179|gb|EGG25954.1| tRNA pseudouridine synthase A [Propionibacterium sp. P08]
          Length = 279

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 120/253 (47%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
           M R+ + I Y+G+ + GW  Q +  ++QG +E+ I  V        +  AGRTD+GVHA 
Sbjct: 1   MTRWRLDIAYDGANFSGWAVQPDRRTVQGDLERWIPRVLRLSVPTPLTVAGRTDAGVHAR 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH DL        + + L+  L     + + ++  V  +F ARFSA+ R Y+YR+  
Sbjct: 61  GQVAHVDLPDGVDTSSMLRRLSRVL--DPDVVVKSIRSVPDEFDARFSALWRRYVYRLWD 118

Query: 119 -RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
               P  + +     +P+ LD + +  A   L+G  DF  F     + ++ IRT+     
Sbjct: 119 ESSRPDPVTRFHVASVPRHLDLDRLNAAGASLLGLRDFAAFCKYR-EGATTIRTLLDCHA 177

Query: 178 NSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
               +    +E+ V A +F H+ +RS VG+L  V  G+     L++   +  R     + 
Sbjct: 178 ERLDDPCGTVEVTVRADAFCHSMVRSLVGALTAVASGQRNQGWLDEVAASASRASSVLVM 237

Query: 235 PPEGLYFDSVEYS 247
           P  GL  + V Y 
Sbjct: 238 PACGLTLEEVGYP 250


>gi|327288532|ref|XP_003228980.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Anolis
           carolinensis]
          Length = 293

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 87/274 (31%), Positives = 134/274 (48%), Gaps = 31/274 (11%)

Query: 3   RYCMIIEYNGSGYFG-WQRQKNGSS--IQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY +  +Y+G+ Y G  +   + ++  +Q  +EKA   +     V    + RTD+GVHAL
Sbjct: 7   RYLISFQYSGTMYSGVMETPPHQATLGVQNYLEKAAEKLRPLVPVKFVISSRTDTGVHAL 66

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      +   +L +ALN  LK  + I +L    V   FHARFSA+ R+Y+
Sbjct: 67  CNTAHIDIERSGGKPPFSESVLVQALNRNLK-HEPIRVLAARRVSDTFHARFSALSRTYV 125

Query: 114 YRIITRQAPL----ALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQ--AS 166
           YR++T  +        E+   W+  +  LD   M+ AA  LVG HDF+TFRS   +  A 
Sbjct: 126 YRVVTGCSCPSDLPVFERNLCWVTQRGHLDLTAMQEAAGLLVGTHDFSTFRSASSELPAK 185

Query: 167 SPIRTIDHFDVNSFGNL------------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           +P++TID  ++                   E+   +RSFL+ Q+R   G L  VG  +  
Sbjct: 186 NPVKTIDQLEIRPSSGFLMHHVKSSDLKFWELEFTSRSFLYKQVRRMAGVLVAVGQHRLD 245

Query: 215 STDLEKALQAQDRKECGP--LAPPEGLYFDSVEY 246
              ++  L  +D     P  +AP  GL+  +VEY
Sbjct: 246 PECVKTLLDIRDLMAYPPSTIAPACGLFLKNVEY 279


>gi|308233892|ref|ZP_07664629.1| tRNA pseudouridine synthase A [Atopobium vaginae DSM 15829]
 gi|328943600|ref|ZP_08241065.1| tRNA pseudouridine synthase A [Atopobium vaginae DSM 15829]
 gi|327491569|gb|EGF23343.1| tRNA pseudouridine synthase A [Atopobium vaginae DSM 15829]
          Length = 311

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/256 (26%), Positives = 108/256 (42%), Gaps = 14/256 (5%)

Query: 6   MIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           +   Y G+ + G+  Q     S++G + +A+       + +  AGRTD+GVHA  Q   F
Sbjct: 46  IRFGYVGTHFCGYAAQNESVRSVEGCLTRALSTFLRRNITLTCAGRTDAGVHAHAQYVSF 105

Query: 65  DLVREWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            + +  + +   K ++A   +  D ISI  L      F ARFSA  RSY YRI       
Sbjct: 106 PITQSELGMSKHKIMSALSGLCPDDISIRTLYRAPLDFSARFSACERSYTYRIALGPLKP 165

Query: 124 ALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIHC------QASSPIRTIDHF 175
            L     W +     +  ++M  A ++L G H+F +F           Q  S  R +   
Sbjct: 166 ILTHEFVWWVKNIPHVCMDDMNAAGEYLAGEHNFKSFCKASSAQLLEEQGLSLNRCLTSI 225

Query: 176 DVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
            V+        ++ + +   +FLH  +R    SL  VG G      ++  L+ Q R    
Sbjct: 226 KVSRDYIVGEQILRLDITGNAFLHNMVRIITASLLEVGRGARQPDWIQDVLRQQTRTAAA 285

Query: 232 PLAPPEGLYFDSVEYS 247
             AP +GL  + V Y 
Sbjct: 286 MTAPAQGLTLERVGYP 301


>gi|227487069|ref|ZP_03917385.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227541767|ref|ZP_03971816.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227093143|gb|EEI28455.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227182473|gb|EEI63445.1| tRNA pseudouridine synthase A [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 284

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/263 (31%), Positives = 121/263 (46%), Gaps = 20/263 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVHAL 58
           +     I Y+G+ + GW  QK G  ++Q +IE+A+ LV    +   +  AGRTD+GVHA 
Sbjct: 3   VNLRFDIAYDGTNFHGWATQKGGLRTVQQTIEEALRLVLRLDDSYQLTVAGRTDAGVHAT 62

Query: 59  RQVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
            QVA+  +             P  L + LN  L   D IS+L +S   + F ARF A+RR
Sbjct: 63  GQVANMVVPESCLEQRSIDGDPARLTRRLNKLL--PDDISLLAVSAAPEAFDARFGALRR 120

Query: 111 SYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            Y YR+ TR   PL L +       K +D + +   A   VG HDF         A + I
Sbjct: 121 YYEYRVTTRPGGPLPLRRFDTATWKKPVDIDVVSACASAFVGLHDFAALCKHKPHA-TTI 179

Query: 170 RTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           RT++ F                +V A +F  + +RS VG+   VG+G+   +     L  
Sbjct: 180 RTVETFTWEDISTPCEPQTYLAKVSADAFCWSMVRSLVGACLAVGEGRRDLSFAPHLLTL 239

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           ++R    P+A   GL    V+Y 
Sbjct: 240 KERAADVPVASACGLTLTGVDYP 262


>gi|289706561|ref|ZP_06502911.1| tRNA pseudouridine synthase A [Micrococcus luteus SK58]
 gi|289556696|gb|EFD50037.1| tRNA pseudouridine synthase A [Micrococcus luteus SK58]
          Length = 297

 Score =  219 bits (559), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 77/261 (29%), Positives = 115/261 (44%), Gaps = 16/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW RQ    S+QG++E  +  +    V    AGRTD+GVHA  QV
Sbjct: 19  VRVRLDLAYDGGAFHGWARQPGLDSVQGALEDGLERILRRPVRTVVAGRTDAGVHARGQV 78

Query: 62  AHFDLVRE------------WVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAI 108
           AH DL                    L + L   L      + +         F ARFSA+
Sbjct: 79  AHLDLTETEWAGLTRGRPGLEPAASLTRRLGGVLSGWGGAVVVHGAGRAPAGFDARFSAL 138

Query: 109 RRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R Y YRI     A     +G       +LD   M + A  ++G HDF +F       ++
Sbjct: 139 WREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAVLGLHDFLSFCRPRA-GAT 197

Query: 168 PIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            IR + H +V    + ++ +R+ A +F H  +R+ VG+L  VG+G      L + +    
Sbjct: 198 TIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVGEGAREPGWLARRVARPA 257

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R     LAPP GL   +V Y 
Sbjct: 258 RDSEVRLAPPGGLTLLAVGYP 278


>gi|239918171|ref|YP_002957729.1| pseudouridylate synthase I [Micrococcus luteus NCTC 2665]
 gi|281415639|ref|ZP_06247381.1| tRNA pseudouridine synthase A [Micrococcus luteus NCTC 2665]
 gi|239839378|gb|ACS31175.1| pseudouridylate synthase I [Micrococcus luteus NCTC 2665]
          Length = 297

 Score =  219 bits (559), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 76/261 (29%), Positives = 113/261 (43%), Gaps = 16/261 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW RQ    S+QG++E  +  +    V    AGRTD+GVHA  QV
Sbjct: 19  VRVRLDLAYDGGAFHGWARQPGLDSVQGALEDGLERILRRPVRTVVAGRTDAGVHARGQV 78

Query: 62  AHFDL------------VREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAI 108
            H DL                    L + L   L      + +         F ARFSA+
Sbjct: 79  VHLDLAETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVVVHGARRAPAGFDARFSAL 138

Query: 109 RRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R Y YRI     A     +G       +LD   M + A  ++G HDF +F       ++
Sbjct: 139 WREYEYRIDDVPAARDPRTRGFTHWHGAALDDRLMALEADAVLGLHDFLSFCRPRA-GAT 197

Query: 168 PIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            IR + H +V    + ++ +R+ A +F H  +R+ VG+L  VG+G      L   +    
Sbjct: 198 TIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAMVGALLQVGEGVREPGWLAHRVARPA 257

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R     LAPP GL   +V Y 
Sbjct: 258 RDSEVRLAPPGGLTLLAVGYP 278


>gi|218135248|ref|ZP_03464052.1| hypothetical protein BACPEC_03153 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990633|gb|EEC56644.1| hypothetical protein BACPEC_03153 [Bacteroides pectinophilus ATCC
           43243]
          Length = 196

 Score =  219 bits (559), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 64/178 (35%), Positives = 94/178 (52%), Gaps = 2/178 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q N  +I+G +  A+  + GE + V GA RTD+GVHAL  
Sbjct: 1   MRRIKLIVAYDGTKYSGWQVQNNADTIEGRLNAALSSICGENIRVIGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +A FD            ALNA L   + I +     V   +H R  +  ++Y Y I+ R 
Sbjct: 61  IAVFDTESRIPAEKFAYALNARL--PEDIVVQKSCEVPPDYHPRHCSTIKTYEYHILNRT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
             L   +   +    +LD E M  AAQ+L+G HDF +F S++ QA + +RTI   +V 
Sbjct: 119 FRLPQMRNNTFFCHYALDLETMNEAAQYLLGEHDFKSFCSVNTQAETTVRTIYSIEVT 176


>gi|283457578|ref|YP_003362161.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
 gi|283133576|dbj|BAI64341.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
          Length = 348

 Score =  219 bits (559), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 84/279 (30%), Positives = 121/279 (43%), Gaps = 35/279 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +   Y+GS + GW  Q N  ++QG IE A+ L+      V  AGRTD+GVHA  Q  
Sbjct: 47  RVRIDCAYDGSLFSGWAAQPNLVTVQGVIENALELILRAPHRVVVAGRTDAGVHAEAQTL 106

Query: 63  HF------------DLVREWVPVILCKAL-------------------NAYLKISDTISI 91
           H                 +     L + L                   N    +   I I
Sbjct: 107 HCDLSDEDWTRLQGRTGEDDPTAALGRRLTGALQRCLYDAEEQLNLPKNVRGILQGAIQI 166

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAP--LALEKGRAWLIPKSLDCENMRIAAQHL 149
             ++ V   F ARFSA  R Y+YRI    A     L +   W +P+ LDC ++  +AQ L
Sbjct: 167 HRVAEVPFDFDARFSATGRRYVYRIADGAADGLNPLHRTYTWAVPEHLDCADLNESAQQL 226

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLV 208
           +G  DF +F     + ++ IR +         + LIE+ VVA +F H  +RS VG+L L 
Sbjct: 227 LGLRDFLSFCKPR-EGATTIRELRELSFTRTESALIEVCVVADAFCHHMVRSLVGALVLY 285

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G GK  +  L + ++   R+    LAPP  L    + Y 
Sbjct: 286 GTGKRDAAWLRERIENPGREASLTLAPPHALALAEIYYP 324


>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 =  219 bits (559), Expect = 2e-55,   Method: Composition-based stats.
 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|294660547|ref|NP_853358.2| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str.
           R(low)]
 gi|298286877|sp|Q7NAQ9|TRUA_MYCGA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|284812210|gb|AAP56926.2| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str.
           R(low)]
 gi|284930851|gb|ADC30790.1| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str.
           R(high)]
          Length = 263

 Score =  219 bits (559), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 112/245 (45%), Gaps = 5/245 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              + I Y+G+ + G+  Q +  ++Q  ++ A+  +    + V+ +GRTD GVHA+ Q  
Sbjct: 24  NVLINISYHGTKFHGYAVQNDYETVQSKLQDALAWIYESKIYVNASGRTDKGVHAINQYI 83

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F +        L + LN Y +  +   I  +  VD+ FHARFSA  ++YLY I    A 
Sbjct: 84  SFYIDDRISLEKLREILNRYGQ--NKWYIKWIKEVDRNFHARFSAKAKTYLYLI-DYCAN 140

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L    AW++   LD   +  A   L G H+F +F +        +RTI   D+    N
Sbjct: 141 NPLFYDHAWIVNFQLDFNLIEKAIPILEGTHNFWSFSTADKDKG--LRTIHKIDLKQEDN 198

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + I +    FL + +R  VG+L  +G  K+    L+  L    +      AP  GLY  
Sbjct: 199 KVYIYITGDGFLRSMVRMIVGALYNIGIKKYDLNHLKWLLDNPKKGRAITKAPASGLYLY 258

Query: 243 SVEYS 247
            V Y 
Sbjct: 259 EVYYE 263


>gi|288919692|ref|ZP_06414019.1| tRNA pseudouridine synthase A [Frankia sp. EUN1f]
 gi|288348881|gb|EFC83131.1| tRNA pseudouridine synthase A [Frankia sp. EUN1f]
          Length = 275

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 113/241 (46%), Gaps = 5/241 (2%)

Query: 9   EYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVAHFDLV 67
            Y+G+ + GW RQ    ++QG +E A+  V     V +  AGRTDSGVHA+ QVAH DL 
Sbjct: 15  AYDGTPFAGWARQPGQRTVQGDVEDALMRVARLPAVRLTVAGRTDSGVHAIGQVAHVDLP 74

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALE 126
                  L + LN  L     + +  L+     F ARFSA+ R Y+YRI         L 
Sbjct: 75  TGTPVGGLARRLNGVL--DRAVRVKGLAPAPAGFDARFSALSRRYVYRITDAPFGAEPLR 132

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +      P+ LD   M  AA  L+G HDF  F     + ++ +RT+   DV+    +I  
Sbjct: 133 RFDTLASPRPLDVPAMAEAALLLLGEHDFAAFCRRR-EGATTVRTLLRLDVSRVEGVILA 191

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            V A +F H+ +R+ VG+L  VG+G+         L    R     + P  GL    V Y
Sbjct: 192 DVEADAFCHSMVRALVGALVAVGEGRRRPEWAAAVLGRGVRDSGVTVLPAHGLTLVEVRY 251

Query: 247 S 247
            
Sbjct: 252 P 252


>gi|325964130|ref|YP_004242036.1| pseudouridylate synthase I [Arthrobacter phenanthrenivorans Sphe3]
 gi|323470217|gb|ADX73902.1| pseudouridylate synthase I [Arthrobacter phenanthrenivorans Sphe3]
          Length = 296

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 74/263 (28%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G  + GW  Q    ++QG +E+A+ L+    V V  AGRTD+GVHA  QV 
Sbjct: 18  RVRLDLSYDGGPFSGWALQPGLRTVQGVLEEALHLLVRRPVRVTVAGRTDAGVHARGQVV 77

Query: 63  HFD-LVREW----------VPVILCKALNAYL-----KISDTISILNLSIVDKQFHARFS 106
           H D    EW            V + + +   L      ++  + +  + +    F ARFS
Sbjct: 78  HLDLTEAEWLGLPRGHELDPAVAMLRRIRGALSRILGDLTGAVEVHRIILAPPGFDARFS 137

Query: 107 AIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R Y YRI    A    L +         LD + +   A  L+G  +F +F     + 
Sbjct: 138 ALWRRYSYRIADGPALWDPLGRYSTLWHKNPLDVDLLNEGASKLLGLQNFLSFCKPR-EG 196

Query: 166 SSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           ++ IR +  F+     + + +  V A +F H  +R+ +GS   VG+G      L + L A
Sbjct: 197 ATTIRELQRFEFTRAEDGVIVATVQADAFCHNMVRALIGSALYVGEGVEEPGWLYERLLA 256

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           Q R     LA P  L  + V Y 
Sbjct: 257 QKRDAKSVLAAPHPLVLEEVAYP 279


>gi|311258299|ref|XP_003127542.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Sus scrofa]
          Length = 306

 Score =  219 bits (558), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 129/273 (47%), Gaps = 30/273 (10%)

Query: 3   RYCMIIEYNGSGYFGWQ--RQK-NGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G    R   +   +Q  +E+A   +     V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYLGTDFNGVAAVRGPQHAVGVQNYLEEAAERLNSVVPVKFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR++A  R+YL
Sbjct: 73  SNAAHLDIQRRSGQPPFSPEVLTEALNTHLRHP-AIRVLQAFRVPSHFHARYAATSRTYL 131

Query: 114 YRIITRQAPL----ALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T           E+ R W +    LD   M+ AAQHL+G HDF+ F+S    A+SP
Sbjct: 132 YRLATGCPRPDHLSVFERNRCWPLRADCLDVAAMQEAAQHLLGTHDFSAFQSTGSPATSP 191

Query: 169 IRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V+                    +   ++SFL+ Q+R     L  VG G  T 
Sbjct: 192 VRTLRRASVSPEPSSPLVLPGESRGLRFWSLEFESQSFLYRQVRRMTAVLVAVGLGALTP 251

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             ++  L+++D   +    +AP  GL+  SV Y
Sbjct: 252 AQVKMILESRDPLGRHQSRVAPAHGLFLKSVLY 284


>gi|194334164|ref|YP_002016024.1| tRNA pseudouridine synthase A [Prosthecochloris aestuarii DSM 271]
 gi|194311982|gb|ACF46377.1| tRNA pseudouridine synthase A [Prosthecochloris aestuarii DSM 271]
          Length = 237

 Score =  219 bits (558), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 117/242 (48%), Gaps = 10/242 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           MIIEY+G+ + GWQRQ    S++QG IE  +  +  E V + GAGRTD GVHA+ Q A F
Sbjct: 1   MIIEYDGTDFAGWQRQDGAVSTVQGEIEAVLRRILQEAVSITGAGRTDKGVHAMGQAASF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     LC +LN+ L    +I I++L  VD  FHAR+SA+ R Y Y +  RQ   A
Sbjct: 61  MTGSSMEAGRLCHSLNSLL--PSSIRIMSLIDVDGDFHARYSALSRQYRYML--RQRESA 116

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           + +  +     S D + +   A  L+GRHDF  F        +   T+           +
Sbjct: 117 IFRRFSGYDRASHDLDQLNSRASVLLGRHDFKAFSKSGSDTRTTCCTVSEAQWFREKEFL 176

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
             ++ A  FL + +R  V +       +++  ++  AL ++   +    A P GL+   +
Sbjct: 177 VFQISANRFLRSMVRYLVSATL-----RFSGEEISYALVSRQPIKGLLPADPAGLFLWEI 231

Query: 245 EY 246
            Y
Sbjct: 232 GY 233


>gi|257126804|ref|YP_003164918.1| tRNA pseudouridine synthase A [Leptotrichia buccalis C-1013-b]
 gi|257050743|gb|ACV39927.1| tRNA pseudouridine synthase A [Leptotrichia buccalis C-1013-b]
          Length = 251

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 119/250 (47%), Gaps = 6/250 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               ++ +Y+GS + G+QRQ    ++QG IEK I     + + +  +GRTD GVHA+ QV
Sbjct: 4   RNVKIVYQYDGSKFCGFQRQMGIKTVQGEIEKVISKTFFQNINMISSGRTDKGVHAIEQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           ++F + +      + + LN  LK    I IL++  +D++F++RF A  R+YLY +     
Sbjct: 64  SNFMIDQNIPLNAIKRQLNKRLK--GEIKILDIEEMDEKFNSRFDAQNRTYLYIMKVEDE 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E      I + +D +  +      +G+HDF++F        +P+R I   +     
Sbjct: 122 ITPFETNYITGIKEMIDIDKFQKIMLEFIGKHDFSSFMKKDKAYRNPVREIFFINCYYDK 181

Query: 182 N----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N     I I +    FL T +R  +GS   V  GK     ++K L+  D      LA  E
Sbjct: 182 NGKEKQINIEICGNGFLKTMVRIMIGSALAVYFGKEEKNYIKKKLENPDADGKKILAGSE 241

Query: 238 GLYFDSVEYS 247
           GLY   V Y 
Sbjct: 242 GLYLYKVSYE 251


>gi|21227597|ref|NP_633519.1| tRNA pseudouridine synthase A [Methanosarcina mazei Go1]
 gi|34395892|sp|Q8PWT1|TRUA_METMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|20905982|gb|AAM31191.1| tRNA pseudouridine synthase A [Methanosarcina mazei Go1]
          Length = 269

 Score =  218 bits (557), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 71/249 (28%), Positives = 114/249 (45%), Gaps = 25/249 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R  + + Y G+ + G Q Q +  +++  + KA+  +    + +      AGRTD+GVHA
Sbjct: 1   MRVALKLAYIGTEFHGSQIQPSVETVEKELFKALRNLRIIESPKSANYICAGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  FD  R    + + + +N+ L    TI +   + V   F AR  A+ R Y Y I 
Sbjct: 61  LGQVIAFDTDR--PNLAIPRIINSGL--PPTIWVWAHAEVPYDFDARRHAVSRHYRYVIS 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                            +  D   MR A++ L+G HDF  F   + +  S +RT++  +V
Sbjct: 117 ----------------GEGYDISKMREASKLLLGTHDFENFSRSNGE-KSTVRTLERINV 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G++ +I VV  SFL   +R  V +L ++G G   +  L + L     +E    AP  
Sbjct: 160 RVDGDITKIDVVGNSFLWNMVRKIVTALSMIGKGVRDNDWLIQMLNPDIYEEGIEPAPAY 219

Query: 238 GLYFDSVEY 246
           GL    V Y
Sbjct: 220 GLTLMGVNY 228


>gi|269837096|ref|YP_003319324.1| tRNA pseudouridine synthase A [Sphaerobacter thermophilus DSM
           20745]
 gi|269786359|gb|ACZ38502.1| tRNA pseudouridine synthase A [Sphaerobacter thermophilus DSM
           20745]
          Length = 271

 Score =  218 bits (557), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 84/258 (32%), Positives = 116/258 (44%), Gaps = 17/258 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + + Y+GS +FG QRQ    ++QG++E A   + GE   V  AGRTD GVHA+ QVA 
Sbjct: 10  FRVDLGYDGSAFFGSQRQPGVRTVQGALESAAERLAGEPTRVALAGRTDRGVHAVGQVAS 69

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
             +        L +AL A     D + +     VD++FHARFSA  R Y Y +     P 
Sbjct: 70  LRIRWARSADELARALMAL--TPDDLVVYGAREVDERFHARFSARWREYRYFVWEGPVP- 126

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS----SPIRTIDHFDVN- 178
            L +GR W++   L+   M  AA   +GR DF                  RT+       
Sbjct: 127 TLMRGRVWVVRTPLNLAAMNAAADAFIGRRDFAAVAGAGVGVPWSGIDTTRTVSLARWRI 186

Query: 179 ---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                      G L+E R+ A  FL   +R+ VGSL  VG G       E+ L  +DR+ 
Sbjct: 187 VDQPFERHDRSGRLLEFRIRADGFLPHMVRNIVGSLVAVGRGDRPIGWTEELLAGRDRRR 246

Query: 230 CGPLAPPEGLYFDSVEYS 247
               AP +GL    V Y 
Sbjct: 247 GEAPAPAQGLVLWRVAYD 264


>gi|197294307|ref|YP_001798848.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma australiense]
 gi|171853634|emb|CAM11505.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma australiense]
          Length = 245

 Score =  218 bits (556), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 105/243 (43%), Gaps = 5/243 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +I+ Y+G+ Y G+Q+Q    +IQ ++E A+  +T   +    A RTD GVHA  Q  H
Sbjct: 8   YKLILSYDGTCYCGYQKQPQTKTIQQTLENALKSMTKRQINTFAASRTDKGVHAQEQTIH 67

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              LN  L     I I  +      FHAR+ A  + Y Y I  ++   
Sbjct: 68  FQTAFAIELKRFKNTLNRIL--PPDIRIKKIEKATADFHARYWAKSKIYHY-IFAKKPLN 124

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A        +  +LD   ++ A   ++G+++F +F +   +  +  +T+ +  V      
Sbjct: 125 AFNYHFQVFVA-NLDFAKIKSAMNLIIGKYNFASFTNDKKE-KNFNKTVLNAFVKETSQN 182

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             +   A  FL   +R  VG L  +G  K +    +  L     ++   LAP +GL+   
Sbjct: 183 YILIFHADGFLKYMVRFLVGGLIEIGKNKMSLELFKAMLTNTTNQKVSLLAPAKGLFLKK 242

Query: 244 VEY 246
           + Y
Sbjct: 243 IFY 245


>gi|73668859|ref|YP_304874.1| tRNA pseudouridine synthase A [Methanosarcina barkeri str. Fusaro]
 gi|121729516|sp|Q46CU8|TRUA_METBF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|72396021|gb|AAZ70294.1| pseudouridylate synthase [Methanosarcina barkeri str. Fusaro]
          Length = 269

 Score =  218 bits (556), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 116/250 (46%), Gaps = 25/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R  + + Y G+ + G Q Q N  +++G + KA+  +    + +      AGRTD+GVHA
Sbjct: 1   MRVALKLAYIGTEFHGSQIQPNVETVEGELFKALRNLGIIESPKSANYTCAGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  FD  +  + + + + +N+ L     I +   + V   F AR  A+ R Y Y + 
Sbjct: 61  LEQVVAFDTDK--LNLAIPRVINSELT--PGIWVWAHAEVPLSFDARRDAVSRHYRYVMS 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                            K  D   +R A++ L+G HDF  F   + +  S +RTI+  D 
Sbjct: 117 ----------------GKEYDISKIREASKFLLGTHDFENFSRTNGE-KSTVRTIERIDA 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G LI+I VV  SFL   +R  V +L ++G G   +  L + L  +  +E    AP  
Sbjct: 160 RIDGELIKIDVVGNSFLWNMVRKIVTALSMIGKGVRDTDWLLQMLNPEIYEEGIESAPAY 219

Query: 238 GLYFDSVEYS 247
           GL    V Y+
Sbjct: 220 GLTLLKVNYN 229


>gi|284931225|gb|ADC31163.1| tRNA pseudouridine synthase A [Mycoplasma gallisepticum str. F]
          Length = 263

 Score =  218 bits (556), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 70/245 (28%), Positives = 113/245 (46%), Gaps = 5/245 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
              + I Y+G+ + G+  Q +  ++Q  ++ A+  +    + V+ +GRTD GVHA+ Q  
Sbjct: 24  NVLINISYHGTKFHGYAVQNDYETVQSKLQDALAWIYESKIYVNASGRTDKGVHAINQYI 83

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            F +        L + LN Y +  +   I  +  VD+ FHARFSA  ++YLY I    A 
Sbjct: 84  SFYIDDRISLEKLREILNRYGQ--NKWYIKWIKEVDRNFHARFSAKAKTYLYLI-DYCAN 140

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L    AW++   LD   +  A   L G H+F +F +        +RTI+  ++    N
Sbjct: 141 NPLFYDHAWIVNFQLDFNLIEKAIPILEGTHNFWSFSTADKDKG--LRTINKINLKQEDN 198

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + I +    FL + +R  VG+L  +G  K+    L+  L    +      AP  GLY  
Sbjct: 199 KVYIYITGDGFLRSMVRMIVGALYNIGIKKYDLNHLKWLLDNPKKGRAITKAPASGLYLY 258

Query: 243 SVEYS 247
            V Y 
Sbjct: 259 EVYYE 263


>gi|28493493|ref|NP_787654.1| tRNA pseudouridine synthase A [Tropheryma whipplei str. Twist]
 gi|28476535|gb|AAO44623.1| pseudouridylate synthase I [Tropheryma whipplei str. Twist]
          Length = 315

 Score =  218 bits (556), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 119/248 (47%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ + GW  Q    ++ G I  A+ L+  E   +  A RTD+GVHAL+QV
Sbjct: 52  TRYRLDVAYDGANFCGWAPQPGLRTVGGLILDALRLICSEPPDIVVAARTDAGVHALQQV 111

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            H DL+    PV L   L + LK    + IL+       FHARFSAI R Y+YR+I ++ 
Sbjct: 112 CHVDLISSPDPVWLLHRLRSLLKSETDLHILSAVKAPVNFHARFSAIGRRYVYRVIDKRS 171

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +     +   + +   L    MR AA  L+G  DF  F        S +R +  F+V   
Sbjct: 172 SWYPQNRYFVYRVNAFLQDYRMRRAASGLIGLKDFGAFCKPRRMG-STVRHLRQFEVIRQ 230

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +  I   + + +F H+ +R+ VGSL  VG G  T  DL    +   R    P  PP  L
Sbjct: 231 PDGQIHFFLESDAFCHSMVRNLVGSLIEVGRGALTLQDLFCYTKIAKRTPKIPTLPPHAL 290

Query: 240 YFDSVEYS 247
               ++Y 
Sbjct: 291 TLIGIDYP 298


>gi|42559799|sp|Q83G11|TRUA_TROWT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 267

 Score =  218 bits (556), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 119/248 (47%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ + GW  Q    ++ G I  A+ L+  E   +  A RTD+GVHAL+QV
Sbjct: 4   TRYRLDVAYDGANFCGWAPQPGLRTVGGLILDALRLICSEPPDIVVAARTDAGVHALQQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            H DL+    PV L   L + LK    + IL+       FHARFSAI R Y+YR+I ++ 
Sbjct: 64  CHVDLISSPDPVWLLHRLRSLLKSETDLHILSAVKAPVNFHARFSAIGRRYVYRVIDKRS 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +     +   + +   L    MR AA  L+G  DF  F        S +R +  F+V   
Sbjct: 124 SWYPQNRYFVYRVNAFLQDYRMRRAASGLIGLKDFGAFCKPRRMG-STVRHLRQFEVIRQ 182

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +  I   + + +F H+ +R+ VGSL  VG G  T  DL    +   R    P  PP  L
Sbjct: 183 PDGQIHFFLESDAFCHSMVRNLVGSLIEVGRGALTLQDLFCYTKIAKRTPKIPTLPPHAL 242

Query: 240 YFDSVEYS 247
               ++Y 
Sbjct: 243 TLIGIDYP 250


>gi|284161452|ref|YP_003400075.1| tRNA pseudouridine synthase A [Archaeoglobus profundus DSM 5631]
 gi|284011449|gb|ADB57402.1| tRNA pseudouridine synthase A [Archaeoglobus profundus DSM 5631]
          Length = 262

 Score =  218 bits (555), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 109/248 (43%), Gaps = 25/248 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALR 59
           +R    + Y G+ + G+Q Q N  ++ G + KA     +  +      AGRTD+GVHA  
Sbjct: 1   MRIAYKLAYVGTNFHGFQYQPNVRTVAGELFKAFRALGIDPKKAKFRCAGRTDAGVHAFG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV   ++ +   P    +  NA+L   + ++    + VD++F+ R  A  R+Y+Y +   
Sbjct: 61  QVIAINVEKPIFP----RMFNAHL--PEDVTFWAWTEVDEKFNPRH-AKSRTYVYVMPAE 113

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                             D   MR A++ L+G HDF+ F     +    IRTI + ++  
Sbjct: 114 GY----------------DISAMRKASKLLLGTHDFSNFTKKFGERRRCIRTIYNVELRL 157

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + + +V  +F    +R  V +L+ VG G  +    E  L  +  +E    AP  GL
Sbjct: 158 DDGFVVLEIVGNAFTWNMVRCIVSALREVGSGHRSVEWFEDMLNPERHRERIEPAPAYGL 217

Query: 240 YFDSVEYS 247
               VEY 
Sbjct: 218 ILKDVEYE 225


>gi|116671484|ref|YP_832417.1| tRNA pseudouridine synthase A [Arthrobacter sp. FB24]
 gi|116611593|gb|ABK04317.1| tRNA pseudouridine synthase A [Arthrobacter sp. FB24]
          Length = 280

 Score =  218 bits (555), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 117/264 (44%), Gaps = 19/264 (7%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G  + GW  Q    ++QG +E A+ L+    V V  AGRTD+GVHA  QV
Sbjct: 1   MRIRLDLAYDGGPFSGWAVQPGLRTVQGVLESALALLIRRKVRVTVAGRTDAGVHARGQV 60

Query: 62  AHFD-LVREW----------VPVILCKALNAYL-----KISDTISILNLSIVDKQFHARF 105
            H D    EW            V L + L   L      ++  I + ++++  + F ARF
Sbjct: 61  VHLDLTEEEWQGLNRGVELDPAVALLRRLRGALSRGLGDLTGAIEVHSVTVAPEGFDARF 120

Query: 106 SAIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R Y YRI    A    L +       + LD   +   A  L+G  +F ++     +
Sbjct: 121 SALWRRYSYRIADGPALWDPLGRYSTLWHKEQLDVSLLNEGASKLLGLQNFRSYCKPR-E 179

Query: 165 ASSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            S+ IR +  F+     + + +  V A +F H  +R+ VGS   VG G      L + L 
Sbjct: 180 GSTTIRELQRFEFARGTDGVIVATVQADAFCHNMVRALVGSALYVGSGAEKPGWLYERLL 239

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
            Q R     L+ P  L  + V Y 
Sbjct: 240 EQKRDAKSVLSAPHPLVLEEVAYP 263


>gi|39938715|ref|NP_950481.1| tRNA pseudouridine synthase A [Onion yellows phytoplasma OY-M]
 gi|42559719|sp|P60351|TRUA_ONYPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|39721824|dbj|BAD04314.1| pseudouridylate synthase [Onion yellows phytoplasma OY-M]
          Length = 243

 Score =  218 bits (555), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 104/243 (42%), Gaps = 5/243 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y +I+ Y+G+ Y+G+Q+Q    ++Q + EKA+  +T + +    A RTD GVH+  Q  H
Sbjct: 6   YKLILSYDGTCYYGYQKQPQKITVQQTFEKALKKMTHQNIPTFAASRTDKGVHSQGQTLH 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F       P    K LN  L     I +  ++     FHAR+SA  + Y Y     + PL
Sbjct: 66  FQTTFFLKPTHFQKTLNYLL--PPDIRVRQMNFATPNFHARYSAKSKIYQYVFS--KKPL 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                   +    L  + +  A + + G H+F  F S   Q  +  +TI    +    + 
Sbjct: 122 NAFNHHFQIFADKLYFDKITKALKFIEGTHNFFAFTS-ETQPKNFSKTIFQAFLKETSHK 180

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             +      FL   IR  VGSL  +G  K +    +  L     K+   LAP + L    
Sbjct: 181 YILVFHGNGFLKYMIRFLVGSLIEIGKNKLSLEQFQAMLLGNTTKKATLLAPSKALVLKK 240

Query: 244 VEY 246
           + Y
Sbjct: 241 IFY 243


>gi|28572394|ref|NP_789174.1| tRNA pseudouridine synthase A [Tropheryma whipplei TW08/27]
 gi|42559794|sp|Q820Z2|TRUA_TROW8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|28410525|emb|CAD66911.1| tRNA pseudouridine synthase A [Tropheryma whipplei TW08/27]
          Length = 267

 Score =  218 bits (555), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 119/248 (47%), Gaps = 3/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + + Y+G+ + GW  Q    ++ G I  A+ L+  E   +  A RTD+GVHAL+QV
Sbjct: 4   TRYRLDVAYDGANFCGWAPQPGLRTVGGLILDALRLICSEPPDIVIAARTDAGVHALQQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            H DL+    PV L   L + LK    + IL+       FHARFSAI R Y+YR+I ++ 
Sbjct: 64  CHVDLISSPDPVWLLHRLRSLLKSETDLHILSAVKAPVNFHARFSAIGRRYVYRVIDKRS 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +     +   + +   L    MR AA  L+G  DF  F        S +R +  F+V   
Sbjct: 124 SWYPQNRYFVYRVNAFLQDYRMRRAASGLIGLKDFGAFCKPRRMG-STVRHLRQFEVIRQ 182

Query: 181 GN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            +  I   + + +F H+ +R+ VGSL  VG G  T  DL    +   R    P  PP  L
Sbjct: 183 PDGQIHFFLESDAFCHSMVRNLVGSLIEVGRGALTLQDLFCYTKIAKRTPKIPTLPPHAL 242

Query: 240 YFDSVEYS 247
               ++Y 
Sbjct: 243 TLIGIDYP 250


>gi|255326873|ref|ZP_05367949.1| tRNA pseudouridine synthase A [Rothia mucilaginosa ATCC 25296]
 gi|255296090|gb|EET75431.1| tRNA pseudouridine synthase A [Rothia mucilaginosa ATCC 25296]
          Length = 321

 Score =  217 bits (554), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 86/279 (30%), Positives = 123/279 (44%), Gaps = 35/279 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +   Y+GS + GW  Q N  ++QG+IE A+ L+      V  AGRTD+GVHA  Q  
Sbjct: 20  RVRIDCAYDGSLFSGWAAQPNLVTVQGAIENALELILRAPHRVVVAGRTDAGVHAEAQTL 79

Query: 63  HF------------DLVREWVPVILCKAL-------------------NAYLKISDTISI 91
           H                 +     L + L                   N    +   I I
Sbjct: 80  HCDLNDEDWTRLQGRTGEDDPTAALGRRLTGALQRCLYDAEEQLNLPKNVRGILQGAIQI 139

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAP--LALEKGRAWLIPKSLDCENMRIAAQHL 149
             +S V  +F ARFSA  R Y+YRI    A     L +   W +P+ LDC ++  +AQ L
Sbjct: 140 HRVSEVSFEFDARFSATGRRYVYRIADGAANGLNPLHRTYTWAVPEHLDCADLNQSAQQL 199

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLV 208
           +G  DF +F     + ++ IR +           LIE+RVVA +F H  +RS VG+L L 
Sbjct: 200 LGLRDFLSFCKPR-EGATTIRELRELSFTRTESGLIEVRVVADAFCHHMVRSLVGALVLY 258

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G GK  +  L + ++   R+    LAPP  L    + Y 
Sbjct: 259 GTGKRDAAWLRERIENPGREASLTLAPPHALALAEIYYP 297


>gi|76637689|ref|XP_875031.1| PREDICTED: pseudouridylate synthase-like 1 [Bos taurus]
 gi|297484219|ref|XP_002694181.1| PREDICTED: pseudouridylate synthase-like 1 [Bos taurus]
 gi|296479092|gb|DAA21207.1| pseudouridylate synthase-like 1 [Bos taurus]
          Length = 303

 Score =  217 bits (554), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 88/277 (31%), Positives = 128/277 (46%), Gaps = 36/277 (12%)

Query: 3   RYCMIIEYNGSGY------FGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGV 55
           RY +  +Y G+ +       G QR      +Q  +E+A   +     V    + RTD+GV
Sbjct: 9   RYLVYFQYLGTDFNGVAAVRGVQR---AVGVQNYLEEAAERLNSVMPVKFTISSRTDAGV 65

Query: 56  HALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           HAL   AH D+ R      + P +L +ALN +LK    I +L    V   FHAR +AI R
Sbjct: 66  HALSNAAHLDIQRRSDLPPFSPEVLTEALNTHLKHP-AIRVLQAFRVPSHFHARHAAISR 124

Query: 111 SYLYRIITRQAPL----ALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           +YLYR+ T           E+ R W +    LD   M+ AAQHL+G HDF+ F+S    A
Sbjct: 125 TYLYRLATGCPRPDRLPVFERNRCWALQADCLDVAAMQEAAQHLLGTHDFSAFQSAGSPA 184

Query: 166 SSPIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           SSP+RT+    V+                    +   ++SFL+ Q+R     L  VG G 
Sbjct: 185 SSPVRTLRRASVSPDPASPFVLPEESRQLQFWSMEFESQSFLYKQVRRMTAVLVAVGLGA 244

Query: 213 WTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEYS 247
                ++  L+++D   K    +AP  GL+  SV Y 
Sbjct: 245 LMPAQVKAILESRDPLGKHQSRVAPAHGLFLKSVLYE 281


>gi|296274435|ref|YP_003657066.1| tRNA pseudouridine synthase A [Arcobacter nitrofigilis DSM 7299]
 gi|296098609|gb|ADG94559.1| tRNA pseudouridine synthase A [Arcobacter nitrofigilis DSM 7299]
          Length = 240

 Score =  217 bits (553), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 114/246 (46%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   M I Y+G  Y G QRQ N  S++  + +  F +      +  +GRTD  VHA  QV
Sbjct: 1   MNVKMTISYDGFSYQGSQRQTNKKSVEDRLIEV-FKILNIEPKITLSGRTDKQVHATGQV 59

Query: 62  AHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +  +   W     L + +N  L    +I I  +  V+ +FHARF A +R Y Y I T++
Sbjct: 60  FNIVIPAYWSNFLKLKQVMNYKL--PSSIRIRKIQKVNDEFHARFHAKKRVYRYVISTKE 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                       + K ++ E ++ A +  +G HDF  F     +  + +R I       +
Sbjct: 118 V-SPFLANYVTFV-KEINEEKIKEAIKLFIGVHDFEYFHKSGSEKDNKVREIFDAKFYKY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +    R  A S+L +QIR  VG L  + +GK +  DL+  L ++++      A P GLY
Sbjct: 176 KDFYIFRFEANSYLRSQIRIMVGFLLKISEGKLSKNDLKAQL-SREKYIYKTPALPNGLY 234

Query: 241 FDSVEY 246
              V+Y
Sbjct: 235 LSQVKY 240


>gi|24212680|sp|Q9X796|TRUA_MYCLE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 286

 Score =  217 bits (553), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 75/259 (28%), Positives = 118/259 (45%), Gaps = 15/259 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I Y+G+ + GW  Q    ++ G +++A   V    V +  AGRTD+GVHA  QV
Sbjct: 11  VRLRLDIAYDGTDFAGWAVQAGQRTVAG-LDEAFTTVFRTPVRLRAAGRTDTGVHATGQV 69

Query: 62  AHFDLV------------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AH D+                 P  L         +   + +L+++     F ARFSA+R
Sbjct: 70  AHVDIPGTALSKANPRSPHTGDPEFLPLLRRLSRLLPVDVRVLDIACAPVGFDARFSALR 129

Query: 110 RSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R Y YR+ T    +   +       P+ LD ++M  A++ L+G  DF  F   H   ++ 
Sbjct: 130 RHYRYRLSTAPYGVQPNQARYVTAWPRELDLDSMSAASRDLLGLRDFAVFCR-HRHGATT 188

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IR +   + +  G LI   + A +F  + +RS +G+L  VGD + T     + L    R 
Sbjct: 189 IRELQRLEWSREGYLITAHITADAFCWSMVRSLIGALLAVGDHRRTIGWCGELLTKASRS 248

Query: 229 ECGPLAPPEGLYFDSVEYS 247
                AP  GL F  V+Y 
Sbjct: 249 SDFTTAPAHGLTFIRVDYP 267


>gi|291457231|ref|ZP_06596621.1| tRNA pseudouridine synthase A [Bifidobacterium breve DSM 20213]
 gi|291381066|gb|EFE88584.1| tRNA pseudouridine synthase A [Bifidobacterium breve DSM 20213]
          Length = 303

 Score =  217 bits (553), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 86/287 (29%), Positives = 132/287 (45%), Gaps = 42/287 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q    ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPELRTVQGTIEDALHKVLRVPVGDEREPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + V L +AL   LK  +   I I  ++I  + F AR
Sbjct: 61  GVHASHQVAHLDVSDETLARCQGHMDVPLTEALARRLKAVLPADIVIHGIAIAPQGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R +      +G    + +SLD + M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLRVDESLDLDAMNAAAAMTIGLHDFGSFATPNP 180

Query: 164 QASSPIRTIDHFDVNSFG----------------------NLIEIRVVARSFLHTQIRSF 201
              + IR +                                L+   +VA +F    +RS 
Sbjct: 181 -GGTTIREVKTAYWRRVPVASLVPDVLAENEAYRTPSLESGLVVFTIVADAFARNMVRSL 239

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VGS   VG G+ T       +    R+   GP+AP +GL  + +EY 
Sbjct: 240 VGSSIKVGSGRKTLEWFADKMANPVREGSSGPIAP-QGLTLEHIEYP 285


>gi|282933805|ref|ZP_06339157.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
 gi|281302070|gb|EFA94320.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
          Length = 223

 Score =  217 bits (553), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 69/211 (32%), Positives = 106/211 (50%), Gaps = 5/211 (2%)

Query: 40  GEIVVVHGAGRTDSGVHALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVD 98
           G+ +VVHG+GRTD+GVHAL QV HFD          +  ALN+ +     I   +  IV+
Sbjct: 2   GQRIVVHGSGRTDAGVHALGQVIHFDFPNDNIPANRMVLALNSMM--PTDIIFKDAEIVN 59

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           + FH ++S   + Y Y +   +     ++      P  L+   M+ AA  L+G HDFT+F
Sbjct: 60  EDFHVQYSTHGKWYRYIVNQDRFVDPFKRFYTGHYPYKLNVSKMQEAALDLLGEHDFTSF 119

Query: 159 RSIHCQASSPIRTIDHFDV--NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
            +   Q    +RTI +  +   S  N I    +   FL+  +R  VG+L  +G+ +    
Sbjct: 120 AASGGQIIDKVRTIYYVKIWQKSEENEIIFDFIGNGFLYNMVRIMVGALLEIGNERRPVH 179

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           DL++ + A+DR+E    AP  GLY   V Y 
Sbjct: 180 DLKRVILAKDRQEVINTAPASGLYLYHVFYE 210


>gi|242398608|ref|YP_002994032.1| tRNA pseudouridine synthase A [Thermococcus sibiricus MM 739]
 gi|259550478|sp|C6A238|TRUA_THESM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|242265001|gb|ACS89683.1| tRNA pseudouridine synthase A [Thermococcus sibiricus MM 739]
          Length = 266

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 120/250 (48%), Gaps = 27/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG----EIVVVHGAGRTDSGVHA 57
           +R  + I Y+G+ ++G+QRQ +  +++G + K +  +      +     GA RTD GV A
Sbjct: 1   MRIALKIAYDGTKFYGFQRQPDLRTVEGELIKVLKKLGIIEDVKEANFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L  V  F+  +  +     + LN +L+    I IL  + V + FH RF A  + Y Y   
Sbjct: 61  LGNVIAFNTAKPELAEA--RILNHHLR---DIWILGKAEVPEDFHPRFWAKNKIYRY--- 112

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +L  + +D   ++  A+  +GRHDF+ F  +  +   P+R I+  DV
Sbjct: 113 -------------YLFDEGIDVIKLKACAEAFLGRHDFSNFARLE-EFRKPVREINRIDV 158

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S G +I + +  +SFL    R  + +LKL G G  +  D+E  L+ +  K+  P APPE
Sbjct: 159 FSRGRIIVVEIEGKSFLWEMTRRIITALKLCGLGVLSIGDVELMLKEKVDKKL-PPAPPE 217

Query: 238 GLYFDSVEYS 247
            L    V Y 
Sbjct: 218 NLVLWEVGYE 227


>gi|20089106|ref|NP_615181.1| tRNA pseudouridine synthase A [Methanosarcina acetivorans C2A]
 gi|30913395|sp|Q8TU65|TRUA_METAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|19913971|gb|AAM03661.1| pseudouridylate synthase [Methanosarcina acetivorans C2A]
          Length = 269

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 71/249 (28%), Positives = 115/249 (46%), Gaps = 25/249 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHA 57
           +R  + + Y G+ + G Q Q N  +++  + KA+  ++     +      AGRTD+GVHA
Sbjct: 1   MRVALKLAYIGTEFHGSQIQPNVETVEKELFKALRNLSIIESPKSADYTCAGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  FD  +    + + + +N+ L     I     + V   F AR SA+ R Y Y + 
Sbjct: 61  LGQVVAFDTEK--PNLAIPRVINSEL--PPAIWAWAHAEVPYYFDARRSAVSRHYHYVMS 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                            +  D   MR A++ L+G HDF  F   + +  S +RT++  +V
Sbjct: 117 ----------------GEDYDISKMREASKLLLGTHDFENFSRSNGE-KSTVRTLERINV 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G + +I VV  SFL   +R  V +L ++G+G   +  L + L  +  +E    APP 
Sbjct: 160 RVDGEITKIDVVGNSFLWNMVRKIVTALSMIGNGVRDNDWLLQMLNPEIYEEGIEPAPPY 219

Query: 238 GLYFDSVEY 246
           GL    V Y
Sbjct: 220 GLTLMGVNY 228


>gi|301167543|emb|CBW27126.1| putative tRNA pseudouridine synthase [Bacteriovorax marinus SJ]
          Length = 267

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/248 (29%), Positives = 117/248 (47%), Gaps = 17/248 (6%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           YNG  YFGWQ+QKN  +IQ +IE A+ ++   E +   G+ RTD+GVH+   V    +  
Sbjct: 11  YNGENYFGWQKQKNFKTIQDTIEDALRVIAPSEKIRTMGSSRTDTGVHSRANVCFIQIQE 70

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
           +  P  L K LN  L   + I I       + F   + A R+ YLY      +    +  
Sbjct: 71  DLEPHELTKKLNQEL--PNDIRITKCERTYRHFKVVYFAKRKQYLYIFKINNS----DHS 124

Query: 129 RAWL-IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE-- 185
             +  I ++LD E M+ AA+  +G HDF  F     +     R I    +    + I   
Sbjct: 125 TFYHSIEENLDIEKMKEAAKVFIGTHDFRNFCHKVSENVDKKREIFECKIIEDQDFISEN 184

Query: 186 -------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                  + +    FL   +R  +GSL  +G GK T + +++AL + + K+ G +AP  G
Sbjct: 185 NCHGSYALVIEGSGFLKQMVRIIMGSLINIGLGKTTLSQIQEALVSTEFKKTGFIAPGGG 244

Query: 239 LYFDSVEY 246
           LY + +E+
Sbjct: 245 LYLNEIEF 252


>gi|325191328|emb|CCA26111.1| tRNA pseudouridine synthase A putative [Albugo laibachii Nc14]
          Length = 289

 Score =  216 bits (551), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 80/265 (30%), Positives = 124/265 (46%), Gaps = 23/265 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
              II Y+G+ Y G+Q Q  +   ++Q +IE AIF  TGE V +    RTD GVHA  QV
Sbjct: 27  VKCIIAYDGTDYNGFQAQGKEGTITLQEAIEDAIFRTTGEAVRIRACSRTDRGVHARGQV 86

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVD---KQFHARFSAIRRSYLYRIIT 118
             FD +       L  ALN+ L   D I+ L +  +     +   R  +I + Y YRI++
Sbjct: 87  IVFDTLCTADAEKLRDALNSRL--DDAIACLQVVPLSISSDRMDPRKLSIGKEYEYRIVS 144

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG--RHDFTTFRSIHCQAS---SPIRTID 173
                  E+ + W + + +D ++M+ AAQ L    + D+ +F      A        T+ 
Sbjct: 145 GGVRPVHERFQVWFVRQLVDIKSMKQAAQLLFHREKRDYASFSGERDDAKEGTDTFCTLH 204

Query: 174 HFDVN-----------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             D+               + I IR+    FL+  +R+ VG+L  VG GK  +  +   L
Sbjct: 205 ALDITMDQPRQEVMNHGQQSCIRIRMSGDRFLYKMVRNIVGTLVDVGLGKIDALSIPDIL 264

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
            A+DR++ G  AP +GL    V +S
Sbjct: 265 LARDRRQAGQGAPAKGLTLVRVYFS 289


>gi|11499319|ref|NP_070558.1| tRNA pseudouridine synthase A [Archaeoglobus fulgidus DSM 4304]
 gi|3915163|sp|O28544|TRUA_ARCFU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2648818|gb|AAB89516.1| pseudouridylate synthase I (truA) # [Archaeoglobus fulgidus DSM
           4304]
          Length = 265

 Score =  216 bits (551), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 100/247 (40%), Gaps = 23/247 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+++   I Y G  + G Q Q +  +++G +  A+  +  E   +  AGRTD+GVHA  Q
Sbjct: 1   MMKFAFKIAYFGDNFHGSQFQPDQRTVEGEVINALRRLGVENPRLRSAGRTDAGVHAYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F    +  P    + LNA L   + I+    + V + F  R  A  R Y Y +    
Sbjct: 61  VISFYSEDKIFP----RMLNAEL--PEDITAWAWAKVSEDFDPR-RAKSRVYTYVMYGSD 113

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                            D   MR A + L+G HDF+ F     +  S +R I   D+ + 
Sbjct: 114 Y----------------DISAMRKAVKELIGVHDFSNFTKKFGEGESCVREIISADIRAD 157

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I   +   +F    +R  V ++  +G    +       L  +  KE    APP GL 
Sbjct: 158 REFIIFEIEGNAFTWNMVRCIVTAIMEIGKQHRSIEWFRDLLNPEKHKERVEPAPPYGLI 217

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 218 LKDVKYD 224


>gi|225010595|ref|ZP_03701066.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
 gi|225005424|gb|EEG43375.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
          Length = 218

 Score =  216 bits (551), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 71/216 (32%), Positives = 110/216 (50%), Gaps = 4/216 (1%)

Query: 32  EKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           E+A  L+    + + GAGRTD+GVHA + VAHFD    +   I+   LNA+L     ISI
Sbjct: 2   EQAFSLLLATPIELMGAGRTDAGVHAKKMVAHFDTELGFDKQIIKDRLNAFLAA--DISI 59

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
             +  V ++ HARF+A  R+Y Y ++ ++     +   A  + + LD ++M  AAQ L+G
Sbjct: 60  DQILAVTQETHARFTATSRTYEYIVVNQK--DPFQHHGAHYVFQPLDIQSMNKAAQILLG 117

Query: 152 RHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
             DF  F   +    + I  I H    +    +   + A  FL   +R+ VG+L  +G G
Sbjct: 118 EKDFECFSKSNSDVHTFICDITHAKWVATKGQLVFTITANRFLRNMVRAIVGTLLEIGTG 177

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           K   TD+   L+ + R + GP  P +GLY   + Y 
Sbjct: 178 KRPVTDIPLLLETKSRSKAGPSVPAKGLYLTQINYP 213


>gi|281202734|gb|EFA76936.1| hypothetical protein PPL_09688 [Polysphondylium pallidum PN500]
          Length = 275

 Score =  216 bits (551), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 90/276 (32%), Positives = 133/276 (48%), Gaps = 47/276 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +                    +Q  +E+++ +   + V + G+ RTD+GV+AL Q
Sbjct: 1   MTRYRIK-----------------KPVQQVLEESLEVFIRKKVRLVGSSRTDTGVNALHQ 43

Query: 61  VAHFDLV----------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           VAHFD+               P ++  ALN  ++    + +++  IVD  FH+RFSA  R
Sbjct: 44  VAHFDVDTRISKTGEEIDMMPPEVITMALNQNVQGYP-VRVISTEIVDDSFHSRFSAKSR 102

Query: 111 SYLYRIITRQAPL--ALE-KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           +YLYR++          E K R W +   LD   M+ AA  L GRH+F +FRS  CQA +
Sbjct: 103 TYLYRMLGGMHRNQAPFELKDRVWAVTNQLDVPKMQEAATLLCGRHNFNSFRSSKCQADN 162

Query: 168 PIRTIDHFDVNS----------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           P+RTI  F V                     LI I V AR+FLH Q+R  V +L+ VG  
Sbjct: 163 PVRTISSFQVFDLPNPDIWQYNSAPLGVNPQLIGIEVKARAFLHNQVRIMVSTLERVGSH 222

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + +   L++ + A+DR++  P APP  L    V Y 
Sbjct: 223 QMSLDQLQELIDAKDRQKAPPTAPPYPLTLTKVSYE 258


>gi|330470142|ref|YP_004407885.1| tRNA-pseudouridine synthase i [Verrucosispora maris AB-18-032]
 gi|328813113|gb|AEB47285.1| tRNA-pseudouridine synthase i [Verrucosispora maris AB-18-032]
          Length = 276

 Score =  216 bits (550), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 110/251 (43%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW  Q +  ++ G + + + LV G      +  AGRTD+GVHA  
Sbjct: 5   VRLRLDVAYDGTDFSGWAAQPDRRTVAGVLVQTLDLVLGAGTATGLTVAGRTDAGVHASG 64

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL    W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHLDLPVEVWREHEGRLLRRLARLLPGDVRVRAMTEVPATFDARFSATFRRYEYRVTD 124

Query: 119 RQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +      P+ LD + +  A+  LVG HDF  +     + ++ +R +   D 
Sbjct: 125 APWGAEPLRRHEVLAWPRPLDTDRLAAASAGLVGEHDFAAYCRRK-ENATTLREVTRLDW 183

Query: 178 NSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               + I    V A +F    +RS VG++ + GDG+         L  ++R     +AP 
Sbjct: 184 RRDPDGILVATVQADAFCQAMVRSLVGAMLVAGDGRRPVEWPAGLLTRRERSSEVTVAPA 243

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 244 HGLTLVAVGYP 254


>gi|256420466|ref|YP_003121119.1| tRNA pseudouridine synthase A [Chitinophaga pinensis DSM 2588]
 gi|256035374|gb|ACU58918.1| tRNA pseudouridine synthase A [Chitinophaga pinensis DSM 2588]
          Length = 250

 Score =  215 bits (549), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 5/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y G+ + G+Q Q N  ++Q  I+ AI  +    +V  G+ RTD+GVHA +  
Sbjct: 1   MRYFIEVAYKGTSFGGFQIQDNVETVQSVIDHAISTLMRGAIVTTGSSRTDAGVHARQNF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+ +   P  L K +NA L     + + N+  V    H+RF+A+ RSY Y +   + 
Sbjct: 61  LHFDMEQPLHPQFLYK-VNAIL--PPDVVMRNIYRVADDAHSRFAALSRSYEYTLYMEK- 116

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                + R +  P +L  E +  AA  L    +F TF   + Q  +    I   +     
Sbjct: 117 -DPFMRDRGYFFPYTLHPELLHEAASVLREYENFMTFSKRNTQVKTYNCNIMSSEWEVGE 175

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  RV A  FL   +R  VG++  VG GK T     +A+++++        PP+GL+ 
Sbjct: 176 DRIVYRVTANRFLRGMVRGMVGTMLRVGRGKLTMDGFREAIESRNCVNADFAVPPQGLFL 235

Query: 242 DSVEYS 247
             V Y 
Sbjct: 236 MKVAYP 241


>gi|23503259|ref|NP_699170.1| tRNA pseudouridine synthase-like 1 [Homo sapiens]
 gi|52783232|sp|Q8N0Z8|PUSL1_HUMAN RecName: Full=tRNA pseudouridine synthase-like 1; AltName:
           Full=tRNA pseudouridylate synthase-like 1; AltName:
           Full=tRNA-uridine isomerase-like 1
 gi|21706547|gb|AAH34304.1| Pseudouridylate synthase-like 1 [Homo sapiens]
 gi|22761287|dbj|BAC11527.1| unnamed protein product [Homo sapiens]
 gi|56204950|emb|CAI23172.1| pseudouridylate synthase-like 1 [Homo sapiens]
 gi|119576649|gb|EAW56245.1| pseudouridylate synthase-like 1 [Homo sapiens]
          Length = 303

 Score =  215 bits (549), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 125/273 (45%), Gaps = 30/273 (10%)

Query: 3   RYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G       +    +Q  +E+A   +   E V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYVGTDFNGVAAVRGTQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR +A  R+YL
Sbjct: 73  SNAAHLDVQRRSGRPPFPPEVLAEALNTHLRHP-AIRVLRAFRVPSDFHARHAATSRTYL 131

Query: 114 YRIITRQAP----LALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T           E+   W +P   LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 132 YRLATGCHRRDELPVFERNLCWTLPADCLDMVAMQEAAQHLLGTHDFSAFQSAGSPVPSP 191

Query: 169 IRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V+                    +   ++SFL+ Q+R     L  VG G    
Sbjct: 192 VRTLRRVSVSPGQASPLVTPEESRKLRFWNLEFESQSFLYRQVRRMTAVLVAVGLGALAP 251

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 252 AQVKTILESQDPLGKHQTRVAPAHGLFLKSVLY 284


>gi|269124177|ref|YP_003306754.1| tRNA pseudouridine synthase A [Streptobacillus moniliformis DSM
           12112]
 gi|268315503|gb|ACZ01877.1| tRNA pseudouridine synthase A [Streptobacillus moniliformis DSM
           12112]
          Length = 244

 Score =  215 bits (549), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 119/246 (48%), Gaps = 3/246 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +I +Y+GS ++G QRQK+  ++QG+IE  +     E V +  +GRTD GVHA  Q
Sbjct: 1   MNNIKIIYQYDGSAFYGSQRQKDKVTVQGTIEDILINSFNEKVNMISSGRTDRGVHAKMQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V++F + ++    I+   +  Y   +  I IL++  VD ++++RF  + R+Y + +  R+
Sbjct: 61  VSNFIINKDIKLDIIKSKIEKY--SNYAIKILSIEKVDIKYNSRFDCMERTYEFILSNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNS 179
                 +     I   +D E +    +  +G+H+F+ F     +A  +PIR I       
Sbjct: 119 NITPFNRKYITSINYEIDVEKLNDILKQFIGKHNFSNFSKKENKANKNPIREIYECYSIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I +   SFL + +R  +G+   +  GK +   +++A    +      +    GL
Sbjct: 179 KDKNIHIYIKGNSFLKSMVRIIIGTTLAIYSGKISKHFIKEAFDNPNPNTKKYILDGNGL 238

Query: 240 YFDSVE 245
           Y   V+
Sbjct: 239 YLYHVK 244


>gi|312150754|gb|ADQ31889.1| pseudouridylate synthase-like 1 [synthetic construct]
          Length = 303

 Score =  215 bits (549), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 125/273 (45%), Gaps = 30/273 (10%)

Query: 3   RYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G       +    +Q  +E+A   +   E V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYVGTDFNGVAAVRGTQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR +A  R+YL
Sbjct: 73  SNAAHLDVQRRSGRPPFPPEVLAEALNTHLRHP-AIRVLRAFRVPSDFHARHAATSRTYL 131

Query: 114 YRIITRQAP----LALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T           E+   W +P   LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 132 YRLATGCHRRDELPVFERNLCWTLPADCLDMVAMQEAAQHLLGTHDFSAFQSAGSPVPSP 191

Query: 169 IRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V+                    +   ++SFL+ Q+R     L  VG G    
Sbjct: 192 VRTLRRVSVSPGQASPLVTPEESRKLRFWNLEFESQSFLYRQVRRMTAVLVAVGLGALAP 251

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 252 AQVKTILESQDPLGKHQTRVAPAHGLFLKSVLY 284


>gi|317483422|ref|ZP_07942412.1| tRNA pseudouridine synthase A [Bifidobacterium sp. 12_1_47BFAA]
 gi|316915108|gb|EFV36540.1| tRNA pseudouridine synthase A [Bifidobacterium sp. 12_1_47BFAA]
          Length = 303

 Score =  215 bits (548), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 131/287 (45%), Gaps = 42/287 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPTDDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R +      +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 180

Query: 164 QASSPIRTIDHFDVNSFG----------------------NLIEIRVVARSFLHTQIRSF 201
              + IR +                                L+   +VA +F    +RS 
Sbjct: 181 -GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSL 239

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VGS   VG G+ +       +    R+   GP+AP +GL  + + Y 
Sbjct: 240 VGSCIKVGSGRKSLEWFADKMAEPVREGSSGPIAP-QGLTLEHIAYP 285


>gi|12045035|ref|NP_072845.1| tRNA pseudouridine synthase A [Mycoplasma genitalium G37]
 gi|255660331|ref|ZP_05405740.1| tRNA pseudouridine synthase A [Mycoplasma genitalium G37]
 gi|1351308|sp|P47428|TRUA_MYCGE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3844778|gb|AAC71401.1| tRNA pseudouridine synthase A [Mycoplasma genitalium G37]
 gi|166078658|gb|ABY79276.1| tRNA pseudouridine synthase A [synthetic Mycoplasma genitalium
           JCVI-1.0]
          Length = 244

 Score =  215 bits (547), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 116/248 (46%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  I+ Y+GS + GW  Q N ++IQG +E++  L+ G  + V G+GRTD GVHA+ Q
Sbjct: 1   MARYLGIVSYDGSYFKGWAIQPNLATIQGLLEQSFSLIIGRKIKVIGSGRTDKGVHAINQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             H D+  E    +L + +N  L     I +  L +V+  FHARF    + Y Y I    
Sbjct: 61  TFHVDINGEINLNLLIRKINQ-LIKPHCI-VKTLVLVNDSFHARFQVKTKVYEYLINCGN 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L+    W + + LD E ++  A   +G+ +F +F S     +  IRTI    +   
Sbjct: 119 L-NPLQFNYVWQLNQQLDLEKLKADATLFLGKKNFLSFSS--SIHTDSIRTISKITIQKE 175

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              L+ +      FL +Q+R  V  L  +   K     + K  +   +  C   AP  GL
Sbjct: 176 TNQLVRLTFFGSGFLRSQVRMIVACLVNLNTNKMALETVAKLFEHPKKGSCVVKAPSCGL 235

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 236 YLKTVVYE 243


>gi|251772807|gb|EES53368.1| Pseudouridylate synthase [Leptospirillum ferrodiazotrophum]
          Length = 294

 Score =  215 bits (547), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 71/253 (28%), Positives = 105/253 (41%), Gaps = 9/253 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R  +++ Y+G  + GWQ Q N  ++QG++ +A+  +    V V G+GRTD+GV A  QV
Sbjct: 12  RRIALLLAYDGRDFSGWQVQPNRWTVQGTLGEALATLCRAPVGVTGSGRTDAGVSAWGQV 71

Query: 62  AHFDLVR--EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AH DL          L + LN  L    ++ +L+   V   FHAR SA  + Y Y     
Sbjct: 72  AHADLPEGFSIPVDRLPRILNTRL--PGSLRVLDCRSVSSSFHARHSARGKIYRYVFRHL 129

Query: 120 QA---PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            A      L    +  +P +      R A+   +G HDF  F           R ID   
Sbjct: 130 PASLSHHPLATPFSAPLPPNFFLPRAREASTFFLGTHDFRHFSVASSLPDDSTRRIDGIL 189

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRKECGPLA 234
                  + + V    FLH  +R   G L   G+G+    ++   L+  A          
Sbjct: 190 WEERCAELILWVTGPGFLHKMVRMIGGYLLEAGEGRRPLEEIPALLRKGAPPPFRAVEPL 249

Query: 235 PPEGLYFDSVEYS 247
           PP+GL    V Y 
Sbjct: 250 PPDGLALARVLYD 262


>gi|83409929|emb|CAI64350.1| tRNA pseudouridine synthase A [uncultured archaeon]
          Length = 276

 Score =  215 bits (547), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 114/250 (45%), Gaps = 25/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R  + I Y G+ Y G+Q Q +  +I+  + + +  +      +     G+GRTD+GV+A
Sbjct: 1   MRIALKIAYIGTEYHGYQIQPDVPTIEKELFRTLEELKIITDPKSARYIGSGRTDAGVNA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV  F+       + + + +N+ L    +I + + + V   F  R  A+ R Y Y + 
Sbjct: 61  LGQVVAFNTDN--PKLAIPRVINSKL--PPSIWVWSRAEVPDDFDPRRHAVSREYKYFV- 115

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                            + L+   +R A++ L G HDF  F +      S +RT++  D+
Sbjct: 116 ---------------CGECLNISLLRKASKLLRGTHDFANFATPDMD-KSTVRTVERIDI 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G LI + + A SF+   +R  V +L++VGD       L++ L   + +E    AP  
Sbjct: 160 RVEGRLINLDIKADSFVWHMVRKIVTALRMVGDQTREVEWLKRMLHPDEFEEGLEPAPAC 219

Query: 238 GLYFDSVEYS 247
           GL   +V Y 
Sbjct: 220 GLLLKNVNYD 229


>gi|124516114|gb|EAY57622.1| Pseudouridylate synthase [Leptospirillum rubarum]
          Length = 268

 Score =  214 bits (546), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 81/253 (32%), Positives = 118/253 (46%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  ++ Y+G G+ GWQ Q  G+++Q  IE+A   +T + V + G+GRTD+GV A  Q
Sbjct: 1   MPRFAFVVSYDGRGFQGWQSQIRGNAVQDHIEEAFCRLTRQDVRISGSGRTDTGVSAAGQ 60

Query: 61  VAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI--I 117
           V H D+    W P  L + LN +L  S  I IL  + V   FHAR   +R+ Y YR   +
Sbjct: 61  VFHCDIAGPGWTPDSLSRGLNHFL--SPAIRILQAAAVAPDFHARHDVVRKIYRYRWVSL 118

Query: 118 TRQAP--LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +R+A      E     +    +D   ++ A + L G +DFT F           R+ID  
Sbjct: 119 SRKAREVPPTEDPFCGIFFPPVDWTLLQQATKLLEGANDFTRFTVQKSCPEDARRSIDAI 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPL 233
              +  N +++ V  R FLH  IR    +L   G  K T    +  L             
Sbjct: 179 QWIAGPNTLDLWVAGRGFLHMMIRYLAMALLETGQQKRTLKSFQDLLLPGSLPPVPALHP 238

Query: 234 APPEGLYFDSVEY 246
           APP+GL    V Y
Sbjct: 239 APPQGLSLMRVFY 251


>gi|320459238|dbj|BAJ69859.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. infantis
           ATCC 15697]
          Length = 303

 Score =  214 bits (546), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 83/287 (28%), Positives = 131/287 (45%), Gaps = 42/287 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPADDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPAGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R +      +G    + +SLD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEIDPRLRGCVLTVDESLDLELMNRAAALTIGLHDFGSFATPNP 180

Query: 164 QASSPIRTIDHFDVNSFG----------------------NLIEIRVVARSFLHTQIRSF 201
              + IR +                                L+   +VA +F    +RS 
Sbjct: 181 -GGTTIREVKTAYWRRVPITPLVPDAMASHEAYRTPSLESGLVVFTIVADAFARNMVRSL 239

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VGS   VG G+ +       +    R+   GP+AP +GL  + + Y 
Sbjct: 240 VGSCIKVGSGRKSLEWFAGKMADPVREGSSGPIAP-QGLTLEHIAYP 285


>gi|225351017|ref|ZP_03742040.1| hypothetical protein BIFPSEUDO_02599 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225158473|gb|EEG71715.1| hypothetical protein BIFPSEUDO_02599 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 331

 Score =  214 bits (546), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 75/288 (26%), Positives = 124/288 (43%), Gaps = 46/288 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSG 54
           +R  + + Y+G+ ++GW +Q +  ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 30  VRLRIDLAYDGTDFYGWAKQPDIRTVQGEIERVLHTILRVPEGDDNEPLRLTVAGRTDTG 89

Query: 55  VHALRQVAHFDLVRE-----------WVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           VHA  QV H D+  E              + L + L   L   + I+I ++    + F A
Sbjct: 90  VHASHQVCHLDINEETLARCVGHMQVEPVMALTRRLQRML--PNDIAIRSIKEAPEGFDA 147

Query: 104 RFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R+Y+YRI  R +      +     I  +LD   M  AA+  +G HDF +F + +
Sbjct: 148 RFSALERTYVYRIADRSSEIDPRTRNSVLHIDDNLDIGAMNKAAEMTIGLHDFGSFATPN 207

Query: 163 CQASSPIRTIDHFDVNSFGN----------------------LIEIRVVARSFLHTQIRS 200
               + IR +                                L+   +VA +F    +RS
Sbjct: 208 P-GGTTIREVKTAYWRRIPQHPLIDDGTTMGERYRTPALESGLLCFTIVADAFARNMVRS 266

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            V     VG GK +       +    R+   GP+AP +GL  + +EY 
Sbjct: 267 LVNGCVQVGIGKRSLDWFAGKMATPLREGSTGPIAP-QGLTLEHIEYP 313


>gi|152990852|ref|YP_001356574.1| tRNA pseudouridine synthase A [Nitratiruptor sp. SB155-2]
 gi|151422713|dbj|BAF70217.1| tRNA pseudouridine synthase A [Nitratiruptor sp. SB155-2]
          Length = 241

 Score =  214 bits (546), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 115/247 (46%), Gaps = 8/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R   +I Y+GS + G+Q QK+  +++   +  A+  V  E   + G+GRTD GVHA  Q
Sbjct: 1   MRIKAVISYDGSRFDGFQIQKHTANTVMHHLYNALQRVGIES-KIVGSGRTDKGVHATAQ 59

Query: 61  VAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFDL   W     L   LN  L+    I I  +  V K+FHAR+SA RR+Y Y +   
Sbjct: 60  VIHFDLPPFWSELERLQNLLNESLR--PYIQIKRVVKVPKEFHARYSAKRRAYRYLLKKS 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P   E      +  +LD E ++       GRHDF  F        S +R I    +  
Sbjct: 118 E-PSVFENAYLHHVS-NLDIEIIKRNISLFEGRHDFRYFMKTGSDTKSSVRRIFKTALYE 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +L  +      FL  QIR  VG+L  +G G+     +   L  + R     LAPP GL
Sbjct: 176 KDDLYVLYFEGDGFLRAQIRLIVGALIKLGKGELKPEQIIDQLACKAR-YTSTLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLCKIIY 241


>gi|296206475|ref|XP_002750239.1| PREDICTED: tRNA pseudouridine synthase-like 1-like, partial
           [Callithrix jacchus]
          Length = 301

 Score =  214 bits (546), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 126/273 (46%), Gaps = 30/273 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY + ++Y G+ + G    +       +Q  +E+A   +   E V    + RTD+GVHAL
Sbjct: 11  RYLVYLQYVGTDFNGVAAVRGAQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 70

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR +A  R+YL
Sbjct: 71  SNAAHLDVQRRSGRPPFPPEVLTEALNTHLRHP-AIRVLRAFRVPSDFHARHAATSRTYL 129

Query: 114 YRIITRQAP----LALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR++T           E+   W +    LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 130 YRLVTGCHRSDELPVFERNLCWALRADRLDVAAMQEAAQHLLGTHDFSAFQSAGSPVPSP 189

Query: 169 IRTIDHFDV-------------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V             +       +   ++SFL+ Q+R     L  VG G    
Sbjct: 190 VRTLRRVSVSPGLTSPLVTPQESRKLQFWSLEFESQSFLYRQVRRMTAVLVAVGLGALAP 249

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
             ++  L++QD   K    LAP  GL+  SV Y
Sbjct: 250 AQVKTILESQDPLGKHQTRLAPAHGLFLKSVVY 282


>gi|213693060|ref|YP_002323646.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 15697]
 gi|213524521|gb|ACJ53268.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 305

 Score =  214 bits (546), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 83/287 (28%), Positives = 131/287 (45%), Gaps = 42/287 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 3   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPADDAAEPLRLTVAGRTDT 62

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 63  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPAGFDAR 122

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R +      +G    + +SLD E M  AA   +G HDF +F + + 
Sbjct: 123 FSALERTYVYRVADRSSEIDPRLRGCVLTVDESLDLELMNRAAALTIGLHDFGSFATPNP 182

Query: 164 QASSPIRTIDHFDVNSFG----------------------NLIEIRVVARSFLHTQIRSF 201
              + IR +                                L+   +VA +F    +RS 
Sbjct: 183 -GGTTIREVKTAYWRRVPITPLVPDAMASHEAYRTPSLESGLVVFTIVADAFARNMVRSL 241

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VGS   VG G+ +       +    R+   GP+AP +GL  + + Y 
Sbjct: 242 VGSCIKVGSGRKSLEWFAGKMADPVREGSSGPIAP-QGLTLEHIAYP 287


>gi|212716584|ref|ZP_03324712.1| hypothetical protein BIFCAT_01513 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660288|gb|EEB20863.1| hypothetical protein BIFCAT_01513 [Bifidobacterium catenulatum DSM
           16992]
          Length = 306

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/288 (26%), Positives = 124/288 (43%), Gaps = 46/288 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSG 54
           +R  + + Y+G+ ++GW +Q +  ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 5   VRLRIDLAYDGTDFYGWAKQPDMRTVQGEIERVLHTILRVPEGDDNEPLRLTVAGRTDTG 64

Query: 55  VHALRQVAHFDLVRE-----------WVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           VHA  QV H D+  E              + L + L   L   + I+I ++    + F A
Sbjct: 65  VHASHQVCHLDINEETLARCVGHMQVEPVMALTRRLQRML--PNDIAIHSIKEAPEGFDA 122

Query: 104 RFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R+Y+YRI  R +      +     I  +LD   M  AA+  +G HDF +F + +
Sbjct: 123 RFSALERTYVYRIADRSSEIDPRTRNSVLHIDDNLDIAVMNKAAEMTIGLHDFGSFATPN 182

Query: 163 CQASSPIRTIDHFDVNSFGN----------------------LIEIRVVARSFLHTQIRS 200
               + IR +                                L+   +VA +F    +RS
Sbjct: 183 P-GGTTIREVKTAYWRRIPQHPLIDDGTTMGERYRTPALESGLLCFTIVADAFARNMVRS 241

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            V     VG GK +       +    R+   GP+AP +GL  + +EY 
Sbjct: 242 LVNGCVQVGIGKRSLDWFAGKMATPLREGSTGPIAP-QGLTLEHIEYP 288


>gi|294786442|ref|ZP_06751696.1| tRNA pseudouridine synthase A [Parascardovia denticolens F0305]
 gi|315226006|ref|ZP_07867794.1| tRNA pseudouridine synthase A [Parascardovia denticolens DSM 10105]
 gi|294485275|gb|EFG32909.1| tRNA pseudouridine synthase A [Parascardovia denticolens F0305]
 gi|315120138|gb|EFT83270.1| tRNA pseudouridine synthase A [Parascardovia denticolens DSM 10105]
          Length = 338

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 80/320 (25%), Positives = 115/320 (35%), Gaps = 75/320 (23%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT--------GEIVVVHGAGRTDS 53
           +R  +   Y+G+ + GW RQ    ++QG +E  I  V         G  + +  AGRTD+
Sbjct: 1   MRLRIDCSYDGTAFHGWARQPGQRTVQGELEATIAKVLHLWKPDDDGHPITLVVAGRTDA 60

Query: 54  GVHALRQVAHFDLVR--------EWVPVILC--KALNAYLK--ISDTISILNLSIVDKQF 101
           GVHA  QV H DL             P      +AL   L+  +   IS+ ++      F
Sbjct: 61  GVHASGQVCHLDLEDEVLSVAMGHLDPATYRPWEALAYRLRRILPADISVRSIFPSPAGF 120

Query: 102 HARFSAIRRSYLYRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
            ARFSA  R Y+YR+     A     +G    +P+ LD + M  AAQ LVG HDF +F S
Sbjct: 121 DARFSASDRVYVYRVADESSAYDPRLRGFVLNLPRRLDLDLMNQAAQSLVGLHDFGSFSS 180

Query: 161 IHCQASSPIRTIDHFDVNSFG--------------------------------------- 181
            +    + IR +                                                
Sbjct: 181 PNP-GGTTIREVKFARWERVPTHPLGSSSYAGGASLSPTQAIGADPSAAGSISGFESCSG 239

Query: 182 --------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                          L+   ++A +F    +RS V +   VG GK         L    R
Sbjct: 240 SNPDSPYRVDSVESGLLIFTIIADAFAKNMVRSLVNACLQVGMGKKGLDWFAGKLAHPVR 299

Query: 228 KECGPLAPPEGLYFDSVEYS 247
           +     AP  GL  + V Y 
Sbjct: 300 EGASGPAPACGLTLEKVNYP 319


>gi|260891283|ref|ZP_05902546.1| tRNA pseudouridine synthase A [Leptotrichia hofstadii F0254]
 gi|260858959|gb|EEX73459.1| tRNA pseudouridine synthase A [Leptotrichia hofstadii F0254]
          Length = 250

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 117/249 (46%), Gaps = 6/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               MI +Y+GS + G+QRQK   ++QG IE+A+F    + + +  +GRTD GVHA+ QV
Sbjct: 4   RNLKMIYQYDGSKFCGFQRQKKMKTVQGEIERAVFKTFNQEINMISSGRTDKGVHAMEQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           ++F +        + + +N  LK    + +L +    K F+ARF A  R+YLY +   + 
Sbjct: 64  SNFVIDENIPIEAIKRQINKCLK--GEVKVLEVEEAGKDFNARFDAKSRTYLYIMRNEED 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
               E      +  S+  E  +      VG++DF++F        +P+R I +       
Sbjct: 122 ITPFEANYVTGLRASVSVEKFQEIMNDFVGKYDFSSFMKKDKAYRNPVREIVYIKCYYDE 181

Query: 182 NL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +    + + +    FL T +R  +GS   V  G      +++ L+  +  +   LA  E
Sbjct: 182 KIGQKQLNVEICGNGFLKTMVRIMIGSALAVYFGNVEEDYIKRRLENPNADDKKILAASE 241

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 242 GLYLYKVNY 250


>gi|23466158|ref|NP_696761.1| tRNA pseudouridine synthase A [Bifidobacterium longum NCC2705]
 gi|46190438|ref|ZP_00121526.2| COG0101: Pseudouridylate synthase [Bifidobacterium longum DJO10A]
 gi|189440597|ref|YP_001955678.1| pseudouridylate synthase [Bifidobacterium longum DJO10A]
 gi|239621038|ref|ZP_04664069.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|296454842|ref|YP_003661986.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp. longum
           JDM301]
 gi|312133902|ref|YP_004001241.1| trua [Bifidobacterium longum subsp. longum BBMN68]
 gi|322689901|ref|YP_004209635.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
 gi|42559815|sp|Q8CY46|TRUA_BIFLO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238692041|sp|B3DQE2|TRUA_BIFLD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|23326895|gb|AAN25397.1| tRNA pseudouridine synthase A [Bifidobacterium longum NCC2705]
 gi|189429032|gb|ACD99180.1| Pseudouridylate synthase [Bifidobacterium longum DJO10A]
 gi|239516139|gb|EEQ56006.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|291516444|emb|CBK70060.1| pseudouridylate synthase I [Bifidobacterium longum subsp. longum
           F8]
 gi|296184274|gb|ADH01156.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp. longum
           JDM301]
 gi|311773196|gb|ADQ02684.1| TruA [Bifidobacterium longum subsp. longum BBMN68]
 gi|320461237|dbj|BAJ71857.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
          Length = 303

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 131/287 (45%), Gaps = 42/287 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPTDDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R +      +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 180

Query: 164 QASSPIRTIDHFDVNSFG----------------------NLIEIRVVARSFLHTQIRSF 201
              + IR +                                L+   +VA +F    +RS 
Sbjct: 181 -GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSL 239

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VGS   VG G+ +       +    R+   GP+AP +GL  + + Y 
Sbjct: 240 VGSCIKVGSGRKSLEWFAGKMAEPVREGSSGPIAP-QGLTLEHIAYP 285


>gi|206895862|ref|YP_002247302.1| tRNA pseudouridine synthase A [Coprothermobacter proteolyticus DSM
           5265]
 gi|238057727|sp|B5Y955|TRUA_COPPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|206738479|gb|ACI17557.1| tRNA pseudouridine synthase A [Coprothermobacter proteolyticus DSM
           5265]
          Length = 259

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 65/244 (26%), Positives = 109/244 (44%), Gaps = 4/244 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++Y  ++++ G+ Y G+QRQKNG++IQ  +E  +  +     VV  +GRTD+GVHA   
Sbjct: 1   MVKYAGLLQFKGTNYAGFQRQKNGTAIQNVLESTLSQINNRATVVRYSGRTDAGVHAWGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F    +         LN  L     + ++++     +F  + SA+ + YLY     +
Sbjct: 61  PFVFWGREDLSADKWMFILNRML--PKDMRVISVVRTSPEFDPQLSAVAKQYLYCATQER 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +   A+L   S++   +  AA+ LVG HDF  F        S  R +    V   
Sbjct: 119 LGPLWDDFFAYLPNLSIETSAVISAARKLVGEHDFKGFSKKGSSVKSTRRKLYEVSVMFT 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + +    V   FL+  +R  VG+L  +G GK     +++ L           AP +GL+
Sbjct: 179 HSRMYFSFVGNGFLYGMVRLMVGTLLQIGWGKQDVNFIDEVLSGN--AVANYSAPAQGLH 236

Query: 241 FDSV 244
              V
Sbjct: 237 LVKV 240


>gi|322691842|ref|YP_004221412.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. longum
           JCM 1217]
 gi|320456698|dbj|BAJ67320.1| tRNA pseudouridine synthase [Bifidobacterium longum subsp. longum
           JCM 1217]
          Length = 303

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 131/287 (45%), Gaps = 42/287 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 1   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPADDAAEPLRLTVAGRTDT 60

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 61  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 120

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R +      +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 121 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 180

Query: 164 QASSPIRTIDHFDVNSFG----------------------NLIEIRVVARSFLHTQIRSF 201
              + IR +                                L+   +VA +F    +RS 
Sbjct: 181 -GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSL 239

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VGS   VG G+ +       +    R+   GP+AP +GL  + + Y 
Sbjct: 240 VGSCIKVGSGRKSLEWFAGKMAEPVREGSSGPIAP-QGLTLEHIAYP 285


>gi|227546504|ref|ZP_03976553.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 55813]
 gi|227213053|gb|EEI80932.1| tRNA pseudouridine synthase A [Bifidobacterium longum subsp.
           infantis ATCC 55813]
          Length = 305

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 131/287 (45%), Gaps = 42/287 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDS 53
           M R  + + Y+G G++GW +Q N  ++QG+IE A+  V         E + +  AGRTD+
Sbjct: 3   MTRLRIDLAYDGGGFYGWAKQPNLRTVQGTIEDALHKVLRVPTDDAAEPLRLTVAGRTDT 62

Query: 54  GVHALRQVAHFDLVRE-------WVPVILCKALNAYLK--ISDTISILNLSIVDKQFHAR 104
           GVHA  QVAH D+  E        + + + +AL   LK  +   I I  +++    F AR
Sbjct: 63  GVHASHQVAHLDVSDEVLNRCVGHMTIPVTEALTRRLKAVLPSDIVIHGIAVAPVGFDAR 122

Query: 105 FSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           FSA+ R+Y+YR+  R +      +G    + ++LD E M  AA   +G HDF +F + + 
Sbjct: 123 FSALERTYVYRVADRSSEVDPRLRGCVLTVDEALDLELMNRAASLTIGLHDFGSFATPNP 182

Query: 164 QASSPIRTIDHFDVNSFG----------------------NLIEIRVVARSFLHTQIRSF 201
              + IR +                                L+   +VA +F    +RS 
Sbjct: 183 -GGTTIREVKTAYWRRVPITPLVPDEMASHEAYRTPSLESGLVVFTIVADAFARNMVRSL 241

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VGS   VG G+ +       +    R+   GP+AP +GL  + + Y 
Sbjct: 242 VGSCIKVGSGRKSLEWFAGKMAEPVREGSSGPIAP-QGLTLEHIAYP 287


>gi|213964809|ref|ZP_03393008.1| tRNA pseudouridine synthase A [Corynebacterium amycolatum SK46]
 gi|213952345|gb|EEB63728.1| tRNA pseudouridine synthase A [Corynebacterium amycolatum SK46]
          Length = 333

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 118/266 (44%), Gaps = 23/266 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN------GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           +R    I Y+G+ + GW  Q++        ++Q ++E  +  V    V +  AGRTD+GV
Sbjct: 46  VRLRFDIAYDGTDFHGWAAQRDKPTGEPVRTVQATLESTLEKVLRTPVQLTVAGRTDAGV 105

Query: 56  HALRQVAHFDLVREW--------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           HA  QVAH D+             P  L + +   L     +++   S     F ARFSA
Sbjct: 106 HASGQVAHADVPVSCLDTRSIAGDPGNLVRRVARLL--PADVTLRGASFAPSGFDARFSA 163

Query: 108 IRRSYLYRI-ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           +RR Y+YR+      PL           +S+D + M++AA  L+G +DF  F      A+
Sbjct: 164 LRRHYVYRVTSCVSGPLPTRARDTAHWRRSVDIDRMQVAADALLGLNDFAAFCRHKPHAT 223

Query: 167 SPIRTIDHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           +  R +  F            L E  V A +F  + +RS VG+   VG+G+      E+ 
Sbjct: 224 TT-RDLQRFQWFDVSTRQEPELYEAHVTADAFCWSMVRSLVGACLSVGEGRREVGFTEQL 282

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
           L  + R    P+A   GL    V+Y 
Sbjct: 283 LSEEKRSPLVPVAEARGLSLVGVDYP 308


>gi|218886490|ref|YP_002435811.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           'Miyazaki F']
 gi|226708648|sp|B8DRQ6|TRUA_DESVM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|218757444|gb|ACL08343.1| tRNA pseudouridine synthase A [Desulfovibrio vulgaris str.
           'Miyazaki F']
          Length = 277

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 82/279 (29%), Positives = 117/279 (41%), Gaps = 35/279 (12%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M R  + + Y G+   GWQ Q         ++QG +E+    + G  V +HGAGRTDSGV
Sbjct: 1   MARLALTVSYVGTRLAGWQIQARTDRPQPRTVQGELERIAERIVGAPVRLHGAGRTDSGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA  QVAH D+      +   +A NA L   D IS+  +  V  +FHARF A  ++Y YR
Sbjct: 61  HAEAQVAHMDVPDHRADLDWQRAFNAGL--PDDISVAAVVRVPDEFHARFDARGKTYTYR 118

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +   +  +             LD + M  AA +L G HDF +F++      + +RT+   
Sbjct: 119 LWPERRWVPPRLAPFAWATGQLDMDAMDAAAAYLHGMHDFASFQNTGTDIVTTVRTVTRV 178

Query: 176 DVNSFGN----------------------------LIEIRVVARSFLHTQIRSFVGSLKL 207
                G                             ++     A  FL   +R+ +G L  
Sbjct: 179 ARRHEGEAPVQPALPGAQPLAGAEETANAMAGGLRVMAWDFEADGFLKQMVRNMMGLLVA 238

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           VG GK     +   L A+DRK     AP  GL    V Y
Sbjct: 239 VGRGKLPPDAVPAILAARDRKTAPATAPAHGLTLTRVHY 277


>gi|86157969|ref|YP_464754.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85774480|gb|ABC81317.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 272

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 81/262 (30%), Positives = 119/262 (45%), Gaps = 22/262 (8%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  Y + + Y+G  + G+QRQ    ++Q ++E+A+  + G    +H A RTD+GVHAL
Sbjct: 1   MERRSYALRLAYDGGRFRGFQRQPGLPTVQQALEEALERL-GVRAQLHVAARTDAGVHAL 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F       P  L + LN  L   + I +L+ + V   FHAR SA  R+Y+Y +  
Sbjct: 60  AQVVSFSARAALDPAALRRGLNEGL--PEGILVLDAARVGPSFHARGSAASRTYVYLV-- 115

Query: 119 RQAPLALEKGRAWLIPK-----------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
              P    +  AW +P             LD   MR A    VG HDF  F     Q   
Sbjct: 116 GAPPPEGLRPYAWTLPDARAFPELAEVPPLDAAAMREALGAAVGEHDFVGFARPGEQRG- 174

Query: 168 PIRTIDHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +RT+   +V   G   L+ + +  + FL   +R+ VG+   VG G+     +   L  +
Sbjct: 175 TVRTLLRAEVVEAGWAPLVAVVLEGKGFLRAMVRNLVGTAVAVGLGRAPPDVIRTLLATR 234

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R   G  AP  GL   +V Y 
Sbjct: 235 GRYR-GVRAPGWGLTLAAVRYP 255


>gi|317418864|emb|CBN80902.1| tRNA pseudouridine synthase-like 1 [Dicentrarchus labrax]
          Length = 285

 Score =  213 bits (544), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 93/276 (33%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 3   RYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHA 57
           RY +  +Y G+ Y G  +    Q     +Q  +E AI  +     V +  + RTD GVHA
Sbjct: 6   RYLIFFQYIGTKYSGVVKVPPHQLPSKGVQDHLEDAIRKLMPLNPVSLSVSSRTDRGVHA 65

Query: 58  LRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           L   AHFDL R      +   IL +ALN YLK  + I I N   V   FHAR+ A  R+Y
Sbjct: 66  LSNSAHFDLQRKNNLPPFTEGILIEALNFYLKT-EQIRITNAHRVPDDFHARYQAQSRTY 124

Query: 113 LYRIITRQAPLAL-----EKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQA- 165
           +YRI     P  L     E    W +    LD   MR AA  LVG HDF++FR++  +  
Sbjct: 125 VYRIALG-IPNQLLLPLTELKFCWSLRNTELDVGAMRKAAALLVGNHDFSSFRAVSTEMA 183

Query: 166 -SSPIRTIDHFDVNSFGNL-----------IEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
             +P++ +D   +   G+             E+   ARSFL+ Q+R   G+L  VG G+ 
Sbjct: 184 FKNPVKVLDVASIQPGGSFVQSHFQREVLFWEVTFKARSFLYKQVRRMTGALVAVGQGRL 243

Query: 214 TSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
           +   L++ L+A+D     P   +AP  GL+   V+Y
Sbjct: 244 SVPQLKEILEARD-TMAYPKNLVAPAHGLFLTRVDY 278


>gi|212223540|ref|YP_002306776.1| tRNA pseudouridine synthase A [Thermococcus onnurineus NA1]
 gi|229470756|sp|B6YTJ2|TRUA_THEON RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|212008497|gb|ACJ15879.1| tRNA pseudouridine synthase A [Thermococcus onnurineus NA1]
          Length = 267

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 112/250 (44%), Gaps = 26/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG----EIVVVHGAGRTDSGVHA 57
           +R  + I Y+G+ ++G+QRQ    +++G I +A+  +      E     GA RTD GV A
Sbjct: 1   MRLALRIAYDGTAFYGFQRQPGLRTVEGEIIRALTKLGIIEDVESSNFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              V  FD+      ++  + LN +L     + +L  + V + FH RF A  ++Y Y   
Sbjct: 61  FFNVVAFDVAS-RPDLVRPEVLNFHL---KDVWVLGTAEVPEDFHPRFWAKSKTYRY--- 113

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +LI    D + MR  A+  +G HDF+ F  +     +P+R +   D+
Sbjct: 114 -------------YLIDAGFDEKAMRECAKLFIGTHDFSAFARLEPH-KNPVRELIRADI 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                   I +  +SFL    R  V +L+  G G  T  ++EK L   +     P A PE
Sbjct: 160 IKRQGYYIIELEGKSFLWEMARRIVNALRFCGLGILTEEEVEKMLNG-EYSRKIPPARPE 218

Query: 238 GLYFDSVEYS 247
           GL    +EY 
Sbjct: 219 GLVLWGIEYE 228


>gi|119025367|ref|YP_909212.1| tRNA pseudouridine synthase A [Bifidobacterium adolescentis ATCC
           15703]
 gi|118764951|dbj|BAF39130.1| tRNA pseudouridine synthase A [Bifidobacterium adolescentis ATCC
           15703]
          Length = 306

 Score =  213 bits (542), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 74/286 (25%), Positives = 121/286 (42%), Gaps = 42/286 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G+G++GW +Q    ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 5   VRLRIDLAYDGTGFYGWAKQPEIRTVQGEIERVLHTILRVPEGDPTEPLRLTVAGRTDTG 64

Query: 55  VHALRQVAHF---------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H           +    VP ++         +   I+I  ++     F ARF
Sbjct: 65  VHASHQVCHLDVNEDVLKRCVGHMDVPPVIALTRRLQRMLPADIAIRGIAPAPDGFDARF 124

Query: 106 SAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y+YRI  R +      +     I   LD ++M  AA   +G HDF +F + +  
Sbjct: 125 SALERTYVYRIADRSSEVDPRTRNFVLHIDDELDLKSMNEAAAMTIGLHDFGSFATPNP- 183

Query: 165 ASSPIRTIDHFDVNSFGN----------------------LIEIRVVARSFLHTQIRSFV 202
             + IR +                                L+   +VA +F    +RS V
Sbjct: 184 GGTTIREVKTAYWRRVPQRTLIDDGMTMGERYRTPTVESGLVCFVIVADAFARNMVRSLV 243

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
                VG GK +       + A  R+   GP+AP +GL  + +EY 
Sbjct: 244 NGCVQVGIGKRSLDWFAGKMAAPLREGSTGPIAP-QGLTLEHIEYP 288


>gi|162456345|ref|YP_001618712.1| tRNA pseudouridine synthase A [Sorangium cellulosum 'So ce 56']
 gi|161166927|emb|CAN98232.1| tRNA pseudouridine synthase A [Sorangium cellulosum 'So ce 56']
          Length = 281

 Score =  213 bits (542), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 117/246 (47%), Gaps = 7/246 (2%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            + + Y+G  + G+ RQ++  ++ G +  A+ ++   I  + GA RTD+GVHA  Q   F
Sbjct: 1   MLSVAYDGRPFAGFARQRDQRTVSGELLGALRVIDPGIREIRGASRTDAGVHARDQRVAF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           D      P     A   +L   D I I   ++V   F  RF ++R+ Y Y I+       
Sbjct: 61  DTTAPLPPRGWVLATARHL--PDEIVIRRAAVVRLGFSPRFESLRKRYRYLILRDLVRDP 118

Query: 125 LEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN---S 179
               RAW +    D   E  R  A    G HDF  FR+   + ++ +RT+   +++   +
Sbjct: 119 FLSRRAWRVEGITDEAIERARAEALAAKGTHDFAAFRTSADERTTTVRTLYGVELSLDPA 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              ++ I V   +FLH  +R  VG+L  V  G      + +AL + DR++ G  APP+GL
Sbjct: 179 DPRVVRIDVEGNAFLHNMVRILVGTLMDVARGHLAPGAIARALSSLDRRDAGITAPPDGL 238

Query: 240 YFDSVE 245
           Y + + 
Sbjct: 239 YLERIH 244


>gi|154486775|ref|ZP_02028182.1| hypothetical protein BIFADO_00600 [Bifidobacterium adolescentis
           L2-32]
 gi|154084638|gb|EDN83683.1| hypothetical protein BIFADO_00600 [Bifidobacterium adolescentis
           L2-32]
          Length = 306

 Score =  213 bits (542), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 74/286 (25%), Positives = 120/286 (41%), Gaps = 42/286 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G+G++GW +Q    ++QG IE+ +  +         E + +  AGRTD+G
Sbjct: 5   VRLRIDLAYDGTGFYGWAKQPEIRTVQGEIERVLHTILRVPEGDPTEPLRLTVAGRTDTG 64

Query: 55  VHALRQVAHF---------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H           +    VP ++         +   I+I  ++     F ARF
Sbjct: 65  VHASHQVCHLDVNEDVLKRCVGHMDVPPVIALTRRLQRMLPADIAIRGIAPAPNGFDARF 124

Query: 106 SAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y+YRI  R +      +     I   LD + M  AA   +G HDF +F + +  
Sbjct: 125 SALERTYVYRIADRSSEVDPRTRNFVLHIDDELDLKAMNEAAAMTIGLHDFGSFATPNP- 183

Query: 165 ASSPIRTIDHFDVNSFGN----------------------LIEIRVVARSFLHTQIRSFV 202
             + IR +                                L+   +VA +F    +RS V
Sbjct: 184 GGTTIREVKTAYWRRVPQRTLIDDGMTMGERYRTPTVESGLVCFVIVADAFARNMVRSLV 243

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
                VG GK +       + A  R+   GP+AP +GL  + +EY 
Sbjct: 244 NGCVQVGIGKRSLDWFAGKMAAPLREGSTGPIAP-QGLTLEHIEYP 288


>gi|301788920|ref|XP_002929883.1| PREDICTED: LOW QUALITY PROTEIN: tRNA pseudouridine synthase-like
           1-like [Ailuropoda melanoleuca]
          Length = 290

 Score =  213 bits (542), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 130/273 (47%), Gaps = 31/273 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-GSSI--QGSIEKAIFLVTGE-IVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G    +    ++  Q  +E+A   +     V    + RTD+GVHAL
Sbjct: 11  RYLVYFQYLGTDFNGVAAVRGSQRAVAXQNYLEEAAKRLNSVVPVKFTISSRTDAGVHAL 70

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALNA+L+    I IL    V   FHAR +A  R+YL
Sbjct: 71  CNAAHLDVQRRSGQPPFSPEVLAEALNAHLRHP-AIRILQAFRVPSDFHARHAATSRTYL 129

Query: 114 YRIITRQAPL----ALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR++T           E+ R W +    LD + M+ AAQHL+G HDF+ F+S    A+S 
Sbjct: 130 YRLVTGCHRPDQLSVFERNRCWPLRAGCLDVDAMQEAAQHLLGTHDFSAFQSAGSPAASS 189

Query: 169 IRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           +RT+    V+                   +   ++SFL+ Q+R     L  VG G     
Sbjct: 190 VRTLRRASVSPDPGSPFVLPQENRLRFWNLEFESQSFLYRQVRRMTAVLVAVGLGALMPA 249

Query: 217 DLEKALQAQD---RKECGPLAPPEGLYFDSVEY 246
            ++  L+++D   R +   +AP  GL+  SV Y
Sbjct: 250 QVKVILESRDPLGRHQAR-VAPAHGLFLKSVLY 281


>gi|145596404|ref|YP_001160701.1| tRNA-pseudouridine synthase I [Salinispora tropica CNB-440]
 gi|145305741|gb|ABP56323.1| tRNA-pseudouridine synthase I [Salinispora tropica CNB-440]
          Length = 276

 Score =  212 bits (541), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 109/251 (43%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
            R  + + Y+G+ + GW  Q    ++ G++ +A+ LV G      +  AGRTD+GVHA  
Sbjct: 5   TRVRLDVSYDGADFSGWAVQPERRTVAGALVQALDLVLGVGAATGLTVAGRTDAGVHATG 64

Query: 60  QVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL    W              +   + I  ++     F ARFSA  R Y YR+  
Sbjct: 65  QVCHVDLLTEVWHRHEHTLLRRLARLLPADVRIRAMTEAPDDFDARFSATFRRYEYRVTD 124

Query: 119 RQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +      P  LD   + +AA  LVG HDF  +     + ++ +R +   + 
Sbjct: 125 APWGAEPLRRHDTLAWPSRLDLAALNVAADGLVGEHDFAAYCRRK-ENATTLREVTRLEW 183

Query: 178 NSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               +  +   V A +F    +RS VG++  VGDG+  +      L  ++R     +AP 
Sbjct: 184 RRAPDGTLVATVQADAFCQAMVRSLVGAMLAVGDGRRPADWPAGLLTRRERASEVNVAPA 243

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 244 HGLTLVAVGYP 254


>gi|220917510|ref|YP_002492814.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219955364|gb|ACL65748.1| tRNA pseudouridine synthase A [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 272

 Score =  212 bits (541), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 83/262 (31%), Positives = 120/262 (45%), Gaps = 22/262 (8%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  Y + + Y+G  + G+QRQ    ++Q ++E+A+  + G    +H A RTD+GVHAL
Sbjct: 1   MERRSYALRLAYDGGRFRGFQRQPGLPTVQQALEEALERL-GVRAQLHVAARTDAGVHAL 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F       PV L   LN  L   + I +L+ + V   FHAR SAI R+Y+Y +  
Sbjct: 60  AQVVSFSARAALDPVALRGGLNEGL--PEGILVLDAARVGPSFHARGSAIARTYVYLV-- 115

Query: 119 RQAPLALEKGRAWLIPK-----------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
              P    +  AW +P             LD   MR A  H VG HDF  F     Q   
Sbjct: 116 GAPPPVGLRPYAWTLPDARAFPDLAEVPPLDAAAMREALGHAVGEHDFVGFARPGEQRG- 174

Query: 168 PIRTIDHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +RT+   +V   G   L+ + +  + FL   +R+ VG+    G G+     +   L  +
Sbjct: 175 TVRTLLRAEVIEAGWAPLVAVVLEGKGFLRAMVRNLVGTAVAAGLGRAPPDVIRTLLATR 234

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R   G  AP  GL   +V Y 
Sbjct: 235 GRYR-GVRAPGWGLTLAAVRYP 255


>gi|319956627|ref|YP_004167890.1| tRNA pseudouridine synthase a [Nitratifractor salsuginis DSM 16511]
 gi|319419031|gb|ADV46141.1| tRNA pseudouridine synthase A [Nitratifractor salsuginis DSM 16511]
          Length = 242

 Score =  212 bits (541), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 120/250 (48%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R   +I Y+GS + G+QRQK    ++QG++E+A+  + G    + G+GRTD+GVHA  
Sbjct: 1   MQRIKAVIAYDGSAFEGFQRQKRTPRTVQGALERALASL-GIGTPIVGSGRTDAGVHATG 59

Query: 60  QVAHFDLVREW---VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFDL   W       L   LN  L   D I   +L+ V   FHAR+ A  R Y Y  
Sbjct: 60  QVIHFDLPPHWAKQPLDELQIHLNRRL---DAIRFKHLTPVPADFHARYDAKERIYRYIF 116

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             R+ P   E+     +  + D   +  A +   GRHDF+ F     + +  IRTI    
Sbjct: 117 --RREPSIFERKYVAGLAIA-DEAKLSEALKTFQGRHDFSHFLKTGSETAHNIRTITRAY 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G    I   A  FL  Q+R  V +   V +G+ +   L++ L+   R     LAPP
Sbjct: 174 FLRRGKYGYIYFHADGFLRAQVRMMVHAAAAVANGELSLEQLKEQLELGKR-YTTRLAPP 232

Query: 237 EGLYFDSVEY 246
           EGLY   V Y
Sbjct: 233 EGLYLARVIY 242


>gi|311745752|ref|ZP_07719537.1| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
 gi|311302425|gb|EAZ79545.2| tRNA pseudouridine synthase A [Algoriphagus sp. PR1]
          Length = 274

 Score =  212 bits (541), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 100/250 (40%), Gaps = 12/250 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVA 62
           Y   I Y G+ Y GW  Q N  ++Q  +E+ +  V G E   + GA RTDSGV  +    
Sbjct: 8   YLFSISYYGARYKGWAPQPNQQTVQRRLERVLRHVLGHEDFSLIGASRTDSGVSCVGGFV 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
              L  E    +L    N +L     I + ++  V   F+   S  +++Y Y        
Sbjct: 68  QVFLRDEVEMDLLLPQFNEHL--PQDIHLNSVKEVSTTFNLIQSVKKKTYRYYFSNSSDF 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                       + L+ E M  A +  +G+HDF +F       +   R +   ++     
Sbjct: 126 HPFASAFMVNASEELNWEAMNEACKSFIGKHDFKSFCKPSENKTDYNREVLSAEICDSNE 185

Query: 183 LI---------EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            +           ++    FLH Q+R  + +L  +G G+   +++E   ++ DR E  P 
Sbjct: 186 FMGQYFPHKIYYFQITGTGFLHHQVRMMMSALWQIGKGEMDLSEIEARFESSDRFEKLPP 245

Query: 234 APPEGLYFDS 243
           AP  GL    
Sbjct: 246 APANGLVLWE 255


>gi|309802980|ref|ZP_07697081.1| tRNA pseudouridine synthase A [Bifidobacterium dentium JCVIHMP022]
 gi|308220447|gb|EFO76758.1| tRNA pseudouridine synthase A [Bifidobacterium dentium JCVIHMP022]
          Length = 302

 Score =  212 bits (540), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 123/288 (42%), Gaps = 46/288 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSG 54
           +R  + + Y+G G+FGW +Q +  ++QG IE+ +  V        GE + +  AGRTD+G
Sbjct: 1   MRLRIDLAYDGGGFFGWAKQPDRRTVQGEIERILHTVLRVPVDDAGEPLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREW-----------VPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           VHA  QV H D+                 V L + L   L   + I+I  ++   + F A
Sbjct: 61  VHASHQVCHLDVSETILARCVGHMDVPPVVALTRRLQRML--PNDITIHGINEAPQGFDA 118

Query: 104 RFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R+Y+YRI  R +      +G    +   LD E M  AA   +G HDF +F + +
Sbjct: 119 RFSALERTYVYRIADRSSEIDPRMRGFVLHVDDDLDLETMNQAAAMTIGLHDFGSFATPN 178

Query: 163 CQASSPIRTIDHFDVNSFGN----------------------LIEIRVVARSFLHTQIRS 200
               + IR +                                L    +VA +F    +RS
Sbjct: 179 P-GGTTIREVKTAYWRRIPQRPLIDGEMTMGERYHTPSMESGLACFTIVADAFARNMVRS 237

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            V     VG GK +       +    R+   GP+AP +GL  + +EY 
Sbjct: 238 LVNGCVQVGIGKRSLDWFADKMATPLREGSTGPIAP-QGLTLEHIEYP 284


>gi|147903104|ref|NP_001085529.1| tRNA pseudouridine synthase-like 1 [Xenopus laevis]
 gi|82236585|sp|Q6GQ53|PUSL1_XENLA RecName: Full=tRNA pseudouridine synthase-like 1; AltName:
           Full=tRNA pseudouridylate synthase-like 1; AltName:
           Full=tRNA-uridine isomerase-like 1
 gi|49115069|gb|AAH72895.1| MGC80334 protein [Xenopus laevis]
          Length = 298

 Score =  212 bits (540), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 81/273 (29%), Positives = 128/273 (46%), Gaps = 29/273 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSI---QGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ Y G        S+   Q  +E A   +     +    + RTDSGVHA+
Sbjct: 7   RYLVFFQYYGTKYSGVMETPITQSVLGVQNYLEVAAQKLRPVGTIKFFISSRTDSGVHAI 66

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
             +AH D+ R      +   IL +A+N +L+  + I +L    V   FHAR +A+ R+Y+
Sbjct: 67  CNLAHVDIERAKGKPPFTEEILVQAMNHHLQ-PEPIRLLKAIRVCDNFHARHNALSRTYV 125

Query: 114 YRIITRQAPL---ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSP 168
           YR+    +       E    W I   L+   +  A++ L+G H+F+ FRS + +    SP
Sbjct: 126 YRVAAGCSRPELPVFEGNLCWAIQDGLNVTAINEASKMLLGTHNFSAFRSANSENAFKSP 185

Query: 169 IRTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           I+T+   D+N                  +    ARSFL+ Q+R   G+L  VG G+ T  
Sbjct: 186 IKTLQQADINPSCGILTHHWQSRNLQFWDFTFRARSFLYKQVRRMTGALVAVGQGRLTPQ 245

Query: 217 DLEKALQAQDRK--ECGPLAPPEGLYFDSVEYS 247
            +++ L+ QD        +APP GL+   VEY 
Sbjct: 246 QIKEFLENQDPNCFLGNFVAPPHGLFLKDVEYD 278


>gi|222630953|gb|EEE63085.1| hypothetical protein OsJ_17893 [Oryza sativa Japonica Group]
          Length = 279

 Score =  211 bits (539), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 72/212 (33%), Positives = 110/212 (51%), Gaps = 8/212 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ M+I Y+G+ + GWQ Q +  +IQ SIE A+  +T    + + + GAGRTD+GVHA  
Sbjct: 64  KWRMVIAYDGTKFKGWQYQPSPPTIQCSIENALTRITKLDRKELCLVGAGRTDTGVHAWG 123

Query: 60  QVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF           +  A+N  L     I +  +S    +FHAR S   + Y Y+I  
Sbjct: 124 QVAHFTTPFSYHCLDSMHSAINGLL--PHEIRVREISAAKPEFHARTSTRSKIYHYKIYN 181

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFD 176
                      A+     L+ + MR AA+H VG HDFT+F +   + +  SPI+ I  FD
Sbjct: 182 GPVMDPFHNHYAYHSAYKLNSQAMREAAKHFVGTHDFTSFANAVHNDRVRSPIKKIMRFD 241

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
           V   G ++++ +    FL+ Q+R+  GS   V
Sbjct: 242 VIEMGAILQLEIEGTGFLYRQVRNMAGSSLAV 273


>gi|197122727|ref|YP_002134678.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
 gi|196172576|gb|ACG73549.1| tRNA pseudouridine synthase A [Anaeromyxobacter sp. K]
          Length = 272

 Score =  211 bits (539), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 82/262 (31%), Positives = 120/262 (45%), Gaps = 22/262 (8%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  Y + + Y+G  + G+QRQ    ++Q ++E+A+  + G    +H A RTD+GVHAL
Sbjct: 1   MERRSYALRLAYDGGRFRGFQRQPGLPTVQQALEEALERL-GLRAQLHVAARTDAGVHAL 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F       P  L + LN  L   + I +L+ + V   FHAR SAI R+Y+Y +  
Sbjct: 60  AQVVSFSARAALDPAALRRGLNEGL--PEGILVLDAARVGPSFHARGSAIARTYVYLV-- 115

Query: 119 RQAPLALEKGRAWLIPK-----------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
              P    +  AW +P             LD   MR A  H VG HDF  F     Q   
Sbjct: 116 GAPPPEGLRPYAWTLPDARAFPDLAEVPPLDAAAMREALGHAVGEHDFVGFARPGEQRG- 174

Query: 168 PIRTIDHFDVNSFG--NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            +RT+   +V   G   L+ + +  + FL   +R+ VG+    G G+     +   L  +
Sbjct: 175 TVRTLLRAEVIEAGWAPLVAVVLEGKGFLRAMVRNLVGTAVAAGLGRAPPDVIRTLLATR 234

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R   G  AP  GL   +V Y 
Sbjct: 235 GRYR-GVRAPGWGLTLAAVRYP 255


>gi|229818212|ref|ZP_04448494.1| hypothetical protein BIFANG_03510 [Bifidobacterium angulatum DSM
           20098]
 gi|229784463|gb|EEP20577.1| hypothetical protein BIFANG_03510 [Bifidobacterium angulatum DSM
           20098]
          Length = 302

 Score =  211 bits (539), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 125/285 (43%), Gaps = 41/285 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW  Q +  ++QG IE+A+  +         E + +  AGRTD+G
Sbjct: 1   MRLRIDLAYDGGGFYGWAVQPDIRTVQGEIEQALHRILRVDPNDASEPLRLVVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVILCK-------ALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  + +   +         AL   L+  + D I+I  +S     F ARF
Sbjct: 61  VHASHQVCHIDMSPDILERAVGHMKVPAVTALEHRLQRVLPDDITIHRISEAPVGFDARF 120

Query: 106 SAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y+YRI  R +      +G    I   LD E M +AA   +G HDF +F + +  
Sbjct: 121 SALERTYVYRIADRSSEVDPRLRGCVLHIDGDLDIEAMNLAAAQTIGLHDFGSFATPNP- 179

Query: 165 ASSPIRTIDHFDVNSFG---------------------NLIEIRVVARSFLHTQIRSFVG 203
             + IR +   D                           L+   +VA +F    +RS V 
Sbjct: 180 GGTTIREVKQADWARVPAQPLIAQPMAGKGYVVPTFESGLVCFTIVADAFARNMVRSLVN 239

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
               VG  K      +  +    R+   GP+AP +GL  + V Y 
Sbjct: 240 GCVQVGLDKRDLDWFKGKMAVPKREGSTGPIAP-QGLTLEHVAYP 283


>gi|219682884|ref|YP_002469267.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis AD011]
 gi|254789603|sp|B8DW40|TRUA_BIFA0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219620534|gb|ACL28691.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis AD011]
 gi|289178185|gb|ADC85431.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis BB-12]
          Length = 298

 Score =  211 bits (539), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 80/282 (28%), Positives = 125/282 (44%), Gaps = 37/282 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI----VVVHGAGRTDSGVH 56
           M R  + + YNG+ + GW  Q    ++QG++E+A+  +T       + +  AGRTD+GVH
Sbjct: 1   MTRLRIDLAYNGAAFHGWAAQPGCRTVQGTVEEALRRITRMPDAGSLRLTVAGRTDAGVH 60

Query: 57  ALRQVAHFDLVRE-------WVPVILCKALNAYL--KISDTISILNLSIVDKQFHARFSA 107
           A  QV H D+  +        + +   +AL   L   + D I+I  +S+    F ARFSA
Sbjct: 61  ATHQVCHVDVPDQTLGQCVGHMNLTPVQALQTRLSRMMPDDIAIHGISVAPAGFDARFSA 120

Query: 108 IRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           + R+Y+YRI   + P     K  AW   + LD   M  AA   +G HDF +F   +    
Sbjct: 121 LERTYVYRIADARVPWDPRLKDFAWRTDRELDIAQMNAAAALTLGLHDFGSFAIANP-GG 179

Query: 167 SPIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFVGSLK 206
           + IR +                              L+   +VA +F    +RS VG+  
Sbjct: 180 TTIREVKTAYWQRVPTRPLLGPGMGERYHTPAVESGLLCFTIVADAFARNMVRSLVGACV 239

Query: 207 LVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            VG GK         ++   R+   GP+AP +GL  + + Y 
Sbjct: 240 QVGMGKRDVDWFAGKMRVPLREGSTGPIAP-QGLTLEHIAYP 280


>gi|307721208|ref|YP_003892348.1| tRNA pseudouridine synthase A [Sulfurimonas autotrophica DSM 16294]
 gi|306979301|gb|ADN09336.1| tRNA pseudouridine synthase A [Sulfurimonas autotrophica DSM 16294]
          Length = 236

 Score =  211 bits (539), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 116/247 (46%), Gaps = 13/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + + YNG+ +FG Q QK    ++ G +E  +  +  E   V  +GRTD GVHA  Q
Sbjct: 1   MRVALHLAYNGTHFFGSQTQKETSKTVLGELENVLKKLGIEQ-KVIASGRTDKGVHATMQ 59

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL   W     L + LN  L   D + +  +  V   FHAR+SA +R+Y Y I T 
Sbjct: 60  VCHIDLPPYWEDTQKLKRVLNEMLN--DALHVKRIRPVSDDFHARYSAKKRTYRYIIKTT 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q+    EK     + K ++ EN++      VG+HDF  F     +  S  R I       
Sbjct: 118 QS-NPFEKDFVTFL-KDINFENIQENIALFVGKHDFKQFMKTGSEVKSTTRIIYKAFAYK 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + + + +   A  FL +QIR  VG+L         +  +++ L   +  +  P AP  GL
Sbjct: 176 YKDYVVLNFQANGFLRSQIRLMVGALLS-----LNAQQIQEQLNCSNNYKIKP-APANGL 229

Query: 240 YFDSVEY 246
           Y  ++ Y
Sbjct: 230 YLSTITY 236


>gi|149278992|ref|ZP_01885126.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
 gi|149230271|gb|EDM35656.1| tRNA pseudouridine synthase A [Pedobacter sp. BAL39]
          Length = 267

 Score =  211 bits (538), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 75/248 (30%), Positives = 117/248 (47%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I Y+G  Y GWQ+Q    ++QG +EK +  V    V + G GRTD+ VHA +  
Sbjct: 1   MRYFVHIGYHGLHYNGWQKQPGVLNVQGVLEKTLSQVLKRPVEIIGCGRTDAHVHASQFF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D+   W    L   LN  L     I++ ++  +    HARF A++RSY Y + T + 
Sbjct: 61  FHMDIEEAWD-FDLIFRLNKSL--PTNIAVFDVIPMPGLQHARFDAVQRSYDYFLHTYKN 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--VNS 179
           P  L+   ++ + K L  + M+ AA  L    DF  F +   +    I  +      V+ 
Sbjct: 118 PF-LQGLSSYYLLKDLKFDEMKAAAAILPKYKDFRPFCTSPDKYEHTICNVMSASLTVDP 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +  ++ +  FL   IR  +G L  VG G  +  + E+ L  +   E    A P+GL
Sbjct: 177 NGDRMRFQISSNRFLSKMIRIIMGQLLKVGRGVLSVDEFEQYLIDKRTPELITPAHPQGL 236

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 237 YLSKVTYP 244


>gi|260906021|ref|ZP_05914343.1| pseudouridylate synthase I [Brevibacterium linens BL2]
          Length = 284

 Score =  211 bits (538), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 85/266 (31%), Positives = 117/266 (43%), Gaps = 20/266 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + + Y G+ + GW +Q    ++Q S+E  +  +TG  V    AGRTD+GVHA RQ
Sbjct: 1   MTRFRIDLGYRGTDFHGWAKQPGLRTVQDSLEAGLSRITGAEVATIVAGRTDAGVHARRQ 60

Query: 61  VAHFDLV-----------REWVPVILCKALNAYLKIS--DTISILNLSIVDKQFHARFSA 107
           V H DL                   L   L   L +   D I I  +S V + F ARFSA
Sbjct: 61  VVHIDLAEEGIEKLIGKSSRPAEAALLSRLRGVLTVDDTDDIVIHAVSEVPEDFDARFSA 120

Query: 108 IRRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           + R+Y YR+  R+     L           LD E M  AA+   G HDF  F     + +
Sbjct: 121 LWRTYQYRLADRRSFIDPLLTPVTPRHKGELDAEAMAEAAREAQGLHDFIPFCKPR-EGA 179

Query: 167 SPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           + IRT+   +V      +I I + A +F H  +R+ VG L  VG G W  T   + L   
Sbjct: 180 TTIRTLHELEVTRDQEAVITIDLRADAFCHHMVRALVGGLIKVGSGTWPVTRPAELLTEA 239

Query: 226 D--RKECGPLA--PPEGLYFDSVEYS 247
           D       P+   P  GL    V Y 
Sbjct: 240 DSGVDPDVPMFVSPAHGLVLTGVGYP 265


>gi|255533538|ref|YP_003093910.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
 gi|255346522|gb|ACU05848.1| tRNA pseudouridine synthase A [Pedobacter heparinus DSM 2366]
          Length = 269

 Score =  211 bits (538), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 115/248 (46%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + I YNG  Y GWQ+Q    ++QG IE A+  V    V + G GRTD+ VHA +  
Sbjct: 1   MRYFVHIGYNGLKYNGWQKQPGVMNVQGVIENALSKVLKTPVFIIGCGRTDAHVHASQFF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D+ ++W    L   +N  L     I+I  +  +D   HARF A+ RSY Y I T + 
Sbjct: 61  FHMDVEQDWD-FDLVFRMNKLL--PAGIAIFEVIQMDGLQHARFDAVLRSYDYFIHTYKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD--VNS 179
           P  L    ++ +   LD + M+ AA  L    DF  F +   +    +  +      V+ 
Sbjct: 118 PF-LNGLSSFYLLDKLDFDKMKQAAAILPKYKDFRAFCTSPDKYEHTLCNVMSASLAVDE 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +  ++ +  FL   IR  +G L  +G G  +  + E  L      E    A P+GL
Sbjct: 177 NGDKLRFQISSNRFLSKMIRIIMGQLLKIGRGVLSVDEFEHYLIYNQTPELITPAHPQGL 236

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 237 YLSKVTYP 244


>gi|153824082|ref|ZP_01976749.1| tRNA pseudouridine synthase A [Vibrio cholerae B33]
 gi|126518399|gb|EAZ75622.1| tRNA pseudouridine synthase A [Vibrio cholerae B33]
          Length = 205

 Score =  211 bits (538), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 65/187 (34%), Positives = 91/187 (48%), Gaps = 2/187 (1%)

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I    
Sbjct: 1   MVHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHV 58

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +           LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 59  YRPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 118

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY
Sbjct: 119 GRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLY 178

Query: 241 FDSVEYS 247
             SV+Y 
Sbjct: 179 LVSVDYP 185


>gi|317125837|ref|YP_004099949.1| tRNA pseudouridine synthase A [Intrasporangium calvum DSM 43043]
 gi|315589925|gb|ADU49222.1| tRNA pseudouridine synthase A [Intrasporangium calvum DSM 43043]
          Length = 303

 Score =  211 bits (537), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 114/260 (43%), Gaps = 16/260 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVHALR 59
           +R  + + Y G+ + GW  Q    +++G +  A+  V      V +  AGRTD+GVHA  
Sbjct: 20  VRLRLDLAYEGTAFSGWAAQPGLRTVEGELATAVTTVLRAPAPVSLTVAGRTDAGVHARG 79

Query: 60  QVAHFDLV----------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           QV H D+               P            +   + +  ++   + F ARFSA  
Sbjct: 80  QVVHVDVEPAALAALPGRSNRTPEE-ALLRRLGGLLDPDVVVHRVARAPEGFDARFSAQE 138

Query: 110 RSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R YLYR+    A    L +      P+ LD E M  AA+ LVG  DF  F     + ++ 
Sbjct: 139 RRYLYRLADADALRDPLRRHDTVWWPRPLDAERMDEAARPLVGLRDFAAFCKRR-EGATT 197

Query: 169 IRTIDHFDVNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           +RT+  +     G+ +    V A +F H+ +RS VG+   VG+G+  ++   +  Q   R
Sbjct: 198 VRTLLEYRWVRLGDGVLAATVRADAFCHSMVRSLVGAAVAVGEGRRPTSWPAELQQRTQR 257

Query: 228 KECGPLAPPEGLYFDSVEYS 247
                + P  GL  ++V Y 
Sbjct: 258 AADVRVMPAHGLSLEAVTYP 277


>gi|297242940|ref|ZP_06926878.1| tRNA pseudouridine synthase [Gardnerella vaginalis AMD]
 gi|296889151|gb|EFH27885.1| tRNA pseudouridine synthase [Gardnerella vaginalis AMD]
          Length = 301

 Score =  211 bits (537), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 79/281 (28%), Positives = 126/281 (44%), Gaps = 36/281 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW +Q    ++QG IE A+ +V         E + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGGFYGWAKQPTLRTVQGDIEAALHMVLRVPENDPTESLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVILCK-------ALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  E +   +         AL   L+  ++  I I  +S+    F ARF
Sbjct: 61  VHASHQVCHLDISDETLQRCIGHTGLDGVSALEYRLRHVLAQDIVIHKVSVAPYGFDARF 120

Query: 106 SAIRRSYLYRI---ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           SA+ R+Y+YRI     +       +G        LD + M  AA+ +VG HDF +F   +
Sbjct: 121 SALERTYVYRIADGYCKAKYDPRMRGFVLRFDSELDIDAMNQAARLMVGLHDFGSFAKPN 180

Query: 163 CQASSPIRTIDHFDVNSFGN----------------LIEIRVVARSFLHTQIRSFVGSLK 206
               + IR +     +  G+                L+E  +VA +F H  +RS V +  
Sbjct: 181 P-GGTTIRKVKQARWHRVGSKDAQNSTGFVLPIEQSLLEFTIVADAFAHNMVRSLVQACV 239

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +G GK +    E+ +    R+       P GL  + V Y 
Sbjct: 240 QIGCGKRSVDWFEEKINVPLREGSTGPIDPHGLTLEYVAYP 280


>gi|15639816|ref|NP_219266.1| tRNA pseudouridine synthase A [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189026054|ref|YP_001933826.1| tRNA pseudouridine synthase A [Treponema pallidum subsp. pallidum
           SS14]
 gi|6136049|sp|O83802|TRUA_TREPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238689345|sp|B2S468|TRUA_TREPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|3323141|gb|AAC65796.1| pseudouridylate synthase (hisT) [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018629|gb|ACD71247.1| pseudouridylate synthase [Treponema pallidum subsp. pallidum SS14]
          Length = 280

 Score =  210 bits (535), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 70/238 (29%), Positives = 111/238 (46%), Gaps = 8/238 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ-----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
            +  + I Y+G+ + GWQ+Q     +   S+QG +EK    +  + + V G+GRTDSGVH
Sbjct: 5   RKILLRISYDGTRFCGWQKQVSGSRERAPSVQGELEKVAEKIHHQKIAVIGSGRTDSGVH 64

Query: 57  ALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           A+ Q AHF    R  +      A N+ L    +I I +   V  Q HARFSA+ R+Y Y 
Sbjct: 65  AVGQAAHFCTPMRNILAYRFIPAFNSLL--PHSIRITDAREVSSQLHARFSAVMRTYRYH 122

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +       A E    W I +  D   +   A  L G  D T+F +   +++S  R     
Sbjct: 123 LHCAPVAYAHELPYCWHIARMPDIHLLNQYAATLKGELDCTSFAAAGDKSASKSRYFYDT 182

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             +    ++   + A +FL   +RS  G+L      + +  +  + L A+DR+  GP 
Sbjct: 183 HFSFNHRVLTFEISANAFLWKMVRSLTGTLLHCEKKRCSVREFVRILHAKDRRLQGPP 240


>gi|294494718|ref|YP_003541211.1| tRNA pseudouridine synthase A [Methanohalophilus mahii DSM 5219]
 gi|292665717|gb|ADE35566.1| tRNA pseudouridine synthase A [Methanohalophilus mahii DSM 5219]
          Length = 273

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 81/249 (32%), Positives = 107/249 (42%), Gaps = 25/249 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R  + I Y GS Y G Q Q   S+I+G I +A+  +             +GRTD+GVHA
Sbjct: 1   MRVALKIAYIGSSYRGSQVQPGVSTIEGKIFEALQSLEIIEDPSSARFVSSGRTDTGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           + QV  FD  +    + + + +N+ L     I   + + VD  FH R  AI R+Y Y   
Sbjct: 61  MGQVVAFDTDK--PKLAIPRVINSKL--PGDIWAWSRAEVDSDFHPRRYAINRTYRYITP 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           +  A                D   +R A   L G HDF  F        S IR I+  DV
Sbjct: 117 SMDA----------------DISKLRAACSILEGSHDFANFC-FRDTGRSTIRRIEKIDV 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              GNL+ I + A SFL   IR  V  L LVG G      LE  L     +E    A P 
Sbjct: 160 RLAGNLLRIDITANSFLWKMIRKIVTVLLLVGSGARDLDWLENMLDPASYEEGIKPAKPY 219

Query: 238 GLYFDSVEY 246
           GL   +V Y
Sbjct: 220 GLILTNVNY 228


>gi|212697539|ref|ZP_03305667.1| hypothetical protein ANHYDRO_02112 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675538|gb|EEB35145.1| hypothetical protein ANHYDRO_02112 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 242

 Score =  210 bits (534), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/219 (32%), Positives = 104/219 (47%), Gaps = 3/219 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
               + I+Y+GS + G+Q QK+  ++Q  +E+AI  VTGE   +  +GRTDSGVHA    
Sbjct: 4   QNILLKIQYDGSLFEGFQIQKDKRTVQKELEEAIRKVTGEKNRIIASGRTDSGVHANEMY 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +F   ++         L  YL     I  L+   VDK FHARFS   ++Y Y I   + 
Sbjct: 64  VNFLTAKDIRADKFHFHLKKYL--PADILALSSKKVDKNFHARFSVKTKTYKYVISLEKI 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSF 180
              + +     I   LD + ++   + L G HDF  F  S      + IR ID       
Sbjct: 122 LHPIYRNYMEQITYKLDFDKLKQGMEILKGEHDFRAFMLSEKNDIINTIRKIDDCYYILD 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            N++ +   A SFLH Q+R   GSL  +  GK +  D +
Sbjct: 182 NNILFLYFKAESFLHNQVRIMAGSLIELSRGKISLDDFK 220


>gi|241896974|ref|NP_001028662.1| tRNA pseudouridine synthase-like 1 [Mus musculus]
 gi|218525914|sp|A2ADA5|PUSL1_MOUSE RecName: Full=tRNA pseudouridine synthase-like 1; AltName:
           Full=tRNA pseudouridylate synthase-like 1; AltName:
           Full=tRNA-uridine isomerase-like 1
 gi|123295163|emb|CAM18398.1| pseudouridylate synthase-like 1 [Mus musculus]
          Length = 291

 Score =  210 bits (534), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 80/274 (29%), Positives = 125/274 (45%), Gaps = 30/274 (10%)

Query: 3   RYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY + ++Y G+ + G            +   +E+A   +   + V    + RTD+GVHAL
Sbjct: 13  RYLVFLQYLGTDFNGVAAVRGNPRAVGVLNFLEEAAKRLNSVDPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P ++ KALN +LK    I +L    V   FHAR +A  R+Y 
Sbjct: 73  SNAAHLDIQRRPGQSPFSPEVVAKALNTHLKHP-AIRVLKAFRVPNDFHARHAATSRTYQ 131

Query: 114 YRIITRQAPL----ALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T  +        E+   W +  + LD   M+ AAQHL+G HDF+ F+S     ++ 
Sbjct: 132 YRLATGCSWPNQLPVFEQNVCWALQTEYLDMAAMQEAAQHLLGTHDFSAFQSAGSPVTNT 191

Query: 169 IRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           +RT+    V+                    +   ++SFL+ Q+R     L  VG G    
Sbjct: 192 VRTLRRVSVSPGPASPFVLPEGSRRLQFWTLEFESQSFLYRQVRRMTAVLVAVGLGILAP 251

Query: 216 TDLEKALQAQDR--KECGPLAPPEGLYFDSVEYS 247
           T ++  L++QD   K    +AP  GL+  SV Y 
Sbjct: 252 TQVKVILESQDPLGKYQARVAPARGLFLKSVLYD 285


>gi|13507935|ref|NP_109884.1| tRNA pseudouridine synthase A [Mycoplasma pneumoniae M129]
 gi|2499079|sp|Q50291|TRUA_MYCPN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1215692|gb|AAC43685.1| hypothetical 28k protein (alkaline endoglucanase); GT9_orf321
           [Mycoplasma pneumoniae]
 gi|1674340|gb|AAB96283.1| pseudouridylate synthase I [Mycoplasma pneumoniae M129]
 gi|301633310|gb|ADK86864.1| tRNA pseudouridine synthase A [Mycoplasma pneumoniae FH]
          Length = 243

 Score =  210 bits (534), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 72/248 (29%), Positives = 106/248 (42%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  I+ YNG+ + GW +Q    ++QG IE+ + L+    + ++G+GRTD GVHA+ Q
Sbjct: 1   MPRYLAIVAYNGAPFRGWAKQPGYHTVQGQIEQNLALIYQTPINIYGSGRTDKGVHAINQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             H DL  +     L   LN        I +  L  V  +FHARF+   + Y Y I TR 
Sbjct: 61  TFHVDLPDKLPLKQLIAKLNQLNY--PDIFVKALVPVAPRFHARFAVKTKVYEYLINTRA 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                +    W     LD   +       +GR DF +F +         RTI    V   
Sbjct: 119 F-NPAQYHTVWQYNHPLDLAQLEADTTLFLGRKDFWSFSTAS--QKDTQRTISKIIVQQD 175

Query: 181 G-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +++      FL  QIR  V SL  + +       +++      +  C   AP  GL
Sbjct: 176 HTGTVKLTFFGNGFLRNQIRMMVASLVALNNRTLMRETVQQLFDQPQKGGCKVKAPACGL 235

Query: 240 YFDSVEYS 247
           Y  +V Y 
Sbjct: 236 YLKTVLYE 243


>gi|282163988|ref|YP_003356373.1| tRNA pseudouridine synthase A [Methanocella paludicola SANAE]
 gi|282156302|dbj|BAI61390.1| tRNA pseudouridine synthase A [Methanocella paludicola SANAE]
          Length = 279

 Score =  209 bits (533), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 112/247 (45%), Gaps = 23/247 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQ 60
           +    + Y G+ + G Q Q    +++G + K +    + GE   V  +GRTD+GVHAL Q
Sbjct: 14  KVAFKLAYVGTDFSGSQSQPGRRTVEGELRKGLVEKGIIGEKTKVEFSGRTDAGVHALGQ 73

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F    + +     + +N+ L     + +   ++V   F  R  A+ R+Y Y +    
Sbjct: 74  VIAFVPKNDKLTE--PRIINSVL--PADMWVYAKAVVPDDFDPRRHAVSRTYRYLLY--- 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP  +E+                  +Q   G HDFT F S+     +P+RT+    V   
Sbjct: 127 APDVIERRIVTY-------------SQLFPGTHDFTNFSSVEPN-KNPVRTVKSISVTKR 172

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++  I + A SFL   +R  V  L+LVG  K  +  +E+ L+  + +E  P A   GLY
Sbjct: 173 GDMYVIDIEADSFLWNMVRKIVTGLRLVGSNKRPAQWIEQMLKPDEYREGIPPALAAGLY 232

Query: 241 FDSVEYS 247
              VEY 
Sbjct: 233 LMKVEYP 239


>gi|313140894|ref|ZP_07803087.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum NCIMB 41171]
 gi|313133404|gb|EFR51021.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum NCIMB 41171]
          Length = 304

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 75/284 (26%), Positives = 123/284 (43%), Gaps = 40/284 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+G
Sbjct: 5   MRLRIDLAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDTG 64

Query: 55  VHALRQVAHF---------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H           +    VP  +         +   I+I ++++    F ARF
Sbjct: 65  VHASHQVCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPADITIHDVTVAPSGFDARF 124

Query: 106 SAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y+YR+  R +      +G    +   LD   M  AA   +G HDF +F + +  
Sbjct: 125 SALERTYVYRVADRASEVDPRLRGFVLHLDADLDVAAMNEAAAMTIGLHDFGSFATPNP- 183

Query: 165 ASSPIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFVGS 204
             + IR +                             +L+   +VA +F    +RS VG 
Sbjct: 184 GGTTIREVKTAYWRRIPTRPLVVDGVGERYRTPAAESDLLCFTIVADAFARNMVRSLVGG 243

Query: 205 LKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
              VG GK ++    + +    R+   GP+AP +GL  + V Y 
Sbjct: 244 CIQVGMGKRSTDWFREKMAVPLREGSTGPIAP-QGLTLEHVAYP 286


>gi|159039803|ref|YP_001539056.1| tRNA pseudouridine synthase A [Salinispora arenicola CNS-205]
 gi|157918638|gb|ABW00066.1| tRNA pseudouridine synthase A [Salinispora arenicola CNS-205]
          Length = 276

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 109/251 (43%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVHALR 59
            R  + + Y+G+ + GW  Q +  ++ G + +A  LV G      +  AGRTD+GVHA  
Sbjct: 5   TRVRLDVSYDGTDFSGWAVQPDRRTVAGVLVQAFDLVLGSDAATGLTVAGRTDAGVHATG 64

Query: 60  QVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL    W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHVDLLTEVWRRHEGTLLRRLARLLPGDVRVRAVTGVPGDFDARFSATFRRYEYRVTD 124

Query: 119 RQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +         LD + +  AA  LVG HDF  +     + ++ +R +   D 
Sbjct: 125 APWGAEPLRRHDTLAWSSRLDQDALNAAADGLVGEHDFAAYCRRK-ENATTLREVTRLDW 183

Query: 178 NSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               + +    V A +F    +RS VG++ +VGDG+  +      L  ++R     +AP 
Sbjct: 184 RRSADGVLVATVQADAFCQAMVRSLVGAMLVVGDGRRPAGWPAGLLARRERANEVNVAPA 243

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 244 HGLTLVAVGYP 254


>gi|295395151|ref|ZP_06805359.1| tRNA pseudouridine synthase A [Brevibacterium mcbrellneri ATCC
           49030]
 gi|294971913|gb|EFG47780.1| tRNA pseudouridine synthase A [Brevibacterium mcbrellneri ATCC
           49030]
          Length = 303

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 85/269 (31%), Positives = 118/269 (43%), Gaps = 24/269 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            R+ + + Y G+ + GW  Q +  ++QG +E A+  +    V V  AGRTD+GVHA RQV
Sbjct: 17  QRFRIDLGYVGTHFHGWALQPHLRTVQGELETALARILSAPVRVTVAGRTDAGVHARRQV 76

Query: 62  AHFDLVREWVPVI----------------LCKALNAYLKISD--TISILNLSIVDKQFHA 103
            H D+     P +                L   L   L   D   I I +++ V   F A
Sbjct: 77  VHVDIPHTDFPRLVGQPRARAEQRTPARGLTSRLRGVLARQDASDIVIHDVTAVHADFDA 136

Query: 104 RFSAIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ RSY YR+   QA    L           LD   M  AAQ + G  DF  F    
Sbjct: 137 RFSALWRSYTYRLADPQAFTDPLTAAFTVEHRAELDVAAMSAAAQQVCGLRDFLPFCKPR 196

Query: 163 CQASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            + S+ IRT++   V   G  +IE  + A +F H  +R+ VG L  VG+GKW    L   
Sbjct: 197 -EGSTTIRTLEELRVERVGSGVIEFFLRADAFCHHMVRALVGGLVKVGEGKWGPGRLAGM 255

Query: 222 LQAQDRKECG---PLAPPEGLYFDSVEYS 247
            +   R        + P  GL  + V Y 
Sbjct: 256 CEEAGRGGSEFPMFVFPAHGLVLEDVGYP 284


>gi|315452593|ref|YP_004072863.1| tRNA pseudouridine synthase A [Helicobacter felis ATCC 49179]
 gi|315131645|emb|CBY82273.1| tRNA pseudouridine synthase A [Helicobacter felis ATCC 49179]
          Length = 246

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 75/251 (29%), Positives = 104/251 (41%), Gaps = 14/251 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ M++ Y+GS ++G+ +Q N  S++G++E A+  + G    +  AGRTD GVHAL Q
Sbjct: 1   MGRFQMLLAYDGSAFYGYAKQPNLPSVEGALESALLKL-GISSPILCAGRTDRGVHALCQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F          L + L   L     I    +  V   FH RF A  R Y Y      
Sbjct: 60  VISFSTP--LSLQTLQRHLPPKLPAP--ILCKGIQEVPLDFHPRFDATWRLYRYICTNIP 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
            P                 + ++ A    VG HDF  F     +     RTI    V   
Sbjct: 116 -PSPFLSRFIAHCAYGP-LKLIQEALNLFVGTHDFKFFCKR--ETRHTQRTIHSTKVYQR 171

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  I I + A SFL  Q+R  V +      GK +  DL+  +  + R     LAPP
Sbjct: 172 VLYNHPCIVIAIRAPSFLRAQVRLMVSAALAHSLGKLSLEDLKAQIATRARHH-HLLAPP 230

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 231 QGLYLARVAYP 241


>gi|311064868|ref|YP_003971594.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum PRL2010]
 gi|310867188|gb|ADP36557.1| TruA tRNA pseudouridine synthase A [Bifidobacterium bifidum
           PRL2010]
          Length = 303

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 75/284 (26%), Positives = 123/284 (43%), Gaps = 40/284 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+G
Sbjct: 4   MRLRIDLAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDTG 63

Query: 55  VHALRQVAHF---------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           VHA  QV H           +    VP  +         +   I+I ++++    F ARF
Sbjct: 64  VHASHQVCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPADITIHDVTVAPSGFDARF 123

Query: 106 SAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           SA+ R+Y+YR+  R +      +G    +   LD   M  AA   +G HDF +F + +  
Sbjct: 124 SALERTYVYRVADRASEVDPRLRGFVLHLDADLDVAAMNEAAAMTIGLHDFGSFATPNP- 182

Query: 165 ASSPIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFVGS 204
             + IR +                             +L+   +VA +F    +RS VG 
Sbjct: 183 GGTTIREVKTAYWRRIPTRPLVVDGMGERYRTPAAESDLLCFTIVADAFARNMVRSLVGG 242

Query: 205 LKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
              VG GK ++    + +    R+   GP+AP +GL  + V Y 
Sbjct: 243 CIQVGMGKRSTDWFREKMAVPLREGSTGPIAP-QGLTLEHVAYP 285


>gi|194246764|ref|YP_002004403.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma mali]
 gi|254764860|sp|B3R022|TRUA_PHYMT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|193807121|emb|CAP18559.1| tRNA pseudouridine synthase A [Candidatus Phytoplasma mali]
          Length = 244

 Score =  209 bits (532), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 113/245 (46%), Gaps = 6/245 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQV 61
            Y +++ Y+G+ Y+G+Q+Q + ++IQ  +E  +  +   + + ++GA RTD GVHA  QV
Sbjct: 5   NYKLVLSYDGTNYYGFQKQLHLNTIQSVLENVLNKITKQKKIKIYGASRTDKGVHASGQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF L          K LN  L     I I  + ++ K+FH RF A  + Y Y    ++ 
Sbjct: 65  VHFQLPFLIPNDHFQKILNFCL--PSDIQITKIILISKEFHCRFQAKSKIYHYVFSKKKL 122

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                      IP ++D   ++ A   + G+HDF+ F S      +  R I    +    
Sbjct: 123 -NVFNYRFQVYIP-NMDFNKIKEAILFIEGKHDFSLFTSQKS-LKNYQRIIFKAFIKETK 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
               + +   SF+   IR  VG L  +   K T ++ ++ L  +  ++   LAP +GL  
Sbjct: 180 QKYFLIIHGNSFIQHMIRFLVGFLIEIAQNKKTLSEFKQMLDLKINQKARLLAPAKGLIL 239

Query: 242 DSVEY 246
             + Y
Sbjct: 240 KKIFY 244


>gi|153807552|ref|ZP_01960220.1| hypothetical protein BACCAC_01832 [Bacteroides caccae ATCC 43185]
 gi|149129914|gb|EDM21126.1| hypothetical protein BACCAC_01832 [Bacteroides caccae ATCC 43185]
          Length = 220

 Score =  209 bits (532), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 74/218 (33%), Positives = 104/218 (47%), Gaps = 7/218 (3%)

Query: 33  KAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISIL 92
           KA+       + V GAGRTD+GVHA   VAHFD       V + + LN  L     IS+ 
Sbjct: 2   KALSTFLRCEIEVVGAGRTDAGVHASLMVAHFDYDGLLDTVSVAEKLNRLL--PPDISVY 59

Query: 93  NLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
            +  V  + HARF A  R+Y Y +   + P    +   W I  SLD E M  AA+ L   
Sbjct: 60  RVCRVKPEAHARFDATARTYKYYVTAVKYP--FNRQYRWRIYSSLDYERMNEAARTLFEY 117

Query: 153 HDFTTFRSIHCQASSPIRTIDHFDVNSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVG 209
            DFT+F  +H    + I  I H +     +        + A  FL   +R+ VG+L  VG
Sbjct: 118 SDFTSFSKLHTDVKTNICHITHAEWTKVTDDEATWVFTIRADRFLRNMVRAIVGTLIEVG 177

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            GK +  D  + ++ QDR + G  AP + L+  +VEY 
Sbjct: 178 RGKLSVEDFRRIIEQQDRCKAGTSAPGQALFLVNVEYP 215


>gi|303328364|ref|ZP_07358802.1| tRNA pseudouridine synthase A [Desulfovibrio sp. 3_1_syn3]
 gi|302861694|gb|EFL84630.1| tRNA pseudouridine synthase A [Desulfovibrio sp. 3_1_syn3]
          Length = 226

 Score =  208 bits (531), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 73/227 (32%), Positives = 110/227 (48%), Gaps = 14/227 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R  +++ Y G+GY GWQ Q+      +IQG +E A+ ++ G  V VHG+GRTD+GVHA 
Sbjct: 1   MRLKLLLAYLGTGYSGWQIQEKPSPPPTIQGELEAALRVLAGAPVRVHGSGRTDAGVHAH 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVAH D+      +   ++LNA L     I IL        FHAR  A+R++Y+Y+   
Sbjct: 61  GQVAHCDVPDAKAGLRWQRSLNALL--PPEIRILAAEPAAADFHARKDALRKTYVYQFWQ 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +A +  +    +     LD E MR A  HL+G HDF   ++      S  RT+   +++
Sbjct: 119 ERAFVPPQLAPFFWNCGPLDVEAMRAALPHLLGEHDFAGLQNAGTDMESTTRTVFRAELD 178

Query: 179 ---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                         + + V A  FL   +R+  G L   G GK    
Sbjct: 179 IPPPCEFYPPHAPGLRLTVTANGFLKQMVRNMAGLLAACGQGKIRPE 225


>gi|13358100|ref|NP_078374.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 3 str.
           ATCC 700970]
 gi|170761947|ref|YP_001752621.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 3 str.
           ATCC 27815]
 gi|183508635|ref|ZP_02958135.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 14 str.
           ATCC 33697]
 gi|26006901|sp|Q9PPV4|TRUA_UREPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030149|sp|B1AJH7|TRUA_UREP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|11269468|pir||B82879 pseudouridylate synthase I UU536 [imported] - Ureaplasma
           urealyticum
 gi|6899540|gb|AAF30949.1|AE002152_8 pseudouridylate synthase I [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|168827524|gb|ACA32786.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 3 str.
           ATCC 27815]
 gi|182676096|gb|EDT88001.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 14 str.
           ATCC 33697]
          Length = 241

 Score =  208 bits (531), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 113/247 (45%), Gaps = 8/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           + Y + + Y+GS ++GW RQ    ++QG +E+    +     + + G+GRTD GVHA  Q
Sbjct: 1   MNYKISLRYDGSLFYGWARQPQKRTVQGDLEEIFKSIFKINNIRIIGSGRTDKGVHAYEQ 60

Query: 61  VAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                    ++   I+ +AL +  + S  I IL +  VD  FHA+++A  ++Y Y I   
Sbjct: 61  TFSVKHSALKYDSHIIYQALCS--RTSSDIQILEVQKVDDSFHAQYNATSKTYQYVINDY 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +            + + ++ + +  A +  VG HDF +F +   + +  IR I+   +  
Sbjct: 119 EF-DLFRNNYELFVNQKINDQKILEALELFVGEHDFKSFST--SELTMTIRRINWVKIKR 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             +LI I + A  FL   +R  V S       K +   + + L    +     LAP  GL
Sbjct: 176 DTHLI-IYINANGFLKNMVRMIVASCLDYAFNKISLAKIHELLIYPKKGASIKLAPACGL 234

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 235 YLYKVYY 241


>gi|328875656|gb|EGG24020.1| hypothetical protein DFA_06158 [Dictyostelium fasciculatum]
          Length = 403

 Score =  208 bits (531), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 88/258 (34%), Positives = 130/258 (50%), Gaps = 33/258 (12%)

Query: 22  KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREW----------- 70
           +NG SIQ +IE  +  +  + + + G+ RTDSGV++L QVAH DL  +            
Sbjct: 81  ENGRSIQYAIEHGLSHIMRQRIQIVGSSRTDSGVNSLCQVAHCDLPNQRYDKKGTIEQEQ 140

Query: 71  -VPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP---LAL 125
             P I+  ALN  LK  +  I I+++  VD +FH+R++A  R+YLY+I+T   P      
Sbjct: 141 LTPSIIKIALNQQLKRHNHDIRIVSVEKVDNEFHSRYNATSRTYLYKIMTGVRPTEVPLE 200

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--------DV 177
            K + W I ++LD + M+  A  L G HDF + RS  CQA SPIR+I H         D+
Sbjct: 201 LKNKVWPIWETLDIDQMKETASFLQGLHDFDSLRSAKCQAKSPIRSISHIKIIDLPLPDI 260

Query: 178 NSFGN---------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
             + N          I + +  RSFLH Q+R     L  +G G  T  +L++ ++ +DR 
Sbjct: 261 WRYNNDDSTPPKIQYIGLEIKGRSFLHNQVRIMSSCLAEIGRGHMTLDNLKEIMKGRDRT 320

Query: 229 ECGPLAPPEGLYFDSVEY 246
                AP   L    V Y
Sbjct: 321 LAPATAPAYPLTLVKVSY 338


>gi|332295380|ref|YP_004437303.1| tRNA pseudouridine synthase A [Thermodesulfobium narugense DSM
           14796]
 gi|332178483|gb|AEE14172.1| tRNA pseudouridine synthase A [Thermodesulfobium narugense DSM
           14796]
          Length = 283

 Score =  208 bits (531), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 75/254 (29%), Positives = 115/254 (45%), Gaps = 13/254 (5%)

Query: 1   MIR-------YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDS 53
           M R          II Y+G+ + G+Q Q    ++Q  IE+ +  +  E V V  AGRTD+
Sbjct: 1   MPRSFSLKMDIAAIISYDGTNFHGFQMQNQSRTVQLVIEQKLEKIFKERVCVVPAGRTDA 60

Query: 54  GVHALRQVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GVHA+ QV  F L +  +    L   LN +L   D I I  + ++   F++RFSA  R Y
Sbjct: 61  GVHAIGQVISFRLAKCPFDVEKLQNILNYHL--PDDIRISEMRLMPADFNSRFSAKSRVY 118

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +Y I  ++   A      W +  SL  E+++     +  R  F +F  +         T+
Sbjct: 119 VYAISAKKDICAHLNRYFWNLDISL--EDLKATLNLIPNRFCFRSFSRVSKDRKLNFGTV 176

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                  F + +   + A SFL   +R   G    V  GK T  D ++AL+ + R     
Sbjct: 177 TFSKCVVFEDFLYFIIEAPSFLWHTVRFLFGEAVAVAKGKRTLEDYKEALEGKKR-LVLY 235

Query: 233 LAPPEGLYFDSVEY 246
            APP+GL+   V Y
Sbjct: 236 KAPPKGLHLWGVSY 249


>gi|302851591|ref|XP_002957319.1| tRNA pseudouridine synthase [Volvox carteri f. nagariensis]
 gi|300257414|gb|EFJ41663.1| tRNA pseudouridine synthase [Volvox carteri f. nagariensis]
          Length = 226

 Score =  208 bits (529), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 73/224 (32%), Positives = 103/224 (45%), Gaps = 6/224 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---AGRTDSGVHALRQ 60
           Y MI+ Y+G+ Y GWQ Q +  ++Q  +E A+  V  E   V G   AGRTD+GVHA  Q
Sbjct: 5   YRMIVSYDGTAYCGWQLQPSAPTVQRFLEGALCTVLREERAVLGVRAAGRTDAGVHARGQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   +E     +   LN+ L     I +L +S     F    SA+ + Y Y I   +
Sbjct: 65  VVQFSCDKELDVTKMPYKLNSVL--PHDIRVLRMSRTAPDFSVTCSALGKCYRYSITNGE 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A  + + LD   MR AA  L G HDF+ F +I  +  SP         N  
Sbjct: 123 THDPLRHRYALHVRRHLDLAAMRSAAALLTGTHDFSQFSNIGEEGGSPDVQRRRRQRNPV 182

Query: 181 GNLIEIRVV-ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             L  + VV    FL+  +R   G L  VG+GK  +  + + L+
Sbjct: 183 KTLRRVDVVEGNGFLYKMVRHISGVLVAVGEGKLQTKAVGRMLE 226


>gi|91215693|ref|ZP_01252663.1| putative tRNA pseudouridine synthase A [Psychroflexus torquis ATCC
           700755]
 gi|91186159|gb|EAS72532.1| putative tRNA pseudouridine synthase A [Psychroflexus torquis ATCC
           700755]
          Length = 224

 Score =  208 bits (529), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 109/225 (48%), Gaps = 3/225 (1%)

Query: 23  NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAY 82
           +  S+Q  +  A+     E V V GAGRTD+GVHA   VAHFD  ++     +  A    
Sbjct: 2   HEISVQSQVNLALKTALQETVDVVGAGRTDTGVHASGYVAHFDSSQKIFDFKML-AFKLN 60

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM 142
             +   I++ ++  V   FHARF AI R+Y Y II  + P ++  GR++L+   L+ + M
Sbjct: 61  SILPPDIAVQSVVGVKDDFHARFDAISRTYRYSIIQTKDPFSV--GRSYLVKNELNLQVM 118

Query: 143 RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
           + A+  L    +F +F  +     +    I+  +    G+ +   + A  FL   +R+ V
Sbjct: 119 QNASNLLFNHKNFKSFSKVKTDVYTFDCHIEKVEWQKEGHHLFFEITANRFLRNMVRAIV 178

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G+L  VG  K +  +    + A+DR + G   P   L   +++Y 
Sbjct: 179 GTLIEVGLEKISVEEFNDIILAKDRSKAGKSVPAHALVLTNIKYP 223


>gi|171920141|ref|ZP_02931545.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 1 str.
           ATCC 27813]
 gi|186701850|ref|ZP_02971512.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 6 str.
           ATCC 27818]
 gi|171902508|gb|EDT48797.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 1 str.
           ATCC 27813]
 gi|186701145|gb|EDU19427.1| tRNA pseudouridine synthase A [Ureaplasma parvum serovar 6 str.
           ATCC 27818]
          Length = 241

 Score =  208 bits (529), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 113/247 (45%), Gaps = 8/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           + Y + + Y+GS ++GW RQ    ++QG +E+    +     + + G+GRTD GVHA  Q
Sbjct: 1   MNYKISLRYDGSLFYGWARQPQKRTVQGDLEEIFKSIFKINNIRIIGSGRTDKGVHAYEQ 60

Query: 61  VAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +        ++   I+ +AL +  + S  I IL +  VD  FHA+++A  ++Y Y I   
Sbjct: 61  IFSVKHSALKYDSHIIYQALCS--RTSSDIQILEVQKVDDSFHAQYNATSKTYQYVINDY 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +            + + ++ + +  A +  VG HDF +F +   + +  IR I+   +  
Sbjct: 119 EF-DLFRNNYELFVNQKINDQKILEALELFVGEHDFKSFST--SELTMTIRRINWVKIKR 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              LI I + A  FL   +R  V S       K +   + + L    +     LAP  GL
Sbjct: 176 DTRLI-IYINANGFLKNMVRMIVASCLDYAFNKISLAKIHELLIYPKKGASIKLAPACGL 234

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 235 YLYKVYY 241


>gi|197303254|ref|ZP_03168295.1| hypothetical protein RUMLAC_01977 [Ruminococcus lactaris ATCC
           29176]
 gi|197297680|gb|EDY32239.1| hypothetical protein RUMLAC_01977 [Ruminococcus lactaris ATCC
           29176]
          Length = 242

 Score =  207 bits (528), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 62/247 (25%), Positives = 112/247 (45%), Gaps = 6/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  + M ++Y+G+ Y GW +  K+  ++   +E+ +  + G+ V +H A RT+  VHA  
Sbjct: 1   MNNFKMTLQYDGTRYLGWTKNEKSVKTVSYKLEQVLTRLLGQPVTLHAAVRTEPCVHASC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  F+    + P +L K +N YL     I +L+L  V  +F A       +Y Y + T 
Sbjct: 61  QVCSFEADLPFSPEVLKKQMNQYL--PMDIKVLSLLPVSGRFRADLGIRAYTYEYNVCTA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                           + D   M+ AA  L+G+HDF +F  +  +     + + + D   
Sbjct: 119 SVYDVFHSRYQAHFFPAPDLALMKQAASCLIGKHDFQSFSPVR-KKKGTKKELLYLDFIQ 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +  R+ A +FL +  +  VG+L  +G GK +   +    +  +    G   P +GL
Sbjct: 178 NKEQLSFRLTANAFLPSMPQLIVGTLLEIGQGKRSPDCILSIFEGNETP--GNFCPSDGL 235

Query: 240 YFDSVEY 246
           +   ++Y
Sbjct: 236 FLTEIQY 242


>gi|283782782|ref|YP_003373536.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 409-05]
 gi|283442111|gb|ADB14577.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 409-05]
          Length = 305

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 82/286 (28%), Positives = 127/286 (44%), Gaps = 42/286 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW +Q    ++QG IE A+  V         E + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGGFYGWAKQPTLRTVQGEIEGALHTVLRVPEGDSAEPLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVILCK-------ALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  E +   +         AL   LK  +   IS+  +S+    F ARF
Sbjct: 61  VHASHQVCHLDVCEETLLRCVGHTGLDGVCALEYRLKHVLPQDISLHKVSVAPIGFDARF 120

Query: 106 SAIRRSYLYRIITR---QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           SA+ R+Y+YRI             +G    +   LD + M  AA+ ++G HDF +F   +
Sbjct: 121 SALERTYVYRICDASDYCDYDPRMRGFVLKLDDVLDVDAMNQAARLMIGLHDFGSFARPN 180

Query: 163 CQASSPIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFV 202
               + IR +        G                     L+E  +VA +F H  +RS V
Sbjct: 181 P-GGTTIRDVKSACWERVGTRANDVRVKLKTGCVPPVEQGLLEFTIVADAFAHNMVRSLV 239

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            +   +G GK T     + +    R+   GP+AP +GL  + V Y 
Sbjct: 240 QACVQIGCGKRTLDWFVEKINTPLREGSTGPIAP-QGLTLEYVAYP 284


>gi|118101049|ref|XP_417580.2| PREDICTED: similar to MGC80334 protein [Gallus gallus]
          Length = 291

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 90/276 (32%), Positives = 134/276 (48%), Gaps = 31/276 (11%)

Query: 2   IRYCMIIEYNGSGYFG-WQRQKN--GSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHA 57
            RY +  +Y G+ Y G  Q      G  +Q  +EKA   +     +  H + RTDSGVHA
Sbjct: 6   TRYLVFFQYWGTKYSGVMQTSAEQSGIGVQNYLEKAAQNLKPVVPIKFHISSRTDSGVHA 65

Query: 58  LRQVAHFDLVREWVPVILCKA-----LNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           L   AH D+ R        +      LN +LK  + I IL+   V   FHARFSA+ R+Y
Sbjct: 66  LCNSAHLDIQRAPGKPAFQERVLIGCLNHHLK-PEPIRILSAYRVTNNFHARFSALSRTY 124

Query: 113 LYRIITRQAP----LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQA-- 165
           +YR++            E+   W  P   L+   M+ AAQ L+G HDF+TF S++ +   
Sbjct: 125 IYRLLMGCTHHSEIPVFERDLCWAPPGGYLNVPAMQDAAQFLLGTHDFSTFCSLNSETPF 184

Query: 166 SSPIRTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
            SP++TI   D+                   E++  +RSFL+ Q+R  VG+L  VG GK 
Sbjct: 185 RSPVKTILQADIQPSSGFLSHHYEYRGLQFWELKFKSRSFLYRQVRRMVGALVAVGQGKL 244

Query: 214 TSTDLEKALQAQDRKE--CGPLAPPEGLYFDSVEYS 247
               +++ L+ +D +      +AP  GL+  SVEY+
Sbjct: 245 APHHIKELLEMKDARAFPAFAMAPSSGLFLKSVEYN 280


>gi|171920798|ref|ZP_02931982.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 13
           str. ATCC 33698]
 gi|185179091|ref|ZP_02964822.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 5
           str. ATCC 27817]
 gi|188024013|ref|ZP_02996773.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 7
           str. ATCC 27819]
 gi|188518366|ref|ZP_03003873.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 11
           str. ATCC 33695]
 gi|188524280|ref|ZP_03004323.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 12
           str. ATCC 33696]
 gi|195867909|ref|ZP_03079907.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 9
           str. ATCC 33175]
 gi|198273508|ref|ZP_03206044.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 4
           str. ATCC 27816]
 gi|209554225|ref|YP_002284984.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 10
           str. ATCC 33699]
 gi|225550684|ref|ZP_03771633.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 2
           str. ATCC 27814]
 gi|225551354|ref|ZP_03772300.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 8
           str. ATCC 27618]
 gi|238057738|sp|B5ZC44|TRUA_UREU1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|171903560|gb|EDT49849.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 13
           str. ATCC 33698]
 gi|184208984|gb|EDU06027.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 5
           str. ATCC 27817]
 gi|188019040|gb|EDU57080.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 7
           str. ATCC 27819]
 gi|188998036|gb|EDU67133.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 11
           str. ATCC 33695]
 gi|195659898|gb|EDX53278.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 12
           str. ATCC 33696]
 gi|195660386|gb|EDX53645.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 9
           str. ATCC 33175]
 gi|198250028|gb|EDY74808.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 4
           str. ATCC 27816]
 gi|209541726|gb|ACI59955.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 10
           str. ATCC 33699]
 gi|225379169|gb|EEH01534.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 8
           str. ATCC 27618]
 gi|225379838|gb|EEH02200.1| tRNA pseudouridine synthase A [Ureaplasma urealyticum serovar 2
           str. ATCC 27814]
          Length = 241

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 110/247 (44%), Gaps = 8/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQ 60
           + Y + I Y+GS ++GW +Q    ++Q  +E     +     + + G+GRTD GVHA  Q
Sbjct: 1   MNYKISIRYDGSLFYGWAKQPQKRTVQEHLETVFKTIFKINDIKIIGSGRTDRGVHAYEQ 60

Query: 61  VAHF-DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V         + P ++ +AL +  +I   + IL +  V   FHA+  AI ++Y Y I   
Sbjct: 61  VFSVNHHQLNYEPQVIYQALCS--QIDPDVQILKVQSVHDTFHAQHDAISKTYQYIINDY 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     +    + I + ++ + +  A +  VG +DF +F +   +     R I+   +  
Sbjct: 119 EF-DLFKHNYEYFIHQKINDQKLLEALELFVGEYDFKSFST--SELPLTTRKINWVKITR 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
              L EI +    FL   +R  + +       K + T ++  L    +     LAPP GL
Sbjct: 176 NTRL-EIYINGNGFLKNMVRMIISACIDYVFNKISLTQIKTLLTNPKKGASVKLAPPCGL 234

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 235 YLYKVYY 241


>gi|315636694|ref|ZP_07891924.1| tRNA pseudouridine synthase A [Arcobacter butzleri JV22]
 gi|315479009|gb|EFU69712.1| tRNA pseudouridine synthase A [Arcobacter butzleri JV22]
          Length = 240

 Score =  207 bits (527), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 117/246 (47%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +    ++ Y+GS + G Q+Q NG +++  + KA   +  +   +  +GRTD  VH+  QV
Sbjct: 1   MNLKFVVAYDGSLFQGSQKQPNGKTVENELLKAFENINIKT-QIVLSGRTDKEVHSSGQV 59

Query: 62  AHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +  +   W     L + LN  L    +I I  +S V++ FH+RFSA +R Y Y I T++
Sbjct: 60  FNCQIPSYWEDFFKLKEILNKNL--PTSIKIKKISKVEESFHSRFSAKKRVYRYLITTKE 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                       + KS+D + ++ A +  +G HDF  F        +  R I       +
Sbjct: 118 T-TPFNDKFITYV-KSVDEKLLKKAIKEFIGVHDFKYFHKTGSDKENTNREIFDTKFYKY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++   +  A S+L +QIR  VG L  + D K T  DL+K L  +      P+  P GLY
Sbjct: 176 KDIYVFKFTANSYLRSQIRLMVGFLLAINDKKLTIEDLKKQLNCEKSIFKTPI-KPNGLY 234

Query: 241 FDSVEY 246
              ++Y
Sbjct: 235 LAKIKY 240


>gi|308178101|ref|YP_003917507.1| tRNA pseudouridylate synthase A [Arthrobacter arilaitensis Re117]
 gi|307745564|emb|CBT76536.1| tRNA pseudouridylate synthase A [Arthrobacter arilaitensis Re117]
          Length = 311

 Score =  207 bits (527), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 81/259 (31%), Positives = 122/259 (47%), Gaps = 15/259 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  M++ Y+G+ Y GW RQ N   +Q  +E+A+ ++    V V  AGRTD+GVHA RQV 
Sbjct: 26  RMRMVLGYDGAAYSGWARQPNVLGVQQLVEEALEMLIRRQVRVVVAGRTDAGVHARRQVV 85

Query: 63  HFDLVREW-----------VPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           HFDL  E                L + +N  L +    + +       + F ARFSA+ R
Sbjct: 86  HFDLTEEEYTSLPRKAPLAPGPALVRRINGILGRQDGAVWVHEAERAPEGFDARFSALAR 145

Query: 111 SYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            Y YRI   Q     L +       + LD E M   A+ ++GRHDF T+      A + I
Sbjct: 146 RYSYRIADGQQRWDPLTRQLTTWHREELDVEAMNREARSVLGRHDFLTYCKPRPHA-TTI 204

Query: 170 RTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           RT+  F      + + +  + A +F H  +R+ +G+  +VGDG+     L + L+   R 
Sbjct: 205 RTLQEFTFTRGADGLVLAHLKADAFCHNMVRALIGAAMMVGDGREQPGFLAERLELMVRD 264

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               L+ P  L  + V Y 
Sbjct: 265 SKTKLSHPRALVLEEVYYP 283


>gi|66811154|ref|XP_639285.1| hypothetical protein DDB_G0283061 [Dictyostelium discoideum AX4]
 gi|60467961|gb|EAL65974.1| hypothetical protein DDB_G0283061 [Dictyostelium discoideum AX4]
          Length = 343

 Score =  207 bits (527), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 90/301 (29%), Positives = 137/301 (45%), Gaps = 55/301 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
            RY +I EY G  + G+QR K       +Q  +E ++  + G  + + G+ RTD GV A+
Sbjct: 3   PRYKIIYEYIGKSFTGFQRLKYPVVKLPVQQVLEDSLEKIHGYKIPIVGSSRTDHGVSAV 62

Query: 59  RQVAHFDLVRE----------WVPVILCKALNAYLKIS--DTISILNLSIVDKQFHARFS 106
            QV+HFD+               P  L  A+N  +      +I I+   IVD +FH RF+
Sbjct: 63  GQVSHFDVKTRTSKSGIEMPLLSPEELTMAINYNVGKEYLKSIRIIKTEIVDDKFHCRFN 122

Query: 107 AIRRSYLYRII--TRQAPLALEK-GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A  R+YLYR++    +  + LE   R +L+   L+ + MR A++  +G HDF++FRS  C
Sbjct: 123 ATSRTYLYRVMANCGRKQIPLELLDRVYLVGPILNLDEMRKASEMFIGTHDFSSFRSAKC 182

Query: 164 QASSPIRTIDHFDVNSFG-------------------------------------NLIEI 186
            ++ PIR+I H  +                                             I
Sbjct: 183 SSTRPIRSISHIKIYDLPLPDIFQYNPSFQNISRSNTNYPIGDGEKNLDKKNTGLQYFGI 242

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + AR+FLH Q+R  V SL  VG+G+ +   LE+    +DR    P A PE L   +V Y
Sbjct: 243 EIKARAFLHNQVRIMVASLIKVGEGEISIQQLEEIKDKKDRGAAPPTASPEPLTLLTVSY 302

Query: 247 S 247
            
Sbjct: 303 D 303


>gi|118462566|ref|YP_883531.1| tRNA pseudouridine synthase A [Mycobacterium avium 104]
 gi|254776828|ref|ZP_05218344.1| tRNA pseudouridine synthase A [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|118163853|gb|ABK64750.1| tRNA pseudouridine synthase A [Mycobacterium avium 104]
          Length = 251

 Score =  207 bits (527), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 111/232 (47%), Gaps = 14/232 (6%)

Query: 29  GSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA---------- 78
           G +++A+  V    V +  AGRTD+GVHA  QVAH D+    +P    +A          
Sbjct: 3   GVLDEALTTVFRTPVRLRAAGRTDAGVHATGQVAHLDVPGTALPNAYPRAPHVGEAEFGP 62

Query: 79  --LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPK 135
                   +   + +++++     F ARFSA+RR Y+YR+ T     L  +       P+
Sbjct: 63  LLRRLGRFLPTDVRVVDITRAPAGFDARFSALRRHYVYRLSTAPWGVLPQQARYVTAWPR 122

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
            LD E M  A++ L+G HDF  F   H + ++ IR +   D    G+LI  RV A +F  
Sbjct: 123 PLDVEAMAAASRDLLGLHDFAAFCR-HRENATTIRDLQRLDWTRDGDLIIARVSADAFCW 181

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + +RS VG+L  VG+ +   +   + L A +R      AP  GL    V+Y 
Sbjct: 182 SMVRSLVGALLAVGENRRPVSWCRELLSATNRSSDYATAPAHGLTLVGVDYP 233


>gi|224438205|ref|ZP_03659140.1| tRNA pseudouridine synthase A [Helicobacter cinaedi CCUG 18818]
 gi|313144651|ref|ZP_07806844.1| tRNA pseudouridine synthase A [Helicobacter cinaedi CCUG 18818]
 gi|313129682|gb|EFR47299.1| tRNA pseudouridine synthase A [Helicobacter cinaedi CCUG 18818]
          Length = 245

 Score =  207 bits (527), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 112/247 (45%), Gaps = 6/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  +I Y+GS ++G+  QK+  S+ G+++     V G    + G  RTD GVH+  Q
Sbjct: 1   MPRYKAVISYDGSAFYGFALQKHKPSVLGALQDGFSRV-GIRGEILGTSRTDKGVHSTGQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F+         L   LNA L     I++  L  V++ FH RF A+ R+Y + + +  
Sbjct: 60  VISFESRHFEDSHTLQNLLNAKLYPH--IAVRRLERVNEDFHPRFHALWRAYRFLLSSH- 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   +        K  +    + A     G+H+F  F+         IR I        
Sbjct: 117 APSPFQSAYVS-YEKIGNRALFQSALSMFKGKHNFALFKKNGSFTKDSIRDIFRIFSYQH 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L  + +    FL +Q+R  VG+   V  G+ +   L++ +QA+ R    P++P  GLY
Sbjct: 176 KGLDIVYIKGNGFLRSQVRLMVGAALSVSRGELSLESLQEQIQAKKRHYNFPISP-NGLY 234

Query: 241 FDSVEYS 247
              V YS
Sbjct: 235 LCGVGYS 241


>gi|41410333|ref|NP_963169.1| tRNA pseudouridine synthase A [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|51316707|sp|Q73S41|TRUA_MYCPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|41399167|gb|AAS06785.1| TruA [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 251

 Score =  207 bits (527), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 111/232 (47%), Gaps = 14/232 (6%)

Query: 29  GSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA---------- 78
           G +++A+  V    V +  AGRTD+GVHA  QVAH D+    +P    +A          
Sbjct: 3   GVLDEALTTVFRTPVRLRAAGRTDAGVHATGQVAHLDVPGTALPNAYPRAPHVGEAEFGP 62

Query: 79  --LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPK 135
                   +   + +++++     F ARFSA+RR Y+YR+ T     L  +       P+
Sbjct: 63  LLRRLGRFLPTDVRVVDITRAPAGFDARFSALRRHYVYRLSTAPWGVLPQQARYVTAWPR 122

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
            LD E M  A++ L+G HDF  F   H + ++ IR +   D    G+LI  RV A +F  
Sbjct: 123 PLDVEAMAAASRDLLGLHDFAAFCR-HRENATTIRDLQRLDWTRDGDLITARVSADAFCW 181

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + +RS VG+L  VG+ +   +   + L A +R      AP  GL    V+Y 
Sbjct: 182 SMVRSLVGALLAVGENRRPVSWCRELLSATNRSSDYATAPAHGLTLVGVDYP 233


>gi|317498140|ref|ZP_07956442.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894617|gb|EFV16797.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 206

 Score =  207 bits (527), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 71/205 (34%), Positives = 103/205 (50%), Gaps = 13/205 (6%)

Query: 1   MIR-YCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVH 56
           M R   + IEY+GS Y GWQR     N ++IQG +E  +  +TGE V ++G+GRTD+GVH
Sbjct: 1   MKRNIRLTIEYDGSRYQGWQRLGGDSNANTIQGKLESVLSKMTGEDVNINGSGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QVA+F          +   L  YL     I I+ +S   ++FH+R +A  ++YLYRI
Sbjct: 61  AYGQVANFHTDCMMSVNEIKNYLTKYL--PSDIGIVEVSEASERFHSRLNAKEKTYLYRI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                    E+   W  P++LD + M  AA  L+G HDF  F SI     S +RTI + +
Sbjct: 119 AIPGVSNVFERKYLWYFPETLDIKKMEEAASLLIGTHDFKGFSSIKKTKKSTVRTIYNIE 178

Query: 177 VNSFG-------NLIEIRVVARSFL 194
           +             +   +    FL
Sbjct: 179 IKKTKKKSRSLIQEMASFITWSGFL 203


>gi|91773587|ref|YP_566279.1| tRNA pseudouridine synthase A [Methanococcoides burtonii DSM 6242]
 gi|121691685|sp|Q12VJ7|TRUA_METBU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91712602|gb|ABE52529.1| tRNA pseudouridine synthase A [Methanococcoides burtonii DSM 6242]
          Length = 275

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 106/250 (42%), Gaps = 25/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R  + I Y GS + G Q Q N  +++G + K +  +             +GRTDSGVHA
Sbjct: 1   MRVALKIAYIGSNFHGSQVQLNDPTVEGELFKVLKELGIMEDPRTANFISSGRTDSGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           + QV  FD       + + + +N+ L    TI     +IV + F  R  A+ RSY Y + 
Sbjct: 61  MGQVVAFDTDA--PNLAMPRVINSKL--PGTIWAWAHAIVPENFDPRRHALSRSYRYIL- 115

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                            +  D   +R A++ L+G HDF+ F +        +R +   D+
Sbjct: 116 ---------------YGEQFDISKIRSASKLLLGSHDFSNFSTSRGSKK-TVRIVKRIDI 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              GNL  I V A SFL   +R  V +L +VG G      L   L  +  +E    A   
Sbjct: 160 RVSGNLTRIDVEANSFLWNMVRKIVAALMMVGSGVRDEEWLGHMLDPESYEEGLEPAHGY 219

Query: 238 GLYFDSVEYS 247
           GL    V Y 
Sbjct: 220 GLVLMDVNYP 229


>gi|224119986|ref|XP_002331109.1| predicted protein [Populus trichocarpa]
 gi|222872837|gb|EEF09968.1| predicted protein [Populus trichocarpa]
          Length = 326

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 86/319 (26%), Positives = 128/319 (40%), Gaps = 73/319 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + +EY G+ + G Q+Q N  ++ G +++A     G+ V +  + RTD+GVHAL  V
Sbjct: 6   QRYLVAVEYIGTRFCGSQQQLNHRTVVGVLQEAFHKFIGQPVTICLSSRTDAGVHALSNV 65

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ KA+N +L+  +  I + ++  V   FHARF A  
Sbjct: 66  CHVDVERISKRKPGEVLPPHEPAVVRKAVNHFLQKKEGDIMVTDVRSVSAHFHARFKAQE 125

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLV------------------ 150
           R+Y YR++         EK RAW + + LD  +M+ A + LV                  
Sbjct: 126 RTYFYRLLIGPELLSTFEKDRAWHVSEELDLVSMQEACKVLVGHHDFSSFRASGCQAKSP 185

Query: 151 --------------------------------GRHDFTTFRSIH----------CQASSP 168
                                           G H F                     S 
Sbjct: 186 FRTLEELSVLEVVSTPYFPSITEREQNSSNGEGPHSFHNKCKTGLPTGSISNGFMAGGSN 245

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
             T   F +        I   +RSFL+ Q+R  VG LK VG G  T +D+E+ L A+   
Sbjct: 246 SGTDLGFGIRRRHRCYVITARSRSFLYHQVRLLVGVLKSVGTGDLTVSDVERILNARSIT 305

Query: 229 ECGPLAPPEGLYFDSVEYS 247
              P+AP  GLY   V+Y 
Sbjct: 306 AASPMAPACGLYLGHVKYE 324


>gi|238061092|ref|ZP_04605801.1| tRNA-pseudouridine synthase I [Micromonospora sp. ATCC 39149]
 gi|237882903|gb|EEP71731.1| tRNA-pseudouridine synthase I [Micromonospora sp. ATCC 39149]
          Length = 276

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/251 (28%), Positives = 109/251 (43%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV--VHGAGRTDSGVHALR 59
           +R  + + Y+G+ + GW  Q    ++ G +   + LV G  V   +  AGRTD+GVHA  
Sbjct: 5   VRLRLTVAYDGTNFSGWAAQPARRTVAGVLTGTLDLVLGAGVATGLTVAGRTDAGVHATG 64

Query: 60  QVAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL    W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHLDLPAAVWREHEGRLLRRLARLLPTDVRVRAMTEVPADFDARFSATFRRYEYRVTD 124

Query: 119 RQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +      PK LD   +  AA  LVG HDF  +     + ++ +R +   D 
Sbjct: 125 APFGAEPLRRHEVLAWPKPLDPALLNAAAAGLVGEHDFAAYCRRK-ENATTLREVTRLDW 183

Query: 178 NSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G L+   V A +F    +RS VG++ + GDG+         L  ++R     +AP 
Sbjct: 184 RRDPGGLLVATVQADAFCQAMVRSLVGAMLVAGDGRRPVDWPGSLLTRRERSSEVTVAPA 243

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 244 HGLTLVAVGYP 254


>gi|116754296|ref|YP_843414.1| tRNA pseudouridine synthase A [Methanosaeta thermophila PT]
 gi|121692939|sp|A0B7V0|TRUA_METTP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|116665747|gb|ABK14774.1| tRNA pseudouridine synthase A [Methanosaeta thermophila PT]
          Length = 267

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 106/246 (43%), Gaps = 22/246 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + I Y G  Y+G+QRQ    +++  +  A+  +         AGRTD GV AL QV
Sbjct: 1   MKIALKIAYLGDRYYGFQRQPGLRTVESVMRDALLRIGVANGDFCYAGRTDRGVSALGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F +  +   +   + +N+ L     +     ++    F AR+SA+ R Y Y +     
Sbjct: 61  IDFWIEEDRAYLAFPRVINSLL--PSDVWAWARAVAPVGFSARWSALWREYRYFL----- 113

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                          +D   +R AA HLVG HDF  F          +R I   DVN+  
Sbjct: 114 -----------FSPDIDLSAVREAAGHLVGTHDFRNFSMSKVD---TVRRIISIDVNAHC 159

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++   V A  F+   +R  VG+L+L+G G+     + + L         P APPEGL  
Sbjct: 160 GIVVFDVRAEGFIWNMVRRIVGALELIGIGEKPVDWILELLDPSTPHGA-PTAPPEGLML 218

Query: 242 DSVEYS 247
             V YS
Sbjct: 219 MDVGYS 224


>gi|330790485|ref|XP_003283327.1| hypothetical protein DICPUDRAFT_25596 [Dictyostelium purpureum]
 gi|325086752|gb|EGC40137.1| hypothetical protein DICPUDRAFT_25596 [Dictyostelium purpureum]
          Length = 323

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 89/290 (30%), Positives = 128/290 (44%), Gaps = 45/290 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
            RY +  EY G  + GWQR     N   +Q  +E ++  +  + + V G+ RTDSGV AL
Sbjct: 3   PRYKITYEYVGKYFTGWQRLTYDINPLPVQNVLENSLKHICNKEIKVFGSSRTDSGVSAL 62

Query: 59  RQVAHFDLVRE----------WVPVILCKALNAYLKIS--DTISILNLSIVDKQFHARFS 106
              +HFD+ +                L  A+N  +     D + I+   IVD  FH+RF 
Sbjct: 63  GNTSHFDIDQRTSRKGKPLPLLTTDELTMAINYNVGEQYLDRVRIIKTEIVDDNFHSRFH 122

Query: 107 AIRRSYLYRII--TRQAPLALEK-GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A  R+YLY+I+    +    LE   R   I   LD   M+ AA+ LVGRHDF++FRS  C
Sbjct: 123 ATSRTYLYKILANCGKKQTPLELLDRVLEISFILDVNKMKEAAEILVGRHDFSSFRSKDC 182

Query: 164 QASSPIRTIDHFDVNSFG--------------------------NLIEIRVVARSFLHTQ 197
              +P+RTI++  +                                I I + A+SFLH Q
Sbjct: 183 -TKNPVRTIEYIKIIELPTPEIIRYHPDFINCSKEINNNVNHGLQYIGIEIKAQSFLHNQ 241

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +R    +L  VG G  T   L++ L+ +DR         E L    V Y 
Sbjct: 242 VRIMSSALIEVGKGTITKDQLKEILEKKDRLAAPSTIASEPLTLIKVSYD 291


>gi|157738399|ref|YP_001491083.1| tRNA pseudouridine synthase A [Arcobacter butzleri RM4018]
 gi|157700253|gb|ABV68413.1| tRNA pseudouridine synthase A [Arcobacter butzleri RM4018]
          Length = 240

 Score =  206 bits (525), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 116/246 (47%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +    ++ Y+GS + G Q+Q NG +++  + KA   +  +   +  +GRTD  VH+  QV
Sbjct: 1   MNLKFVVAYDGSLFQGSQKQPNGKTVENELLKAFENINIKT-QIVLSGRTDKEVHSSGQV 59

Query: 62  AHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +  +   W     L + LN  L    +I I  +S VD+ FH+RFSA +R Y Y I T++
Sbjct: 60  FNCQIPSYWEDFFKLKEILNKNL--PTSIKIKKISKVDESFHSRFSAKKRVYRYLITTKE 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                       + KS+D + ++ A +  +G HDF  F        +  R I       +
Sbjct: 118 T-TPFNDKFITYV-KSVDEKLLKKAIKEFIGIHDFKYFHKTGSDKENTNREIFDTKFYKY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++   +  A S+L +QIR  VG L  + D K T  DL K L  +      P+  P GLY
Sbjct: 176 KDIYVFKFTANSYLRSQIRLMVGFLLAINDKKLTIEDLRKQLNCEKIIFKTPI-KPNGLY 234

Query: 241 FDSVEY 246
              ++Y
Sbjct: 235 LAKIKY 240


>gi|261338249|ref|ZP_05966133.1| tRNA pseudouridine synthase A [Bifidobacterium gallicum DSM 20093]
 gi|270276903|gb|EFA22757.1| tRNA pseudouridine synthase A [Bifidobacterium gallicum DSM 20093]
          Length = 313

 Score =  206 bits (525), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 77/286 (26%), Positives = 120/286 (41%), Gaps = 41/286 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVT------GEIVVVHGAGRTD 52
           M+R  + + Y+G  + GW  Q   N  ++QG IE+A+  +         +  +  AGRTD
Sbjct: 1   MVRLRIDLAYDGFSFNGWAVQPQSNIRTVQGEIEQALARLLHDGNEPDYVPRLTVAGRTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVIL-------CKALNAYL--KISDTISILNLSIVDKQFHA 103
           +GVHA  QV H D+    +   +        KAL   L   + D I+I  +S   + F A
Sbjct: 61  AGVHASHQVCHLDVTEPMLDACVGHMRVEPVKALETRLSRMMPDDIAIHRVSFAPEGFDA 120

Query: 104 RFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           RFSA+ R+Y+YRI          +    W     L+ + M  AA   +G HDF +F + +
Sbjct: 121 RFSALERTYVYRISDAATDYDPRQLSYVWHTDHLLNMDAMNEAAALTLGLHDFGSFATPN 180

Query: 163 CQASSPIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFV 202
               + IR +     +                        L+   +VA +F    +RS V
Sbjct: 181 P-GGTTIREVKTAYWSRIPTRPLIANPMGERYHTPAIESGLLCFTIVADAFARNMVRSLV 239

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            +   VG GK         +    R+   GP+AP +GL  + V Y 
Sbjct: 240 NACVQVGLGKRDVAWFAHKMAVPLREGSTGPIAP-QGLTLEHVAYP 284


>gi|224373193|ref|YP_002607565.1| tRNA pseudouridine synthase A [Nautilia profundicola AmH]
 gi|223588941|gb|ACM92677.1| tRNA pseudouridine synthase A [Nautilia profundicola AmH]
          Length = 223

 Score =  206 bits (524), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 103/229 (44%), Gaps = 6/229 (2%)

Query: 18  WQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCK 77
            Q+Q +  ++QGSIE A+  +      V  AGRTD GVHAL QV  F L   W    L  
Sbjct: 1   MQKQPDKITVQGSIENALKRLNI-NSDVLHAGRTDRGVHALNQVVSFKLPSFWNQNKLLT 59

Query: 78  ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSL 137
            LN  L  +  I I     V+  F+ RF A +RSY Y +                 P  +
Sbjct: 60  ELNKILHPN--IHIKKFYNVNDDFNPRFDAKKRSYRYIL--NPNFNPFSANYTTYYPHKI 115

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           +   ++ A +   G HDF  F       ++ IR I   DV  + N   I++V   FL  Q
Sbjct: 116 NISLLKKALKEFEGIHDFEYFAKTGSDVNNYIREIYKTDVYKYKNFTVIKIVGNGFLRAQ 175

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           IR  V  +  + + K T  DL+K L ++       LAPP GLY D + Y
Sbjct: 176 IRLIVDFVLKINENKLTVQDLQKQL-SKQELISKHLAPPNGLYLDRIWY 223


>gi|184200291|ref|YP_001854498.1| tRNA pseudouridine synthase TruA [Kocuria rhizophila DC2201]
 gi|183580521|dbj|BAG28992.1| tRNA pseudouridine synthase TruA [Kocuria rhizophila DC2201]
          Length = 331

 Score =  206 bits (524), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 76/306 (24%), Positives = 123/306 (40%), Gaps = 61/306 (19%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GW RQ    S+Q ++E A+ LV         AGRTD+GVHA  Q 
Sbjct: 8   VRLRIDLAYDGAPFRGWARQPGLPSVQEAVEDALCLVFRVRCPTVVAGRTDTGVHARSQT 67

Query: 62  AHFDLVREWVPVI--------------------------------------------LCK 77
            H D+ RE    +                                            L +
Sbjct: 68  VHVDVPREAWERVTRSRGTGRVAGALPASPDPAHASAPAATTGTVAASDARGPVDPVLAR 127

Query: 78  ALNAYLK--ISDTISILNLSI------------VDKQFHARFSAIRRSYLYRIITRQA-P 122
            LN  L   +    +                      F ARFSA+ R+Y YR+   +   
Sbjct: 128 RLNGALNRVLGKDRADRGWEPVVGAVVVQSVAQAPPGFDARFSALSRAYRYRVADARTGH 187

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L +  +W +   LD   M  A + L+G HDF ++       ++ +R +    V+   +
Sbjct: 188 DPLTRTFSWWVDPQLDVAAMDGAVRELLGLHDFLSYCKPRA-GATTVRELQRATVDRDEH 246

Query: 183 -LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +I + + A +F H  +RS VG+L  VG+G+   +   + L+A+ R     +AP  GL  
Sbjct: 247 GMITVALTADAFCHHMVRSVVGALVRVGEGRHGPSWPGERLRARTRDAAIVMAPAHGLVL 306

Query: 242 DSVEYS 247
           D+V Y 
Sbjct: 307 DAVAYP 312


>gi|206602902|gb|EDZ39382.1| Pseudouridylate synthase [Leptospirillum sp. Group II '5-way CG']
          Length = 268

 Score =  205 bits (523), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 79/253 (31%), Positives = 114/253 (45%), Gaps = 9/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  ++ Y+G G+ GWQ Q  G+++Q  IE+A   +T + V + G+GRTD+GV A  Q
Sbjct: 1   MQRFAFVVSYDGRGFQGWQSQIRGNAVQDHIEEAFCRLTRQDVRISGSGRTDTGVSAAGQ 60

Query: 61  VAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL    W P  L + LN +L  S  I IL  + V   FHAR   +R+ Y YR ++R
Sbjct: 61  VFHCDLAGPGWTPDSLSRGLNHFL--SPAIRILQAAAVAPDFHARHDVVRKIYRYRWVSR 118

Query: 120 QAPL----ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              +      E          +    ++ A + L G +DFT F           RTID  
Sbjct: 119 SRKMREVGPTEDPFCGTFLPPVHWTLLQQATKLLEGSNDFTRFTVQKSCPEDARRTIDAI 178

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPL 233
              +    +++ V  R FLH  IR    +L   G  K +    +  L             
Sbjct: 179 QWIAGPYTLDLWVAGRGFLHMMIRYLAMALLETGQQKRSLKSFQDLLLTGSLPPVPALHP 238

Query: 234 APPEGLYFDSVEY 246
           APP+GL    V Y
Sbjct: 239 APPQGLSLVRVLY 251


>gi|119963259|ref|YP_948625.1| tRNA pseudouridine synthase A [Arthrobacter aurescens TC1]
 gi|119950118|gb|ABM09029.1| tRNA pseudouridine synthase A [Arthrobacter aurescens TC1]
          Length = 296

 Score =  205 bits (523), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 80/263 (30%), Positives = 118/263 (44%), Gaps = 19/263 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+G  + GW  Q    ++QGS+E+A+ L+    V V  AGRTD+GVHA  QV 
Sbjct: 18  RVRLDLSYDGGPFSGWALQPGLRTVQGSLEEALALLLQRPVRVTVAGRTDAGVHARGQVV 77

Query: 63  HFD-LVREW----------VPVILCKALNAYL-----KISDTISILNLSIVDKQFHARFS 106
           H D    EW            V L + L   L      ++ +I + +  +  + F ARFS
Sbjct: 78  HLDLTEAEWLSLPRGHELDPAVALLRRLRGALSRILGDLTGSIEVHDAGLAPEGFDARFS 137

Query: 107 AIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           A+ R Y YRI         + +G        L+ E M   A  L+G  DF ++     + 
Sbjct: 138 ALWRRYSYRIADGPERWDPVLRGITLWHKAPLNVELMNEGAFALLGLQDFRSYCKPR-EG 196

Query: 166 SSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           ++ IR +  F  +    ++I   V A +F H  +RS VGS   VG+G  T   L   L  
Sbjct: 197 ATTIRELQQFSFDRGSDDVIVATVQADAFCHNMVRSLVGSALRVGEGLETPGWLHSRLLE 256

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           + R     LA P  L  + V Y 
Sbjct: 257 RKRDAKSVLAAPHPLVLEEVAYP 279


>gi|240103716|ref|YP_002960025.1| tRNA pseudouridine synthase A [Thermococcus gammatolerans EJ3]
 gi|259550472|sp|C5A7E9|TRUA_THEGJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|239911270|gb|ACS34161.1| tRNA-pseudouridine synthase A (truA) [Thermococcus gammatolerans
           EJ3]
          Length = 267

 Score =  205 bits (522), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 108/250 (43%), Gaps = 26/250 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           ++  + I Y+G+ ++G+QRQ    +++G +   +  +    + E     GA RTD GV A
Sbjct: 1   MKLALRIAYDGTAFYGFQRQPGIRTVEGELINVLTKLKIIESPEKNDFKGASRTDRGVSA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              V  F +  E   +   + LN  L     + +L ++ V   FH RF AI ++Y Y   
Sbjct: 61  FFNVVSF-VPGERADLARPEVLNHNLH---DLWVLGVAEVPDDFHPRFWAISKTYRY--- 113

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +LI +  + E M   A+   GRHDF+ F  +      P+R I H  +
Sbjct: 114 -------------YLIDEGFELEKMVGCAKLFEGRHDFSAFARLEP-GRDPVREITHISI 159

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                   I +  +SFL   +R  V +L+  G       ++   L +   ++  P APPE
Sbjct: 160 TPRHGYYVIEITGKSFLWEMVRRIVNALRFCGLSLLEPEEVGAML-SGVYEKKVPPAPPE 218

Query: 238 GLYFDSVEYS 247
            L    +EY 
Sbjct: 219 NLILWHIEYP 228


>gi|118616627|ref|YP_904959.1| tRNA pseudouridine synthase A [Mycobacterium ulcerans Agy99]
 gi|118568737|gb|ABL03488.1| pseudouridine synthase a, TruA [Mycobacterium ulcerans Agy99]
          Length = 260

 Score =  205 bits (521), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 71/240 (29%), Positives = 114/240 (47%), Gaps = 14/240 (5%)

Query: 21  QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV------------R 68
           Q    ++ G +++A+  V    V +  AGRTD+GVHA  QVAH D+             R
Sbjct: 2   QTGQRTVAGVLDEALTTVLRTPVRLRAAGRTDAGVHATGQVAHADVPVDALPNAYSRSAR 61

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEK 127
              P  L         +   + +L+++     F ARFSA+RR Y+YR+ T    +   + 
Sbjct: 62  AGDPEFLPLVRRLARFLPADLRVLDIARAPTAFDARFSALRRHYVYRLSTAPYGVEPQQA 121

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
               + P+ LD + M +A+Q L+G H+F  F     + ++ IR +   D +  G+L+  +
Sbjct: 122 RYVTVWPRELDIDAMTVASQELLGLHNFAAFCRRR-EGATTIRDLQRLDWSRNGHLVTAQ 180

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           V A +F  + +RS VG+L  VG+ + T     + L A  R      AP  GL    V+Y 
Sbjct: 181 VSADAFCWSMVRSLVGALLAVGEHRRTPDWCRELLTATARSSDFAAAPAHGLVLAKVDYP 240


>gi|312892081|ref|ZP_07751581.1| tRNA-pseudouridine synthase I [Mucilaginibacter paludis DSM 18603]
 gi|311295453|gb|EFQ72622.1| tRNA-pseudouridine synthase I [Mucilaginibacter paludis DSM 18603]
          Length = 268

 Score =  205 bits (521), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 109/248 (43%), Gaps = 6/248 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + + Y+G+ Y GWQ+     SIQ  +E ++  V      + G GRTD+ VHA +  
Sbjct: 1   MRYFVHLGYHGTQYSGWQKHAGVMSIQQVLENSLSQVLKTPTAIVGCGRTDAKVHASQFF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D+        L   LN  L     I+I ++  +    HARF A +RSY Y I T + 
Sbjct: 61  FHVDIDNPR-EFDLLFRLNKIL--PADIAIFDIIPMAGLPHARFDATQRSYDYFIHTYKD 117

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN--S 179
           P  L    ++   +SLD   M+ A   L   HD+  F     +    +  +   ++    
Sbjct: 118 PF-LNGFSSYYNEQSLDLHEMKKAVALLPLYHDYRAFCKSPDRNEHTLCHVTSAELFACK 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I   + A  FL   IR  VG L  +G G+ +  + E+ L      +    A P+GL
Sbjct: 177 NADRIRFNISANRFLSKMIRVIVGRLISIGTGEMSVDEFEQNLIKPQNAQTISPAHPQGL 236

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 237 YLSKVTYP 244


>gi|99034196|ref|ZP_01314273.1| hypothetical protein Wendoof_01000930 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 166

 Score =  205 bits (521), Expect = 7e-51,   Method: Composition-based stats.
 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|148273765|ref|YP_001223326.1| tRNA pseudouridine synthase A [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147831695|emb|CAN02664.1| putative tRNA pseudouridine synthase [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 334

 Score =  204 bits (520), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 79/279 (28%), Positives = 123/279 (44%), Gaps = 34/279 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHAL 58
            R  + I Y+G+G+ GW +Q    ++QG++E A+  +         +  AGRTD+GVHA 
Sbjct: 12  TRLRLDIAYDGTGFAGWAKQPGLRTVQGALEDALAQLLARTPPAPTLVVAGRTDAGVHAT 71

Query: 59  RQVAHFDLVREWVP----------------------------VILCKALNAYLKISDTIS 90
            QVAH DL  E +                               L + LN  L     + 
Sbjct: 72  GQVAHLDLTDEQIASLDRPPRGRAAAADAGEGAHVPSVDRAAAALARRLNGVLGARSDVV 131

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHL 149
           +L  +     F ARFSA  R+Y YRI     P   L++ R   +P +LD   ++ AA  L
Sbjct: 132 VLACAPAPDGFDARFSATWRAYRYRISDVDGPRDPLQRHRTVELPVALDAAVLQEAADAL 191

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLV 208
           +G HDF  +     + +S IRT+         +  +E  V A +F H+ +R+ VG+    
Sbjct: 192 LGLHDFAAYCKPR-EGASTIRTLQELTWTRASDGALEATVRADAFCHSMVRALVGACVAA 250

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             G+   T L + L+ ++R     + P  GL  + V Y 
Sbjct: 251 ASGRVGVTRLRELLELRERTSEFTVMPARGLVLERVGYP 289


>gi|283455394|ref|YP_003359958.1| 50S ribosomal protein L17 [Bifidobacterium dentium Bd1]
 gi|283102028|gb|ADB09134.1| rplQ 50S ribosomal protein L17 [Bifidobacterium dentium Bd1]
          Length = 296

 Score =  204 bits (520), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 79/282 (28%), Positives = 120/282 (42%), Gaps = 46/282 (16%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSGVHALRQ 60
           + Y+G G+FGW +Q +  ++QG IE+ +  V        GE + +  AGRTD+GVHA  Q
Sbjct: 1   MAYDGGGFFGWAKQPDRRTVQGEIERILHTVLRVPVDDAGEPLRLTVAGRTDTGVHASHQ 60

Query: 61  VAHFDLVREW-----------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           V H D+                 V L + L   L   + I+I  ++   + F ARFSA+ 
Sbjct: 61  VCHLDISETILARCVGHMNVPPVVALTRRLQRML--PNDITIHGINEAPQGFDARFSALE 118

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y+YRI  R +      +G    +   LD E M  AA   +G HDF +F + +    + 
Sbjct: 119 RTYVYRIADRSSEIDPRMRGFVLHVDDDLDLETMNQAAAMTIGLHDFGSFATPNP-GGTT 177

Query: 169 IRTIDHFDVNSFGN----------------------LIEIRVVARSFLHTQIRSFVGSLK 206
           IR +                                L    +VA +F    +RS V    
Sbjct: 178 IREVKTAYWRRIPQRPLVDGEMTMGERYRTPSMESGLACFTIVADAFARNMVRSLVNGCV 237

Query: 207 LVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            VG GK +       +    R+   GP+AP +GL  + +EY 
Sbjct: 238 QVGIGKRSLDWFADKMATPLREGSTGPIAP-QGLTLEHIEYP 278


>gi|224283738|ref|ZP_03647060.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum NCIMB 41171]
          Length = 298

 Score =  204 bits (519), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 74/281 (26%), Positives = 121/281 (43%), Gaps = 40/281 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSGVHA 57
            + + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+GVHA
Sbjct: 2   RIDLAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDTGVHA 61

Query: 58  LRQVAHF---------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
             QV H           +    VP  +         +   I+I ++++    F ARFSA+
Sbjct: 62  SHQVCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPADITIHDVTVAPSGFDARFSAL 121

Query: 109 RRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R+Y+YR+  R +      +G    +   LD   M  AA   +G HDF +F + +    +
Sbjct: 122 ERTYVYRVADRASEVDPRLRGFVLHLDADLDVAAMNEAAAMTIGLHDFGSFATPNP-GGT 180

Query: 168 PIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFVGSLKL 207
            IR +                             +L+   +VA +F    +RS VG    
Sbjct: 181 TIREVKTAYWRRIPTRPLVVDGVGERYRTPAAESDLLCFTIVADAFARNMVRSLVGGCIQ 240

Query: 208 VGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VG GK ++    + +    R+   GP+AP +GL  + V Y 
Sbjct: 241 VGMGKRSTDWFREKMAVPLREGSTGPIAP-QGLTLEHVAYP 280


>gi|88603643|ref|YP_503821.1| tRNA pseudouridine synthase ACD [Methanospirillum hungatei JF-1]
 gi|88189105|gb|ABD42102.1| tRNA pseudouridine synthase A [Methanospirillum hungatei JF-1]
          Length = 276

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 74/247 (29%), Positives = 110/247 (44%), Gaps = 27/247 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R    I Y G+ +FG Q Q +  +++G IE A        + ++  +  +GRTD GVHA
Sbjct: 11  VRLAFRIGYIGTSFFGSQYQPDQRTVEGEIEAACLRAGIITSRQVSRLALSGRTDRGVHA 70

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             Q+          P +  +ALN  L     I +   +   + F+ R+  I R+Y Y   
Sbjct: 71  KCQILALST---HNPDLAVRALNGQL--PPDIWVSAWAYAPESFYPRYDVIIRTYRY--- 122

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +      D   MR AA   +G HDF  F  I     SP++TID  +V
Sbjct: 123 -------------YFSRPPSDINAMRDAAGLFLGTHDFRCFARIEP-GKSPVKTIDRIEV 168

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            S  N   + V A+SFL   +R   GSL  V +G+    DL + L+ + + +  P APPE
Sbjct: 169 ISDENGCRLEVTAQSFLWHMVRCMAGSLYQVSEGEMAIRDLTQYLKGECKNKVKP-APPE 227

Query: 238 GLYFDSV 244
           GL    V
Sbjct: 228 GLILWDV 234


>gi|213622844|ref|ZP_03375627.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
          Length = 188

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 59/173 (34%), Positives = 88/173 (50%), Gaps = 2/173 (1%)

Query: 75  LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
               +NA L     I++  +  V   FHARFSA  R Y Y I   +   A+         
Sbjct: 1   WTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLAKGVTHYY 58

Query: 135 KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFL 194
           + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + + + A +F+
Sbjct: 59  EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFV 118

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y 
Sbjct: 119 HHMVRNIVGSLLEVGAHNQPESWIAELLAARDRTLAAATAKAEGLYLVAVDYP 171


>gi|242310521|ref|ZP_04809676.1| tRNA pseudouridine synthase A [Helicobacter pullorum MIT 98-5489]
 gi|239522919|gb|EEQ62785.1| tRNA pseudouridine synthase A [Helicobacter pullorum MIT 98-5489]
          Length = 241

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 111/250 (44%), Gaps = 14/250 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  M I YNG+ + G+Q+QK+  S+ G +E+    V G    + G+GRTD GVHA  Q
Sbjct: 2   MMKVAMKIAYNGANFCGFQKQKDRQSVSGFLEEVFGSV-GIFEKIIGSGRTDKGVHASAQ 60

Query: 61  VAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V    +         L + LN  LK+   + I  +  VD  FHARF A RR Y Y I   
Sbjct: 61  VISLKIPDFHKDLQKLQEILN--LKLYPLVKIKKIWRVDDDFHARFDAKRRGYCYVISQE 118

Query: 120 QAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFD 176
            +P          +      +   ++ A +   G H+F  F       A   +R I    
Sbjct: 119 YSPFIAPFAHYYCFQ-----NVGIIKEALREFEGLHNFKAFMKNDGSGAKGSVREIYKAR 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G           FL +QIR  VG L  +  G    +DL+K L   +R    P APP
Sbjct: 174 LLKRGKFYIFLFWGNGFLRSQIRLMVGYLLEIDKGNLQISDLKKQLLG-ERIFSIP-APP 231

Query: 237 EGLYFDSVEY 246
            GL+  SV+Y
Sbjct: 232 NGLFLSSVKY 241


>gi|306823540|ref|ZP_07456915.1| tRNA pseudouridine synthase A [Bifidobacterium dentium ATCC 27679]
 gi|304553247|gb|EFM41159.1| tRNA pseudouridine synthase A [Bifidobacterium dentium ATCC 27679]
          Length = 296

 Score =  203 bits (518), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 79/282 (28%), Positives = 120/282 (42%), Gaps = 46/282 (16%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSGVHALRQ 60
           + Y+G G+FGW +Q +  ++QG IE+ +  V        GE + +  AGRTD+GVHA  Q
Sbjct: 1   MAYDGGGFFGWAKQPDRRTVQGEIERILHTVLRVPVDDAGEPLRLTVAGRTDTGVHASHQ 60

Query: 61  VAHFDLVREW-----------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           V H D+                 V L + L   L   + I+I  ++   + F ARFSA+ 
Sbjct: 61  VCHLDVSETILARCVGHMDVPPVVALTRRLQRML--PNDITIHGINEAPQGFDARFSALE 118

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y+YRI  R +      +G    +   LD E M  AA   +G HDF +F + +    + 
Sbjct: 119 RTYVYRIADRSSEIDPRMRGFVLHVDDDLDLETMNQAAAMTIGLHDFGSFATPNP-GGTT 177

Query: 169 IRTIDHFDVNSFGN----------------------LIEIRVVARSFLHTQIRSFVGSLK 206
           IR +                                L    +VA +F    +RS V    
Sbjct: 178 IREVKTAYWRRIPQRPLIDGEMTMGERYHTPSMESGLACFTIVADAFARNMVRSLVNGCV 237

Query: 207 LVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
            VG GK +       +    R+   GP+AP +GL  + +EY 
Sbjct: 238 QVGIGKRSLDWFADKMATPLREGSTGPIAP-QGLTLEHIEYP 278


>gi|310287995|ref|YP_003939254.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum S17]
 gi|309251932|gb|ADO53680.1| tRNA pseudouridine synthase A [Bifidobacterium bifidum S17]
          Length = 298

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 74/281 (26%), Positives = 121/281 (43%), Gaps = 40/281 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSGVHA 57
            + + Y+G G+FGW +Q    ++QG IE+ +  +T        E + +  AGRTD+GVHA
Sbjct: 2   RIDLAYDGGGFFGWAKQPTIRTVQGEIERVLHTITRVPVDDPAEPLRLTVAGRTDTGVHA 61

Query: 58  LRQVAHF---------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
             QV H           +    VP  +         +   I+I ++++    F ARFSA+
Sbjct: 62  SHQVCHLDIGEETLSRCVGHMSVPPTVALKHRLQRMLPADITIHDVTVAPSGFDARFSAL 121

Query: 109 RRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R+Y+YR+  R +      +G    +   LD   M  AA   +G HDF +F + +    +
Sbjct: 122 ERTYVYRVADRASEVDPRLRGFVLHLDADLDVVAMNEAAAMTIGLHDFGSFATPNP-GGT 180

Query: 168 PIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFVGSLKL 207
            IR +                             +L+   +VA +F    +RS VG    
Sbjct: 181 TIREVKTAYWRRIPTRPLVVDGMGERYRTPAAESDLLCFTIVADAFARNMVRSLVGGCIQ 240

Query: 208 VGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
           VG GK ++    + +    R+   GP+AP +GL  + V Y 
Sbjct: 241 VGMGKRSTDWFREKMAVPLREGSTGPIAP-QGLTLEHVAYP 280


>gi|269925860|ref|YP_003322483.1| tRNA pseudouridine synthase A [Thermobaculum terrenum ATCC BAA-798]
 gi|269789520|gb|ACZ41661.1| tRNA pseudouridine synthase A [Thermobaculum terrenum ATCC BAA-798]
          Length = 240

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 107/250 (42%), Gaps = 17/250 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + ++I Y G  + G Q Q    ++Q  +E A   VTG       AGRTD+GV AL Q
Sbjct: 1   MSTWKLVISYKGEYFSGSQIQPGKRTVQEELENAWEKVTGSRCRAVLAGRTDAGVSALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA         P  L + L  YL     I I  +  V   F AR SAI R Y Y     +
Sbjct: 61  VATIKADWPGTPEELLEKLRKYLT--QGIEIRKVERVSDNFDARKSAIWRRYRYVFSKDE 118

Query: 121 -APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFD-- 176
            A               +  E+MR AA+ LVG  DF  F S         +R I   +  
Sbjct: 119 IARFGF-----------ISVESMRQAARALVGEKDFAAFASQSELGPRGTVRRILDINVI 167

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            +   N + I +VA +FL   +R  V +L  VG GK    +L +A++ + R+     AP 
Sbjct: 168 WDKAANNLCIEIVADAFLRQMVRRIVSALIWVGTGKIEVVELLRAVEIKARQLLPGPAPA 227

Query: 237 EGLYFDSVEY 246
           + L    V Y
Sbjct: 228 KNLTLVEVGY 237


>gi|147919589|ref|YP_686671.1| tRNA pseudouridine synthase A [uncultured methanogenic archaeon
           RC-I]
 gi|121687867|sp|Q0W2P8|TRUA_UNCMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|110622067|emb|CAJ37345.1| tRNA pseudouridine synthase [uncultured methanogenic archaeon RC-I]
          Length = 266

 Score =  203 bits (516), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 68/248 (27%), Positives = 108/248 (43%), Gaps = 24/248 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVHALR 59
           ++  + I Y G+ ++G Q Q    +++  + KA+           +  AGRTD+GVHAL 
Sbjct: 1   MKTALKIAYVGTNFYGSQAQPGLPTVESELRKALEEAGAIKLGTKIAMAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  F+       +   + +N+ L     +     + V   F  R  A  R Y Y +   
Sbjct: 61  QVVAFEQAD--PKLTAPRIINSKL--PKDLWAYARAEVPDDFDPRRHATSREYRYILY-- 114

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            AP  +E+              ++  +   +G HDFT F S+      P+RT+   D+  
Sbjct: 115 -APDVIER-------------RLKECSSRFLGTHDFTNFSSVEA-GKYPVRTVTRLDIAK 159

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+   I + A SFL   +R  V +L+LVG+ K     +EK    + R+   P AP  GL
Sbjct: 160 RGDFYIIDIEADSFLWNMVRKIVTALRLVGENKRPDGWIEKMFDPEYREGIPPAAPG-GL 218

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 219 YLSRVNYD 226


>gi|322378343|ref|ZP_08052800.1| tRNA pseudouridine synthase A [Helicobacter suis HS1]
 gi|321149229|gb|EFX43672.1| tRNA pseudouridine synthase A [Helicobacter suis HS1]
          Length = 244

 Score =  203 bits (516), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 107/250 (42%), Gaps = 10/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +++ Y+GS + G+ +Q    +++G + KA+  +      +  AGRTD GVHA  Q
Sbjct: 1   MRRFKLVLAYDGSAFSGFAKQAGLYTVEGRLIKALESLQI-PSKILAAGRTDRGVHATHQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F+    W    L K L   L     I+  +L  V   FH RF A RR Y Y +   +
Sbjct: 60  VIAFNTCDIWSSSKLLKHLAPKLGY--FIACKSLEEVPLSFHPRFEATRRRYRYFLSLAK 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P           P   D   ++ A +   G HDF  F        S IR+I       +
Sbjct: 118 -PSPFLSRFVGYHPCG-DMGILKQALELFKGEHDFKFFSKSGSDPKSTIRSIYKAFCYPY 175

Query: 181 G----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  + +   A SFL +Q+R  +G+       + +  DL K +  Q R     ++P 
Sbjct: 176 MLYNLPCLVLVFEANSFLRSQVRLMLGAALACSLKQISLEDLYKQITLQRRFLMRAVSP- 234

Query: 237 EGLYFDSVEY 246
            GLY  SV Y
Sbjct: 235 SGLYLSSVFY 244


>gi|115730971|ref|XP_781664.2| PREDICTED: similar to MGC80334 protein [Strongylocentrotus
           purpuratus]
 gi|115939533|ref|XP_001190679.1| PREDICTED: similar to MGC80334 protein [Strongylocentrotus
           purpuratus]
          Length = 306

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 83/283 (29%), Positives = 126/283 (44%), Gaps = 38/283 (13%)

Query: 1   MIRYCMIIEYNGSGYFG-------WQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTD 52
           M R+ +  +Y G+ Y G           +    +Q  IE A+  +     V +H + RTD
Sbjct: 1   MGRFLIYFQYIGTRYRGVVRATSLSASGEKFVGVQDVIEGALDELKPVIPVKLHVSSRTD 60

Query: 53  SGVHALRQVAHFDL---------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           +GVHAL   AHFD+          R+ +   +  A+N  L+    I I+    V   FH+
Sbjct: 61  TGVHALCNTAHFDMIFKSKRTGEPRDILAESITAAVNKKLE-DHDIRIIKTLRVQDSFHS 119

Query: 104 RFSAIRRSYLYRIITRQAP---LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR- 159
           +  A+ R+YLYR+            EK R+W   + LD  +M+ A+   VG HDFT FR 
Sbjct: 120 QHLAMGRTYLYRLAMGCRQIELPVFEKNRSWAFDQRLDIPSMKEASGRFVGTHDFTAFRN 179

Query: 160 -SIHCQASSPIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSL 205
            S+     SPI+TID  +                    +E+   +RSFL+ QIR   G+L
Sbjct: 180 SSMDDDKKSPIKTIDMIEFRRTRGFLYHHCNKMAQLEFLELTFHSRSFLYKQIRRMTGAL 239

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPL--APPEGLYFDSVEY 246
             VG G+   + +   L+++D         AP  GLY   + Y
Sbjct: 240 VAVGLGRIAPSHITTILESRDNSHMHRTTMAPAHGLYLKEISY 282


>gi|255994429|ref|ZP_05427564.1| tRNA pseudouridine synthase A [Eubacterium saphenum ATCC 49989]
 gi|255993142|gb|EEU03231.1| tRNA pseudouridine synthase A [Eubacterium saphenum ATCC 49989]
          Length = 304

 Score =  202 bits (515), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 71/289 (24%), Positives = 112/289 (38%), Gaps = 48/289 (16%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      I Y+GS + G+Q+    +S+QG IE A+  + G  V +    RTD+GVHA  Q
Sbjct: 1   MKHIAFKISYDGSAFKGFQKNHGITSVQGEIENALKPIVG-DVEISAVSRTDAGVHAFSQ 59

Query: 61  VAHFDLVREWVPVILCKAL-NAYLKISDT------ISILNLSIVDKQFHARFSAIRRSYL 113
           +  F          L + L NA+            I+I   + + +  + R+    + Y+
Sbjct: 60  IFSFSYDTNIPHGRLAEVLTNAFSTRKSDYRKQAAIAIEGWAELGRAMNPRYFVKGKRYI 119

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y            +    L    L+   M+  A+  VG HDF+ FR+      SPIR + 
Sbjct: 120 YVFKKNAGSDIFARNYMLLTNGDLNVGRMKEEAKAFVGEHDFSAFRTQ--DGRSPIRKVF 177

Query: 174 HFDVNSFGNL-------------------------------------IEIRVVARSFLHT 196
             +V S   L                                     +   V    FL+ 
Sbjct: 178 SANVISCEELNDGFHEPLTDEYGRISDIIALKKRLLPRLNLSNLQGYVFFAVTGEGFLYN 237

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            +R   G+L  VG  K+    +   L++++R+  G  APP+GLY D V 
Sbjct: 238 MVRIMAGTLLEVGKNKFDKP-VCDVLKSKNRQMAGITAPPQGLYLDEVF 285


>gi|298674065|ref|YP_003725815.1| tRNA pseudouridine synthase A [Methanohalobium evestigatum Z-7303]
 gi|298287053|gb|ADI73019.1| tRNA pseudouridine synthase A [Methanohalobium evestigatum Z-7303]
          Length = 277

 Score =  202 bits (515), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 68/248 (27%), Positives = 114/248 (45%), Gaps = 25/248 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
           R  + + Y G+ Y G Q Q    +I+G + K++  +      +      +GRTD+GVH+L
Sbjct: 4   RMALKLAYIGTEYHGSQVQPELPTIEGELFKSLKNLEIIDDPKSANFVSSGRTDTGVHSL 63

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  FD       + + + +N+ L   ++I     ++V  +F+ R  A  R YLY +  
Sbjct: 64  GQVVTFDTDNPR--LAVPRVINSQL--PESIWAWAYAVVPDEFNPRHGAFSRRYLYIMSG 119

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +                 D   +R A+++L+G HDF  F +   +  S +RT+   ++ 
Sbjct: 120 EEY----------------DISRIRTASKYLIGTHDFANFCTP-VKGKSTVRTVQRINIR 162

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G L  I + A SFL   +R  V +L +VG G   +  LE+ L  +  +E    AP  G
Sbjct: 163 VKGTLTLIDIQADSFLWKMVRKIVTALMMVGYGTRDTEWLEQMLNPEYYEEGIEPAPSYG 222

Query: 239 LYFDSVEY 246
           L    V+Y
Sbjct: 223 LILKDVDY 230


>gi|332261432|ref|XP_003279774.1| PREDICTED: LOW QUALITY PROTEIN: tRNA pseudouridine synthase-like
           1-like [Nomascus leucogenys]
          Length = 287

 Score =  202 bits (515), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 115/245 (46%), Gaps = 26/245 (10%)

Query: 27  IQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVR-----EWVPVILCKALN 80
           +Q  +E+A   +   E V    + RTD+GVHAL   AH D+ R      + P +L +ALN
Sbjct: 25  VQNYLEEAAERLNSVEPVRFTISSRTDAGVHALSNAAHLDVQRRSGRPPFPPEVLTEALN 84

Query: 81  AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP----LALEKGRAWLIPKS 136
            +L+    I +L    V   FHAR +A  R+YLYR+ T           E+   W +P  
Sbjct: 85  THLRHP-AIRVLRAFRVPNDFHARHAATSRTYLYRLATGCNRRDELPVFERNLCWALPAD 143

Query: 137 -LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG------------NL 183
            LD   M+ AAQHL+G HDF+ F+S      SP+RT+    V+                 
Sbjct: 144 CLDVVAMQEAAQHLLGTHDFSAFQSTGSPVPSPVRTLRRVSVSPGQASPLVTQESRKLRF 203

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYF 241
             +   ++SFL+ Q+R     L  VG G      ++  L++QD   K    +AP  GL+ 
Sbjct: 204 WSLEFESQSFLYRQVRRMTAVLVAVGLGALAPAQVKTILESQDPLGKHQTRVAPAHGLFL 263

Query: 242 DSVEY 246
            SV Y
Sbjct: 264 KSVLY 268


>gi|326932368|ref|XP_003212291.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Meleagris
           gallopavo]
          Length = 292

 Score =  202 bits (515), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 91/277 (32%), Positives = 137/277 (49%), Gaps = 33/277 (11%)

Query: 2   IRYCMIIEYNGSGYFG----WQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVH 56
            RY +  +Y G+ Y G       Q +G  +Q  +EKA   +     +  H + RTDSGVH
Sbjct: 6   TRYLVFFQYWGTKYSGVMHTSAEQ-SGVGVQNYLEKAAQNLKPVVPIKFHISSRTDSGVH 64

Query: 57  ALRQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           AL   AH D+ R      +   +L   LN +LK  + I IL+   V   FHARFSA+ R+
Sbjct: 65  ALCNSAHLDIQRAPGKPAFQEKMLIGCLNHHLK-PEPIRILSAYRVTNNFHARFSALSRT 123

Query: 112 YLYRIITRQAP----LALEKGRAWLIPK-SLDCENMRIAAQHLVGRHDFTTFRSIHCQA- 165
           Y+YR++            E+   W      L+   M+ AAQ L+G HDF+TF S++ +  
Sbjct: 124 YIYRLLMGCTHHSEIPVFERDLCWAPTGGYLNVPAMQDAAQFLLGTHDFSTFCSLNSETP 183

Query: 166 -SSPIRTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
             SP++TI   D+                   E++  +RSFL+ Q+R  VG+L  VG GK
Sbjct: 184 FRSPVKTILQADIQPSSGFLSHHYEYRGLQFWELKFKSRSFLYRQVRRMVGALVAVGQGK 243

Query: 213 WTSTDLEKALQAQDRKECGP--LAPPEGLYFDSVEYS 247
                +++ L+ +D +   P  +AP  GL+  SVEY+
Sbjct: 244 LAPYHIKELLEMKDARAFPPFAMAPSSGLFLKSVEYN 280


>gi|150390096|ref|YP_001320145.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
 gi|149949958|gb|ABR48486.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
          Length = 248

 Score =  202 bits (514), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 119/251 (47%), Gaps = 8/251 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y M+I Y+G  Y G+ + K+    SIQG +E  +  +  E V V  A  TD+GVH+ 
Sbjct: 1   MQNYKMMIAYDGRKYTGYNKSKDNLEKSIQGKLELILSKLYEEEVEVISAVSTDAGVHSK 60

Query: 59  RQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            Q+ +F           +      YL   D I IL++   D++FH+R+     +Y YR+ 
Sbjct: 61  GQIVNFIAPNSRLDEKEIFDYFEKYLT--DDIIILSVETADERFHSRYLMKSATYEYRLW 118

Query: 118 --TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                     E+    L+ +++D   ++ A ++LVG HDF  F +      S I+T+   
Sbjct: 119 KKDAPNRPLFERQYVNLMNQTVDVTKIKKAGKYLVGEHDFLAFTTNRKTTKS-IKTMVSL 177

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           DV    N I I + A  FL    R  VG+L  +G G+     +EKA ++++  + G  A 
Sbjct: 178 DVMETRNEIIITMTANGFLLNMERVIVGTLIQIGLGQLPMNTIEKAFESKNMNDVGHKAS 237

Query: 236 PEGLYFDSVEY 246
              L   SVEY
Sbjct: 238 AGALCLLSVEY 248


>gi|26554422|ref|NP_758356.1| tRNA pseudouridine synthase A [Mycoplasma penetrans HF-2]
 gi|42559813|sp|Q8CXQ1|TRUA_MYCPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|26454432|dbj|BAC44760.1| tRNA pseudouridine synthase [Mycoplasma penetrans HF-2]
          Length = 241

 Score =  202 bits (514), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 107/247 (43%), Gaps = 8/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           + Y + I Y+GS + G+ +QK  N  ++Q  +EK + L     +   G+GRTD  VHA+ 
Sbjct: 1   MTYKLKISYDGSFFRGYAKQKDENLITVQSELEKYLSLFFNTKISTFGSGRTDKYVHAID 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q   F    ++ P  +   LN+ L     I + ++  V   FHARFS   ++Y+Y I T 
Sbjct: 61  QTVSFKCDSDYDPKSIQNFLNSKLT---NIYVNSIEKVPNSFHARFSIKSKTYMYVINTG 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     ++   +   KS+D +         +G  DF +F +   + ++  RTI    +  
Sbjct: 118 EF-DVFKQRYEYQYNKSIDIKKCEDIINLFIGTKDFLSFSTSKLENTT--RTIRWIRIIK 174

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I +    FL   +R  VG +    + K T  ++    +   +       P  GL
Sbjct: 175 KNKKIYIFINGEGFLRNMVRMIVGIILTYCENKITYQEVLDLFKNPKKGSAVIKVPGCGL 234

Query: 240 YFDSVEY 246
           Y     Y
Sbjct: 235 YLYRTIY 241


>gi|170780769|ref|YP_001709101.1| tRNA pseudouridine synthase A [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169155337|emb|CAQ00440.1| putative pseudouridylate synthase [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 323

 Score =  202 bits (514), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 123/279 (44%), Gaps = 34/279 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHAL 58
           +R  + + Y+G+G+ GW +Q    ++QGS+E A+  +         +  AGRTD+GVHA 
Sbjct: 1   MRLRLDVAYDGTGFAGWAKQPGLRTVQGSLEDALAQLLARTPPAPTLVVAGRTDAGVHAT 60

Query: 59  RQVAHFDLVR------EWVP----------------------VILCKALNAYLKISDTIS 90
            QVAH DL        +  P                        L + LN  L     + 
Sbjct: 61  GQVAHLDLTEAQIASLDRPPRGRAAEATAGEGQHVPTAARAASALARRLNGVLGARSDVV 120

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHL 149
           +L  +     F ARFSA  R+Y YR+     P   L++ R   +P +LD   ++ AA  L
Sbjct: 121 VLACAPAPDGFDARFSATWRAYRYRVADADGPRDPLQRHRTVEVPVALDAAVLQEAADAL 180

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLV 208
           +G HDF  +     + +S IRT+         +  +E  V A +F H+ +R+ VG+    
Sbjct: 181 LGLHDFAAYCKPR-EGASTIRTLQELTWIRAADGALEAVVRADAFCHSMVRALVGACVAA 239

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             G+     L + L+ ++R     + P  GL  + V Y 
Sbjct: 240 ASGRVPVARLRELLELRERTSEFTVMPARGLVLERVGYP 278


>gi|254819223|ref|ZP_05224224.1| tRNA pseudouridine synthase A [Mycobacterium intracellulare ATCC
           13950]
          Length = 251

 Score =  201 bits (513), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 14/232 (6%)

Query: 29  GSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA---------- 78
           G +++A+  +    V +  AGRTD+GVHA  QVAH D+    +P    +A          
Sbjct: 3   GVLDEALTTIFRTPVRLRAAGRTDAGVHATGQVAHVDVPAAALPNAYSRAPHVGEAEFLP 62

Query: 79  --LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPK 135
                   +   + ++++      F ARFSA+RR Y+YR+ T        +       P+
Sbjct: 63  LLRRLGRFLPTDVRVVDIVRAPAGFDARFSALRRHYVYRLSTAPWGVDPQQVRYVTAWPR 122

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
            LD E M  A++ L+G HDF  F   H + ++ IR +   +    G+LI  RV A +F  
Sbjct: 123 PLDVEAMATASRDLLGLHDFAAFCR-HRENATTIRDLQRLEWTREGDLITARVSADAFCW 181

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + +RS VG+L  VG+ +   +   + L A  R      AP  GL    V+Y 
Sbjct: 182 SMVRSLVGALLAVGEHRRPVSWCRELLSATARSSDYATAPAHGLTLVGVDYP 233


>gi|304314991|ref|YP_003850138.1| tRNA pseudouridine synthase A [Methanothermobacter marburgensis
           str. Marburg]
 gi|302588450|gb|ADL58825.1| tRNA pseudouridine synthase A [Methanothermobacter marburgensis
           str. Marburg]
          Length = 273

 Score =  201 bits (513), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 106/250 (42%), Gaps = 29/250 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M +  + + Y G+ Y G+QRQ +  +++G +  A+       +        AGRTD GVH
Sbjct: 1   MRKIALKVAYIGTNYHGFQRQPDVPTVEGKLLDALKEAGVIRSPGDSRFQIAGRTDRGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL     F    E     +   L         I +L  + V   F  R+  + R Y Y +
Sbjct: 61  ALGNFVSFFTEEEIHVNQINDLL------PHDIKVLAWASVMYPFKVRY-PLERHYRYIL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +               S+D + M  AA+H  G HDF+ F     +  +PIR I+   
Sbjct: 114 HRGE---------------SMDIDAMAKAAEHFRGTHDFSNFSRRRDR--NPIRKINDVR 156

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+   N I + V   SFL   +R  V  L LV +G+ +  D+ + L   +R    P APP
Sbjct: 157 VSEDDNSILVDVYGESFLWQMVRKMVRVLLLVSEGELSPDDVPRLLDTDERVFIDP-APP 215

Query: 237 EGLYFDSVEY 246
           E L    ++Y
Sbjct: 216 ENLILMDLKY 225


>gi|330507400|ref|YP_004383828.1| tRNA pseudouridine synthase A [Methanosaeta concilii GP-6]
 gi|328928208|gb|AEB68010.1| tRNA pseudouridine synthase A [Methanosaeta concilii GP-6]
          Length = 271

 Score =  201 bits (513), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 62/246 (25%), Positives = 102/246 (41%), Gaps = 22/246 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + + Y G  Y+G+Q+Q +  ++   + +A+  +         AGRTD GV AL QV
Sbjct: 1   MKVALKLAYLGDNYYGFQKQPDRVTVDSQVRRALAQIGVIHGDFCYAGRTDRGVSALGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F +  + + +   + +N  L     I     SI    F AR++A+ R Y Y +     
Sbjct: 61  IDFWIDEDKIDLTRPRCVNGRL--PRDIWTWAWSIAPVGFSARWNALWREYQYLLW---- 114

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                          LD + M  AA  L+G HDF  F S        ++ ++  ++    
Sbjct: 115 ------------HPGLDRDLMEEAADMLLGEHDFRNFSSAKVG---TVKRVEKLEIRERD 159

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L    + A  FL   +R  VG+ + VG G+      +  L+  +     P AP EGL  
Sbjct: 160 GLFIFDIRADGFLWNMVRKIVGATEKVGSGQKDMRWFKDLLR-PELNHGAPTAPAEGLIL 218

Query: 242 DSVEYS 247
             V Y 
Sbjct: 219 MEVGYD 224


>gi|254282596|ref|ZP_04957564.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR51-B]
 gi|219678799|gb|EED35148.1| tRNA pseudouridine synthase A [gamma proteobacterium NOR51-B]
          Length = 222

 Score =  201 bits (513), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 70/201 (34%), Positives = 100/201 (49%), Gaps = 2/201 (0%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
            AGRTD+GVH   Q+ HFD              N+ L    T+ +     V+  FHARFS
Sbjct: 5   CAGRTDTGVHGFAQIVHFDDPVGRSEKAWVMGTNSAL--PSTVRVHWAHPVEDDFHARFS 62

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
           A  R+Y Y I   +   A   G    + ++LD + M  AAQ LVG HDF+ FR+  C A+
Sbjct: 63  AELRTYRYVIANTRVHPAQLAGLVTWVRRALDADVMNKAAQALVGEHDFSAFRAASCGAN 122

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           +P+R ++   +   G+L+ I + A +FLH  +R+  GSL +VG G  T+       + +D
Sbjct: 123 TPMRRVEQISITRRGDLVVIEIAANAFLHHMVRNIAGSLIMVGSGLRTADWFRDIFRGRD 182

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R      A   GLY   V Y 
Sbjct: 183 RTVAADTAAAAGLYLIHVSYP 203


>gi|303233145|ref|ZP_07319818.1| tRNA pseudouridine synthase A [Atopobium vaginae PB189-T1-4]
 gi|302480730|gb|EFL43817.1| tRNA pseudouridine synthase A [Atopobium vaginae PB189-T1-4]
          Length = 321

 Score =  201 bits (511), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 75/257 (29%), Positives = 107/257 (41%), Gaps = 17/257 (6%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y G  + G+  Q+   +++G +   +  V    V +  AGRTD+GVHA  Q   F 
Sbjct: 58  LRLGYEGEQFAGYAFQEGQRTVEGCVRDVLQRVLRRDVTLTCAGRTDAGVHAHAQYVSFP 117

Query: 66  LVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +  E        L ++LN  +     I+I  +      F ARF A  RSY YRI T    
Sbjct: 118 VTHEECACAKSSLLRSLN--MLCPADIAIRTIYQAAPDFSARFDARSRSYTYRIATAPLK 175

Query: 123 LALEKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSI------HCQASSPIRTIDH 174
             L     W       +  ++M  AAQ L+G H+F +F           Q  S  R I  
Sbjct: 176 PVLTAPFVWWNRHVHHVCMDDMNAAAQALIGEHNFESFCKATSADVLKSQGLSLQRCITS 235

Query: 175 FDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            +V+        LI I +   +FLH  +R   GSL  VG G  +   L   L A+ R   
Sbjct: 236 INVHRDYVLGEQLICIDIEGNAFLHNMVRIIAGSLLEVGRGARSVAWLGDVLAARTRTAA 295

Query: 231 GPLAPPEGLYFDSVEYS 247
              AP  GL  + V Y 
Sbjct: 296 AQTAPACGLTLEHVAYP 312


>gi|237752928|ref|ZP_04583408.1| tRNA pseudouridine synthase A [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375195|gb|EEO25286.1| tRNA pseudouridine synthase A [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 249

 Score =  201 bits (511), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 74/246 (30%), Positives = 108/246 (43%), Gaps = 9/246 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  M I YNG  +FG+Q Q N  S+   +E   F   G    +  +GRTD GVH+  QV 
Sbjct: 11  KVAMRIAYNGGAFFGFQSQSNVQSVANVLEDV-FKSVGVFSKIAASGRTDKGVHSSAQVI 69

Query: 63  HFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             ++   W     L   LNA L  +  I   ++  V   FHARFSA RR Y Y +   + 
Sbjct: 70  SLEIPYFWKNLENLKVCLNAKLAPNLFI--KHIWEVGDDFHARFSATRRGYCYVLS--KH 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                   +       +   ++ A + LVG H+F  F+       S +R+I   D+  F 
Sbjct: 126 FSPFLTPFSLHYNLK-NPNLIKQALKLLVGTHNFGAFKKQGSGEKSSVRSIFRADLREFK 184

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
               +      FL +Q+R  VG L  +  G  T   LE  L  + R    P+AP  GLY 
Sbjct: 185 GFWILSFWGNGFLRSQVRLMVGFLLEIDKGNLTLEALEAQLNGEMRYRI-PIAP-NGLYL 242

Query: 242 DSVEYS 247
             V+++
Sbjct: 243 SRVDFN 248


>gi|84489200|ref|YP_447432.1| tRNA pseudouridine synthase A [Methanosphaera stadtmanae DSM 3091]
 gi|121725515|sp|Q2NHB4|TRUA_METST RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|84372519|gb|ABC56789.1| TruA [Methanosphaera stadtmanae DSM 3091]
          Length = 274

 Score =  200 bits (510), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 69/252 (27%), Positives = 106/252 (42%), Gaps = 26/252 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG----AGRTDSGVH 56
           M R  + I Y GS + G+QRQ N  +++G + +                  AGRTD GVH
Sbjct: 1   MRRVALKIAYIGSNFHGYQRQPNYRTVEGELLRVFKETNIIEDTWTAHYSVAGRTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +   V  F    +         LN  L   D I I+  + V   F  RF  + R+Y Y  
Sbjct: 61  STGNVISFITDEDIH----INQLNGLL--PDDIKIIGEARVPYGFKVRF-PLTRTYTYI- 112

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              Q     EK       K+LD   M +A +  +G+H+F  F        +P R I   +
Sbjct: 113 ---QPISPFEK-------KNLDITKMHVAMESFIGKHNFRNFSKR--NEKNPNRKIIDVN 160

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP--LA 234
           +    +++   +V  SFL   +R  V S+  VG GK    D+ + L+ ++ ++      A
Sbjct: 161 LEVDEDVLIFTIVGESFLWNMVRKMVTSIMEVGYGKLDINDINELLKPKELRQFIRLQPA 220

Query: 235 PPEGLYFDSVEY 246
           P  GL    +EY
Sbjct: 221 PANGLILSDMEY 232


>gi|298253049|ref|ZP_06976841.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 5-1]
 gi|297532444|gb|EFH71330.1| tRNA pseudouridine synthase A [Gardnerella vaginalis 5-1]
          Length = 305

 Score =  200 bits (510), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 79/285 (27%), Positives = 124/285 (43%), Gaps = 40/285 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------EIVVVHGAGRTDSG 54
           +R  + + Y+G G++GW +Q    ++QG IE A+ +V         E + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGGFYGWAKQPVLRTVQGDIEAALHMVLRVPKNDPTESLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREWVPVILCK-------ALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  E +   +         AL   LK  +   IS+  +S+    F ARF
Sbjct: 61  VHASHQVCHLDVCEETLLRCVGHTGLDGVCALEYRLKHVLPQDISLHKVSVAPIGFDARF 120

Query: 106 SAIRRSYLYRIITR---QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           SA+ R+Y+YRI             +G    +   LD + M  AA+ ++G HDF +F   +
Sbjct: 121 SALERTYVYRICDASDYCDYDPRMRGFVLKLDDVLDVDAMNQAARLMIGLHDFGSFARPN 180

Query: 163 CQASSPIRTIDHFDVNSFG--------------------NLIEIRVVARSFLHTQIRSFV 202
               + IR +        G                     L+E  +VA +F H  +RS V
Sbjct: 181 P-GGTTIRDVKSVCWERVGTRANDVRVKLKTGCVPPVEQGLLEFTIVADAFAHNMVRSLV 239

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +   +G GK +    E+ +    R+       P GL  + V Y 
Sbjct: 240 QACVQIGCGKRSFDWFEEKINVPLREGSTGPIDPHGLTLEYVAYP 284


>gi|298709054|emb|CBJ31003.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 412

 Score =  200 bits (509), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 63/275 (22%), Positives = 117/275 (42%), Gaps = 31/275 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R+   + Y+G+ Y G+Q Q +G  ++QG +EKA+       V V  AGRTD+GVH++ Q
Sbjct: 137 TRFVSRVMYDGTNYKGFQLQGHGLPTVQGVLEKALSTRFQTYVPVVAAGRTDTGVHSVGQ 196

Query: 61  VAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQ----------FHARFSAIR 109
             HFDL         L  ++N  +   + + + N+S+              + +  +A  
Sbjct: 197 AVHFDLPNANEDLSQLAYSMNQMM--PEDVRVWNMSVAPPSSPWQVEKGWPWSSMLNARG 254

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPK----SLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           + Y YR+        L++       +     ++ + +      LVG+HDF  F +   + 
Sbjct: 255 KRYSYRLFVGPVMSPLDRLYRAHASQAAGSPINVDLLYQTIPKLVGKHDFAGFSNEVTKR 314

Query: 166 SS-----------PIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           ++            +RT+   ++ +  G  I +       L+  +R+ VG+L  V  G+ 
Sbjct: 315 ATLKKEDGLGEFNTVRTVYSAEIIDEGGGNIRLDFHLDGALYRMVRNMVGALLAVAAGRL 374

Query: 214 TSTDLEKALQAQDR-KECGPLAPPEGLYFDSVEYS 247
               +++    + R       AP  GL  D+V Y 
Sbjct: 375 EPEVIDEIFATRVRDSRLIYAAPAHGLTLDTVLYD 409


>gi|322374718|ref|ZP_08049232.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
 gi|321280218|gb|EFX57257.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
          Length = 191

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 55/190 (28%), Positives = 90/190 (47%), Gaps = 4/190 (2%)

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + +   
Sbjct: 3   QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEFIVDRG 60

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH--FDV 177
           +    + +  A   P  LD E M+ A + L G HDFT F +        +RTI      V
Sbjct: 61  RPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFTGFTASGTSVEDKVRTITEASLSV 120

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  +        FL+ QIR+ VG+L  +G+ +     ++  L+ +DR+  GP A P 
Sbjct: 121 DETGQFLTFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPTAAPN 180

Query: 238 GLYFDSVEYS 247
           GLY   + Y 
Sbjct: 181 GLYLKEIRYE 190


>gi|283954398|ref|ZP_06371918.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           414]
 gi|283794015|gb|EFC32764.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           414]
          Length = 240

 Score =  199 bits (507), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 102/246 (41%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +  S+Q  + +A+  + G    +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGSAFLGSATQPHKKSVQDVLGEALSHL-GIFSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVECGEYFTNLEYLKKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHA 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D +         VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLDKANELLSFFVGKKDLKFFCKSGGDNKTTLREIFLARAYTY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +    R  A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY
Sbjct: 176 KDFSIFRFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNRFLAPPNGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRIHY 240


>gi|288932131|ref|YP_003436191.1| tRNA pseudouridine synthase A [Ferroglobus placidus DSM 10642]
 gi|288894379|gb|ADC65916.1| tRNA pseudouridine synthase A [Ferroglobus placidus DSM 10642]
          Length = 256

 Score =  199 bits (507), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 105/242 (43%), Gaps = 29/242 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
              I Y G+ + G Q Q    +++G I KA      E   +  AGRTD+GVHA+  V  F
Sbjct: 2   AFKIAYIGTNFHGSQYQPELRTVEGEIRKAFEKAGIEYGKIMFAGRTDAGVHAIGNV--F 59

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               E     + K LN+ L   + +S+    +VD+ F  R  A  R Y Y I        
Sbjct: 60  ATDLEEFSKKVVKKLNSNL--PEDVSVWGYKVVDENFKPRK-AKWRKYCYVI-------- 108

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L++G         + E M+ AA+H VG+HDF  F      + S +R +   DV   GNLI
Sbjct: 109 LDEGY--------NLEEMKEAAKHFVGKHDFGIFVR---GSESCVREVYESDVEKRGNLI 157

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
              + A +F    +R    SL +   GK    +  K L+ +        APP GL    V
Sbjct: 158 YFSIKANAFAWNMVRRMASSLMIA--GKEGIEEFFKILKGE---RAVSAAPPNGLVLVDV 212

Query: 245 EY 246
            Y
Sbjct: 213 HY 214


>gi|153951132|ref|YP_001398256.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. doylei
           269.97]
 gi|166228691|sp|A7H426|TRUA_CAMJD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|152938578|gb|ABS43319.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. doylei
           269.97]
          Length = 241

 Score =  199 bits (506), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 100/247 (40%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q  + +A+  + G    +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSATQPHKKGVQDVLSEALSHL-GIFSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA  +    +     L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +         +  PK  D           VG+ D   F        + +R I      +
Sbjct: 117 SSYSPFMASYVYFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ +     LAPP GL
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAKKQCN-HFLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLSRICY 241


>gi|255022149|ref|ZP_05294152.1| tRNA pseudouridine synthase A [Acidithiobacillus caldus ATCC 51756]
 gi|254968413|gb|EET25972.1| tRNA pseudouridine synthase A [Acidithiobacillus caldus ATCC 51756]
          Length = 206

 Score =  198 bits (505), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 69/187 (36%), Positives = 98/187 (52%), Gaps = 2/187 (1%)

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           + HFD       +   + +N YL    +IS+L    V + FHARF+A+ R Y Y I+ R 
Sbjct: 1   MVHFDAPVTRPALAWTRGVNRYL--PSSISVLWARPVPRDFHARFAAVGRRYRYCILNRS 58

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL  GRA  +P+ L  E M+ AA  L+GRHDF+ FR+  CQA  PIR +    V+  
Sbjct: 59  ERSALYAGRAAWVPRPLAVEPMQEAASLLLGRHDFSAFRAAACQAKHPIRELRQLRVSRQ 118

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + +   A +FLH  +R+ VG L  +G G        + L ++ R   G  AP EGLY
Sbjct: 119 GDWVFVDAEANAFLHHMVRNLVGVLLGIGWGDRPPHWAAEVLASRKRALAGVTAPAEGLY 178

Query: 241 FDSVEYS 247
           F +  Y 
Sbjct: 179 FVAALYP 185


>gi|73956519|ref|XP_546716.2| PREDICTED: similar to pseudouridylate synthase-like 1 [Canis
           familiaris]
          Length = 294

 Score =  198 bits (504), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 79/258 (30%), Positives = 120/258 (46%), Gaps = 31/258 (12%)

Query: 16  FGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVAHFDLVR-----E 69
            G QR      +   +E+A   +     V    + RTD+GVHAL   AH D+ R      
Sbjct: 30  RGSQR---AVGVLNYLEEAAKRLNSVVPVRFTISSRTDAGVHALSNAAHLDVQRRSGQPP 86

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL----AL 125
           + P +L +ALNA+++    I +L    V   FHAR +A  R+YLYR++T           
Sbjct: 87  FSPEVLAEALNAHVRHP-AIRVLQAFRVPSDFHARHAATSRTYLYRLVTGCHRPDQLSVF 145

Query: 126 EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG--- 181
           E+ R W +    LD + M+ AAQHL+G HDF  F+S     +S +RT+    V+      
Sbjct: 146 ERNRCWPLRADCLDVDAMQEAAQHLLGTHDFRAFQSAGSPTTSSVRTLRRASVSPDPGSP 205

Query: 182 ---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD---RKE 229
                    +   +   +RSFL+ Q+R     L  VG G      ++  L+++D   R +
Sbjct: 206 FVLAQEKRLHFWNLEFESRSFLYRQVRRMTAVLVAVGLGALRPAQVKVILESRDPLGRHQ 265

Query: 230 CGPLAPPEGLYFDSVEYS 247
              +AP  GL+  SV Y 
Sbjct: 266 AR-VAPAHGLFLKSVLYE 282


>gi|301094360|ref|XP_002896286.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
 gi|262109681|gb|EEY67733.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
          Length = 300

 Score =  198 bits (504), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 115/273 (42%), Gaps = 29/273 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVH 56
           +R   ++EY+G+ +FG Q Q       ++Q  IE A+F  TGE     +  A RTD+GVH
Sbjct: 30  VRRRCVVEYDGAAFFGSQAQDQPGALRTVQEVIEDALFRTTGEKGLPRLRFASRTDTGVH 89

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLS---IVDKQFHARFSAIRRSYL 113
           AL QV  F         +   ALN  L   D +   +++     +  F  R    R+ Y 
Sbjct: 90  ALGQVMVFVSQCIESDRVFRDALNTRL--PDDVLCHSMTTMTEAEADFDPRSDTKRKRYE 147

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG---RHDFTTFR--SIHCQASSP 168
           Y +I         +   W + K LD   M+ A  HL+      DF+ F       +    
Sbjct: 148 YELIVGGLRPVAHRRNVWYVHKPLDVAKMQEAIDHLMTPPTTKDFSAFTPQKAVDRERGN 207

Query: 169 IRTIDHFDVNS-----FGN---------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           I TI   +++S      G+          I +      F +  +R  VG+L  +G G+  
Sbjct: 208 ICTISTIELHSTMMDDRGDAQYREDVATRIRLVFEGNRFRYKMVRILVGTLVDIGLGRLK 267

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             D+   L +Q+R + G  AP +GL    V+Y 
Sbjct: 268 PDDIPVILASQNRGKAGQGAPSQGLTLIWVKYD 300


>gi|260188510|ref|ZP_05765984.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis CPHL_A]
 gi|289449159|ref|ZP_06438903.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289422117|gb|EFD19318.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           CPHL_A]
          Length = 256

 Score =  198 bits (503), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 70/238 (29%), Positives = 114/238 (47%), Gaps = 14/238 (5%)

Query: 23  NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA---- 78
              ++ G ++ A+  +    V +  AGRTD+GVHA  QVAH D+  + +P    +A    
Sbjct: 2   GQRTVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQVAHVDVPADALPNAYPRAGHVG 61

Query: 79  --------LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGR 129
                         +   + IL+++     F ARFSA+RR Y+YR+ T    +   +   
Sbjct: 62  DPEFLPLLRRLGRFLPADVRILDITRAPAGFDARFSALRRHYVYRLSTAPYGVEPQQARY 121

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
               P+ LD + M  A++ L+G HDF  F   H + ++ IR +   D +  G+L+   V 
Sbjct: 122 ITAWPRELDLDAMTAASRDLMGLHDFAAFCR-HREGATTIRDLQRLDWSRAGSLVTAHVT 180

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           A +F  + +RS VG+L  VG+ +  +T   + L A  R     +AP  GL    V+Y 
Sbjct: 181 ADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRSSDFAVAPAHGLTLIQVDYP 238


>gi|219853269|ref|YP_002467701.1| tRNA pseudouridine synthase ACD [Methanosphaerula palustris E1-9c]
 gi|254789642|sp|B8GFU5|TRUA_METPE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219547528|gb|ACL17978.1| tRNA pseudouridine synthase A [Methanosphaerula palustris E1-9c]
          Length = 280

 Score =  198 bits (503), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 100/248 (40%), Gaps = 28/248 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +R    + Y+G+ + G Q Q    +++G +  A   V             AGRTD GVHA
Sbjct: 1   MRLAFQLSYDGNQFRGSQLQPAYRTVEGELITACQRVQLFDDPCKAGFALAGRTDRGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV  F       P    +ALN  L  S  +     + V   FH RF AI R+Y Y   
Sbjct: 61  RGQVGAFSTP---FPERAVEALNGQL--SPDLWCNGFAEVPPSFHPRFDAISRTYRYFFA 115

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                              LD   M  AA  L+G HDF+  R    +  SPIRT+    V
Sbjct: 116 ----------------DWPLDIRAMDQAAAALIGTHDFS--RLARVREKSPIRTVKSARV 157

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                +    V A ++L   +R    +L L+G  +     +E+ L  + R+   P AP +
Sbjct: 158 FQDRGIPVFEVTAHTYLWHMVRCMAAALLLIGTHEREPELMERLLSGKCRRN-PPAAPAD 216

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 217 GLVLWDVD 224


>gi|326671566|ref|XP_683563.5| PREDICTED: tRNA pseudouridine synthase-like 1-like [Danio rerio]
          Length = 291

 Score =  198 bits (503), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 84/274 (30%), Positives = 129/274 (47%), Gaps = 32/274 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGS---IEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY +  +Y GS Y G  +     ++QG    +E A+  +     V V  + RTD+GVHAL
Sbjct: 7   RYLIFFQYTGSKYSGVMKAPAHQAVQGVGNHLENAVRKLKPVNEVCVSISSRTDTGVHAL 66

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R           L +ALN  LK  + I I     V   FHAR+ A  R+Y+
Sbjct: 67  CNSAHVDIQRRADKPPLSEQSLLEALNFQLKE-EPIRITRAYRVHSDFHARYQAQSRTYV 125

Query: 114 YRIITRQAPLAL----EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQA--S 166
           YR+        L    EK   W +  + L+ + MR A+  L+G HDF+TFR++   A   
Sbjct: 126 YRLALGCQHHTLMPLTEKDLCWALRDTRLNIDAMREASALLLGTHDFSTFRALSSDAPFK 185

Query: 167 SPIRTIDHFDVNSFG-----------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
            P++T+D   +                  E+   +RSFL+ Q+R   G L  +G G+ + 
Sbjct: 186 CPVKTLDLAQLEPGESFSQRHFQRDIQFWELTFKSRSFLYRQVRRMTGVLVAIGQGRLSV 245

Query: 216 TDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
           + ++  L+A+D     P    AP  GL+  +V+Y
Sbjct: 246 SKIQDLLEARD-SLAFPNNLTAPAHGLFLTNVQY 278


>gi|302869940|ref|YP_003838577.1| tRNA-pseudouridine synthase I [Micromonospora aurantiaca ATCC
           27029]
 gi|315501401|ref|YP_004080288.1| tRNA-pseudouridine synthase i [Micromonospora sp. L5]
 gi|302572799|gb|ADL49001.1| tRNA-pseudouridine synthase I [Micromonospora aurantiaca ATCC
           27029]
 gi|315408020|gb|ADU06137.1| tRNA-pseudouridine synthase I [Micromonospora sp. L5]
          Length = 277

 Score =  198 bits (503), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 71/251 (28%), Positives = 108/251 (43%), Gaps = 6/251 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHALR 59
            R  + + Y+G+ + GW  Q    ++ G + + + LV G      +  AGRTD+GVHA  
Sbjct: 5   TRLRLDVSYDGTDFSGWAPQPARRTVAGVLMQTLDLVLGAGTATGLTVAGRTDAGVHATG 64

Query: 60  QVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL    W              +   + +  ++ V   F ARFSA  R Y YR+  
Sbjct: 65  QVCHLDLPTPVWREHEGRLLRRLARLLPPDVRVRAMTEVPADFDARFSATFRRYEYRVTD 124

Query: 119 RQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  L +G     PK LD   +  AA  LVG HDF  +     + ++ +R +   D 
Sbjct: 125 APWGAEPLRRGDTLAWPKPLDLAALNAAAAGLVGEHDFAAYCRRK-ENATTLREVTRLDW 183

Query: 178 NSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               + I    V A +F    +RS VG++ + GDG+         L  ++R     +AP 
Sbjct: 184 RRDPDGILVATVQADAFCQNMVRSLVGAMLVAGDGRRPVQWPAGLLTRRERSSEVTVAPA 243

Query: 237 EGLYFDSVEYS 247
            GL   +V Y 
Sbjct: 244 HGLALVAVGYP 254


>gi|294464718|gb|ADE77866.1| unknown [Picea sitchensis]
          Length = 382

 Score =  197 bits (502), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 70/193 (36%), Positives = 106/193 (54%), Gaps = 13/193 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + ++Y G+ + G Q+Q N  ++QG +E A     G+ V    + RTD+GVHAL  V
Sbjct: 29  QRYLVAVDYIGTNFAGMQKQPNFRTVQGVLEDAFNKFIGQPVSSASSSRTDAGVHALTNV 88

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIR 109
            H D+ R              P ++ +A+N +L+     ISI+++  V   FHAR+ A  
Sbjct: 89  CHVDVERISKRKPGEVLPPHEPEVVKRAVNHFLQKDAGDISIIDVRFVPMTFHARYRAQE 148

Query: 110 RSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           R+Y YRI++ + P    EK RAW +P+ L    M+ A + LVG HDF++FR+  CQA SP
Sbjct: 149 RTYYYRILSGKEPLSIFEKDRAWHVPEDLGLSCMQEACKVLVGHHDFSSFRASGCQAKSP 208

Query: 169 IRTIDHFDVNSFG 181
           I+ +D   V    
Sbjct: 209 IKILDELRVCEMP 221



 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 40/77 (51%)

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            +  F          +   A+SFL+ Q+R  VG+LK VG GK +  D+E  L+A+     
Sbjct: 292 EVLEFGHRRGHRGYVVVARAQSFLYHQVRLLVGTLKCVGTGKLSVDDVESILKARTITVA 351

Query: 231 GPLAPPEGLYFDSVEYS 247
            P+AP  GLY  +V+Y 
Sbjct: 352 PPMAPACGLYLAAVKYD 368


>gi|121639375|ref|YP_979599.1| tRNA pseudouridine synthase A [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148663320|ref|YP_001284843.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Ra]
 gi|215405494|ref|ZP_03417675.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis 02_1987]
 gi|215413368|ref|ZP_03422053.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis
           94_M4241A]
 gi|215428962|ref|ZP_03426881.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T92]
 gi|215432426|ref|ZP_03430345.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis EAS054]
 gi|215447792|ref|ZP_03434544.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T85]
 gi|218755231|ref|ZP_03534027.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis GM 1503]
 gi|219559524|ref|ZP_03538600.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T17]
 gi|224991871|ref|YP_002646560.1| tRNA pseudouridine synthase A [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|254552559|ref|ZP_05143006.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260202637|ref|ZP_05770128.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T46]
 gi|260206826|ref|ZP_05774317.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis K85]
 gi|289445055|ref|ZP_06434799.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T46]
 gi|289571689|ref|ZP_06451916.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T17]
 gi|289576191|ref|ZP_06456418.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis K85]
 gi|289752179|ref|ZP_06511557.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T92]
 gi|289755588|ref|ZP_06514966.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           EAS054]
 gi|289759618|ref|ZP_06518996.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T85]
 gi|289763637|ref|ZP_06523015.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis GM
           1503]
 gi|297636114|ref|ZP_06953894.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis KZN 4207]
 gi|297733114|ref|ZP_06962232.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis KZN R506]
 gi|306777802|ref|ZP_07416139.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu001]
 gi|306782521|ref|ZP_07420858.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu002]
 gi|306809459|ref|ZP_07446127.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu007]
 gi|313660445|ref|ZP_07817325.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis KZN
           V2475]
 gi|2104378|emb|CAB08721.1| PROBABLE TRNA PSEUDOURIDINE SYNTHASE A TRUA (PSEUDOURIDYLATE
           SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL
           HYDROLYASE) [Mycobacterium tuberculosis H37Rv]
 gi|31620228|emb|CAD95671.1| PROBABLE TRNA PSEUDOURIDINE SYNTHASE A TRUA (PSEUDOURIDYLATE
           SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL
           HYDROLYASE) [Mycobacterium bovis AF2122/97]
 gi|121495023|emb|CAL73509.1| Probable tRNA pseudouridine synthase A truA [Mycobacterium bovis
           BCG str. Pasteur 1173P2]
 gi|148507472|gb|ABQ75281.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Ra]
 gi|224774986|dbj|BAH27792.1| tRNA pseudouridine synthase A [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|289417974|gb|EFD15214.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis T46]
 gi|289540622|gb|EFD45200.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis K85]
 gi|289545443|gb|EFD49091.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T17]
 gi|289692766|gb|EFD60195.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T92]
 gi|289696175|gb|EFD63604.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           EAS054]
 gi|289711143|gb|EFD75159.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis GM
           1503]
 gi|289715182|gb|EFD79194.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis T85]
 gi|308213887|gb|EFO73286.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu001]
 gi|308324838|gb|EFP13689.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu002]
 gi|308344299|gb|EFP33150.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           SUMu007]
 gi|326905301|gb|EGE52234.1| tRNA pseudouridine synthase A truA [Mycobacterium tuberculosis
           W-148]
          Length = 256

 Score =  197 bits (502), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 70/238 (29%), Positives = 113/238 (47%), Gaps = 14/238 (5%)

Query: 23  NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA---- 78
              ++ G ++ A+  +    V +  AGRTD+GVHA  QVAH D+  + +P    +A    
Sbjct: 2   GQRTVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQVAHVDVPADALPNAYPRAGHVG 61

Query: 79  --------LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGR 129
                         +   + IL+++     F ARFSA+RR Y+YR+ T    +   +   
Sbjct: 62  DPEFLPLLRRLGRFLPADVRILDITRAPAGFDARFSALRRHYVYRLSTAPYGVEPQQARY 121

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
               P+ LD + M  A++ L+G HDF  F   H + ++ IR +   D +  G L+   V 
Sbjct: 122 ITAWPRELDLDAMTAASRDLMGLHDFAAFCR-HREGATTIRDLQRLDWSRAGTLVTAHVT 180

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           A +F  + +RS VG+L  VG+ +  +T   + L A  R     +AP  GL    V+Y 
Sbjct: 181 ADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRSSDFAVAPAHGLTLIQVDYP 238


>gi|86153529|ref|ZP_01071733.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           HB93-13]
 gi|85843255|gb|EAQ60466.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           HB93-13]
          Length = 241

 Score =  197 bits (501), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 102/247 (41%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA  +    +     L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +            PK  D +         VG+ D   F        + +R I      +
Sbjct: 117 SSYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GL
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLSRICY 241


>gi|121613330|ref|YP_001000512.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|166228692|sp|A1VZH1|TRUA_CAMJJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|121504241|gb|EAQ72335.2| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81-176]
          Length = 241

 Score =  197 bits (501), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 101/247 (40%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA       +     L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVGCGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +            PK  D +         VG+ D   F        + +R I      +
Sbjct: 117 SSYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GL
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLSRICY 241


>gi|78777192|ref|YP_393507.1| pseudouridylate synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497732|gb|ABB44272.1| Pseudouridylate synthase [Sulfurimonas denitrificans DSM 1251]
          Length = 236

 Score =  197 bits (501), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 109/247 (44%), Gaps = 13/247 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  +II YNG+ + G Q QK   ++I G++E A+  +  E   +  +GRTD GVHA  Q
Sbjct: 1   MRCALIIAYNGTNFLGSQTQKESKNTILGTLEIALKKINIET-KIVASGRTDRGVHASGQ 59

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL   W  +  L  +L   L    +I I  + IVD  FHAR+SA RR Y Y I   
Sbjct: 60  VCHIDLPPYWSDITKLQDSLGRVL--PPSILIKKIKIVDDTFHARYSAKRRVYRYIIKKA 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++    E+     I  + D   ++   +   G  DF  F        S  R I       
Sbjct: 118 KS-NPFEENFVTFIDDT-DFFEIQKNIKLFCGAFDFKFFMKSGGDIKSTTRVIYRAFAYE 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I +   A  FL +QIR  VG+L           ++   L+ +   +  P A   GL
Sbjct: 176 HKGFIVLNFEANGFLRSQIRLMVGALLS-----LNEDEILDKLECRVNHKIKP-AKSNGL 229

Query: 240 YFDSVEY 246
           Y   ++Y
Sbjct: 230 YLSKIKY 236


>gi|294621109|ref|ZP_06700300.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|291599345|gb|EFF30371.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
          Length = 165

 Score =  197 bits (501), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 56/161 (34%), Positives = 92/161 (57%), Gaps = 3/161 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M+RY  II Y+G+ + G+Q+Q NG ++Q  +EK +  +  G+ + V G+GRTD+GVHA+ 
Sbjct: 1   MVRYKAIIAYDGTNFNGFQKQPNGRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E     +  AL+   +  + I++  + IV + FHAR+    ++Y +R+   
Sbjct: 61  QVIHFDYPEERPLERMRFALDT--QSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           +      +  A   P  LD E ++ A   L+G HDFT+F +
Sbjct: 119 KPRSPFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCA 159


>gi|154503357|ref|ZP_02040417.1| hypothetical protein RUMGNA_01181 [Ruminococcus gnavus ATCC 29149]
 gi|153796024|gb|EDN78444.1| hypothetical protein RUMGNA_01181 [Ruminococcus gnavus ATCC 29149]
          Length = 252

 Score =  197 bits (501), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 58/249 (23%), Positives = 103/249 (41%), Gaps = 8/249 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQ---RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + +EY+G+ Y GW+   +++N  ++ G I  A+  +  E + +  A +TD GVHA
Sbjct: 1   MQTLMLTVEYDGTRYAGWKAAPKKENLDTVLGRIHTALARLLKEDIQLFCAAKTDPGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             Q+  F      +P  L  +LN  L     I++L+   V ++FHA        +   I 
Sbjct: 61  RGQILSFQTTSSLLPSALKSSLNQVL--PQDIAVLDARQVSERFHAELLPKHCIWELCIK 118

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T   P    +     +P   D   M+ A   L GRHD   F  +  +  + +R +    +
Sbjct: 119 TGPTPDVFRQKYTLFLPDLPDPLRMQEAFSFLKGRHDVRCFSPVK-KKKAIMRELYSLRI 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + +++ +    FL     + +  L  +G G   +  +     A +    G  AP  
Sbjct: 178 EHSDDEMQLFLEGSDFLPFMPATLMQLLLDIGTGTLDACCIPSIF-AGEHSYSGH-APAH 235

Query: 238 GLYFDSVEY 246
            LY   + Y
Sbjct: 236 ALYLHDIVY 244


>gi|57167827|ref|ZP_00366967.1| tRNA pseudouridine synthase A [Campylobacter coli RM2228]
 gi|57020949|gb|EAL57613.1| tRNA pseudouridine synthase A [Campylobacter coli RM2228]
          Length = 240

 Score =  196 bits (499), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 102/246 (41%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +  S+Q +++ A+  + G    V  A RTD GVHA   V
Sbjct: 1   MKLKIIFSYDGSKFLGSATQPHKKSVQDALQDALSHL-GIFSSVLMASRTDKGVHASYAV 59

Query: 62  AHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +          L K +N +      I + NL I+   F  R+    R Y Y      
Sbjct: 60  ACVECGEHFRDLNYLKKQINKF--SHPFIHVKNLKIMPSNFEVRYDVKSREYRYIFYHG- 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                        P  +D     +  Q+ VG  DF  F        + IR I      S+
Sbjct: 117 VYNPFLASYVHFYPF-IDVLKADLVLQNFVGIKDFKFFCKSGGDNKTTIREIFLAKAYSY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +    R  A  FL  QIR  V S+  V + K +  +L++ ++A+ ++    LAPP GLY
Sbjct: 176 KDFTIFRFKANGFLRAQIRLMVASVLKVLENKMSIEELKEQIEAK-KQYNHFLAPPCGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRISY 240


>gi|290999771|ref|XP_002682453.1| predicted protein [Naegleria gruberi]
 gi|284096080|gb|EFC49709.1| predicted protein [Naegleria gruberi]
          Length = 377

 Score =  196 bits (498), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 87/304 (28%), Positives = 127/304 (41%), Gaps = 61/304 (20%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN-----GSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVH 56
           RY +I +Y G+ Y G+Q+Q N     G++IQ  IE ++  +     + + G+ RTDSGVH
Sbjct: 58  RYKLIFQYRGNNYDGYQKQNNKGEPRGNTIQKHIEGSLHKLFNTNDIYIVGSSRTDSGVH 117

Query: 57  ALRQVAHFDLVREWVPVI-------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           AL    HFD+  E +          +   LN YLK  + I I +    D  FHAR     
Sbjct: 118 ALHNTCHFDVASEIIEKRENYTAKNVIFGLNFYLK-DEDIVICSCEKKDMNFHARHRVKE 176

Query: 110 RSYLYR-IITRQAPL-----ALEKGRAWLIPK-------------SLD---------CEN 141
           R Y YR ++T   P         + + W++               SLD          ++
Sbjct: 177 REYQYRVLLTGPKPDLAYKVPFIQDQYWIVNGAKYEQGGPTKQEISLDFRSLETYFRIDD 236

Query: 142 MRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVNSFG-----------------NL 183
           +R A Q+ +G H+F  F      +  S I+TI+   V                       
Sbjct: 237 VREACQYFIGTHNFNNFCKSDLPERVSRIKTINSVTVEEIDLQQDQTISPLFFSTSKCKE 296

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD-RKECGPLAPPEGLYFD 242
           I   +   SFLH Q+R  V +L  VG GK   T L   +Q  + R      APP GL+  
Sbjct: 297 IRFTIRGNSFLHNQVRIMVDALVKVGIGKMNPTYLRALVQNPNMRYPEKGSAPPHGLFLT 356

Query: 243 SVEY 246
           +V Y
Sbjct: 357 NVVY 360


>gi|152993424|ref|YP_001359145.1| tRNA pseudouridine synthase A [Sulfurovum sp. NBC37-1]
 gi|151425285|dbj|BAF72788.1| tRNA pseudouridine synthase A [Sulfurovum sp. NBC37-1]
          Length = 240

 Score =  195 bits (497), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 113/247 (45%), Gaps = 9/247 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGS-IEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R   +I Y+GS + G+Q+Q   +    + IE A+  +   I  + G+GRTD+GVHA  Q
Sbjct: 1   MRVKAVIAYDGSAFQGFQKQTRTNRTVTTTIENALADLQI-ISPLTGSGRTDAGVHASGQ 59

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V HFDL   W     L  +LN  L    TI   ++S     FHARFSA +R Y Y     
Sbjct: 60  VIHFDLPEFWSDLNRLKNSLNKKLS---TIRFKHISAAPDDFHARFSAKKRIYRYIFKEN 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +     E+        S D + ++ A    VG HDF  F        + +R I   +   
Sbjct: 117 EL-SVFERKYVAHYS-SFDPDILKRALLMFVGEHDFIYFHKTGSDIHTTVRKIYDANYRQ 174

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G    +   A  FL +Q+R  V S  L    + T   L+K + A+ R     L+PPEGL
Sbjct: 175 EGKYHFLYFTANGFLRSQVRMMVESAMLCAQNELTLEQLQKQINAEKRYHSR-LSPPEGL 233

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 234 YLARILY 240


>gi|86150269|ref|ZP_01068496.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88597547|ref|ZP_01100781.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|148926529|ref|ZP_01810211.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|218562455|ref|YP_002344234.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           NCTC 11168]
 gi|24212598|sp|Q9PP96|TRUA_CAMJE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|85839385|gb|EAQ56647.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88190139|gb|EAQ94114.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|112360161|emb|CAL34955.1| tRNA pseudouridine synthase [Campylobacter jejuni subsp. jejuni
           NCTC 11168]
 gi|145845223|gb|EDK22317.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni CG8486]
          Length = 241

 Score =  195 bits (497), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 100/247 (40%), Gaps = 7/247 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +I  Y+GS + G   Q +   +Q ++  A+  + G    +  A RTD GVHA   
Sbjct: 1   MMKIKIIFSYDGSAFLGSATQPHKKGVQDALSGALSHL-GIFSPLLMASRTDKGVHASYA 59

Query: 61  VAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA  +    +     L K LN +      I I  +  V   F  RF    R Y Y I + 
Sbjct: 60  VASVECGDYFTNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +            PK  D           VG+ D   F        + +R I      +
Sbjct: 117 ASYSPFMASYVHFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYA 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GL
Sbjct: 176 YKDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGL 234

Query: 240 YFDSVEY 246
           Y   + Y
Sbjct: 235 YLSRICY 241


>gi|301629805|ref|XP_002944022.1| PREDICTED: tRNA pseudouridine synthase A-like [Xenopus (Silurana)
           tropicalis]
          Length = 207

 Score =  195 bits (497), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 61/192 (31%), Positives = 89/192 (46%), Gaps = 6/192 (3%)

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD      P    +  N +L     I++     V   FHAR  A  R Y Y ++  
Sbjct: 2   QVVHFDTPLRRTPFAWVRGSNTFL--PPDIAVQWAQAVPASFHARACATARRYAYVLLQS 59

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               ++E  R   + + LD   MR AAQHL+G HDFT+FR+  CQA +P++T+    +  
Sbjct: 60  PVRPSVESARVGWVFQPLDGAAMRAAAQHLLGEHDFTSFRASACQAKTPVKTLHRIGITR 119

Query: 180 FG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            G              +FLH  +R+ +G L  VG G+  +  + + L A+ R    P   
Sbjct: 120 RGAGPHGYWRFEFEGNAFLHHMVRNIMGCLIAVGQGRKPADWMAEVLAARSRDAAAPTFA 179

Query: 236 PEGLYFDSVEYS 247
           P+GLYF    Y 
Sbjct: 180 PDGLYFLGPVYD 191


>gi|254756839|ref|ZP_05208867.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Australia
           94]
          Length = 185

 Score =  195 bits (496), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 58/182 (31%), Positives = 87/182 (47%), Gaps = 3/182 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+G  + G+Q Q    ++Q  IEKA+  +  GE+V V  +GRTDS VHA  
Sbjct: 6   MDRIKCTVAYDGMHFCGYQIQPQHRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKG 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD            ALN  L   D I I  +    ++FHAR+   R+ Y YR++  
Sbjct: 66  QVIHFDTPLSLEEWQWSNALNTML--PDDIVITQVEKKTEEFHARYGVERKEYRYRVLVS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +   +  P  L+  ++R A  + +G HDFT+F S        +RTI   ++  
Sbjct: 124 KTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIELIE 183

Query: 180 FG 181
             
Sbjct: 184 QD 185


>gi|52548278|gb|AAU82127.1| pseudouridylate synthase [uncultured archaeon GZfos10C7]
          Length = 284

 Score =  195 bits (496), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 107/255 (41%), Gaps = 29/255 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVH 56
           R  + I Y G+ Y G+Q Q      +I+G + KA+         +      AGRTD+GVH
Sbjct: 9   RIALKIGYIGTNYHGFQIQPRSALPTIEGELFKALKKQGIIEDRKTANYSAAGRTDTGVH 68

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV  F    +       + +N+ L    +I +  ++     F+AR  AI R Y Y +
Sbjct: 69  ALAQVVSFVTSNQNTT---PRMINSVL-PDGSIWVSAIAKPYSGFNARRDAISREYRYYL 124

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-----ASSPIRT 171
             +                 LD   MR A++  VG HDF+ F  +          S IR 
Sbjct: 125 FLQTELD-------------LDITRMREASELFVGTHDFSNFSLLQGNEYEVAGYSTIRD 171

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           I   +V +    + I + A  FL   +R  V +L++VG G      +E  L  +  KE  
Sbjct: 172 IKRIEVKTKKPFVIIDIEASGFLRKMVRKIVSALRMVGSGMKDKRWIEDLLDLRI-KEGI 230

Query: 232 PLAPPEGLYFDSVEY 246
             AP  GL   +V Y
Sbjct: 231 EPAPAFGLVLKNVSY 245


>gi|157164133|ref|YP_001466582.1| tRNA pseudouridine synthase A [Campylobacter concisus 13826]
 gi|112800733|gb|EAT98077.1| tRNA pseudouridine synthase A [Campylobacter concisus 13826]
          Length = 243

 Score =  195 bits (496), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 104/245 (42%), Gaps = 5/245 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G Q Q + + ++  +E+A+  V G    V  + RTD  VHA  Q 
Sbjct: 1   MKIQLIYSYDGSKFQGSQTQPHENGVEDELERALAHV-GIFERVVSSSRTDKSVHANNQS 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           +       +  +   + L  +     +I I  +++VD+ F ARF A+ RSY Y I   + 
Sbjct: 60  SSVICGDHFTNLERLRDLINHHAHP-SIHIKRINLVDESFQARFDAVARSYRYVIDHGKF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                      +PK  D E      ++ +G HDF+ +        SP+R I      ++ 
Sbjct: 119 -DVFSSNYKVFLPK-FDIEKANEILRNFIGEHDFSAYMKTGSDTKSPVREIYKAFCYTYK 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
               I   A  FL  Q+R  V +L      K     ++ +L           AP EGLY 
Sbjct: 177 EQTIIVFKANGFLRGQVRLMVANLLKALKQKDGGKLIKASLNGHP-ALTRIPAPAEGLYL 235

Query: 242 DSVEY 246
           + V Y
Sbjct: 236 NRVFY 240


>gi|224079884|ref|XP_002194368.1| PREDICTED: similar to MGC80334 protein [Taeniopygia guttata]
          Length = 427

 Score =  195 bits (496), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 125/248 (50%), Gaps = 28/248 (11%)

Query: 27  IQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVAHFDLVRE-----WVPVILCKALN 80
           +Q  +EKA   +     +  H + RTD+GVHAL   AH D+ R      +    L + LN
Sbjct: 153 VQNYLEKAAERLKPSAPIKFHISSRTDAGVHALANAAHLDIQRPPGKAPFSGQQLVQGLN 212

Query: 81  AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP----LALEKGRAWLIPK- 135
            +L+  + I IL+   V   FHARF A+ R+Y+YR++   A        E+   W     
Sbjct: 213 HHLR-PEPIRILSAQRVSSTFHARFCALSRTYIYRLLLGCAHHSQIPVFEQDLCWAPAGG 271

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTIDHFDVNSFG------------ 181
            LD   MR AAQ L+G HDF++FRS+H +A+  SP+RT+    +                
Sbjct: 272 PLDVAAMREAAQFLLGTHDFSSFRSLHAEAAAQSPVRTLQQLQLQPAPGFLQQHYLHSGL 331

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP--LAPPEGL 239
              E++V +RSFL+ Q+R  VG+L  VG G+     L + L+ +D     P  +AP  GL
Sbjct: 332 EFWEVKVKSRSFLYRQVRRMVGALVAVGQGRLAPVQLRELLELRDPHAFPPHAMAPAAGL 391

Query: 240 YFDSVEYS 247
           +   VEYS
Sbjct: 392 FLQRVEYS 399



 Score = 89.1 bits (220), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 41/139 (29%), Positives = 63/139 (45%), Gaps = 21/139 (15%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQV 61
           RY +  +Y G+ Y           I   + +A   +     +  H + RTD+GVHAL   
Sbjct: 7   RYLVFFQYLGTRYR----------IIAELTRAAERLKPSAPIKFHISSRTDAGVHALANA 56

Query: 62  AHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AH D+ R      +    L + LN +L+  + I IL+   V   FHARF A+ R+Y+YR+
Sbjct: 57  AHLDIQRPPGKAPFSSQQLVQGLNHHLR-PEPIRILSAQRVSSTFHARFCALSRTYIYRL 115

Query: 117 ITRQAP----LALEKGRAW 131
           +   A        E+   W
Sbjct: 116 LLGCAHHSQIPVFEQDLCW 134


>gi|305432148|ref|ZP_07401314.1| tRNA pseudouridine synthase A [Campylobacter coli JV20]
 gi|304444813|gb|EFM37460.1| tRNA pseudouridine synthase A [Campylobacter coli JV20]
          Length = 240

 Score =  194 bits (494), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 101/246 (41%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +  S+Q +++ A+  + G    V  A RTD GVHA   V
Sbjct: 1   MKLKIIFSYDGSKFLGSATQPHKKSVQDALQDALSHL-GIFSSVLMASRTDKGVHASYAV 59

Query: 62  AHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +          L K +N +      I + NL I+   F  R+    R Y Y      
Sbjct: 60  ACVECGEHFRDLNYLKKQINKF--SHPFIHVKNLKIMPSNFEVRYDVKSREYRYIFYHG- 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                        P  +D     +  Q+ VG  DF  F        + IR I      S+
Sbjct: 117 VYNPFLASYVHFYPF-IDVLKADLVLQNFVGIKDFKFFCKSGGDNKTTIREIFLAKAYSY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +    R  A  FL  QIR  V S+  V + K +  +L++ ++ + ++    LAPP GLY
Sbjct: 176 KDFTIFRFKANGFLRAQIRLMVASVLKVLENKMSIEELKEQIEVK-KQYNHFLAPPCGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRISY 240


>gi|325959678|ref|YP_004291144.1| tRNA pseudouridine synthase A [Methanobacterium sp. AL-21]
 gi|325331110|gb|ADZ10172.1| tRNA pseudouridine synthase A [Methanobacterium sp. AL-21]
          Length = 271

 Score =  194 bits (494), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 104/251 (41%), Gaps = 26/251 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVH 56
           M++    + Y G+ Y G+QRQ N  +I+G + +A        + E      AGRTD GV 
Sbjct: 1   MLKIAFKVAYIGTDYHGFQRQPNLPTIEGELLRAFKKSGISDSPEKSDYSIAGRTDRGVS 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL  V      +     +    +N YL     I I+  ++V   F  R+ A  R Y Y +
Sbjct: 61  ALGNVVCLKTDK----DVTINRINYYL--PSNIRIIGSTMVSNGFKPRY-AKLRHYRYIL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                          L P +L+ + M+ AA+ + G+H++  F     +A  P R +   D
Sbjct: 114 DKS------------LCPNTLNLKLMKQAAKQMEGKHNYINFSKRSERA--PERMVYSVD 159

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +    + I   VV  SFL   +R  V  L + G  + T  +LE            P+A  
Sbjct: 160 LVETPDNIVFDVVGESFLWNMVRKMVKVLVMFGREELTLENLETLFNPDVPAAIKPVA-S 218

Query: 237 EGLYFDSVEYS 247
           +GL    V Y 
Sbjct: 219 DGLILMDVVYD 229


>gi|313682232|ref|YP_004059970.1| tRNA pseudouridine synthase a [Sulfuricurvum kujiense DSM 16994]
 gi|313155092|gb|ADR33770.1| tRNA pseudouridine synthase A [Sulfuricurvum kujiense DSM 16994]
          Length = 242

 Score =  194 bits (494), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 107/248 (43%), Gaps = 8/248 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + + YNGS + G Q+Q N  +++ G +   +  +         +GRTD GVHA  
Sbjct: 1   MSRVKITLSYNGSAFMGSQQQPNTDNTVMGHLITVLHRLKITATP-KASGRTDRGVHATH 59

Query: 60  QVAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV H DL   W     L + LN  L    ++ I  +  V+  FHAR+SA RR Y Y I  
Sbjct: 60  QVIHVDLPDFWTDLHRLREMLNVQL--PPSMRIQRIEFVEDDFHARYSAKRRVYRYVIKE 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
             +    E      +P SL+ E +  A    VG HDF  F+          R I      
Sbjct: 118 GLS-NPFEDNFITFVP-SLNREAICDAIGCFVGTHDFEFFKKSGNDLEHHTRIIYRAYAY 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           S+     I      FL +QIR  VG L  +  GK T   L + +    R     +AP  G
Sbjct: 176 SYKGHFIIVFEGNGFLRSQIRLMVGFLLRISAGKATKEQLIEQINCVKRHTTD-IAPHNG 234

Query: 239 LYFDSVEY 246
           LY   ++Y
Sbjct: 235 LYLTHIKY 242


>gi|57237668|ref|YP_178916.1| tRNA pseudouridine synthase A [Campylobacter jejuni RM1221]
 gi|62901173|sp|Q5HUW9|TRUA_CAMJR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57166472|gb|AAW35251.1| tRNA pseudouridine synthase A [Campylobacter jejuni RM1221]
 gi|315058277|gb|ADT72606.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           S3]
          Length = 240

 Score =  193 bits (492), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 62/246 (25%), Positives = 100/246 (40%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+G+ + G   Q +   +Q ++  A+  + G    +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGTAFLGSATQPHKKGVQDALSGALSHL-GIFSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVECGDYFTNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHS 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D +         VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY
Sbjct: 176 KDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRICY 240


>gi|313674169|ref|YP_004052165.1| tRNA pseudouridine synthase a [Marivirga tractuosa DSM 4126]
 gi|312940867|gb|ADR20057.1| tRNA pseudouridine synthase A [Marivirga tractuosa DSM 4126]
          Length = 261

 Score =  193 bits (492), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 69/253 (27%), Positives = 102/253 (40%), Gaps = 12/253 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GWQ Q    ++QG +EK + FL  GE   + GAGRTD+ V A     
Sbjct: 9   YLVEIQYLGFRYHGWQFQHGLKTLQGMLEKTLNFLFQGEKFKILGAGRTDAMVSAESAYF 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                +        + LN  L     I++LN+ IVD +F+       ++Y Y   +    
Sbjct: 69  ELFTNQALDLESFARELNENL--PADINVLNVEIVDSKFNIIQDVRLKTYQYYFASVNKK 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-- 180
                     I  SLD   M+ AA+   G +DF  F     +  S +R I    +     
Sbjct: 127 YPFAAPLMNCIHHSLDISKMKEAARLFEGENDFRHFMVGDAENKSIVREIKESRIEENTA 186

Query: 181 -------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                         V  + F+  Q+R  +G+L  +G  + +  DLE ALQ          
Sbjct: 187 LRASFFPEKSYVFIVKGKGFMRYQVRMMMGALIRIGRNEISLQDLEHALQGNPPNFTKLN 246

Query: 234 APPEGLYFDSVEY 246
           A   GL    VE+
Sbjct: 247 AAASGLMVKEVEF 259


>gi|225011098|ref|ZP_03701561.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
 gi|225004732|gb|EEG42691.1| tRNA pseudouridine synthase A [Flavobacteria bacterium MS024-3C]
          Length = 268

 Score =  193 bits (492), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 58/256 (22%), Positives = 106/256 (41%), Gaps = 12/256 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVHALRQV 61
           Y + + Y G  Y GWQ+Q    +I+  + K I  V GE     + GAGRTD+ V ++   
Sbjct: 8   YLVRVSYLGFRYSGWQKQPGVKTIESMLTKTISFVLGETRSFKILGAGRTDAKVSSIHGA 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               +  E +  +        L +   I + +++ V+++F+   SA  ++Y Y       
Sbjct: 68  FELFIEHEPLKNLDALMDLFNLNLPADIRVESITAVEEKFNIIHSAKEKTYCYLFSFGSK 127

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS-PIRTIDHFDVNSF 180
                       P+ L+   M+ AA+   G HDF  F +   + +S  IRTI   ++   
Sbjct: 128 AHPFCAPIMANYPEDLNITLMQEAAKLFEGTHDFKNFTARKDKKNSQTIRTIASCELKKN 187

Query: 181 ---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                     +   + V  + FL  QIR  +G+L  +G  +     +++ L +       
Sbjct: 188 KAISASFFPEDSYVLEVRGKGFLRYQIRLMMGALICLGRNEIDLEGIKRLLNSDLDDFIP 247

Query: 232 PLAPPEGLYFDSVEYS 247
            +A   GL+   + + 
Sbjct: 248 YVAAGSGLHLKELLFD 263


>gi|224010986|ref|XP_002294450.1| hypothetical protein THAPSDRAFT_264420 [Thalassiosira pseudonana
           CCMP1335]
 gi|220969945|gb|EED88284.1| hypothetical protein THAPSDRAFT_264420 [Thalassiosira pseudonana
           CCMP1335]
          Length = 264

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 73/266 (27%), Positives = 113/266 (42%), Gaps = 30/266 (11%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+G+ + GWQ Q   S++QG IE+ +       + V GAGRTD+GVHA  Q  HFDL 
Sbjct: 2   VAYHGTPFNGWQLQPGRSTVQGEIEEVLTRRFHRRIPVVGAGRTDAGVHARGQAIHFDLF 61

Query: 68  R-------EWVPVILCKALNAYLKISDTISILNLSIVDKQ-FHARFSAIRRSYLYRIITR 119
                      P IL  ++N  +     I + +L +     +HA   A  + Y YR+   
Sbjct: 62  HDEIPFKPPTPPEILQHSMNRMM--PLDIRMFHLQLAPYTPWHAIQRAQSKWYSYRLTLG 119

Query: 120 QA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF---------RSIHCQASSPI 169
                 +E+         LD E +    Q  VG HDF  F         +    +  + +
Sbjct: 120 PTLWNPMERFTRTHFVH-LDMERLESILQLYVGTHDFGAFGGQLEQNAKKRNDGKRINTV 178

Query: 170 RTIDHFDVNSFGNL--------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           RT+   ++     L          I  + +  L+  +R+ VG+   V  G+     L + 
Sbjct: 179 RTVFRVELIQQEQLGFIGEEGNYRIDFLLKGALYKMVRNMVGTAMEVWLGRMKEEQLAEL 238

Query: 222 LQAQDRKECG-PLAPPEGLYFDSVEY 246
           L+  DRK+     APPEGL  + V Y
Sbjct: 239 LKIPDRKDNPSKPAPPEGLTLECVYY 264


>gi|307352726|ref|YP_003893777.1| tRNA pseudouridine synthase A [Methanoplanus petrolearius DSM
           11571]
 gi|307155959|gb|ADN35339.1| tRNA pseudouridine synthase A [Methanoplanus petrolearius DSM
           11571]
          Length = 261

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 100/246 (40%), Gaps = 28/246 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA---IFLVTG-EIVVVHGAGRTDSGVHA 57
           +R   ++ Y G+ ++G Q+Q    +++G    A   + L +         +GRTD+GVHA
Sbjct: 1   MRIAFLVSYIGTDFYGSQQQPGIRTVEGEFIGACIDLGLFSDWRDARFQFSGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             Q+  FD      P     A+N  L     I     + V + F+ RF    R Y Y   
Sbjct: 61  RSQICAFDTDY---PERAVSAINRKL--PGDIRCRGWAGVPEGFNPRFEVSERIYRYFFP 115

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                             +LD   M +AA++L G HDF+ F  +  +  +P R I   ++
Sbjct: 116 DG----------------NLDWGKMSLAAEYLPGVHDFSRFARV--EGKNPERKIFLAEI 157

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I   +   SFL   +R    +L LVG G  +   +  AL   D     P APPE
Sbjct: 158 IPDKEGIIFEIRGESFLWNMVRCISHALWLVGSGSESPEVISAALSNTD-GPRFPAAPPE 216

Query: 238 GLYFDS 243
           GL    
Sbjct: 217 GLVLWD 222


>gi|86152100|ref|ZP_01070312.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           260.94]
 gi|85840885|gb|EAQ58135.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           260.94]
          Length = 240

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 101/246 (41%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHS 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D +         VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY
Sbjct: 176 KDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRICY 240


>gi|167005448|ref|ZP_02271206.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81-176]
          Length = 240

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 100/246 (40%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A       +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVGCGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHS 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D +         VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY
Sbjct: 176 KDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRICY 240


>gi|15678860|ref|NP_275977.1| tRNA pseudouridine synthase A [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|3915162|sp|O26928|TRUA_METTH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2621931|gb|AAB85338.1| pseudouridylate synthase I [Methanothermobacter thermautotrophicus
           str. Delta H]
          Length = 275

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 105/250 (42%), Gaps = 29/250 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF----LVTGEIVVVHGAGRTDSGVH 56
           M +  + + Y G+ Y G+QRQ +  +++G + +A+     +   +      AGRTD GVH
Sbjct: 1   MRKIALKVAYIGTNYHGFQRQPDVPTVEGKLLEALEGAGIIEDPKRARFQIAGRTDRGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL     F    +     +   L         I +L  + V   F  R+  + R Y Y +
Sbjct: 61  ALGNFVSFFTEEDIHVNQINDLL------PRDIRVLAWASVMYPFKVRY-PLERHYRYIL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                             +S+D  +M  AA H  G HDF+ F     +   P+R I+   
Sbjct: 114 ---------------HREESMDTYSMAEAAAHFRGTHDFSNFSRRSDR--DPVRRINDVR 156

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++  G+ I I V   SFL   +R  V +L +V +G+    D+   L   DR+      PP
Sbjct: 157 ISEVGDSIIIDVYGESFLWQMVRKMVRALLMVSEGELAPDDMAGLLDT-DRRVFLEPMPP 215

Query: 237 EGLYFDSVEY 246
           E L    ++Y
Sbjct: 216 ENLILMDLKY 225


>gi|149193965|ref|ZP_01871063.1| Pseudouridylate synthase [Caminibacter mediatlanticus TB-2]
 gi|149135918|gb|EDM24396.1| Pseudouridylate synthase [Caminibacter mediatlanticus TB-2]
          Length = 223

 Score =  193 bits (490), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 109/229 (47%), Gaps = 6/229 (2%)

Query: 18  WQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCK 77
            Q+Q N  +IQG IE A+  +    + V  AGRTD GVHAL QV  F +   W    L  
Sbjct: 1   MQKQPNKKTIQGEIELALNKLNINSI-VQHAGRTDKGVHALNQVISFTIPNFWDLNKLQT 59

Query: 78  ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSL 137
           +LN  +       I  +  +   F+ RF+A +RSY Y I         +        K +
Sbjct: 60  SLNKIIHPYIH--IKKIKFIKNDFNPRFNAKKRSYRYIIS--PIFSPHKADYETYYDKKI 115

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           + E ++ A +   G +DF  F     + ++ IRTI   D+  + N + ++++   FL  Q
Sbjct: 116 NIELLKKAIKKFEGTYDFEYFAKTGSEVNNYIRTIYKTDIIEYKNKVILKIIGNGFLRGQ 175

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           IR     L ++ + K T  DL+K L  +D+     LAPP GLY + + Y
Sbjct: 176 IRIITNFLLMINENKLTIDDLQKQLN-KDQLFTKHLAPPNGLYLERIWY 223


>gi|222823975|ref|YP_002575549.1| tRNA pseudouridine synthase A [Campylobacter lari RM2100]
 gi|222539197|gb|ACM64298.1| tRNA pseudouridine synthase A [Campylobacter lari RM2100]
          Length = 244

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 103/244 (42%), Gaps = 7/244 (2%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             +   Y+GS + G   Q +  S+Q ++E+A+  +      +  A RTD GVHA   VA 
Sbjct: 3   LKLTFSYDGSKFQGSATQPHKLSVQDALEQALSHLGIYNKTLF-ASRTDKGVHANNGVAC 61

Query: 64  FDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
             +   +   + L   +N +      I I ++  V + F  RF   +R+Y Y I   +  
Sbjct: 62  VKVGEHFKDLLYLKNKINHF--AHPFIHIKHIQKVHENFQVRFDVKKRAYRYIISHERY- 118

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                      PK ++ +  +  A    G HDF  F+       +  R I    V ++ N
Sbjct: 119 NPFLASYVHFYPK-INIQLAKKIASLFEGEHDFKLFQKEGSDNKTTTRIIYKSKVYTYKN 177

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
                  A  FL +QIR  + S+  V + K +  +L++ + A+ +     LAP  GLY  
Sbjct: 178 CTIFYFEANGFLRSQIRMMIASILKVLEKKISQENLKEQIDAK-KAHIRLLAPASGLYLS 236

Query: 243 SVEY 246
            + Y
Sbjct: 237 KISY 240


>gi|226325156|ref|ZP_03800674.1| hypothetical protein COPCOM_02948 [Coprococcus comes ATCC 27758]
 gi|225206504|gb|EEG88858.1| hypothetical protein COPCOM_02948 [Coprococcus comes ATCC 27758]
          Length = 255

 Score =  192 bits (489), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 114/247 (46%), Gaps = 9/247 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    + IEY+GS Y G+  +K  +SI+  +  AI  VTG+   +  A +T+ GVHA  Q
Sbjct: 12  MTTIKLTIEYDGSRYPGFSTKKKSTSIESKLTLAIRDVTGQSTQLFAAVKTEPGVHAAHQ 71

Query: 61  VAHFDLVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           +  F L +E       +L   LNA L     I++ +L I D++F A  +    +Y  RI 
Sbjct: 72  IVSFQLEKESFSDNTELLKMKLNAAL--PADIAVTSLEIADERFVASLAVKSCTYTCRIA 129

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           T  A     +    ++ +SLD E+M+ AAQ L G HDF  F +      S +RT++   +
Sbjct: 130 TDPAAALFSRPYTCVVTESLDLESMQQAAQLLTGTHDFAAFSN-GRTRKSTVRTVETIKI 188

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N    LI+I++ A SFL    +   G++   G  K T       L     +   P  P  
Sbjct: 189 NREDQLIQIQLTANSFLRHMPQLLAGTILTAGKEKKTDG---TTLTLAGVESVAPACPSH 245

Query: 238 GLYFDSV 244
                 V
Sbjct: 246 AFTLTDV 252


>gi|268324810|emb|CBH38398.1| tRNA pseudouridine synthase A [uncultured archaeon]
          Length = 275

 Score =  192 bits (489), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 72/251 (28%), Positives = 112/251 (44%), Gaps = 28/251 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           R  + I Y G+ Y G+Q Q      +++G + KA+  +      +      AGRTD GVH
Sbjct: 7   RVALKIGYLGTNYHGFQIQPQAELQTVEGELFKALKRLGILEDRKTANYSYAGRTDKGVH 66

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV  FD + + +     + +N  L   + I  L ++     F+AR  AIRR Y Y +
Sbjct: 67  ALAQVVSFDTLNQNMT---PRMINTML--PNDIWALAIAKPHAGFNARKEAIRREYRYFL 121

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHF 175
                           +   LD   MR A++ L+G HDF+ F      +  S I+ I   
Sbjct: 122 ---------------FLQTELDISRMRDASELLIGAHDFSNFSQRDGLEGKSLIKEIKQV 166

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           ++      I I + A  FL   +R  V +L +VG GK   + ++  L  + +++  P AP
Sbjct: 167 NIVKSDLFIIIDIAASGFLRKMVREIVSALSMVGSGKRAKSWIQDLLDLKIKEQIEP-AP 225

Query: 236 PEGLYFDSVEY 246
             GL    V Y
Sbjct: 226 AFGLVLKDVSY 236


>gi|260062928|ref|YP_003196008.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
 gi|88784496|gb|EAR15666.1| tRNA pseudouridine synthase A [Robiginitalea biformata HTCC2501]
          Length = 274

 Score =  192 bits (489), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 62/263 (23%), Positives = 97/263 (36%), Gaps = 22/263 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + + I + G  + GWQ Q    ++ G I K   F++    V + GAGRTD+ V A     
Sbjct: 9   FLIRIAFLGFRFHGWQEQPGQRTVAGMIRKTFRFVLPDTPVKILGAGRTDARVSARDFAV 68

Query: 63  HFDLVREWVPV--ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                   +P   +L  ALN  L     I + ++  V   F+       ++Y Y   T  
Sbjct: 69  QVIARAPELPPFGVLADALNENL--PPDIRVNSIRPVPPGFNPIRDCASKTYRYYFQTGN 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--- 177
            P A        +P S D   MR AA    G H+F  F +   +    +R +    +   
Sbjct: 127 HPDAYWTPFVGFLPGSPDITRMREAAPLFEGMHNFRCFTASPSEDKKYVRRVTRCRLGVG 186

Query: 178 ----------NSFGNL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                     +  G+       + V A  F   Q+R  + +L  VG  +     L K L 
Sbjct: 187 SPMDGVVAGKDPEGDTGFTAHMLEVRAPGFGRNQVRLMMAALAAVGRQELQPETLVKVLD 246

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
                    + P  GL+   VE+
Sbjct: 247 EGQGWMSDSIVPASGLHLMHVEF 269


>gi|34557089|ref|NP_906904.1| tRNA pseudouridine synthase A [Wolinella succinogenes DSM 1740]
 gi|34482804|emb|CAE09804.1| TRNA PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 267

 Score =  192 bits (488), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 109/248 (43%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      +EY+GS +FG Q QK   S+  ++++ +  + G    V  +GRTD GVHA RQ
Sbjct: 15  MPTLLAFLEYDGSAFFGSQIQKEEPSVALALQRGLKSM-GIASKVRFSGRTDRGVHATRQ 73

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              F++  +        + LN  L     + +  L  + +    RF A  R+Y Y +   
Sbjct: 74  AVSFEVPYKKSDWGYFKEELNKKLF--PYLRVRRLYPIREGLDPRFEAKSRAYRYLLSEE 131

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               A             D   ++ A + LVG HDF  F+    Q  S +R +    +  
Sbjct: 132 PL-SAFASRYVTHAHLG-DERKIQEAMKLLVGWHDFALFKKSGSQEKSTLREMRRCWLYR 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  VG+L  VG G+ +  + ++ L+A+ R  C   APP GL
Sbjct: 190 YRSYWVFYFEANGFLRLQIRLLVGALLKVGRGEMSLEEFKEQLEAKRRFFC-EGAPPYGL 248

Query: 240 YFDSVEYS 247
           Y   V + 
Sbjct: 249 YLCKVSFE 256


>gi|291550669|emb|CBL26931.1| Pseudouridylate synthase [Ruminococcus torques L2-14]
          Length = 260

 Score =  192 bits (488), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 61/265 (23%), Positives = 103/265 (38%), Gaps = 24/265 (9%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + ++Y+G+ Y GW+R +   N  ++   IE  +  VTG  V +    RT+ GVHA
Sbjct: 1   MQNIKLTLQYDGTRYLGWKRPEKDHNDRTVSYKIENVLEKVTGTPVTLFSGVRTEPGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
                +F    +  P      LN YL     I++L+     ++F A  +A   +Y Y + 
Sbjct: 61  RNLTVNFLTESQLTPAEFKTVLNQYL--PQDIAVLDAVSTPERFRADLNAREITYEYAMD 118

Query: 118 TRQAPLALEKGRAWLIPKSL----------------DCENMRIAAQHLVGRHDFTTFRSI 161
                    K     +   L                +   M  AA  L+G HDF  F SI
Sbjct: 119 LSPIYDLFHKNYRGRLTDLLSDSLFDLPPEQTAELPNILLMETAAHSLLGTHDFKHFSSI 178

Query: 162 HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
             +     + I      +  + + IR+ A  FL+      +G+L  +G GK     +   
Sbjct: 179 R-KKKGTEKEIKTITFVTEESTLYIRMTANDFLYQMAPFILGTLLDIGIGKRPVECINAI 237

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEY 246
           L+ +++         +GL    + Y
Sbjct: 238 LEGKEKPSA--SCDTKGLILYDIVY 260


>gi|153005130|ref|YP_001379455.1| tRNA-pseudouridine synthase I [Anaeromyxobacter sp. Fw109-5]
 gi|152028703|gb|ABS26471.1| tRNA-pseudouridine synthase I [Anaeromyxobacter sp. Fw109-5]
          Length = 265

 Score =  191 bits (487), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 84/260 (32%), Positives = 115/260 (44%), Gaps = 20/260 (7%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M R  Y + + Y G  + G+QRQ    ++Q ++E A+ L  G    +  A RTD+GVHAL
Sbjct: 1   MERRFYALRVAYEGGRFRGFQRQPGLPTVQDALEGAL-LAAGVRATLAVAARTDAGVHAL 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F       P  L  ALNA L   + +++L +  V   FHAR +A  R Y+Y +  
Sbjct: 60  DQVVSFSARAALDPAALRGALNAAL--PEGVAVLEVLRVAPSFHARNTARARRYVYLV-- 115

Query: 119 RQAPLALEKGRAWLIPKS---------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
              P       AW +P           LD   M  A  H VG HDFT F     Q    +
Sbjct: 116 GAPPPESLAAYAWTLPDPRAFPDGEARLDVAAMSAALAHAVGTHDFTAFARPGEQRG-TV 174

Query: 170 RTIDHFDVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           RT+   +V S  +  L  +      FL   IR+  G+   VG G+     + + L A+ R
Sbjct: 175 RTVTRAEVVSATWAPLHALVFEGHGFLRAMIRNLAGTAVTVGVGRAAPEIVRELLLARGR 234

Query: 228 KECGPLAPPEGLYFDSVEYS 247
              G  AP  GL   SV Y 
Sbjct: 235 YR-GVRAPGWGLTLASVVYP 253


>gi|119477629|ref|ZP_01617779.1| hypothetical protein GP2143_09210 [marine gamma proteobacterium
           HTCC2143]
 gi|119449132|gb|EAW30372.1| hypothetical protein GP2143_09210 [marine gamma proteobacterium
           HTCC2143]
          Length = 261

 Score =  191 bits (487), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 69/261 (26%), Positives = 111/261 (42%), Gaps = 19/261 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDS 53
           M  + + I Y G+ YFGWQ Q      +   +I+G+I KA+  ++  +   +  A RTD 
Sbjct: 1   MHYFRVTIAYKGTHYFGWQAQSKDTLKEEYPTIEGTILKALKKMSNYQHCTISAASRTDG 60

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA  Q+A   L  +     L   LN+ L     I IL  +   K F    S++ + Y 
Sbjct: 61  GVHAQGQLAKISLSIDISADHLLLGLNSAL--PLDIRILECASSTKNFQPNVSSVSKEYH 118

Query: 114 YRIITRQAPLA----LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           Y     +        +    +      +D   +R A Q  VGRHDF  F       +S +
Sbjct: 119 YYFTASKTDNVAISEISLRLSTHDDGPIDMALLRTACQLFVGRHDFYNFSVRDLNNASSV 178

Query: 170 RTIDHFDVNS------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           R I + D+           +  ++++   FL   IR  +G+L  +G G+ T  D+   LQ
Sbjct: 179 RQISYCDILQANFSPLVDEVYYLKIIGDGFLKYMIRYVMGALIELGKGRITLEDIAFYLQ 238

Query: 224 AQDRKECGPLAPPEGLYFDSV 244
            Q   +    A  +GL+   +
Sbjct: 239 HQQDDKLSAKAKAKGLHLIKI 259


>gi|195490008|ref|XP_002092963.1| GE26463, isoform B [Drosophila yakuba]
 gi|194179064|gb|EDW92675.1| GE26463, isoform B [Drosophila yakuba]
          Length = 306

 Score =  191 bits (487), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 85/301 (28%), Positives = 125/301 (41%), Gaps = 55/301 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTG-EIVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MNRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALRVFHPINEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL      DL R     +    L   LN  L      I +L+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQGLPIRVLSSKLVSNSFHCRYH 120

Query: 107 AIRRSYLYRIITRQAP----------------LALEKGRAWLIPKS-LDCENMRIAAQHL 149
           AI R+YLYR    + P                   E  R + +  S  D   ++ AA+  
Sbjct: 121 AIGRTYLYRFAVAKDPSLEDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVQAAARMF 180

Query: 150 VGRHDFTTFRSIHCQASS------PIRTIDHFDVNSFG---------------NLIEIRV 188
           +G HDF TF S+  Q  S       +R ID  ++                   N  +I +
Sbjct: 181 IGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDIEI 240

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVE 245
            A+SFL+ Q+R  VG+L  +G+G+     L + L    +    P   LAP  GLY   V 
Sbjct: 241 KAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNSWDPRILLAPACGLYLCKVH 300

Query: 246 Y 246
           Y
Sbjct: 301 Y 301


>gi|295133853|ref|YP_003584529.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
 gi|294981868|gb|ADF52333.1| tRNA pseudouridine synthase A [Zunongwangia profunda SM-A87]
          Length = 262

 Score =  191 bits (486), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 100/262 (38%), Gaps = 15/262 (5%)

Query: 1   MIR----YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGV 55
           M R    Y + ++Y G    GWQ+Q N  +++G I K +  V  E    V G  RTD+ V
Sbjct: 1   MQRVRYYYLIKVQYLGYRLHGWQKQPNFKTVEGLITKTLRYVMPETRYKVLGCSRTDAMV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            +        +  + +  +        L +   I + ++  V   F+    +  + Y Y 
Sbjct: 61  SSNGSAFELFVDEQPLENLEDFLALFNLNLPQDIRVTDIEEVGANFNIIQHSKIKEYAYL 120

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                                LD + M+  AQ   G H+F  +     + S+  R I   
Sbjct: 121 FSFGSKNHPFCAPFMANFQFDLDIDKMKKGAQLFNGTHNFRNYCVRVSEKSTFEREILKA 180

Query: 176 DVNSF---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           ++                   V  + FL  Q+R  +G++  +G G+++  D+E++L+  +
Sbjct: 181 EIVENKLYTANFFPKKSYIFHVHGKGFLRHQVRLMMGAMIQLGRGEFSLGDIEQSLKEGN 240

Query: 227 RK-ECGPLAPPEGLYFDSVEYS 247
              +    AP  GL  + + + 
Sbjct: 241 EHLQMDYSAPASGLILNDIHFD 262


>gi|283957185|ref|ZP_06374649.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni 1336]
 gi|283791361|gb|EFC30166.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni 1336]
          Length = 240

 Score =  191 bits (486), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 100/246 (40%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGSAFLGSATQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHS 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D           VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY
Sbjct: 176 KDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRICY 240


>gi|157415094|ref|YP_001482350.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           81116]
 gi|172047118|sp|A8FLN6|TRUA_CAMJ8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157386058|gb|ABV52373.1| putative tRNA pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|284926072|gb|ADC28424.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           IA3902]
 gi|307747736|gb|ADN91006.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           M1]
 gi|315927713|gb|EFV07042.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           DFVF1099]
 gi|315931164|gb|EFV10137.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           327]
          Length = 240

 Score =  191 bits (486), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 99/246 (40%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +   +Q ++  A+  + G    +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGSAFLGSATQPHKKGVQDALSGALSHL-GIFSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVECGDYFTNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHA 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D           VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLGKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +       A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY
Sbjct: 176 KDFSIFHFKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRICY 240


>gi|312136442|ref|YP_004003779.1| tRNA pseudouridine synthase a [Methanothermus fervidus DSM 2088]
 gi|311224161|gb|ADP77017.1| tRNA pseudouridine synthase A [Methanothermus fervidus DSM 2088]
          Length = 277

 Score =  191 bits (486), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 112/250 (44%), Gaps = 29/250 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGE--IVVVHGAGRTDSGVH 56
           M +  + + Y G+ +FG+QRQ +  +++G + KA+    +  E  +     AGRTD GVH
Sbjct: 1   MKKIALKVAYIGTHFFGFQRQPDLRTVEGELIKALVETGILDESGVARFRSAGRTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL  V  F         ++   +N+ L   D + IL  + V   F  R++  R      +
Sbjct: 61  ALGNVVTFFTDE----DVIINQINSCL--PDDVYILGKASVPYGFKTRYAYRRHYRY-VL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                               L+ E M+ A++   GRHDFT F S   +  +PIR I+  D
Sbjct: 114 PND----------------GLNIELMKEASKKFEGRHDFTNF-SRRVEERNPIRYIEKVD 156

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  I + V+  SFL   +R  V  L  +G  ++    +++ L  +++    P+ PP
Sbjct: 157 VVDKGEYIWVDVIGESFLWQMVRKMVKVLFDIGKEEYEPEKIDEFLDTEEKVYIEPM-PP 215

Query: 237 EGLYFDSVEY 246
           E L    V Y
Sbjct: 216 ENLILMKVMY 225


>gi|65317910|ref|ZP_00390869.1| COG0101: Pseudouridylate synthase [Bacillus anthracis str. A2012]
          Length = 175

 Score =  191 bits (486), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 63/160 (39%), Positives = 95/160 (59%), Gaps = 3/160 (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 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F 
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFS 158


>gi|42559739|sp|Q7M9U3|TRUA_WOLSU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 253

 Score =  191 bits (486), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 109/248 (43%), Gaps = 7/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      +EY+GS +FG Q QK   S+  ++++ +  + G    V  +GRTD GVHA RQ
Sbjct: 1   MPTLLAFLEYDGSAFFGSQIQKEEPSVALALQRGLKSM-GIASKVRFSGRTDRGVHATRQ 59

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              F++  +        + LN  L     + +  L  + +    RF A  R+Y Y +   
Sbjct: 60  AVSFEVPYKKSDWGYFKEELNKKLF--PYLRVRRLYPIREGLDPRFEAKSRAYRYLLSEE 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               A             D   ++ A + LVG HDF  F+    Q  S +R +    +  
Sbjct: 118 PL-SAFASRYVTHAHLG-DERKIQEAMKLLVGWHDFALFKKSGSQEKSTLREMRRCWLYR 175

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           + +       A  FL  QIR  VG+L  VG G+ +  + ++ L+A+ R  C   APP GL
Sbjct: 176 YRSYWVFYFEANGFLRLQIRLLVGALLKVGRGEMSLEEFKEQLEAKRRFFC-EGAPPYGL 234

Query: 240 YFDSVEYS 247
           Y   V + 
Sbjct: 235 YLCKVSFE 242


>gi|194208171|ref|XP_001496445.2| PREDICTED: similar to LOC617640 protein [Equus caballus]
          Length = 389

 Score =  191 bits (486), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 80/240 (33%), Positives = 115/240 (47%), Gaps = 26/240 (10%)

Query: 32  EKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKIS 86
           E A  L +   V +  + RTD+GVHAL   AH D+ R      + P +L KALN +L+  
Sbjct: 131 EAAERLNSVVPVKLTISSRTDAGVHALSNAAHLDVQRRSGQPPFSPEVLAKALNTHLRHP 190

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITR-QAPL---ALEKGRAWLIP-KSLDCEN 141
             I +L    V   FHAR+SA  R+YLYR+ T    P      E+ R W +   SLD   
Sbjct: 191 -AIRVLQAFRVPSDFHARYSATSRTYLYRLATGCPQPDQLSVFEQNRCWALRADSLDVAA 249

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-------------NSFGNLIEIRV 188
           M  AAQHL+G HDF+ F+S     +S +RT+    V             +       +  
Sbjct: 250 MEEAAQHLLGTHDFSAFQSAGSPTTSSVRTLRRASVSPDLPSPFVLPQESRRLRFWSLEF 309

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            ++SFL+ Q+R     L  VG G  T   ++  L+++D   +    +AP  GL+  SV Y
Sbjct: 310 ESQSFLYRQVRRMTAVLVAVGLGALTPAQVKMILESRDPLGRHQTRVAPAHGLFLKSVLY 369


>gi|126640496|ref|YP_001083480.1| tRNA pseudouridine synthase A [Acinetobacter baumannii ATCC 17978]
          Length = 205

 Score =  191 bits (485), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 62/188 (32%), Positives = 90/188 (47%), Gaps = 2/188 (1%)

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD              N+ L     ISI  +  +D++FHARF A  R Y Y +   
Sbjct: 1   MVAHFDTNAIRPERGWIMGANSQL--PKDISIQWIKQMDEEFHARFKATARRYRYVVYNA 58

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H  +  
Sbjct: 59  PHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKHCRLFE 118

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  APP+GL
Sbjct: 119 HGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDAMFAAEDRKAAGITAPPDGL 178

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 179 YFIQCYYP 186


>gi|307110841|gb|EFN59076.1| hypothetical protein CHLNCDRAFT_19189 [Chlorella variabilis]
          Length = 300

 Score =  191 bits (485), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 71/265 (26%), Positives = 114/265 (43%), Gaps = 25/265 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKN------GSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSG 54
           Y  +++Y+G+ Y+G+Q Q          ++Q  +E+A+   TG+    + V  AGRTD+G
Sbjct: 4   YAAVLQYDGTAYWGFQLQPAPQGRRAKPTVQLRVEQALCRATGQGRQALRVQAAGRTDAG 63

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA  QV  F   R      L +ALNA +     I  + +  V   ++ R+ A R++Y Y
Sbjct: 64  VHARGQVVQFCCARRQGAAPLLRALNALM--PPDIRAVAVQEVPLDWNVRY-ASRKTYAY 120

Query: 115 RIITRQAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSPIR 170
            +                  +   L  + M  AA   VG HDF+ F ++   A   SP++
Sbjct: 121 DLHLDPVADPFLHRWRCHPRRPERLRLDAMADAAALFVGTHDFSRFANLGPDATRKSPVK 180

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
           T+  + +        + V    FL+ Q+R   G+L  VG G   + D+  AL   +R   
Sbjct: 181 TVLSYRLLPLEGGARLEVTGTGFLYKQVRHMTGALLAVGGGSLGADDIAAALAGGERARS 240

Query: 231 GP---------LAPPEGLYFDSVEY 246
                      +A   GL    V Y
Sbjct: 241 AAQRNAFRGWQVAEARGLCLQQVVY 265


>gi|88807910|ref|ZP_01123421.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7805]
 gi|88787949|gb|EAR19105.1| tRNA pseudouridine synthase A [Synechococcus sp. WH 7805]
          Length = 251

 Score =  191 bits (485), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 67/222 (30%), Positives = 98/222 (44%), Gaps = 4/222 (1%)

Query: 28  QGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS 86
           QG +E+AI  +     V    AGRTD+GVHA  QV HFD            ALN  L   
Sbjct: 2   QGVLEQAIADLDPHRPVHAVAAGRTDAGVHAAGQVVHFDSSGPIPANRWAPALNGRL--P 59

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIA 145
            +I +         +HA +SA  R Y Y +   + P       +W   +  LD   M  A
Sbjct: 60  ASIRVREAVERPLSWHACYSATYRRYRYTLYNGRRPNLFLAPWSWHRYQARLDEHAMADA 119

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
              ++G HDF  F+    + +    TI    V   G+LI++ + A  FL+  +R  +G L
Sbjct: 120 LGGMLGSHDFAAFQRAGSRRAHSRTTIQDVSVQRRGDLIDLEIQATGFLYGMVRLLMGQL 179

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             VG+ + T    E+  + + R+E    APP+GL      Y 
Sbjct: 180 VAVGEHRLTPEQFERRWRERRREEVKDGAPPQGLCLLRAGYE 221


>gi|332293112|ref|YP_004431721.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171198|gb|AEE20453.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Krokinobacter diaphorus 4H-3-7-5]
          Length = 259

 Score =  190 bits (484), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 98/252 (38%), Gaps = 13/252 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GWQ+Q +  +++  +E+    V       +  +GRTD+ V A     
Sbjct: 8   YLLKIQYLGFRYHGWQKQPDVLTVERMMERTFSYVLDRKNFKLLASGRTDAKVSANVAYV 67

Query: 63  HFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              L           K LN  L     I  L ++ VDK+F+   + I + Y+Y     + 
Sbjct: 68  ELFLNDSPLPEEGFLKLLNNNL--PQDIRCLEITQVDKKFNVMDAPIAKEYVYLFSYGEK 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                      I  SLD E M+ AA+   G HDF ++       +  I  I    +    
Sbjct: 126 NHPFAAPYMINIAGSLDIELMKEAARLFEGEHDFRSYAYKPNPETKTIGNISSSLIEPNE 185

Query: 182 ---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                         RV  + F   QIR  +G L  +G+GK      +K L A +  +   
Sbjct: 186 LYTANFFPKESFAFRVSGKGFKRHQIRLMMGMLFDIGEGKVDLDFFKKTLDASNDIKLSR 245

Query: 233 LAPPEGLYFDSV 244
           +A   GL   +V
Sbjct: 246 IAQASGLLLQNV 257


>gi|195436014|ref|XP_002065973.1| GK25867, isoform B [Drosophila willistoni]
 gi|194162058|gb|EDW76959.1| GK25867, isoform B [Drosophila willistoni]
          Length = 313

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 93/303 (30%), Positives = 130/303 (42%), Gaps = 58/303 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQR------QK--NGSSIQGSIEKAI--FLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+      Q   + +S+QG +E A+  F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLDQPRLDTNSVQGCLELALRVFRPTNEIQTVL-SSR 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L      I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTIHVDLERYDGQPYALTTLTGVLNRTLGKQRLPIRVLSTELVPDTFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALE-----KGRAWLIP------------KSLDCENMRIAAQH 148
            AI R+YLYR    +     +     +G    IP             S D E +R AA+ 
Sbjct: 120 HAIGRTYLYRFAVARNSPVDDGKLKNRGYEAFIPVEELDRCYFLQAASFDIERVRSAARL 179

Query: 149 LVGRHDFTTFRSIHCQASS-------PIRTIDHFDV---------------NSFGNLIEI 186
            +G HDF TF S+  Q           +R ID  ++               N   +  EI
Sbjct: 180 FLGIHDFRTFMSVSRQKGPSRDHPMFTVRKIDEINIRPGHSLALNAHAKLANETYDHWEI 239

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDS 243
            + A+SFL+ Q+R  VG+L  +G GK     + + L    +    P   LAP  GLY   
Sbjct: 240 EIKAKSFLYKQVRRIVGTLLALGTGKIDEKCIYQMLTIPSKNSWEPRILLAPACGLYLCQ 299

Query: 244 VEY 246
           V Y
Sbjct: 300 VHY 302


>gi|58699741|ref|ZP_00374392.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533741|gb|EAL58089.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 156

 Score =  190 bits (482), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 71/155 (45%), Positives = 92/155 (59%)

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
           LN  +VD  FHARFSA +R Y YRI+ R AP ALE G  W +   LD   MR AA+HL+G
Sbjct: 2   LNAEVVDDAFHARFSAKKRYYEYRIVNRYAPAALETGYVWQVFSPLDVNIMREAAKHLLG 61

Query: 152 RHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           +HD ++FRS  C A++PIRTID  D+   GN I I++ A SFLH Q+R   G+L   G  
Sbjct: 62  KHDLSSFRSKDCHAANPIRTIDDIDIVQNGNHIHIKISAISFLHNQVRIIAGTLVEFGKN 121

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +    ++   L    R   G  APP GLY   ++Y
Sbjct: 122 RTNPQEMLHILSQCKRSAAGVTAPPFGLYLVKIDY 156


>gi|156538761|ref|XP_001607889.1| PREDICTED: similar to CG34140-PA [Nasonia vitripennis]
          Length = 298

 Score =  189 bits (481), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 86/285 (30%), Positives = 125/285 (43%), Gaps = 40/285 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLVTGEIVVVHG-AGRTDSGV 55
            RY + + Y G+ Y G Q+  N       +IQG+IE ++       +     AGRTD+GV
Sbjct: 6   RRYLLKLSYIGTSYRGSQKHVNNAVVDIDTIQGAIEYSMRRFNFSNIPTISLAGRTDAGV 65

Query: 56  HALRQVAHFDLVR--EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSY 112
           HAL   AH DL          L + +N  L   +  I I++   V K FHAR+SA  R+Y
Sbjct: 66  HALCTSAHVDLEHSGTLDTEYLVRMMNRNLINANHEIRIMSAHEVSKDFHARYSAKSRTY 125

Query: 113 LYRIITRQAP-----LALEKGRAWL---IPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           LYR+I  + P        E  R+      P++ D E +R   +   G  DF TF +    
Sbjct: 126 LYRLIIPKDPLDHRFPIAEANRSLFLNMYPQNFDIERLRSGIKLFCGTKDFMTFSARKRD 185

Query: 165 A-------SSPIRTIDHFDVNSFG------------NLIEIRVVARSFLHTQIRSFVGSL 205
                    + +RT+ H  +   G            +   +   +RSFL+ QIR  VGSL
Sbjct: 186 RNPEFEMRRNFVRTL-HVTMKEAGPLMSFDPLSKNLDYWHLEFTSRSFLYNQIRRIVGSL 244

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEYS 247
             +G  K +  D++  +Q        P    A P GLY  +VEY 
Sbjct: 245 IALGSHKVSEEDIQTMIQVPSHHNWNPHVTPAAPRGLYLKNVEYD 289


>gi|116072175|ref|ZP_01469443.1| tRNA pseudouridine synthase [Synechococcus sp. BL107]
 gi|116065798|gb|EAU71556.1| tRNA pseudouridine synthase [Synechococcus sp. BL107]
          Length = 253

 Score =  189 bits (481), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 64/221 (28%), Positives = 94/221 (42%), Gaps = 4/221 (1%)

Query: 28  QGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS 86
           Q  +E AI  +     +    AGRTD+GVHA  QV HFD            ALN  L   
Sbjct: 2   QAVLETAIAQLDPLRPIQSFAAGRTDAGVHAAAQVVHFDCSGPIPAAKWAPALNGRL--P 59

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWL-IPKSLDCENMRIA 145
            +I +       + +HA +SA+ R Y Y I   + P        W      L+ ENMR+A
Sbjct: 60  ASIRVRESVERPQDWHACYSAVYRRYRYIIHNGRRPNLFLTPWTWHRYHHRLNEENMRVA 119

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
            + ++G HDF  F     +      TI    V   G+LI + + A  FL+  +R  +  L
Sbjct: 120 LEGMIGLHDFAAFMRAGSRRLHSRTTIQDVLVEREGDLIRVEIQASGFLYGMVRLLMAQL 179

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             VG+ + +    E+  + + R +    AP  GL      Y
Sbjct: 180 VAVGEHRLSVEAFEQRWRDRRRDQVKEAAPARGLCLLRAGY 220


>gi|148683104|gb|EDL15051.1| mCG23338, isoform CRA_b [Mus musculus]
          Length = 284

 Score =  189 bits (480), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 78/252 (30%), Positives = 115/252 (45%), Gaps = 29/252 (11%)

Query: 21  QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR-----EWVPVIL 75
           Q      Q   E A  L + + V    + RTD+GVHAL   AH D+ R      + P ++
Sbjct: 3   QPPVRFPQ---EAAKRLNSVDPVRFTISSRTDAGVHALSNAAHLDIQRRPGQSPFSPEVV 59

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL----ALEKGRAW 131
            KALN +LK    I +L    V   FHAR +A  R+Y YR+ T  +        E+   W
Sbjct: 60  AKALNTHLKHP-AIRVLKAFRVPNDFHARHAATSRTYQYRLATGCSWPNQLPVFEQNVCW 118

Query: 132 LIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG--------- 181
            +  + LD   M+ AAQHL+G HDF+ F+S     ++ +RT+    V+            
Sbjct: 119 ALQTEYLDMAAMQEAAQHLLGTHDFSAFQSAGSPVTNTVRTLRRVSVSPGPASPFVLPEG 178

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAP 235
                   +   ++SFL+ Q+R     L  VG G    T ++  L++QD   K    +AP
Sbjct: 179 SRRLQFWTLEFESQSFLYRQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAP 238

Query: 236 PEGLYFDSVEYS 247
             GL+  SV Y 
Sbjct: 239 ARGLFLKSVLYD 250


>gi|319955610|ref|YP_004166877.1| tRNA pseudouridine synthase a [Cellulophaga algicola DSM 14237]
 gi|319424270|gb|ADV51379.1| tRNA pseudouridine synthase A [Cellulophaga algicola DSM 14237]
          Length = 264

 Score =  189 bits (480), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 112/262 (42%), Gaps = 18/262 (6%)

Query: 1   MIR----YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGV 55
           M R    Y + +++ G  Y GWQ+Q    +I+  + K + F++  +   + GAGRTD+ V
Sbjct: 1   MQRIRYYYLVKLQFLGFRYSGWQKQPGQKTIEAMLVKTLKFILPDQKFKILGAGRTDAKV 60

Query: 56  HALRQVAHFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            AL       L    +          N  L     I IL+++ VD+ F+   ++  + Y+
Sbjct: 61  SALDAAFELYLDDTPIEVLEDFLALFNKNL--PPDIRILSMTEVDESFNIIQNSKEKEYI 118

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y     +               +LD + M+  A++  G H+F ++ +   + +  IRT++
Sbjct: 119 YLFSFGEKSHPFCAPYLVTFLDNLDLDKMKTVAKYFEGTHNFKSYTARIQENTKVIRTVN 178

Query: 174 HFDVNSF---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
              +                   V    F+  QIR  +G L  VG G+ +  ++  +L+ 
Sbjct: 179 SCGIIENKILEANFFPEKSYAFHVKGEGFMRYQIRMMMGVLVQVGKGELSEEEVLNSLKE 238

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
           ++  +   +AP  GL  + V++
Sbjct: 239 ENNMQLPFVAPGSGLILNQVDF 260


>gi|195375299|ref|XP_002046439.1| GJ12898 [Drosophila virilis]
 gi|194153597|gb|EDW68781.1| GJ12898 [Drosophila virilis]
          Length = 513

 Score =  189 bits (480), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 125/301 (41%), Gaps = 58/301 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +   +  +    + RT
Sbjct: 1   MRRYLLNIAYIGTNFRGIQKTVNKLEEARLDTNSVQGCLELALRVFRPKNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    L   LN  L   +  I +L+   V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLERSDNKFYDTTTLTGVLNRTLDKQNLPIRVLSTQRVPDTFHCRYH 120

Query: 107 AIRRSYLYRIITRQA-------PLALEKGRAWLIP------------KSLDCENMRIAAQ 147
           AI R+YLYR+   +             KG    +P             + D E ++ AA+
Sbjct: 121 AIGRTYLYRVAVAKNVTQSNTINSLRNKGYESFVPVEEIDRCYFLQNNNFDIERLKNAAR 180

Query: 148 HLVGRHDFTTFRSIHCQASS-------PIRTIDHFDVN---------------SFGNLIE 185
             +G HDF +F S+  Q S         +R ID  ++                   +  +
Sbjct: 181 MFLGVHDFRSFMSVSRQKSPSRDHPMFTVRKIDEINIRAGQSLALGPNATLASQIYDYWD 240

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFD 242
           I + A+SFL+ Q+R  VG+L  + +G+     + + L    +    P   +AP  GLY  
Sbjct: 241 IEIKAKSFLYKQVRRIVGTLLALANGRIDERCIYEMLTIPSKHTWEPRILVAPASGLYLC 300

Query: 243 S 243
            
Sbjct: 301 R 301


>gi|291276765|ref|YP_003516537.1| putative tRNA pseudouridine synthase [Helicobacter mustelae 12198]
 gi|290963959|emb|CBG39798.1| putative tRNA pseudouridine synthase [Helicobacter mustelae 12198]
          Length = 245

 Score =  188 bits (479), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 72/251 (28%), Positives = 107/251 (42%), Gaps = 11/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+     I Y+GS +FG+ +Q +G  S+  ++E A+    G    + GAGRTD GVHA  
Sbjct: 1   MMFIAAKIAYDGSKFFGFAKQDDGHKSVVQALEFAL-KSLGITSNIIGAGRTDRGVHATG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV   ++   W    L   LN  L  S  I +  +  V+  FH RFSA +R Y Y     
Sbjct: 60  QVIRVEIPDFWELERLRNLLNQKLHPS--IFLRRIWRVEASFHPRFSAKKREYRYIFGNY 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                             D + +  A    VG+ DF  F        + IR I H  + +
Sbjct: 118 LG-NVWMASYVSWERYG-DKKRISEALNLFVGKRDFGYFCKSGSDNKTTIRQIYHTRLYT 175

Query: 180 F----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                 + +   + A  FL+ QIR  +G++      + T  +LE  + A+ R    P A 
Sbjct: 176 HQIFKHDYLVACIQANGFLYGQIRLMMGAVLAYSRKELTYEELELQVLAKKRFYSIP-AS 234

Query: 236 PEGLYFDSVEY 246
           P GLY   + Y
Sbjct: 235 PNGLYLSKIFY 245


>gi|222834648|gb|EEE73111.1| predicted protein [Populus trichocarpa]
          Length = 225

 Score =  188 bits (478), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 59/210 (28%), Positives = 93/210 (44%), Gaps = 24/210 (11%)

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +  P    +  N +L     I++     V   FH+R  A  R Y Y ++  
Sbjct: 2   QVVHFDTPLDRAPFSWVRGTNTFL--PPDIAVQWAQPVPDAFHSRACATARRYAYVLLQS 59

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               ++E GR   +  +LD + M+ AAQHL+G HDF++FR+  CQA SP++T+    +  
Sbjct: 60  PVRPSVEAGRVGWVFHALDGDAMQAAAQHLLGEHDFSSFRASGCQAKSPVKTLHRLSITR 119

Query: 180 F--GN--------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
              G+                             +FLH  +R+ +G L  +G G +    
Sbjct: 120 RMAGDGAQMAAASSMRPGDAAMECCYWRFEFEGSAFLHHMVRNIMGCLIAIGQGAYAPQW 179

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +++ L A+ R    P   P+GLYF    Y 
Sbjct: 180 MQQVLDARSRDAAAPTFSPDGLYFLGPVYD 209


>gi|240167785|ref|ZP_04746444.1| tRNA pseudouridine synthase A [Mycobacterium kansasii ATCC 12478]
          Length = 248

 Score =  188 bits (477), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 108/230 (46%), Gaps = 14/230 (6%)

Query: 31  IEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLK------ 84
           ++ A+  +    + +  AGRTD+GVHA  QVAH D+  + +P     ++ A         
Sbjct: 2   LDAALTTIFRTPIRLRAAGRTDAGVHASGQVAHADVPVDALPNAYSHSVRAGHPEFRPLV 61

Query: 85  ------ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSL 137
                 +   + ++++    + F ARFSA+ R Y+YR+ T    +           P+ L
Sbjct: 62  RRLSRFLPSDVRVIDIVRAPRDFDARFSALCRHYVYRLSTAPYGVVPQLARYVTAWPRDL 121

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           D E M IA++ L+G HDF  F   H   ++ IR +   D    G+L+   V A +F  + 
Sbjct: 122 DVEAMTIASRELLGLHDFAAFCR-HRDGATTIRDLQRLDWARDGDLVTAHVTADAFCWSM 180

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +RS VG++  VG+ + ++    + L A  R      AP  GL    V+Y 
Sbjct: 181 VRSLVGAVLAVGEHRRSTAWCRELLTATGRSSDFAAAPAHGLTLVQVDYP 230


>gi|297666734|ref|XP_002811665.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Pongo abelii]
          Length = 287

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 75/243 (30%), Positives = 111/243 (45%), Gaps = 27/243 (11%)

Query: 30  SIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVR-----EWVPVILCKALNAYL 83
            +++A   +   E V    + RTD+GVHAL   AH D+ R      + P +L + LN +L
Sbjct: 27  VLQEAAERLNSVEPVRFTISSRTDAGVHALSNAAHLDVQRRSGRPPFPPEVLAEVLNRHL 86

Query: 84  KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP----LALEKGRAWLIPKS-LD 138
           +    I +L    V   FHAR +A  R YLYR+ T           E+   W +P   LD
Sbjct: 87  RHP-AIRVLRAFRVPSDFHARHAATSRIYLYRLATGCHRRDELPVFERNLCWALPADCLD 145

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-------------NLIE 185
              ++ AAQHL+G HDF+ F+S      SP+RT+    V+                    
Sbjct: 146 VVAVQEAAQHLLGTHDFSAFQSTGSPVPSPVRTMRRVSVSPGQASPLVTPEESRKLRFWN 205

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDS 243
           +   ++SFL+ Q+R     L  VG G      ++  L++QD   K    +AP  GL+  S
Sbjct: 206 LEFESQSFLYRQVRRMTAVLVAVGLGALAPAQVKTILESQDPLGKHQTRVAPAHGLFLKS 265

Query: 244 VEY 246
           V Y
Sbjct: 266 VLY 268


>gi|120436099|ref|YP_861785.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
 gi|117578249|emb|CAL66718.1| tRNA pseudouridine synthase A [Gramella forsetii KT0803]
          Length = 262

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 103/262 (39%), Gaps = 15/262 (5%)

Query: 1   MIR----YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGV 55
           M R    Y + ++Y G    GWQ+Q +  +++G + K +  ++      + G  RTD+ V
Sbjct: 1   MFRKRFYYFIKVQYLGYRLHGWQKQPDVKTVEGLVTKTLGWVIPDAKYKILGTSRTDAMV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A        L  E +  +          +   I  L++  VD +F+    +  + Y Y 
Sbjct: 61  SAEESAFELFLDHEPLEDLDGFLHLFNKNLPQDIRALSIEEVDDKFNIIQHSKTKEYAYL 120

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                              + LD + M+ AA+   G H+F  +     + S+  R +   
Sbjct: 121 FSIGDKFHPFCAPFMANFQEDLDVDRMKEAAKLFHGIHNFRNYCIRVSEKSTFEREMLKS 180

Query: 176 DVNSFGNL---------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           ++                   + A  FL  Q+R  +GSL LVG G+ +  D+E +L+   
Sbjct: 181 ELVENDIYTANFFPEKSYIFHIHASGFLRHQVRLMMGSLVLVGRGELSLQDIEDSLKPDS 240

Query: 227 RK-ECGPLAPPEGLYFDSVEYS 247
            + +   +AP  GL    +E+ 
Sbjct: 241 PQLQMDYIAPASGLILRKIEFE 262


>gi|325287844|ref|YP_004263634.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
 gi|324323298|gb|ADY30763.1| tRNA pseudouridine synthase A [Cellulophaga lytica DSM 7489]
          Length = 270

 Score =  187 bits (475), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 109/255 (42%), Gaps = 14/255 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
           Y + +++ G  + GWQ+Q    +I+G + K +  +  E    + GAGRTD+ V AL    
Sbjct: 14  YLIRLQFLGYRFSGWQKQPGYKTIEGMLAKTLKFILPERQYKILGAGRTDAKVSALDAAF 73

Query: 63  HFDLVREW--VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              L  E         K  N  L     I I+++  V ++F+    +  + Y+Y     +
Sbjct: 74  ELFLDGEPLQDLDFFLKDFNKNL--PSDIRIVSVKHVKEKFNIIQHSKEKEYVYLFSFGE 131

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                       I  +LD + M+ A    VG H+F +F +   +    IR ++  ++   
Sbjct: 132 KNHPYTAPFMANIQDNLDLDLMKKATSLFVGTHNFKSFTAKPKENGKFIRKVNSAEIKEN 191

Query: 181 ---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                           +    F+  Q+R  +G+L  +G G+ T +D+E+AL+     +  
Sbjct: 192 TILKANFFPKKSYAFHIKGEGFMRYQVRMLMGALIQLGKGEVTLSDIEEALKPNSTTKFV 251

Query: 232 PLAPPEGLYFDSVEY 246
            +AP  GL   S+++
Sbjct: 252 FVAPGSGLMLHSLDF 266


>gi|118474657|ref|YP_891922.1| tRNA pseudouridine synthase A [Campylobacter fetus subsp. fetus
           82-40]
 gi|166228690|sp|A0RNY9|TRUA_CAMFF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|118413883|gb|ABK82303.1| tRNA pseudouridine synthase A [Campylobacter fetus subsp. fetus
           82-40]
          Length = 258

 Score =  187 bits (475), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 68/266 (25%), Positives = 108/266 (40%), Gaps = 28/266 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M++  +   YNGS + G Q Q + ++++  +  A+  V G    V  + RTD GVHA+ Q
Sbjct: 1   MMKIALTYSYNGSKFKGSQTQPDKNAVEDCLNFALNRV-GIFKPVVSSSRTDKGVHAISQ 59

Query: 61  VAHFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V+  +    W      L   +N + K    I I N+  V  +FH R+ A+ RSY Y I  
Sbjct: 60  VSCVECGEFWNERFERLKNQINKHTK--PYIYIKNIQKVSDEFHPRYDAVARSYRYIIYH 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
            +              K+L+ + + IA +  +G+HDFT F  +     S +R I +    
Sbjct: 118 DEQ-NVFLADYV-HFYKTLNIQRLNIALKLFIGKHDFTPFYKVGSGEKSTVREIFYAKAY 175

Query: 178 ---------------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
                               L  I   A  FL  Q+R  V +         +  +L K +
Sbjct: 176 QIYKTKDAKFSAKFKTQKPTLTIINFKANGFLRAQVRLMVANALQACK---SDENLYKFI 232

Query: 223 QA--QDRKECGPLAPPEGLYFDSVEY 246
               + +      +PP GLY   V Y
Sbjct: 233 SNFKEQKPLTRMPSPPNGLYLKRVFY 258


>gi|124486487|ref|YP_001031103.1| tRNA pseudouridine synthase ACD [Methanocorpusculum labreanum Z]
 gi|166228737|sp|A2SU30|TRUA_METLZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|124364028|gb|ABN07836.1| tRNA pseudouridine synthase A [Methanocorpusculum labreanum Z]
          Length = 281

 Score =  186 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 107/249 (42%), Gaps = 32/249 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGS-----IEKAIFLVTGEIVVVHGAGRTDSGVH 56
           ++   +  Y G  + G Q Q +  +++G      IE  +F    E      AGRTD GV 
Sbjct: 1   MKLAFLAGYRGQNFAGSQYQPHKRTVEGEFVAGGIELGLFSDAKE-AHFRTAGRTDKGVS 59

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A RQ+      +   P +  +ALN +L   D I  +  + VD++F+ R++A  RSY Y  
Sbjct: 60  ARRQLFSITTEK---PELAIEALNFHL--PDDIWCIGAAEVDEEFYPRYAARERSYRYY- 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                            P   D   M+ AA  L+G H+F+ F  +      P+RT+   +
Sbjct: 114 ----------------FPYPADVSRMQDAASRLIGTHNFSGFAKMEA-GRDPVRTVTRAE 156

Query: 177 VNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           V    +      V A+SFL   +R   G+L+ +G G      +E+ L +         AP
Sbjct: 157 VFEGKDGCPVFEVAAKSFLWNMVRGMAGALQTIGLGLCEPDVIEELLSSP--TARVHPAP 214

Query: 236 PEGLYFDSV 244
            EGL F  V
Sbjct: 215 AEGLVFWDV 223


>gi|126180241|ref|YP_001048206.1| tRNA pseudouridine synthase ACD [Methanoculleus marisnigri JR1]
 gi|166228738|sp|A3CXX4|TRUA_METMJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|125863035|gb|ABN58224.1| tRNA pseudouridine synthase A [Methanoculleus marisnigri JR1]
          Length = 270

 Score =  186 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 96/250 (38%), Gaps = 31/250 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           +       Y G  +FG Q Q +  +++G    A  L+             AGRTD GVHA
Sbjct: 1   MNLAFRFSYFGDRFFGSQMQPDLCTVEGEFIGACRLLRLFDDWREANFATAGRTDRGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV  F   +   P    +ALN  L     I     +     FH R+SA+ R+Y Y   
Sbjct: 61  RSQVCSFLTDK---PERAIEALNRVL--PADIWCTGWAEAPDGFHPRYSAVSRTYRYYFS 115

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                               D   M  AAQ  +GRHDF+ F     +  +P R I    V
Sbjct: 116 -----------------APGDAAAMHEAAQEFLGRHDFSAFARAGDR--NPERRILASRV 156

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPP 236
              G      V   SFL   +R     L  VG G+  + ++ + L    +R+     APP
Sbjct: 157 FIDGEFAVFEVTGESFLWNMVRCMATMLGRVGRGEAEAGEIARLLTGPVERRVAA--APP 214

Query: 237 EGLYFDSVEY 246
           EGL    ++Y
Sbjct: 215 EGLILWDIDY 224


>gi|241745612|ref|XP_002412440.1| pseudouridylate synthase, putative [Ixodes scapularis]
 gi|215505839|gb|EEC15333.1| pseudouridylate synthase, putative [Ixodes scapularis]
          Length = 350

 Score =  186 bits (473), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/293 (25%), Positives = 124/293 (42%), Gaps = 49/293 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLV--TGEIVVVHGAGRTDSGV 55
           RY +   Y G+ Y G QRQ +       ++QG+IE A+  +    E V++  A RTD+GV
Sbjct: 4   RYLLKFSYLGTRYRGMQRQSSRPCLENWTVQGAIEGALRNLRPLSEPVLIL-ASRTDTGV 62

Query: 56  HALRQVAHF-----DLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIR 109
           HA     H      +  + + P+ +   LN +  +    I +  +  V   FHAR+ A  
Sbjct: 63  HASLSAGHVDLVPANTAQCYQPLQIFSVLNRHFARRDHDIVVREVLPVPSWFHARYLAKS 122

Query: 110 RSYLYRI---------------ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHD 154
           RSY+YR+                T +  L L +  +      LD   +  A + L G HD
Sbjct: 123 RSYVYRVAVLRPHVLEQSTVLGTTIRHLLPLNEINSCCAVPPLDFSRVHEAMELLSGEHD 182

Query: 155 FTTFRSIHCQAS----SPIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQ 197
           F TF+++    +    + +R +  F +                 +L E  + +RSFL+ Q
Sbjct: 183 FRTFKNVGRTKAEDEVNTVRNVLDFTLRPSQPASAVADPLYDNVDLWEFHIKSRSFLYRQ 242

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC---GPLAPPEGLYFDSVEYS 247
           +R  V  +  VG    +   + + L+   +        +AP  GLY  ++EY 
Sbjct: 243 VRRMVSVVLHVGMHPESLPLVRRMLENPHKDSWDNKVRIAPACGLYLTNIEYD 295


>gi|268679755|ref|YP_003304186.1| tRNA pseudouridine synthase A [Sulfurospirillum deleyianum DSM
           6946]
 gi|268617786|gb|ACZ12151.1| tRNA pseudouridine synthase A [Sulfurospirillum deleyianum DSM
           6946]
          Length = 247

 Score =  186 bits (473), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 76/252 (30%), Positives = 115/252 (45%), Gaps = 12/252 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS----SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           +R  +I+ Y+GS ++G+QRQ N +    ++ G +EK++    G    + G+GRTD GVHA
Sbjct: 1   MRVKLILSYDGSHFYGFQRQNNENEHFQTVTGILEKSL-KALGIHTPIVGSGRTDRGVHA 59

Query: 58  LRQVAHFDLVREWVPV--ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           LRQV H DL   W      L   LN  L     I    +      FHARFSA +R Y Y 
Sbjct: 60  LRQVVHLDLPLFWEKEYEKLRSLLNRSLMPHLYI--QQIHPTLPNFHARFSAQKRLYRYF 117

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +             A  +  +LD + +   AQ   G H+F  F+      +   R +   
Sbjct: 118 LYDG-VYQPFYAHYALHV-NALDVQRLHHVAQSFQGAHNFEFFKKQGGGLTRDERILYKV 175

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
               + +LI I  +  +FL +QIR    +L  V   +    +L   L+ +++K    L P
Sbjct: 176 GAYRYKHLIVIYFLGDAFLRSQIRMMCDALLKVCYDEIREEELIAQLR-REKKVSTTLLP 234

Query: 236 PEGLYFDSVEYS 247
           P GLY   + Y 
Sbjct: 235 PSGLYLSRIFYE 246


>gi|89890078|ref|ZP_01201589.1| tRNA pseudouridine synthase A [Flavobacteria bacterium BBFL7]
 gi|89518351|gb|EAS21007.1| tRNA  pseudouridine synthase A [Flavobacteria bacterium BBFL7]
          Length = 267

 Score =  186 bits (472), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 92/251 (36%), Gaps = 13/251 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G  + GWQ+Q +  +++  +++ +  V       V  AGRTD+ V     + 
Sbjct: 11  YLIKLQYLGFRFHGWQKQPDVPTVEKMVKRTLRFVLDHHNFKVLAAGRTDARVSVNETII 70

Query: 63  HFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              L  E           N  L +   I  L++   + QF+       + Y+Y     + 
Sbjct: 71  ELFLDDEALNLDTFLAEFN--LNLPSDIRALDIEETNAQFNVIQHPKEKEYIYLFSHGEK 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
                      +   LD E M+ AA+   G H+F ++       +  + T++   +    
Sbjct: 129 FHPFCASLMVYMKTELDIELMKTAARLFEGTHNFWSYTYKPSDTTDTVSTVNSCHIEENN 188

Query: 181 --------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                         RV    F   Q+R  +G+L  +G  K T  D +  L    +     
Sbjct: 189 LFTANFFPEESFVFRVTGMGFKRHQVRLMMGALFDLGMHKITLEDFKATLDGSKKIHLSH 248

Query: 233 LAPPEGLYFDS 243
           +AP  GL    
Sbjct: 249 IAPASGLMLYR 259


>gi|224418450|ref|ZP_03656456.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|253827766|ref|ZP_04870651.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|313141982|ref|ZP_07804175.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|253511172|gb|EES89831.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
 gi|313131013|gb|EFR48630.1| tRNA pseudouridine synthase A [Helicobacter canadensis MIT 98-5491]
          Length = 240

 Score =  186 bits (472), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 107/248 (43%), Gaps = 10/248 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MI+  M I Y G  +FG+QRQK+  +I G +E+  F   G   V  G+GRTD GVHA  Q
Sbjct: 1   MIKVAMRIAYYGGEFFGFQRQKDKITICGVLEEV-FRSVGIFDVCMGSGRTDKGVHASAQ 59

Query: 61  VAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V    +         L + LN  L     I I  +  V+ +FH RFS  RR Y Y +  +
Sbjct: 60  VISVSIPEFHRDLQRLKQLLNVKLYPW--IKIKQIWQVENEFHVRFSVKRRGYCYVLSQK 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVN 178
            +P        + +        ++ +     G +DF+ F           +R I H  + 
Sbjct: 118 YSPFLALFSHFYPLKNPF---LVQESLDIFRGVYDFSAFMKNGGSGCEGSVREIFHTKLL 174

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G    I      FL +QIR  VG L  +  G     DL+K L  +  K     APP G
Sbjct: 175 KRGEFYLISFWGNGFLRSQIRLMVGFLLEIDRGNLGIEDLKKQLLGE--KIFSIPAPPNG 232

Query: 239 LYFDSVEY 246
           L+   V+Y
Sbjct: 233 LFLSRVDY 240


>gi|154174016|ref|YP_001408137.1| tRNA pseudouridine synthase A [Campylobacter curvus 525.92]
 gi|153793037|gb|EAU00484.2| tRNA pseudouridine synthase A [Campylobacter curvus 525.92]
          Length = 241

 Score =  185 bits (471), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 98/246 (39%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G Q Q + + +Q ++ +A+  V G    +  + RTD GVHA  Q 
Sbjct: 1   MKIQLIFSYDGSKFQGSQTQPHENGVQDALSRALAHV-GIFDKLALSSRTDKGVHATAQS 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L   +N +      I I N+  V+  F AR+ A  R Y Y I   +
Sbjct: 60  ATVECGEHFKDLDRLKNLINRH--AHPFIHIKNIKRVNDDFQARYDAKARLYRYIIDHGR 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                        PK  D        +  +G HDF+ F        SPIR I       +
Sbjct: 118 Y-DVFHAEHCLFAPK-FDTARANHILKIFIGEHDFSAFMKTGSGTKSPIREIYKAYCYEY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            N   I   A  FL  Q+R  V SL    + K     L  A+  +      P A  +GLY
Sbjct: 176 KNKTVIVFKANGFLRAQVRLMVASLLKALNLKDGDELLNLAINHKKPLTRIPAA-AQGLY 234

Query: 241 FDSVEY 246
              V Y
Sbjct: 235 LSRVFY 240


>gi|195012380|ref|XP_001983614.1| GH25313, isoform B [Drosophila grimshawi]
 gi|193897096|gb|EDV95962.1| GH25313, isoform B [Drosophila grimshawi]
          Length = 317

 Score =  185 bits (470), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 80/304 (26%), Positives = 122/304 (40%), Gaps = 58/304 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +SIQG +E A+ +   +  +    + RT
Sbjct: 1   MHRYLLNISYIGTNFRGIQKTINKLEEARLDTNSIQGCLELALRVFRPKNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    L   LN  L      I IL+   V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLERSDGKPYDTSTLTGVLNRTLDKHKLPIRILSSQRVVDTFHCRYH 120

Query: 107 AIRRSYLYRIITRQ------------------APLALEKGRAWLIP-KSLDCENMRIAAQ 147
           A  R+YLYR+   +                       E  R + +   + D E +  AA+
Sbjct: 121 ATGRTYLYRVAVAKSVSEASKGSSLKNKGYESFVPVEEIDRCYFLHCDNFDVERLHGAAR 180

Query: 148 HLVGRHDFTTFRSIHCQASS-------PIRTIDHFDVN---------------SFGNLIE 185
             +G HDF TF S+  Q S         +R ID  ++                   +  +
Sbjct: 181 MFLGLHDFRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGQTLALGPNAKLATQTYDYWD 240

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC---GPLAPPEGLYFD 242
           I + A+SFL+ Q+R  VG+L  + + +     + + L    +        +AP  GLY  
Sbjct: 241 IEIKAKSFLYKQVRRIVGTLLALANSRIDERCIYQMLTIPSKHNWDSRVVVAPACGLYLC 300

Query: 243 SVEY 246
            V Y
Sbjct: 301 RVHY 304


>gi|290984657|ref|XP_002675043.1| predicted protein [Naegleria gruberi]
 gi|284088637|gb|EFC42299.1| predicted protein [Naegleria gruberi]
          Length = 430

 Score =  185 bits (470), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 66/263 (25%), Positives = 107/263 (40%), Gaps = 37/263 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G  +Q +   +I+  + +A+  +      +       GRTD GV AL
Sbjct: 70  IALKIAYLGFNYQGLSKQLHTPNTIEHHLFEALKTLKLIEHEDNCEFTKCGRTDKGVSAL 129

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV  F+           + +N+ L   D I +L    V K F ARF  ++R+Y Y    
Sbjct: 130 GQVVSFNCRYNPKKNDYVRLINSLL--PDDIRVLAWCPVSKDFDARFGCLQRTYKY---- 183

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV- 177
                       + I ++L+ E M+ AA H VG HDF  F  I+ + ++  R I   ++ 
Sbjct: 184 ------------YFIRQNLNIEKMKQAAAHFVGEHDFRNFCKINEEVTNFRRRILSMEII 231

Query: 178 -----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
                      + +  + EI V   SFL  Q+R     L L+G+GK   + + + L  + 
Sbjct: 232 KSDLLHQQHGNDEYFEIYEIVVCGTSFLWHQVRCMTAILFLIGEGKEEPSVIPELLDIEK 291

Query: 227 RKE--CGPLAPPEGLYFDSVEYS 247
            K      +A    L      + 
Sbjct: 292 YKARPVYHIASEFPLVLYDCVFE 314


>gi|194746922|ref|XP_001955903.1| GF24924 [Drosophila ananassae]
 gi|190623185|gb|EDV38709.1| GF24924 [Drosophila ananassae]
          Length = 307

 Score =  185 bits (470), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 87/303 (28%), Positives = 126/303 (41%), Gaps = 57/303 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQR------QK--NGSSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+      Q   + ++IQG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTSFRGIQKTVNKSEQPRLDTNTIQGCLELALRVFRPTNDIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    L   LN  L      I IL+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLQRYDGQPYDTGTLTGVLNRTLDKQRLPIRILSSQVVSDSFHCRYH 120

Query: 107 AIRRSYLYRIITRQAPLALEKG-----------------RAWLIPK-SLDCENMRIAAQH 148
           A  R+YLYR    +   A+E G                 R + +   S D E +R AA+ 
Sbjct: 121 ATGRTYLYRFAVSRNTGAVESGNLRNKGYESFIPVEELDRCYFLQSTSFDIERVRNAARM 180

Query: 149 LVGRHDFTTFRSIHCQASS-------PIRTIDHFDVNS---------------FGNLIEI 186
            +G HDF TF S+  Q S         +R ID   +                   +  EI
Sbjct: 181 FIGVHDFRTFMSVSRQKSPSRDHPRFTLRKIDDISIRPGRALAVAGNAALAANSYDYWEI 240

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDS 243
            + A+SFL+ Q+R  VG+L  +G G+     + + L    +        LAP  GLY   
Sbjct: 241 EIRAKSFLYKQVRRIVGTLLALGCGRIDEKSVYQMLTIPSKNSWDHRVLLAPACGLYLCR 300

Query: 244 VEY 246
           V Y
Sbjct: 301 VHY 303


>gi|167583949|ref|ZP_02376337.1| tRNA pseudouridine synthase A [Burkholderia ubonensis Bu]
          Length = 193

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 54/167 (32%), Positives = 83/167 (49%)

Query: 81  AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCE 140
               +  T+++     +   FHARFSA  R+Y Y +        +   RA  I   LD +
Sbjct: 1   TNAFLPPTVAVQWAKPMPDAFHARFSAFERTYYYALYVHPVRSPMLDARAGWIHTPLDDD 60

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
            MR AA HL+G HDF+ FRS  CQ+ +P++ +   D+   G+ +  R  A +FLH  +R+
Sbjct: 61  AMRAAAAHLIGEHDFSAFRSSECQSKTPVKHLYQIDIRRAGHFLHFRFRANAFLHHMVRN 120

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +G L  VG G++ +  +   L  +DR    P    +GLY   V Y 
Sbjct: 121 LMGCLVAVGRGRYPAEWIADVLAGRDRNRAAPTFMADGLYLAHVGYP 167


>gi|51246208|ref|YP_066092.1| tRNA pseudouridine synthase A [Desulfotalea psychrophila LSv54]
 gi|62901427|sp|Q6AKP0|TRUA2_DESPS RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|50877245|emb|CAG37085.1| related to tRNA pseudouridine synthase A [Desulfotalea psychrophila
           LSv54]
          Length = 261

 Score =  183 bits (466), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 110/262 (41%), Gaps = 21/262 (8%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDS 53
           M  + + I Y G+ YFGWQ Q      +   +++G+I  A+  +T  +   V GA RTD 
Sbjct: 1   MNYFRVKIAYKGTHYFGWQAQSIDTLHEEKPTVEGTILNALKKITNYQPCTVSGASRTDG 60

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA  Q+A   + ++  P  L         +   I IL      K++ A   ++ + Y 
Sbjct: 61  GVHARGQIAKITISQKISPEHLLLG--LNSLLPTDIRILECVPSTKEYQASRGSVSKEYH 118

Query: 114 YRIITRQAPLALEKGRAWLIP----KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           Y  I            A  +P       D   +R A +  VGRHDF  F S      +  
Sbjct: 119 YYFIASPVDNVATSDIALHLPIDSIGPDDLALLRSACRLFVGRHDFYNFSSRGS--GTSF 176

Query: 170 RTIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           R I + D++         ++  ++++   FL   IR  +G+L  +  G+    D+   LQ
Sbjct: 177 REIFYCDIHRANFSPLANDMFYLKIIGDGFLKYMIRYIMGALLELVRGRIVLDDISLYLQ 236

Query: 224 AQDRKECGPLAPPEGLYFDSVE 245
                +  P A  +GL+   +E
Sbjct: 237 QHQEDKLSPRAKAKGLHLIRIE 258


>gi|261885752|ref|ZP_06009791.1| tRNA pseudouridine synthase A [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 257

 Score =  183 bits (465), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 67/265 (25%), Positives = 107/265 (40%), Gaps = 28/265 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +   YNGS + G Q Q + ++++  +  A+  V G    V  + RTD GVHA+ QV
Sbjct: 1   MKIALTYSYNGSKFKGSQTQPDKNAVEDCLNFALNRV-GIFKPVVSSSRTDKGVHAISQV 59

Query: 62  AHFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +  +    W      L   +N + K    I I N+  V  +FH R+ A+ RSY Y I   
Sbjct: 60  SCVECGEFWNERFERLKNQINKHTK--PYIYIKNIQKVSDEFHPRYDAVARSYRYIIYHD 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-- 177
           +              K+L+ + + IA +  +G+HDFT F  +     S +R I +     
Sbjct: 118 EQ-NVFLADYV-HFYKTLNIQRLNIALKLFIGKHDFTPFYKVGSGEKSTVREIFYAKAYQ 175

Query: 178 --------------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                              L  I   A  FL  Q+R  V +         +  +L K + 
Sbjct: 176 IYKTKDAKFSAKFKTQKPTLTIINFKANGFLRAQVRLMVANALQACK---SDENLYKFIS 232

Query: 224 A--QDRKECGPLAPPEGLYFDSVEY 246
              + +      +PP GLY   V Y
Sbjct: 233 NFKEQKPLTRMPSPPNGLYLKRVFY 257


>gi|116007752|ref|NP_001036574.1| CG34140 [Drosophila melanogaster]
 gi|113194868|gb|ABI31225.1| CG34140 [Drosophila melanogaster]
 gi|238231868|gb|ACR40402.1| RE01995p [Drosophila melanogaster]
          Length = 306

 Score =  183 bits (464), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 85/301 (28%), Positives = 124/301 (41%), Gaps = 55/301 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N          SIQG +E A+ +      +    + RT
Sbjct: 1   MYRYLLNISYIGTTFRGIQKTVNKLEQSRLDTKSIQGCLELALQVFHPTNEIHTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL      DL R     +   IL   LN  L      I +L+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVQVDLERPNGQPYDTTILTGVLNRTLNKQRLPIRVLSSKLVANSFHCRYD 120

Query: 107 AIRRSYLYRIITRQAP----------------LALEKGRAWLIPKS-LDCENMRIAAQHL 149
           AI R+YLYR    + P                   E  R + +  S  D + ++ AA+  
Sbjct: 121 AIGRTYLYRFAVAKVPTLGDCSLRNRSFETFIPVEEIDRCYFLQSSSFDIKRVQAAARMF 180

Query: 150 VGRHDFTTFRSIHCQASS------PIRTIDHFDVNSFG---------------NLIEIRV 188
           +G HDF TF S+  Q          +R ID  ++                   N  +I +
Sbjct: 181 IGVHDFRTFMSVSRQKVCRDHPMFTVRKIDEINIRPGETRALSSNAIQAAETYNYWDIEI 240

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVE 245
            A+SFL+ Q+R  VG+L  +G+G+     L + L    +        LAP  GLY   V 
Sbjct: 241 RAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNSWDHRVLLAPACGLYLCRVH 300

Query: 246 Y 246
           Y
Sbjct: 301 Y 301


>gi|86130141|ref|ZP_01048741.1| tRNA pseudouridine synthase A [Dokdonia donghaensis MED134]
 gi|85818816|gb|EAQ39975.1| tRNA pseudouridine synthase A [Dokdonia donghaensis MED134]
          Length = 259

 Score =  183 bits (464), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 94/252 (37%), Gaps = 13/252 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GWQ+Q +  +++  +E+    V       +  +GRTD+ V A     
Sbjct: 8   YLLKIQYLGFRYHGWQKQPDVLTVERMMERTFSYVLDRKNFKLLASGRTDAKVSANVAYV 67

Query: 63  HFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              L             LN  L     I  L ++ VDK+F+   + I + Y+Y     + 
Sbjct: 68  ELFLNDSPLPAEGFLTLLNDNL--PQDIRCLQITQVDKKFNVMDAPIAKEYVYLFSYGEK 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                      I   LD E M+ AA+   G HDF ++       +  I  +    +    
Sbjct: 126 NHPFAAPYMINIAGDLDIELMKEAARLFEGEHDFRSYAYKPNPQTQTIGHVLSSTIEIND 185

Query: 182 ---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                         RV  + F   QIR  +G+L  +G G       +K L A +  +   
Sbjct: 186 LYTASFFPEESYAFRVSGKGFKRHQIRLMMGALFDLGQGNIDLEFFKKTLDASNDIKLTR 245

Query: 233 LAPPEGLYFDSV 244
           +A   GL    V
Sbjct: 246 IAQASGLLLQDV 257


>gi|195135262|ref|XP_002012053.1| GI24889, isoform B [Drosophila mojavensis]
 gi|193918317|gb|EDW17184.1| GI24889, isoform B [Drosophila mojavensis]
          Length = 320

 Score =  182 bits (463), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 82/307 (26%), Positives = 126/307 (41%), Gaps = 61/307 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTG-EIVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTRFRGIQKTINKLEESRVDTNSVQGCLELALRVFRPVNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +   IL   LN  L   S  I +L+   V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLERNDGKCYDTTILTGVLNRTLDKQSLPIRVLSTQRVADTFHCRYH 120

Query: 107 AIRRSYLYRIITRQAP---------------------LALEKGRAWLI-PKSLDCENMRI 144
           AI R+YLYR+   +                          E  R + +   + D E +  
Sbjct: 121 AIGRTYLYRVAVSKQKTTVLPDAKSSSLRNRAFEAFLPVEEWDRCYFLQNNNFDIERLIA 180

Query: 145 AAQHLVGRHDFTTFRSIHCQASS-------PIRTIDHFDVN---------------SFGN 182
           A++ L+G HD+ TF S+  Q S         +R ID  ++                   +
Sbjct: 181 ASRMLIGVHDYRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGRSLALGPNATLATENYD 240

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGL 239
             +I + A+SFL+ Q+R  VG+L  + +G+     + + L    +        LAP  GL
Sbjct: 241 YWDIEIKAKSFLYKQVRRIVGTLLALAEGRIDERCIYQMLTIPSKHSWDHRIQLAPACGL 300

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 301 YLCRVHY 307


>gi|284166628|ref|YP_003404907.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Haloterrigena turkmenica DSM 5511]
 gi|284016283|gb|ADB62234.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Haloterrigena turkmenica DSM 5511]
          Length = 295

 Score =  182 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 66/266 (24%), Positives = 107/266 (40%), Gaps = 30/266 (11%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSG 54
           M      I Y+G+GY G+QRQ +  +++ +I  A+  +               AGRTD+G
Sbjct: 1   MPTRAFRIAYDGTGYHGFQRQPDVPTVEDAIFDALRDLEVLAADADRPDGYAAAGRTDAG 60

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V AL Q    +      P    +ALN  L     I     +    +FHA   A RR Y Y
Sbjct: 61  VSALAQTVALEAPDWLTP----RALNGEL--PADIRAWAAADAPPEFHATHHAERREYAY 114

Query: 115 RIITRQAPLALEKGRAWLI-----------PKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
            +    A  +  + RA  +            +++D +  R A + L G HD   F ++  
Sbjct: 115 HLYAPPA-DSRRRDRAAPVSDRAGTRGSPGQRAVDDDRFRAACEALSGSHD---FHNLTP 170

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
              +  R+    +    G+ + + V A  F+   +R  V   + VG G      +++A  
Sbjct: 171 DDRNTERSPT-LEAIRDGDFLVVTVTAGGFVRELVRRLVSLARAVGTGDAPLEKIDRAFD 229

Query: 224 AQDR--KECGPLAPPEGLYFDSVEYS 247
            +     E    APPE L   +V+Y 
Sbjct: 230 PEPLPGHEGVAPAPPEPLVLTAVDYP 255


>gi|154149764|ref|YP_001403382.1| tRNA pseudouridine synthase ACD [Candidatus Methanoregula boonei
           6A8]
 gi|153998316|gb|ABS54739.1| tRNA pseudouridine synthase A [Methanoregula boonei 6A8]
          Length = 276

 Score =  182 bits (462), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 99/247 (40%), Gaps = 30/247 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHA 57
           +R    + Y G+ ++G Q+Q++  +++G   +A   +             AGRTD GVHA
Sbjct: 15  VRLACRVSYLGTRFYGSQQQESSRTVEGEFIEACRRLALFSDWRTAGFASAGRTDRGVHA 74

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV  F       P    +ALN+ L     I     ++V   FH R+ A  R+Y Y   
Sbjct: 75  CGQVIAFSTQ---TPDRARQALNSQL--PPDIWCTATAVVPDHFHPRYDARSRTYRY--- 126

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                        +      D   M  AA+   G H+FT F  +     +P R I    +
Sbjct: 127 -------------YFGEPPRDPVAMETAAREFSGDHNFTNFARVGD--KNPWRKILEIRI 171

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-QAQDRKECGPLAPP 236
            + G+   + V A+SFL  Q+R    +    G G+  +  +   L +A  R      AP 
Sbjct: 172 GTEGSFTYLEVKAQSFLWHQVRCMAAAALSAGMGEQDADGIRLLLNEAASRP--IQPAPA 229

Query: 237 EGLYFDS 243
           EGL    
Sbjct: 230 EGLVLWD 236


>gi|89266772|emb|CAJ81267.1| pseudouridine synthase 3 [Xenopus (Silurana) tropicalis]
          Length = 505

 Score =  182 bits (462), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 69/265 (26%), Positives = 105/265 (39%), Gaps = 39/265 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G GY G+  Q+N  ++++ ++  A+       + +    H  GRTD GV AL
Sbjct: 64  VALRLAYLGWGYQGFASQENTKNTVEETVFNALIKTRLVESRQTSNYHRCGRTDRGVSAL 123

Query: 59  RQVAHFDLV---REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QV   DL         +     LN  L     I +L+ + V   F ARFS   R+Y Y 
Sbjct: 124 GQVISLDLRCSGEGKPEIRYVHILNRVL--PPDIRVLSWAAVPPSFSARFSCRSRTYRYL 181

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTID 173
               Q                LD E M  AA+ L G HDF     +       + IRT+ 
Sbjct: 182 FSCAQ----------------LDVEAMDKAARLLEGTHDFRNLCKMDVANGVMNFIRTVL 225

Query: 174 HFDVNSFGN---------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ- 223
              V              L  +++   +FL+ Q+R  +G L LVG GK     + + L  
Sbjct: 226 SARVEPVPEIPGDMGPFQLYRLQITGLAFLYHQVRCIMGVLFLVGQGKEKPEVITELLDV 285

Query: 224 AQD-RKECGPLAPPEGLYFDSVEYS 247
           A++ RK    +A    L   +  + 
Sbjct: 286 AKNPRKPQYNMAVEFPLVLYNCHFD 310


>gi|45360593|ref|NP_988969.1| pseudouridylate synthase 3 [Xenopus (Silurana) tropicalis]
 gi|38174435|gb|AAH61416.1| pseudouridylate synthase 3 [Xenopus (Silurana) tropicalis]
          Length = 505

 Score =  181 bits (461), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 69/265 (26%), Positives = 105/265 (39%), Gaps = 39/265 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G GY G+  Q+N  ++++ ++  A+       + +    H  GRTD GV AL
Sbjct: 64  VALRLAYLGWGYQGFASQENTKNTVEETVFNALIKTRLVESRQTSNYHRCGRTDRGVSAL 123

Query: 59  RQVAHFDLV---REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QV   DL         +     LN  L     I +L+ + V   F ARFS   R+Y Y 
Sbjct: 124 GQVISLDLRCSGEGKPEIRYVHILNRVL--PPDIRVLSWAAVPPSFSARFSCRSRTYRYL 181

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTID 173
               Q                LD E M  AA+ L G HDF     +       + IRT+ 
Sbjct: 182 FPCAQ----------------LDVEAMDKAARLLEGTHDFRNLCKMDVANGVMNFIRTVL 225

Query: 174 HFDVNSFGN---------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ- 223
              V              L  +++   +FL+ Q+R  +G L LVG GK     + + L  
Sbjct: 226 SARVEPVPEIPGDMGPFQLYRLQITGLAFLYHQVRCIMGVLFLVGQGKEKPEVITELLDV 285

Query: 224 AQD-RKECGPLAPPEGLYFDSVEYS 247
           A++ RK    +A    L   +  + 
Sbjct: 286 AKNPRKPQYNMAVEFPLVLYNCHFD 310


>gi|94266218|ref|ZP_01289926.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
 gi|93453191|gb|EAT03652.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
          Length = 319

 Score =  181 bits (460), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 56/165 (33%), Positives = 84/165 (50%), Gaps = 2/165 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   + I ++G+ + GWQRQ++  +IQ ++E  +  + GE VV+HGAGRTD+GVHA   V
Sbjct: 1   MNIKLTIAFDGTAFAGWQRQRHQPTIQATLEDGLARLLGEKVVLHGAGRTDAGVHAAGMV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A F   R+         LN+ L     I IL    V   FHARFSA  + Y+Y   T   
Sbjct: 61  ASFQTARQLPLAAYRHGLNSML--PPAIRILAAREVAADFHARFSAKGKIYVYGFTTAAI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
                +  +   P S +   ++ A   L+G HDFT+F +   +  
Sbjct: 119 ISPRRRLYSAHFPGSFNPGPVQEALPGLLGEHDFTSFEAAGSRRR 163



 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 24/66 (36%), Positives = 32/66 (48%)

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+   + V    FL   +R+ VG+L  +G GK T   L + L  +DR   GP AP  GL 
Sbjct: 254 GDDYYLVVAGDGFLRHMVRNLVGTLLEIGRGKRTPESLPQLLAGRDRCRAGPTAPAHGLT 313

Query: 241 FDSVEY 246
              V Y
Sbjct: 314 LWRVLY 319


>gi|322374719|ref|ZP_08049233.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
 gi|321280219|gb|EFX57258.1| tRNA pseudouridine synthase A [Streptococcus sp. C300]
          Length = 163

 Score =  181 bits (459), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 59/157 (37%), Positives = 87/157 (55%), Gaps = 3/157 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVHAL 
Sbjct: 1   MTRYKATISYDGFAFAGFQRQPHARSVQEEIEKTLTRLNKGQAIAVHGAGRTDSGVHALE 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL  +     L  AL+   +  + I ++++ IV   FH R++   ++Y + +   
Sbjct: 61  QVIHFDLPYQMDEEKLRFALDT--QSPEDIDVISIEIVADDFHCRYAKHSKTYEFIVDRG 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           +    + +  A   P  LD E M+ A + L G HDFT
Sbjct: 119 RPKNPMRRHYATHFPYPLDVERMQEAVKKLEGTHDFT 155


>gi|55379749|ref|YP_137599.1| tRNA pseudouridine synthase A [Haloarcula marismortui ATCC 43049]
 gi|62901222|sp|Q5UXW0|TRUA_HALMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|55232474|gb|AAV47893.1| tRNA pseudouridine synthase A [Haloarcula marismortui ATCC 43049]
          Length = 275

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/255 (23%), Positives = 100/255 (39%), Gaps = 27/255 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSG 54
           M  Y   + Y+G  Y G+QRQ +  +++G +  A+  +       G       AGRTD+G
Sbjct: 1   MRAYR--VAYDGQPYHGFQRQPDVDTVEGRLRSALVRLGVCERGEGLPDRYAAAGRTDAG 58

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A  Q   FD      P           ++ + + +   + V + FHA   A  R+Y Y
Sbjct: 59  VSARTQTVAFDAPAWLSPAAF------NGELPNDVRVWASADVPEDFHATHDAAERTYTY 112

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +    AP   ++       + +D      A   L G HD   F ++    +   RT+  
Sbjct: 113 YLY---APADADRPE----HEPVDDGRWADAVDALAGTHD---FHNLTTDETGTERTV-A 161

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK--ECGP 232
            D    G  + +++ A  F    +R  V     V DG    + +++ L  +     +  P
Sbjct: 162 IDWTRDGQFLVVQLTAGGFCRQLVRRLVSLAAAVADGSAPLSKVDRILSPEPVSGPDGVP 221

Query: 233 LAPPEGLYFDSVEYS 247
            APPE L    V Y 
Sbjct: 222 PAPPEPLVLTDVRYP 236


>gi|270014158|gb|EFA10606.1| hypothetical protein TcasGA2_TC012867 [Tribolium castaneum]
          Length = 315

 Score =  180 bits (458), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 86/296 (29%), Positives = 120/296 (40%), Gaps = 51/296 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--------SIQGSIEKAIFLVTGE-IVVVHGAGRTDS 53
           RY +   Y G+ + G QRQ  G         ++QG +E A+  +      VV+ + RTDS
Sbjct: 5   RYLLHFSYIGTPFMGAQRQVTGRMPRPDDPSTVQGQLEMALKRLNPTNDPVVYLSSRTDS 64

Query: 54  GVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAI 108
           GVHAL    H DL R    E+ P  +   LN Y   ++  I ++    V   FH R +AI
Sbjct: 65  GVHALNSTCHVDLYRSNELEYEPKTITICLNRYFDKNEVPIRVIKTYWVPPDFHCRHTAI 124

Query: 109 RRSYLYRIITRQA------------PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            R+YLYRI   +             P+   +   +    S + + M+ AA+   G HDF 
Sbjct: 125 SRTYLYRIAIAKTGVTEHATILNLLPIEEYQRCLFFYCDSFNIDEMKEAAKVFEGLHDFR 184

Query: 157 TFRSIHCQASSPI--RTIDHFDVN--------------------SFGNLIEIRVVARSFL 194
           TF          I  R +   DV                           +I V A  FL
Sbjct: 185 TFMGRGSHDPDKITRRVVTRVDVCDGRALTYSSFSWPRFASGSAENYQFYDIYVQATGFL 244

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC---GPLAPPEGLYFDSVEYS 247
           + Q+R  V SL  VG GK T  +L+  L+    +         P  GLY   VEYS
Sbjct: 245 YRQVRRMVASLIAVGQGKKTRRELKLMLEVPSHRSWDERIKTVPAYGLYLCEVEYS 300


>gi|50364970|ref|YP_053395.1| tRNA pseudouridine synthase A [Mesoplasma florum L1]
 gi|62901303|sp|Q6F1W2|TRUA_MESFL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|50363526|gb|AAT75511.1| tRNA pseudouridine synthase I [Mesoplasma florum L1]
          Length = 251

 Score =  180 bits (458), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 117/253 (46%), Gaps = 11/253 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV-VVHGAGRTDSGVHALR 59
           M ++ + +EY+GS + GW  Q   S+IQG + KAI  VT   V    GA +TD+GVHA+ 
Sbjct: 1   MFKFLITLEYDGSDFHGWIEQPKTSTIQGELNKAINRVTKNAVFKTIGASKTDTGVHAID 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q    DL       +  KA+N  L   +TI + ++  V + F+ R   + + Y Y I  +
Sbjct: 61  QKVLLDLGFNPKLDLFKKAINKAL--PETIKVRSIEEVKQDFNIR-DVLYKEYSYTINDK 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-----IHCQASSPIRTIDH 174
           +  +   +       + +D + ++      +G H+F  F       +     + IR I+ 
Sbjct: 118 EYNILSNRFELNWDFEEIDIDKLQNIFNLFIGEHEFKLFSGLNHKELDSNKITTIREIES 177

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG-KWTSTDLEKALQAQDRKECGPL 233
            DV    + + I   A+ F+  QIR  V S        K ++ ++++ LQ +  K     
Sbjct: 178 IDVKRALDKVVITFKAKGFIRYQIRMIVQSALNCYLNKKISADEIKEKLQGKGNKP-PFN 236

Query: 234 APPEGLYFDSVEY 246
           AP +GL  + + +
Sbjct: 237 APAKGLKLNKIVF 249


>gi|157137669|ref|XP_001657123.1| hypothetical protein AaeL_AAEL003683 [Aedes aegypti]
 gi|108880780|gb|EAT45005.1| conserved hypothetical protein [Aedes aegypti]
          Length = 325

 Score =  180 bits (458), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 76/300 (25%), Positives = 121/300 (40%), Gaps = 53/300 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTG-EIVVVHGAGRT 51
           M RY + + Y G+ + G Q+         ++  S++G +E A+          +  + RT
Sbjct: 1   MNRYLINLSYIGTHFRGIQKNLLKDSGYLEDPHSVEGVLEIALKKFAPVNEFKIKLSSRT 60

Query: 52  DSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    L + LN         I IL+  +V    HAR  
Sbjct: 61  DAGVHALHNTVHVDLERPSGKPYKTYKLTQGLNRTFGSQGLPIRILDTKLVPMSCHARLC 120

Query: 107 AIRRSYLYRI------ITRQAPL-ALEK-------GRAWLI-PKSLDCENMRIAAQHLVG 151
           A  R+YLYR+         +       +        R + I  K  D E ++  A    G
Sbjct: 121 AKSRTYLYRLGVLRPQYCDKVESHPFNRFVPIDEYDRCYFIAHKHFDIERLKRVASTFQG 180

Query: 152 RHDFTTFRSIHC------QASSPIRTIDHFDV---------------NSFGNLIEIRVVA 190
            HDF TF S+          S  +RTI+H  +                 + +  +IR+  
Sbjct: 181 YHDFRTFMSVARGNDRQHDPSFTLRTIEHISIDRGISMASAFNREQAERYYDYWDIRIKG 240

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC---GPLAPPEGLYFDSVEYS 247
           RSFL+ Q+R  VG+     + + +  D+ + L    ++       +AP  GL+   VEY 
Sbjct: 241 RSFLYKQVRRMVGAWIGAAENRLSERDIYRMLTVPSQRSWCDQAVVAPAYGLFLCRVEYD 300


>gi|307168411|gb|EFN61571.1| tRNA pseudouridine synthase-like 1 [Camponotus floridanus]
          Length = 305

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 77/284 (27%), Positives = 124/284 (43%), Gaps = 37/284 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIFLVTGEIVV---VHGAGRT 51
           M+RY +   Y G+ Y G Q+Q      ++  SIQG++E A+  ++ + ++   +  + RT
Sbjct: 1   MVRYLLKFSYIGTQYRGLQKQIGNDFVRDTDSIQGALETALLTISPKSLIRPFIILSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAY-LKISDTISILNLSIVDKQFHARFS 106
           D+GVHAL    H +L       +    + + +N Y  K    I +L    + + FHAR+ 
Sbjct: 61  DAGVHALCNTGHVELENKYGQIYDTSRIKQYVNRYFTKCGHNIRLLECIPITQDFHARYC 120

Query: 107 AIRRSYLYRIIT------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
              R+Y+YR +        + PL        L   + D +  +   +  +G  DFTTF +
Sbjct: 121 VKSRTYIYRFMIPKVDEEHRIPLVEGIHTFHLRTYNFDIDRTKRGTKLFMGIKDFTTFSA 180

Query: 161 IHCQASS--PIRTIDHFDVNS------------FGNLIEIRVVARSFLHTQIRSFVGSLK 206
                 +   +R++  F +                        ARSFL+ QIR  VG+L 
Sbjct: 181 KDEGKRNIRYVRSLHSFTLEETQPLMPFDPLSKHFTYWNFICSARSFLYNQIRRMVGALF 240

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEYS 247
            +G GK T  D+   LQ        P    APP GL+  +VEY 
Sbjct: 241 ALGLGKITEKDIIVMLQVPSHYNWNPHATCAPPHGLHLLNVEYD 284


>gi|94270473|ref|ZP_01291754.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
 gi|93450785|gb|EAT01835.1| tRNA pseudouridine synthase [delta proteobacterium MLMS-1]
          Length = 319

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 56/165 (33%), Positives = 84/165 (50%), Gaps = 2/165 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   + I ++G+ + GWQRQ++  +IQ ++E  +  + GE VV+HGAGRTD+GVHA   V
Sbjct: 1   MNIKLTIAFDGTAFAGWQRQRHQPTIQATLEDGLARLLGEKVVLHGAGRTDAGVHAAGMV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A F   R+         LN+ L     I IL    V   FHARFSA  + Y+Y   T   
Sbjct: 61  ASFQTARQLPLAAYRHGLNSML--PPAIRILAAREVAADFHARFSARGKIYVYGFTTAAI 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
                +  +   P S +   ++ A   L+G HDFT+F +   +  
Sbjct: 119 ISPRRRLYSAHFPGSFNPGPVQEALPGLLGEHDFTSFEAAGSRRR 163



 Score =  100 bits (249), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 24/66 (36%), Positives = 32/66 (48%)

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+   + V    FL   +R+ VG+L  +G GK T   L + L  +DR   GP AP  GL 
Sbjct: 254 GDDYYLVVAGDGFLRHMVRNLVGTLLEIGRGKRTPESLPQLLAGRDRCRAGPTAPAHGLT 313

Query: 241 FDSVEY 246
              V Y
Sbjct: 314 LWRVLY 319


>gi|288560959|ref|YP_003424445.1| tRNA pseudouridine synthase A TruA [Methanobrevibacter ruminantium
           M1]
 gi|288543669|gb|ADC47553.1| tRNA pseudouridine synthase A TruA [Methanobrevibacter ruminantium
           M1]
          Length = 290

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 64/272 (23%), Positives = 104/272 (38%), Gaps = 50/272 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +   +  +      +      AGRTD+GVH
Sbjct: 1   MKRTALKIAYIGTHFHGFQRQPDVRTVEEELIYHLRKLEYIDDLKASRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E     +  +L       D I I+  + V   F  RF A RR Y Y +
Sbjct: 61  SLGNVISFQSEKEVRVNQINNSL------PDDIQIIAWAPVRFGFKPRF-AKRRWYRYIL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                             + LD + +R  A+   G HDFT F        + +RTI+   
Sbjct: 114 ----------------FEEDLDIDLLRKTAEVFKGTHDFTNFTKRK--QKTTVRTIEDIR 155

Query: 177 V-------------------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           +                   N   + I + +   SFL   +R  +     V  GK T  D
Sbjct: 156 ITKPIIDEEDKNKKSDFAHLNKSYSPIFVDIYGESFLWNMVRKMMRIFLDVNYGKLTLDD 215

Query: 218 LEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           +E+ L  +  + +    +   E L    +EY 
Sbjct: 216 VERLLNPEEGEPRAYIKVVDAENLILMDIEYE 247


>gi|183981112|ref|YP_001849403.1| pseudouridine synthase a, TruA [Mycobacterium marinum M]
 gi|183174438|gb|ACC39548.1| pseudouridine synthase a, TruA [Mycobacterium marinum M]
          Length = 237

 Score =  180 bits (456), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/217 (29%), Positives = 103/217 (47%), Gaps = 14/217 (6%)

Query: 44  VVHGAGRTDSGVHALRQVAHFDLV------------REWVPVILCKALNAYLKISDTISI 91
            +  AGRTD+GVHA  QVAH D+             R   P  L         +   + +
Sbjct: 2   RLRAAGRTDAGVHATGQVAHADVPVDALPNAYSRSARAGDPEFLPLVRRLARFLPADLRV 61

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+++     F ARFSA+RR Y+YR+ T    +   +     + P+ LD + M +A++ L+
Sbjct: 62  LDIARAPTAFDARFSALRRHYVYRLSTAPYGVEPQQARYVTVWPRELDIDAMTVASRELL 121

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
           G H+F  F     + ++ IR +   D +  G+L+  +V A +F  + +RS VG+L  VG+
Sbjct: 122 GLHNFAAFCRRR-EGATTIRDLQRLDWSRNGHLVTAQVSADAFCWSMVRSLVGALLAVGE 180

Query: 211 GKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + T     + L A  R      AP  GL    V+Y 
Sbjct: 181 HRRTPDWCRELLTATARSSDFAAAPAHGLVLAKVDYP 217


>gi|328783921|ref|XP_001121186.2| PREDICTED: tRNA pseudouridine synthase-like 1-like [Apis mellifera]
          Length = 313

 Score =  180 bits (456), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 75/285 (26%), Positives = 118/285 (41%), Gaps = 39/285 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTGEIVV---VHGAG 49
           M RY +   Y G+ Y G Q+         ++  +IQG++E A   +  + +    +  + 
Sbjct: 1   MTRYLIKFSYLGTQYRGMQKNVIQTENVIRDIDTIQGALETAFTTLIPKCIEWPKITCSS 60

Query: 50  RTDSGVHALRQVAHFDL----VREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHAR 104
           RTD GVH++  +AH D+       + P    K +N Y       I +L    V K FH R
Sbjct: 61  RTDIGVHSMCNLAHIDIKNKYDSIYYPNDTLKYVNRYFFDCHHNIRLLEFIPVKKTFHVR 120

Query: 105 FSAIRRSYLYRIITRQAPLAL-----EKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTF 158
                R+YLYR    +          E  R + I   + D E ++ A Q  +G  DF TF
Sbjct: 121 KFIHSRTYLYRFSVTKNKDEHRIPITEINRCFHIRSDTFDLERIKRATQLFIGTKDFRTF 180

Query: 159 RS--IHCQASSPIRTIDHFDVN------------SFGNLIEIRVVARSFLHTQIRSFVGS 204
            +  +  +  + +R ++   +                    I   +R FL+ Q+R  VG+
Sbjct: 181 SAKIVGNKPINYVRNLNSLTIEKGYPLMPNDPLSQNFEYWNIICSSRGFLYKQVRRIVGA 240

Query: 205 LKLVGDGKWTSTDLEKALQAQ---DRKECGPLAPPEGLYFDSVEY 246
           L  +G GK T  D+   LQ     +       AP  GLY  +VEY
Sbjct: 241 LFALGSGKITEKDITVMLQVPGCHNYLSQIETAPAYGLYLMNVEY 285


>gi|317180826|dbj|BAJ58612.1| tRNA pseudouridine synthase A [Helicobacter pylori F32]
          Length = 242

 Score =  180 bits (456), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFCTPKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P RTI +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRTIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +V+  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKVIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|305666822|ref|YP_003863109.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
 gi|88709046|gb|EAR01280.1| tRNA pseudouridine synthase A [Maribacter sp. HTCC2170]
          Length = 282

 Score =  180 bits (456), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 99/253 (39%), Gaps = 13/253 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G  + GWQ+Q    +++G I K + F++      +  AGRTDS V AL    
Sbjct: 30  YVIKLQYLGFRFSGWQKQPGQKTVEGMITKTLKFILPNSEFKILSAGRTDSKVSALDAAF 89

Query: 63  HFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              +              N  L     I ++++  V++ F+       + Y+Y       
Sbjct: 90  ELFINEPLTDFEAFIGLFNKNL--PSDIRVMSIKEVNEDFNIIQDPKVKEYVYLFSYGSK 147

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
                      +   LD E M+ AA   VG HD + +       +   RTI   ++    
Sbjct: 148 NHPYSSPFITNVLDELDLELMKKAASLYVGTHDLSVYTVKAQNNAHKKRTITSCEIIENK 207

Query: 181 --------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                         RV    F+  QIR  +G+L  +G G+    D+E +L   +  E   
Sbjct: 208 ILQANFFPEKSYAFRVEGPGFMRYQIRMMMGALIQLGKGELLFADIENSLSNPESIELTY 267

Query: 233 LAPPEGLYFDSVE 245
           +AP  GL  + ++
Sbjct: 268 VAPGSGLLLNRLD 280


>gi|154148265|ref|YP_001406534.1| tRNA pseudouridine synthase A [Campylobacter hominis ATCC BAA-381]
 gi|153804274|gb|ABS51281.1| tRNA pseudouridine synthase A [Campylobacter hominis ATCC BAA-381]
          Length = 278

 Score =  180 bits (456), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 64/279 (22%), Positives = 103/279 (36%), Gaps = 41/279 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  +I  ++GS + G Q Q NG +++  +  A+F   G    V  A RTD GVHAL QV+
Sbjct: 6   KIRLIYSFDGSKFCGSQTQPNGKAVEDRLNSALFR-CGINEKVISASRTDKGVHALSQVS 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                  W    L   +N +     +I +  +   D+ F  RF A  RSY Y I+     
Sbjct: 65  TTHCAAFWDLQNLRHFINRH--AKPSIYVRKIERADENFQVRFDAKARSYRY-ILNHDEF 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                   +  P+ +    + ++    VG+HDF+ F      + S +R I       + N
Sbjct: 122 SPFFSNYFYFYPE-ISPFLLNLSLGIFVGKHDFSEFMKSGSASGS-VREIYKAFAYRYKN 179

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGD------GKWTSTDLE------------KALQA 224
              I   A  FL  Q+R  V +                  ++             + L+ 
Sbjct: 180 FTIINFKANGFLRAQVRLMVANALKCVKILEKSFSNKKIDEISNFYKNNKNLKFNEILKN 239

Query: 225 QD-----------------RKECGPLAPPEGLYFDSVEY 246
           +D                 +      APP GLY + + Y
Sbjct: 240 KDFNIEKIINDNNFPLNINKAITRIPAPPNGLYLNKIWY 278


>gi|91217701|ref|ZP_01254658.1| tRNA pseudouridine synthase A [Psychroflexus torquis ATCC 700755]
 gi|91184205|gb|EAS70591.1| tRNA pseudouridine synthase A [Psychroflexus torquis ATCC 700755]
          Length = 261

 Score =  179 bits (455), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 55/252 (21%), Positives = 99/252 (39%), Gaps = 13/252 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G  Y GWQ+Q +  +++  + K + F++  +   V  AGRTD+ V A +   
Sbjct: 8   YLIQLQYLGFRYHGWQKQPDVLTVEHMLHKTLNFILENQRFKVLAAGRTDAMVSANQTYI 67

Query: 63  H-FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F    E       +  N  L     I  L++      F+       + Y Y    ++ 
Sbjct: 68  ELFIYEDELDLETFLEQFNKNL--PQDIRALSIEETTADFNIIQHPKIKEYFYFFCVKEK 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                      + + LD E M++ A+   G HDF +F       +     I+  ++    
Sbjct: 126 MHPFCAPFMVNLQEDLDIELMKLGAKLFEGEHDFYSFTFRPNPETKTEGNIERCELTEND 185

Query: 182 ---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                        ++VV   F   QIR  +G+L  +G  K +  +LEK +    + +   
Sbjct: 186 IYTANFFPNQSFVLKVVGEGFKRQQIRLMMGALIDLGRHKISLEELEKTIDGSHKIKLEH 245

Query: 233 LAPPEGLYFDSV 244
           +A   GL  + V
Sbjct: 246 IAQASGLILNKV 257


>gi|298208691|ref|YP_003716870.1| tRNA pseudouridine synthase A [Croceibacter atlanticus HTCC2559]
 gi|83848614|gb|EAP86483.1| tRNA pseudouridine synthase A [Croceibacter atlanticus HTCC2559]
          Length = 266

 Score =  179 bits (455), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 55/252 (21%), Positives = 100/252 (39%), Gaps = 13/252 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVA 62
           Y + ++Y G  + GWQ+Q + ++++  +E+ +  V G +   +  +GRTD+ V       
Sbjct: 14  YIIQLQYLGFRFHGWQKQPDVNTVERMVERTLAYVLGHKKFKLLASGRTDAKVSVNNTFV 73

Query: 63  H-FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
             F   +        K  N  L     I  L++   D  F+       + Y+Y     + 
Sbjct: 74  ELFIDDKPLEVDSFFKDFNVNL--PQDIKALSIKETDANFNIIQHPKLKEYIYLFTYGEK 131

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF- 180
                        K L+ E M+ AA    G HDF  +     + +  I  ID  +++   
Sbjct: 132 MHPFCAPYMVCYNKPLNIELMQEAAALFQGEHDFKNYTYKPTEDTQTIGVIDACELSENT 191

Query: 181 --------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                        ++VV + F   QIR  +G+L  +G G++     +K L + +  +   
Sbjct: 192 VYTANFFPEKSYMLKVVGQGFKRHQIRLMMGALFDLGSGEFDMQFFKKTLTSTEFIKLTH 251

Query: 233 LAPPEGLYFDSV 244
           +A   GL   SV
Sbjct: 252 IAQASGLILQSV 263


>gi|195170621|ref|XP_002026110.1| GL16086 [Drosophila persimilis]
 gi|194110990|gb|EDW33033.1| GL16086 [Drosophila persimilis]
          Length = 504

 Score =  179 bits (454), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 81/297 (27%), Positives = 121/297 (40%), Gaps = 56/297 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTINKLEPQSLDTNSVQGCLELALRVFHPTNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    L   LN  L      I +L+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLARRDGQPYDTTTLTGVLNRTLDKQRLPIRVLSSQVVPDTFHCRYH 120

Query: 107 AIRRSYLYRIITRQAP----------------LALEKGRAWLI-PKSLDCENMRIAAQHL 149
           AI R+YLYR    + P                   E  R + +   + D E +R AA+  
Sbjct: 121 AIGRTYLYRFAVARKPLFDDGKLRNKGFEAFVPVEEIDRCYFLLAPTFDIERIRNAARMF 180

Query: 150 VGRHDFTTFRSIHCQAS-------SPIRTIDHFDVN---------------SFGNLIEIR 187
           +G HDF TF S+  Q S         +R ID  ++                   +  +I 
Sbjct: 181 IGVHDFRTFMSVSRQKSLSRDHPMFTLRKIDEINIRPGRTLALPSNATLAAETYDYWDIE 240

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC---GPLAPPEGLYF 241
           + A+SFL+ Q+R  VGSL  +G  +     + + L    +         AP  GLY 
Sbjct: 241 IKAKSFLYKQVRRIVGSLLSLGSDRIDEKCIYQMLTIPSKHSWDSRVVPAPACGLYL 297


>gi|15644989|ref|NP_207159.1| tRNA pseudouridine synthase A [Helicobacter pylori 26695]
 gi|2499078|sp|P56144|TRUA_HELPY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|2313463|gb|AAD07429.1| pseudouridylate synthase I (hisT) [Helicobacter pylori 26695]
          Length = 242

 Score =  179 bits (454), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIEDALNALGIKSV-VIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P RTI +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRTIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|261839825|gb|ACX99590.1| pseudo uridylate synthase I [Helicobacter pylori 52]
          Length = 242

 Score =  179 bits (454), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWNAAKLFYHLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P RTI +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRTIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  V +       K T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAEIQAQIHNAKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|198462560|ref|XP_001352470.2| GA20054 [Drosophila pseudoobscura pseudoobscura]
 gi|198150878|gb|EAL29967.2| GA20054 [Drosophila pseudoobscura pseudoobscura]
          Length = 504

 Score =  179 bits (454), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 81/297 (27%), Positives = 121/297 (40%), Gaps = 56/297 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTINKLEPQSLDTNSVQGCLELALRVFHPTNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    L   LN  L      I +L+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLARRDGQPYDTTTLTGVLNRTLDKQRLPIRVLSSQVVPDTFHCRYH 120

Query: 107 AIRRSYLYRIITRQAP----------------LALEKGRAWLI-PKSLDCENMRIAAQHL 149
           AI R+YLYR    + P                   E  R + +   + D E +R AA+  
Sbjct: 121 AIGRTYLYRFAVARRPLFDDGKLRNKGFEAFVPVEEIDRCYFLLAPTFDIERIRNAARMF 180

Query: 150 VGRHDFTTFRSIHCQAS-------SPIRTIDHFDVN---------------SFGNLIEIR 187
           +G HDF TF S+  Q S         +R ID  ++                   +  +I 
Sbjct: 181 IGVHDFRTFMSVSRQKSLSRDHPMFTLRKIDEINIRPGRTLALPSNATLAAETYDYWDIE 240

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC---GPLAPPEGLYF 241
           + A+SFL+ Q+R  VGSL  +G  +     + + L    +         AP  GLY 
Sbjct: 241 IKAKSFLYKQVRRIVGSLLSLGSDRIDEKCIYQMLTIPSKHSWDSRVVPAPACGLYL 297


>gi|163788523|ref|ZP_02182969.1| tRNA pseudouridine synthase A [Flavobacteriales bacterium ALC-1]
 gi|159876843|gb|EDP70901.1| tRNA pseudouridine synthase A [Flavobacteriales bacterium ALC-1]
          Length = 261

 Score =  179 bits (454), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 99/256 (38%), Gaps = 14/256 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHAL--RQ 60
           Y + I+Y G  + GWQ+Q +  +I   I++ +  +  ++     GAGRTD+ V A     
Sbjct: 8   YLIKIQYLGYRFHGWQKQPDVKTIHLMIDRTLKFILKDVRFKTLGAGRTDAMVSANEAAL 67

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                           K  N  L     I  L++S VDK F+    +  + Y Y     +
Sbjct: 68  ELFIYNEPITDFEAFLKLFNHNL--PQDIRALSISEVDKAFNIIQDSKIKEYHYVFSEGE 125

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                       I + LD E M+  A+   G H+F T+           RTI+  ++   
Sbjct: 126 KNHPFCAPILTTILEPLDVELMKKGAKLFEGSHNFKTYCYRATDKGEYFRTIESSEIIDN 185

Query: 181 ---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                          +V  + F+  QIR   G L  +G G+ T   +E  L+    +   
Sbjct: 186 SLYTANFFPEQSYVFKVRGKGFMRNQIRLMFGCLIKLGRGEVTLQYIENTLKHDSTEVMD 245

Query: 232 PLAPPEGLYFDSVEYS 247
            +AP  GL   S+++ 
Sbjct: 246 YIAPASGLILHSIDFE 261


>gi|32266100|ref|NP_860132.1| tRNA pseudouridine synthase A [Helicobacter hepaticus ATCC 51449]
 gi|42559757|sp|Q7U328|TRUA_HELHP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|32262149|gb|AAP77198.1| tRNA pseudouridine synthase [Helicobacter hepaticus ATCC 51449]
          Length = 248

 Score =  178 bits (453), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 75/253 (29%), Positives = 109/253 (43%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M  Y  +I Y+GS + G+  QK+    S+ G++++    V G    + GAGRTD GVHA 
Sbjct: 1   MPTYKAVIAYDGSVFSGFALQKDKRLKSVLGTLKEGFARV-GIKSDIIGAGRTDKGVHAT 59

Query: 59  RQVAHFDLVREWVP-----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            QV  F               L   LNA L     I + +L IVD  FH RF A+ RSY 
Sbjct: 60  GQVICFQSAHFLDSQVQAIESLRFLLNAKLYPH--IMVRSLHIVDDTFHPRFDALWRSYR 117

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           + +   Q P            K  D    + A Q   G+H+F  F+       + IRTI 
Sbjct: 118 FLLSPTQ-PSPFAAPYVS-YEKIGDETLFKNALQAFQGQHNFVFFKKNGSYTKNCIRTIF 175

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                ++  L  + V    FL  Q+R  VG+       + +   L++ +  Q +    P+
Sbjct: 176 AIKHYTYKGLDIVYVRGNGFLRAQVRLMVGAALAYSRAELSFHSLQEQINGQKQHYTYPI 235

Query: 234 APPEGLYFDSVEY 246
           +P  GLY   V Y
Sbjct: 236 SP-NGLYLCEVGY 247


>gi|323455279|gb|EGB11148.1| hypothetical protein AURANDRAFT_21872 [Aureococcus anophagefferens]
          Length = 264

 Score =  178 bits (453), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 66/267 (24%), Positives = 102/267 (38%), Gaps = 28/267 (10%)

Query: 2   IRYCMI--IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +R  ++  ++Y G  + GWQ Q N  S+      A+            AGRTD GV+A  
Sbjct: 1   MRSKLVFELQYLGDAFAGWQPQPNERSVHDVFAAALSNAGITDCGAVAAGRTDRGVNAAH 60

Query: 60  QVAHFDLVREWVPVILCKALN-AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QV       +     L   L      +   + +L+       FHA  SA  + Y Y +  
Sbjct: 61  QVVSVRSDADRGDEDLSAVLRDVSAALPGDVRVLSCRQAPASFHAITSARSKRYAYYLGF 120

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDV 177
            +         +W  P  LD   +R  A  LVG  DF  F +   +   S +R++   ++
Sbjct: 121 SEDA----ARYSWQAPPGLDVGRVRRGAALLVGERDFRAFCAPGGRKCGSTVRSLRSVEI 176

Query: 178 N-----------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           +               L+ I      FL  Q R  VG+L  +G G  +   +E AL   D
Sbjct: 177 DDLETAELPFVGRVRGLLRIAFDGDGFLKHQCRKIVGALVRLGTGALSEAQVEAALA--D 234

Query: 227 RKECGP-------LAPPEGLYFDSVEY 246
            +   P        AP  GL+ + V+Y
Sbjct: 235 PRGAHPAVSSRRFAAPARGLWLERVDY 261


>gi|323454991|gb|EGB10860.1| hypothetical protein AURANDRAFT_58785 [Aureococcus anophagefferens]
          Length = 305

 Score =  178 bits (453), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 106/273 (38%), Gaps = 29/273 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
            RY + + Y+G+ + GWQ Q  G  ++QG +  A+     G  +   GA RTD+GVHA  
Sbjct: 33  TRYALRVAYDGTRFKGWQVQPGGARTVQGELNAALRTRFGGADIPTLGASRTDAGVHARG 92

Query: 60  QVAHFDLVREW----VPVILCKALNAYLKISDTISILNLSIVDK----------QFHARF 105
           Q AH DL           +L   +N  L   D   + +L                +HA  
Sbjct: 93  QCAHADLPVAPLGGAPLELLEHQINRLL--PDDARVHDLRPAPAPKPWQAREGLPWHAIA 150

Query: 106 SAIRRSYLYRIITRQ-APLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRS--- 160
           +A  + Y YR+  R+ +   L +     +  + +D   +  A    VG HDF  F +   
Sbjct: 151 NAAGKRYAYRLTARRGSADPLGRLYRGHVAYRDVDFGRLDDALSCFVGEHDFAAFANNAP 210

Query: 161 ---IHCQASSPIRTIDHFD-VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                  A S  R I     ++  G    +       L+  +R+ VG+   V DG     
Sbjct: 211 GLDPSGAARSTTRAIRSATLLDEGGGDATLTFELDGALYKMVRNVVGAAVAVADGALPRD 270

Query: 217 DLEKALQAQDRKECGP--LAPPEGLYFDSVEYS 247
            +   L    R+   P   AP  GL  + V Y 
Sbjct: 271 AIPALLAPGARRADNPAKAAPACGLCLEEVYYD 303


>gi|110004220|emb|CAK98558.1| hypothetical trna pseudouridine synthase a protein [Spiroplasma
           citri]
          Length = 246

 Score =  178 bits (452), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 109/249 (43%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+   + IEY+G  Y GW +QKN  +IQG +EKA F +  + +   GA +TD+GVHA  Q
Sbjct: 1   MLYLLLSIEYDGYDYSGWVKQKNAWTIQGELEKAFFGICHQKIWTLGASKTDAGVHASDQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                L  +   ++      +   +   I+I    +V + F  R +A  + Y+Y I   Q
Sbjct: 61  KVLVKLPFQSQHLVFFIKTVSK-TLPPNINIKGYQLVSENFSVR-TAKVKEYVYTI-NDQ 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVNS 179
                       +   L+   +   +Q  VG HDF  F  +   +     RTI+   V  
Sbjct: 118 EYDLFNHRYELKVNTPLNVRKLHQISQIFVGTHDFGYFAGVKPTENIVTQRTINKIWVKR 177

Query: 180 FG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE-CGPLAPPE 237
                IEI  + +SF+  QIR    ++     GK + ++L+  L+   +       A P 
Sbjct: 178 NKAKKIEIHFMGKSFIRYQIRMLTQNILACYAGKVSLSELQAQLKHPPQGATTKYCAKPY 237

Query: 238 GLYFDSVEY 246
           GL    ++Y
Sbjct: 238 GLCLKKIKY 246


>gi|153792349|ref|NP_001093370.1| pseudouridylate synthase 3 [Xenopus laevis]
 gi|148745611|gb|AAI42593.1| LOC100101318 protein [Xenopus laevis]
          Length = 507

 Score =  178 bits (451), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 65/265 (24%), Positives = 99/265 (37%), Gaps = 39/265 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G GY G+  Q+N  ++++ ++  A+       + +    H  GRTD GV AL
Sbjct: 61  VALRLAYLGWGYQGFASQENTKNTVEETVFNALLKTRLVESRQTSNYHRCGRTDRGVSAL 120

Query: 59  RQVAHF---DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QV              +     LN  L     I +L+ + V   F ARFS   R+Y Y 
Sbjct: 121 AQVISLDLRCSAEGKPEIRYVHILNRVL--PPDIRVLSWAPVPPSFSARFSCGSRTYRYL 178

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTID 173
               Q                LD E M  AA+ L G HDF     +       +  RT+ 
Sbjct: 179 FPCAQ----------------LDVEAMDKAARLLEGTHDFRNLCKMDVANGVLNFTRTVL 222

Query: 174 HFDVNSFGN---------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ- 223
              V              L  +++   +FL+ Q+R  +G L LVG GK     + + L  
Sbjct: 223 SARVGPVPEIPGDMGPFQLYHLQITGLAFLYHQVRCIMGVLFLVGQGKEKPEVITELLDV 282

Query: 224 -AQDRKECGPLAPPEGLYFDSVEYS 247
               RK    +A    L   +  + 
Sbjct: 283 VKNPRKPQYNMAVEFPLVLYNCHFD 307


>gi|42559721|sp|P60353|TRUA_SPIKU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|34849384|gb|AAP58883.1| tRNA pseudouridine synthase [Spiroplasma kunkelii CR2-3x]
          Length = 260

 Score =  178 bits (451), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 107/250 (42%), Gaps = 8/250 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+   + IEY+G  Y GW +QKN  +IQG +EKA F +  + +   GA +TD+GVHA  Q
Sbjct: 1   MLYLLLSIEYDGYDYSGWVKQKNARTIQGELEKAFFGICHQKIWTLGASKTDAGVHACDQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                L   + P  L   +    + +   I+I     V + F  R +   + Y+Y I   
Sbjct: 61  KVLVKLT--FQPRHLAFFIKTVSQTLPPNINIKGYQFVAENFSVR-TVKVKEYVYTI-ND 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVN 178
           Q            +   L+ + +   +Q  VG HDF  F  +   +  + + TI+   V 
Sbjct: 117 QEYDLFNHRYELKVNAPLNVKKLHQISQIFVGTHDFAYFAGVKPTEDIATVHTINKIWVK 176

Query: 179 SFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPP 236
                 IEI    + F+  QIR    ++     GK + T+L+  L    +       A P
Sbjct: 177 RNKAKKIEIHFRGKIFIRYQIRMLTQNILACYAGKVSLTELQAQLNCPPKGTTTKYCAKP 236

Query: 237 EGLYFDSVEY 246
            GL    ++Y
Sbjct: 237 YGLCLKKIKY 246


>gi|217032587|ref|ZP_03438076.1| hypothetical protein HPB128_159g13 [Helicobacter pylori B128]
 gi|298735906|ref|YP_003728431.1| tRNA pseudouridine synthase A [Helicobacter pylori B8]
 gi|216945723|gb|EEC24348.1| hypothetical protein HPB128_159g13 [Helicobacter pylori B128]
 gi|298355095|emb|CBI65967.1| tRNA pseudouridine synthase A [Helicobacter pylori B8]
          Length = 242

 Score =  178 bits (451), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + I Y+G+ + G+ +Q N   +Q  IE A+  + G   VV  AGRTD GVHA  Q
Sbjct: 1   MRCFKVTIAYDGAYFLGYAKQPNKLGVQDKIESAL-NMLGIKSVVVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWNAAKLFYCLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  ++E  +         P+   
Sbjct: 174 SIMGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|291234813|ref|XP_002737344.1| PREDICTED: MGC80334 protein-like [Saccoglossus kowalevskii]
          Length = 520

 Score =  177 bits (450), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 100/231 (43%), Gaps = 31/231 (13%)

Query: 1   MIRYCMIIEYNGSGYFGW-QRQKNGSSIQGSIEKAIFLV-TGEIVVVHGAGRTDSGVHAL 58
           M RY + I Y G+ + G  Q      ++Q  IE A+  +   E   ++ + RTD+GVHAL
Sbjct: 1   MCRYLLYISYLGTNFRGVVQTNSTSPTVQRVIEGALHTLKPQEAAKLYFSSRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKAL------NAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
              AH D VR          +      N  L     I I ++  V  +FHARF A  R+Y
Sbjct: 61  NNTAHVDFVRRNNQQPFSGEVLKTILNNKLLIAQQDIRINDVKKVPDEFHARFQAKGRTY 120

Query: 113 LYRIITR-----QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-- 165
           +YRI +            E  R W++   LD E M+ A +  +G HDF  FRS + +   
Sbjct: 121 VYRIASNWNCALNHIPLFENHRCWMVSYRLDIEKMKQACEVFIGTHDFAAFRSKNNKNVH 180

Query: 166 SSPIRTIDHFDVNSFG---------------NLIEIRVVARSFLHTQIRSF 201
            S +RTID  ++                      EI   A+SFL+ Q R  
Sbjct: 181 KSTVRTIDSINIRKSHGILQHLSPCETDARIEYYEIEFKAKSFLYKQ-RCI 230


>gi|313229675|emb|CBY18490.1| unnamed protein product [Oikopleura dioica]
          Length = 402

 Score =  177 bits (450), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 101/267 (37%), Gaps = 37/267 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSG 54
            +  +   Y+G+ Y G QR       ++I+  I  AI                 GRTD G
Sbjct: 65  RKIALRFSYDGTKYNGLQRSPVPAGKTTIEDVIFDAILRTKVVDDIGTADYIAGGRTDKG 124

Query: 55  VHALRQVAHFDLVREWVPVILCKALNA---------YLKISDTISILNLSIVDKQFHARF 105
           VHA+  V    +        + + +             ++ D I I + + +   F ARF
Sbjct: 125 VHAVNNVISLFVNSRLSEDEINENVTVGERNFVAIINRQLPDDIWITSWAPISFDFSARF 184

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           S   R Y Y   +                  LD E M+ AA +L+G HDF  F     + 
Sbjct: 185 SCKSRHYNYIFDSS----------------GLDVELMKEAASYLIGEHDFRNFSQAQLER 228

Query: 166 SSPIRTIDHFDVNSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
            + +R     D+    N   +    + A  FL+ QIR  +  L LVG+    ST +++ L
Sbjct: 229 QNTVRVCFAADIKQVPNMSSMCVFSIKASGFLYHQIRLTMAILALVGNKLEKSTIVKELL 288

Query: 223 QAQD--RKECGPLAPPEGLYFDSVEYS 247
             +   R+     A P+GL     EY 
Sbjct: 289 DVEKYPRRPSYKYANPDGLVLIDCEYE 315


>gi|67484392|ref|XP_657416.1| pseudouridine synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56474668|gb|EAL52030.1| pseudouridine synthase, putative [Entamoeba histolytica HM-1:IMSS]
          Length = 366

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/274 (23%), Positives = 97/274 (35%), Gaps = 49/274 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQK-------------NGSSIQGSIEKAIFLV----TGEIVVVH 46
             + + Y G  Y G Q                N  +I+  + KA+F        +    +
Sbjct: 38  IAIRLTYIGIDYNGIQCTLLNDVTDATFDSVINDGTIEYQLFKALFKTRLIQNTKDCKYN 97

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVIL-----------CKALNAYLKISDTISILNLS 95
             GRTD GV A  QV    +        +           C+ LN  L     I  L   
Sbjct: 98  RCGRTDKGVSAFGQVVDLWVRSNLKDETILYTKREGELDYCRMLNGLL--PTDIRCLGWC 155

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            V   F++RFS   R+Y Y                +  P S D   M+ AAQ  +G HDF
Sbjct: 156 GVPDDFNSRFSCQSRTYHY----------------YFDPSSYDVPKMKEAAQLFLGEHDF 199

Query: 156 TTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           T F       S  +R ++ F+V     L    V   +F+  Q+R  VG+L  +G G    
Sbjct: 200 TNFCKKDPAVSHCVRRVNSFEVEETDGLSRFVVCGTAFVWHQVRYMVGALFAIGQG-ANP 258

Query: 216 TDLEKALQAQDRKECG--PLAPPEGLYFDSVEYS 247
             +++ L  +   +      AP   L     +Y 
Sbjct: 259 ESIKQLLDVEHYTKPNYFKYAPAYPLVLYECKYD 292


>gi|300782641|ref|YP_003762932.1| tRNA pseudouridine synthase A [Amycolatopsis mediterranei U32]
 gi|299792155|gb|ADJ42530.1| tRNA pseudouridine synthase A [Amycolatopsis mediterranei U32]
          Length = 238

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/221 (31%), Positives = 98/221 (44%), Gaps = 18/221 (8%)

Query: 42  IVVVHGAGRTDSGVHALRQVAHFDLVREWV-------------PVILCKALNAYLKISDT 88
              V  AGRTD+GVHA  QV H D+V                 P +   A      +   
Sbjct: 2   PKSVVVAGRTDAGVHATGQVVHVDVVPLAPGSAGRVPVFAEGIPDLTRMAGRWNRLLPGD 61

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQ 147
           + +L   I  + F ARFSA+RR Y YR+         L +       + L  + M  AA 
Sbjct: 62  VRVLGARIAPEGFDARFSAVRRHYRYRVSDAPWGVDPLRRHDTLAWNRPLSTDAMNAAAA 121

Query: 148 HLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLK 206
            L+G HDF  +     +  + IR +   +      +L+E+RV A +F H+ +RS VG L 
Sbjct: 122 ELLGLHDFAAYCKQR-ETGTTIRELQRLEWTRVDEHLLEVRVSADAFCHSMVRSLVGVLL 180

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           LVGDG+ T     K L++  R     +AP  GL    V+Y 
Sbjct: 181 LVGDGRRTDAWPAKVLESGIRDSA--VAPAHGLTLLGVDYP 219


>gi|217034467|ref|ZP_03439879.1| hypothetical protein HP9810_890g12 [Helicobacter pylori 98-10]
 gi|216943069|gb|EEC22546.1| hypothetical protein HP9810_890g12 [Helicobacter pylori 98-10]
          Length = 242

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 105/250 (42%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N  S+Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLSVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFCAQKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGAMTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +      GK T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKIIGDAFLRSSVRLIIQACVQYSLGKITLAEIQAQIHNIKAAIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|313125232|ref|YP_004035496.1| pseudouridylate synthase i [Halogeometricum borinquense DSM 11551]
 gi|312291597|gb|ADQ66057.1| pseudouridylate synthase I [Halogeometricum borinquense DSM 11551]
          Length = 272

 Score =  177 bits (449), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/254 (25%), Positives = 106/254 (41%), Gaps = 35/254 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSGV 55
           +R    I Y+G  ++G+QRQ +  +++ SI  A+  +        +      AGRTD+GV
Sbjct: 1   MR-AFRIAYDGRPFYGFQRQPSVPTVEDSIFDALRSLGVLDEDARKPTGYAAAGRTDAGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            AL Q   FD      P    +A+NA L   +++     + V ++FHA   A RR+Y+Y 
Sbjct: 60  SALAQTVAFDCPEWCTP----RAMNAEL--PESVRAWAAADVGERFHATHDAARRAYVYD 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +   +A                D    + AA  L G HD   F ++    +  +R +   
Sbjct: 114 LYAPEA----------------DESKAQAAADALTGEHD---FHNLTPDDTGTVRDVT-V 153

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPL 233
            V + G  + + V A  F +  +R     +  V  G     D+E  L  +     E  P 
Sbjct: 154 SVEADGEFLVLSVAAGGFPYNLVRRLASIVHSVATGDRPLADIETVLGPETVPGPEGVPT 213

Query: 234 APPEGLYFDSVEYS 247
           AP E L  + V Y 
Sbjct: 214 APAEPLVLERVVYP 227


>gi|109947020|ref|YP_664248.1| tRNA pseudouridine synthase A [Helicobacter acinonychis str.
           Sheeba]
 gi|122973397|sp|Q17YM7|TRUA_HELAH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|109714241|emb|CAJ99249.1| pseudouridylate synthase I [Helicobacter acinonychis str. Sheeba]
          Length = 242

 Score =  177 bits (449), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 107/250 (42%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q +   +Q  IE A+ L+  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPDKLGVQDKIESALNLLGIKSV-VIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAQKHWSADKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKSL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
               L    A     SLD  ++  A +  +G+HDF+ F+     A++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--SLNTALKQFIGKHDFSMFKKEGGAATNPKRIIFNAFAYKA 173

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 SIMGHECVVFKIIGDAFLRSSVRLIMQACVQYSLEKITLAEIKTQINNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVHY 242


>gi|312892438|ref|ZP_07751932.1| tRNA pseudouridine synthase A [Mucilaginibacter paludis DSM 18603]
 gi|311295072|gb|EFQ72247.1| tRNA pseudouridine synthase A [Mucilaginibacter paludis DSM 18603]
          Length = 358

 Score =  176 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 46/172 (26%), Positives = 76/172 (44%), Gaps = 4/172 (2%)

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK 135
            ++LNA L     I++  +  V    HARF A  RSY Y +   +         +W +  
Sbjct: 189 TRSLNALL--PHDIAVKRIIPVHADAHARFDATLRSYEYHVHFEK--DPFLNNLSWQLRD 244

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
             D   M  AAQ ++   DF+ F   + Q  +    I   +  S G+ +   + A  FL 
Sbjct: 245 RPDVGLMNQAAQIVMEYTDFSCFSKSNTQVKTNNCKISRAEWVSNGDKLIFHISADRFLR 304

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +R+ VG+L +VG G     ++ + +++++R   G   P  GLY   V Y 
Sbjct: 305 NMVRAIVGTLMMVGKGDIKPEEVRRIIESKNRSNAGVSVPACGLYLTEVRYP 356



 Score = 98.4 bits (244), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 42/71 (59%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+G+ Y GWQ Q N  S+Q  + KA+  +    V   G GRTD+GVHA +  
Sbjct: 5  QRYFIELAYDGTNYHGWQIQHNAISVQQVLNKALSTLLRMPVETLGCGRTDTGVHAKQLY 64

Query: 62 AHFDLVREWVP 72
          AHFD+ R+  P
Sbjct: 65 AHFDIGRQEQP 75


>gi|224102643|ref|XP_002312761.1| predicted protein [Populus trichocarpa]
 gi|222852581|gb|EEE90128.1| predicted protein [Populus trichocarpa]
          Length = 232

 Score =  176 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/176 (34%), Positives = 92/176 (52%), Gaps = 8/176 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ ++I Y+G+ Y GWQ Q+   +IQ  +EKA+   T    + + + GA RTD GVHA  
Sbjct: 58  KWRLLISYDGTHYKGWQFQQTPPTIQCILEKALTRATKLERKDLHLVGASRTDGGVHAWG 117

Query: 60  QVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +     +  ALN  L     I +  +S V  +FHARFSA  ++Y Y+I  
Sbjct: 118 QVAHFVTPFNYDSLDSIHAALNGLL--PPDIRVREISAVVPEFHARFSAKGKTYHYKIFN 175

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSPIRTI 172
                  ++  A+ +   L+   MR AA H +G  DF+ F   S +    +P++TI
Sbjct: 176 DTVMDPFQRLYAYHVTHKLNAAVMREAANHFIGTRDFSAFVNSSRNDGVPNPVKTI 231


>gi|167377399|ref|XP_001734387.1| tRNA pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165904128|gb|EDR29463.1| tRNA pseudouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 366

 Score =  176 bits (447), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/274 (23%), Positives = 96/274 (35%), Gaps = 49/274 (17%)

Query: 4   YCMIIEYNGSGYFGWQ-------------RQKNGSSIQGSIEKAIFLV----TGEIVVVH 46
             + + Y G  Y G Q                N  +I+  + KA+F        +    +
Sbjct: 38  IAIHLTYIGIDYNGIQCTLLNDVTDSTFDSVVNDGTIEYQLFKALFKTRLIQNTKDCKYN 97

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVIL-----------CKALNAYLKISDTISILNLS 95
             GRTD GV A  QV    +        +           C+ LN  L     I  L   
Sbjct: 98  RCGRTDKGVSAFGQVVDLWVRSNLKDETILYTKREGELDYCRMLNGLL--PIDIRCLGWC 155

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            V   F++RFS   R+Y Y                +  P S D   M+ AAQ  +G HDF
Sbjct: 156 GVPDDFNSRFSCQSRTYHY----------------YFDPSSYDVPKMKEAAQLFLGEHDF 199

Query: 156 TTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
           T F          IR ++ F+V     L    V   +F+  Q+R  VG+L  +G G    
Sbjct: 200 TNFCKKDPAVPHCIRRVNSFEVEEINGLSRFVVCGTAFVWHQVRYMVGALFAIGQG-ANP 258

Query: 216 TDLEKALQAQDRKECG--PLAPPEGLYFDSVEYS 247
             +++ L  +   +      AP   L     +Y 
Sbjct: 259 ESIKQLLDVEHYTKPNYFKYAPAYPLVLYECKYD 292


>gi|146093784|ref|XP_001467003.1| pseudouridine synthase A-like protein [Leishmania infantum JPCM5]
 gi|134071367|emb|CAM70054.1| putative pseudouridine synthase A-like protein [Leishmania infantum
           JPCM5]
          Length = 499

 Score =  176 bits (446), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 109/264 (41%), Gaps = 36/264 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  + G  +QK   ++++G +  A+  +              GRTD GV 
Sbjct: 60  RKIALRLAYHGHVHDGLAKQKETDNTVEGLVCDALRRLRLIPEDGPHNFGRCGRTDKGVS 119

Query: 57  ALRQ--------VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL              D   +  P+  C  LN  L    TI I+  ++VD  F ARFS +
Sbjct: 120 ALGNALSLTARASCTADAEPQLPPLDYCSMLNNVL--PSTIRIVGCALVDDTFDARFSCV 177

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
            R+Y Y                +   + L+ E M+ AA   +G H+F  F  +     S+
Sbjct: 178 HRTYRY----------------YFFHRGLNLEAMQEAAAFFLGTHNFRNFCKMDVVNVSN 221

Query: 168 PIRTIDHFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +RT+    ++    L E+     + A SFL+ QIR  +  L LVG G    + ++  L+
Sbjct: 222 FVRTVFSVGLHPSEALPELISYLEIRANSFLYHQIRCIMEVLFLVGRGLEVPSVVQTLLE 281

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             DRK   PLA    L      + 
Sbjct: 282 RGDRKPTYPLADGTPLVLWDCGFD 305


>gi|317014476|gb|ADU81912.1| tRNA pseudouridine synthase A [Helicobacter pylori Gambia94/24]
          Length = 242

 Score =  176 bits (446), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSGVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWNAAKLFHYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +  +G+HDF+ F+     A++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLDL--LNTALKQFIGKHDFSMFKKEGGAATNPNRIIFNALAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIMGHECVAFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|15612084|ref|NP_223736.1| tRNA pseudouridine synthase A [Helicobacter pylori J99]
 gi|8134768|sp|Q9ZKC0|TRUA_HELPJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|4155610|gb|AAD06601.1| PSEUDOURIDYLATE SYNTHASE I [Helicobacter pylori J99]
          Length = 242

 Score =  176 bits (446), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +  I+ Y+G+ + G+ +Q N   +Q  IE A+    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKAIVAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSGVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  ALSFHAPKHWNAAKLFHYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   + IA +  +G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNIALKQFIGKHDFSMFKKEGGATTNPNRIIFNALAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIMGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|313245560|emb|CBY40253.1| unnamed protein product [Oikopleura dioica]
          Length = 402

 Score =  176 bits (446), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 101/267 (37%), Gaps = 37/267 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSG 54
            +  +   Y+G+ Y G QR       ++I+  I  A+                 GRTD G
Sbjct: 65  RKIALRFSYDGTKYNGLQRSPVPAGKTTIEDVIFDAMLRTKVVDDIGTADYIAGGRTDKG 124

Query: 55  VHALRQVAHFDLVREWVPVILCKALNA---------YLKISDTISILNLSIVDKQFHARF 105
           VHA+  V    +        + + +             ++ D I I + + +   F ARF
Sbjct: 125 VHAVNNVISLFVNSRLSEDEINENVTVGERNFVAIINRQLPDDIWITSWAQISSDFSARF 184

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           +   R Y Y   +                  LD E M+ AA +L+G HDF  F     + 
Sbjct: 185 NCKSRHYNYIFDSS----------------GLDVELMKEAASYLIGEHDFRNFSQAQLER 228

Query: 166 SSPIRTIDHFDVNSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
            + +R     D+    N   +    + A  FL+ QIR  +  L LVG+    ST +++ L
Sbjct: 229 QNTVRVCFAADIKQVPNMSSMCVFSIKASGFLYHQIRLTMAILALVGNKLEKSTIVKELL 288

Query: 223 QAQD--RKECGPLAPPEGLYFDSVEYS 247
             +   R+     A P+GL     EY 
Sbjct: 289 DVEKYPRRPSYKYANPDGLVLIDCEYE 315


>gi|221230534|ref|YP_002503950.1| putative pseudouridylate synthase [Mycobacterium leprae Br4923]
 gi|4539110|emb|CAB39831.1| putative tRNA pseudouridine synthase A [Mycobacterium leprae]
 gi|13093610|emb|CAC30910.1| probable pseudouridylate synthase [Mycobacterium leprae]
 gi|219933641|emb|CAR72052.1| probable pseudouridylate synthase [Mycobacterium leprae Br4923]
          Length = 249

 Score =  176 bits (446), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 103/230 (44%), Gaps = 14/230 (6%)

Query: 31  IEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV------------REWVPVILCKA 78
           +++A   V    V +  AGRTD+GVHA  QVAH D+                 P  L   
Sbjct: 2   LDEAFTTVFRTPVRLRAAGRTDTGVHATGQVAHVDIPGTALSKANPRSPHTGDPEFLPLL 61

Query: 79  LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLIPKSL 137
                 +   + +L+++     F ARFSA+RR Y YR+ T    +   +       P+ L
Sbjct: 62  RRLSRLLPVDVRVLDIACAPVGFDARFSALRRHYRYRLSTAPYGVQPNQARYVTAWPREL 121

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           D ++M  A++ L+G  DF  F   H   ++ IR +   + +  G LI   + A +F  + 
Sbjct: 122 DLDSMSAASRDLLGLRDFAVFCR-HRHGATTIRELQRLEWSREGYLITAHITADAFCWSM 180

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +RS +G+L  VGD + T     + L    R      AP  GL F  V+Y 
Sbjct: 181 VRSLIGALLAVGDHRRTIGWCGELLTKASRSSDFTTAPAHGLTFIRVDYP 230


>gi|215737309|dbj|BAG96238.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 223

 Score =  176 bits (446), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/196 (31%), Positives = 91/196 (46%), Gaps = 8/196 (4%)

Query: 58  LRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +  VAHF           +  A+N  L     I +  +S    +FHAR S   + Y Y+I
Sbjct: 1   MHGVAHFTTPFSYHCLDSMHSAINGLL--PHEIRVREISAAKPEFHARTSTRSKIYHYKI 58

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDH 174
                        A+     L+ + MR AA+H VG HDFT+F +   + +  SPI+ I  
Sbjct: 59  YNGPVMDPFHNHYAYHSAYKLNSQAMREAAKHFVGTHDFTSFANAVHNDRVRSPIKKIMR 118

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL- 233
           FDV   G ++++ +    FL+ Q+R+ V  L  VG        + K + A+DRKE   + 
Sbjct: 119 FDVIEMGAILQLEIEGTGFLYRQVRNMVALLLQVGREALPPDIVAKIIAARDRKELAKVA 178

Query: 234 --APPEGLYFDSVEYS 247
             APP GLY  SV Y 
Sbjct: 179 LSAPPHGLYLMSVNYD 194


>gi|74191686|dbj|BAE30412.1| unnamed protein product [Mus musculus]
          Length = 280

 Score =  175 bits (445), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 115/276 (41%), Gaps = 53/276 (19%)

Query: 21  QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR-----EWVPVIL 75
           Q      Q   E A  L + + V    + RTD+GVHAL   AH D+ R      + P ++
Sbjct: 3   QPPVRFPQ---EAAKRLNSVDPVRFTISSRTDAGVHALSNAAHLDIQRRPGQSPFSPEVV 59

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL----ALEKGRAW 131
            KALN +LK    I +L    V   FHAR +A  R+Y YR+ T  +        E+   W
Sbjct: 60  AKALNTHLKHP-AIRVLKAFRVPNDFHARHAATSRTYQYRLATGCSWPNQLPVFEQNVCW 118

Query: 132 LIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG--------- 181
            +  + LD   M+ AAQHL+G HDF+ F+S     ++ +RT+    V+            
Sbjct: 119 ALQTEYLDMAAMQEAAQHLLGTHDFSAFQSAGSPVTNTVRTLRRVSVSPGPASPFVLPEG 178

Query: 182 ----NLIEIRVVARSFLHT------------------------QIRSFVGSLKLVGDGKW 213
                   +   ++SFL+                         Q+R     L  VG G  
Sbjct: 179 SRRLQFWTLEFESQSFLYRQVGCLNPHRMGSGRHTCDNLSSLLQVRRMTAVLVAVGLGIL 238

Query: 214 TSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEYS 247
             T ++  L++QD   K    +AP  GL+  SV Y 
Sbjct: 239 APTQVKVILESQDPLGKYQARVAPARGLFLKSVLYD 274


>gi|322501100|emb|CBZ36178.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 499

 Score =  175 bits (445), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 109/264 (41%), Gaps = 36/264 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  + G  +QK   ++++G +  A+  +              GRTD GV 
Sbjct: 60  RKIALRLAYHGHVHDGLAKQKETDNTVEGLVCDALRRLRLIPEDGPHNFGRCGRTDKGVS 119

Query: 57  ALRQ--------VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL              D   +  P+  C  LN  L    TI I+  ++VD  F ARFS +
Sbjct: 120 ALGNALSLTARASCTADAEPQLPPLDYCSMLNNVL--PSTIRIVGCALVDDAFDARFSCV 177

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
            R+Y Y                +   + L+ E M+ AA   +G H+F  F  +     S+
Sbjct: 178 HRTYRY----------------YFFHRGLNLEAMQEAAAFFLGTHNFRNFCKMDVVNVSN 221

Query: 168 PIRTIDHFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +RT+    ++    L E+     + A SFL+ QIR  +  L LVG G    + ++  L+
Sbjct: 222 FVRTVFSVGLHPSEALPELISYLEIRANSFLYHQIRCIMEVLFLVGRGLEVPSVVQTLLE 281

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             DRK   PLA    L      + 
Sbjct: 282 RGDRKPTYPLADGTPLVLWDCGFD 305


>gi|210135252|ref|YP_002301691.1| tRNA pseudouridine synthase A [Helicobacter pylori P12]
 gi|238057731|sp|B6JMT3|TRUA_HELP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|210133220|gb|ACJ08211.1| pseudouridylate synthase I [Helicobacter pylori P12]
          Length = 242

 Score =  175 bits (445), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 102/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSAVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWSADKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +    + 
Sbjct: 116 KTPFLAPYIACGDYGSLDL--LNTALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYTT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIMGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQMQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|317182345|dbj|BAJ60129.1| tRNA pseudouridine synthase A [Helicobacter pylori F57]
          Length = 242

 Score =  175 bits (445), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAQKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P RTI +      
Sbjct: 116 KTPFLVPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGAITNPKRTIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  V +       K T  +++  +         P+   
Sbjct: 174 FITGHECVVFKIIGDAFLRSSVRLIVQACVKYSLEKITLAEIQAQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|261838425|gb|ACX98191.1| pseudouridylate synthase I [Helicobacter pylori 51]
          Length = 242

 Score =  175 bits (445), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAQKHWNAAKLFYHLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P RTI +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRTIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|15669871|ref|NP_248685.1| tRNA pseudouridine synthase A [Methanocaldococcus jannaschii DSM
           2661]
 gi|3915177|sp|Q59069|TRUA_METJA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|1500579|gb|AAB99697.1| pseudouridylate synthase I (truA) [Methanocaldococcus jannaschii
           DSM 2661]
          Length = 259

 Score =  175 bits (444), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 106/250 (42%), Gaps = 35/250 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALRQV 61
           Y + I Y+G  Y  +Q+Q +  ++   +  A+       +  V++  GRTD GV AL   
Sbjct: 2   YILKIAYDG-RYS-FQQQPHKQTVCDILLDALEETGFLAKKKVIYSGGRTDKGVSALGNF 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              +L +      +   +NA LK    I +L    +D+    ++    R Y Y +     
Sbjct: 60  VVVELKK----EPILSYINAKLK-DKGIWVLGYREIDEIPKVKY----RHYRYILPN--- 107

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSF 180
                 G         D + ++  A+ ++G H F         +  SPIRTI    ++  
Sbjct: 108 -----IGY--------DVDAIKEGAKKMIGTHSFHNLSKRDRTKEKSPIRTIYDIKISEN 154

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + ++  SFL   +R  VG+L LVG GK     ++K L  ++ +E  P  PPEGL 
Sbjct: 155 EFYLTVDIIGESFLWNMVRKIVGALDLVGRGKKPVEWIDKLLD-ENHREGVPTFPPEGLI 213

Query: 241 F----DSVEY 246
                  +EY
Sbjct: 214 LVEAKVDIEY 223


>gi|308184830|ref|YP_003928963.1| tRNA pseudouridine synthase A [Helicobacter pylori SJM180]
 gi|308060750|gb|ADO02646.1| tRNA pseudouridine synthase A [Helicobacter pylori SJM180]
          Length = 242

 Score =  175 bits (443), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +  I+ Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKAIVAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWNADKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKSL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLDL--LNTALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  ++E  +         P+   
Sbjct: 174 SIMGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|289581033|ref|YP_003479499.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Natrialba magadii ATCC 43099]
 gi|289530586|gb|ADD04937.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Natrialba magadii ATCC 43099]
          Length = 293

 Score =  174 bits (442), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 106/261 (40%), Gaps = 27/261 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSGV 55
           +R    + Y+G+GY+G+QRQ +  +++ ++  A+  +        +      AGRTD+GV
Sbjct: 1   MR-AFRLAYDGTGYYGFQRQPDVPTVEDAMFDALRALDVLAPDADKPAGYAAAGRTDAGV 59

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            AL Q   F+      P    +A N  L     I     +    +FHA   A  R Y Y 
Sbjct: 60  SALAQTVAFEAPDWLTP----RAFNGEL--PADIRAWAAADAPDEFHATHHAREREYTYY 113

Query: 116 II----TRQAPLA----LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           +        AP A     +     +   ++D +  + A   L G HD   F ++     +
Sbjct: 114 LYAPPANDDAPPASDTDEDHAGTPVTAHTVDDDRFQAACDALSGPHD---FHNLTPDDHN 170

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             R+    +    G+   + V A  F    +R  V   + VG G+     +E+AL++   
Sbjct: 171 TERS-PVLESTRDGHFRILTVTAGGFCRELVRRLVSLARDVGTGEANLQTIERALESDPL 229

Query: 228 --KECGPLAPPEGLYFDSVEY 246
              E    APPE L    VEY
Sbjct: 230 PGHEGIAPAPPEPLVLTDVEY 250


>gi|208434988|ref|YP_002266654.1| pseudo uridylate synthase I [Helicobacter pylori G27]
 gi|238057732|sp|B5Z889|TRUA_HELPG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|208432917|gb|ACI27788.1| pseudo uridylate synthase I [Helicobacter pylori G27]
          Length = 242

 Score =  174 bits (442), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 102/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  TLSFHAPKHWNAAKLFYCLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSLFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  ++E  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|307637758|gb|ADN80208.1| tRNA pseudo uridine synthase A [Helicobacter pylori 908]
 gi|325996359|gb|ADZ51764.1| tRNA pseudouridine synthase A [Helicobacter pylori 2018]
 gi|325997947|gb|ADZ50155.1| tRNA pseudouridine synthase A [Helicobacter pylori 2017]
          Length = 242

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +  I+ Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKAIVAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  ALSFHAPKHWNADKLFHYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +  +G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLDL--LNTALKQFIGKHDFSMFKKEGGATTNPNRIIFNALAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K    +++  +         P+   
Sbjct: 174 FIMGHECVVFKIIGDAFLRSSVRLIIKACVQYSLEKIALAEIQAQIHNLKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|219129673|ref|XP_002185007.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403502|gb|EEC43454.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 373

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 87/359 (24%), Positives = 129/359 (35%), Gaps = 116/359 (32%)

Query: 3   RYCMIIEYNGSGYFG--WQRQ------KNG------SSIQGSIEKAIFLVTGEIV--VVH 46
           RY + ++Y G  + G  WQR        NG       S++G + +A+  + G      + 
Sbjct: 9   RYAVSLQYRGPPFLGFSWQRTQEDCILPNGTDLRGRQSVEGRLREALDKLVGRDGYDKIQ 68

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPV----------ILCKALNAYLKIS---------- 86
            + RTD GVHAL+   H D+   +              L + L  Y+             
Sbjct: 69  VSSRTDRGVHALKNTCHIDVRTSFPDESGNVLTPYSRTLFEGLQYYIAKQASTAVEQGGK 128

Query: 87  ------------------------------DTISILNLSIVDK----------------- 99
                                           + +LN+                      
Sbjct: 129 GLEVSKRRSIDLKDVLSGKERFPAVQQFQIKDMRLLNIREAPHFMDNPLYDVQSTIQPNK 188

Query: 100 -QFHARFSAIRRSYLYRII----TRQAPLALEKGRAWLIPK--SLDCENMRIAAQHLVGR 152
            ++ ARFSA +R+YLYRI+         +  E  R+W I     LD E M+ AA++L G 
Sbjct: 189 VRWDARFSATQRTYLYRILHMCNDTDWAVPFEWNRSWRIRNSIPLDLEAMQRAAKYLTGT 248

Query: 153 HDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI--------------------------EI 186
           HDFT+FR+  C   SP+ T++   V S    I                           I
Sbjct: 249 HDFTSFRASGCSRYSPVVTLNQICVQSQPYGIAGLSGTFAKECALFGIPTTIDPLCLTTI 308

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
                SFL+ Q+R+ VG L  VG G     D    L A+DR +    AP  GL+   V+
Sbjct: 309 SFQGNSFLYRQVRNMVGYLVAVGKGWINCEDTVAVLNARDRTKAQSTAPAHGLFLVDVK 367


>gi|108563457|ref|YP_627773.1| tRNA pseudouridine synthase A [Helicobacter pylori HPAG1]
 gi|122980474|sp|Q1CSH3|TRUA_HELPH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|107837230|gb|ABF85099.1| pseudouridylate synthase I [Helicobacter pylori HPAG1]
          Length = 242

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 105/250 (42%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIENALNTLGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWNVAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +    + 
Sbjct: 116 KTPFLAPYIACGDYGSLDL--LNSALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYTA 173

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  ++E  +         P+   
Sbjct: 174 FIMGHECVVFKIIGDAFLRSSVRLIIQTCVQYSLEKITLAEIEMQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 233 DGLYLHRVYY 242


>gi|254756838|ref|ZP_05208866.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Australia
           94]
          Length = 145

 Score =  173 bits (440), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 42/144 (29%), Positives = 69/144 (47%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           R+   R+ Y YR++  +      +   +  P  L+  ++R A  + +G HDFT+F S   
Sbjct: 1   RYGVERKEYRYRVLVSKTADVFRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKT 60

Query: 164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                +RTI   ++    + +  R V   FL+  +R  VG+L  VG GK     + + L 
Sbjct: 61  DKKDKVRTIYEIELIEQDDELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILA 120

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
            Q+R+  G +AP  GLY   V Y+
Sbjct: 121 KQNRQFAGKMAPGHGLYLWQVNYN 144


>gi|261328820|emb|CBH11798.1| pseudouridine synthase A-like protein, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 458

 Score =  173 bits (440), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 102/264 (38%), Gaps = 36/264 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  Y G  RQ     +++  +  A+  +              GRTD GV 
Sbjct: 55  RKIALRLAYHGHIYCGLVRQAETPNTVEAYLVAALERLRFVEPSGPKDFSRCGRTDKGVS 114

Query: 57  ALRQVAHFDL--------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL  V  F            +  P+  C+ LN  L    TI I+  S V+  F ARFS  
Sbjct: 115 ALGNVVSFTSRASSWATDEHQQPPLDYCEKLNNVL--PPTIRIVGWSYVNADFDARFSCT 172

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
            R+Y Y                +   + L+ E MR A  +L G H+F  F        ++
Sbjct: 173 GRTYRY----------------YFCNRGLNLEAMRKAVGYLKGVHNFRNFCKTDVVNVNN 216

Query: 168 PIRTIDHFDV---NSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             R + H D+       +L+    + A SFL+ QIR  +  L LVG        +++ L 
Sbjct: 217 YERHVRHADIVGSEMLPDLVSYFEIEANSFLYNQIRCTMEVLFLVGRCLEEPEVVKQLLD 276

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             DRK   PLA    L      + 
Sbjct: 277 CGDRKPVYPLADATPLVLWECHFE 300


>gi|167948002|ref|ZP_02535076.1| tRNA pseudouridine synthase A [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 201

 Score =  173 bits (440), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 56/151 (37%), Positives = 77/151 (50%), Gaps = 2/151 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+GSG+ GWQ+Q +  S+Q  +E A+  V  + V VH AGRTD+GVH   QV
Sbjct: 19  MKIALGVEYDGSGFNGWQKQSHARSVQEDLEAALSRVADQPVRVHCAGRTDTGVHGTGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   E  P       N  L   + +S+     V   FHARFSA  R Y Y I+ R  
Sbjct: 79  VHFETTAERPPRAWVLGSNVNL--PNDVSVSWARQVADDFHARFSATGRHYRYLILNRGT 136

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
             AL + RA      LD   M+ A   + G 
Sbjct: 137 RSALWRNRATWHHHPLDEHRMQPAGTGIGGH 167


>gi|296471772|gb|DAA13887.1| tRNA pseudouridine synthase 3 [Bos taurus]
          Length = 481

 Score =  173 bits (440), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+         +    H  GRTD GV A 
Sbjct: 65  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVENRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL          +  N                     +   I +L  + V+  F
Sbjct: 125 GQVISLDLRSHIPKGRDSEHFNLKNEVNDVATEIRYTHILNRVLPPDIRVLAWAPVETSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +    +LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRANLDIVTMNYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI    V   G             L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQRVGQNLGEEGWQEPFQLCQFEVTGQAFLYHQVRCMMAVLFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEVIDELLN 304


>gi|255086349|ref|XP_002509141.1| predicted protein [Micromonas sp. RCC299]
 gi|226524419|gb|ACO70399.1| predicted protein [Micromonas sp. RCC299]
          Length = 452

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 108/236 (45%), Gaps = 59/236 (25%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT------------------GEIV 43
            RY + ++Y+G+ + G+QRQ N  ++QG +E A+                         +
Sbjct: 63  PRYLLRVQYDGTNFHGFQRQANARTVQGCVEDALDAFAGGGGGGGGGGGGDGADTMRSSI 122

Query: 44  VVHGAGRTDSGVHALRQVAHFDLV------------REWVPVILCKALNAYLKI--SDTI 89
           V HG+ RTD+GVHAL    H DL                 P ++  ALN +LK   +  +
Sbjct: 123 VTHGSSRTDAGVHALDNTMHVDLPPRVSRREPTRALPPHEPHVVASALNHFLKKRGAPDV 182

Query: 90  SILNLSIVDKQ-FHARFSAIRRSYLYRIITRQAPL-ALEKGRAWLI-------------- 133
           ++     VD   FHARFSA  R+Y YR+     P    E+GR W +              
Sbjct: 183 AVTRCIRVDPNAFHARFSATGRTYHYRMHVSPTPPSLFERGRVWHVCSGAGDRDAAGGGA 242

Query: 134 -----------PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                         LD + MR+AA HLVG HDF+TFR+  CQASSP+RT+    V+
Sbjct: 243 DGCHENAGHDGRWGLDVDAMRVAAAHLVGTHDFSTFRASGCQASSPVRTLWDVRVD 298



 Score = 81.8 bits (201), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 31/64 (48%)

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + +  V  SFL+ Q+R  V +L+ VG G+     +   L A+  +    +AP  GLY   
Sbjct: 371 VVVTAVGPSFLYHQVRLMVATLRAVGAGEIDPASVPALLAARTPRAVPAMAPAHGLYLGR 430

Query: 244 VEYS 247
           V Y 
Sbjct: 431 VHYD 434


>gi|77735971|ref|NP_001029684.1| tRNA pseudouridine synthase 3 [Bos taurus]
 gi|119391067|sp|Q3SX07|PUS3_BOVIN RecName: Full=tRNA pseudouridine synthase 3; AltName: Full=tRNA
           pseudouridylate synthase 3; AltName: Full=tRNA-uridine
           isomerase 3
 gi|74356305|gb|AAI04570.1| Pseudouridylate synthase 3 [Bos taurus]
          Length = 481

 Score =  173 bits (439), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+         +    H  GRTD GV A 
Sbjct: 65  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVENRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL          +  N                     +   I +L  + V+  F
Sbjct: 125 GQVISLDLRSHIPKGRDSEHFNLKNEVNDVATEIRYTHILNRVLPPDIRVLAWAPVETSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +    +LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRANLDIVTMNYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI    V   G             L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQRVGQNLGEEGWQEPFQLCQFEVTGQAFLYHQVRCMMAVLFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEVIDELLN 304


>gi|308183197|ref|YP_003927324.1| tRNA pseudouridine synthase A [Helicobacter pylori PeCan4]
 gi|308065382|gb|ADO07274.1| tRNA pseudouridine synthase A [Helicobacter pylori PeCan4]
          Length = 242

 Score =  173 bits (439), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIEDALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAQKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKRFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +V+  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIIGHECVVFKVIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|157872401|ref|XP_001684749.1| pseudouridine synthase A-like protein [Leishmania major strain
           Friedlin]
 gi|68127819|emb|CAJ06260.1| putative pseudouridine synthase A-like protein [Leishmania major
           strain Friedlin]
          Length = 498

 Score =  173 bits (439), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 108/264 (40%), Gaps = 36/264 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  + G  +QK   ++++G +  A+  +              GRTD GV 
Sbjct: 60  RKIALRLAYHGHVHDGLAKQKETDNTVEGLVCDALRRLRLIPEDGPHNFGRCGRTDKGVS 119

Query: 57  ALRQ--------VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL              D   +  P+  C  LN  L    TI I+  ++VD  F ARFS +
Sbjct: 120 ALGNAFSLTARASCTGDAEPQLPPLDYCSMLNNVL--PSTIRIVGCALVDDAFDARFSCV 177

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
            R+Y Y                +   + L+   M+ AA   +G H+F  F  +     S+
Sbjct: 178 HRTYRY----------------YFFHRGLNLAAMQEAAAFFLGTHNFRNFCKMDVVNVSN 221

Query: 168 PIRTIDHFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +RT+    ++    L E+     + A SFL+ QIR  +  L LVG G    + ++  L+
Sbjct: 222 FVRTVFSVGLHPSEALPELISYLEIRANSFLYHQIRCIMEVLFLVGRGLEVPSVVQTLLE 281

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             DRK   PLA    L      + 
Sbjct: 282 LGDRKPTYPLADGTPLILWDCGFD 305


>gi|315586982|gb|ADU41363.1| tRNA-pseudouridine synthase I [Helicobacter pylori 35A]
          Length = 242

 Score =  173 bits (439), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G  + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGVYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     + +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAPKHWNAAKLFYYLAPKLAPH--VVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P RTI +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRTIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +V+  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKVIGDAFLRSSVRLIIQACVQYSLEKITLAEIQTQIHNTKAAIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|20094324|ref|NP_614171.1| TruD family pseudouridine synthase [Methanopyrus kandleri AV19]
 gi|30913397|sp|Q8TWZ3|TRUA_METKA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|19887376|gb|AAM02101.1| Pseudouridylate synthase of the TruA family [Methanopyrus kandleri
           AV19]
          Length = 256

 Score =  173 bits (439), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 110/248 (44%), Gaps = 28/248 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+GS Y G+Q Q +  +I+G++ KA+  +  E+V    A RTD+G HA  QV
Sbjct: 1   MRVALRVAYDGSRYHGFQYQPDVPTIEGALRKALSELGLELVGY--ASRTDAGAHARYQV 58

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              +       +     +NA L     I ++  + V ++F  R  A+R+ Y Y +     
Sbjct: 59  VVVEGD---PELAQPDPINARL--PKDIRVIAKTEVHEEFDPRRDALRKEYRYFLG---- 109

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNSF 180
              L +            E    AA+ L G+HDF+ FR       +PI T++  + V   
Sbjct: 110 --PLNRP-----------EAAARAARKLEGKHDFSAFRRE--DGRNPIITVERCELVEIT 154

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-DRKECGPLAPPEGL 239
            N   +RVVA  FL   +R   G +  VG G     D E  L  + +  +     P EGL
Sbjct: 155 PNAYVLRVVAPRFLWEMVRRIAGFVWEVGHGLREEGDAEALLSGKFEPSKKPRCLPAEGL 214

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 215 ILWHIEYD 222


>gi|308062368|gb|ADO04256.1| tRNA pseudouridine synthase A [Helicobacter pylori Cuz20]
          Length = 242

 Score =  173 bits (439), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 101/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSTVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     + +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYTQKHWNAAKLFYHLAPKLAPH--VVLKRLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGAITNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  V +       K T  +++  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAEIQAQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|317178604|dbj|BAJ56392.1| tRNA pseudouridine synthase A [Helicobacter pylori F30]
          Length = 242

 Score =  173 bits (439), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFCAPKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQVQIHNIKAAIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|332673893|gb|AEE70710.1| tRNA pseudouridine synthase A [Helicobacter pylori 83]
          Length = 242

 Score =  173 bits (438), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 102/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHADNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAPKHWNAAKLFYHLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I        
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFDAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  V +       K T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAEIQAQIHNIKAAIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|317177844|dbj|BAJ55633.1| tRNA pseudouridine synthase A [Helicobacter pylori F16]
          Length = 242

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 102/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+    G   +V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSIVVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAPKHWNAAKLFYHLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLVPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIAGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNIKAAIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|72390247|ref|XP_845418.1| pseudouridine synthase A-like protein [Trypanosoma brucei TREU927]
 gi|62360588|gb|AAX81000.1| pseudouridine synthase A-like protein, putative [Trypanosoma
           brucei]
 gi|70801953|gb|AAZ11859.1| pseudouridine synthase A-like protein, putative [Trypanosoma brucei
           brucei strain 927/4 GUTat10.1]
          Length = 428

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 103/264 (39%), Gaps = 36/264 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  Y G  RQ     +++  +  A+  +              GRTD GV 
Sbjct: 25  RKIALRLAYHGHIYCGLVRQAETPNTVEAYLVAALERLRFVEPSGPKDFSRCGRTDKGVS 84

Query: 57  ALRQVAHFDL--------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL  V  F           ++  P+  C+ LN  L    TI I+  S V+  F ARFS  
Sbjct: 85  ALGNVVSFTSRASSWATDEQQQPPLDYCEKLNNVL--PPTIRIVGWSYVNADFDARFSCT 142

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
            R+Y Y                +   + L+ E MR A  +L G H+F  F        ++
Sbjct: 143 GRTYRY----------------YFCNRGLNLEAMRKAVGYLKGVHNFRNFCKTDVVNVNN 186

Query: 168 PIRTIDHFDVNSFG---NLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             R + H D+       +L+    + A SFL+ QIR  +  L LVG        +++ L 
Sbjct: 187 YERHVRHADIVGSDMLPDLVSYFEIEANSFLYNQIRCTMEVLFLVGRCLEEPEVVKQLLD 246

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             DRK   PLA    L      + 
Sbjct: 247 CGDRKPVYPLADATPLVLWECHFE 270


>gi|255322348|ref|ZP_05363494.1| tRNA pseudouridine synthase A [Campylobacter showae RM3277]
 gi|255300721|gb|EET79992.1| tRNA pseudouridine synthase A [Campylobacter showae RM3277]
          Length = 317

 Score =  172 bits (437), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 54/207 (26%), Positives = 84/207 (40%), Gaps = 4/207 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G Q Q + + ++ ++  A+  V G    +  + RTD GVHA  QV
Sbjct: 1   MRLKLVFSYDGSKFQGSQTQPHENGVEDALGVALAHV-GIFSKIISSSRTDKGVHANNQV 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A  +    +   +  ++L         I +  +S V   FH R+ A  R+Y Y I   + 
Sbjct: 60  ACVECGEHFKDFVRLRSL-VNRHAHPAIHVKFISRVKDGFHPRYDATARAYRYVINHGEF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                      IPK  D           VG HDF+ F  +     SP+R +        G
Sbjct: 119 -SPFLSPYETFIPK-FDLNLANELLALFVGEHDFSAFMKLGSDVKSPVRRVSKAFCYERG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLV 208
               I   A  FL  Q+R  V S+   
Sbjct: 177 ERTIIVFKANGFLRAQVRLMVASVLKA 203


>gi|311264306|ref|XP_003130101.1| PREDICTED: tRNA pseudouridine synthase 3-like [Sus scrofa]
          Length = 479

 Score =  172 bits (437), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 95/256 (37%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+         +    H  GRTD GV A 
Sbjct: 64  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVENRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL   ++     + +N                     +   I +L  + V+  F
Sbjct: 124 GQVISLDLRSHFLKDKDSEDINLKDEVNDATKEIRYTHILNRVLPPDIRVLAWAPVEPSF 183

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 184 SARFSCLERTYRY----------------FFPHADLDIVTMNYAAQKYVGTHDFRNLCKM 227

Query: 162 H--CQASSPIRTI------------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                 ++  RTI            +         L +  VV ++FL+ Q+R  +  L L
Sbjct: 228 DVANGVTNFQRTILSAQVQLLSQSLEEERWQEAFQLCQFEVVGQAFLYHQVRCMMAVLFL 287

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 288 IGQGMEKPEVIDELLN 303


>gi|308063876|gb|ADO05763.1| tRNA pseudouridine synthase A [Helicobacter pylori Sat464]
          Length = 242

 Score =  172 bits (437), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 101/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSAVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     + +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAQKHWNAAKLFYYLAPKLAPH--VVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  V +       K T  +++  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAEIQAQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|317012865|gb|ADU83473.1| tRNA pseudouridine synthase A [Helicobacter pylori Lithuania75]
          Length = 242

 Score =  172 bits (437), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 100/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE  +    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIEGTL-NALGIKSAVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFHAPKHWNAAKLFHYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  V +       K T  ++E  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAEIEMQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|188527873|ref|YP_001910560.1| tRNA pseudouridine synthase A [Helicobacter pylori Shi470]
 gi|238691941|sp|B2UUJ8|TRUA_HELPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|188144113|gb|ACD48530.1| tRNA pseudouridine synthase A [Helicobacter pylori Shi470]
          Length = 242

 Score =  172 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     + +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAQKHWNAAKLFYYLAPKLAPH--VVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  V +       K T  +++  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIVQACVQYSLEKITLAEIQAQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|317011288|gb|ADU85035.1| tRNA pseudouridine synthase A [Helicobacter pylori SouthAfrica7]
          Length = 242

 Score =  172 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 101/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  + G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFSGYAKQPNKLGVQDKIESAL-NLLGIKSAVVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAPKHWNADRLFSYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKSL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +  +G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDFGSLDL--LNTALKQFIGKHDFSMFKKEGGALTNPKRIIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T   +   +         P+   
Sbjct: 174 SIMGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAAITAQIHNIQAAIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|256810921|ref|YP_003128290.1| tRNA pseudouridine synthase A [Methanocaldococcus fervens AG86]
 gi|256794121|gb|ACV24790.1| tRNA pseudouridine synthase A [Methanocaldococcus fervens AG86]
          Length = 259

 Score =  172 bits (436), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 105/250 (42%), Gaps = 35/250 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALRQV 61
           Y + I Y+G  Y  +Q+Q +  ++   +   +       +  +++  GRTD GV AL   
Sbjct: 2   YILKIAYDG-RYS-FQQQPHKQTVCDILLDTLENTDFLAKKKIIYSGGRTDKGVSALGNF 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              +L +      +   +NA LK S  I +L    +D+    ++    R Y Y +     
Sbjct: 60  VVLELKK----EPILSYINAKLK-SKGIWVLGYREIDEIPKVKY----RYYRYILPNINY 110

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSF 180
                           + + ++  A+ ++G H F         +  SPIRTI    ++  
Sbjct: 111 ----------------NVDAIKEGAKKMIGTHSFHNLSKRDRTKEKSPIRTIYDIKISEN 154

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I ++  SFL   +R  VG+L L+G GK     ++K L  ++ +E  P  PP+GL 
Sbjct: 155 EFYLTIDIIGESFLWNMVRKIVGALDLIGRGKKPVEWIDKLLD-ENYREGVPTFPPDGLI 213

Query: 241 F----DSVEY 246
                  V+Y
Sbjct: 214 LVEAKVDVDY 223


>gi|261350284|ref|ZP_05975701.1| tRNA pseudouridine synthase A [Methanobrevibacter smithii DSM 2374]
 gi|288861068|gb|EFC93366.1| tRNA pseudouridine synthase A [Methanobrevibacter smithii DSM 2374]
          Length = 288

 Score =  172 bits (436), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 99/269 (36%), Gaps = 47/269 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +   +  +      +      AGRTD+GVH
Sbjct: 1   MKRTALKIGYIGTNFHGFQRQPDLRTVEEELIYHLRKLGYIDDLKKSRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E     +  +L       D I IL  + V   F  R+ A  R Y Y +
Sbjct: 61  SLGNVISFQSEKEVRVNEINNSL------PDDIQILAKAPVRFGFKPRY-AEMRQYRYVL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                               LD   +   A+   G H+FT F        +  RTID   
Sbjct: 114 ----------------FRSDLDLYKLNEVAEIFKGTHNFTNFTKRF--QKTTTRTIDDIK 155

Query: 177 VN----------SFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +            F NL      + + +   SFL   +R  +     V  GK +   +E+
Sbjct: 156 ITKANLNDYHKKEFPNLHDTLSPVFVDIYGESFLWNMVRKMMRVFVDVAIGKLSLEKVEE 215

Query: 221 AL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            L     D +    +  P+ L    ++Y 
Sbjct: 216 LLNPAENDPRANIKVLDPDYLILMDIKYD 244


>gi|254779646|ref|YP_003057752.1| tRNA pseudouridine synthase A [Helicobacter pylori B38]
 gi|254001558|emb|CAX29576.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Helicobacter pylori B38]
          Length = 242

 Score =  171 bits (435), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 104/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIEGALNALGIKSV-VIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAPKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +    + 
Sbjct: 116 KTPFLAPYIARGDYGSLDL--LNTALKQFTGKHDFSLFKKEGGATTNPNRIIFNAFAYTA 173

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  ++E  +         P+   
Sbjct: 174 FIMGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|308807767|ref|XP_003081194.1| Exopolyphosphatases and related proteins (ISS) [Ostreococcus tauri]
 gi|116059656|emb|CAL55363.1| Exopolyphosphatases and related proteins (ISS) [Ostreococcus tauri]
          Length = 813

 Score =  171 bits (435), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 99/265 (37%), Gaps = 38/265 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQ---KNGSSIQGSIEKAIFLV--------TGEIVVVHGAGRTD 52
             + + Y G  Y G+  Q       +++ ++ +A+             +       GRTD
Sbjct: 456 IALKVAYLGWPYRGFASQGPEATTPTVEWTLFEALAKTRLVAAAADVFKTASYARCGRTD 515

Query: 53  SGVHALRQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
            GV  L Q+    +           +     LN  L     +  L  + VD++ +ARF  
Sbjct: 516 RGVSGLGQIVTLQVRSNGASDPREELDYVGLLNRAL--PSDVRALGWAPVDEELNARFDC 573

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-AS 166
             R Y Y           EK  A      LD E M  AA+   G HDF  F  +  +   
Sbjct: 574 KWRQYKYF---------FEKTTA------LDLEAMGEAARAFEGVHDFRNFCRMDAENVK 618

Query: 167 SPIRTIDHFDVNSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA--L 222
           S  R +    +   G+  L+ I V   +FL  Q+R+    L +VG G    + +E+   L
Sbjct: 619 SFTRRVLECTIEEAGDGKLMYINVRGTAFLWHQVRNMASVLFMVGLGHEPPSVVERLLDL 678

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
           +   RK   P+AP E L      Y 
Sbjct: 679 ERTPRKPQYPMAPEESLLLWRSGYD 703


>gi|148642915|ref|YP_001273428.1| tRNA pseudouridine synthase A [Methanobrevibacter smithii ATCC
           35061]
 gi|226708656|sp|A5ULI2|TRUA_METS3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148551932|gb|ABQ87060.1| tRNA pseudouridine synthase A, TruA [Methanobrevibacter smithii
           ATCC 35061]
          Length = 290

 Score =  171 bits (435), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 99/269 (36%), Gaps = 47/269 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +   +  +      +      AGRTD+GVH
Sbjct: 1   MKRTALKIGYIGTNFHGFQRQPDLRTVEEELIYHLRKLGYIDDLKKSRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E     +  +L       D I IL  + V   F  R+ A  R Y Y +
Sbjct: 61  SLGNVISFQSEKEVRVNEINNSL------PDDIQILAKAPVRFGFKPRY-AEMRQYRYVL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                               LD   +   A+   G H+FT F        +  RTID   
Sbjct: 114 ----------------FRSDLDLYKLNEVAEIFKGTHNFTNFTKRF--QKTTTRTIDDIK 155

Query: 177 VN----------SFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +            F NL      + + +   SFL   +R  +     V  GK +   +E+
Sbjct: 156 ITKANLNDYHKKEFPNLHDTLSPVFVDIYGESFLWNMVRKMMRVFVDVAIGKLSLEKVEE 215

Query: 221 AL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            L     D +    +  P+ L    ++Y 
Sbjct: 216 LLNPAENDPRANIKVLDPDYLILMDIKYD 244


>gi|260797314|ref|XP_002593648.1| hypothetical protein BRAFLDRAFT_252211 [Branchiostoma floridae]
 gi|229278875|gb|EEN49659.1| hypothetical protein BRAFLDRAFT_252211 [Branchiostoma floridae]
          Length = 259

 Score =  171 bits (435), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 76/254 (29%), Positives = 116/254 (45%), Gaps = 37/254 (14%)

Query: 31  IEKAIFLV-TGEIVVVHGAGRTDSGVHALRQVAHFDLV-----REWVPVILCKALNA--Y 82
           ++ A   +   E   +H + RTDSGVHAL   AH DL+       + P  +  A+N    
Sbjct: 1   LQDAFSHLKLAEPPNIHVSSRTDSGVHALCNTAHADLIYGDDKEPFDPDSIVHAVNRSIL 60

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL---EKGRAWLIPKSLDC 139
                 I ++N   V   F +R  A+ R+YLYR+++      L   E  R+W I + LD 
Sbjct: 61  HMGRTDIRLMNCRPVSPTFSSRHQALGRTYLYRVVSGCYHSRLPIPEVNRSWGIKERLDI 120

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHFDVNSFG-------------NLI 184
           E M+ AA+H +G HDFTTFRS   +     P++T+   +V                  ++
Sbjct: 121 EAMQEAAKHFLGTHDFTTFRSKTPETWTKDPVKTMKVVEVRRASCFLKEHDPFCRDLEVL 180

Query: 185 EIRVVARSFLHT--------QIRSFVGSLKLVGDGKWTSTDLEKALQAQD---RKECGPL 233
           E+   +RSFL+         Q+R   G L  +G GK    D+   L  +      +   +
Sbjct: 181 ELIFKSRSFLYRQAIVLSLLQVRRMTGLLVAIGRGKLQPEDVCTLLAVRKIAAYPKAAQV 240

Query: 234 APPEGLYFDSVEYS 247
           AP  GLY  +VEY+
Sbjct: 241 APAHGLYLCNVEYN 254


>gi|261403437|ref|YP_003247661.1| tRNA pseudouridine synthase A [Methanocaldococcus vulcanius M7]
 gi|261370430|gb|ACX73179.1| tRNA pseudouridine synthase A [Methanocaldococcus vulcanius M7]
          Length = 259

 Score =  171 bits (435), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 107/250 (42%), Gaps = 35/250 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQV 61
           Y + I Y+G  Y  +Q Q + +++   +   +  +       +++  GRTD GV AL   
Sbjct: 2   YILKIAYDG-RYS-FQTQPHRNTVCDKVLNTLDEIDLLERRKIIYCGGRTDKGVSALGNF 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              +L +E  P      +NA LK ++ I +L    ++K    R+    R Y Y +     
Sbjct: 60  IVVELKKEPSPS----YINAKLK-NEGIWVLGYREIEKIPEVRY----RHYRYILPNMGY 110

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSF 180
                           D E ++  A  L G H F         +  SPIRTI   DV+  
Sbjct: 111 ----------------DVEAIKRGASILTGTHSFHNLSKKDRTKDRSPIRTIFKIDVSEN 154

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I + +  +SFL   +R  VG+L LVG G+     +EK L+ +D KE  P  PP+GL 
Sbjct: 155 EFYITLDIFGKSFLWNMVRKMVGALDLVGRGERPVNWIEKLLR-EDHKEGVPTFPPDGLI 213

Query: 241 F----DSVEY 246
                  V+Y
Sbjct: 214 LVEANVDVDY 223


>gi|223040118|ref|ZP_03610398.1| tRNA pseudouridine synthase A (tRNA-uridine isomeraseI) (tRNA
           pseudouridylate synthase I) [Campylobacter rectus
           RM3267]
 gi|222878595|gb|EEF13696.1| tRNA pseudouridine synthase A (tRNA-uridine isomeraseI) (tRNA
           pseudouridylate synthase I) [Campylobacter rectus
           RM3267]
          Length = 483

 Score =  171 bits (434), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 93/223 (41%), Gaps = 8/223 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G Q Q + + ++ ++  A+  V G    +  + RTD GVHA  QV
Sbjct: 1   MRLKLVFSYDGSKFQGSQTQPHENGVEDALGAALAHV-GIFSKIISSSRTDKGVHANNQV 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           A  +    +      K+L         + +  +S     FH R+ A  R+Y Y I   + 
Sbjct: 60  ACVECGEHFRDFTRLKSL-INRHAHPAVHVKFISRARDCFHPRYDATARAYRYVINHGEF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                      +P+  D           VG HDF+ F  +     SP+R +      + G
Sbjct: 119 -SPFLAPYETFLPR-FDLNLANELLALFVGEHDFSAFMKLGSDVKSPVRRVSKAFCYARG 176

Query: 182 NLIEIRVVARSFLHTQIRSFVG----SLKLVGDGKWTSTDLEK 220
               I   A  FL  Q+R  V     +L+L  +GK+  TD+ +
Sbjct: 177 ERSIIVFKANGFLRAQVRLMVASVFKALELAKNGKFKETDVRE 219


>gi|224083654|ref|XP_002193509.1| PREDICTED: similar to Pseudouridylate synthase 3 [Taeniopygia
           guttata]
          Length = 462

 Score =  171 bits (434), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 66/277 (23%), Positives = 97/277 (35%), Gaps = 49/277 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N   +I+  + +A+         +    H  GRTD GV A 
Sbjct: 68  VALRIAYLGWGYQGFASQENTPNTIEEKLFEALKKTRLVDDRQTSNYHRCGRTDKGVSAF 127

Query: 59  RQVAHFDLVREWVP-------------VILCKALNAYLKISDTISILNLSIVDKQFHARF 105
            QV   DL                     L         +   I +L  + V  +F ARF
Sbjct: 128 GQVISLDLRSSLPEGQQLNGHGGEGQQEELRYTHILNRVLPPDIRVLAWAPVGPEFSARF 187

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           S + R+Y Y     Q                LD   M  AAQ  VG HDF     +    
Sbjct: 188 SCLSRTYRYFFPCAQ----------------LDVALMDTAAQRYVGTHDFRNLCKMDVAN 231

Query: 166 S--SPIRTIDHFDVNSF-----------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
              +  RTI    V                L +  V  ++FL+ Q+R  +  L L+G G 
Sbjct: 232 GVLNFQRTILRARVTRVSGGGEARPRDPFQLCQFEVTGQAFLYHQVRCMMAVLFLIGQGM 291

Query: 213 WTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            +   +++ L  +   RK    +A    L     E+ 
Sbjct: 292 ESPDVIDELLNVEKNPRKPQYSMAVEFPLVLYDCEFP 328


>gi|289192063|ref|YP_003458004.1| tRNA pseudouridine synthase A [Methanocaldococcus sp. FS406-22]
 gi|288938513|gb|ADC69268.1| tRNA pseudouridine synthase A [Methanocaldococcus sp. FS406-22]
          Length = 262

 Score =  171 bits (434), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 103/248 (41%), Gaps = 35/248 (14%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQVAH 63
           + I Y+G  Y  +Q+Q +  ++   +   +  +    +  +++  GRTD GV AL     
Sbjct: 8   LKIAYDG-RYS-FQQQPHKQTVCDILLDTLEEIDFLAKKKIIYSGGRTDKGVSALGNFVI 65

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            +L +      +   +NA LK    I +L    +D+    ++    R Y Y +       
Sbjct: 66  VELKK----EPILSYINAKLK-DKGIWVLGYREIDEIPKVKY----RHYRYILPNINY-- 114

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSFGN 182
                         + + ++  A+ ++G H F         +  SPIRTI    ++    
Sbjct: 115 --------------NIDAIKEGAKKMIGTHSFHNLSKRDKSKEKSPIRTIYDIKISENEF 160

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF- 241
            + I ++  SFL   +R  VG+L LVG GK     + K L  ++ +E  P  PP+GL   
Sbjct: 161 YLTIDIIGESFLWNMVRKIVGALDLVGRGKKPVDWIGKLLD-ENHREGVPTFPPDGLILV 219

Query: 242 ---DSVEY 246
                V+Y
Sbjct: 220 EAKVDVDY 227


>gi|222445148|ref|ZP_03607663.1| hypothetical protein METSMIALI_00769 [Methanobrevibacter smithii
           DSM 2375]
 gi|222434713|gb|EEE41878.1| hypothetical protein METSMIALI_00769 [Methanobrevibacter smithii
           DSM 2375]
          Length = 288

 Score =  171 bits (434), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 99/269 (36%), Gaps = 47/269 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M R  + I Y G+ + G+QRQ +  +++  +   +  +      +      AGRTD+GVH
Sbjct: 1   MKRTALKIGYIGTNFHGFQRQPDLRTVEEELIYHLRKLGYIDDLKKSRFRIAGRTDAGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           +L  V  F   +E     +  +L       D I IL  + V   F  R+ A  R Y Y +
Sbjct: 61  SLGNVISFQSEKEVRVNEINNSL------PDDIQILAKAPVRFGFKPRY-AEMRQYRYVL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                               LD   +   A+   G H+FT F        +  RTID   
Sbjct: 114 ----------------FRSDLDLYKLNEVAEIFKGTHNFTNFTKRF--QKTTTRTIDDIK 155

Query: 177 VN----------SFGNL------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +            F NL      + + +   SFL   +R  +     V  GK +   +E+
Sbjct: 156 ITKANLNDYHKKEFPNLHDTLSPVFVDIYGESFLWNMVRKMMRVFVDVAIGKLSLEKVEE 215

Query: 221 AL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            L     D +    +  P+ L    ++Y 
Sbjct: 216 LLNPAENDLRANIKVLDPDYLILMDIKYD 244


>gi|219120077|ref|XP_002180785.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407501|gb|EEC47437.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 347

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 117/306 (38%), Gaps = 64/306 (20%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ---------------------KNGSSIQGSIEKAIFLVTG 40
           +RY   + Y+G+ + G+Q Q                     K   ++QG +E  +     
Sbjct: 37  VRYRARVAYDGTSFQGFQIQGSNKVVDDKNCNGITHQNRKDKQQRTVQGELETVLSTRWN 96

Query: 41  EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV---ILCKALNAYLKISDTISILNLSIV 97
           + V V  AGRTD+GVHA  Q  HFD+     P     L ++L   L    T+  L  +  
Sbjct: 97  QPVRVVAAGRTDAGVHARGQAIHFDVNVSETPTDHASLERSLARMLPTDVTLWNLQFAPS 156

Query: 98  DKQ-----------FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD-------- 138
            +            ++  +    + Y YR+ T      L +   W  P ++D        
Sbjct: 157 ARTKLVDGQERVLPWNVMYDNTHKLYSYRLSTAAVMDPLSRQHRWH-PDNVDAYVVGKAG 215

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQAS-------SPIRTIDHFDVNSFGNL--IEIRVV 189
              +    +H  G HDF  F S   Q           +RT+   +V    N   + I  V
Sbjct: 216 LAQLTRLLKHYEGTHDFRAFASAMEQLEKHSDGPIDTVRTVYSVNVVPEANEGDVRIDFV 275

Query: 190 ARSFLHTQIRSFVGSLKLVGDGK-WTSTDLEKALQAQDRKECG--------PLAPPEGLY 240
            +  L+ Q+R+ VG++     G+    +D+ + L  QD    G          APP+GL 
Sbjct: 276 LKGALYKQVRNMVGTVLETCRGEIMKESDMLRLL--QDATASGLSRADNPSKPAPPQGLT 333

Query: 241 FDSVEY 246
            ++V +
Sbjct: 334 LENVYF 339


>gi|291383625|ref|XP_002708689.1| PREDICTED: CG3045-like [Oryctolagus cuniculus]
          Length = 480

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/282 (22%), Positives = 102/282 (36%), Gaps = 54/282 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 64  VALRIAYLGWGYQGFASQENTTNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      ++ N+                    +   I IL  + VD  F
Sbjct: 124 GQVISLDLRSQFPMAKDSESCNSKDEANDVAEEIRYTHILNRVLPPDIRILAWAPVDPGF 183

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 184 SARFSCLERTYHY----------------FFPRADLDIVTMNCAAQKYVGTHDFRNLCKM 227

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 228 DVANGVINFQRTILSAKVQLVGQSLGEERWQEHFQLCQFEVTGQAFLYHQVRCMMAILFL 287

Query: 208 VGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           +G G      +++ L  +   +K    +A    L     ++ 
Sbjct: 288 IGQGMEKPDIIDELLNVEKNPQKPQYSMAVEFPLVLHDCKFE 329


>gi|237751255|ref|ZP_04581735.1| tRNA pseudouridine synthase A [Helicobacter bilis ATCC 43879]
 gi|229372621|gb|EEO23012.1| tRNA pseudouridine synthase A [Helicobacter bilis ATCC 43879]
          Length = 253

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 103/255 (40%), Gaps = 16/255 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
               II Y+GS + G+  QK+     S+    E  +  + G    + G+GRTD  VHA  
Sbjct: 4   NIVCIIAYDGSKFCGFSHQKHTKGVLSVANFFELTLQKI-GIKAKIIGSGRTDKDVHATN 62

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV +F          + K LN  L     + I  + I D  FHARFSA  R Y Y     
Sbjct: 63  QVINFHAKLYMPLDKMKKLLNDRLY--PFVLIKRIFIADSSFHARFSAKLRIYRYVFTQA 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +  L         +    D   ++ A    +G HDF+ F+    +    IRTI    +  
Sbjct: 121 EL-LPFYSNYIAKVRHG-DISLLQTALNEFIGTHDFSLFKKNGSETKDFIRTIVKAHIFP 178

Query: 180 FG----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ---DRKECG- 231
                 +     + A  FL +Q+R  + +      G+ T  +L + +Q     ++  C  
Sbjct: 179 AKIHNISCFVAHIGANGFLRSQVRIMLKACFEFSLGRITLQNLVRQIQNDITLEKSLCVR 238

Query: 232 PLAPPEGLYFDSVEY 246
            LAP  GLY   + Y
Sbjct: 239 ELAPACGLYLHRIIY 253


>gi|195436012|ref|XP_002065972.1| GK25867, isoform A [Drosophila willistoni]
 gi|194162057|gb|EDW76958.1| GK25867, isoform A [Drosophila willistoni]
          Length = 508

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 85/286 (29%), Positives = 122/286 (42%), Gaps = 55/286 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQR------QK--NGSSIQGSIEKAI--FLVTGEIVVVHGAGR 50
           M RY + I Y G+ + G Q+      Q   + +S+QG +E A+  F  T EI  V  + R
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLDQPRLDTNSVQGCLELALRVFRPTNEIQTVL-SSR 59

Query: 51  TDSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARF 105
           TD+GVHAL    H DL R     +    L   LN  L      I +L+  +V   FH R+
Sbjct: 60  TDAGVHALHSTIHVDLERYDGQPYALTTLTGVLNRTLGKQRLPIRVLSTELVPDTFHCRY 119

Query: 106 SAIRRSYLYRIITRQAPLALE-----KGRAWLIP------------KSLDCENMRIAAQH 148
            AI R+YLYR    +     +     +G    IP             S D E +R AA+ 
Sbjct: 120 HAIGRTYLYRFAVARNSPVDDGKLKNRGYEAFIPVEELDRCYFLQAASFDIERVRSAARL 179

Query: 149 LVGRHDFTTFRSIHCQASS-------PIRTIDHFDV---------------NSFGNLIEI 186
            +G HDF TF S+  Q           +R ID  ++               N   +  EI
Sbjct: 180 FLGIHDFRTFMSVSRQKGPSRDHPMFTVRKIDEINIRPGHSLALNAHAKLANETYDHWEI 239

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            + A+SFL+ Q+R  VG+L  +G GK     + + L    +    P
Sbjct: 240 EIKAKSFLYKQVRRIVGTLLALGTGKIDEKCIYQMLTIPSKNSWEP 285


>gi|224370989|ref|YP_002605153.1| TruA2 [Desulfobacterium autotrophicum HRM2]
 gi|223693706|gb|ACN16989.1| TruA2 [Desulfobacterium autotrophicum HRM2]
          Length = 257

 Score =  170 bits (432), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 98/253 (38%), Gaps = 12/253 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GW +Q    +++  +EK +  + G     + G+ RTD+ V A     
Sbjct: 6   YLIHIQYLGFRYHGWLKQPGLKTVEAMVEKTVAFILGHSDFKILGSSRTDAMVSANHSAF 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
              +        L K  N  L   + I ++    VD+ F    +   ++Y+Y     +  
Sbjct: 66  ELFVHEPLNVEQLVKDFNQNL--PNDIRVIKAQGVDRNFSIINAPRTKAYIYLFAFGEKC 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-- 180
                         LD + M+  A    GRH+F ++ +     ++  R +    +     
Sbjct: 124 HPFCAPLISSFCHWLDIDLMKQGALLFQGRHNFRSYCTKPGTRTTFKREVLVSKIEENRI 183

Query: 181 -------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                         + ++ F+  Q+R  +G L  +G G+    D++ +L+         +
Sbjct: 184 FKANFFPAESYAYHIHSKGFMRYQVRLIMGQLLSLGRGEIGLEDIKVSLKGMSHLPLRHI 243

Query: 234 APPEGLYFDSVEY 246
           AP  GL  + +E+
Sbjct: 244 APSSGLMLNKIEF 256


>gi|195490006|ref|XP_002092962.1| GE26463, isoform A [Drosophila yakuba]
 gi|194179063|gb|EDW92674.1| GE26463, isoform A [Drosophila yakuba]
          Length = 495

 Score =  170 bits (432), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 77/284 (27%), Positives = 117/284 (41%), Gaps = 52/284 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTG-EIVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MNRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALRVFHPINEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL      DL R     +    L   LN  L      I +L+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQGLPIRVLSSKLVSNSFHCRYH 120

Query: 107 AIRRSYLYRIITRQAP----------------LALEKGRAWLIPKS-LDCENMRIAAQHL 149
           AI R+YLYR    + P                   E  R + +  S  D   ++ AA+  
Sbjct: 121 AIGRTYLYRFAVAKDPSLEDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVQAAARMF 180

Query: 150 VGRHDFTTFRSIHCQASS------PIRTIDHFDVNSFG---------------NLIEIRV 188
           +G HDF TF S+  Q  S       +R ID  ++                   N  +I +
Sbjct: 181 IGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDIEI 240

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            A+SFL+ Q+R  VG+L  +G+G+     L + L    +    P
Sbjct: 241 KAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNSWDP 284


>gi|322493546|emb|CBZ28834.1| putative pseudouridine synthase A-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 499

 Score =  170 bits (432), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 66/264 (25%), Positives = 106/264 (40%), Gaps = 36/264 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  + G  +QK   ++++G +  A+  +              GRTD GV 
Sbjct: 60  RKIALRLAYHGHVHDGLAKQKETDNTVEGLVCDALRRLRLIPEDGPHNFGRCGRTDKGVS 119

Query: 57  ALRQ--------VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL              D   +  P+  C  LN  L    TI I+  ++VD  F ARFS +
Sbjct: 120 ALGNALSLTARASCTADAEPQLPPLDYCSMLNNVL--PSTIRIVGCALVDDAFDARFSCV 177

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
            R+Y Y                +   + L+   M+ AA   +G H+F  F  +     S+
Sbjct: 178 HRTYRY----------------YFFHRGLNLAAMQEAAAFFLGTHNFRNFCKMDVVNVSN 221

Query: 168 PIRTIDHFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +RT+    +     L E+     + A SFL+ QIR  +  L LVG G    + ++  L+
Sbjct: 222 FVRTVFSVGLYPSEELPELISYLEIRANSFLYHQIRCTMEVLFLVGRGLEAPSVVQTLLE 281

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             D K   PLA    L      + 
Sbjct: 282 LGDCKPTYPLADGTPLVLWDCGFD 305


>gi|226533212|ref|NP_001145731.1| hypothetical protein LOC100279238 [Zea mays]
 gi|219884209|gb|ACL52479.1| unknown [Zea mays]
          Length = 486

 Score =  170 bits (432), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 96/270 (35%), Gaps = 44/270 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + + Y G  ++G+  + N   +++  I KA+          +       GRTD GV A
Sbjct: 151 VALKVMYFGQRFYGFSSEGNIEPTVESEIFKALERAKLMVANRKESCYSRCGRTDKGVSA 210

Query: 58  LRQVAHFDLVREW-----------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
             QV    L                 +   K LN  L     I +L    V   FHARF+
Sbjct: 211 TGQVISLYLRSNIKDVGGDMLDERSEIDYVKVLNRIL--PRDIRVLGWCPVPADFHARFT 268

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QA 165
            + R Y Y                      LD   M+ AA   +G HDF  F  +     
Sbjct: 269 CLSREYKYLFW----------------KGDLDILEMQKAASKFIGEHDFRNFCKMDAANV 312

Query: 166 SSPIRTIDHFDVNS------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           S+  R I  F +++         L  + +   +FL  Q+R  V  L L+G G  + + ++
Sbjct: 313 SNYRRHITEFTISACDRRSNNDELCSMTIKGSAFLWHQVRCMVAVLFLIGQGLESPSVVD 372

Query: 220 KALQ--AQDRKECGPLAPPEGLYFDSVEYS 247
             L      RK    +AP   L   S  + 
Sbjct: 373 SLLDIMKTSRKPQYKMAPELPLILQSCLFD 402


>gi|110667083|ref|YP_656894.1| tRNA pseudouridine synthase A [Haloquadratum walsbyi DSM 16790]
 gi|109624830|emb|CAJ51238.1| tRNA-pseudouridine synthase [Haloquadratum walsbyi DSM 16790]
          Length = 276

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 67/255 (26%), Positives = 103/255 (40%), Gaps = 36/255 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSG 54
           +R    + Y+G  + G+QRQ +  +++ ++  A+  +         +      AGRTD+G
Sbjct: 5   MR-AFRLAYDGRPFSGFQRQPSVPTVEDALFDALDSLDVFNRDTDSKPSGYAAAGRTDAG 63

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V ALRQ   F+      P    +ALN+ L    ++     + V   FHA   A++R+Y Y
Sbjct: 64  VSALRQTVGFECPSWCTP----RALNSEL--PTSVRAWASADVQSGFHATHDALQRTYTY 117

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                           +L    LD   +  AA+ L G+HDF  F S     +  +     
Sbjct: 118 ----------------YLYGPELDMNRLNTAAEILSGKHDFHNFTSDDDGTTRKLSITLE 161

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRKECGP 232
           FD       I  R+ A  F  + IR  + +L+ VG    T   L   L    Q   +  P
Sbjct: 162 FD----DPFITARITADGFPRSLIRRLMSALRGVGSESMTIETLTGLLNTVPQTGPDGIP 217

Query: 233 LAPPEGLYFDSVEYS 247
            A PE L    V Y 
Sbjct: 218 TASPEPLILTRVTYP 232


>gi|223558061|gb|ACM91066.1| tRNA pseudouridine synthase A [uncultured bacterium 34R1]
          Length = 189

 Score =  170 bits (430), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 53/189 (28%), Positives = 84/189 (44%), Gaps = 5/189 (2%)

Query: 60  QVAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             AHFD+         LC++LN  L     +++  +  V    HARF A  R+Y Y + T
Sbjct: 1   MYAHFDVDAPIADTDGLCRSLNGLLGR--DVAVYAIFPVADDAHARFDATSRTYKYFLHT 58

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            ++P       +W     LD E M  AA+HL+   DFT+F  +H    +    + +    
Sbjct: 59  AKSP--FLYPLSWECHFDLDFELMNEAAEHLLHYTDFTSFSKLHTDVKTNNCRVTYAHWE 116

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G      + A  FL   +R+ VG+L  VG  + T  +  + ++A+DR E G   P   
Sbjct: 117 RVGEQWVFTITADRFLRNMVRAVVGTLVEVGRHRITVDEFCRIIEAKDRCEAGNSMPGNA 176

Query: 239 LYFDSVEYS 247
           L+   + Y 
Sbjct: 177 LFLWDITYP 185


>gi|194706182|gb|ACF87175.1| unknown [Zea mays]
 gi|195612012|gb|ACG27836.1| hypothetical protein [Zea mays]
          Length = 457

 Score =  170 bits (430), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 96/270 (35%), Gaps = 44/270 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + + Y G  ++G+  + N   +++  I KA+          +       GRTD GV A
Sbjct: 122 VALKVMYFGQRFYGFSSEGNIEPTVESEIFKALERAKLMVANRKESCYSRCGRTDKGVSA 181

Query: 58  LRQVAHFDLVREW-----------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
             QV    L                 +   K LN  L     I +L    V   FHARF+
Sbjct: 182 TGQVISLYLRSNIKDVGGDMLDERSEIDYVKVLNRIL--PRDIRVLGWCPVPADFHARFT 239

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QA 165
            + R Y Y                      LD   M+ AA   +G HDF  F  +     
Sbjct: 240 CLSREYKYLFW----------------KGDLDILEMQKAASKFIGEHDFRNFCKMDAANV 283

Query: 166 SSPIRTIDHFDVNS------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           S+  R I  F +++         L  + +   +FL  Q+R  V  L L+G G  + + ++
Sbjct: 284 SNYRRHITEFTISACDRRSNNDELCSMTIKGSAFLWHQVRCMVAVLFLIGQGLESPSVVD 343

Query: 220 KALQ--AQDRKECGPLAPPEGLYFDSVEYS 247
             L      RK    +AP   L   S  + 
Sbjct: 344 SLLDIMKTSRKPQYKMAPELPLILQSCLFD 373


>gi|297380269|gb|ADI35156.1| tRNA pseudouridine synthase A [Helicobacter pylori v225d]
          Length = 242

 Score =  170 bits (430), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 103/250 (41%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VVAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     + +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAQKHWNAAKLFYHLAPKLAPH--VVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SLD   +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQVQIHNIKATIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|327282044|ref|XP_003225754.1| PREDICTED: tRNA pseudouridine synthase 3-like [Anolis carolinensis]
          Length = 455

 Score =  170 bits (430), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 98/281 (34%), Gaps = 55/281 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q+N + +I+  + +A+         +    H  GRTD GV A 
Sbjct: 66  VALKIAYLGWEYQGFASQENTNNTIEEKLFEALGKTRLVKNRQTSNYHRCGRTDKGVSAF 125

Query: 59  RQVAHFDLVREWVPVI-----------------LCKALNAYLKISDTISILNLSIVDKQF 101
            QV   DL                             LN  L     I +L  + V+  F
Sbjct: 126 GQVISLDLRSNLPENKPGDTATNKATKASEEIHYTHILNQVL--PPDIRVLAWAPVEPNF 183

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARF+ ++R+Y Y                     +LD   M  AAQ  VG HDF     +
Sbjct: 184 SARFNCLKRTYRYFFPCA----------------TLDVALMNRAAQKFVGTHDFRNLCKM 227

Query: 162 H--CQASSPIRTIDHFDVNSFGN-----------LIEIRVVARSFLHTQIRSFVGSLKLV 208
                 +S  RTI   +V                +    V  ++FL+ Q+R  +  L L+
Sbjct: 228 DVANGVTSFHRTILAAEVQPVDGESETEQQNPFRMYYFEVTGQAFLYHQVRCMMAILFLI 287

Query: 209 GDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           G        +++ L  +   RK    +A    L     ++ 
Sbjct: 288 GQRMERPEIIDELLDIEKNPRKPQYSMAVEFPLVLYDCDFE 328


>gi|303284649|ref|XP_003061615.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456945|gb|EEH54245.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 390

 Score =  170 bits (430), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 78/257 (30%), Positives = 112/257 (43%), Gaps = 44/257 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH---GAGRTDSGVHALR 59
           RY + I+Y+G  + G+QRQ N  ++QG +E+A+   TG    VH   G+ RTD+GVHAL 
Sbjct: 7   RYLLRIQYDGGAFHGFQRQANARTVQGCVEEAMAKFTGVEGGVHAITGSSRTDAGVHALD 66

Query: 60  QVAHF----------DLVREWVPVILCKALNAYLK-ISDTISILNLSIV-DKQFHARFSA 107
             AH                     + KA+N YL+  +   SI + + V  + FHAR+ A
Sbjct: 67  ATAHVDIDDGDAGDAPPPPPHSARTVMKAVNHYLRKTAPMASIASCARVCPETFHARYCA 126

Query: 108 IRRSYLYRIITRQA-PLALEKGRAWLIPK---------------------SLDCENMRIA 145
             R+Y Y I   +  P   ++G+AW +                        LD + M  A
Sbjct: 127 TARTYRYLIYLGRDEPSVFDRGKAWHVYDGRNASGAGVNTHEPSGGCALGGLDVDAMNAA 186

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
           A+  VG HDF+ FR+  CQASSPIR +    V+          +A         S V   
Sbjct: 187 ARRFVGEHDFSAFRANGCQASSPIRRLHVLRVDRAMPWPSFPSIASQD------SMVMHS 240

Query: 206 KLVGDGKWTSTDLEKAL 222
             V        DL + L
Sbjct: 241 FDVAK-PMEEDDLSEVL 256



 Score = 88.7 bits (219), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA-QDRKECGPLAPPEGLY 240
             I I   A SFL+ Q+R  VG+L+ VG G+ +  D+   L+   D     P+AP  GLY
Sbjct: 284 GHIVITARAPSFLYHQVRLMVGTLRAVGAGELSPDDVTDLLEGTTDASRAPPMAPAHGLY 343

Query: 241 FDSVEYS 247
            + V Y 
Sbjct: 344 LERVHYD 350


>gi|317009700|gb|ADU80280.1| tRNA pseudouridine synthase A [Helicobacter pylori India7]
          Length = 242

 Score =  169 bits (429), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 102/250 (40%), Gaps = 12/250 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+  +  + V V  AGRTD GVHA  Q
Sbjct: 1   MRCFKTTIAYDGAYFLGYAKQPNKLGVQDKIESALNALGIKSV-VIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F   + W    L   L   L     I +  L    K FHARF A +R+Y Y +    
Sbjct: 60  VLSFYAPKHWNAAKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRAYRYLLTKNL 115

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L    A     SL    +  A +   G+HDF+ F+      ++P R I +      
Sbjct: 116 KTPFLAPYIACGDYGSL--VALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKT 173

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                  +  +++  +FL + +R  + +       K T  +++  +         P+   
Sbjct: 174 FIIGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIQAQIHNIKAAIRTPIM-A 232

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 233 NGLYLHRVYY 242


>gi|242040775|ref|XP_002467782.1| hypothetical protein SORBIDRAFT_01g033960 [Sorghum bicolor]
 gi|241921636|gb|EER94780.1| hypothetical protein SORBIDRAFT_01g033960 [Sorghum bicolor]
          Length = 459

 Score =  169 bits (428), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 95/264 (35%), Gaps = 44/264 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + + Y G  ++G+  + N   +++  I KA+        + +       GRTD GV A
Sbjct: 124 VALKVMYFGQRFYGFSSEGNTEPTVESEIFKALERAKLMVGSRKESCYSRCGRTDKGVSA 183

Query: 58  LRQVAHFDLVREW-----------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
             QV    L                 +   K LN  L     I +L    V   FHARF+
Sbjct: 184 TGQVISLYLRSNIKDVGGDMLDERSEIDYVKVLNRIL--PRDIRVLGWCPVPADFHARFT 241

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQA 165
            + R Y Y                      LD   M+ AA   +G HDF  F  +     
Sbjct: 242 CLSREYKYLFW----------------KGDLDILEMQKAASKFIGEHDFRNFCKMDAANV 285

Query: 166 SSPIRTIDHFDVNS------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           S+  R I  F +++         L  + +   +FL  Q+R  V  L L+G G  + + ++
Sbjct: 286 SNYRRRITEFTISACDRRSNNDELCSMMIKGSAFLWHQVRCMVAVLFLIGQGLESPSVVD 345

Query: 220 KALQ--AQDRKECGPLAPPEGLYF 241
             L      RK    +AP   L  
Sbjct: 346 SLLDITKTPRKPQYKMAPELPLIL 369


>gi|150403192|ref|YP_001330486.1| tRNA pseudouridine synthase A [Methanococcus maripaludis C7]
 gi|150034222|gb|ABR66335.1| tRNA pseudouridine synthase [Methanococcus maripaludis C7]
          Length = 262

 Score =  169 bits (428), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 99/248 (39%), Gaps = 33/248 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGR--LSFQTQPHGETVCDKISNALLDCGYLDDKDRVPLYHGGRTDRGVSALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
               +++ ++ V   +   L       D I +L    +D      +    R Y Y +   
Sbjct: 60  NYIVYEMDKKPVLPRVQSNL-----KKDGIWVLGCKEIDTFPEIEY----RHYQYNLPN- 109

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVN 178
                          K+ D E M+ A++ L+G H F         +   P+RT+    ++
Sbjct: 110 ---------------KNHDVELMKKASEKLIGTHYFQNLSKRDKTKVKDPVRTLHDIKIS 154

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW-TSTDLEKALQAQDRKECGPLAPPE 237
           S    I I +   SFL   +R  +  L  VG  K+       + + ++D  +  P +P E
Sbjct: 155 SNDYFITIDIFGESFLWNMVRRIIRLLSDVGKHKFEDPEKFIELILSKDYNKGYPPSPAE 214

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 215 GLILVDVK 222


>gi|301117110|ref|XP_002906283.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
 gi|262107632|gb|EEY65684.1| tRNA pseudouridine synthase A, putative [Phytophthora infestans
           T30-4]
          Length = 316

 Score =  168 bits (427), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 72/287 (25%), Positives = 120/287 (41%), Gaps = 50/287 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-------NGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDS 53
           RYC+ I Y G+G+ GWQRQ+          S+Q  +E A+    G  + V V G  RTD+
Sbjct: 18  RYCLHIAYYGTGFVGWQRQQQETKSSSGHDSVQEVVEAAVTETLGTSKRVNVTGVSRTDA 77

Query: 54  GVHALRQVAHFDLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           G HAL Q     L  E       L   +N  L I   +++L ++ V     +R  +  + 
Sbjct: 78  GTHALYQFGFIRLDSELPMTMDELKDRVNTKLDIGR-VAVLGVT-VPTTGPSRIRSRYKK 135

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR----SIHCQASS 167
           Y+Y +     P       +W + + LD + +R A + L G HDF  F         +  +
Sbjct: 136 YIYYLQQGHRPDLELGKYSWFLGRRLDIQRIRDALKFLEGTHDFRPFSQGLQKPKFEDMT 195

Query: 168 PIRTIDHFDVNSFGN-------------------------------LIEIRVVARSFLHT 196
            +RT+    V +  N                                + I +VA  FL  
Sbjct: 196 TLRTVMSAKVVARRNVNFSLDPPVSGSGEIIDAADMYREPGNTPVHFVCIELVANGFLRH 255

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
            +R  +G+L+ +G+G   ++ +++ L  +   + GP AP +GL+   
Sbjct: 256 MVRRIIGTLRPIGEGTQPASRMQQVLAGEV--QPGPSAPTKGLWLHR 300


>gi|209882282|ref|XP_002142578.1| tRNA pseudouridine synthase A family protein [Cryptosporidium muris
           RN66]
 gi|209558184|gb|EEA08229.1| tRNA pseudouridine synthase A family protein [Cryptosporidium muris
           RN66]
          Length = 332

 Score =  168 bits (427), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 68/272 (25%), Positives = 98/272 (36%), Gaps = 38/272 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHA 57
           R+   I Y G+ Y+G   Q     +I+     A   +      E   +   GRTD GVH+
Sbjct: 26  RFLFRISYIGTNYYGMAYQNETIPTIEREFYNACLRLKLIKNREDCDLIRCGRTDKGVHS 85

Query: 58  LRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
                  +L  R+  P    + +N  L     I IL    V+  F ARF    R Y Y  
Sbjct: 86  TGNYISINLRTRDTSPYNYQEMINGVL--PWDIRILGFCQVNNNFSARFDCDSRVYKYIF 143

Query: 117 ITRQAPLALEKGRAWLIPKSLDC---ENMRIAAQHLVGRHDFTTFRSIHCQAS---SPIR 170
              Q     E          L+    + M  + +  +G HDF  F  +  +     + +R
Sbjct: 144 PIDQIQN-FEHNY----FPKLNINHIDQMNKSCKQFIGTHDFRVFCKMDIKNRPNQTYVR 198

Query: 171 TIDHFDVNSFGN----------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           TI  F V  F N                L  I ++  +FL  Q+R  VG L  +  GK  
Sbjct: 199 TIYDFRVEVFNNNKISSSSFDNSINDTKLGVITIIGSAFLWHQVRLMVGILFEISLGKIR 258

Query: 215 STDLEKALQA---QDRKECGPLAPPEGLYFDS 243
           S  + K L     +D     P+A   GL    
Sbjct: 259 SECITKLLDNYFDKDEIPFFPMASEIGLILWD 290


>gi|159905071|ref|YP_001548733.1| tRNA pseudouridine synthase A [Methanococcus maripaludis C6]
 gi|238686937|sp|A9A828|TRUA_METM6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|159886564|gb|ABX01501.1| tRNA pseudouridine synthase [Methanococcus maripaludis C6]
          Length = 262

 Score =  168 bits (427), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 99/248 (39%), Gaps = 33/248 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGR--LSFQTQPHGETVCDKISNALLDCGYLDNKDRVPLYHGGRTDRGVSALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
               +++ ++ V   +   L       D + +L    +D      +    R Y Y +   
Sbjct: 60  NYIVYEMDKKPVLPRVQSKLKW-----DGVWVLGCKEIDTFPEIEY----RHYQYNLPN- 109

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVN 178
                          K+ D E M+ A++ L+G H F         +   P+RT+ +  ++
Sbjct: 110 ---------------KNHDVELMKKASEKLIGTHYFQNLSKRDKSKVKDPVRTLYNIKIS 154

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT-STDLEKALQAQDRKECGPLAPPE 237
           S    I I +   SFL   +R  +  L  +G  K        + + ++D  +  P +P E
Sbjct: 155 SNDYFITIDIFGESFLWNMVRRIIRLLSDIGKHKIKDPEKFIELILSEDYSKGYPPSPAE 214

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 215 GLILVDVK 222


>gi|118350997|ref|XP_001008777.1| tRNA pseudouridine synthase A family protein [Tetrahymena
           thermophila]
 gi|89290544|gb|EAR88532.1| tRNA pseudouridine synthase A family protein [Tetrahymena
           thermophila SB210]
          Length = 481

 Score =  168 bits (427), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 98/262 (37%), Gaps = 41/262 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           Y + + Y G  Y G   Q+   ++++  + KA+   T     +      +GRTD GV AL
Sbjct: 114 YALKMSYVGINYQGLAYQQETDNTVEEQLFKALEKTTLIKNRDNCNFTRSGRTDKGVSAL 173

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV    L            +   +   D I IL  S VD  F+ARF   +R Y Y    
Sbjct: 174 GQVIGITLRTSIK-------IGENIDEIDDIRILGCSKVDPAFNARFDCQKRIYKY---- 222

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDV 177
                       +     +D + M+ AA   +G HDF  F  I   Q  + +R I   D+
Sbjct: 223 ------------YFFENQMDIQRMKEAANLFLGEHDFRNFCKIDVLQTLNYVRIIYQLDI 270

Query: 178 NS----------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                          L    +   +FL  QIR+ +  L LVG  +   + + + L  Q  
Sbjct: 271 EEVQANFGTLDPRSKLYVATIQGSAFLWHQIRNMMAILFLVGRKQEEPSIVTELLDIQKN 330

Query: 228 --KECGPLAPPEGLYFDSVEYS 247
             K    +AP   L      Y+
Sbjct: 331 PSKPNYEMAPDYPLVLFDCLYN 352


>gi|57242355|ref|ZP_00370294.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis RM3195]
 gi|57017035|gb|EAL53817.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis RM3195]
          Length = 240

 Score =  168 bits (427), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 100/246 (40%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G   Q + +S+Q +   A     G    V  A RTD GVHALR V
Sbjct: 1   MRLKLVFSYDGSAFLGSACQPHLNSVQDA-LAAALAHLGIFSPVLFASRTDKGVHALRAV 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +   V L + +N +      I I +L  V + +  RF    R Y Y     +
Sbjct: 60  ACVECGEHFKDLVYLKRQINRFTH--PFIHIKSLERVSENYAVRFDVRAREYRYIFHHGE 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                         +  D +       H VG  DF  F+     A + +R +      ++
Sbjct: 118 F-NPFLSPYVCFSER-FDIKKANELLSHFVGEKDFKFFQKAGGSAKTSVRIMFFARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +L      A  FL  QIR  V S+  V  G+ +   L++ ++A+       LAP  GLY
Sbjct: 176 KDLSIFCFRANGFLRAQIRLSVASVMAVLRGELSEDKLKEQIEAKKCHY-RFLAPANGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRIIY 240


>gi|294901661|ref|XP_002777462.1| tRNA pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239885099|gb|EER09278.1| tRNA pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 387

 Score =  168 bits (427), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 64/278 (23%), Positives = 98/278 (35%), Gaps = 50/278 (17%)

Query: 3   RYCMIIEYNGSG--------------------YFG--WQRQK--NGSSIQGSIEKAIFLV 38
           R+ M   Y G+                     Y G  WQ Q+    ++++  + K +   
Sbjct: 34  RFVMKFAYVGTRQASFPSTTMALKVCVEAVLRYAGVAWQNQEAFGVNTVENELFKGLVKT 93

Query: 39  T----GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNL 94
                         GRTD GVHA    A   L  +               + D I +L +
Sbjct: 94  CLIESRMSCDFSRCGRTDKGVHARGNYATLRLRLKPDGTEFPYIQMINRVLPDDIRVLRI 153

Query: 95  SIVD-KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
             V    F ARFS   R+Y Y   +                  LD E M  AAQ LVG+H
Sbjct: 154 CSVPSDDFDARFSCKSRTYKYFFPST----------------GLDLEVMAEAAQRLVGQH 197

Query: 154 DFTTFRSIHCQASSPI-RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           D+  F  +  + ++   RTI  F++ +   +    +   +FL  Q+R  +  L L+G G 
Sbjct: 198 DYRNFCRMDVEQTTNFERTIYSFEICNGDVISHAVITGSAFLWHQVRCMMEVLMLIGKGL 257

Query: 213 WTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEYS 247
                +   L   ++    P   LA   GL     +Y 
Sbjct: 258 EKPEVI-DMLFDINKTPGKPSYDLADGAGLVLFDCKYD 294


>gi|219888663|gb|ACL54706.1| unknown [Zea mays]
          Length = 271

 Score =  168 bits (427), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/194 (29%), Positives = 86/194 (44%), Gaps = 8/194 (4%)

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           QVAHF     +  +  +  A+N        I +  +S    +FHAR S   + Y Y+I  
Sbjct: 51  QVAHFTTPFSYSCLSSIHSAMNGL--PPPEIRVREISAARPEFHARSSTKSKVYRYKIYN 108

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFD 176
                      A+     L+   M+ AA + VG HDFT+F +   +     P + I  FD
Sbjct: 109 EAIMDPFHNHYAYHSAYKLNPHAMQEAANYFVGIHDFTSFANAAHNDGERRPTKKITRFD 168

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL--- 233
           V   G ++++ V    FL+ Q+R+ V  L  VG        +   + A+DRKE   +   
Sbjct: 169 VTEMGAVLQLEVEGTGFLYRQVRNMVALLLQVGKEALPPDIVPAIIAARDRKELAKVALS 228

Query: 234 APPEGLYFDSVEYS 247
           APP GLY  SV Y 
Sbjct: 229 APPHGLYLMSVNYD 242


>gi|222480083|ref|YP_002566320.1| tRNA pseudouridine synthase [Halorubrum lacusprofundi ATCC 49239]
 gi|222452985|gb|ACM57250.1| tRNA pseudouridine synthase [Halorubrum lacusprofundi ATCC 49239]
          Length = 293

 Score =  168 bits (425), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 106/255 (41%), Gaps = 28/255 (10%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL----------VTGEIVVVHGAGRTDSG 54
              + Y+G  Y G+QRQ + ++++G++ +A+                      AGRTD+G
Sbjct: 10  AFRVAYDGREYAGFQRQPHATTVEGTLLRALAKHGILDRGDGPTHATPPGYAAAGRTDAG 69

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A+ Q   F+      P    +A N +L    ++ +   + V   FHA   A+RR+Y Y
Sbjct: 70  VSAVAQTVAFEAPDWLTP----RAFNGHL--PGSVRVWAAADVPAGFHATHDAVRRTYRY 123

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       A  +        ++D   +R A   L G  D   F ++    +  +R +  
Sbjct: 124 HLY------APARVEETDHDHAVDDGRVRDALARLSGEQD---FHNLTSDETGTVRDLT- 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGP 232
                 G+++ + V A  F    +R  V +++ VG G    + +++ L ++    +    
Sbjct: 174 TTATREGDILVVEVSAGGFPRALVRRLVAAVRAVGRGTADPSLIDRLLASEPISGEFGIG 233

Query: 233 LAPPEGLYFDSVEYS 247
            APPE L    V Y 
Sbjct: 234 PAPPEPLVLWDVSYE 248


>gi|86143390|ref|ZP_01061792.1| tRNA pseudouridine synthase A [Leeuwenhoekiella blandensis MED217]
 gi|85830295|gb|EAQ48755.1| tRNA pseudouridine synthase A [Leeuwenhoekiella blandensis MED217]
          Length = 261

 Score =  168 bits (425), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 90/253 (35%), Gaps = 14/253 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
           Y + I+Y G  Y GWQ+Q +  +++  +++ +  V G        AGRTD+ V       
Sbjct: 8   YLLKIQYLGFRYHGWQKQPDLLTVERMMQRTLKYVLGRNNFKFIAAGRTDAKVSVNETYV 67

Query: 63  HFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              L            K  N  L     I +L +     Q +   +   + Y+Y     +
Sbjct: 68  ELILKEESLTDLQEFHKLFNENL--PQDIRLLEIIEKADQTNIIQAPKLKEYIYLFSFGE 125

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                           L+ E M+  A  + G HD+  +       +  + TI+   +   
Sbjct: 126 KNHPFCAPYMINAKGELNIELMQKGAALMQGTHDYRNYAYKASAETQTVMTIESSVIEEN 185

Query: 181 ---------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                     +    RVV   F   Q+R  +G+L  +G G  +    EK+L  +   +  
Sbjct: 186 TLYTANFFPKHSYVFRVVGAGFKRHQVRLMMGALFDLGSGVLSWEAFEKSLDGKIPFKLT 245

Query: 232 PLAPPEGLYFDSV 244
            +A   GL    V
Sbjct: 246 HIAQASGLILQEV 258


>gi|163755611|ref|ZP_02162730.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
 gi|161324524|gb|EDP95854.1| tRNA pseudouridine synthase A [Kordia algicida OT-1]
          Length = 262

 Score =  168 bits (425), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 95/258 (36%), Gaps = 17/258 (6%)

Query: 1   MIR----YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGV 55
           M R    Y + ++Y G  Y GWQ+Q + +++Q   E+ +  V G     +  +GRTD+ V
Sbjct: 1   MKRNRKYYLITLQYLGFRYHGWQKQPDVNTVQRMTERTLAYVFGHKNFKLLASGRTDAKV 60

Query: 56  HALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            A        L              N  L     I  L ++  +++F+       + Y+Y
Sbjct: 61  SANEIAIELFLDNETLNIPEFLPLFNKNL--PQDIRALAITETNEKFNIIQHPKVKEYIY 118

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                +            +   LD E M+  A+   G H   T+     + +     I+ 
Sbjct: 119 LFAFGEKYHPFAAPYMTNVLGDLDVELMKKGAKLFEGNHYLKTYCYKPTEHTILEGEIEL 178

Query: 175 FDVNSFG---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            ++                 +RV    F   QIR  +G+L L+G  +     ++++L   
Sbjct: 179 CEITENDLYTASFFPEKSYVLRVQGAGFKRHQIRMMMGTLILLGRHELDLDFIKRSLLPN 238

Query: 226 DRKECGPLAPPEGLYFDS 243
              E   +AP  GL  + 
Sbjct: 239 STLEVNYIAPASGLMLNK 256


>gi|149716663|ref|XP_001505142.1| PREDICTED: pseudouridylate synthase 3 [Equus caballus]
          Length = 479

 Score =  168 bits (425), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 94/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 63  VALRIAYLGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 122

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL   +      +  N                     +   I +L  + V+  F
Sbjct: 123 GQVISLDLRSHFPNGRDSEDFNLKDEVNDAAKEIRYTHILNRVLPPDIRVLAWAPVEPSF 182

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 183 SARFSCLERTYRY----------------FFPRADLDIITMNSAAQKYVGTHDFRNLCKM 226

Query: 162 H--CQASSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI    V   G             L +  V+ ++FL+ Q+R  +  L L
Sbjct: 227 DVANGVINFQRTILSAQVQLVGQSLAEERGQEPFQLCQFEVIGQAFLYHQVRCMMAILFL 286

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 287 IGQGMEKPEVIDELLN 302


>gi|134046431|ref|YP_001097916.1| tRNA pseudouridine synthase A [Methanococcus maripaludis C5]
 gi|132664056|gb|ABO35702.1| tRNA pseudouridine synthase [Methanococcus maripaludis C5]
          Length = 262

 Score =  168 bits (425), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 98/248 (39%), Gaps = 33/248 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGK--LSFQTQPHGETVCDKISNALLDCGYLDNKDKVPLYHGGRTDRGVAALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
               +++ ++ V   +   L       D I +L    ++           R Y Y +   
Sbjct: 60  NYVVYEMDKKPVLPRVQSKLKW-----DGIWVLGCKEIE----IFPEIEHRHYQYTLPN- 109

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVN 178
                          K+ D E M+ A++ L+G H F         +   P+RT+    ++
Sbjct: 110 ---------------KNHDVELMKKASEKLIGTHYFQNLSKRDKTKVKDPVRTLYDIKIS 154

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW-TSTDLEKALQAQDRKECGPLAPPE 237
           S    I I +   SFL   +R  +  L  +G  K        + + +++ K+  P +P E
Sbjct: 155 SNDYFITIDIFGESFLWNMVRRIIRLLSDIGKHKIEDPEKFIELILSEEYKKGYPPSPAE 214

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 215 GLILVDVK 222


>gi|296216591|ref|XP_002754614.1| PREDICTED: tRNA pseudouridine synthase 3 [Callithrix jacchus]
          Length = 477

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/253 (24%), Positives = 94/253 (37%), Gaps = 49/253 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 64  VALKIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWVPVILCKALNA--------------YLKISDTISILNLSIVDKQFHAR 104
            QV   DL  ++      +  N                  +   I IL  + V+  F AR
Sbjct: 124 GQVISLDLRSQFPRRRDSEDFNVKEEAAEEIRYTHILNRVLPPDIRILAWAPVEPSFSAR 183

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-- 162
           FS + R+Y Y                +     LD   M  AAQ  VG HDF     +   
Sbjct: 184 FSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKMDVA 227

Query: 163 CQASSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKLVGD 210
               +  RTI    V   G             L +  V  ++FL+ Q+R  +  L L+G 
Sbjct: 228 NGVINFQRTILSAQVQPVGQSPDEERWQVPFQLCQFEVTGQAFLYHQVRCMMAILFLIGQ 287

Query: 211 GKWTSTDLEKALQ 223
           G      +++ L 
Sbjct: 288 GMEKPEIIDELLN 300


>gi|57085889|ref|XP_536533.1| PREDICTED: similar to tRNA pseudouridine synthase 3 (tRNA-uridine
           isomerase 3) (tRNA pseudouridylate synthase 3) [Canis
           familiaris]
          Length = 480

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  +  A+       + +    H  GRTD GV A 
Sbjct: 64  VALKIAYLGWGYQGFASQENTNNTIEEKLFDALTKTRLVESRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL   +      +  N                     +   I +L  + V+  F
Sbjct: 124 GQVISLDLRSHFPEGSTSEDSNLKNEVNDVAKEIRYTHILNRVLPPDIRVLAWAPVEPSF 183

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 184 SARFSCLERTYRY----------------FFPRADLDIITMNYAAQKYVGTHDFRNLCKM 227

Query: 162 H--CQASSPIRTI------------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RT+            D         L +  VV ++FL+ Q+R  +  L L
Sbjct: 228 DVANGVINFQRTVLFAQVELVGQSLDKEQWQEPFQLCQFEVVGQAFLYHQVRCMMAILFL 287

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 288 IGQGMEKPEIIDELLN 303


>gi|315638468|ref|ZP_07893645.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis JV21]
 gi|315481459|gb|EFU72086.1| tRNA pseudouridine synthase A [Campylobacter upsaliensis JV21]
          Length = 240

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 101/246 (41%), Gaps = 7/246 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  ++  Y+GS + G   Q + +S+Q +   A     G    V  A RTD GVHALR V
Sbjct: 1   MRLKLVFSYDGSAFLGSASQPHLNSVQDA-LAAALAHLGIFSPVLFASRTDKGVHALRAV 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +  + +   V L + +N +      I I +L  V + +  RF    R Y Y     +
Sbjct: 60  ACVECGKHFKDLVYLKRQINRF--AHPFIHIKSLERVSENYAVRFDVRAREYRYIFHHGE 117

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                         +  D +       H VG  DF  F+     A + +R +      ++
Sbjct: 118 F-NPFLSRYVCFSER-FDIKRANELLSHFVGEKDFKFFQKAGGSAKTSVRIMFFARAYAY 175

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            +L      A  FL  QIR  V S+  V  G+ +   L++ ++A+       LAP  GLY
Sbjct: 176 KDLSIFCFRANGFLRAQIRLSVASVMAVLRGELSEDKLKEQIEAKACHY-RLLAPANGLY 234

Query: 241 FDSVEY 246
              + Y
Sbjct: 235 LSRIIY 240


>gi|324505293|gb|ADY42276.1| tRNA pseudouridine synthase A [Ascaris suum]
          Length = 491

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 106/268 (39%), Gaps = 26/268 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---VTGEIVV------VHGAGRTD 52
            RY M+I Y G  Y G Q QK+  +I+G +  A+     +T E V+         A RTD
Sbjct: 62  TRYAMLIAYQGKNYCGMQVQKDAPTIEGCLLNAMQKYGLITDEEVIKPNLFFFQRAARTD 121

Query: 53  SGVHALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
             V A+RQ+    L   E +P  +   LN  L   + I ++ +    + F+A+     R+
Sbjct: 122 RAVSAVRQMCSMMLNFDEQLPKTVPDELNKLL--PEDIRVMGIRRATRTFNAQKDCDART 179

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIR 170
           Y Y + T       E   +           +    Q  VG H+F  +         S  R
Sbjct: 180 YSYTLPTYAFAKVDELTSSAYRITDETINEINALLQIFVGTHNFFNYTSKREFSDRSCFR 239

Query: 171 TIDHFDV-----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            I  F             N     + I +  +SF+  QIR  +G +  +  G    +D++
Sbjct: 240 YIIDFKCGAKFLFKNELRNEDVEFLTISIKGQSFMLHQIRKMIGMVIAISRGLLYKSDIQ 299

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++ ++   +   P AP  GL  + V Y 
Sbjct: 300 RSFESA--RMDVPKAPGLGLLLEKVHYD 325


>gi|218460354|ref|ZP_03500445.1| tRNA pseudouridine synthase A [Rhizobium etli Kim 5]
          Length = 141

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 78/121 (64%), Positives = 95/121 (78%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G+AW +PK+LD E M  AAQ LVGRHDF+TFRS HCQA+SP+RT+D  DV   G LIEI
Sbjct: 1   AGKAWWVPKTLDHEVMHAAAQRLVGRHDFSTFRSAHCQANSPVRTLDRLDVTRSGALIEI 60

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           R  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A++RK CGP+APP+GLYF  V+Y
Sbjct: 61  RATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARNRKACGPVAPPDGLYFLQVDY 120

Query: 247 S 247
            
Sbjct: 121 P 121


>gi|271962666|ref|YP_003336862.1| tRNA-pseudouridine synthase I [Streptosporangium roseum DSM 43021]
 gi|270505841|gb|ACZ84119.1| tRNA-pseudouridine synthase I [Streptosporangium roseum DSM 43021]
          Length = 360

 Score =  167 bits (423), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 45/164 (27%), Positives = 75/164 (45%), Gaps = 2/164 (1%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMR 143
           +   + +  +++  + F ARFSA+ R Y YR+         L +       + LD + + 
Sbjct: 178 LPPDVRVYRVTVAPRGFDARFSAMSRRYAYRVSDAPGGVDPLRRREVIWYGRPLDVDRLN 237

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVG 203
            AA  L+G HDF  F     + ++ IR +   D     +++   VVA +F H+ +R+ VG
Sbjct: 238 AAAAVLLGEHDFAAFCKKR-EGATTIRELQRLDWVRQDDILVATVVADAFCHSMVRALVG 296

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           SL  VG+G+       + L    R     +AP  GL  + V Y 
Sbjct: 297 SLLPVGEGRLAVDWPGRVLTRAVRDSGVHVAPAHGLCLEEVRYP 340



 Score = 97.2 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 29/68 (42%), Positives = 43/68 (63%), Gaps = 2/68 (2%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG--EIVVVHGAGRTDSGVHAL 58
          M+R  + + Y+G+ + GW +Q    ++QG IE+A+  +    E  V+  AGRTD+GVHA 
Sbjct: 1  MVRLRLDLAYDGTDFSGWAKQPGRRTVQGEIEEALGKILRLPEPPVLTVAGRTDAGVHAR 60

Query: 59 RQVAHFDL 66
           QVAH DL
Sbjct: 61 GQVAHVDL 68


>gi|219123859|ref|XP_002182234.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406195|gb|EEC46135.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 308

 Score =  167 bits (423), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 75/311 (24%), Positives = 113/311 (36%), Gaps = 67/311 (21%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQ--------------KN-----------GSSIQGSIEKAI 35
           M  Y +I+ Y+G+ + G+QRQ               +             ++Q  +E+A+
Sbjct: 1   MPLYKLIVAYDGTRFNGFQRQSTTTDMSKKIALKRPHWDSATGKRKGIALTVQECLEQAL 60

Query: 36  FLVTGEIVVVHG-----AGRTDSGVHALRQVAHFDLVREWVPVILCK---ALNAYLKISD 87
              TG    V       AGRTD GVHA  QV    L     P  L +   ALN+ L    
Sbjct: 61  MDWTGNETNVEAFRFRFAGRTDKGVHARGQVVAVQLPIVVEPTELWRVHKALNSRL--PV 118

Query: 88  TISILNLSIVDK--QFHARFSAIRRSYLYRIITRQ-------------------APLALE 126
            IS+  + + +    F  R     + Y Y I  R+                   A  A++
Sbjct: 119 DISVERVELCENQLDFDPRHDVQSKQYSYTIKFRRKAYNEEGQLLPICTSGPQSARSAMD 178

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVN------S 179
               WL P  LD   +    Q L G+H F +F           I T+D   V        
Sbjct: 179 SPCLWLCPWVLDDSKLYELCQRLQGQHSFRSFVHRADRNLRDHILTLDRVWVEALSCTRE 238

Query: 180 FGNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-KECGPLAPP 236
              ++ +R    A+ F  + +R+ VG    V  G +     +   +  D   +    AP 
Sbjct: 239 DAPVVTVRLWFQAKGFRRSMVRNLVGFCVDVCRGMYQPDW-DALWEGSDEIAQKVHSAPA 297

Query: 237 EGLYFDSVEYS 247
            GL  +SV YS
Sbjct: 298 CGLCLESVAYS 308


>gi|45357831|ref|NP_987388.1| tRNA pseudouridine synthase A [Methanococcus maripaludis S2]
 gi|62901319|sp|Q6M0K2|TRUA_METMP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|45047391|emb|CAF29824.1| tRNA pseudouridine synthase Related [Methanococcus maripaludis S2]
          Length = 262

 Score =  167 bits (423), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 57/248 (22%), Positives = 98/248 (39%), Gaps = 33/248 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHALR 59
           Y   I Y+G     +Q Q +G ++   I  A+    +L   + V ++  GRTD GV AL 
Sbjct: 2   YIFKIAYDGK--LSFQTQPHGETVCDKISNALLDCGYLDNKDRVPLYHGGRTDRGVAALG 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
               +++ ++ V   +   L       D I +L    ++           R Y Y +   
Sbjct: 60  NYVVYEMDKKPVLPRVQSKLKW-----DGIWVLGCKKIE----IFPEIEHRHYQYTLPN- 109

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVN 178
                          K+ D E M+ A++ L+G H F         +   P+RT+    ++
Sbjct: 110 ---------------KNHDVELMKKASEKLIGTHYFQNLSKRDKTKVKDPVRTLYDIKIS 154

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT-STDLEKALQAQDRKECGPLAPPE 237
           S    I I +   SFL   +R  +  L  +G  K        + + ++D K+  P +P E
Sbjct: 155 SNDYFITIDIFGESFLWNMVRRIIRLLSDIGKHKIENPEKFIELILSEDYKKGYPPSPAE 214

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 215 GLILVDVK 222


>gi|328702786|ref|XP_003242010.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Acyrthosiphon
           pisum]
          Length = 358

 Score =  166 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 119/287 (41%), Gaps = 42/287 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDS 53
           RY +   Y G+ + G QRQ         + SS+QG +E A+  +       +H + RTD 
Sbjct: 5   RYLLYFSYIGTRFRGVQRQLTYDMVHNDDPSSVQGLLEYALKQLQPLNTPKLHLSSRTDQ 64

Query: 54  GVHALRQVAHFDLVREWV--PVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRR 110
           GVH+ +  AH DL   +   P  L   +N +L   +  I +++  IV   F+AR  A  R
Sbjct: 65  GVHSFKSSAHLDLELPYTCHPNKLVFQVNNFLSSCEVPIKLVSAQIVPNDFNARSCAKWR 124

Query: 111 SYLYRIITRQA--------PLAL-----EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFT 156
            YLYR+   ++                 E  R + I KS  D E ++      +G  D+ 
Sbjct: 125 KYLYRLAVVKSEFKDLYAERFVFPIPITEDKRCYFIQKSDFDVELVKNVLPLFIGTKDYK 184

Query: 157 TFRSIHCQAS--SPIRT-----------IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVG 203
           TF       +  S IRT               D++ + N  +IRV ARSFL+ QIR  VG
Sbjct: 185 TFMGKSGLNTELSTIRTWNNIEIVPGRSFYPTDIDKYYNYWDIRVNARSFLYKQIRRTVG 244

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEYS 247
            L  V     T  D++            P    AP  GLY   + Y 
Sbjct: 245 VLIKVAQNIITYDDVKYMFDNPSINSWNPKISTAPSYGLYLYDIGYD 291


>gi|148693449|gb|EDL25396.1| pseudouridine synthase 3, isoform CRA_b [Mus musculus]
          Length = 322

 Score =  166 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 94/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 72  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 131

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I +L  + V+  F
Sbjct: 132 GQVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSF 191

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 192 SARFSCLERTYRY----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 235

Query: 162 H--CQASSPIRTIDHFDVN------------SFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI    V                 L +  V+ ++FL+ Q+R  +  L L
Sbjct: 236 DVANGVINFQRTILCAQVQLVAQSPGEERRQEPFQLCQFEVIGQAFLYHQVRCMMAILFL 295

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 296 IGQGMEKPEIIDELLN 311


>gi|12847644|dbj|BAB27651.1| unnamed protein product [Mus musculus]
          Length = 316

 Score =  166 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 94/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 66  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 125

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I +L  + V+  F
Sbjct: 126 GQVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSF 185

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 186 SARFSCLERTYRY----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 229

Query: 162 H--CQASSPIRTIDHFDVN------------SFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI    V                 L +  V+ ++FL+ Q+R  +  L L
Sbjct: 230 DVANGVINFQRTILCAQVQLVAQSPGEERRQEPFQLCQFEVIGQAFLYHQVRCMMAILFL 289

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 290 IGQGMEKPEIIDELLN 305


>gi|296187338|ref|ZP_06855733.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
 gi|296047860|gb|EFG87299.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
          Length = 141

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 46/137 (33%), Positives = 72/137 (52%)

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           ++YLY I   +      +  A+ + ++L+   MR AA+ L G HDF +F S+     S +
Sbjct: 5   KTYLYTINNNKFRNVFNRKYAYHVEENLNLSEMRDAAEVLTGTHDFQSFTSLKSNTKSTV 64

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           RTI++  +     +I I V   SFL   +R  VG+L  VG G    +D+EK L  + R E
Sbjct: 65  RTINYISITEEHGMIGIEVNGNSFLLNMVRIIVGTLLDVGKGILKPSDVEKILYEKKRAE 124

Query: 230 CGPLAPPEGLYFDSVEY 246
            GP+A  +GL    ++Y
Sbjct: 125 AGPMAAAKGLCLKDIQY 141


>gi|322368335|ref|ZP_08042904.1| tRNA pseudouridine synthase A [Haladaptatus paucihalophilus DX253]
 gi|320552351|gb|EFW93996.1| tRNA pseudouridine synthase A [Haladaptatus paucihalophilus DX253]
          Length = 263

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 91/251 (36%), Gaps = 32/251 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK---AIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R    + Y+G  ++G+QRQ +  +++ S+ +   A+ +          AGRTDSGV AL
Sbjct: 1   MR-AFRVAYDGRPFYGFQRQPDVPTVEDSLFESLRALGVADRVPDGYAAAGRTDSGVSAL 59

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            Q   F+      P           ++   I +   + V   FHA   A  R Y+Y    
Sbjct: 60  AQTVAFECPEWLTPSAF------NSELPAEIRVWASADVVPAFHATHDAYYREYVYHCYA 113

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +A                +    + A+  L G HD   F ++       +R +   DV 
Sbjct: 114 PRA----------------NLGLAKEASDRLSGEHD---FHNLTSDTEGTVRDL-GIDVV 153

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPP 236
             G  +     A  F    +R  V  +  +  G      ++  L  +  D +   P A  
Sbjct: 154 QDGEYLVFTFQAGGFARNLVRRVVSLIHSIATGDAEMAKIDTVLAPEPLDGRAGVPCASA 213

Query: 237 EGLYFDSVEYS 247
             LY   V Y 
Sbjct: 214 HPLYLADVGYD 224


>gi|194864517|ref|XP_001970978.1| GG25359, isoform B [Drosophila erecta]
 gi|190652761|gb|EDV50004.1| GG25359, isoform B [Drosophila erecta]
          Length = 288

 Score =  166 bits (420), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 76/281 (27%), Positives = 116/281 (41%), Gaps = 52/281 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALQVFHPTNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL      DL R     +    L   LN  L      I +L+  +VD  FH R+ 
Sbjct: 61  DAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQRLPIRVLSSQLVDNSFHCRYD 120

Query: 107 AIRRSYLYRIITRQ----------------APLALEKGRAWLIPKS-LDCENMRIAAQHL 149
           AI R+YLYR    +                     E  R + +  S  D   ++ AA+  
Sbjct: 121 AIGRTYLYRFAVAKDSSLGDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVKAAARMF 180

Query: 150 VGRHDFTTFRSIHCQASS------PIRTIDHFDVNSFG---------------NLIEIRV 188
           +G HDF TF S+  Q  S       +R ID  ++                   N  +I +
Sbjct: 181 IGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDIEI 240

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            A+SFL+ Q+R  VG+L  +G+G+     L + L    +  
Sbjct: 241 KAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNS 281


>gi|26347775|dbj|BAC37536.1| unnamed protein product [Mus musculus]
          Length = 481

 Score =  165 bits (419), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 94/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 66  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 125

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I +L  + V+  F
Sbjct: 126 GQVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSF 185

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 186 SARFSCLERTYRY----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 229

Query: 162 H--CQASSPIRTIDHFDVN------------SFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI    V                 L +  V+ ++FL+ Q+R  +  L L
Sbjct: 230 DVANGVINFQRTILCAQVQLVAQSPGEERRQEPFQLCQFEVIGQAFLYHQVRCMMAILFL 289

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 290 IGQGMEKPEIIDELLN 305


>gi|194864515|ref|XP_001970977.1| GG25359, isoform A [Drosophila erecta]
 gi|190652760|gb|EDV50003.1| GG25359, isoform A [Drosophila erecta]
          Length = 499

 Score =  165 bits (419), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 76/281 (27%), Positives = 116/281 (41%), Gaps = 52/281 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSVQGCLELALQVFHPTNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL      DL R     +    L   LN  L      I +L+  +VD  FH R+ 
Sbjct: 61  DAGVHALHSTVQVDLERPNGQPYDTTTLTGVLNRTLNKQRLPIRVLSSQLVDNSFHCRYD 120

Query: 107 AIRRSYLYRIITRQ----------------APLALEKGRAWLIPKS-LDCENMRIAAQHL 149
           AI R+YLYR    +                     E  R + +  S  D   ++ AA+  
Sbjct: 121 AIGRTYLYRFAVAKDSSLGDCNLRNKAYETFIPVEEIDRCYFLQSSSFDINRVKAAARMF 180

Query: 150 VGRHDFTTFRSIHCQASS------PIRTIDHFDVNSFG---------------NLIEIRV 188
           +G HDF TF S+  Q  S       +R ID  ++                   N  +I +
Sbjct: 181 IGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSSAILAAETYNYWDIEI 240

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            A+SFL+ Q+R  VG+L  +G+G+     L + L    +  
Sbjct: 241 KAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTVPSKNS 281


>gi|227499255|ref|NP_075781.3| tRNA pseudouridine synthase 3 [Mus musculus]
 gi|52783242|sp|Q9JI38|PUS3_MOUSE RecName: Full=tRNA pseudouridine synthase 3; AltName: Full=tRNA
           pseudouridylate synthase 3; AltName: Full=tRNA-uridine
           isomerase 3
 gi|22137577|gb|AAH29253.1| Pseudouridine synthase 3 [Mus musculus]
 gi|148693450|gb|EDL25397.1| pseudouridine synthase 3, isoform CRA_c [Mus musculus]
          Length = 481

 Score =  165 bits (419), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 94/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 66  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 125

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I +L  + V+  F
Sbjct: 126 GQVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSF 185

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 186 SARFSCLERTYRY----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 229

Query: 162 H--CQASSPIRTIDHFDVN------------SFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI    V                 L +  V+ ++FL+ Q+R  +  L L
Sbjct: 230 DVANGVINFQRTILCAQVQLVAQSPGEERRQEPFQLCQFEVIGQAFLYHQVRCMMAILFL 289

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 290 IGQGMEKPEIIDELLN 305


>gi|109109191|ref|XP_001111887.1| PREDICTED: tRNA pseudouridine synthase 3 [Macaca mulatta]
          Length = 480

 Score =  165 bits (419), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 64  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALSKTRLVESRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I IL  + V+  F
Sbjct: 124 GQVISLDLRSQFPRGRDSEDFNVKEEANATAEEIRYTHILNRVLPPDIRILAWAPVEPSF 183

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 184 SARFSCLERTYRY----------------FFPRADLDIVAMDYAAQKYVGTHDFRNLCKM 227

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 228 DVANGVINFQRTILSAQVRLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 287

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 288 IGQGMEKPEIIDELLN 303


>gi|16550495|dbj|BAB70990.1| unnamed protein product [Homo sapiens]
          Length = 481

 Score =  165 bits (419), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 93/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      + LN                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSQFPRGRDSEDLNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEIIDELLN 304


>gi|219363303|ref|NP_001136956.1| hypothetical protein LOC100217116 [Zea mays]
 gi|194697754|gb|ACF82961.1| unknown [Zea mays]
          Length = 201

 Score =  165 bits (419), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 51/168 (30%), Positives = 76/168 (45%), Gaps = 5/168 (2%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           +   I +  +S    +FHAR S   + Y Y+I             A+     L+   M+ 
Sbjct: 5   LPPEIRVREISAARPEFHARSSTKSKVYRYKIYNEAIMDPFHNHYAYHSAYKLNPHAMQE 64

Query: 145 AAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
           AA + VG HDFT+F +   +     P + I  FDV   G ++++ V    FL+ Q+R+ V
Sbjct: 65  AANYFVGIHDFTSFANAAHNDGERRPTKKITRFDVTEMGAVLQLEVEGTGFLYRQVRNMV 124

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEYS 247
             L  VG        +   + A+DRKE   +   APP GLY  SV Y 
Sbjct: 125 ALLLQVGKEALPPDIVPAIIAARDRKELAKVALSAPPHGLYLMSVNYD 172


>gi|153840131|ref|ZP_01992798.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
 gi|149746249|gb|EDM57337.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ3810]
          Length = 142

 Score =  165 bits (418), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 44/118 (37%), Positives = 67/118 (56%)

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
                  LD + M  A Q+L+G +DF++FR+ HCQ+ SP R + H +V   G+ + I + 
Sbjct: 5   VSHYHGELDEKKMHEAGQYLLGENDFSSFRAAHCQSLSPCRNLMHLNVTRHGDYVVIDIK 64

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY   V+Y 
Sbjct: 65  ANAFVHHMVRNITGSLIKVGRGEEKPEWIKWLLEAKDRKLAGATAKAEGLYLVDVDYP 122


>gi|307595363|ref|YP_003901680.1| tRNA-pseudouridine synthase I [Vulcanisaeta distributa DSM 14429]
 gi|307550564|gb|ADN50629.1| tRNA-pseudouridine synthase I [Vulcanisaeta distributa DSM 14429]
          Length = 272

 Score =  165 bits (418), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 114/246 (46%), Gaps = 26/246 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      + Y+GS + G+    + +SI+  + +AI     +   +  A RTD GV A+  
Sbjct: 1   MPTVAFKVFYDGSLFSGFT--GSTNSIEYYLRRAI-RYFIKDFKLSKASRTDPGVSAIGN 57

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V   + +      ++   LN+ L   + I     + VD+ F AR +A+ R+Y+Y +    
Sbjct: 58  VVSINYIDSI--RLVPGMLNSRL--PNGIRAWAWAEVDEGFRAR-AAVSRTYVYVMP--- 109

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                     WL     D + MR AA+  VG HD + F+       + +  I++ ++  F
Sbjct: 110 ----------WLYE---DIDLMRSAAKLFVGVHDLSNFQVKEKGVPTTVM-INNVNIERF 155

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +   V+ R F +  IR  V +L++VG G  T  +L   ++ + RK   P APP GL 
Sbjct: 156 GDYLVFIVIGRGFRNKMIRKIVNALRMVGSGILTIDELRDLIELRIRKPI-PPAPPYGLL 214

Query: 241 FDSVEY 246
             +V Y
Sbjct: 215 LLNVNY 220


>gi|9652099|gb|AAF91402.1|AF266505_1 pseudouridine synthase 3 [Mus musculus]
          Length = 481

 Score =  164 bits (417), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 93/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 66  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 125

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I +L  + V+  F
Sbjct: 126 GQVISLDLRSQFPTSRDSEDSNLKHEADDLAKEIRYTHILNRVLPADIRVLAWAPVEPSF 185

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 186 SARFSCLERTYRY----------------FFPRADLDIATMNYAAQKYVGTHDFRNLCKM 229

Query: 162 H--CQASSPIRTIDHFDVN------------SFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                     RTI    V                 L +  V+ ++FL+ Q+R  +  L L
Sbjct: 230 DVANGVIDFQRTILCAQVQLVAQSPGEERRQEPFQLCQFEVIGQAFLYHQVRCMMAILFL 289

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 290 IGQGMEKPEIIDELLN 305


>gi|126327379|ref|XP_001371991.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 575

 Score =  164 bits (417), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 62/284 (21%), Positives = 102/284 (35%), Gaps = 56/284 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 68  VALKIAYLGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 127

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   +L  +       +  N                     +   I +L  + V+  F
Sbjct: 128 GQVISLNLRSQLPRDKDPEDKNLKDTVNDSVEEICYTHILNRVLPPDIRVLAWATVESSF 187

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                     +LD E M  AAQ  VG HDF     +
Sbjct: 188 SARFSCLERTYRYFFPCA----------------NLDIEAMNDAAQKYVGTHDFRNLCKM 231

Query: 162 H--CQASSPIRTIDHFDVN--------------SFGNLIEIRVVARSFLHTQIRSFVGSL 205
                  +  RTI    V                   L +  V+ ++FL+ Q+R  +  L
Sbjct: 232 DVANGVINFQRTILSAKVQLVAFGSPEEKLQQQESFQLCQFEVIGQAFLYHQVRCMMAIL 291

Query: 206 KLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            L+G     +  +++ L  +   +K    +A    L     ++ 
Sbjct: 292 FLIGQRMEKAEIIDELLNIEKNPQKPQYSMAVEFPLVLYDCKFE 335


>gi|297690638|ref|XP_002822721.1| PREDICTED: tRNA pseudouridine synthase 3-like [Pongo abelii]
          Length = 481

 Score =  164 bits (417), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSQFPRGKDSEDFNVKGEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEIIDELLN 304


>gi|19115377|ref|NP_594465.1| tRNA-pseudouridine synthase (predicted) [Schizosaccharomyces pombe
           972h-]
 gi|74698445|sp|Q9UTB3|YL85_SCHPO RecName: Full=Putative tRNA pseudouridine synthase C25B8.05
 gi|6469292|emb|CAB61771.1| tRNA-pseudouridine synthase (predicted) [Schizosaccharomyces pombe]
          Length = 450

 Score =  164 bits (417), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 95/259 (36%), Gaps = 29/259 (11%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
                 Y G  Y G   Q       +++G + +A+                 GRTD GV 
Sbjct: 94  VAFKFAYCGWNYNGLAYQLEPTPLPTVEGKVFEALLRAHLITDPSSCSFSRCGRTDKGVS 153

Query: 57  ALRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           A+ QV   ++   E  P+I C  LN  L     I I   +   + F ARFS  +R Y Y 
Sbjct: 154 AMGQVISLNVRHSERRPIIYCDVLNRLL--PADIRITGYAFPPEGFDARFSCKQRHYKY- 210

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTID 173
           + T+  P             SLD + M  AA   +G HDF  F  I    Q ++  R I 
Sbjct: 211 LFTKDYP-----------GGSLDIDRMNEAAALYLGEHDFRNFCKIDASKQITNYHRRIL 259

Query: 174 H---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--K 228
                 ++    L    +   +FL  Q+R  +  L L+G     ++ +   L  +    K
Sbjct: 260 SSKVICIDPSTGLYAFDLQGTAFLWHQVRCMMAILFLIGQKLEPASLINDLLDIKKVPTK 319

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               +A    L     ++ 
Sbjct: 320 PIYDMASEYPLILYDCDFD 338


>gi|114641137|ref|XP_001148378.1| PREDICTED: tRNA pseudouridine synthase 3 [Pan troglodytes]
          Length = 481

 Score =  164 bits (416), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 91/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL   +      +  N                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSHFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEIIDELLN 304


>gi|301320977|gb|ADK69620.1| putative tRNA pseudouridine synthase A [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 251

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 107/250 (42%), Gaps = 11/250 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQV 61
             + + Y+GS Y GW  Q N  SIQ ++ KAI  V  TG+   + GA +TD+ VHAL Q 
Sbjct: 5   ILLSLCYDGSNYHGWINQTNAISIQTTLNKAIKKVIKTGQFKTI-GASKTDTNVHALDQK 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               +    +     KA+N  L     I IL+   VD  F+ R     + Y Y I   Q 
Sbjct: 64  VLLIIYFTPILEKFIKAINKAL--PSDIKILDAKFVDPNFNIR-EVEYKIYHYYINDHQF 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS---PIRTIDHFDVN 178
            +   +   +   + +D   ++      +G H+F  F  +     +     RTID   V 
Sbjct: 121 DIFTNRYEYFWKHQKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVL 180

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVG-SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              N + I   A  F+  QIR  +   L    + K ++T L + LQ    K+   +   +
Sbjct: 181 RINNKVVIEFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLQG-IGKKTPFIIDAK 239

Query: 238 GLYFDSVEYS 247
           GL    ++++
Sbjct: 240 GLVLQKIQFN 249


>gi|242062120|ref|XP_002452349.1| hypothetical protein SORBIDRAFT_04g024110 [Sorghum bicolor]
 gi|241932180|gb|EES05325.1| hypothetical protein SORBIDRAFT_04g024110 [Sorghum bicolor]
          Length = 201

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 49/169 (28%), Positives = 74/169 (43%), Gaps = 7/169 (4%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           +   I +  +S    +FHAR S   + Y Y+I             A+     L+   M+ 
Sbjct: 5   LPPEIRVREISAARPEFHARTSTKSKVYRYKIYNEAIMDPFHNRYAYHSAYKLNPHAMQE 64

Query: 145 AAQHLVGRHDFTTFRSI---HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
           AA + VG HDFT+F +      +  S  + I  FDV   G ++++ V    FL+ Q+R+ 
Sbjct: 65  AANYFVGTHDFTSFANAAHNDRERRST-KKITRFDVTEMGAVLQLEVEGTGFLYRQVRNM 123

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEYS 247
           V  L  VG        +   +  +DRKE   +   APP GL   SV Y 
Sbjct: 124 VALLLQVGKEALPPDIVPAIIAVRDRKELAKVALSAPPHGLCLMSVNYD 172


>gi|171184695|ref|YP_001793614.1| tRNA pseudouridine synthase ACD [Thermoproteus neutrophilus V24Sta]
 gi|229470755|sp|B1YAT9|TRUA_THENV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|170933907|gb|ACB39168.1| tRNA-pseudouridine synthase I [Thermoproteus neutrophilus V24Sta]
          Length = 255

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 99/246 (40%), Gaps = 35/246 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y   I Y+G+ ++G+       S++  + +A+  V G         RTD GV A+  
Sbjct: 1   MP-YLYRIAYDGTLFYGFTGHP--RSLEPHLRRALGDVLG------RGSRTDPGVSAVGN 51

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V       +  P        A  K+   + +   + V + F+ R  A  R YLY      
Sbjct: 52  VV--MTSAKVQPAA------ANSKLPRGVWVWAAAEVPEGFNPR-RARSRHYLYVAP--- 99

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                            D ++MR AA+ L G HD+ +F     + +S + TI    V + 
Sbjct: 100 -------------HWGEDLDSMREAAELLAGTHDYASFVQRRGEPASTVTTIFSITVETR 146

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+L+ +  V R F +  IR    ++   G G     D+   L+ + +    P AP EGL 
Sbjct: 147 GDLVFLHFVGRGFRNKMIRKLAWAILAAGRGVLRKRDIADLLE-RPKPGAVPSAPAEGLV 205

Query: 241 FDSVEY 246
              ++Y
Sbjct: 206 LLDIDY 211


>gi|18312431|ref|NP_559098.1| tRNA pseudouridine synthase ACD [Pyrobaculum aerophilum str. IM2]
 gi|24212564|sp|Q8ZXR6|TRUA_PYRAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|18159888|gb|AAL63280.1| tRNA pseudouridine synthase A [Pyrobaculum aerophilum str. IM2]
          Length = 256

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 98/249 (39%), Gaps = 38/249 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y   I Y+G+ ++G+    N       +E  + L+ GEI  +    RTD GV A+  
Sbjct: 1   MP-YLYRIAYDGTMFYGFTGHPNS------LEPRLRLIFGEI--LGRGSRTDPGVSAVGN 51

Query: 61  VAHFDLVREWVPVILCKALNA-YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V                AL     K+        ++ V + F+ R  A  R YLY     
Sbjct: 52  VVMTG---------RKMALGYVNSKMPKGAWAWGIAEVPEGFNPR-RAKLRRYLYVAP-- 99

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVN 178
                             D + MR AA+ L G HD+++F  +  +  +P + T+   DV 
Sbjct: 100 --------------HWGEDVDVMREAAKLLTGTHDYSSFIQLRGEKHTPTVTTVYDIDVT 145

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+LI I    R F +  IR    +L   G G  +  DL   L+ + R    P AP EG
Sbjct: 146 LRGDLIFIYFAGRGFRNKMIRKMAWALLAAGRGVLSVDDLADLLK-KPRPGAVPSAPAEG 204

Query: 239 LYFDSVEYS 247
           L    + Y 
Sbjct: 205 LVLLDIVYD 213


>gi|119588071|gb|EAW67667.1| pseudouridylate synthase 3 [Homo sapiens]
          Length = 481

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEIIDELLN 304


>gi|14919399|gb|AAH04822.1| Pseudouridylate synthase 3 [Homo sapiens]
 gi|124000287|gb|ABM87652.1| pseudouridylate synthase 3 [synthetic construct]
 gi|124000289|gb|ABM87653.1| pseudouridylate synthase 3 [synthetic construct]
 gi|157928602|gb|ABW03597.1| pseudouridylate synthase 3 [synthetic construct]
 gi|157929242|gb|ABW03906.1| pseudouridylate synthase 3 [synthetic construct]
          Length = 481

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEIIDELLN 304


>gi|303275814|ref|XP_003057201.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461553|gb|EEH58846.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 281

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 69/274 (25%), Positives = 100/274 (36%), Gaps = 51/274 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG------SSIQGSIEKAIFL-------VTGEIVVVHGAGR 50
             + + Y G  Y G+  Q N        +I+G++  A+          T   V     GR
Sbjct: 18  IALHVAYAGWDYHGFASQGNDAAEARSPTIEGALFAALKRTRLIADDATWTDVDYTRCGR 77

Query: 51  TDSGVHALRQVAHFD---------------LVREWVPVILCKALNAYLKISDTISILNLS 95
           TD+GV A+ Q+                     ++   +     LN  L   D I +    
Sbjct: 78  TDAGVSAMGQLVSLRARSRGTRYTPPSPPPPAKDADELDYPSILNRAL--PDDIRVTGWC 135

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            VD+ F ARF    R Y Y                 L    LD E MR AA+ L G HDF
Sbjct: 136 YVDEAFSARFDCEWRHYKYFFT--------------LHDGGLDLEKMRDAARRLEGEHDF 181

Query: 156 TTFRSIHCQA--SSPIRTIDHFDVNSFG---NLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
             F  +  +   +   R ++    ++ G    L  I V   +FL  Q+R     L LVG 
Sbjct: 182 RNFCKMDVKNVHNHARRILESASSSASGAPPRLCYISVKGTAFLWHQVRCVAAVLFLVGL 241

Query: 211 GKWTSTDLEKA--LQAQDRKECGPLAPPEGLYFD 242
           GK   + ++    L+   RK    +AP E L   
Sbjct: 242 GKEPPSVIDDLLDLEKTTRKPQYEMAPEEPLLLW 275


>gi|195336235|ref|XP_002034747.1| GM14299 [Drosophila sechellia]
 gi|194127840|gb|EDW49883.1| GM14299 [Drosophila sechellia]
          Length = 499

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 76/281 (27%), Positives = 116/281 (41%), Gaps = 52/281 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +SIQG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLERSRLDTNSIQGCLELALQVFHPTNEIHTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL      DL R     +   IL   LN  L      I +L+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVQVDLERTNGQPYDTTILTGVLNRTLNKQRLPIRVLSSKLVANSFHCRYD 120

Query: 107 AIRRSYLYRIITRQAPLA-----LEKGRAWLIP------------KSLDCENMRIAAQHL 149
           A  R+YLYR    + P         +     IP             S D + ++ A++  
Sbjct: 121 ATGRTYLYRFAVAKDPPLGDCSLRNRSFETFIPIEEIDRCYFLQSSSFDIKRVQAASRMF 180

Query: 150 VGRHDFTTFRSIHCQASS------PIRTIDHFDVNSFG---------------NLIEIRV 188
           +G HDF TF S+  Q  S       +R ID  ++                   N  +I +
Sbjct: 181 IGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSNAILAAETYNYWDIEI 240

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            A+SFL+ Q+R  VG+L  +G+G+     L + L    +  
Sbjct: 241 RAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTIPSKNS 281


>gi|195586672|ref|XP_002083097.1| GD13536 [Drosophila simulans]
 gi|194195106|gb|EDX08682.1| GD13536 [Drosophila simulans]
          Length = 499

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 76/281 (27%), Positives = 117/281 (41%), Gaps = 52/281 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +SIQG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTTFRGIQKTVNKLEQSRLDTNSIQGCLELALQVFHPTNEIHTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL      DL R     +   IL   LN  L      I +L+  +V   FH R+ 
Sbjct: 61  DAGVHALHSTVQVDLERTNGQPYDTTILTGVLNRTLNKQRLPIRVLSSKLVANSFHCRYD 120

Query: 107 AIRRSYLYRIITRQAPL----------------ALEKGRAWLIPKS-LDCENMRIAAQHL 149
           A  R+YLYR    + P                   E  R + +  S  D + ++ A++  
Sbjct: 121 ATGRTYLYRFAVAKDPPLGDCSLRNRSFETFIPVEEIDRCYFLQSSSFDIKRVQAASRMF 180

Query: 150 VGRHDFTTFRSIHCQASS------PIRTIDHFDVNSFG---------------NLIEIRV 188
           +G HDF TF S+  Q  S       +R ID  ++                   N  +I +
Sbjct: 181 IGVHDFRTFMSVSRQKVSRDHPMFTVRKIDEINIRPGETRALSSNAILAAETYNYWDIEI 240

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            A+SFL+ Q+R  VG+L  +G+G+     L + L    +  
Sbjct: 241 RAKSFLYKQVRRIVGALIALGNGRIDERCLYQMLTIPSKNS 281


>gi|242003078|ref|XP_002422603.1| tRNA pseudouridine synthase A, putative [Pediculus humanus
           corporis]
 gi|212505404|gb|EEB09865.1| tRNA pseudouridine synthase A, putative [Pediculus humanus
           corporis]
          Length = 410

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 92/262 (35%), Gaps = 24/262 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---------VVVHGAGRTD 52
               +++ YNGS Y G Q+  +  +I+  +  A+                +    A RTD
Sbjct: 74  RNVALLMAYNGSNYHGMQKNLDFKTIEYELLNALVKANLIPSEAIDNLPLIHFQRAARTD 133

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A +QV  F +   +    +       + + + I + ++  V K F+ +     R+Y
Sbjct: 134 KGVSAAKQVVSFKIAENFQVEKI------NMFLPEDIRVFSIKRVTKGFNCKNQCTARTY 187

Query: 113 LYRIITRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIR 170
            Y + T                   L  +         +G H F  F      +  S  R
Sbjct: 188 SYTLPTFALAPEFHDEYPKNYRIDKLTIQKTNEILSQYLGTHPFHNFTSKKDGRDPSAKR 247

Query: 171 TIDHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            I  F+       +    I ++V  +SF+  QIR  VG    V  G  +     K    +
Sbjct: 248 YIMSFEAEEPFLENEEEFITLKVKGQSFMLHQIRKMVGYTIAVMKGFASEAIQSKIWTNE 307

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
                 P+AP  GL  + V Y 
Sbjct: 308 KVSL--PMAPGLGLVLEDVHYD 327


>gi|199559785|ref|NP_112597.3| tRNA pseudouridine synthase 3 [Homo sapiens]
          Length = 481

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEIIDELLN 304


>gi|332208632|ref|XP_003253411.1| PREDICTED: tRNA pseudouridine synthase 3 [Nomascus leucogenys]
          Length = 481

 Score =  164 bits (415), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/282 (22%), Positives = 100/282 (35%), Gaps = 54/282 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSQFPRGRESEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVVNFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           +G G      +++ L  +   +K    +A    L     ++ 
Sbjct: 289 IGQGMEKPELIDELLNIEKNPQKPQYSMAVEFPLVLYDCKFE 330


>gi|326933214|ref|XP_003212702.1| PREDICTED: tRNA pseudouridine synthase 3-like [Meleagris gallopavo]
          Length = 710

 Score =  163 bits (414), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/283 (22%), Positives = 98/283 (34%), Gaps = 55/283 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 66  VALRIAYLGWGYQGFASQENTSNTIEEKLFEALKKTRLVDSRQTSNYHRCGRTDKGVSAF 125

Query: 59  RQVAHFDLVREWV-------------------PVILCKALNAYLKISDTISILNLSIVDK 99
            QV   DL                           L         +   I +L  + V+ 
Sbjct: 126 GQVISLDLRSNLSKEKKLNGCTGDSEGKSSKSEEELRYTHILNRVLPPDIRVLAWAPVEP 185

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS ++R+Y Y                      LD   M+ AAQ  VG HDF    
Sbjct: 186 DFSARFSCLKRTYRYFFPCA----------------DLDVALMQAAAQRYVGTHDFRNLC 229

Query: 160 SIH--CQASSPIRTIDHFDVNSFGN-----------LIEIRVVARSFLHTQIRSFVGSLK 206
            +       +  RTI    V                L +  V  ++FL+ Q+R  +  L 
Sbjct: 230 KMDVANGVINFQRTILSAQVTWVDGGAEGGLRDPFRLCQFEVTGQAFLYHQVRCMMAILF 289

Query: 207 LVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           L+G        +++ L  +   RK    +A    L     E+ 
Sbjct: 290 LIGQRMEGPEIIDELLDVEKNPRKPQYSMAVEFPLVLYDCEFE 332


>gi|126302589|sp|Q9BZE2|PUS3_HUMAN RecName: Full=tRNA pseudouridine synthase 3; AltName: Full=tRNA
           pseudouridylate synthase 3; AltName: Full=tRNA-uridine
           isomerase 3
 gi|12276176|gb|AAG50280.1|AF325689_1 FKSG32 [Homo sapiens]
 gi|189055315|dbj|BAG36917.1| unnamed protein product [Homo sapiens]
          Length = 481

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 92/256 (35%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 65  VALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREWVPVILCKALNA-----------------YLKISDTISILNLSIVDKQF 101
            QV   DL  ++      +  N                     +   I IL  + V+  F
Sbjct: 125 GQVISLDLRSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPVEPSF 184

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                +     LD   M  AAQ  VG HDF     +
Sbjct: 185 SARFSCLERTYRY----------------FFPRADLDIVTMDYAAQKYVGTHDFRNLCKM 228

Query: 162 H--CQASSPIRTIDHF------------DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
                  +  RTI                      L +  V  ++FL+ Q+R  +  L L
Sbjct: 229 DVANGVINFQRTILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFL 288

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 289 IGQGMEKPEIIDELLN 304


>gi|301782183|ref|XP_002926505.1| PREDICTED: tRNA pseudouridine synthase 3-like [Ailuropoda
           melanoleuca]
          Length = 480

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 94/258 (36%), Gaps = 56/258 (21%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 64  VALKIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWV-------------------PVILCKALNAYLKISDTISILNLSIVDK 99
            QV   DL   ++                    +     LN  L     I +L  + V+ 
Sbjct: 124 GQVISLDLRSHFLKGRASEDFHVKDEVSDAAKEIRYTHILNRVL--PPDIRVLAWAPVEP 181

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS + R+Y Y                +     LD   M  AAQ  VG HDF    
Sbjct: 182 SFSARFSCLERTYRY----------------FFPRADLDIVTMNYAAQKYVGTHDFRNLC 225

Query: 160 SIH--CQASSPIRTI------------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
            +       +  RTI            D         L +  V  ++FL+ Q+R  +  L
Sbjct: 226 KMDVANGVINFQRTILSAQVQLVGQSLDKETWQEAFQLCQFEVTGQAFLYHQVRCMMAIL 285

Query: 206 KLVGDGKWTSTDLEKALQ 223
            L+G G      +++ L 
Sbjct: 286 FLIGQGMEKPEIIDELLN 303


>gi|195012378|ref|XP_001983613.1| GH25313, isoform A [Drosophila grimshawi]
 gi|193897095|gb|EDV95961.1| GH25313, isoform A [Drosophila grimshawi]
          Length = 496

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 114/283 (40%), Gaps = 55/283 (19%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTGE-IVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +SIQG +E A+ +   +  +    + RT
Sbjct: 1   MHRYLLNISYIGTNFRGIQKTINKLEEARLDTNSIQGCLELALRVFRPKNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    L   LN  L      I IL+   V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLERSDGKPYDTSTLTGVLNRTLDKHKLPIRILSSQRVVDTFHCRYH 120

Query: 107 AIRRSYLYRIITRQ------------------APLALEKGRAWLIP-KSLDCENMRIAAQ 147
           A  R+YLYR+   +                       E  R + +   + D E +  AA+
Sbjct: 121 ATGRTYLYRVAVAKSVSEASKGSSLKNKGYESFVPVEEIDRCYFLHCDNFDVERLHGAAR 180

Query: 148 HLVGRHDFTTFRSIHCQASS-------PIRTIDHFDVN---------------SFGNLIE 185
             +G HDF TF S+  Q S         +R ID  ++                   +  +
Sbjct: 181 MFLGLHDFRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGQTLALGPNAKLATQTYDYWD 240

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           I + A+SFL+ Q+R  VG+L  + + +     + + L    + 
Sbjct: 241 IEIKAKSFLYKQVRRIVGTLLALANSRIDERCIYQMLTIPSKH 283


>gi|157822367|ref|NP_001101604.1| tRNA pseudouridine synthase 3 [Rattus norvegicus]
 gi|149027806|gb|EDL83266.1| pseudouridylate synthase 3 (predicted) [Rattus norvegicus]
 gi|165971639|gb|AAI58694.1| Pseudouridylate synthase 3 [Rattus norvegicus]
          Length = 479

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 94/256 (36%), Gaps = 52/256 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+       + +    H  GRTD GV A 
Sbjct: 64  VALKIAYLGWGYQGFASQENTSNTIEEKLFEALIKTRLVESRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWV-----------------PVILCKALNAYLKISDTISILNLSIVDKQF 101
            QV   DL  ++                     +  A      +   I +L  +  +  F
Sbjct: 124 GQVISLDLRSQFPRSRDSEDSNLKDGADDIAKEIRYAHILNRVLPADIRVLAWAPAEPSF 183

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R+Y Y                      LD   M  AAQ  VG HDF     +
Sbjct: 184 SARFSCLERTYRYFFPCA----------------DLDIATMNYAAQKYVGTHDFRNLCKM 227

Query: 162 H--CQASSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKL 207
                 ++  RTI    V +               L +  V+ ++FL+ Q+R  +  L L
Sbjct: 228 DVANGVTNFQRTILSAQVQTVAQSPGEEGRQGPFQLCQFEVIGQAFLYHQVRCMMAILFL 287

Query: 208 VGDGKWTSTDLEKALQ 223
           +G G      +++ L 
Sbjct: 288 IGQGMEKPEIIDELLN 303


>gi|281338704|gb|EFB14288.1| hypothetical protein PANDA_016156 [Ailuropoda melanoleuca]
          Length = 479

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 94/258 (36%), Gaps = 56/258 (21%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+       + +    H  GRTD GV A 
Sbjct: 64  VALKIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWV-------------------PVILCKALNAYLKISDTISILNLSIVDK 99
            QV   DL   ++                    +     LN  L     I +L  + V+ 
Sbjct: 124 GQVISLDLRSHFLKGRASEDFHVKDEVSDAAKEIRYTHILNRVL--PPDIRVLAWAPVEP 181

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS + R+Y Y                +     LD   M  AAQ  VG HDF    
Sbjct: 182 SFSARFSCLERTYRY----------------FFPRADLDIVTMNYAAQKYVGTHDFRNLC 225

Query: 160 SIH--CQASSPIRTI------------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSL 205
            +       +  RTI            D         L +  V  ++FL+ Q+R  +  L
Sbjct: 226 KMDVANGVINFQRTILSAQVQLVGQSLDKETWQEAFQLCQFEVTGQAFLYHQVRCMMAIL 285

Query: 206 KLVGDGKWTSTDLEKALQ 223
            L+G G      +++ L 
Sbjct: 286 FLIGQGMEKPEIIDELLN 303


>gi|42561241|ref|NP_975692.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|62901321|sp|Q6MSQ4|TRUA_MYCMS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|42492739|emb|CAE77334.1| pseudouridylate synthase I [Mycoplasma mycoides subsp. mycoides SC
           str. PG1]
          Length = 251

 Score =  163 bits (413), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 108/250 (43%), Gaps = 11/250 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQV 61
             + + Y+GS Y GW  Q N  SIQ ++ KAI  V  TG+   + GA +TD+ VHAL Q 
Sbjct: 5   ILLSLCYDGSNYHGWINQTNAISIQTTLNKAIKKVIKTGQFKTI-GASKTDTNVHALDQK 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               +    +     KA+N  L     I IL+   VD  F+ R     + Y Y I   Q 
Sbjct: 64  VLLIIYFTPILEKFIKAINKAL--PSDIKILDAKFVDPNFNIR-EVEYKIYHYYINDHQF 120

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS---PIRTIDHFDVN 178
            +   +   +   + +D   ++      +G H+F  F  +     +     RTID   V 
Sbjct: 121 DIFTNRYEYFWKHQKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVL 180

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVG-SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              N + I+  A  F+  QIR  +   L    + K ++T L + LQ    K+   +   +
Sbjct: 181 RINNKVVIQFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLQG-IGKKTPFIIDAK 239

Query: 238 GLYFDSVEYS 247
           GL    ++++
Sbjct: 240 GLVLQKIQFN 249


>gi|195135260|ref|XP_002012052.1| GI24889, isoform A [Drosophila mojavensis]
 gi|193918316|gb|EDW17183.1| GI24889, isoform A [Drosophila mojavensis]
          Length = 499

 Score =  163 bits (413), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 118/287 (41%), Gaps = 58/287 (20%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG--------SSIQGSIEKAIFLVTG-EIVVVHGAGRT 51
           M RY + I Y G+ + G Q+  N         +S+QG +E A+ +      +    + RT
Sbjct: 1   MHRYLLNISYIGTRFRGIQKTINKLEESRVDTNSVQGCLELALRVFRPVNEIQTVLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLK-ISDTISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +   IL   LN  L   S  I +L+   V   FH R+ 
Sbjct: 61  DAGVHALHSTVHVDLERNDGKCYDTTILTGVLNRTLDKQSLPIRVLSTQRVADTFHCRYH 120

Query: 107 AIRRSYLYRIITRQAP---------------------LALEKGRAWLI-PKSLDCENMRI 144
           AI R+YLYR+   +                          E  R + +   + D E +  
Sbjct: 121 AIGRTYLYRVAVSKQKTTVLPDAKSSSLRNRAFEAFLPVEEWDRCYFLQNNNFDIERLIA 180

Query: 145 AAQHLVGRHDFTTFRSIHCQASS-------PIRTIDHFDVN---------------SFGN 182
           A++ L+G HD+ TF S+  Q S         +R ID  ++                   +
Sbjct: 181 ASRMLIGVHDYRTFMSVSRQKSPSRDHPMFTVRKIDEINIRPGRSLALGPNATLATENYD 240

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
             +I + A+SFL+ Q+R  VG+L  + +G+     + + L    +  
Sbjct: 241 YWDIEIKAKSFLYKQVRRIVGTLLALAEGRIDERCIYQMLTIPSKHS 287


>gi|50293511|ref|XP_449167.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49528480|emb|CAG62137.1| unnamed protein product [Candida glabrata]
          Length = 438

 Score =  163 bits (413), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 90/243 (37%), Gaps = 39/243 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK+     +I+G+I +A+        +T +       GRTD G
Sbjct: 88  IALRFAYLGWNYNGLAIQKDPTPLPTIEGTIIEALNKCKLVPSITPQEFEFSRCGRTDKG 147

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLK----------ISDTISILNLSIVDKQ-FHA 103
           V A+ QV    +             N + +          + D I I  + +     F A
Sbjct: 148 VSAMNQVISLRVRSNLTDEEQKDPRNDHKEIQYVAILNQLLPDDIRISAVCLRPPNSFDA 207

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS   R Y Y                      LD + M+ AA+   G HDF  F  +  
Sbjct: 208 RFSCEYRHYKYL----------------FHKDGLDLDRMQKAAKLYEGEHDFRNFCKLDG 251

Query: 163 -CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RT+   ++   + +     ++  +FL  Q+R     L LVG G    T +EK
Sbjct: 252 SKQITNYNRTMISANIKHVYNDFYCFDLIGSAFLWHQVRCMTAILFLVGQGLEEPTLIEK 311

Query: 221 ALQ 223
            L 
Sbjct: 312 MLD 314


>gi|227497212|ref|ZP_03927460.1| pseudouridylate synthase [Actinomyces urogenitalis DSM 15434]
 gi|226833297|gb|EEH65680.1| pseudouridylate synthase [Actinomyces urogenitalis DSM 15434]
          Length = 229

 Score =  163 bits (412), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 53/171 (30%), Positives = 87/171 (50%), Gaps = 12/171 (7%)

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIIT------RQAPLALEKGRAWLIPKSLDCEN 141
            + +     V   F ARFSA+ R Y+YRI        R+A     +G+   + ++LD E+
Sbjct: 32  DVVLRGARRVPADFDARFSALERRYVYRIDDGAPSQGRRAYDPCRRGQVLWVGQALDVES 91

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-----FGNLIEIRVVARSFLHT 196
           M ++A+ L+G HDF ++     + ++ IRT+   D           L+ + VVA +F H+
Sbjct: 92  MALSARGLLGEHDFLSYCKPR-EGATTIRTLRRLDWQRASSGPDAGLVTLTVVADAFCHS 150

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +RS VG+   VG G+   +   + L A+ R +  P+APP GL  + V Y 
Sbjct: 151 MVRSLVGAGLAVGQGRQPVSWPARLLAARSRDQAAPVAPPYGLTLEEVVYP 201


>gi|71665382|ref|XP_819661.1| pseudouridine synthase A-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70884973|gb|EAN97810.1| pseudouridine synthase A-like protein, putative [Trypanosoma cruzi]
          Length = 429

 Score =  163 bits (412), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 105/263 (39%), Gaps = 36/263 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  Y G  +Q+   ++++  +  A+  V        + +   GRTD GV 
Sbjct: 40  RKVAIRLAYHGHLYDGLAKQEETSNTVEAYVVAALKHVRLIPQDGPIDLARCGRTDKGVS 99

Query: 57  ALRQVAH-------FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL  V         +       P    C  LN+ L    TI I+  + VD  F ARFS +
Sbjct: 100 ALGNVFSLTVRASSWPTDSPQKPALDYCAMLNSAL--PVTIRIVGWAYVDDTFDARFSCV 157

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH----CQ 164
            R+Y Y                +   + L+ E M  AA  L G H+F  F          
Sbjct: 158 GRTYRY----------------YFCHRGLNVEAMGNAAARLKGVHNFRNFCKTDVVNVSN 201

Query: 165 ASSPIRTIDHFDVNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
               +R++  F   +F  L+  + + A SFL+ QIR  +  L LVG G      + + L+
Sbjct: 202 YERDVRSVGIFASEAFPELVSYLEIHANSFLYHQIRCTMEVLFLVGRGLEDPEVVTQLLE 261

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
             DRK   PLA    L      +
Sbjct: 262 RGDRKPVYPLADGTPLVLWDCHF 284


>gi|296108989|ref|YP_003615938.1| tRNA pseudouridine synthase A [Methanocaldococcus infernus ME]
 gi|295433803|gb|ADG12974.1| tRNA pseudouridine synthase A [Methanocaldococcus infernus ME]
          Length = 258

 Score =  163 bits (412), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 98/243 (40%), Gaps = 31/243 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQV 61
           Y + I Y+G  Y  +Q+Q +  ++   +   +  +    E  +++  GRTD GV AL   
Sbjct: 2   YILKIAYDG-RYS-FQQQPHKETVCDKLLNTLEKLNFLEERKIIYSGGRTDKGVSALGNF 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               L +E +   +   L  +      I IL    +++    ++    R Y Y +     
Sbjct: 60  VILKLKKEPILSYINHELKKF-----GIWILGYKEIEEIPKVQY----RHYRYIMPNLDY 110

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSF 180
                           + E MR A + L+G H F         +  SPIR I    +N +
Sbjct: 111 ----------------NLELMRKAGEKLIGEHSFHNLSKRDRSKEKSPIRKIYDIKINDY 154

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +E+ VV  SFL   +R  VG L L+G  + +   ++K L   + +E     P EGL 
Sbjct: 155 GFFLEVDVVGESFLWQMVRKIVGLLHLIGREEKSLEWVDKILD-PNYREGVITFPAEGLI 213

Query: 241 FDS 243
              
Sbjct: 214 LVE 216


>gi|154341677|ref|XP_001566790.1| pseudouridine synthase A-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134064115|emb|CAM40310.1| putative pseudouridine synthase A-like protein [Leishmania
           braziliensis MHOM/BR/75/M2904]
          Length = 499

 Score =  163 bits (412), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 107/264 (40%), Gaps = 36/264 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  + G  +QK   ++++G +  A+  V              GRTD GV 
Sbjct: 60  RKIGLRLAYHGHVHDGLAKQKETDNTVEGLVCDALRRVRLIPEDGPHNFGRCGRTDKGVS 119

Query: 57  ALRQ--------VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL              D   +  P+  C  LN  L    TI I+  ++VD +F ARFS +
Sbjct: 120 ALGNAFSLTARASCTADADPQLPPLDYCSMLNNVL--PSTIRIVGCALVDDRFDARFSCV 177

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
            R+Y Y                +   + L+   M+ AA   +G H+F  F  +     S+
Sbjct: 178 HRTYRY----------------YFCHRGLNLAAMQEAAAFFLGTHNFRNFCQMDVVNVSN 221

Query: 168 PIRTIDHFDVNSFGNLIEI----RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             RT+    ++    L E+     + A SFL+ QIR  +  L LVG G    + ++  L+
Sbjct: 222 FTRTVLSVGLHPSEELPELISYLEITANSFLYHQIRCTMEVLFLVGRGLEAPSVVQTMLE 281

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             D K   PLA    L      + 
Sbjct: 282 LGDCKPTYPLADGTPLILWDCAFD 305


>gi|255572341|ref|XP_002527109.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223533532|gb|EEF35272.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 438

 Score =  162 bits (411), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 62/281 (22%), Positives = 103/281 (36%), Gaps = 54/281 (19%)

Query: 3   RY-CMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGV 55
           RY  + + Y G  ++G+  +     +++  I KA+          + +     GRTD GV
Sbjct: 102 RYVALKVMYFGQRFYGFSSEGQMDPTVESEIFKALERTRLLIGDKKEIQYSRCGRTDKGV 161

Query: 56  HALRQVAHFDLVREWV--------------------PVILCKALNAYLKISDTISILNLS 95
            A+ QV    L  +                       +   + LN  L   + I I+   
Sbjct: 162 SAVGQVIALLLRSKVKDIDEIGKVFGETASQKHSEGEIDYVRVLNRVL--PNDIRIIGWC 219

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            V   F ARFS + R Y Y            +G       +L+   M  A +  +G HDF
Sbjct: 220 PVPNDFSARFSCLSREYKY----------FFRG------DNLNLLAMESAGKKFIGEHDF 263

Query: 156 TTFRSIHC-QASSPIRTIDHFDVNSFGNLIE------IRVVARSFLHTQIRSFVGSLKLV 208
             F  +      +  R I  F+++      E      I++   +FL  Q+R  V  L ++
Sbjct: 264 RNFCKMDAMNVHNYRRNITSFEISPCHERYEGNQLFAIKIRGSAFLWHQVRCMVAVLFMI 323

Query: 209 GDGKWTSTDLEKALQA--QDRKECGPLAPPEGLYFDSVEYS 247
           G G  +   ++  L      RK   P+AP   L   S ++ 
Sbjct: 324 GQGLESPDVIDVLLDTVRTPRKPQYPMAPEIPLVLHSCDFE 364


>gi|118101846|ref|XP_417852.2| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 390

 Score =  162 bits (411), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 64/283 (22%), Positives = 96/283 (33%), Gaps = 55/283 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N  ++I+  + +A+         +    H  GRTD GV A 
Sbjct: 68  VALRIAYLGWGYQGFASQENTSNTIEEKLFEALKKTRLVDDRQTSNYHRCGRTDKGVSAF 127

Query: 59  RQVAHFDLVREWVPVI-------------------LCKALNAYLKISDTISILNLSIVDK 99
            QV   DL                           L         +   I +L  + V+ 
Sbjct: 128 GQVISLDLRSNLSEEKKLNGCTGDSEGKSSKSEEELRYTHILNRVLPPDIRVLAWAPVEP 187

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS ++R+Y Y                      LD   M  AAQ  VG HDF    
Sbjct: 188 DFSARFSCLKRTYRYFFPCA----------------DLDVALMHTAAQRYVGTHDFRNLC 231

Query: 160 SIH--CQASSPIRTIDHFDVNSFGN-----------LIEIRVVARSFLHTQIRSFVGSLK 206
            +       +  RTI    V                L +  V  ++FL+ Q+R  +  L 
Sbjct: 232 KMDVANGVINFQRTILSAQVTWADGGAESGLRDPFRLCQFEVTGQAFLYHQVRCMMAILF 291

Query: 207 LVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           L+G        +++ L  +   RK    +A    L     E+ 
Sbjct: 292 LIGQRMEGPEIIDELLDVEKNPRKPQYSMAVEFPLVLYDCEFE 334


>gi|145590498|ref|YP_001152500.1| pseudouridylate synthase [Pyrobaculum arsenaticum DSM 13514]
 gi|166228752|sp|A4WHI1|TRUA_PYRAR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145282266|gb|ABP49848.1| Pseudouridylate synthase [Pyrobaculum arsenaticum DSM 13514]
          Length = 257

 Score =  162 bits (410), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 62/247 (25%), Positives = 100/247 (40%), Gaps = 36/247 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y   I Y+G+ ++G+    N  S++  +  A+  + G         RTD GV A+  
Sbjct: 1   MP-YLYRIAYDGTLFYGFTGHPN--SLEPKLRAALGEILG------RGSRTDPGVSAVAN 51

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V                 +N+ L     +    ++ V + F+ R  A  R YLY      
Sbjct: 52  VVMTSQRLHL------GYVNSKL--PRGVWAWGVAEVPEGFNPR-RAKARRYLYVAP--- 99

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNS 179
                            D E MR AA  LVG HD+++F       ++P + T+   +V  
Sbjct: 100 -------------HWGEDVEAMREAAAVLVGTHDYSSFIKRRGDKATPTVTTVYKIEVEQ 146

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LI +  V R F +  IR    ++   G G   ++DL + ++ + R    P AP EGL
Sbjct: 147 RGGLIYMMFVGRGFRNKMIRKMAWAILATGRGVLKASDLRELVE-RPRPGAVPSAPAEGL 205

Query: 240 YFDSVEY 246
               ++Y
Sbjct: 206 VLLDIDY 212


>gi|331703685|ref|YP_004400372.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802240|emb|CBW54394.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 251

 Score =  162 bits (410), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 103/249 (41%), Gaps = 9/249 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
             + + Y+GS Y GW  Q N  SIQ ++ KAI  V         GA +TD+ VHAL Q  
Sbjct: 5   ILLSLCYDGSNYHGWINQTNAISIQATLNKAIKKVIKTDQFKTIGASKTDTNVHALDQKV 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
              +    +     KA+N  L     I IL+   VD  F+ R     + Y Y I   Q  
Sbjct: 65  LLIIYFTPILEKFIKAINKAL--PSDIKILDAKFVDSNFNIR-EVEYKIYHYYINDYQFD 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS---PIRTIDHFDVNS 179
           +   +   +   + +D   ++      +G H+F  F  +     +     RTID   V  
Sbjct: 122 IFTNRYEYFWKHQKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVLR 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVG-SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N + I   A  F+  QIR  +   L    + K ++T L + L+    K+   +   +G
Sbjct: 182 INNKVVIEFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLKG-IGKKTPFIIDAKG 240

Query: 239 LYFDSVEYS 247
           L    ++++
Sbjct: 241 LVLQKIQFN 249


>gi|281201760|gb|EFA75968.1| tRNA pseudouridylate synthase [Polysphondylium pallidum PN500]
          Length = 531

 Score =  162 bits (410), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 109/274 (39%), Gaps = 34/274 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSG 54
             + + Y+G+ Y G Q+     +I+  +EKAIF V G           +      RTD G
Sbjct: 132 VAICVGYSGTNYRGMQKNPGFPTIEDELEKAIFKVGGISPDNMYCHRKIDWIRCARTDKG 191

Query: 55  VHALRQVAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           V A+R +    L  +      +  A+NA L   + I +  +  V+  FHA+    RRSY+
Sbjct: 192 VSAIRNMVSCKLEYDPPTLDEMKTAINAQL--PNDIRVFAIKRVNNTFHAKNCVDRRSYI 249

Query: 114 YRIITRQAPLALEKGRAWLI-PKSLDCENMRIAAQHLVGR---HDFTTFRSIHCQASSPI 169
           Y   T          +        L+   +    +  VG    H++T+         S +
Sbjct: 250 YITPTFAFEPIFANNKPAQYKFDELERTRLNSLLKLFVGTRKYHNYTS--KKESNDPSAV 307

Query: 170 RTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDG---------KWTS 215
           RT++ F+ +         L+ I +V +SF+  QIR  +G                 +   
Sbjct: 308 RTVNSFECSEPFMNEGVELVAINIVGQSFMLHQIRKMIGVTMQFMRKGFFADSESDEAAL 367

Query: 216 TDLEKALQAQ--DRKECGPLAPPEGLYFDSVEYS 247
           + ++K ++A    R+   P+AP  GL  D   Y 
Sbjct: 368 SKMKKLVEATFAHRQFNLPMAPGAGLLLDRCLYD 401


>gi|256384180|gb|ACU78750.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256385012|gb|ACU79581.1| tRNA pseudouridine synthase A [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455760|gb|ADH21995.1| tRNA pseudouridine synthase A (tRNA-uridine isomeraseI) (tRNA
           pseudouridylate synthase I) [synthetic Mycoplasma
           mycoides JCVI-syn1.0]
          Length = 251

 Score =  161 bits (409), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 101/249 (40%), Gaps = 9/249 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQVA 62
             + + Y+GS Y GW  Q N  SIQ ++ KAI  V         GA +TD+ VHAL Q  
Sbjct: 5   ILLSLCYDGSNYHGWINQTNAISIQTTLNKAIKKVIKTDQFKTIGASKTDTNVHALDQKV 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
              +    +     KA+N  L     I IL+   VD  F+ R     + Y Y I      
Sbjct: 65  LLIIYFTPILEKFIKAINKAL--PSDIKILDAKFVDPNFNIR-EVEYKIYHYYINDHHFD 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS---PIRTIDHFDVNS 179
           +   +   +     +D   ++      +G H+F  F  +     +     RTID   V  
Sbjct: 122 IFTNRYEYFWKHSKIDIIKLQEIFNLFIGEHEFKLFSGLKENEWNQYQTKRTIDDIKVLR 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVG-SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             N + I   A  F+  QIR  +   L    + K ++T L + L+    K+   +   +G
Sbjct: 182 INNKVVIEFKASGFIRYQIRIIIANCLNAYLNHKISTTKLVEMLKG-IGKKTPFIIDAKG 240

Query: 239 LYFDSVEYS 247
           L    ++++
Sbjct: 241 LVLQKIQFN 249


>gi|213406756|ref|XP_002174149.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|212002196|gb|EEB07856.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 426

 Score =  161 bits (409), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 97/261 (37%), Gaps = 32/261 (12%)

Query: 4   YCMIIEYNGSGYFG--WQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
             +   Y G  Y G  +Q +     +++G + +A+                 GRTD GV 
Sbjct: 74  IALRFAYLGWNYNGLAFQTEPTPLPTVEGKLFEALMRAHLIKDPSTCSFSRCGRTDKGVS 133

Query: 57  ALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQ-FHARFSAIRRSYLY 114
           A+ QV   ++   E  P+  C  LN  L   + I ++  S    + F ARFS +RR Y Y
Sbjct: 134 AMGQVVSLNVRYSEERPIAYCDVLNRLL--PEDIRVIAYSPNPPEGFDARFSCVRRHYKY 191

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTI 172
                       K         LD E M  AA   +G HDF  F  I    Q ++  R I
Sbjct: 192 ---------LFLKQYPG---GELDIERMSQAAALYLGEHDFRNFCKIDASKQITNYNRGI 239

Query: 173 DH---FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            H     V+    L    +   +FL  Q+R  +  L LVG        + + L   ++  
Sbjct: 240 LHSKIICVDPQKQLYAFDLQGTAFLWHQVRCMMAILFLVGQHLEPVDIVSELLNV-EKNP 298

Query: 230 CGP---LAPPEGLYFDSVEYS 247
           C P   +A    L      + 
Sbjct: 299 CKPVYDMASDLPLVLYDCVFD 319


>gi|71663014|ref|XP_818505.1| pseudouridine synthase A-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70883761|gb|EAN96654.1| pseudouridine synthase A-like protein, putative [Trypanosoma cruzi]
          Length = 409

 Score =  161 bits (409), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 107/263 (40%), Gaps = 36/263 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  Y G  +Q+   ++++  +  A+  V        + +   GRTD GV 
Sbjct: 20  RKVAIRLAYHGHLYDGLAKQEETSNTVEAYVVAALKHVRLIPQDGPIDLARCGRTDKGVS 79

Query: 57  ALRQVAHFDLVR--------EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL  V    +          +  P+  C  LN+ L    TI I+  + VD  F ARFS +
Sbjct: 80  ALGNVFSLTVRASSWPTDSPQKPPLDYCAMLNSAL--PVTIRIVGWAYVDDTFDARFSCV 137

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH----CQ 164
            R+Y Y                +   + L+ E M  AA  L G H+F  F          
Sbjct: 138 GRTYRY----------------YFCHRGLNVEAMGNAAARLKGVHNFRNFCKTDVVNVSN 181

Query: 165 ASSPIRTIDHFDVNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
               +R++  F   +F  L+  + + A SFL+ QIR  +  L LVG G      + + L+
Sbjct: 182 YERDVRSVGIFASEAFPELVSYLEIHANSFLYHQIRCTMEVLFLVGRGLEDPEVVTQLLE 241

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
             DRK   PLA    L      +
Sbjct: 242 RGDRKPVYPLADGTPLLLWDCHF 264


>gi|260220773|emb|CBA28673.1| tRNA pseudouridine synthase A [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 192

 Score =  161 bits (409), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 56/172 (32%), Positives = 84/172 (48%)

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK 135
            ++   +++      +         FH R SAI R Y Y ++      ++E GR      
Sbjct: 5   ARSFRRHVQRPGIPGLAKXXXXXXXFHCRASAISRRYAYVLLESPIRPSVETGRVGWTFN 64

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLH 195
           +LD  +MR AA +L+G HDFT+FR+  CQA SP++ +   D +  G    I   A +FLH
Sbjct: 65  NLDEMSMRKAADYLIGEHDFTSFRAAQCQALSPVKNVMRIDFHKRGAYWRIEFEANAFLH 124

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             IR+ +G L  +G  K     +E+ L A+ RK   P   P+GLYF    Y 
Sbjct: 125 HMIRNIMGCLVQIGQRKKPPEWMEEVLAARSRKVAAPTFSPDGLYFLGPRYD 176


>gi|149580877|ref|XP_001519338.1| PREDICTED: similar to FKSG32 [Ornithorhynchus anatinus]
          Length = 695

 Score =  161 bits (408), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 65/282 (23%), Positives = 99/282 (35%), Gaps = 56/282 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + I Y G GY G+  Q+N + +I+  + +A+         +    H  GRTD GV A 
Sbjct: 63  VALRIAYLGWGYQGFASQENTNNTIEERLFEALTKTRLIERRQTANYHRCGRTDKGVSAF 122

Query: 59  RQVAHF------------------DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
            QV                      +      +     LN  L     I +L  + V   
Sbjct: 123 GQVISLDLRSQTVRGGQEEEGSKDRMDARTAEIRYTHILNRVL--PPDIRVLAWAPVGSG 180

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F ARF+ ++R+Y Y                +     LD E M  AAQ  VG HDF     
Sbjct: 181 FSARFNCLQRTYRY----------------FFPRADLDLEAMDRAAQKYVGTHDFRNLCK 224

Query: 161 IH--CQASSPIRTIDHFDVNSFGN-----------LIEIRVVARSFLHTQIRSFVGSLKL 207
           +      +S  RTI    V                L +  V  ++FL+ Q+R  +  L L
Sbjct: 225 MDVANGVTSFQRTILSAQVRRVDQSEETDRRDPFRLCQFEVTGQAFLYHQVRCMMAILFL 284

Query: 208 VGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           VG        +++ L  +   RK    +A    L     ++ 
Sbjct: 285 VGQRMEGPEVIDELLDVEKNPRKPQYSMAVELPLVLYDCQFE 326


>gi|320094548|ref|ZP_08026315.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178 str.
           F0338]
 gi|319978528|gb|EFW10104.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178 str.
           F0338]
          Length = 218

 Score =  161 bits (407), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 63/196 (32%), Positives = 94/196 (47%), Gaps = 5/196 (2%)

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +   AL + A+  L R W      +       +SD + +L+ S V   F ARFSA  RSY
Sbjct: 3   ACAAALVRRANALLARAWAQREQGRGERPPRGVSDAL-VLSASPVSADFDARFSATGRSY 61

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
           +YRI  R  P  L +       + LD   +  AA+ L+G HDF +F     + ++ IR +
Sbjct: 62  VYRIADRPTP--LRRWDCVWDDRPLDLAAVNRAAEALLGEHDFLSFCRPR-EGATTIRAL 118

Query: 173 DHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
              +     + L+E  V A +F H+ +RS VG+L LVG G   +      L A+ R    
Sbjct: 119 TRLEAVRAPDGLVEFHVGADAFCHSMVRSLVGALALVGRGARPAPWPRALLDARSRASAA 178

Query: 232 PLAPPEGLYFDSVEYS 247
           P+AP  GL  + V+Y 
Sbjct: 179 PIAPARGLTLERVDYP 194


>gi|302802211|ref|XP_002982861.1| hypothetical protein SELMODRAFT_117099 [Selaginella moellendorffii]
 gi|300149451|gb|EFJ16106.1| hypothetical protein SELMODRAFT_117099 [Selaginella moellendorffii]
          Length = 289

 Score =  161 bits (407), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 103/270 (38%), Gaps = 43/270 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------------EIVVVHGAGR 50
           + +++ Y+G+ + GWQ+Q    ++Q  +EK +                  +  +V  AGR
Sbjct: 14  FKIVLSYSGTAFAGWQKQPGFLTVQSVLEKQLGRFVDGKRASNLEKQGKIKEALVSVAGR 73

Query: 51  TDSGVHALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GVHA  QV  F    RE     +  A+N+ +     +  ++ S V++ FH  FSA  
Sbjct: 74  TDKGVHACGQVCSFYTWMRECKEEDVKSAVNSAM--PTILRAVSASEVNRDFHPIFSAKW 131

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT--FRS----IHC 163
           R Y+Y    R                 +D   +    + L G H  +   F         
Sbjct: 132 RRYIYIFPLR-------------SRDEIDVSKVATLLRGLEG-HSLSYAIFARDTKIARS 177

Query: 164 QASSPIRTIDHFD-------VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
              + + T+ H         V +  N++ + +VA  FL   +R  V +            
Sbjct: 178 SGPATVCTLYHARAALAKLPVPNEENVMVVELVADRFLRKMVRVLVSTAIKEAFAGANDD 237

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            L   ++  DR+   P AP  GL    V Y
Sbjct: 238 ALVALMEETDRRASAPPAPAHGLCLAEVGY 267


>gi|88802196|ref|ZP_01117723.1| pseudouridylate synthase I [Polaribacter irgensii 23-P]
 gi|88781054|gb|EAR12232.1| pseudouridylate synthase I [Polaribacter irgensii 23-P]
          Length = 260

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 97/253 (38%), Gaps = 13/253 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + +E+ G  + GWQ+Q N  ++   ++K++ F+         G GRTD+ V A     
Sbjct: 7   YLIRLEFLGFRFSGWQKQLNAKTVHDIVDKSLSFVFEDSAYKTIGVGRTDAKVSANAYYF 66

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                 E   V    +LN+          + +  V   ++   ++ R+ Y Y        
Sbjct: 67  QLFRDSEIKEVSFLASLNSN--FPPDFRAITVQEVGTDYNVIQASKRKEYHYYFSFGAKN 124

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-- 180
                     +   LD + M  AA+   G H F  + +     +   R ID  ++     
Sbjct: 125 HPFAAPFLVNVAADLDLKKMMDAARLFEGEHYFHKYCTKPSAQTVFKRVIDVCEIVENTI 184

Query: 181 -------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-QAQDRKECGP 232
                       +RV  + FL  QIR  + +L  VG G   +T +  +L +  DRK    
Sbjct: 185 LTASFFPEKSYMLRVQGKGFLRYQIRLMMATLFEVGKGTLDATFIIASLKEDNDRKFMRN 244

Query: 233 LAPPEGLYFDSVE 245
           +AP  GL    +E
Sbjct: 245 IAPSSGLQLYDIE 257


>gi|322823466|gb|EFZ29213.1| hypothetical protein TCSYLVIO_4538 [Trypanosoma cruzi]
          Length = 409

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 67/263 (25%), Positives = 104/263 (39%), Gaps = 36/263 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            +  + + Y+G  Y G  +Q+   ++++  +  A+  V        + +   GRTD GV 
Sbjct: 20  RKVAIRLAYHGHLYDGLAKQEETSNTVEAYVVAALKHVRLIPQDGPIDLARCGRTDKGVS 79

Query: 57  ALRQVAH-------FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           AL  V         +       P    C  LN+ L    TI I+  + VD  F ARFS +
Sbjct: 80  ALGNVFSLTVRASSWPTDSPQKPALDYCAMLNSAL--PVTIRIVGWAYVDDTFDARFSCV 137

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH----CQ 164
            R+Y Y                +   + L+ E M  AA  L G H+F  F          
Sbjct: 138 GRTYRY----------------YFCHRGLNVEAMGNAAARLKGVHNFRNFCKTDVVNVSN 181

Query: 165 ASSPIRTIDHFDVNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
               +R++  F   +   L+  + + A SFL+ QIR  +  L LVG G      + + L+
Sbjct: 182 YERDVRSVGIFASEALPELVSYLEIHANSFLYHQIRCTMEVLFLVGRGLEDPEVVTQLLE 241

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
             DRK   PLA    L      +
Sbjct: 242 RGDRKPVYPLADGTPLVLWDCHF 264


>gi|156844606|ref|XP_001645365.1| hypothetical protein Kpol_1058p44 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156116026|gb|EDO17507.1| hypothetical protein Kpol_1058p44 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 446

 Score =  160 bits (406), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 97/269 (36%), Gaps = 41/269 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK      +++G I +A+        +  +       GRTD G
Sbjct: 97  IALKFAYLGWNYNGLAIQKEPTPLPTVEGVILEAMNKCRLVPSMNPQDYKFSRCGRTDKG 156

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV    +     P     + N              + D I +  +     K F A
Sbjct: 157 VSAMSQVISLKVRSNLTPEEQANSDNDSKEIQYVDILNQLLPDDIRVSAVCLRPPKDFDA 216

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS   R Y Y                    + LD E M  AA++  G +DF  F  +  
Sbjct: 217 RFSCKHRHYKYL----------------FNKEGLDLEKMEQAAKYYEGENDFRNFCKLDG 260

Query: 163 -CQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RTI    + +  G+     ++  +FL  Q+R  + +L LVG G    T ++ 
Sbjct: 261 SKQITNYKRTIISASIMHVSGDFYCFDLIGSAFLWHQVRCMMANLFLVGQGLEDHTLIKD 320

Query: 221 AL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            L  +   RK    +A    L     ++ 
Sbjct: 321 MLDIEKTPRKPIYDMASDVPLILYDCKFE 349


>gi|145350766|ref|XP_001419769.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580001|gb|ABO98062.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 257

 Score =  160 bits (406), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/264 (22%), Positives = 92/264 (34%), Gaps = 40/264 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFLV--------TGEIVVVHGA 48
            +  + + Y G  Y G+  Q         +++ ++  A+             ++      
Sbjct: 11  RKIALHVCYLGWDYHGFASQGAANAAAPRTVEQALFDALAKTKLVESARDVFKVADYARC 70

Query: 49  GRTDSGVHALRQVAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           GRTD GV  L Q+                +     LN  L   + +  L  + VD + +A
Sbjct: 71  GRTDRGVSGLGQIVTLRARSNGAEGVDEELDYVALLNRAL--PNDVRALGWAPVDDELNA 128

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           RF    R Y Y                      LD   MR AA+   G HDF  F  +  
Sbjct: 129 RFDCEWRQYKYFFEKTNG---------------LDLGAMREAARAFEGVHDFRNFCRMDA 173

Query: 164 Q-ASSPIRTIDHFDVNS--FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +   S  R +    +     G L+ I V   +FL  Q+R     L +VG G  + T + +
Sbjct: 174 ENVKSFTRNVLECTIEESHDGKLMYINVRGTAFLWHQVRCMASVLFMVGLGHESPTVVTE 233

Query: 221 A--LQAQDRKECGPLAPPEGLYFD 242
              L+   RK   P+AP   L   
Sbjct: 234 LLDLERTPRKPQYPMAPEHALLLW 257


>gi|149184026|ref|ZP_01862387.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
 gi|148848263|gb|EDL62552.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
          Length = 150

 Score =  160 bits (406), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 46/141 (32%), Positives = 71/141 (50%), Gaps = 3/141 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M R    + Y+GS + G+Q Q    ++Q  IEKA+  +  G+ V +  +GRTD+GVHA  
Sbjct: 11  MQRIKCTVAYDGSPFAGYQVQPGKRTVQLEIEKALSAIHKGDQVKITASGRTDAGVHAKG 70

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD             LN+ L     I + +   V++ FHARFSA+++ Y Y +   
Sbjct: 71  QVFHFDTGLSIPEEKWPTVLNSKL--PPEIVVTSAEEVEEGFHARFSAVKKEYRYSVYQT 128

Query: 120 QAPLALEKGRAWLIPKSLDCE 140
           +     ++  A   P  L+ E
Sbjct: 129 KTADPFKRDFALHYPFPLNIE 149


>gi|328350038|emb|CCA36438.1| pseudouridylate synthase [Pichia pastoris CBS 7435]
          Length = 422

 Score =  160 bits (406), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/271 (20%), Positives = 86/271 (31%), Gaps = 43/271 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   Q+   +  +I+  I +A+        +          GRTD G
Sbjct: 50  IALKFSYLGWNYQGLAVQREATDLPTIEFKILEALRQCRMIPSLNPIDCAFSRCGRTDKG 109

Query: 55  VHALRQVAHFDLVREWVPVIL---------CKALN-AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++     P  L            +N     +   I I  +     K F A
Sbjct: 110 VSAMNQVIGLNVRSRLTPEELESPENDIKELDYINILNQLLPSDIRIHGVCLRPPKGFDA 169

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS   R Y Y                    + LD E+M+ AA    G HDF  F  +  
Sbjct: 170 RFSCRGRHYKYV----------------FQDEGLDLESMKKAAPMFEGVHDFRNFCKVDG 213

Query: 163 ----CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
                  +  +R+     +          +   +FL  Q+R  V  L ++G G  +   +
Sbjct: 214 AKQMTNYTRAVRSSQILPLEGHPGYYVFDLKGTAFLWHQVRCMVAILLMIGQGFESPDIV 273

Query: 219 EKALQAQDRKECGPLAPPE--GLYFDSVEYS 247
            K L  Q   +           L      Y 
Sbjct: 274 SKLLDIQSHPQKPVYVMAHDIPLVLYDCIYD 304


>gi|320582058|gb|EFW96276.1| Non-essential tRNA:pseudouridine synthase [Pichia angusta DL-1]
          Length = 404

 Score =  160 bits (406), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/273 (22%), Positives = 94/273 (34%), Gaps = 43/273 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFL------VTGEIVVVHGAGRTD 52
            R  +   Y G  Y G   Q    N  +++  I KA+        +          GRTD
Sbjct: 58  RRIALKFSYLGWNYHGLAYQNDTSNIPTVELFILKALEKTKLIRNLDPTDCDFSRCGRTD 117

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLSIVDKQ-F 101
            GV A+ QV    +        +   LN              + + I I ++ +   + F
Sbjct: 118 KGVSAMNQVISLVVRSNLTQDEMANPLNDVKELDYVKILNKVLPEDIRIHSICLRPPEGF 177

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS + R Y Y                     +L+ E M+ AA + VG  DF  F  +
Sbjct: 178 DARFSCLSRHYKYFFEQA----------------NLNIEKMQQAASYFVGEQDFRNFCKV 221

Query: 162 H--CQASSPIRTIDHFDVNS--FGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
               Q  +  R I    +    FG+      +   +FL  Q+RS +  L LVG       
Sbjct: 222 DGSKQIVNYKRKIISSSIERTKFGHKTYVFSLRGSAFLWHQVRSMMSILFLVGQELEEPE 281

Query: 217 DLEKALQAQ--DRKECGPLAPPEGLYFDSVEYS 247
            + K L  +    +    +A P  L     E+ 
Sbjct: 282 IVRKLLDVKLFPGRPNYTIASPLPLVLYDCEFD 314


>gi|332862130|ref|XP_513709.3| PREDICTED: pseudouridylate synthase-like 1 [Pan troglodytes]
          Length = 261

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 64/191 (33%), Positives = 95/191 (49%), Gaps = 15/191 (7%)

Query: 3   RYCMIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ + G       +    +Q  +E+A   +   E V    + RTD+GVHAL
Sbjct: 13  RYLVYFQYVGTDFNGVAAVRGTQRAVGVQNYLEEAAERLNSVEPVRFTISSRTDAGVHAL 72

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      + P +L +ALN +L+    I +L    V   FHAR++A  R+YL
Sbjct: 73  SNAAHLDVQRRSGRPPFPPEVLAEALNTHLRHP-AIRVLRAFRVPSDFHARYAATSRTYL 131

Query: 114 YRIITRQAP----LALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           YR+ T           E+   W +P   LD   M+ AAQHL+G HDF+ F+S      SP
Sbjct: 132 YRLATGCHRRDELPVFERNLCWTLPADCLDVVAMQEAAQHLLGTHDFSAFQSAGSPVPSP 191

Query: 169 IRTIDHFDVNS 179
           +RT+    V+ 
Sbjct: 192 VRTLRRVSVSP 202


>gi|254565011|ref|XP_002489616.1| Non-essential tRNA:pseudouridine synthase [Pichia pastoris GS115]
 gi|238029412|emb|CAY67335.1| Non-essential tRNA:pseudouridine synthase [Pichia pastoris GS115]
          Length = 438

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/271 (20%), Positives = 86/271 (31%), Gaps = 43/271 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   Q+   +  +I+  I +A+        +          GRTD G
Sbjct: 66  IALKFSYLGWNYQGLAVQREATDLPTIEFKILEALRQCRMIPSLNPIDCAFSRCGRTDKG 125

Query: 55  VHALRQVAHFDLVREWVPVIL---------CKALN-AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++     P  L            +N     +   I I  +     K F A
Sbjct: 126 VSAMNQVIGLNVRSRLTPEELESPENDIKELDYINILNQLLPSDIRIHGVCLRPPKGFDA 185

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS   R Y Y                    + LD E+M+ AA    G HDF  F  +  
Sbjct: 186 RFSCRGRHYKYV----------------FQDEGLDLESMKKAAPMFEGVHDFRNFCKVDG 229

Query: 163 ----CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
                  +  +R+     +          +   +FL  Q+R  V  L ++G G  +   +
Sbjct: 230 AKQMTNYTRAVRSSQILPLEGHPGYYVFDLKGTAFLWHQVRCMVAILLMIGQGFESPDIV 289

Query: 219 EKALQAQDRKECGPLAPPE--GLYFDSVEYS 247
            K L  Q   +           L      Y 
Sbjct: 290 SKLLDIQSHPQKPVYVMAHDIPLVLYDCIYD 320


>gi|242001376|ref|XP_002435331.1| pseudouridylate synthase, putative [Ixodes scapularis]
 gi|215498661|gb|EEC08155.1| pseudouridylate synthase, putative [Ixodes scapularis]
          Length = 442

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 102/260 (39%), Gaps = 19/260 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---VTGEIVVV------HGAGRTDS 53
           +  + + YNG  Y G QR     +I+  + +A++    +  E V V        A RTD 
Sbjct: 72  KMALCMSYNGKDYLGMQRNPGTKTIEDDLLQAMYKGDLILKEHVDVPQAMKFQRAARTDK 131

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+RQ+    L        +   +N++L   D I ++++    + F+ + S   R+Y 
Sbjct: 132 GVSAVRQIVSLKLPTNLTVEEMVDKINSHLV--DQIRVIDIKRTTRGFNCKNSCDSRTYT 189

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTI 172
           Y + T                       +        G H++  F S    +  S +R I
Sbjct: 190 YVLPTFAFAPPESPAEESYRITEERIGEVNNVLALYKGCHNYHNFTSGKKSEDPSAMRYI 249

Query: 173 DHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
              +     V      +++++  +SF+  QIR  VG +  +  G    T + +A   +  
Sbjct: 250 ISAECAQPFVQGDQEFVQVQIKGQSFMLHQIRKMVGLVIAIMRGCTKETTIRRAWGPEKL 309

Query: 228 KECGPLAPPEGLYFDSVEYS 247
               P+AP  GL  + V Y 
Sbjct: 310 DL--PIAPALGLMLEEVHYD 327


>gi|328873128|gb|EGG21495.1| tRNA pseudouridylate synthase [Dictyostelium fasciculatum]
          Length = 510

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 101/300 (33%), Gaps = 79/300 (26%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q+    +I+G +  A+         +      +GRTD GV A 
Sbjct: 93  VALKVAYLGWHYHGFAAQQCTEETIEGHLFSALQKTCLIRDIKECNYTKSGRTDKGVSAF 152

Query: 59  RQVAHFDLVREW------------------------------------VPVILCKALNAY 82
            QV    +                                        +     + LN  
Sbjct: 153 GQVISLYVRSNLKQGDGIIPPVIPDDDNKNQQQKNKNNNKKNNNHVTPIEYPYVRMLNGV 212

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM 142
           L     I +L  + V   F+ARFS + R+Y Y                +  P  LD E M
Sbjct: 213 L--PPYIRVLAWTPVPFHFNARFSTLYRTYKY----------------YFNPAGLDIEAM 254

Query: 143 RIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDV-------NSFGNLIEIRVVARSFL 194
           + A  H +G HDF+ F  I  +A  S  R I  FD+          G L E  +   +FL
Sbjct: 255 KEAGNHFLGSHDFSNFCKIDLEAVKSFTRVILSFDIAPVPVGQFQSGGLYEATICGYAFL 314

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE-------GLYFDSVEYS 247
             QIR  +  L L+G  K+ +T ++  L          +A P         L      Y 
Sbjct: 315 WHQIRCMMAMLLLIGQKKFPTTIIKDLLDT-----SSAIAKPSYEMASEIPLVLYDCGYE 369


>gi|325969586|ref|YP_004245778.1| tRNA-pseudouridine synthase I [Vulcanisaeta moutnovskia 768-28]
 gi|323708789|gb|ADY02276.1| tRNA-pseudouridine synthase I [Vulcanisaeta moutnovskia 768-28]
          Length = 272

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 62/246 (25%), Positives = 105/246 (42%), Gaps = 26/246 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M      + Y+GS + G+      +SI+  + +AI     +   +  A RTD GV A+  
Sbjct: 1   MPTMAFKVLYDGSLFSGFT--GGTNSIEYYLRRAI-RYFIKDFGLSKASRTDPGVSAVGN 57

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V            ++   LN+ L   + I +   + V   FHAR +A+ R+Y+Y +    
Sbjct: 58  VISIKYDDGI--RLMPGMLNSRL--PNGIRVWAWAEVSDDFHAR-AAVSRTYVYVMP--- 109

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                     WL     D + MR A +  VG HD + F+       + +  I   +V   
Sbjct: 110 ----------WLYE---DVDLMRRATELFVGVHDLSNFQVKERGVPTTVM-ISSVNVERL 155

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +   +V + F +  IR  V ++++VG    T  +L   ++ + R+   P A P GL 
Sbjct: 156 GDYLVFTIVGKGFRNKMIRKIVNAIRMVGISNLTLDELRDLIELRVRRPI-PPASPYGLL 214

Query: 241 FDSVEY 246
             SV Y
Sbjct: 215 LLSVSY 220


>gi|312093536|ref|XP_003147717.1| hypothetical protein LOAG_12156 [Loa loa]
 gi|307757118|gb|EFO16352.1| hypothetical protein LOAG_12156 [Loa loa]
          Length = 414

 Score =  159 bits (404), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 69/294 (23%), Positives = 105/294 (35%), Gaps = 66/294 (22%)

Query: 2   IRYCMIIEYNGSGYFGW-QRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            R  ++  Y G  Y G  ++Q+   +I+  + KA+       + E    +  GRTD GV 
Sbjct: 32  RRIALMFMYFGWEYNGLVEQQEIAGTIEEEMRKALMKTKLVESWENCGWNRCGRTDKGVS 91

Query: 57  ALRQVAHFDLVREWVP---------------------VILCKALNAYLKISDTISILNLS 95
           A +QVA   +                           +   K LN+ L     I +L  +
Sbjct: 92  AFKQVASLIVRSNEPEGEGVFWPAIAHTSSETAVKGELQYVKMLNSTL--PTNIRVLAWA 149

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            V + F AR+   +R+Y Y         A  +        + D E MR A Q LVG HDF
Sbjct: 150 PVPENFSARYRCTQRTYTY---------AFPRA-------NFDIEAMRQACQFLVGEHDF 193

Query: 156 TTFRSIHCQAS----SPIRTIDHFDVN----------------SFGNLIEIRVVARSFLH 195
             F  I         + IRTI + D++                +    +++ V    FL 
Sbjct: 194 RNFCRIDMNKGRVEMNYIRTISYADISLISNNSLLASKQSDEVTHYEFLQLTVKGSGFLW 253

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFDSVEYS 247
            QIR  +  L  +G G      + + L  +    K    LAP   L      Y 
Sbjct: 254 HQIRCIMALLCEIGLGNEKPEVISELLDIKLTPSKPIYGLAPAFPLCLFDCVYD 307


>gi|317501503|ref|ZP_07959701.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088022|ref|ZP_08336944.1| hypothetical protein HMPREF1025_00527 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316897132|gb|EFV19205.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330409170|gb|EGG88625.1| hypothetical protein HMPREF1025_00527 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 252

 Score =  159 bits (403), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 65/260 (25%), Positives = 101/260 (38%), Gaps = 34/260 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + ++Y+G+ Y GW R        +I   I   +  +TGE + +    +T  GVHA
Sbjct: 1   MPNIKLTLQYDGTRYLGWTRPAADGYAKTISYRISSVLQKMTGEDITLFAGAKTAPGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L Q  +F     +        LN YL     I IL+  IV  +F +  +A+ R+YLYRI 
Sbjct: 61  LCQTVNFHTESPFSDTYFLSKLNEYL--PKDIHILSSEIVSDRFRSDLNAVSRTYLYRIC 118

Query: 118 TRQAPLALEKGRAWLIPKSL---DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           T        +     IP+ +   +   +R AA  LVG HDF +   +  +  +    I  
Sbjct: 119 TAPVQNIFTRAYTANIPEIISESEVAAIRKAADSLVGVHDFRSLSGVKKKKGTVK-EIFD 177

Query: 175 FDVNSFGN-------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             V+           L+ I++ A  FL+      +  L   G  K            + R
Sbjct: 178 ISVSHSKETENDSFSLLTIKICANDFLYLMPEHIIEFLIKKGVDK------------EVR 225

Query: 228 KECGPLAPPEGLYFDSVEYS 247
                   P GL   S+ Y 
Sbjct: 226 CN------PAGLLLHSITYP 239


>gi|50309181|ref|XP_454596.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49643731|emb|CAG99683.1| KLLA0E14345p [Kluyveromyces lactis]
          Length = 444

 Score =  159 bits (403), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 101/271 (37%), Gaps = 45/271 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
                 Y G  Y G   QK+     +++G+I + +        +  +       GRTD G
Sbjct: 98  VAFKFAYLGWNYNGLAIQKDATPLPTVEGTILETMNKCKLVPSMVPQEYKFSRCGRTDRG 157

Query: 55  VHALRQVAHFDLVREWVPV------------ILCKALNAYLKISDTISILNLS-IVDKQF 101
           V A+ QV    +                        LN  L   + I +  +     K F
Sbjct: 158 VSAMNQVISLRVRSNLTAEEQLDPSYDDKEIQYVNILNQIL--PEDIRVSAVCLRPPKGF 215

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS   R Y Y   +                + LD E M++AA+H  G HDF  F  +
Sbjct: 216 DARFSCKSRHYKYLFSS----------------EGLDLERMQLAAKHYEGEHDFRNFCKL 259

Query: 162 H--CQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               Q ++  RTI   ++ +   ++    +V  +FL  Q+R  V +L LVG G      +
Sbjct: 260 DGSKQITNYKRTIKSSNIMHVSEDMYCFDLVGSAFLWHQVRCMVANLFLVGQGLEDPNLI 319

Query: 219 EKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           ++ L  +   RK    +A    L     E+S
Sbjct: 320 KEMLDIEKMPRKPIYEMASDIPLILYECEFS 350


>gi|302818580|ref|XP_002990963.1| hypothetical protein SELMODRAFT_132613 [Selaginella moellendorffii]
 gi|300141294|gb|EFJ08007.1| hypothetical protein SELMODRAFT_132613 [Selaginella moellendorffii]
          Length = 289

 Score =  159 bits (403), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 106/257 (41%), Gaps = 17/257 (6%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-------------EIVVVHGAGR 50
           + +++ Y+G+ + GWQ+Q    ++Q  +EK +                  +  +V  AGR
Sbjct: 14  FKIVLSYSGTAFAGWQKQPGFLTVQSVLEKQLGRFVDGKRASNLEKQGKIKEALVSVAGR 73

Query: 51  TDSGVHALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GVHA  QV  F    RE     +  A+N+ +     +  ++ S V++ FH  FSA  
Sbjct: 74  TDKGVHACGQVCSFYTWMRECKEEDVKSAVNSAM--PTILRAVSASEVNRDFHPIFSAKW 131

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           R Y+Y    R +   ++  +   + ++L+  ++  A      +   ++  +  C      
Sbjct: 132 RRYIYIFPLR-SRDEIDVSKVATLLRALEGHSLSYAIFARDTKIARSSGPATVCTLYHAR 190

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
             +      +  N++ + +VA  FL   +R  V +             L   ++  DR+ 
Sbjct: 191 AALAKLPFPNEENVMVVELVADRFLRKMVRVLVSTAIKEAFAGANDDALVALMEETDRRA 250

Query: 230 CGPLAPPEGLYFDSVEY 246
             P AP  GL    V Y
Sbjct: 251 SAPPAPAHGLCLAEVGY 267


>gi|83320035|ref|YP_424629.1| tRNA pseudouridine synthase A [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|123753714|sp|Q2SRI4|TRUA_MYCCT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83283921|gb|ABC01853.1| tRNA pseudouridine synthase A, putative [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
          Length = 249

 Score =  159 bits (403), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 94/248 (37%), Gaps = 9/248 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVA 62
             + + Y+GS Y GW  Q N  S Q  + KAI  V         GA +TD+ VHAL Q  
Sbjct: 5   ILLTLCYDGSNYHGWINQTNSISTQTVLNKAIKKVIKTSEFKTIGASKTDANVHALDQKV 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
              +    +      A+N  L   + I ILN   VD  F+ R     + Y Y I   +  
Sbjct: 65  LLIIYFTPILEKFINAINKAL--PEDIRILNAKFVDPNFNIR-EVDYKIYNYYINDHKFD 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH---CQASSPIRTIDHFDVNS 179
           +   +   +     +D   ++      +G H+F  F  +           R ID   V  
Sbjct: 122 IFTNRYEYFWKHSKIDILKLQEIFNLFIGEHEFKLFSGLKENEWDNYQTKRIIDDIKVLR 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG-KWTSTDLEKALQAQDRKECGPLAPPEG 238
             N + I+  A  F+  QIR  + +        K     L + LQ    K+   +   +G
Sbjct: 182 INNKVVIQFKATGFIRYQIRIIIANCLNAYLNYKVNINTLTEMLQG-IGKKTPFIIKAKG 240

Query: 239 LYFDSVEY 246
           L    +++
Sbjct: 241 LVLQEIKF 248


>gi|119872780|ref|YP_930787.1| tRNA pseudouridine synthase ACD [Pyrobaculum islandicum DSM 4184]
 gi|166228754|sp|A1RU12|TRUA_PYRIL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119674188|gb|ABL88444.1| Pseudouridylate synthase [Pyrobaculum islandicum DSM 4184]
          Length = 255

 Score =  159 bits (403), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 102/247 (41%), Gaps = 35/247 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y   I Y+G+ ++G+    +  S    +E A+  V GEI  +    RTD GV A+  
Sbjct: 1   MP-YLYRIAYDGTLFYGFT--GHSRS----LEPALKRVFGEI--LGRGSRTDPGVSAVAN 51

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                   + +P+ L  +     K+   +    ++ V + F+ R  A  R YLY      
Sbjct: 52  TVMV---SQKLPIALVNS-----KLPRGVWAWAIAEVPQSFNPR-RAKFRHYLYVAP--- 99

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                            D  +M  AA+ L G HDF +F     +  S I T+    V   
Sbjct: 100 -------------HWGEDLGSMHEAAEVLAGTHDFASFIQRRGEKISTIATVMEIKVELR 146

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI +  V R F +  IR    ++   G G +   D+ + L+ + R    P AP EGL 
Sbjct: 147 GDLIYMHFVGRGFKNKMIRKLAWAILAAGRGIFNIRDIRELLE-RPRPGVVPSAPAEGLV 205

Query: 241 FDSVEYS 247
             ++EY 
Sbjct: 206 LLNIEYD 212


>gi|255088059|ref|XP_002505952.1| predicted protein [Micromonas sp. RCC299]
 gi|226521223|gb|ACO67210.1| predicted protein [Micromonas sp. RCC299]
          Length = 290

 Score =  158 bits (401), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 68/281 (24%), Positives = 92/281 (32%), Gaps = 54/281 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQ----KNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTD 52
             + + Y G  Y G+  Q        +++ ++ +A+  V       T +       GRTD
Sbjct: 15  VALHVMYAGWDYRGFASQGAERDGVRTVEEALFRALKRVRLIAPDATWKTCDYTRCGRTD 74

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLK--------------------ISDTISIL 92
           +GV AL QV    L R  VP       +  L                     +   I IL
Sbjct: 75  AGVSALGQVVSARL-RCRVPRRDDDDDDDDLSETGRLHEGDEIDYPAVLNRALPRDIRIL 133

Query: 93  NLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
             + V   F ARF    R Y Y                      LD   M  AA   VG 
Sbjct: 134 GWTYVPPAFSARFDCDYRHYKYFFTDWNG---------------LDVRAMNEAASAFVGE 178

Query: 153 HDFTTFRSIH-CQASSPIRTIDHFDVN----SFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
           HDF  F  +      +  R ID   V         +  I VV  +FL  Q+R     L L
Sbjct: 179 HDFRNFCKMDARNVHNYRRRIDSCRVVLAAGEPPGVAHIEVVGTAFLWHQVRCIASVLFL 238

Query: 208 VGDGKWTSTDLEKA--LQAQDRKECGPLAPPEGLYFDSVEY 246
           VG G+     +     L    RK    +AP E L      +
Sbjct: 239 VGLGREPPGVVAHMLDLARCPRKPQYEMAPEEPLLLWRCGF 279


>gi|149237835|ref|XP_001524794.1| tRNA pseudouridine synthase 3 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146451391|gb|EDK45647.1| tRNA pseudouridine synthase 3 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 491

 Score =  158 bits (401), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 93/249 (37%), Gaps = 43/249 (17%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTD 52
           M    +   Y G  Y G   Q +     +++  I KA+  V       E V     GRTD
Sbjct: 128 MRFVAIKFAYLGWNYNGLAFQNDPTPLPTVEEIILKALAKVKLIREPIEEVEYSKCGRTD 187

Query: 53  SGVHALRQVAHFDLVREWVPVILCK------------ALNAYLKISDTISILNLS-IVDK 99
            GV A+ QV    L     P                  +NA L     I +  +     +
Sbjct: 188 KGVSAMNQVISIKLRSNLTPQEQQDPAFDAKEVDYFTVINANL--PADIKVHAICLRPPE 245

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS   R Y Y          L +  +     +LD + M  AA++  G HDF  F 
Sbjct: 246 NFDARFSCKERHYRY----------LFRKTS-----TLDIDLMAQAAEYYEGLHDFRNFC 290

Query: 160 SIH--CQASSPIRTIDHFDV---NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
            +    Q +S +R I    +   +S GNL    ++  +FL  Q+R  V  L LVG    +
Sbjct: 291 KLDGSKQLTSFVRDIRRSKIIPLDSDGNLYCFDLIGNAFLWHQVRCMVAILFLVGQKLES 350

Query: 215 STDLEKALQ 223
              ++  + 
Sbjct: 351 PEIVKDLMD 359


>gi|221115363|ref|XP_002163885.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 446

 Score =  158 bits (401), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 97/280 (34%), Gaps = 43/280 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--------------TGEIVVVHG 47
            +  +++ Y G+ Y G Q+  +  +I+  +  A+  +                  +    
Sbjct: 90  RKVALLLAYCGANYSGMQKNPDVETIEEKLLDALCEMKAIRAEHKHEFLVNNVNQISFQR 149

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           A RTD GV A RQ     +          + +N  L   D I +  L  V K F+A+   
Sbjct: 150 AARTDKGVSAARQTVSLKITSN----TFLEDVNKLL--PDDIRVFGLERVTKSFNAKCCC 203

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSL-------------DCENMRIAAQHLVGRHD 154
             R+Y Y + +     + +      + +                   +        G H+
Sbjct: 204 SGRAYEYLVPSFAFAPSNDVNFFVFVYRFFLHHIGFQKFISDEQFAKLNRLFSCYEGTHN 263

Query: 155 FTTFRSIHC-QASSPIRTIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
           F  F S       S  R I  F  N          I I +  +SF+  QIR  +G +  V
Sbjct: 264 FHNFTSGKPFSDQSANRYIISFKANKPFECQGHEFIAIEISGQSFMIHQIRKMIGLVIAV 323

Query: 209 GDGKWTSTDLEKA-LQAQDRKECGPLAPPEGLYFDSVEYS 247
             G      +EK+ LQA+      P AP  GL    V Y+
Sbjct: 324 CRGHCPEDTIEKSWLQAK---ADIPKAPGLGLLLCKVFYN 360


>gi|322792295|gb|EFZ16279.1| hypothetical protein SINV_03177 [Solenopsis invicta]
          Length = 290

 Score =  158 bits (401), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 75/269 (27%), Positives = 112/269 (41%), Gaps = 37/269 (13%)

Query: 16  FGWQRQ------KNGSSIQGSIEKAIFLVTGE---IVVVHGAGRTDSGVHALRQVAHFDL 66
            G QRQ      ++  SIQG+IE A+  V+ +     V+  + RTD+GVHA    AH +L
Sbjct: 1   RGLQRQSSDNFVRDTDSIQGAIETALLTVSPKSLIRPVLTLSSRTDAGVHAFGNTAHVEL 60

Query: 67  VREWVPV----ILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYR-----I 116
             ++  +     + K +N Y  K    I +L+ + +   FHAR S   R+YLYR     I
Sbjct: 61  ENKYNTIYNSSDVKKYVNRYFAKCGHFIRLLDSTPITNDFHARHSCKSRTYLYRFMIPKI 120

Query: 117 ITRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTID 173
              Q     E      +     D +  R   Q  +G  DFTTF +     +    +R + 
Sbjct: 121 CNEQRISLPETIHTHHLRAYDFDIDKARRGIQLFMGTKDFTTFSAKSITSRKIQYVRALH 180

Query: 174 HFDVNS------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            F +                         +SFL+ Q+R  +G+L  +G GK T  D+   
Sbjct: 181 AFTLEEAQPLMPFDPLSNNFTYWHFTCKGKSFLYNQVRRMIGALIALGLGKITEKDITVM 240

Query: 222 LQAQDRKECGP---LAPPEGLYFDSVEYS 247
           LQ        P     PP GL+  +VEY 
Sbjct: 241 LQVPSHHNWDPRVTPVPPNGLHLLNVEYD 269


>gi|297739353|emb|CBI29343.3| unnamed protein product [Vitis vinifera]
          Length = 466

 Score =  158 bits (401), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 62/298 (20%), Positives = 102/298 (34%), Gaps = 71/298 (23%)

Query: 3   RY-CMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGV 55
           RY  + + Y G  ++G+  + +   +++  I KA+          + +     GRTD GV
Sbjct: 101 RYVALKVMYFGPRFYGFASEAHMDPTVESEIFKALEKTWLAVGDKKELQYSRCGRTDKGV 160

Query: 56  HALRQVAHFDLVREWV-------------------------------------PVILCKA 78
            ++ QV    L                                           +   + 
Sbjct: 161 SSVGQVIALFLRSNLKEIGAREENSKEVVPEEQYEERREVKDEGGGDSLASEGEIDYMRV 220

Query: 79  LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD 138
           LN  L     I ++    V   FHARFS + R Y Y                     +L+
Sbjct: 221 LNRVL--PKDIRVMGWCPVPIGFHARFSCLSREYKYFFWRG----------------NLN 262

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGN------LIEIRVVAR 191
              M  A +  VG HDF  F  +      +  R I  F++    N      L  I++   
Sbjct: 263 ILAMESAGKKFVGEHDFRNFCKMDAVNVHNYRRHIISFEIAPTNNRYDGNQLWAIKIKGS 322

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFDSVEYS 247
           +FL  Q+R  V  L ++G G  +   ++  L  +   RK    +AP   L  +S E+ 
Sbjct: 323 AFLWHQVRCMVAVLFMIGQGLESPDVVDALLDTERTSRKPQYAMAPEIPLVLESCEFE 380


>gi|302808177|ref|XP_002985783.1| hypothetical protein SELMODRAFT_181988 [Selaginella moellendorffii]
 gi|300146290|gb|EFJ12960.1| hypothetical protein SELMODRAFT_181988 [Selaginella moellendorffii]
          Length = 372

 Score =  158 bits (401), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 96/284 (33%), Gaps = 64/284 (22%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + I Y GS Y G+  Q    ++++  I  A+        +         GRTD GV A
Sbjct: 69  VALKIMYIGSCYHGFASQGCAFNTVESEIFAALQRTNLVVGSIADANYSRCGRTDRGVSA 128

Query: 58  LRQVA------------------------------------HFDLVREWVPVILCKALNA 81
             QV                                      F    +   +    +LN 
Sbjct: 129 TAQVIALYLRSKKKALDDTEESGYGSKDRVIVARSSREEEEMFAAETDDDEIDYVSSLNR 188

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
            L     I +L    V   FHARFS + R Y Y                + I   L+ + 
Sbjct: 189 AL--PADIRVLGWCPVPPGFHARFSCLYREYKY----------------FFIDDGLNIDA 230

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIR 199
           M+ A+Q L+G HDF  F  +      +  R I  FD+      L  + V   +FL  Q+R
Sbjct: 231 MKQASQRLLGEHDFRNFCKMDADNIHNYTRQILAFDILPIEECLWVMHVRGNAFLWHQVR 290

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYF 241
                L ++G G  T T ++  L      RK    +AP   L  
Sbjct: 291 CMAAVLFMIGRGHETLTIIDDLLDVDKTMRKPQYVMAPELPLVL 334


>gi|15790870|ref|NP_280694.1| tRNA pseudouridine synthase A [Halobacterium sp. NRC-1]
 gi|169236616|ref|YP_001689816.1| tRNA pseudouridine synthase A [Halobacterium salinarum R1]
 gi|24212587|sp|Q9HNP6|TRUA_HALSA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|229470757|sp|B0R6V1|TRUA_HALS3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|10581435|gb|AAG20174.1| pseudouridylate synthase I [Halobacterium sp. NRC-1]
 gi|167727682|emb|CAP14470.1| tRNA-pseudouridine synthase A [Halobacterium salinarum R1]
          Length = 266

 Score =  158 bits (401), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/255 (23%), Positives = 95/255 (37%), Gaps = 35/255 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
           M R    + Y+G  Y G+QRQ + S++ G +  A+  +      +      AGRTD+GV 
Sbjct: 1   MPRRAFRVAYDGRPYHGFQRQPDVSTVAGELFGALRRLDVFDGAKPPGYAAAGRTDAGVS 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  Q   FD      P     AL       D I +   +    +FHA   A+ R+Y+Y  
Sbjct: 61  ARAQTVAFDAPAWLTPDAFTGAL------PDPIQVWAHADAPPEFHATHDAVARTYVYYW 114

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               +    ++                 A   L G HD   F ++    ++ +R +D   
Sbjct: 115 YAPDSRATDDRA--------------AGALDRLTGTHD---FHNLTPNTTNTVRELD-AT 156

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG----P 232
           ++  G    I V A  F    +R  V SL  +      +  ++  L   D    G    P
Sbjct: 157 LDRDGAFRVITVRAGGFCRELVRRVV-SLVQLVTETGDTDRIDTVL--GDEPVAGPDGVP 213

Query: 233 LAPPEGLYFDSVEYS 247
            A P  L   +V Y 
Sbjct: 214 PADPHPLVLHAVAYD 228


>gi|145527104|ref|XP_001449352.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124416940|emb|CAK81955.1| unnamed protein product [Paramecium tetraurelia]
          Length = 414

 Score =  158 bits (400), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 106/269 (39%), Gaps = 42/269 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            R    + Y G  Y G ++Q N  ++I+  + KA+  V      +      AGRTD GV 
Sbjct: 49  TRVAFKLAYVGINYHGLEQQINQQNTIENHLFKALQRVRMIDNRDDCNYTRAGRTDKGVS 108

Query: 57  ALRQVAHFDLVREWVPVIL-CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           A+  V   ++ +      L  + LN  L   + I IL+  IVD++F+AR+  I+R Y Y 
Sbjct: 109 AIGNVVALNVRKIGKSDKLYAQILNRVL--PEDIQILDECIVDEKFNARYDCIKRVYKY- 165

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDH 174
                          +      + E M  A    +G HDF  F  +   A+ + +RTI +
Sbjct: 166 ---------------YFYKMDYNIELMTEAMLLFIGEHDFRNFCKLDVIANQNFVRTIMN 210

Query: 175 FDVNSFGN-----------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
             +                      L  + +   +FL  QIR  +  L L+G G   S+ 
Sbjct: 211 ITIEEVFPENAPRCSTLFKDDDRLRLYCVTIEGNAFLWHQIRYMMAVLFLIGKGIEKSSV 270

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +       D K    +AP   L   + E+
Sbjct: 271 ITDLFTKFDGKPNYQMAPDYPLVLHNCEF 299


>gi|297279170|ref|XP_001093509.2| PREDICTED: hypothetical protein LOC705127 [Macaca mulatta]
          Length = 511

 Score =  158 bits (400), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 100/264 (37%), Gaps = 60/264 (22%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY +  +Y G+ + G                        +  V G  R      A+ +V 
Sbjct: 269 RYLVYFQYVGTDFNG------------------------VAAVRGTQR------AIGEVT 298

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                R   PV L               +L    V   FHAR +A  R+YLYR++T    
Sbjct: 299 PGQTGRVVPPVSLT----------CCHRVLRAFRVPSDFHARHAATSRTYLYRLVTGCHR 348

Query: 123 ----LALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  E+   W +    LD   M+ AAQHL+G HDF+ F+S      SP+RT+    V
Sbjct: 349 LAELPVFERNLCWTLQADCLDVAAMQEAAQHLLGTHDFSAFQSAGSPVPSPVRTLRRVSV 408

Query: 178 NSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           +                    +   ++SFL+ Q+R     L  VG G      ++  L++
Sbjct: 409 SPGQASPLVTPEESRKLQFWSLEFESQSFLYRQVRRMTAVLVAVGLGALAPAQVKTILES 468

Query: 225 QDR--KECGPLAPPEGLYFDSVEY 246
           QD   K    +AP  GL+  SV Y
Sbjct: 469 QDPLGKHQARVAPAHGLFLKSVLY 492


>gi|320591696|gb|EFX04135.1| pseudouridylate synthase 3 [Grosmannia clavigera kw1407]
          Length = 522

 Score =  158 bits (400), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 99/293 (33%), Gaps = 52/293 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVT----------GEIVVVHG---- 47
             + + Y G  Y G++ Q +G   +I+  + KA+               E+ +V      
Sbjct: 60  IALKLAYLGKRYGGFEYQPSGALPTIEEELWKALTKACLVFPAPGASADEVDLVRCEYSK 119

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDK-QFHARFS 106
            GRTD GV A  QV    +      V   K LN  L     I +L         F ARFS
Sbjct: 120 CGRTDRGVSAFGQVVALRVRSNKRAV-YAKVLNRLL--PPDIRVLAWCATPPADFSARFS 176

Query: 107 AIRRSYLYRII-------TRQAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTT 157
              R Y Y              P       +   P    LD + MR AA   VG HDF  
Sbjct: 177 CRERQYRYFFTQPAYFTEDGSRPGPTSSAGSASQPPDGWLDIDAMRDAATRFVGLHDFRN 236

Query: 158 FRSIHC--QASSPIRTIDHFDVNSFGNL-------------------IEIRVVARSFLHT 196
           F  +    Q ++  R I    +    ++                       V   +FL  
Sbjct: 237 FCKVDPSKQITNFERRIFAAGITEVADVHSSLRCLSSSASSVSFPRVYSFDVRGSAFLWH 296

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           QIR  V  L LVG G+  +  + + L   AQ  +   P+A    L      + 
Sbjct: 297 QIRHMVAVLFLVGQGREPADVVSQLLGVAAQPGRPNYPMADETPLVLWDCIFP 349


>gi|170097145|ref|XP_001879792.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164645195|gb|EDR09443.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 446

 Score =  158 bits (400), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 64/280 (22%), Positives = 91/280 (32%), Gaps = 50/280 (17%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-------TGEIVVVHGAGRT 51
            +  +   Y+G  Y G   Q       +++G +  A+            E       GRT
Sbjct: 50  RKIALKFSYSGWEYGGLAFQLGPTPLPTVEGVLFDALAKARLIDQEAGFEGCGWEKCGRT 109

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D GV A  QV                       + DTI +L  S V  +F ARFS + R 
Sbjct: 110 DRGVSAAGQVVSLWATTSKPTFEHDYLSILNRLLPDTIRVLAWSPVAPKFSARFSCLYRH 169

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y Y                +  P  LD   M+ AA  LVG HDF     +  Q    I  
Sbjct: 170 YKY----------------FFSPLGLDIPRMQQAALRLVGDHDFRNLCKLDPQKQITIFR 213

Query: 172 -------IDHFDVNSFGNLIE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                  I+   +   G  +    +V  +FL+ Q+R  +  L LVG G    + +   L 
Sbjct: 214 RKVITAEIEPLSLAENGEGVYVFNLVGTAFLYHQVRHIMAILFLVGTGLEPPSVVSSLLN 273

Query: 224 AQ----------------DRKECGPLAPPEGLYFDSVEYS 247
            +                DRK    +A    L      Y 
Sbjct: 274 VEAGVEPTKDGDSPYEVVDRKPEYQMADALPLMLWECGYP 313


>gi|196007746|ref|XP_002113739.1| hypothetical protein TRIADDRAFT_26740 [Trichoplax adhaerens]
 gi|190584143|gb|EDV24213.1| hypothetical protein TRIADDRAFT_26740 [Trichoplax adhaerens]
          Length = 279

 Score =  158 bits (399), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 91/249 (36%), Gaps = 45/249 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
            R    + Y G  Y+G   Q+    +I+  +  A+                +GRTD GV 
Sbjct: 9   RRVAFKLAYIGWDYYGLASQEGIEKTIEAELFNALTKTCLIENRTNSNYSRSGRTDKGVS 68

Query: 57  ALRQVAHFDLVREW-----------VPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           AL QV   ++                 +   K LN  L     I IL  + VD  F ARF
Sbjct: 69  ALGQVISLNVRTNLASGPGVIVETVSELSYVKLLNKVL--PGDIRILAWAPVDNDFSARF 126

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQ 164
           + + R+Y Y                +    +++ E M  AAQ L G HDF  F  +    
Sbjct: 127 NTVSRTYKY----------------YFPRANMNIEAMNEAAQRLKGEHDFRNFCKMDLAN 170

Query: 165 ASSPIRTIDHFDVNSFG----------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
            S+  R I    V S             + EI V  ++FL  Q+R  V  L L+G G   
Sbjct: 171 VSNFRREILSIKVQSIETPYVLQNQGFEMCEIIVCGKAFLWHQVRCMVAILFLIGQGLED 230

Query: 215 STDLEKALQ 223
           +  +   L 
Sbjct: 231 ANIINYMLD 239


>gi|153813978|ref|ZP_01966646.1| hypothetical protein RUMTOR_00185 [Ruminococcus torques ATCC 27756]
 gi|145848374|gb|EDK25292.1| hypothetical protein RUMTOR_00185 [Ruminococcus torques ATCC 27756]
          Length = 221

 Score =  158 bits (399), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 59/224 (26%), Positives = 93/224 (41%), Gaps = 16/224 (7%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           M    + ++Y+G+ Y GW R        +I   I   +  +TGE + +    +T  GVHA
Sbjct: 1   MPNIKLTLQYDGTRYLGWTRPAADGYAKTISYRISSVLQKMTGEDITLFAGAKTAPGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L Q  +F     +        LN YL     I IL+  IV  +F +  +A+ R+YLYRI 
Sbjct: 61  LCQTVNFHTESPFSDTYFLSKLNEYL--PKDIHILSSEIVSDRFRSDLNAVSRTYLYRIC 118

Query: 118 TRQAPLALEKGRAWLIPKSL---DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           T        +     IP+ +   +   +R AA  LVG HDF +   +  +  +    I  
Sbjct: 119 TAPVQNIFTRAYTANIPEIISESEVAAIRKAADSLVGVHDFRSLSGVKKKKGTVK-EIFD 177

Query: 175 FDVNSFGN-------LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
             V+           L+ I++ A  FL+      +  L   G G
Sbjct: 178 ISVSHSKETENDSFSLLTIKICANDFLYLMPEHIIEFLNKKGSG 221


>gi|123976924|ref|XP_001330657.1| tRNA pseudouridine synthase A family protein [Trichomonas vaginalis
           G3]
 gi|121897278|gb|EAY02404.1| tRNA pseudouridine synthase A family protein [Trichomonas vaginalis
           G3]
          Length = 353

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 53/267 (19%), Positives = 93/267 (34%), Gaps = 39/267 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G    G+  Q + + +++  I +A+                 GRTD+GV  +
Sbjct: 22  IALRIAYIGWNLKGFVLQNDTNETVEYHIFEALKRAKLIRNENECNYSLCGRTDAGVSGV 81

Query: 59  RQVAHFDLVREWVP--------------VILCKALNAYLKISDTISILNLSIVDKQFHAR 104
             V    +                      +  A      +  +I +  ++ V   F+AR
Sbjct: 82  GNVISVRVRSVCPTGLGSIPREGAKVQKEEMNYAQILNGILPPSIRVTGVAYVKPDFNAR 141

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           F    R Y Y                       + + M+ AA+HL+G HD+  F      
Sbjct: 142 FDCATRGYRYFFHKFDK----------------NIDLMKEAAEHLLGEHDYRAFCKFSPD 185

Query: 165 A-SSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           +    +R I   +  ++ G +    +V   F+  QIR     L  VG+G    +  ++ L
Sbjct: 186 STKHCVRKIYKCEFGDAGGGVWYFEIVGSGFIWHQIRCIASILFAVGNGFEKPSITKELL 245

Query: 223 QAQDR--KECGPLAPPEGLYFDSVEYS 247
                  +   P+A PE L F +  Y 
Sbjct: 246 NTAKYPGRPNYPIADPEPLVFWNAGYE 272


>gi|320163253|gb|EFW40152.1| tRNA-pseudouridine synthase [Capsaspora owczarzaki ATCC 30864]
          Length = 548

 Score =  157 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 59/269 (21%), Positives = 91/269 (33%), Gaps = 67/269 (24%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL-VTGEIVV---VHGAGRTDSGVHALR 59
             + I Y G  Y G   Q +  +++G +  A+   +    +        GRTD+GV A  
Sbjct: 142 IALKIAYLGWKYNGLAIQPDVETVEGHLISALKTCMLIPDLSWANYSRCGRTDAGVSAFG 201

Query: 60  QVAHFD-------------------------LVREWVPVILCKALNAYLKISDTISILNL 94
           QV   D                                +     LN  L     I ++  
Sbjct: 202 QVVSLDVRTNLTEGVGVIQQESAIPFQKGRKTEATHAELEYVFKLNRQL--PADIRVVAW 259

Query: 95  SIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHD 154
           + V   F ARFS + R Y Y                +    +++ E M+ AAQ+ VG HD
Sbjct: 260 TPVPLAFDARFSCLYRKYKY----------------FFPKNNMNIEAMQRAAQYFVGTHD 303

Query: 155 FTTFRSIHCQ--ASSPIRTIDHFDVNSF------------------GNLIEIRVVARSFL 194
           +  F   +      S +R I  FDV                       + E+ V+  +FL
Sbjct: 304 YRNFCKTNFDNGVKSFVRRILAFDVVKSTCLPINSATDATDLEGQAAEMYELNVLGFAFL 363

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           + Q+R     L +VG G      +E  L 
Sbjct: 364 YHQVRCMTSILFMVGQGLEPPEVVEHMLD 392


>gi|193666867|ref|XP_001946781.1| PREDICTED: tRNA pseudouridine synthase 3-like isoform 1
           [Acyrthosiphon pisum]
 gi|328702018|ref|XP_003241780.1| PREDICTED: tRNA pseudouridine synthase 3-like isoform 2
           [Acyrthosiphon pisum]
          Length = 402

 Score =  157 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 94/267 (35%), Gaps = 41/267 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
               I Y G  Y G+  Q  +  +I+  + +A+ +     + +    H  GRTD GV + 
Sbjct: 59  VVFKILYLGWDYHGFATQDVSEKTIEYELFRALTICCLIESRQTSNYHRCGRTDKGVSSF 118

Query: 59  RQVAHFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            QV    +            CK LN  L     I ++    V   F ARF    R+Y Y 
Sbjct: 119 SQVISLTVRSNGDDSEELPYCKMLNRLL--PKDIRVVAWGPVKDDFSARFDCGSRTYKY- 175

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTID 173
                          W     LD + M  A Q +VG HDF     +          R I 
Sbjct: 176 ---------------WFPRGDLDVDLMNQAIQQVVGTHDFRNLCKMDVANGVVQFYRRIT 220

Query: 174 HFDV-----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             D+           N   ++ E+ +V ++FL  QIR  V  L LVG  K      +  L
Sbjct: 221 SADIKICSENNQFSKNRDYDMCELTIVGKAFLWHQIRCIVSVLILVGCRKENPNIFKDLL 280

Query: 223 --QAQDRKECGPLAPPEGLYFDSVEYS 247
             +   RK    LA    L     ++ 
Sbjct: 281 NIENCPRKPQYCLASDLPLNLFDCQFE 307


>gi|328770686|gb|EGF80727.1| hypothetical protein BATDEDRAFT_3084 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 289

 Score =  157 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 65/275 (23%), Positives = 91/275 (33%), Gaps = 49/275 (17%)

Query: 4   YCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVH 56
             + I Y G  Y+G+      +  +++  I KA+ +       G        GRTD GV 
Sbjct: 26  IALKISYIGDKYYGFASASNDSVPTVESYIFKALEVARLIPSDGGACAWSRCGRTDKGVS 85

Query: 57  ALRQVAHFDL---------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           A  QV    +           +W  +     LN  L   D I +L  S VD  F ARF+ 
Sbjct: 86  AFDQVVSVWVRTARPGDRDTLDWDQLPYLNILNRLL--PDDIRVLAWSPVDPIFDARFTC 143

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
             R Y Y                      LD   MR AA   VG HD      I    ++
Sbjct: 144 SHRKYNYFFDGA----------------GLDLIAMRDAASRFVGTHDCRHICKIDPTKAA 187

Query: 168 ----PIRTIDHFDVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
                +RTI   D+              + V  R+FL  Q+R+ +  L L+G G      
Sbjct: 188 REGFFVRTIMECDIVPVPVDGAPDRFHVLVVKGRAFLWHQVRNMMALLFLIGRGMEMPDM 247

Query: 218 LEKALQAQDRKECG-----PLAPPEGLYFDSVEYS 247
           +   L               +AP   L      Y 
Sbjct: 248 ISDMLDLTKHAPAAGRPFYEMAPDGPLVLVECAYP 282


>gi|115376217|ref|ZP_01463459.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
 gi|115366790|gb|EAU65783.1| tRNA pseudouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 303

 Score =  157 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 68/252 (26%), Positives = 102/252 (40%), Gaps = 18/252 (7%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y G G+ G+QRQ  G ++Q ++E  +   TG    V  AGRTD GVHA  QV    
Sbjct: 31  LWLWYRGGGFHGFQRQPEGPTVQSTLEAVL-RSTGVPATVMPAGRTDRGVHARMQVVSLR 89

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           L     P  L         +   + +  +      FHA++SA  ++Y YR+         
Sbjct: 90  LEAGDTPEALAAR--LPALLPPDLGVCAVRRPPPSFHAQWSAAGKTYCYRVQLGGRVSET 147

Query: 126 EKGRAW-------LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +           L  +++  E +    Q  VG+ DF  F +         RT++   V+
Sbjct: 148 WRPYVLEAAEEPRLAQRAIAPERLAELLQGAVGQRDFWAFHASSSPRKP--RTLESATVH 205

Query: 179 S-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP--LAP 235
              G L EI++   SF   Q+R  VGS  L   G+        AL++    E  P   A 
Sbjct: 206 ELEGGLFEIQLRGDSFARYQVRYLVGSALLTAAGQLPEAQWRAALES---AEAIPGLRAA 262

Query: 236 PEGLYFDSVEYS 247
             GL    V Y 
Sbjct: 263 AAGLILWEVRYP 274


>gi|118374735|ref|XP_001020555.1| tRNA pseudouridine synthase family protein [Tetrahymena
           thermophila]
 gi|89302322|gb|EAS00310.1| tRNA pseudouridine synthase family protein [Tetrahymena thermophila
           SB210]
          Length = 309

 Score =  157 bits (397), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 73/278 (26%), Positives = 110/278 (39%), Gaps = 32/278 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ----KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
           ++Y     Y G  Y G+Q Q    K   SIQ +++ A+  +T +   +H + RTD GV+A
Sbjct: 15  VKYLATCSYIGMNYSGFQTQILNGKRIPSIQDALQDALKKITKQDTPIHTSSRTDQGVNA 74

Query: 58  LRQVAHFDLVRE-----WVPVILCKALNAYL-KISDTISILNLSIVD-KQFHARFSAIRR 110
           L     F + R        P I+ K++N +L      ISI N+  V    F  + +++++
Sbjct: 75  LAHPFVFIINRNQNQKILEPSIIKKSMNMHLKDAKHQISIENIYYVHLTDFDVKANSLKK 134

Query: 111 SYLYRI----ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
            Y Y I        A    +  +   + + +D E +  A Q  VG H+F  F       S
Sbjct: 135 EYNYFIEANLKDNWANTFQQHKQVTTMTERIDQEKLNQALQQYVGTHNFQNFTIKAEHIS 194

Query: 167 S---PIRTIDHFDVN-------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                +RTID   +             I+I   A+SFL  QIR  VG       GK    
Sbjct: 195 HFGCYVRTIDSITIENYSHPFYEEAQCIKIIFKAKSFLAYQIRFMVGEALQYALGKLDFD 254

Query: 217 DLEKALQAQD-------RKECGPLAPPEGLYFDSVEYS 247
              K L            +     A P GL    V+Y 
Sbjct: 255 SFLKLLDPPKELTPQEVHENNRIRAQPRGLMLKRVDYP 292


>gi|108760886|ref|YP_632235.1| putative tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
 gi|108464766|gb|ABF89951.1| putative tRNA pseudouridine synthase A [Myxococcus xanthus DK 1622]
          Length = 281

 Score =  157 bits (397), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 68/252 (26%), Positives = 96/252 (38%), Gaps = 15/252 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + I Y G  + G+QRQ  G ++Q ++E+A+  V G    +  +GRTD GVHA  QV  
Sbjct: 11  VALWIWYRGGIFRGFQRQPEGPTVQSALEEALRSV-GVPATLMPSGRTDRGVHARMQVVS 69

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
             L        L K L   L     + +  +      FHA++SA  + Y YR     A +
Sbjct: 70  VRLEAGDSAESLEKRLPPRL--PPGLGLCGVRR-PTSFHAQWSACGKEYRYRFQLGGAVM 126

Query: 124 ALEKGRAWLIPKSLDC-------ENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                 A  +             E +    +   G  DF  F           RT++   
Sbjct: 127 PEWAPYALDVSAEPLLQATAVTPERLAALLRSAEGTRDFIAFHEKSSPRKP--RTLESAT 184

Query: 177 VNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +++  G L E R+    F   QIR  VGS   V  G         AL+     E G  AP
Sbjct: 185 LHALGGGLYEARLRGDGFARYQIRYLVGSALKVAAGLLPEEAWLAALETGQAME-GFKAP 243

Query: 236 PEGLYFDSVEYS 247
             GL    V Y 
Sbjct: 244 AHGLVLWEVRYP 255


>gi|302676700|ref|XP_003028033.1| hypothetical protein SCHCODRAFT_60363 [Schizophyllum commune H4-8]
 gi|300101721|gb|EFI93130.1| hypothetical protein SCHCODRAFT_60363 [Schizophyllum commune H4-8]
          Length = 455

 Score =  157 bits (397), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/276 (22%), Positives = 90/276 (32%), Gaps = 48/276 (17%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-------TGEIVVVHGAGRT 51
            +  +   Y G  + G   QK+     +++G +  A+            E       GRT
Sbjct: 79  RKIALKFCYGGWDFGGLAIQKDRTPLPTVEGKLFGALVRARLVDPKGGLEGCGWERCGRT 138

Query: 52  DSGVHALRQVAHFD------------LVREWVPVILCKALNAYLKISDTISILNLSIVDK 99
           D GV A  QV                             +N +L   DTI IL  S VD 
Sbjct: 139 DRGVSAAGQVISLWVRSALSQEELTPTATPTEEHPFIYMINRHL--PDTIKILAWSPVDP 196

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F +R+S   R Y Y                +  P  LD   MR A  +L G HDF    
Sbjct: 197 SFSSRYSCTWRHYKY----------------FFSPVGLDVAAMRAACAYLPGTHDFRNLC 240

Query: 160 SIHC--QASSPIRTIDHFDVNSF-----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
            I    Q     R I H  ++       G +    +   SFL+  +R+ +G L  +G   
Sbjct: 241 KIDPTKQLDQFRRDILHASISPVDASNPGGMHVFDLKGSSFLYHMVRNIMGVLLSIGARL 300

Query: 213 WTSTDLEKALQ-AQDRKECGPLAPPEGLYFDSVEYS 247
              T L   +  A   +    +A    L      Y 
Sbjct: 301 EPPTLLPALMNVAPGCRPEYMMADALPLTLWDCGYP 336


>gi|303245000|ref|ZP_07331323.1| tRNA pseudouridine synthase A [Methanothermococcus okinawensis IH1]
 gi|302484652|gb|EFL47593.1| tRNA pseudouridine synthase A [Methanothermococcus okinawensis IH1]
          Length = 263

 Score =  157 bits (397), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 94/250 (37%), Gaps = 30/250 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHALRQV 61
           Y + + YN   Y G+Q Q +  ++   I  A+          ++   GRTD GV A+   
Sbjct: 2   YILKVAYNKHHY-GFQTQPHKETVCDKIMDALKECNYLANDKIIFCGGRTDKGVSAIGNF 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              +L +E +   +   L      +  I I     +D     ++    R Y Y +     
Sbjct: 61  IVVELSQEPILSHIYSKL-----KNKGIWIFGYKKIDTIPEVKY----RHYRYILPIIPH 111

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNSF 180
                           + + M  A++ L+G H F         +  SPIRTI    +   
Sbjct: 112 ID------------EYNIDLMIEASKKLIGEHSFHNLSKKDRTKEKSPIRTIYDIKIEKN 159

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I V+ +SFL   +R  + +L  VG        +++ L  ++ K   P AP EGL 
Sbjct: 160 LYYITIDVIGKSFLWNMVRKIITALSEVGKENKPVGWIDELL-CENHKGGVPPAPAEGLI 218

Query: 241 FD----SVEY 246
                  +EY
Sbjct: 219 LMEAKTDIEY 228


>gi|313665546|ref|YP_004047417.1| tRNA pseudouridine synthase A [Mycoplasma leachii PG50]
 gi|312949580|gb|ADR24176.1| putative tRNA pseudouridine synthase A [Mycoplasma leachii PG50]
          Length = 249

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 95/248 (38%), Gaps = 9/248 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVA 62
             + + Y+GS Y GW  Q N  SIQ  + KAI  V         GA +TD+ VHAL Q  
Sbjct: 5   ILLTLCYDGSNYHGWINQINSISIQTVLNKAIKKVIKTSEFKTIGASKTDANVHALDQKV 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
              +    +     KA+N  L     I ILN   V+  F+ R     + Y Y I   +  
Sbjct: 65  LLIIYFTPILEKFIKAINKAL--PKDIRILNAKFVNSDFNIR-EVEYKIYNYYINDYKFD 121

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH---CQASSPIRTIDHFDVNS 179
           +   +   +     +D   ++      VG H+F  F  +           R ID   V  
Sbjct: 122 IFTNRYEYFWKHSKIDILKLQEIFNLFVGEHEFKLFSGLKENEWDNYQTKRIIDDIKVLR 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG-KWTSTDLEKALQAQDRKECGPLAPPEG 238
             N + I+  A  F+  QIR  + +        K     L + LQ    K+   +   +G
Sbjct: 182 INNKVVIQFKATGFIRYQIRIIIANCLNAYLNYKINVNTLIEMLQG-IGKKTPFIIEAKG 240

Query: 239 LYFDSVEY 246
           L    +++
Sbjct: 241 LVLQQIKF 248


>gi|297789719|ref|XP_002862797.1| hypothetical protein ARALYDRAFT_920264 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297308524|gb|EFH39055.1| hypothetical protein ARALYDRAFT_920264 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 244

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 51/192 (26%), Positives = 79/192 (41%), Gaps = 8/192 (4%)

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +                ALN  L     I +  LS    +FHARFSA  + Y Y+I    
Sbjct: 25  IWKLPTTVHVFLDSFHAALNGLL--PKDIRVRELSAAVPEFHARFSAQSKVYRYQIYNDT 82

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ--ASSPIRTIDHFDVN 178
                ++  A+     L+   MR      VG HD + F +   +     P+++I  F V 
Sbjct: 83  FMDPFQRYWAYHCAYKLNASKMRETVDLFVGMHDVSAFANATREDGVPDPLKSISRFYVI 142

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP----LA 234
             G+L+++ V    FL+ Q+R+ V  L  +G     S  +   L+ +DR+          
Sbjct: 143 QMGSLLQLEVEGSGFLYRQVRNMVALLIHIGKESLDSDIVPMILETKDRRVLAKYTTLPV 202

Query: 235 PPEGLYFDSVEY 246
           PP GL   SV+Y
Sbjct: 203 PPHGLCLVSVKY 214


>gi|194744150|ref|XP_001954558.1| GF18329 [Drosophila ananassae]
 gi|190627595|gb|EDV43119.1| GF18329 [Drosophila ananassae]
          Length = 410

 Score =  156 bits (396), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 74/263 (28%), Positives = 111/263 (42%), Gaps = 29/263 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL------VTGEIVVVHG---AGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+         + E V +     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQVQIACFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L   D I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPDELD----LEAFNADL--PDQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIR 170
           + T     + EK       + I   L  E +R   +   G  +F  F S       S  R
Sbjct: 187 LPTVAFASSEEKIEDLHDTYRITPEL-LEKVRETLKLYEGTKNFHNFTSKKNFLDPSAKR 245

Query: 171 TIDHF-----DVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F      ++  G   + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 246 FIMSFVSSDPFLSPQGIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTTESLERALTE 305

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 306 E--RLDLPMAPGLGLVLDTVHYE 326


>gi|156369650|ref|XP_001628088.1| predicted protein [Nematostella vectensis]
 gi|156215055|gb|EDO36025.1| predicted protein [Nematostella vectensis]
          Length = 464

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 57/295 (19%), Positives = 94/295 (31%), Gaps = 67/295 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
            R  + + Y G    G+  Q+   ++++  +  A+         E       GRTD GV 
Sbjct: 80  RRIALRLSYLGWDMHGFASQEKIDNTVEAHLFDALIKACLVKSRESCSYSRCGRTDKGVS 139

Query: 57  ALRQVAHFDLV-----------------------REWVPVILCKALNAYLKISDTISILN 93
           A  QV   ++                        +    ++    LN  L     I +L 
Sbjct: 140 AFGQVISLNVRTNLDKGPGVILRQESSVGRDTKGKTMKEILYVDILNKVL--PKEIRVLA 197

Query: 94  LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
            + V+  F ARFS   R Y Y   +                 +LD + M +A++ L G H
Sbjct: 198 WAPVELDFDARFSCSYRKYKYLFPSA----------------NLDIDLMNLASKKLEGEH 241

Query: 154 DFTTFRSIH--CQASSPIRTIDHFDVN-----------------SFGNLIEIRVVARSFL 194
           DF  F  +          R I  F V                      + E  +   +FL
Sbjct: 242 DFRNFCKMDVANGVIQFTRNITSFKVQKVSNATYSAPGENKAKQRGYEMCEAVICGSAFL 301

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
             Q+R  +  L +VG G      ++  L  +   ++    +A    L      Y 
Sbjct: 302 WHQVRCMMSILLMVGQGLEQPEVIDWLLDIEKCPQRPQYNMASELPLVLYDCVYE 356


>gi|193706844|ref|XP_001945291.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like
           [Acyrthosiphon pisum]
          Length = 441

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 66/259 (25%), Positives = 112/259 (43%), Gaps = 25/259 (9%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---LVTGE------IVVVHGAGRTDSGV 55
            +++ Y+G GY G QR K   +++  +  A+    L+T E       +    A RTD GV
Sbjct: 69  AILLAYSGLGYLGLQRNKGVKTVEEELLLALKSKNLITDEGFEQIQTMQFQRAARTDKGV 128

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            ALRQ+    L  +    ++  AL       + I +L++  V K F+++ S   R+Y Y 
Sbjct: 129 SALRQIISLLLPEDVDKQVINTAL------PEQIRVLDIRRVTKGFNSKNSCDGRTYSYT 182

Query: 116 IITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTID 173
             T   AP       ++ I  ++  + +    +  +G H++  +         S  R + 
Sbjct: 183 CPTFAFAPAETTIDFSYRIDATV-IDRINEVVKSFLGCHNYHNYTSKKKPGDPSAQRYMV 241

Query: 174 HFDVNSFGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            F  +         LI + V  +SF+  QIR  VG +  +  G      +E+A Q  DR 
Sbjct: 242 SFYCDKPFEKDGVELISLYVRGQSFMLHQIRKMVGVIIAICRGVAKHDVIERAWQ-PDRL 300

Query: 229 ECGPLAPPEGLYFDSVEYS 247
           +  P+AP  GL  + V Y 
Sbjct: 301 DL-PIAPGLGLVLEEVHYD 318


>gi|194699074|gb|ACF83621.1| unknown [Zea mays]
          Length = 414

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 117/287 (40%), Gaps = 43/287 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI---------VVVHGA---- 48
           + + ++I Y+G  + GWQ+Q   +++QG +EK +     E          + + G     
Sbjct: 119 VTFKVVISYHGGSFDGWQKQPGLNTVQGLVEKHLGQFVDERKAKQLEARSLPIEGCAIVA 178

Query: 49  GRTDSGVHALRQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+ V    +  A+N      D +  L++S V ++FH  F+A
Sbjct: 179 GRTDKGVTALQQVCSFYTWRKDVKSGDIKGAINE--AAPDKLKPLHVSEVSREFHPNFAA 236

Query: 108 IRRSYLYRIITRQAPL----------ALEKGRAWLIPKSLDCENMRIAAQHLVGR----- 152
             R Y+Y     +              LE     + P+S D   +    + L G+     
Sbjct: 237 KWRRYMYIFPLDEDADLILGEAQSSKTLENSEHNIKPQSFDVSKVDEILKPLAGKTLSYK 296

Query: 153 ---HDFTTFRSIHC-------QASSPIRTIDHFDVNSFGNLIE--IRVVARSFLHTQIRS 200
               D    RS+          + + +  +   + +  G ++   + +VA  FL   +R 
Sbjct: 297 MFARDTQASRSVGPPTECFMFHSRAAVAKLHSANEDHKGGMVVMCVELVANRFLRKMVRV 356

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            V +          +  L   ++A DR+   P APPEGL    V Y 
Sbjct: 357 LVATAIREAAAGAGADALLNLMEATDRRATAPPAPPEGLCLVDVGYE 403


>gi|323452423|gb|EGB08297.1| hypothetical protein AURANDRAFT_11850 [Aureococcus anophagefferens]
          Length = 266

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 66/264 (25%), Positives = 93/264 (35%), Gaps = 27/264 (10%)

Query: 1   MIRY-----CMIIEYNGSGYFGWQRQ----KNGSSIQGSIEKAIFLVT----GEIVVVHG 47
           M RY      + I Y G  Y G+  Q        +++  +  A+         E      
Sbjct: 11  MSRYEQRCIALWISYEGGAYSGFAEQNIPGAGVDTVERQLFAALKKTCLVESRESCGYSR 70

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALN-AYLKISDTISILNLSIVDKQFHARFS 106
            GRTD GV AL QV    +            +N     + D +  L    V  +F ARFS
Sbjct: 71  CGRTDKGVSALGQVVGLRVRSAARAGEPLDYVNMLNRVLPDDVRALAWRPVVPEFSARFS 130

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QA 165
              R+Y Y      A      G A+      D   M  AA  LVG HDF  F  +     
Sbjct: 131 CASRTYRYFF---PATSP-NTGAAY------DVPAMAAAAARLVGDHDFRNFCKMDVLHV 180

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA- 224
            +  R +   DV   G+     +  ++FL   +RS V  L LVG+G      ++  L   
Sbjct: 181 KNFRRVVYAADVRKTGDGFFFEIHGQAFLWHMVRSLVAVLFLVGEGLEPPAVVDALLDVA 240

Query: 225 -QDRKECGPLAPPEGLYFDSVEYS 247
              RK    +A    L      + 
Sbjct: 241 RTPRKPQYLIADERPLVLHDCAFD 264


>gi|183601972|ref|ZP_02963341.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|241190461|ref|YP_002967855.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|241195867|ref|YP_002969422.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|183218857|gb|EDT89499.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|240248853|gb|ACS45793.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|240250421|gb|ACS47360.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|295793448|gb|ADG32983.1| tRNA pseudouridine synthase A [Bifidobacterium animalis subsp.
           lactis V9]
          Length = 258

 Score =  156 bits (394), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 100/235 (42%), Gaps = 33/235 (14%)

Query: 44  VVHGAGRTDSGVHALRQVAHFDLVRE-------WVPVILCKALNAYL--KISDTISILNL 94
            +  AGRTD+GVHA  QV H D+  +        + +   +AL   L   + D I+I  +
Sbjct: 8   RLTVAGRTDAGVHATHQVCHVDVPDQTLGQCVGHMNLTPVQALQTRLSRMMPDDIAIHGI 67

Query: 95  SIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
           S+    F ARFSA+ R+Y+YRI   + P     K  AW   + LD   M  AA   +G H
Sbjct: 68  SVAPAGFDARFSALERTYVYRIADARVPWDPRLKDFAWRTDRELDIAQMNAAAALTLGLH 127

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNSFG--------------------NLIEIRVVARSF 193
           DF +F   +    + IR +                              L+   +VA +F
Sbjct: 128 DFGSFAIANP-GGTTIREVKTAYWQRVPTRPLLGPGMGERYHTPAVESGLLCFTIVADAF 186

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFDSVEYS 247
               +RS VG+   VG GK         ++   R+   GP+AP +GL  + + Y 
Sbjct: 187 ARNMVRSLVGACVQVGMGKRDVDWFAGKMRVPLREGSTGPIAP-QGLTLEHIAYP 240


>gi|325186551|emb|CCA21092.1| tRNA pseudouridine synthase putative [Albugo laibachii Nc14]
          Length = 493

 Score =  155 bits (393), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 68/297 (22%), Positives = 104/297 (35%), Gaps = 74/297 (24%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF--------LVTGEIVVVHGAGRTDSGV 55
             M   Y+G  Y G+ RQ +   I+ +IEK +F        + + +       GRTD GV
Sbjct: 80  VAMKFLYSGERYCGFARQDH---IEETIEKYLFDTMQRTKLITSIDDCCYSRCGRTDKGV 136

Query: 56  HALRQVAHFDL---------------------------------VREWVPVILCKALNAY 82
            A  QV    +                                 +R+   V    +LN  
Sbjct: 137 SAFGQVIGIKVRSNVPIDAELLDVDSLDQVASGGRVRVKTQDGRIRKITEVDYAASLNRT 196

Query: 83  LKISDTISILNLSIVDKQFHARFSA-IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
           L     I + ++      F ARF+    RSY Y                + + K LD E 
Sbjct: 197 L--PSDIRVYSVVNAPNNFSARFNCDRGRSYRY----------------FFMKKDLDIEK 238

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV---------NSFGNLIEIRVVARS 192
           MR+AA    G HDF  F  I     +  R +  F +         N +  +    +   +
Sbjct: 239 MRLAAIGFEGLHDFRNFCRIDTNCQTFDRNVRSFKIKSSDEIGDKNPYRQMYYFEIHGNA 298

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           FL  Q+R  V  L L+G G+   + ++K L  +   RK    +AP   L      + 
Sbjct: 299 FLWHQVRCMVSILFLIGQGREEPSIVKKMLDIEKYPRKPQYAIAPDHPLVLHDCRFD 355


>gi|257053070|ref|YP_003130903.1| tRNA pseudouridine synthase A [Halorhabdus utahensis DSM 12940]
 gi|256691833|gb|ACV12170.1| tRNA pseudouridine synthase [Halorhabdus utahensis DSM 12940]
          Length = 275

 Score =  155 bits (393), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 62/253 (24%), Positives = 94/253 (37%), Gaps = 34/253 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSGVH 56
           R    I Y+G  + G+QRQ + +++  +I  A+  +               AGRTD+GV 
Sbjct: 6   RRAFRIAYDGRPFHGFQRQPDVATVSDAILDALRELDVLEDGDNVPPGYAAAGRTDAGVS 65

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL Q   FD      P     ALN+ L     +     + V  +FHA   A+ R Y Y +
Sbjct: 66  ALAQTVAFDCPDWLSPA----ALNSEL--PADVRAWASADVPAEFHATHDAVAREYTYHL 119

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
               AP A                    A   L G HDF  F       +  +R +   +
Sbjct: 120 H---APDA-------------SVSRAGDALDALAGEHDFHNFT---PDDTGTVRDLTG-E 159

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLA 234
             S G+ + + + A  F    +R  V  +  +  G      +E+ L     +       A
Sbjct: 160 ARSEGDFLVVTLRADGFPRQFVRRAVTVIDALASGVAELDRIEQLLGDDPVEGPAGVAPA 219

Query: 235 PPEGLYFDSVEYS 247
            PE L   +VEY 
Sbjct: 220 APEALVLTAVEYP 232


>gi|47208381|emb|CAF93145.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 409

 Score =  155 bits (392), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 60/283 (21%), Positives = 91/283 (32%), Gaps = 57/283 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q+N  ++++  + +A+         +    H  GRTD GV A 
Sbjct: 75  VALRLAYLGWAYQGFAVQENTDNTVEARLFEALHKTCLIQDRQSSNYHRCGRTDKGVSAF 134

Query: 59  RQ----------VAHFDLVREWVPVI----------LCKALNAYLKISDTISILNLSIVD 98
            Q             F L                    K LN  L     I I N +   
Sbjct: 135 SQVTAVQSLHTPPFSFKLPENVDADKKSQTAVSELPYVKMLNRVL--PHDIRIWNWAPAA 192

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           + F ARF    R+Y Y                +    SL+ E M  AA+   G HDF   
Sbjct: 193 EGFSARFDCQSRTYRY----------------YFPRGSLNVELMADAAERYEGTHDFRNL 236

Query: 159 RS--IHCQASSPIRTI----------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
               +        RTI          +H       ++    V   +FL+ Q+R  +  L 
Sbjct: 237 CKMDVGNGVLQFERTILSSSVTPVNPEHASSTDQYDIFVFEVRGLAFLYHQVRCMMALLL 296

Query: 207 LVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           L+G        + + L  Q   RK    +A    L      + 
Sbjct: 297 LIGQKLEAPEIINQLLDVQSNPRKPQYSMAVDYPLVLYHCHFE 339


>gi|238882564|gb|EEQ46202.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 491

 Score =  154 bits (391), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 58/277 (20%), Positives = 86/277 (31%), Gaps = 52/277 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTD 52
           M        Y G  Y G   Q       +++    KA+  V       E V     GRTD
Sbjct: 131 MRFVAFKFAYLGWNYNGLALQLEPTPLPTVEEVFLKALAKVKLIKEPIEEVKFSRCGRTD 190

Query: 53  SGVHALRQVAHFDLVREWVPVI------------LCKALNAYLKISDTISILNLS-IVDK 99
            GV A+ QV   ++                        LNA L     I + ++      
Sbjct: 191 KGVSAMNQVISINVRSNITLENQSNPEFDDLEIDYISVLNANL--PSDIKVHSICLRPPP 248

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS + R Y Y                    + LD E M   A+   G HDF  F 
Sbjct: 249 DFDARFSCLSRHYRYI----------------FRKQDLDIELMNQGAKLYQGIHDFRNFC 292

Query: 160 SIH--CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
            +    Q ++ +R I    +     +     +   +FL  Q+R  V  L  +G G  + +
Sbjct: 293 KLDGSKQITNFVREIYQSQIIHLHQDYYCFDLKGSAFLWHQVRCMVAILFTIGQGLESPS 352

Query: 217 DLEKALQAQDRKECGPLAP----PE--GLYFDSVEYS 247
            +   +         P  P         L     E+ 
Sbjct: 353 IITDLMD----TNKFPTKPQYEMAHDIPLVLYDCEFP 385


>gi|86134196|ref|ZP_01052778.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
 gi|85821059|gb|EAQ42206.1| tRNA pseudouridine synthase A [Polaribacter sp. MED152]
          Length = 260

 Score =  154 bits (390), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 97/253 (38%), Gaps = 13/253 (5%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
           Y + + + G  + GWQ+Q N  ++   ++K++  V  +      GAGRTD+ V A R + 
Sbjct: 7   YLISLGFLGFRFSGWQKQTNAKTLHDIVDKSLSFVLKDVDYKTIGAGRTDAKVSANRYLF 66

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                      +    LN+ L          +S V  +F+   +   + Y Y        
Sbjct: 67  QLFTNEVLQQDVFLNELNSNL--PADFKAYTVSEVATKFNIINAPKIKEYHYYFSFGAVN 124

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
                         L+ + M+  A    G H F  + +     +   RTI+   +     
Sbjct: 125 HPFAAPFIVNEESELNIKLMKKGASLFEGEHYFHKYCTKPSAKTEFKRTIESCSIIENSI 184

Query: 183 L---------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-QAQDRKECGP 232
           L           ++V  + FL  QIR  + +L  +G G  +   +E +L +  DR+    
Sbjct: 185 LTASFFPQKSYVLKVRGKGFLRYQIRLMMATLFELGKGNLSLQYIEDSLKEDNDRQFLRT 244

Query: 233 LAPPEGLYFDSVE 245
           +AP  GL   +++
Sbjct: 245 IAPGSGLQLYTID 257


>gi|66361768|ref|XP_627406.1| Deg1p-like type II pseudouridylate synthase TruA [Cryptosporidium
           parvum Iowa II]
 gi|46228868|gb|EAK89738.1| Deg1p-like type II pseudouridylate synthase TruA [Cryptosporidium
           parvum Iowa II]
          Length = 283

 Score =  154 bits (390), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 62/257 (24%), Positives = 98/257 (38%), Gaps = 31/257 (12%)

Query: 15  YFG--WQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHALRQVAHFDL-- 66
           + G  +Q+     +I+G I KA+  +      +   +   GRTD GVH+       +L  
Sbjct: 4   FQGIAFQKDDKIPTIEGEIYKALLQLRLIKDIDSCDLVRCGRTDRGVHSAGNYISVNLRT 63

Query: 67  -VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             +   P    + LN  L     I ++    V   F ARF    R Y Y       PL  
Sbjct: 64  RAKNLEPYNYMEMLNGVL--PWDIRVIGYCEVRPDFSARFDCEYRLYKYFF-----PLNH 116

Query: 126 EKGRAWLIPK--SLDCENMRIAAQHLVGRHDFTTFRSIH---CQASSPIRTIDHFDVNSF 180
           E+ +    PK        M +AA+  +G HD+  F  +     +  + IRTI  FD+N  
Sbjct: 117 ERTKISKFPKIPPEQVPLMNVAAKQFLGTHDYRRFCKMDLKNRKNQTYIRTIYEFDINFV 176

Query: 181 GNLIEI---RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP----L 233
                     +   +FL  Q+R  +G L  +G  K+    + + L   ++K        +
Sbjct: 177 DENRTFAVATIKGSAFLWHQVRLMMGILFEIGQQKFNPEVITQMLTDVEQKNIAELSFQM 236

Query: 234 APPEGLYFDSV---EYS 247
           A   GL        EY 
Sbjct: 237 ATELGLVLWDCVFKEYD 253


>gi|134056983|emb|CAK44330.1| unnamed protein product [Aspergillus niger]
          Length = 517

 Score =  154 bits (390), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 69/277 (24%), Positives = 95/277 (34%), Gaps = 41/277 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------VTGEIVVVHGAGR 50
             +   Y G  Y G     NG      +I+  + KA+          +  +      AGR
Sbjct: 109 IALKFAYLGQRYNGL-EHANGNATPLPTIEEEMYKALRKTRETKPYYINWDGCEYSKAGR 167

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ-FHARFSAIR 109
           TD GV A  QV      R    +     LN  L   + I +L       + F ARFS   
Sbjct: 168 TDRGVSAFGQVIGI---RVRNELPYVSMLNKVL--PEDIRVLAWCPRPPEGFDARFSCGE 222

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKS------------LDCENMRIAAQHLVGRHDFTT 157
           R Y Y   T+ A      G +  +P+             LD E MR AA++  G HDF  
Sbjct: 223 RHYKYFF-TQPAFSP-TPGASGFVPRDGTGKPPKLREGWLDIEAMRKAAKYFEGTHDFRN 280

Query: 158 FRSIH--CQASSPIRTIDHFDVNSFG---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           F  +    Q  S  R I             +    +   +FL  Q+R  V  L LVG G 
Sbjct: 281 FCKLDVTKQIESFYRDIFQSSAAPLPTAAQVYVFHLEGSAFLWHQVRHMVNVLFLVGQGL 340

Query: 213 WTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
              + ++  L      RK    +A    L      Y 
Sbjct: 341 EEPSIVQDLLDVTKNPRKPTYEMASDAPLVLWDCIYP 377


>gi|302309334|ref|NP_986663.2| AGL003Wp [Ashbya gossypii ATCC 10895]
 gi|299788309|gb|AAS54487.2| AGL003Wp [Ashbya gossypii ATCC 10895]
          Length = 432

 Score =  154 bits (390), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 88/245 (35%), Gaps = 43/245 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK+     +++G+I +A+        +  +       GRTD G
Sbjct: 84  IALKFAYLGWNYNGLAIQKDPTPLPTVEGTILEAMNKCRMVPSMVPQDYKFSRCGRTDKG 143

Query: 55  VHALRQVAHFDLVREWVPVI------------LCKALNAYLKISDTISILNLS-IVDKQF 101
           V A+ QV    +     P                  LN  L   D I I  +     K F
Sbjct: 144 VSAMNQVISLRVRSNLTPQEQEDPANDAREIPYIHILNQLL--PDDIRISAICLRPPKGF 201

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS   R Y Y                      LD   M  AA+   G HDF  F  +
Sbjct: 202 DARFSCKYRHYKYL----------------FNKSGLDLSKMEEAARLYEGEHDFRNFCKL 245

Query: 162 H--CQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               Q ++  RTI    + +  G++    ++  +FL  Q+R  + +L +VG G    T +
Sbjct: 246 DGSKQITNFKRTILSAKILHVDGDMYCFDLLGSAFLWHQVRCMMANLFIVGQGLEPLTLI 305

Query: 219 EKALQ 223
              L 
Sbjct: 306 NNLLD 310


>gi|170050837|ref|XP_001861491.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167872293|gb|EDS35676.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 476

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 112/278 (40%), Gaps = 47/278 (16%)

Query: 1   MIRYCMIIEYNGSGYF--GWQRQKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHA 57
           M RY + + Y G+ +   G  R ++  S++G++E A+          +  + RTD+GVHA
Sbjct: 1   MNRYLINLSYVGTHFRDNG--RLEDPQSVEGALEIALKKFRPVNEFKIKLSSRTDAGVHA 58

Query: 58  LRQVAHFDLVRE----WVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRRSY 112
           L    H DL R     + P  L + LN         I +L    V   FHAR  A  R+Y
Sbjct: 59  LNNAVHVDLERYNGKPYEPDKLTQGLNRTFGSQKIPIRVLRTRHVPLTFHARLCAKSRTY 118

Query: 113 LYRI---------------ITRQAPLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFT 156
           LYR+                  +     E  R + I  K+ D + ++ AA    G HDF 
Sbjct: 119 LYRVGVLRPEFCDDPEQIHPFTRFIPIDEHDRCYFIANKNFDPDRLKRAAALCEGYHDFR 178

Query: 157 TFRSIHC------QASSPIRTIDHFDVNS---------------FGNLIEIRVVARSFLH 195
           TF +I          +  +R I+   V                 +    +IR+ ARSFL+
Sbjct: 179 TFMAIARGNLWQQMPTYTLRRIERITVERGSSMASAFSRKLADRYYEYWDIRIKARSFLY 238

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
            Q+R  VG+     + + T  D+++ L    +      
Sbjct: 239 NQVRRMVGAWIAAAEARITERDVQQMLTVPAKSSWSST 276


>gi|308235466|ref|ZP_07666203.1| tRNA pseudouridine synthase A [Gardnerella vaginalis ATCC 14018]
          Length = 173

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 60/173 (34%), Positives = 89/173 (51%), Gaps = 19/173 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-------IVVVHGAGRTDSG 54
           +R  + + Y+G  ++GW RQ N  ++QG++E A++ V           + +  AGRTD+G
Sbjct: 1   MRLRLDLAYDGGDFYGWARQPNLRTVQGTLEDALYKVLRVHDGDSCFPLRLTVAGRTDTG 60

Query: 55  VHALRQVAHFDLVREW-------VPVILCKALNAYLK--ISDTISILNLSIVDKQFHARF 105
           VHA  QV H D+  +          +   KAL   L+  +   ISI ++SI    F ARF
Sbjct: 61  VHASYQVCHLDVEDDILQNCVGHTNLTPVKALEYRLRGVLPKDISIHSVSIAPSGFDARF 120

Query: 106 SAIRRSYLYRII---TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
           SA+ R+Y+YRI     R+      +G    I   LD  +M  AAQ +VG HDF
Sbjct: 121 SALDRTYVYRISDAANRENLDPRMRGFVLQIDYDLDVNSMNQAAQMIVGLHDF 173


>gi|24648455|ref|NP_650899.1| CG4159, isoform A [Drosophila melanogaster]
 gi|7300636|gb|AAF55785.1| CG4159, isoform A [Drosophila melanogaster]
          Length = 410

 Score =  154 bits (389), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 105/263 (39%), Gaps = 29/263 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L     I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPEELD----LEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIR 170
           + T       EK       + I   L  + ++   +   G  +F  F S       S  R
Sbjct: 187 LPTVAFAPFEEKVDDVHDTFRISPEL-LQKVKETLKLYEGTKNFHNFTSKKSFLDPSSKR 245

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F  +           + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 246 FIMSFTSSEPFRSPQDIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAATLERALTE 305

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 306 E--RLDLPMAPGLGLVLDTVHYE 326


>gi|257387360|ref|YP_003177133.1| tRNA pseudouridine synthase A [Halomicrobium mukohataei DSM 12286]
 gi|257169667|gb|ACV47426.1| tRNA pseudouridine synthase [Halomicrobium mukohataei DSM 12286]
          Length = 263

 Score =  154 bits (389), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 95/252 (37%), Gaps = 34/252 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
           M  Y   I Y+G  Y G+QRQ +  +++G +   +  +             AGRTD+GV 
Sbjct: 1   MRAYR--IAYDGQPYHGFQRQPDVETVEGELLATLDRLGVTAGDVPAGYAAAGRTDAGVS 58

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL Q   F+      P           ++  ++ +   + V   FHA   A  R Y+Y +
Sbjct: 59  ALAQTVAFEAPEWLSPAAF------NSELPASVRVWASADVPDDFHATHDAREREYVYYL 112

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                  A E+        +            L G HD   F ++    S  +R +   D
Sbjct: 113 Y------APERHDDRARRAA----------DALSGEHD---FHNLTPDDSGTVRAL-SID 152

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLA 234
           +   G  +  R+ A  F    +R  VG +  +  G    + +++ L ++  D       A
Sbjct: 153 LTREGEFLVCRLRAGGFCRQLVRRVVGLVDEIRRGDAPLSKVDRVLGSKPIDGAAGVGPA 212

Query: 235 PPEGLYFDSVEY 246
            P  L   +V+Y
Sbjct: 213 SPTPLVLVAVDY 224


>gi|157106978|ref|XP_001649570.1| pseudouridylate synthase [Aedes aegypti]
 gi|108879706|gb|EAT43931.1| pseudouridylate synthase [Aedes aegypti]
          Length = 467

 Score =  154 bits (389), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 103/272 (37%), Gaps = 46/272 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q++   +I+  +  A+  V      E    H  GRTD GV A 
Sbjct: 76  ILLRFYYLGWDYQGYASQEDSARTIEHLLFNALTRVCLIENRETSNYHRCGRTDKGVSAF 135

Query: 59  RQVA------HFDLVREWVPVILCKALNA----YLKISDTIS-ILNLSIVDKQFHARFSA 107
            QV        F    +  P  +   +N        +   I  +  + +V+  + ARF  
Sbjct: 136 HQVVSLDVRSKFAPENQLEPESIANEINYCQLLNRVLPQDIRCVAWMPMVNPNYSARFDC 195

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHCQA 165
             R+Y Y                +    SL+ + M+ A   LVG HDF       +    
Sbjct: 196 RSRTYRY----------------FFPRGSLNIDAMKEACTFLVGAHDFRNLCKMDVGNGV 239

Query: 166 SSPIRTIDHFDVN--------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
            +  R I +  +         S  +++ + +  ++FL  Q+R  +  L LVG+GK   + 
Sbjct: 240 VTFTRRISYVSIEDSQSDAKESPYDMLYLELRGKAFLWHQVRCIMAVLFLVGEGKEEPSV 299

Query: 218 LEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
           +++ L   ++  C P   LA    L     EY
Sbjct: 300 VKELLDV-NKNPCKPQYSLASDLPLNLYECEY 330


>gi|195569417|ref|XP_002102706.1| GD20050 [Drosophila simulans]
 gi|194198633|gb|EDX12209.1| GD20050 [Drosophila simulans]
          Length = 411

 Score =  154 bits (389), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 105/263 (39%), Gaps = 29/263 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L     I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPEELD----LEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIR 170
           + T       EK       + I   L  + ++   +   G  +F  F S       S  R
Sbjct: 187 LPTVAFASFEEKVDDVHDTFRISPEL-LQKVKETLKLYEGTKNFHNFTSKKSFLDPSSKR 245

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F  +           + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 246 FIMSFTSSEPFRSPQDIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAATLERALTE 305

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 306 E--RLDLPMAPGLGLVLDTVHYE 326


>gi|194899730|ref|XP_001979411.1| GG15313 [Drosophila erecta]
 gi|190651114|gb|EDV48369.1| GG15313 [Drosophila erecta]
          Length = 410

 Score =  154 bits (389), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 104/263 (39%), Gaps = 29/263 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  +       +A NA L     I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPEDLD----LEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC----QASS 167
           + T       EK       + I   L  + ++   +   G  +F  F S        +  
Sbjct: 187 LPTMAFAPFEEKVEDLHDTFQISPEL-LQKVKETLKLYEGTKNFHNFTSKKSFLDPSSKR 245

Query: 168 PIRTIDHFDVNSFGNLIEI---RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I +    D       IE    +V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 246 FIMSFTSSDPFRSPQGIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAATLERALTE 305

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 306 E--RLDLPMAPGLGLVLDTVHYE 326


>gi|255938179|ref|XP_002559860.1| Pc13g14530 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211584480|emb|CAP92522.1| Pc13g14530 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 548

 Score =  154 bits (389), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 66/292 (22%), Positives = 95/292 (32%), Gaps = 52/292 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFL---VTGEI-------------- 42
             +   Y G  Y G +          +++  + KA+     ++ E               
Sbjct: 117 IALKFAYLGQAYNGLEHTNGNTTPLPTVEEVLWKALRRTRLISPETTSDLEPSDRAERVP 176

Query: 43  ----------VVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISIL 92
                          AGRTD GV A  QV    +      +     LN  L   + I +L
Sbjct: 177 MRPYHLYWDGCEYSKAGRTDKGVSAFGQVIGLRVRT--DEMNYINVLNRVL--PEDIRVL 232

Query: 93  NLSI-VDKQFHARFSAIRRSYLYRIITRQAPLA-----LEKG-------RAWLIPKSLDC 139
                    F ARFS   R Y Y                +         RA      LD 
Sbjct: 233 AWCPNPPPGFDARFSCRERRYKYFFTNPAFSPTPGSIGFQNRAQNGNGPRAEFREGWLDI 292

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           E MR AA+H  G HDF  F  +    Q  +  R I H    S   +    +   +FL  Q
Sbjct: 293 EAMREAAKHFEGSHDFRNFCKLDTNKQIDNFERIIHHSISQSIPQVYSFNLHGSAFLWHQ 352

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQ-AQD-RKECGPLAPPEGLYFDSVEYS 247
           +R  V  L LVG G  + + + + L  A++ RK    +A    L      + 
Sbjct: 353 VRHMVAILFLVGQGLESPSIVPELLDVAKNPRKPTYAMADDAPLVLWDCIFP 404


>gi|302677288|ref|XP_003028327.1| hypothetical protein SCHCODRAFT_42694 [Schizophyllum commune H4-8]
 gi|300102015|gb|EFI93424.1| hypothetical protein SCHCODRAFT_42694 [Schizophyllum commune H4-8]
          Length = 296

 Score =  154 bits (389), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 93/269 (34%), Gaps = 41/269 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-------TGEIVVVHGAGRT 51
            +  +   Y G  Y G   QK+     +++G +  A+            E       GRT
Sbjct: 46  RKIALKFCYGGWDYGGLAIQKDRTPLPTVEGKLFGALVRARLVDPKGGLEGCGWERCGRT 105

Query: 52  DSGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GV A  QV    +       E +P      +N +L   D I IL  S VD  F +R+S
Sbjct: 106 DRGVSAAGQVISLWVRSALSQEELLPHPFTYMINRHL--PDPIKILAWSPVDLSFSSRYS 163

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
              R Y Y                +  P  LD   MR A  +L G H+F     I     
Sbjct: 164 CTWRHYKY----------------FFPPVGLDIPAMRAACAYLPGTHEFRNLCKIDPTKQ 207

Query: 167 -SPIRT------IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
               R       I H D ++ G +    +   SFL+  +R+ +G L  +G      T L 
Sbjct: 208 LDQFRRDILHASISHVDASNPGGMHVFDLKGSSFLYHMVRNIMGVLLSIGARLEPPTLLP 267

Query: 220 KALQ-AQDRKECGPLAPPEGLYFDSVEYS 247
             +  A   +    +A    L      Y 
Sbjct: 268 SLMNVAPGCRPEYMMADALPLTLWDCGYP 296


>gi|47214586|emb|CAG00940.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 412

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 59/286 (20%), Positives = 92/286 (32%), Gaps = 60/286 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q+N  ++++  + +A+         +    H  GRTD GV A 
Sbjct: 75  VALRLAYLGWAYQGFAVQENTDNTVEARLFEALHKTCLIQDRQSSNYHRCGRTDKGVSAF 134

Query: 59  RQVAHFDLVREW-----------------------VPVILCKALNAYLKISDTISILNLS 95
            QV   +                              +   K LN  L     I I N +
Sbjct: 135 SQVITIESRSTQFCGGLGVKLPENVDADKKSQTAVSELPYVKMLNRVL--PHDIRIWNWA 192

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
              + F ARF    R+Y Y                +    SL+ E M  AA+   G HDF
Sbjct: 193 PAAEGFSARFDCQSRTYRY----------------YFPRGSLNVELMADAAERYEGTHDF 236

Query: 156 TTFRS--IHCQASSPIRTI----------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVG 203
                  +        RTI          +H       ++    V   +FL+ Q+R  + 
Sbjct: 237 RNLCKMDVGNGVLQFERTILSSSVTPVNPEHASSTDQYDIFVFEVRGLAFLYHQVRCMMA 296

Query: 204 SLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
            L L+G        + + L  Q   RK    +A    L      + 
Sbjct: 297 LLLLIGQKLEAPEIINQLLDVQSNPRKPQYSMAVDYPLVLYHCHFE 342


>gi|156088547|ref|XP_001611680.1| tRNA pseudouridine synthase A family protein [Babesia bovis]
 gi|154798934|gb|EDO08112.1| tRNA pseudouridine synthase A family protein [Babesia bovis]
          Length = 248

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 93/250 (37%), Gaps = 44/250 (17%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVH----GAGRTDSGVHA 57
           +  M   Y G+GY G   Q +   +++G + +A+ L      V++      GRTD  VHA
Sbjct: 12  KLLMDFSYIGTGYHGLAYQSDEPNTVEGHLFRALSLANVASDVLNNGYERCGRTDRDVHA 71

Query: 58  LRQVAHFDLVREWVP-------------------VILCKALNAYLKISDTISILNLSIVD 98
           L   A F                               KA+N +L     I +  +  V 
Sbjct: 72  LHNYASFFPDPCPPNSPCSTVSPDERGVGPCYRINTFTKAINKHL--PRGIRVNWVKHVP 129

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
             F +R +   R Y Y                     S+D   ++ A +H +G+H+F  F
Sbjct: 130 DDFSSRRNCTFRVYKYFFQLG----------------SMDLSLIQDACRHFLGQHNFNQF 173

Query: 159 RSIH-CQASSPIRTIDHFDVNSFGNLIEI-RVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                        TI  F+V  +  L+ +  +  R+FL  Q+R  +G L  VG+G     
Sbjct: 174 CKTDNRNPKDSHGTIYSFEVERYNELLCVATICGRAFLWHQVRCMMGVLFKVGEGIIPGL 233

Query: 217 DLEKALQAQD 226
            ++  L+  +
Sbjct: 234 KVKWLLEHPE 243


>gi|74227733|dbj|BAE35706.1| unnamed protein product [Mus musculus]
          Length = 219

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/197 (30%), Positives = 92/197 (46%), Gaps = 24/197 (12%)

Query: 53  SGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
            G+HAL   AH D+ R      + P ++ KALN +LK    I +L    V   FHAR +A
Sbjct: 2   PGLHALSNAAHLDIQRRPGQSPFSPEVVAKALNTHLKHP-AIRVLKAFRVPNDFHARHAA 60

Query: 108 IRRSYLYRIITRQAPL----ALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIH 162
             R+Y YR+ T  +        E+   W +  + LD   M+ AAQHL+G HDF+ F+S  
Sbjct: 61  TSRTYQYRLATGCSWPNQLPVFEQNVCWALQTEYLDMAAMQEAAQHLLGTHDFSAFQSAG 120

Query: 163 CQASSPIRTIDHFDVNSFG-------------NLIEIRVVARSFLHTQIRSFVGSLKLVG 209
              ++ +RT+    V+                    +   ++SFL+ Q+R     L  VG
Sbjct: 121 SPVTNTVRTLRRVSVSPGPASPFVLPEGSRRLQFWTLEFESQSFLYRQVRRMTAVLVAVG 180

Query: 210 DGKWTSTDLEKALQAQD 226
            G    T ++  L++QD
Sbjct: 181 LGILAPTQVKVILESQD 197


>gi|195353947|ref|XP_002043463.1| GM23177 [Drosophila sechellia]
 gi|194127604|gb|EDW49647.1| GM23177 [Drosophila sechellia]
          Length = 411

 Score =  153 bits (387), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 105/263 (39%), Gaps = 29/263 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L     I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPEELD----LEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIR 170
           + T       E+       + I   L  + ++   +   G  +F  F S       S  R
Sbjct: 187 LPTVAFASFEEQVEDVHDTFRISPEL-LQKVKETLKLYEGTKNFHNFTSKKSFLDPSSKR 245

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F  +           + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 246 FIMSFTSSEPFRSPQDIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAATLERALTE 305

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 306 E--RLDLPMAPGLGLVLDTVHYE 326


>gi|322786132|gb|EFZ12740.1| hypothetical protein SINV_14818 [Solenopsis invicta]
          Length = 444

 Score =  153 bits (387), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 99/272 (36%), Gaps = 46/272 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q+ N ++I+  +  A+       + E    H  GRTD GV + 
Sbjct: 94  ILLKFYYLGWDYHGFTVQEDNCNTIEHHLFAALLKSCCIESRESANYHRCGRTDKGVSSF 153

Query: 59  RQVAHFDLVREWVPVI---------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
            QV   D+  +  P            CK LN  L     I  +    V   F ARF    
Sbjct: 154 SQVISLDIRSKLAPEDQGNLSNELPYCKMLNRLL--PTNIRCVAWCPVASNFSARFDCKY 211

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC------ 163
           R Y Y                +    +LD + M  AA+++VG HDF     +        
Sbjct: 212 RRYKY----------------FFPRGNLDIDAMNKAAKYVVGDHDFRNICKMDVANGIIN 255

Query: 164 ------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
                  A          + ++  ++ E+ + +++FL  QIR  +G L LVG  K     
Sbjct: 256 FKRTVIDAKVSFVNEQSMEKSTGYDMCELEITSQAFLWHQIRCLMGILLLVGQRKEEPEV 315

Query: 218 LEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           + K L  +   +K    +A    L     +Y 
Sbjct: 316 ILKLLDTETCPQKPQYNMAHQVPLNLWHCDYE 347


>gi|281362146|ref|NP_001163664.1| CG4159, isoform B [Drosophila melanogaster]
 gi|272477072|gb|ACZ94960.1| CG4159, isoform B [Drosophila melanogaster]
          Length = 442

 Score =  153 bits (387), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 105/263 (39%), Gaps = 29/263 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 105 AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDKGV 164

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L     I +  +  V K F+A+     R+Y Y 
Sbjct: 165 SAARQVCSVKLPEELD----LEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYT 218

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIR 170
           + T       EK       + I   L  + ++   +   G  +F  F S       S  R
Sbjct: 219 LPTVAFAPFEEKVDDVHDTFRISPEL-LQKVKETLKLYEGTKNFHNFTSKKSFLDPSSKR 277

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F  +           + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 278 FIMSFTSSEPFRSPQDIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAATLERALTE 337

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 338 E--RLDLPMAPGLGLVLDTVHYE 358


>gi|195113035|ref|XP_002001075.1| GI22173 [Drosophila mojavensis]
 gi|193917669|gb|EDW16536.1| GI22173 [Drosophila mojavensis]
          Length = 401

 Score =  153 bits (387), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 65/260 (25%), Positives = 102/260 (39%), Gaps = 25/260 (9%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQVQIACFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       K L       + I I  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPEELDLEAFNKDL------PEQIRIFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEKGRAWLIPKSLD-CENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTID 173
           + T       ++         ++  E +    +   G  +F  F S       S  R I 
Sbjct: 187 LPTIAFAAFDDQHDQETYRIPIERLEKVSATLKLYEGTKNFHNFTSKKNFLDPSAKRFIM 246

Query: 174 HFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            F  ++          + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  +  
Sbjct: 247 SFTCSTPFLSPQSVEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTTATLERALTEE-- 304

Query: 228 KECGPLAPPEGLYFDSVEYS 247
           +   P+AP  GL  D+V Y 
Sbjct: 305 RLDLPMAPGLGLVLDTVHYE 324


>gi|327311135|ref|YP_004338032.1| Pseudouridylate synthase [Thermoproteus uzoniensis 768-20]
 gi|326947614|gb|AEA12720.1| Pseudouridylate synthase [Thermoproteus uzoniensis 768-20]
          Length = 250

 Score =  153 bits (386), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 100/243 (41%), Gaps = 37/243 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
              ++ Y+GS ++G+    +  S++ ++ +A+  + G         RTD GV AL  V  
Sbjct: 2   IAYLVAYDGSLFYGFT--GHERSVEPALARALGPLLG------RGSRTDPGVSALGNVV- 52

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
             + R   P+    A     ++   + +   + V + F+ R  A  R+Y+Y         
Sbjct: 53  --VARSLKPLGQINA-----ELPRGVWVWGYAEVPEGFNPR-RARARTYVY--------F 96

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A  +G         D   +R AA   VG HD+  F          + TI   +V   G  
Sbjct: 97  APYRGE--------DLGLVREAASLFVGTHDYRNFAK---GVRDAVTTIYSIEVEDRGAY 145

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           IEI    + F +  +R  V +L  VG G     D+ + L++       P AP EGL   S
Sbjct: 146 IEIAFRGKGFRNKMLRKIVWALLAVGRGVLGIDDVRRLLESGGGGP-VPSAPAEGLVLLS 204

Query: 244 VEY 246
           ++Y
Sbjct: 205 IDY 207


>gi|303391559|ref|XP_003074009.1| tRNA pseudouridine synthase A [Encephalitozoon intestinalis ATCC
           50506]
 gi|303303158|gb|ADM12649.1| tRNA pseudouridine synthase A [Encephalitozoon intestinalis ATCC
           50506]
          Length = 317

 Score =  153 bits (386), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 52/223 (23%), Positives = 90/223 (40%), Gaps = 33/223 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA- 62
             + I Y+G  Y G   Q    ++ G +E A+   TG    +  AGRTD+GV A+  V  
Sbjct: 37  VALRISYDGRRYSGMAPQSGKETVGGHLENAL-KFTGLGEKLVYAGRTDAGVSAISMVVS 95

Query: 63  -------------HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
                        +     ++        LN++L     I ++  + V   F ARF+ I+
Sbjct: 96  GVFISRIEMPNRSYVVTESDYKEYKYDMILNSHL--PSDIRVIGWAPVPDTFSARFTCIQ 153

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           R Y Y                +   + LD + MR  A  +    +F  F     + +   
Sbjct: 154 RQYRY----------------YFHKEDLDADRMREMASRIKKMENFYYFSKHSDKNARYE 197

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           R +D   +   G++  + + AR+FLH  +R  V +++  G G+
Sbjct: 198 RKLDECRIVDEGDVYYLDIRARAFLHNMVRKIVWAIQKAGKGE 240


>gi|24215440|ref|NP_712921.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
 gi|42559814|sp|Q8CXS6|TRUA_LEPIN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|24196565|gb|AAN49939.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
          Length = 207

 Score =  152 bits (385), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 55/193 (28%), Positives = 87/193 (45%), Gaps = 7/193 (3%)

Query: 60  QVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            + +F   R          +LNA       +SILN++ VD+ F +RFS   R Y Y I+ 
Sbjct: 1   MIVNFKTQRVIQNFSKFLLSLNA--ITDSGLSILNMTEVDENFDSRFSCNSREYEYWILN 58

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDV 177
            + P    K R +     +D   +    + L G HDF +   +   +  S +RTI    +
Sbjct: 59  TKYPRPTWKNRTFWYQHRIDVPRLEAELELLKGEHDFRSLAKVASLKGRSTVRTILDVKL 118

Query: 178 NSF---GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                   L+++++ A  FLH  IR   G+L  + +GK   T++ + L ++DR   G   
Sbjct: 119 ERSLELEGLLKVKIRANGFLHNMIRILTGTLLEISNGKRKDTNVLEILSSKDRTIAGITL 178

Query: 235 PPEGLYFDSVEYS 247
           PP GLYF    Y 
Sbjct: 179 PPYGLYFIRAYYD 191


>gi|224066589|ref|XP_002302151.1| predicted protein [Populus trichocarpa]
 gi|222843877|gb|EEE81424.1| predicted protein [Populus trichocarpa]
          Length = 465

 Score =  152 bits (385), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 62/304 (20%), Positives = 104/304 (34%), Gaps = 77/304 (25%)

Query: 2   IRY-CMIIEYNGSGYFGW--QRQKNGSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDS 53
            RY  + + Y G  ++G+  + Q +  +++  I KA+          + +     GRTD 
Sbjct: 92  RRYVALKVMYFGQRFYGFSLEAQMD-PTVESEIFKALETTRLLIGDRKEIQYSRCGRTDK 150

Query: 54  GVHALRQVAHFDLVREWV----------------------PVILCKALNAYLKISDTISI 91
           GV A+ QV    L  +                         +   + LN  L     I I
Sbjct: 151 GVSAVGQVIALYLRSKLKDIDAHNKHSGETVPEEQDGQPGEIDYVRVLNGVL--PKDIRI 208

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
           +    V   F ARFS + R Y Y                     +L+   M  A + L+G
Sbjct: 209 VGWCPVPSDFSARFSCLSREYKYFFWND----------------NLNLLVMETAGKKLIG 252

Query: 152 RHDFTTFRSIHC-QASSPIRTIDHFDVN--------------------------SFGNLI 184
            HDF  F  +   +  +  R +  F+++                              L 
Sbjct: 253 EHDFRNFCKMDAVKVHNYRRNVMSFEISPCDMSHSSGMGSVKWMITKPSIRTRFEGHQLY 312

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD-RKECGPLAPPEGLYFDS 243
            I++   +FL  Q+R  V  L ++G G  +   ++  L  +  RK    +AP   L   S
Sbjct: 313 AIKIKGSAFLWHQVRCMVAVLFMIGQGLESPEVIDALLDTRTLRKPQYLMAPEIPLVLLS 372

Query: 244 VEYS 247
            E+ 
Sbjct: 373 CEFE 376


>gi|297846396|ref|XP_002891079.1| hypothetical protein ARALYDRAFT_473569 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297336921|gb|EFH67338.1| hypothetical protein ARALYDRAFT_473569 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 443

 Score =  152 bits (385), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 63/279 (22%), Positives = 95/279 (34%), Gaps = 52/279 (18%)

Query: 3   RY-CMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGV 55
           RY  + I Y G  ++G+  +     SI+  + KA+          +       GRTD GV
Sbjct: 90  RYVALKIMYFGKRFYGFSAEAQMEPSIESEVFKALERTRLLVGDKKDSCYSRCGRTDKGV 149

Query: 56  HALRQVAHFDLVRE------------------WVPVILCKALNAYLKISDTISILNLSIV 97
            +  QV    L                            + LN  L   D I ++  S  
Sbjct: 150 SSTGQVIALFLRSRLKSPPGDSKAQVNGKTGERPEYDYVRVLNRAL--PDDIRVIGWSPA 207

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
              FHARFS   R Y Y                    ++L+   M IA +  +G HDF  
Sbjct: 208 PVDFHARFSCYAREYKYFFW----------------RQNLNLSAMDIAGKKFIGEHDFRN 251

Query: 158 FRSIH-CQASSPIRTIDHFDVN------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
           F  +         R +  F+V+          L    +   +FL  QIR  V  L ++G 
Sbjct: 252 FCKMDVANVHCYTRRVTFFEVSPCQNSHEGDQLCTFTMRGSAFLWHQIRCMVAVLFMIGQ 311

Query: 211 GKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           G  +   ++  L  +   RK    LA    L   + E+ 
Sbjct: 312 GVESVDVIDTLLDTKKTPRKPQYLLASEIPLVLRTCEFE 350


>gi|255726904|ref|XP_002548378.1| tRNA pseudouridine synthase 3 [Candida tropicalis MYA-3404]
 gi|240134302|gb|EER33857.1| tRNA pseudouridine synthase 3 [Candida tropicalis MYA-3404]
          Length = 437

 Score =  152 bits (384), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 60/277 (21%), Positives = 88/277 (31%), Gaps = 52/277 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTD 52
           M        Y G  Y G   Q       +++  I K +  V       E V     GRTD
Sbjct: 73  MRFVAFKFAYLGWNYNGLAFQLEPTPLPTVEEIILKTLAKVKLIKEPIEEVKFSRCGRTD 132

Query: 53  SGVHALRQVAHFDLVREWV------------PVILCKALNAYLKISDTISILNLS-IVDK 99
            GV A+ QV   +L                  V     LNA L     I + ++     +
Sbjct: 133 KGVSAMNQVISIELRSNLSKEDQANPELDDKEVDYLSILNANL--PSDIKVHSICLRPPE 190

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS I R Y Y                    ++LD + M   A    G HDF  F 
Sbjct: 191 DFDARFSCISRHYRYI----------------FKKQNLDIDLMNQGASLYQGIHDFRNFC 234

Query: 160 SIH--CQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
            +    Q ++  R I    + +   +     +   +FL  Q+R  V  L  +G G     
Sbjct: 235 KLDGSKQITNFQREIYSSKILHLHDDYYCFDLKGSAFLWHQVRCMVAILFTIGQGLEKPE 294

Query: 217 DLEKALQAQDRKECGPLAP----PE--GLYFDSVEYS 247
            + + +  +      P  P         L     E+ 
Sbjct: 295 IVTELMDMEK----YPTKPQYEMAHDIPLVLYDCEFP 327


>gi|195498243|ref|XP_002096440.1| GE25055 [Drosophila yakuba]
 gi|194182541|gb|EDW96152.1| GE25055 [Drosophila yakuba]
          Length = 410

 Score =  152 bits (384), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 104/263 (39%), Gaps = 29/263 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---VTGEIVV------VHGAGRTDSGV 55
            +++ Y G+ ++G QR     +I+  + K +     +T E            A RTD GV
Sbjct: 73  AILLSYCGANFYGMQRNPGMQTIEEELFKVMLKHKWITEESFEQIQISCFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L     I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPEELD----LEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIR 170
           + T       EK       + I   L  + ++   +   G  +F  F S       S  R
Sbjct: 187 LPTVAFASFEEKVEDLHDTFQISPEL-LQKVKETLKLYEGTKNFHNFTSKKSFLDPSSKR 245

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F  +           + + V  +SF+  QIR  VG    +  G  T+  LE+AL  
Sbjct: 246 FIMSFTSSEPFRSPQGIEFVTLNVKGQSFMLHQIRKMVGLAIAIVRGNTTAATLERALTE 305

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 306 E--RLDLPMAPGLGLVLDTVHYE 326


>gi|41056053|ref|NP_956361.1| tRNA pseudouridine synthase 3 [Danio rerio]
 gi|29436973|gb|AAH49516.1| Zgc:56653 [Danio rerio]
          Length = 460

 Score =  152 bits (384), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 92/285 (32%), Gaps = 59/285 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q+N  ++++  + +A+         +    H  GRTD GV A 
Sbjct: 60  VALRLAYLGWQYQGFAVQENTDNTVEARLFEALLKTKLIQDRQTSCYHRCGRTDKGVSAF 119

Query: 59  RQVAHFDLVREW---------------------VPVILCKALNAYLKISDTISILNLSIV 97
            QV   DL                           +   K LN  L     I IL  + V
Sbjct: 120 SQVISIDLRSTQYGGGLGVTVPADVDVKGKTSADELPYVKILNRVL--PHDIRILQWAPV 177

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
           +  F ARF    R+Y Y                +     LD E M  AA+   G HDF  
Sbjct: 178 ESGFSARFDCQSRTYRY----------------YFPRGDLDLELMAEAAKRYEGTHDFRN 221

Query: 158 FRS--IHCQASSPIRTIDHFDVNS-----------FGNLIEIRVVARSFLHTQIRSFVGS 204
                +        RTI    V                L   +V   + L+ Q+R  +  
Sbjct: 222 LCKMDVGNGVLQFQRTILSASVQPAQLPHPSVHNDPHQLFVFQVKGLALLYHQVRCMMAL 281

Query: 205 LKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           L L+G        +++ L  +   RK    +A    L      + 
Sbjct: 282 LLLIGQKLEAPEVIDQLLDVEKNPRKPQYSMAVDYPLVLYDCHFE 326


>gi|312378112|gb|EFR24771.1| hypothetical protein AND_10418 [Anopheles darlingi]
          Length = 376

 Score =  151 bits (383), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 103/259 (39%), Gaps = 49/259 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q++   +I+  +  A+  V      E    +  GRTD GV A 
Sbjct: 75  ILLRFFYLGWDYQGFAAQEDSIETIEHHLFTALQKVCLIESRETSNYNRCGRTDKGVSAF 134

Query: 59  RQVAHFDLVREWVPVI-------------LCKALNAYLKISDTISILNLSI-VDKQFHAR 104
            QV   D+  +  P                C  LN  L   + I  L     V+  + AR
Sbjct: 135 HQVISIDVRSKIAPEDDQLSEDSLATELDYCGMLNRVL--PEEIRCLAWMPMVNPGYSAR 192

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IH 162
           F    R+Y Y                +    +L  + M+ A +HLVG HDF       + 
Sbjct: 193 FDCRSRTYRY----------------FFPRGNLRIDAMQEACRHLVGAHDFRNLCKMDVG 236

Query: 163 CQASSPIRTIDHFDVNSFG---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
               + +R+ID   +++           +++ +++  ++FL  Q+R  +  L LVGDGK 
Sbjct: 237 NGVVNFVRSIDECTIHASQTDSSGMGSYDMMYLQLRGKAFLWHQVRCIMAVLLLVGDGKE 296

Query: 214 TSTDLEKALQAQDRKECGP 232
             T +++ L   DR  C P
Sbjct: 297 DPTIVKELLDV-DRNPCKP 314


>gi|195391039|ref|XP_002054173.1| GJ24293 [Drosophila virilis]
 gi|194152259|gb|EDW67693.1| GJ24293 [Drosophila virilis]
          Length = 408

 Score =  151 bits (383), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 103/260 (39%), Gaps = 25/260 (9%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + K +              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKVMLKHKWITEDSFEQVQIASFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L   D I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQVCSVKLPEELD----LQAFNADL--PDQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPLALEKGRAWLIPKSLDC-ENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTID 173
           + T       E+         L   E +    +   G  +F  F S       S  R I 
Sbjct: 187 LPTIAFAAFDEQHEQETYRIPLKLQEVVNTTLKLYEGTKNFHNFTSKKNFLDPSAKRYIM 246

Query: 174 HFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            F  ++          + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  +  
Sbjct: 247 SFTCSAPFLSPQSIEFVTLQVKGQSFMLHQIRKMVGLAIAIVRGNTTTATLERALTEE-- 304

Query: 228 KECGPLAPPEGLYFDSVEYS 247
           +   P+AP  GL  D+V Y 
Sbjct: 305 RLDLPMAPGLGLVLDTVHYE 324


>gi|223945645|gb|ACN26906.1| unknown [Zea mays]
          Length = 222

 Score =  151 bits (383), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 59/218 (27%), Positives = 89/218 (40%), Gaps = 61/218 (27%)

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHL 149
           + ++  V   FHAR+ ++ R+Y YR++    +    EK   W I + LD ++M+ A   L
Sbjct: 2   VTDVCCVAPDFHARYKSLERTYHYRLLAGPESTSVFEKNSVWHISEDLDIQSMKKACSIL 61

Query: 150 VGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI----------------------- 186
           VG HDF++FR+  CQA+SP+RT+D   V      +                         
Sbjct: 62  VGHHDFSSFRAAGCQANSPVRTLDELSVTEVFPFMFFPSSVERSELELSNVSLVYSRKPD 121

Query: 187 ----------------------------RVVARSF---------LHTQIRSFVGSLKLVG 209
                                       R   R F         L+ Q+R  VG LK VG
Sbjct: 122 MESSGKGSDGSCTSSVKSDFENGKDFGKRSRHRCFVVTARARSFLYHQVRLMVGLLKSVG 181

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            G  T+ D+E+ L A+       +AP  GLY  +V+Y 
Sbjct: 182 TGDLTTADVERILDAKTVTAAPSMAPSCGLYLANVKYD 219


>gi|150400022|ref|YP_001323789.1| tRNA pseudouridine synthase A [Methanococcus vannielii SB]
 gi|150012725|gb|ABR55177.1| tRNA pseudouridine synthase [Methanococcus vannielii SB]
          Length = 265

 Score =  151 bits (383), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 93/247 (37%), Gaps = 32/247 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---VTGEIVVVHGAGRTDSGVHALRQ 60
           Y   I Y+G  Y  +Q Q + +++   I   +     +    + +   GRTD GV AL  
Sbjct: 2   YIFKIAYDG-RYS-FQSQPHRNTVCDKITDTLLECGYLKEGEIPISYGGRTDLGVSALGN 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              +++  + V   +   L+ +      I IL  + + +    ++    R Y Y +    
Sbjct: 60  YIVYNITEKPVLSRIYSKLHKH-----GIWILGFNELKELPDVKY----RHYRYILPNTG 110

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNS 179
                            D E M+ A++ L+G H F         +  SPIRTI +  +  
Sbjct: 111 Q----------------DIELMKKASEKLIGTHSFHNLSKRDKTKNRSPIRTIYNIKIAK 154

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS-TDLEKALQAQDRKECGPLAPPEG 238
               I I +  +SFL   +R  V  L  VG  K+         L  +D +     A  EG
Sbjct: 155 NEYFITIEIFGKSFLWNMVRKIVRLLSNVGLSKYKEFEKFIDDLLDRDVRMGVQPASAEG 214

Query: 239 LYFDSVE 245
           L    V+
Sbjct: 215 LILVDVK 221


>gi|289597197|ref|YP_003483893.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Aciduliprofundum boonei T469]
 gi|289534984|gb|ADD09331.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Aciduliprofundum boonei T469]
          Length = 253

 Score =  151 bits (383), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 101/243 (41%), Gaps = 35/243 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +   Y+G+ ++G+QRQK+  +++G I KA+  +  +   +  A RTD GV AL  V   
Sbjct: 2   LLKFAYDGTRFYGYQRQKDVPTVEGEILKALENMGIK--NLKSASRTDRGVSALGNVIWI 59

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                     L   LNA LK      I   S  +   + R+ A  R Y Y ++       
Sbjct: 60  KTD--IDGKELIGRLNANLK-----HIYFHSFANLDINPRY-ARIRWYRYHLLDMGQ--- 108

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
                        D + ++ AA    G HDF  F  +     + +  I   DVN  G++I
Sbjct: 109 -------------DMDRLKEAAMIFQGEHDFRNFTRVR---KNTVIEIKKIDVNKRGSII 152

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I    R++L   IR  V +++    GK    ++        RK  G +APPE L    +
Sbjct: 153 TIDFYGRNYLWNLIRRIVAAMETYSLGKEFGQEIFTI-----RKNFG-IAPPEPLILMDI 206

Query: 245 EYS 247
           +Y 
Sbjct: 207 QYD 209


>gi|68490066|ref|XP_711154.1| likely tRNA pseudouridine synthase [Candida albicans SC5314]
 gi|68490103|ref|XP_711136.1| likely tRNA pseudouridine synthase [Candida albicans SC5314]
 gi|46432414|gb|EAK91897.1| likely tRNA pseudouridine synthase [Candida albicans SC5314]
 gi|46432433|gb|EAK91915.1| likely tRNA pseudouridine synthase [Candida albicans SC5314]
          Length = 489

 Score =  151 bits (383), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 57/277 (20%), Positives = 85/277 (30%), Gaps = 52/277 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTD 52
           M        Y G  Y G   Q       +++    KA+  V       E V     GRTD
Sbjct: 129 MRFVAFKFAYLGWNYNGLALQLEPTPLPTVEEVFLKALAKVKLIKEPIEEVKFSRCGRTD 188

Query: 53  SGVHALRQVAHFDLVREWVPVI------------LCKALNAYLKISDTISILNLS-IVDK 99
            GV A+ QV   ++                        LNA L     I + ++      
Sbjct: 189 KGVSAMNQVISINVRSNITLENQSNPEFDDLEIDYISVLNANL--PSDIKVHSICLRPPP 246

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
            F ARFS + R Y Y                    + LD E M   A+   G HDF  F 
Sbjct: 247 DFDARFSCLSRHYRYI----------------FRKQDLDIELMNQGAKLYQGIHDFRNFC 290

Query: 160 SIH--CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
            +    Q ++ +R I    +     +     +   +FL  Q+R  V  L  +G    + +
Sbjct: 291 KLDGSKQITNFVREIYQSQIIHLHQDYYCFDLKGSAFLWHQVRCMVAILFTIGQSLESPS 350

Query: 217 DLEKALQAQDRKECGPLAP----PE--GLYFDSVEYS 247
            +   +         P  P         L     E+ 
Sbjct: 351 IITDLMD----TNKFPTKPQYEMAHDIPLVLYDCEFP 383


>gi|326429850|gb|EGD75420.1| hypothetical protein PTSG_06496 [Salpingoeca sp. ATCC 50818]
          Length = 460

 Score =  151 bits (382), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 60/291 (20%), Positives = 93/291 (31%), Gaps = 63/291 (21%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVH 56
            +  + + Y G  Y G   Q +   +I+  + +A+         +       GRTD GV 
Sbjct: 61  RKIALKVAYLGEKYHGLAIQISAPDTIEAHLFEALEKSKLVEDIKTADYSRCGRTDKGVS 120

Query: 57  ALRQVAHFDLVREW-----------------------VPVILCKALNAYLKISDTISILN 93
           A  QV    +                             +   K LN  L     I +++
Sbjct: 121 AYCQVVSLVVRSNLNECRGFISKPSVEPAKKKAKATVDELDYTKILNGLL--PPEIRVVD 178

Query: 94  LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
              VD  F ARFS   R Y Y                +    ++D   M+ A  HLVG H
Sbjct: 179 WGAVDTDFSARFSCNARHYKY----------------FFHRANMDTAAMQAACDHLVGEH 222

Query: 154 DFTTFRSIH--CQASSPIRTIDHFDVNS-------------FGNLIEIRVVARSFLHTQI 198
           DF  F         ++ +RTI    V                 +L E  ++  +FL  Q+
Sbjct: 223 DFRNFCKADVAGGVTNFVRTIKEARVCPAEIGDASVHSSDGDFDLWEFNIIGHAFLWHQV 282

Query: 199 RSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           R  +  L +VG G      +   L       K    +A    L     ++ 
Sbjct: 283 RCMMAVLFMVGRGDEQPGMVRHLLNIDECTHKPQYVMASELPLVLYDCKFD 333


>gi|300710278|ref|YP_003736092.1| tRNA pseudouridine synthase A [Halalkalicoccus jeotgali B3]
 gi|299123961|gb|ADJ14300.1| tRNA pseudouridine synthase A [Halalkalicoccus jeotgali B3]
          Length = 266

 Score =  151 bits (382), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 100/253 (39%), Gaps = 34/253 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHA 57
           +R    I Y+G+ Y+G+QRQ +  +++G +  A+  +      +      AGRTD GV A
Sbjct: 1   MR-AFRIAYDGAPYYGFQRQPDVETVEGVLFDALDRLVTFEGEKPAGYAAAGRTDRGVSA 59

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L Q   F+      P           ++  T+     +     FHAR+ A  R+Y Y + 
Sbjct: 60  LAQTVAFEAPEWLTPAAF------NSELPGTVRAWASADAPDDFHARYDARSRTYAYYLH 113

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
              AP A             D E +R     L G HD   F ++  +     RTI     
Sbjct: 114 ---APGA-------------DVEAIRGVLSRLSGTHD---FHNLTPEDGPTTRTITRARA 154

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR---KECGPLA 234
           N  G  + + + A  FL   +R  V  +  V   +   T +E+ L +++R    E    A
Sbjct: 155 NREGPFVVLTLRADGFLKRLVRRVVTLVVDVLRSERDPTYVERVL-SKERLSGPEGIASA 213

Query: 235 PPEGLYFDSVEYS 247
           P E L      Y 
Sbjct: 214 PSEPLVLVHTAYD 226


>gi|171689408|ref|XP_001909644.1| hypothetical protein [Podospora anserina S mat+]
 gi|170944666|emb|CAP70777.1| unnamed protein product [Podospora anserina S mat+]
          Length = 635

 Score =  151 bits (382), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 65/324 (20%), Positives = 93/324 (28%), Gaps = 86/324 (26%)

Query: 4   YCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAI-----------FLVTGEIVVVHGAGR 50
             + + Y G  Y G++     N  SI+  + KA+             +          GR
Sbjct: 133 IALKLSYLGKNYGGFEHSGYSNVPSIEEELWKALVKGCLITPADPSKIDFAPFEYSKCGR 192

Query: 51  TDSGVHALRQVAHFDLVREWVPVI------------------------------------ 74
           TD GV A  QV    +     P                                      
Sbjct: 193 TDRGVSAFGQVISIRVRSNRPPSKSEQPAEEDVVMEGTPEQNNTPQLPGKKQQQNPQKEW 252

Query: 75  --------LCKALNAYLKISDTISILNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLAL 125
                     K LN  L     I +L  +    + F ARFS   R Y Y          L
Sbjct: 253 EDIVDEINYPKVLNRLL--PPDIKVLAWAPTLPEGFSARFSCYERQYRYFFTNPSMAPTL 310

Query: 126 EKG--RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNS-- 179
                ++      LD   M+ AA++  G HDF  F  +    Q +S  R I   D+    
Sbjct: 311 LAPGEKSGW----LDIAAMKKAAKYFEGLHDFRNFCKVDGGKQITSFQRRIFECDIEEVE 366

Query: 180 --------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                          G +    V   +FL  QIR  V  +  VG G      + + L  +
Sbjct: 367 GQDLGVVNFWGGEKKGKVYYFHVRGSAFLWHQIRHMVAIVFNVGQGLERPEVVRELLDVE 426

Query: 226 D--RKECGPLAPPEGLYFDSVEYS 247
              RK    +A    L      + 
Sbjct: 427 RNGRKPGYIMAEEVPLVLWDCVFP 450


>gi|94502328|ref|ZP_01308801.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri str. Hc
           (Homalodisca coagulata)]
 gi|94451115|gb|EAT14067.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri str. Hc
           (Homalodisca coagulata)]
          Length = 192

 Score =  151 bits (382), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 53/188 (28%), Positives = 85/188 (45%), Gaps = 2/188 (1%)

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             AHF+   + + +           +   I I+N+  V K+ HARF+AI R Y YRI   
Sbjct: 1   MFAHFEFYEKKILLYRNFLFKFNSFLPLNIKIINIFTVKKKIHARFTAISRVYEYRISLG 60

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P +L+    WL  K +    +   A+ L    D+++F    C   + I  I +   + 
Sbjct: 61  KNPFSLDISWQWLSKKKIKLNPLNKGAKILKKYKDYSSFCKKKCNYKTYICNIFNAKWHI 120

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             N++   + A  +L   +RS VG+L  +G GK T  D    L A+DR      AP +GL
Sbjct: 121 KNNILYFNIEANRYLRNMVRSIVGTLIELGIGKITIKDFINILYAKDRNII--SAPAKGL 178

Query: 240 YFDSVEYS 247
           +   + Y 
Sbjct: 179 FLTKINYP 186


>gi|18399149|ref|NP_564438.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|13430550|gb|AAK25897.1|AF360187_1 unknown protein [Arabidopsis thaliana]
 gi|14532756|gb|AAK64079.1| unknown protein [Arabidopsis thaliana]
 gi|332193556|gb|AEE31677.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 446

 Score =  151 bits (382), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 62/279 (22%), Positives = 94/279 (33%), Gaps = 52/279 (18%)

Query: 3   RY-CMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGV 55
           RY  + I Y G  ++G+  +     SI+  + KA+          +       GRTD GV
Sbjct: 90  RYVALKIMYFGKRFYGFSAEAQMEPSIESEVFKALERTRLLVGDKKDSCYSRCGRTDKGV 149

Query: 56  HALRQVAHFDLVRE------------------WVPVILCKALNAYLKISDTISILNLSIV 97
            +  QV    L                            + LN  L   D I ++  S  
Sbjct: 150 SSTGQVIALFLRSRLKSPPGDSKAQVNGRTGERPEYDYVRVLNRAL--PDDIRVIGWSPA 207

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
              FHARFS   R Y Y                    ++L+   M  A +  +G HDF  
Sbjct: 208 PIDFHARFSCYAREYKYFFW----------------RQNLNLSAMDFAGKKFIGEHDFRN 251

Query: 158 FRSIH-CQASSPIRTIDHFDVN------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
           F  +         R +  F+V+          L    +   +FL  QIR  V  L ++G 
Sbjct: 252 FCKMDVANVHCYTRRVTFFEVSPCQNSHEGDQLCTFTMRGSAFLWHQIRCMVAVLFMIGQ 311

Query: 211 GKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           G  +   ++  L  +   RK    LA    L   + E+ 
Sbjct: 312 GVESVDVIDTLLDTKKTPRKPQYLLASEIPLVLRTCEFE 350


>gi|125556371|gb|EAZ01977.1| hypothetical protein OsI_24011 [Oryza sativa Indica Group]
 gi|125598125|gb|EAZ37905.1| hypothetical protein OsJ_22255 [Oryza sativa Japonica Group]
          Length = 417

 Score =  151 bits (382), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 112/288 (38%), Gaps = 44/288 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-------------VHGA 48
           + + +++ Y+G  + GWQ+Q   +++QG +EK +     E                   A
Sbjct: 121 VTFKIVLSYHGGSFDGWQKQPGLNTVQGLVEKHLGQFVDEKKAKQLEARSLPLEGCAVVA 180

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+ V    +  A+N      D +  L++S V ++FH  F+A
Sbjct: 181 GRTDKGVTALQQVCSFYTWRKDVKSSDIKDAINK--AAPDKLRPLHVSQVSREFHPNFAA 238

Query: 108 IRRSYLYRIITR----------QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR----- 152
             R YLY               Q+   +E     + P+S D   +    + L G+     
Sbjct: 239 KWRRYLYIFPLDEDVKLISGEEQSAKTVEGPECNIKPQSFDVGKVDKIIRQLEGKSLSYK 298

Query: 153 ---HDFTTFRSIHC-------QASSPIRTIDHFDVNSFGNL---IEIRVVARSFLHTQIR 199
               D    RS+          + + +  +   D N        I I +VA  FL   +R
Sbjct: 299 MFARDTQASRSVGPPTECFMFHSRAAVAKLHTADENCEEGTTRAICIELVANRFLRKMVR 358

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             V +             L   ++A  R+   P APP+GL    V Y 
Sbjct: 359 VLVATAIREAAAGAEEDALLNLMEATCRRATAPPAPPDGLCLVDVGYE 406


>gi|317419455|emb|CBN81492.1| tRNA pseudouridine synthase 3 [Dicentrarchus labrax]
          Length = 472

 Score =  151 bits (382), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 60/286 (20%), Positives = 91/286 (31%), Gaps = 60/286 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q+N  ++++  + +A+         +    H  GRTD GV A 
Sbjct: 73  VALRLAYLGWSYQGFAVQENTDNTVEARLFEALLKTRLIQDRQSSNYHRCGRTDKGVSAF 132

Query: 59  RQVAHFDLVREW-----------------------VPVILCKALNAYLKISDTISILNLS 95
            QV   DL                             +   K LN  L     I IL+ +
Sbjct: 133 SQVITIDLRSTQFCGGLGVTLPENVDVRSKNKASGSELPYVKMLNRVL--PQDIRILDWA 190

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
              + F ARF    R+Y Y                +    SLD   M  AA+   G HDF
Sbjct: 191 PAAEGFSARFDCQSRTYRY----------------YFPRGSLDVALMAEAAKRYEGTHDF 234

Query: 156 TTFRS--IHCQASSPIRTIDHFDVNS----------FGNLIEIRVVARSFLHTQIRSFVG 203
                  +        RTI    V               L    +   +FL+ Q+R  + 
Sbjct: 235 RNLCKMDVGNGVLQFERTILSASVKPVQPQHVSSTDQYELFMFEIKGLAFLYHQVRCMMA 294

Query: 204 SLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
            L L+G        + + +  Q   RK    +A    L      + 
Sbjct: 295 LLLLIGQKLEAPEIINQLMDVQSNPRKPQYSMAVDYPLVLYDCHFE 340


>gi|152964686|ref|YP_001360470.1| tRNA-pseudouridine synthase I [Kineococcus radiotolerans SRS30216]
 gi|151359203|gb|ABS02206.1| tRNA-pseudouridine synthase I [Kineococcus radiotolerans SRS30216]
          Length = 252

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 97/235 (41%), Gaps = 18/235 (7%)

Query: 28  QGSIEKAIFLVT--GEIVVVHGAGRTDSGVHALRQVAHFDLVRE-----------WVPVI 74
           QG +  A+  V        +  AGRTD+GVHA  QVAH DL R                 
Sbjct: 2   QGVLTAALGRVLRLDPAPRLTVAGRTDAGVHASGQVAHADLPRAVWEALPGRSDAPPAAA 61

Query: 75  LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLI 133
           L + L   L     + +         F ARF A+RR Y YR+    A    L +      
Sbjct: 62  LVRRLAGVL--PPDVRVHGARPAPPGFDARFGALRRRYAYRVCDDPAGVPPLRRFDVLHH 119

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-LIEIRVVARS 192
            + LD   M +AA  LVG  +F  F     + +S +RT+  +      + L+   V A +
Sbjct: 120 RRPLDAAAMDLAAGSLVGLREFAAFCRPR-EGASTVRTLLAYSWRRDEDGLLVADVQADA 178

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F H+ +R+ VG++  VGDG+           A  R     +  P+GL  + V Y 
Sbjct: 179 FCHSMVRALVGAVLAVGDGRRDVDWPRVVQDAAVRDPAVAVVGPQGLTLEEVVYP 233


>gi|255566350|ref|XP_002524161.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223536579|gb|EEF38224.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 443

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 111/318 (34%), Gaps = 78/318 (24%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-------------VHGA 48
           + + + + Y+G  + GWQ+Q   +++QG +EK++     E                   A
Sbjct: 120 VNFKIDLSYHGGSFDGWQKQPGLNTVQGLVEKSLGKFVDEKKAQQLKEACKPLEGCAVVA 179

Query: 49  GRTDSGVHALRQVAHFDLVREWV-PVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV ALRQV  F   R+ V P  +  A+N+       I ++++S V + FH  FSA
Sbjct: 180 GRTDKGVSALRQVCSFYTWRKDVRPHEIEDAINS--SAPGKIRVISVSEVSRVFHPNFSA 237

Query: 108 IRRSYLYRIITRQAPLA--------LEKGRAW-----------------LI--------- 133
             R YLY         +        LE  R++                  +         
Sbjct: 238 KWRRYLYIFPINDGEDSEQSFDSEDLENLRSYEKYDEQRNGCAELTSEEHVEELITSDKD 297

Query: 134 -------PKSLDCENMRIAAQHLVGR--------HDFTTFRSIHCQASSPIRTIDHFDVN 178
                  P+      +    Q L G+         D    R++          I H    
Sbjct: 298 ELEGAKKPRIFSICRVNQLLQQLEGKLLSYKIFARDTKASRNVGPP---TECFIYHARAT 354

Query: 179 S-------FGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
                    G    ++ + +VA  FL   +R  V +             L K + A  R+
Sbjct: 355 EARLPCPDHGEGRKVMCVELVANRFLRKMVRVLVATSIREAAAGAEDDALLKLMDASCRR 414

Query: 229 ECGPLAPPEGLYFDSVEY 246
              P APP+GL    V Y
Sbjct: 415 ASAPPAPPDGLCLFDVGY 432


>gi|332024452|gb|EGI64650.1| tRNA pseudouridine synthase 3 [Acromyrmex echinatior]
          Length = 443

 Score =  150 bits (380), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/272 (24%), Positives = 101/272 (37%), Gaps = 46/272 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q+ N  +I+  +  A+       + E    H  GRTD GV + 
Sbjct: 76  ILLKFYYLGWDYHGFAVQEDNTDTIEHHLFAALLKSCCIESRESSNYHRCGRTDKGVSSF 135

Query: 59  RQVAHFDLVREWVPVI---------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
            QV   D+     P            CK LN  L     I  +    V   F ARF    
Sbjct: 136 SQVISLDVRSRLEPENQDNLSDELPYCKILNRLL--PANIRCIAWCPVSSIFSARFDCKF 193

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASS 167
           RSY Y                +    +LD E M  AA++++G HDF     +       +
Sbjct: 194 RSYRY----------------FFPRGNLDIEAMDKAAKYVIGDHDFRNICKMDVANGVIN 237

Query: 168 PIRTIDHFDVNSFGN----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
             RT+    VNS  +          + E+ + +++FL  QIR  +G L L+G  K     
Sbjct: 238 FKRTVMDARVNSLNDQNVEKSTGYDMCELEITSQAFLWHQIRCLMGILLLIGQRKEEPEI 297

Query: 218 LEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           + K L  +   +K    +A    L     +Y 
Sbjct: 298 ILKLLDIETCPQKPQYNMAHQVPLNLWYCDYE 329


>gi|163784111|ref|ZP_02179057.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880615|gb|EDP74173.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
          Length = 175

 Score =  150 bits (380), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 52/173 (30%), Positives = 77/173 (44%), Gaps = 5/173 (2%)

Query: 74  ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
            + + LNA L     ISI     V   FHARFSA  ++Y+Y++ T+  P      R W I
Sbjct: 1   KIKRYLNAVL--PRDISIKECKQVPLSFHARFSAKGKTYIYKVYTQ--PDPFMYQRGWYI 56

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSF 193
            + LD EN+  A Q +    +  +           +  I  F     G L++  + A  F
Sbjct: 57  SQKLDLENIAEAVQLIKNTENLISMSKKGDYLREDV-EIREFRFKYDGFLLKFEISASHF 115

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           L   +R  V  +  VG G+ T    ++ L ++D      +APPEGLY   V Y
Sbjct: 116 LRYMVRKIVAHVVHVGTGRITIDTFKQILDSKDPARALFIAPPEGLYLKEVYY 168


>gi|47097169|ref|ZP_00234734.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 1/2a
           F6854]
 gi|47014428|gb|EAL05396.1| tRNA pseudouridine synthase A [Listeria monocytogenes str. 1/2a
           F6854]
          Length = 133

 Score =  150 bits (380), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 50/135 (37%), Positives = 68/135 (50%), Gaps = 3/135 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  II Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 1   MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEKALTKMHKGKTVRVTASGRTDTGVHAKG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   +       KAL         IS L +  V   FHARF  + + Y Y +   
Sbjct: 61  QVIHFDSELDITAEKFQKALQVM--TPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRT 118

Query: 120 QAPLALEKGRAWLIP 134
           +      +  A   P
Sbjct: 119 KIFDPFSRNFALHYP 133


>gi|52075919|dbj|BAD45865.1| pseudouridylate synthase-like [Oryza sativa Japonica Group]
          Length = 495

 Score =  150 bits (380), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 112/288 (38%), Gaps = 44/288 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-------------VHGA 48
           + + +++ Y+G  + GWQ+Q   +++QG +EK +     E                   A
Sbjct: 121 VTFKIVLSYHGGSFDGWQKQPGLNTVQGLVEKHLGQFVDEKKAKQLEARSLPLEGCAVVA 180

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+ V    +  A+N      D +  L++S V ++FH  F+A
Sbjct: 181 GRTDKGVTALQQVCSFYTWRKDVKSSDIKDAINK--AAPDKLRPLHVSQVSREFHPNFAA 238

Query: 108 IRRSYLYRIITR----------QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR----- 152
             R YLY               Q+   +E     + P+S D   +    + L G+     
Sbjct: 239 KWRRYLYIFPLDEDVKLISGEEQSAKTVEGPECNIKPQSFDVGKVDKIIRQLEGKSLSYK 298

Query: 153 ---HDFTTFRSIHC-------QASSPIRTIDHFDVNSFGNL---IEIRVVARSFLHTQIR 199
               D    RS+          + + +  +   D N        I I +VA  FL   +R
Sbjct: 299 MFARDTQASRSVGPPTECFMFHSRAAVAKLHTADENCEEGTTRAICIELVANRFLRKMVR 358

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             V +             L   ++A  R+   P APP+GL    V Y 
Sbjct: 359 VLVATAIREAAAGAEEDALLNLMEATCRRATAPPAPPDGLCLVDVGYE 406


>gi|328777716|ref|XP_393954.4| PREDICTED: tRNA pseudouridine synthase 3-like [Apis mellifera]
          Length = 400

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 62/271 (22%), Positives = 108/271 (39%), Gaps = 45/271 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q++  ++I+  + +A+       + E    H  GRTD GV + 
Sbjct: 57  ILLKFYYLGWDYNGFVVQESIDNTIEEHLFEALIKSCCIESRETSNYHRCGRTDKGVSSF 116

Query: 59  RQVAHFDLVREWVPVI---------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
            QV   D+  +  P            CK LN  L     I  +    V   F ARF+   
Sbjct: 117 SQVISLDIRSKLNPEDQYKLEDELPYCKILNRLL--PSNIRCIAWCPVPNDFSARFNCKF 174

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASS 167
           R+Y Y                +    +L+ + M  A ++++G HDF     +       +
Sbjct: 175 RTYKY----------------FFPRGNLNIDAMNKAVKYIIGEHDFRNICKMDVANGVIN 218

Query: 168 PIRTIDHFDVN---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            IR + + +V          S  ++ ++ + +++FL  QIR  +G L L+G+GK  +  +
Sbjct: 219 YIRKVINAEVRMYRQDFRNISGYDMYQLIITSQAFLWHQIRCLMGVLFLIGEGKEEAEIM 278

Query: 219 EKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            + L  +   +K    LA    L     EY 
Sbjct: 279 LELLDIENCPKKPQYNLAHEIPLNLWYCEYD 309


>gi|19074961|ref|NP_586467.1| tRNA PSEUDOURIDINE SYNTHASE A [Encephalitozoon cuniculi GB-M1]
 gi|19069686|emb|CAD26071.1| tRNA PSEUDOURIDINE SYNTHASE A [Encephalitozoon cuniculi GB-M1]
          Length = 339

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 100/259 (38%), Gaps = 47/259 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI-FLVTGEIVVVHGAGRTDSGVHALRQVA 62
             + I Y+G  Y G   Q    +I G +E A+     GE   +  AGRTD+GV A+  +A
Sbjct: 61  IALKISYDGRRYSGVSPQSGRETIGGYLEYALKSTRLGEK--LVYAGRTDAGVSAIGMIA 118

Query: 63  HFDLVREWVPVILCKA--------------LNAYLKISDTISILNLSIVDKQFHARFSAI 108
              L           A              LN +L     I ++  + V   F ARF+ I
Sbjct: 119 SGVLTSRIEMPNRSYAVAEDDYKEYKYDVMLNNHL--PPDIRVVGWAPVPDTFSARFTCI 176

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           +R Y Y                +   K LD + M  AA  + G   F  F     + +  
Sbjct: 177 QRQYRY----------------YFHKKGLDIDRMSKAASEIKGMSSFYCFSKHSDKNARY 220

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
            RT+D   V   G+L  + + AR+FLH  +R  V ++K  G G           ++ D +
Sbjct: 221 ERTLDECRVVDDGDLYYLDIRARAFLHNMVRKIVWAIKKSGRG-----------ESYDVQ 269

Query: 229 ECGPLAPPEGLYFDSVEYS 247
             G  + P  L F +  Y 
Sbjct: 270 RIG-TSEPYPLVFCNAVYP 287


>gi|70952957|ref|XP_745611.1| tRNA pseudouridine synthase [Plasmodium chabaudi chabaudi]
 gi|56525989|emb|CAH74339.1| tRNA pseudouridine synthase, putative [Plasmodium chabaudi
           chabaudi]
          Length = 279

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 98/238 (41%), Gaps = 31/238 (13%)

Query: 17  GWQRQK-NGSSIQGSIEKAIF---LVTGEIVVVHGAGRTDSG---VHALRQVAHFDLVR- 68
           G   QK N ++++  + + +    L++          RTD G   ++AL           
Sbjct: 1   GSAYQKDNNNTVENKLIERLHQLDLISDSNCSFSRVSRTDKGSARMNALTIRLKIKYPHL 60

Query: 69  --EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
               +  I  K LN  L     I I+++  V   F AR + I+R+YLY            
Sbjct: 61  SISIIEKIYLKELNKKL---KNIQIVHIQCVPNNFDARLNCIQRTYLY------------ 105

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLIE 185
               + + K+ +   M  AA+  +G HDF+ F        S IRTI  F++     N   
Sbjct: 106 ----FFVNKNYNIPRMNEAAKIFLGEHDFSNFCKKRKNTISFIRTIHKFEIKRIDQNFYY 161

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD-RKECGPLAPPEGLYFD 242
            ++   SFL+ QIR  V SL LVG G+    D++  L+    + +   +A   GL   
Sbjct: 162 FKIKGTSFLYNQIRHMVASLFLVGKGQLDEHDIKSMLENNSVKNKNYKIADECGLLLH 219


>gi|195158909|ref|XP_002020326.1| GL13924 [Drosophila persimilis]
 gi|194117095|gb|EDW39138.1| GL13924 [Drosophila persimilis]
          Length = 409

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 67/261 (25%), Positives = 106/261 (40%), Gaps = 27/261 (10%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFDQVQIACFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQ+    L  E       +A NA L   + I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQICSVKLPEELD----LEAFNADL--PEQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTI 172
           + T       A  +   + I   L  + ++   +   G  +F  F S       S  R I
Sbjct: 187 LPTVAFASCEAESEQDTFRITPEL-LDRVKETLKLYEGTKNFHNFTSKKNFLDPSAKRFI 245

Query: 173 DHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
             F  +           + ++V  +SF+  QIR  VG    +  G  T+  LE+AL  + 
Sbjct: 246 MAFTSSEPFQSPQGVEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAITLERALTEE- 304

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
            +   P+AP  GL  D+V Y 
Sbjct: 305 -RLDLPMAPGLGLVLDTVHYE 324


>gi|190346281|gb|EDK38328.2| hypothetical protein PGUG_02426 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 431

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 84/245 (34%), Gaps = 43/245 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSG 54
             +   Y G  Y G   Q       +++  I +A+            +      GRTD G
Sbjct: 72  IALRFAYAGWNYNGLAFQNEPTPLPTVEQEILEALTKARLITEPDPLVCNFSRCGRTDKG 131

Query: 55  VHALRQVAHFDLVREWVPVILCK------------ALNAYLKISDTISILNLSI-VDKQF 101
           V A+ QV   ++          +             LN+ L    +I I  + +     F
Sbjct: 132 VSAMNQVISLEVRSGLTEEQRSQPGADQKEIPYITILNSLL--PPSIRITGICLNPPPGF 189

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS   R Y Y                      LD E M  AA+   G HDF  F  I
Sbjct: 190 DARFSCSYRHYRYI----------------FRRYDLDLEAMTEAAKKYEGEHDFRNFCKI 233

Query: 162 H--CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               Q ++  RTI   ++     +     +   +FL  Q+R  +G L LVG      + +
Sbjct: 234 DGSKQITNYGRTILSANIMPLKDDYYVFDLKGTAFLWHQVRCMMGILFLVGRKLEKPSLV 293

Query: 219 EKALQ 223
           ++ L 
Sbjct: 294 DELLN 298


>gi|146417456|ref|XP_001484697.1| hypothetical protein PGUG_02426 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 431

 Score =  149 bits (378), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 84/245 (34%), Gaps = 43/245 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSG 54
             +   Y G  Y G   Q       +++  I +A+            +      GRTD G
Sbjct: 72  IALRFAYAGWNYNGLAFQNEPTPLPTVEQEILEALTKARLITEPDPLVCNFSRCGRTDKG 131

Query: 55  VHALRQVAHFDLVREWVPVILCK------------ALNAYLKISDTISILNLSI-VDKQF 101
           V A+ QV   ++          +             LN+ L    +I I  + +     F
Sbjct: 132 VSAMNQVISLEVRSGLTEEQRSQPGADQKEIPYITILNSLL--PPSIRITGICLNPPPGF 189

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
            ARFS   R Y Y                      LD E M  AA+   G HDF  F  I
Sbjct: 190 DARFSCSYRHYRYI----------------FRRYDLDLEAMTEAAKKYEGEHDFRNFCKI 233

Query: 162 H--CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               Q ++  RTI   ++     +     +   +FL  Q+R  +G L LVG      + +
Sbjct: 234 DGSKQITNYGRTILSANIMPLKDDYYVFDLKGTAFLWHQVRCMMGILFLVGRKLEKPSLV 293

Query: 219 EKALQ 223
           ++ L 
Sbjct: 294 DELLN 298


>gi|301122837|ref|XP_002909145.1| tRNA pseudouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262099907|gb|EEY57959.1| tRNA pseudouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 510

 Score =  149 bits (378), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 96/293 (32%), Gaps = 63/293 (21%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFL----VTGEIVVVHGAGRTDSGV 55
           M    +   Y G  Y G+ RQ +   +++  + +A+         +       GRTD GV
Sbjct: 72  MRAVAVKFLYLGEKYAGFARQDHMPETVERYLLEALVRSKLIENIDDAGYSRCGRTDRGV 131

Query: 56  HALRQVAHFDLVREWVPVI-------------------------------LCKALNAYLK 84
            A  QV    +                                       +  A +    
Sbjct: 132 SAFGQVVALRVRSNLPATAELLSAASIDDVRPGEKFQVRLATGEEKTLTEVDYASHINRA 191

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           +   I +  ++    +F ARF    R Y Y                + + + LD E MR 
Sbjct: 192 LPADIRVYAVASCRPEFSARFDCKARMYRY----------------FFVRRDLDIEKMRT 235

Query: 145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG---------NLIEIRVVARSFLH 195
           AAQ+LVG+HDF  F  I        R +  F++              +    V  R+FL 
Sbjct: 236 AAQYLVGKHDFRNFCRIDPNCHVFERNVRSFEIVECPGQRADDPSQQMYRCEVFGRAFLW 295

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEY 246
            Q+R  V  L L+G G+   + + K L      RK    +A    L      +
Sbjct: 296 HQVRCMVEVLFLIGSGREEPSIIPKLLDIAQTPRKPQYDMASDLPLVLHDCYF 348


>gi|115756434|ref|XP_001202324.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115938206|ref|XP_796203.2| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 494

 Score =  149 bits (377), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 99/265 (37%), Gaps = 30/265 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIV-------VVHGAGRTD 52
            +  +++ Y G+ Y G QR     +I+  +  A+       E               RTD
Sbjct: 71  RKVAILLSYAGANYVGMQRNPGVQTIEEDLVNALVKSGAIPEDCGRNMNKMSFQRCARTD 130

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV      +  +   L + +N +L     I ++ ++     F+ + +   R+Y
Sbjct: 131 KGVSAAGQVVSL---KVLMLDNLMERINEHL--PPVIRVMGVTRTTGGFNCKNNCEFRTY 185

Query: 113 LYRIITRQA----PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
           +Y I T          LEK R          E +    +  +G H+F  F S       S
Sbjct: 186 MYLIPTFAFTPLEDFTLEKYRV----SDEKIEEVGEQLKKYIGTHNFHNFTSGKAFTDPS 241

Query: 168 PIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             R I  F               I+V  +SF+  QIR  +G +  V  G    + +E+A 
Sbjct: 242 ANRYIKEFTCEKGFVDDGMEFAVIKVKGQSFMLHQIRKMLGLVLAVVRGLTPPSTVERAF 301

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
           Q    K   P AP  GL  ++V Y 
Sbjct: 302 QEP--KLDIPRAPGLGLVLEAVHYD 324


>gi|254583638|ref|XP_002497387.1| ZYRO0F04334p [Zygosaccharomyces rouxii]
 gi|238940280|emb|CAR28454.1| ZYRO0F04334p [Zygosaccharomyces rouxii]
          Length = 431

 Score =  149 bits (377), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 58/270 (21%), Positives = 94/270 (34%), Gaps = 43/270 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV------TGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK+     +++G I  A+           +       GRTD G
Sbjct: 82  IALKFSYLGWNYNGLAVQKDVTPLPTVEGVIIDALMKCRLVASSNVQDFRFSRCGRTDKG 141

Query: 55  VHALRQVAHFDL------VREWVPVILCKALNA----YLKISDTISILNLSIVDKQ-FHA 103
           V A+ QV   ++        +  P    + L         + + I I  + +   + F A
Sbjct: 142 VSAMNQVISLEVRSNLSDEEQKDPSNDTRELQYAQILNHLLPEDIKISAMCLRPPEGFDA 201

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           R+S   R Y Y                    K L  + M+ AA    G HDF  F  +  
Sbjct: 202 RYSCEYRHYKYLFS----------------GKGLMLDRMQKAAALYHGEHDFRNFCKLDG 245

Query: 163 -CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  R I   ++     N+    +V  +FL  Q+R  +  L LVG G    + +  
Sbjct: 246 SKQITNYTRNILGSEIQHISDNMYCFDLVGSAFLWHQVRCMMAILFLVGQGLEEPSVITN 305

Query: 221 ALQAQDRKECGP---LAPPEGLYFDSVEYS 247
            L   D+    P   +A    L     ++ 
Sbjct: 306 LLDV-DKTPQKPIYEMASDLPLILYDCKFP 334


>gi|195449703|ref|XP_002072187.1| GK22713 [Drosophila willistoni]
 gi|194168272|gb|EDW83173.1| GK22713 [Drosophila willistoni]
          Length = 412

 Score =  149 bits (377), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 68/270 (25%), Positives = 109/270 (40%), Gaps = 37/270 (13%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL------VTGEIVVVHG---AGRTDSGV 55
            +++ Y G+ YFG QR     +I+  + K +         + E V +     A RTD GV
Sbjct: 67  AILLSYCGANYFGMQRNPGMQTIEEELFKVMLKHKWITEDSFEQVQIACFQRAARTDKGV 126

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  +       + L       + I +  +  V K F+A+     R+Y Y 
Sbjct: 127 SAARQVCSVKLPDDLDLKAFNEDL------PEQIRLFGVERVTKGFNAKDQCNARTYTYT 180

Query: 116 IIT-----------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ 164
           + T           ++A    E+    + P+ L  + +R   Q   G  +F  F S    
Sbjct: 181 LPTVAFAPCQSESDKEAQPPEEQSTYCISPEHL--QKVRETLQLYEGTKNFHNFTSKKNF 238

Query: 165 -ASSPIRTIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
              S  R I  F  +           + ++V  +SF+  QIR  VG    +  G  T++ 
Sbjct: 239 LDPSAKRFIMLFSCSDPFKSPQGIEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTTST 298

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           LE+AL  +  +   P+AP  GL  D+V Y 
Sbjct: 299 LERALTEE--RLDLPMAPGLGLVLDTVHYE 326


>gi|281200681|gb|EFA74899.1| tRNA pseudouridylate synthase [Polysphondylium pallidum PN500]
          Length = 1052

 Score =  149 bits (377), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 100/299 (33%), Gaps = 76/299 (25%)

Query: 3    RY-CMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVT----GEIVVVHG---AGRTDS 53
            RY  + + Y G  Y G+  Q+    +I+G + +A+         +         +GRTD 
Sbjct: 767  RYIALKVAYLGWDYHGFAAQQITEETIEGHLIRALQKTCLINDIKNCNYSKYALSGRTDK 826

Query: 54   GVHALRQVAHFDLVREW-------------------------------VPVILCKALNAY 82
            GV A  QV    +                                         K LN  
Sbjct: 827  GVSAFGQVISLYVRSNLTEGNDLIPPTVIDDEAIAKKKANLLKNKKTHEEFQFVKMLNGV 886

Query: 83   LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM 142
            L     I +L  S +   F+ARFS + R+Y Y                +  P +LD   M
Sbjct: 887  L--PPYIRVLGWSPIPFHFNARFSTLYRTYKY----------------FFDPSNLDLNLM 928

Query: 143  RIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDVNSFG-------NLIEIRVVARSFL 194
            + A +  +G HDF+ F  I  +   S  R I  FD+            +    +   +FL
Sbjct: 929  KEAGKSYIGEHDFSNFCKIDLESVKSFTRVILSFDIQPVESGDFSTSGMYVATICGYAFL 988

Query: 195  HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE------GLYFDSVEYS 247
              QIR  +  L L+G  K+ +T +   L        G + PP        L      Y 
Sbjct: 989  WHQIRCMMAMLFLIGQKKFPTTIIADLLDL----SKGIVKPPYEMASEVPLVLFDCGYE 1043


>gi|125773069|ref|XP_001357793.1| GA17995 [Drosophila pseudoobscura pseudoobscura]
 gi|54637526|gb|EAL26928.1| GA17995 [Drosophila pseudoobscura pseudoobscura]
          Length = 409

 Score =  149 bits (376), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 66/261 (25%), Positives = 106/261 (40%), Gaps = 27/261 (10%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 73  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFDQVQIACFQRAARTDKGV 132

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQ+    L  E       +A NA L   + I +  +  V K F+A+     R+Y Y 
Sbjct: 133 SAARQICSVKLPEELD----LEAFNADL--PEQIRLFGVERVTKGFNAKDQCNARTYTYT 186

Query: 116 IITRQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTI 172
           + T       A  +   + I   L  + ++   +   G  +F  F S       S  R I
Sbjct: 187 LPTVAFASCEAESEQDTFRITPEL-LDRVKETLKLYEGTKNFHNFTSKKNFLDPSAKRFI 245

Query: 173 DHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
             F  +           + ++V  +SF+  QIR  VG    +  G  T+  L++AL  + 
Sbjct: 246 MAFTSSEPFQSPQGVEFVTLKVKGQSFMLHQIRKMVGLAIAIVRGNTTAITLDRALTEE- 304

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
            +   P+AP  GL  D+V Y 
Sbjct: 305 -RLDLPMAPGLGLVLDTVHYE 324


>gi|330804770|ref|XP_003290364.1| hypothetical protein DICPUDRAFT_154861 [Dictyostelium purpureum]
 gi|325079531|gb|EGC33127.1| hypothetical protein DICPUDRAFT_154861 [Dictyostelium purpureum]
          Length = 449

 Score =  149 bits (376), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 97/303 (32%), Gaps = 79/303 (26%)

Query: 2   IRY-CMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGV 55
            RY    + Y G  Y G+  Q     +I+G + KA+   +     +      +GRTD GV
Sbjct: 67  RRYVAFKVSYVGWPYHGFAAQDCTDETIEGHLIKALKRTSLISDIKTSNYAKSGRTDKGV 126

Query: 56  HALRQVAHFDLVREWVP-----------------------------------------VI 74
            A  QV    +                                                 
Sbjct: 127 SAFGQVISLYVRSNLTEGEGIIAPLDQSGGPISNRPSKNNNNNSNSNNQKQQNKAKEEFP 186

Query: 75  LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
             K LN  L     I +L  + +   F++RFS + R+Y Y                    
Sbjct: 187 YVKMLNGVL--PPEIRVLGWAPIPFHFNSRFSTLFRTYKYFFTLN--------------- 229

Query: 135 KSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDVNS---FGNLIEIRVVA 190
            ++D   M+ A  H +G HDF+ F  +  +   S  R I  F +       +L    +  
Sbjct: 230 -NMDLNLMKEAGNHYLGEHDFSNFCKMDIENVKSFKRVILEFSIEPVNNHNDLYVATIKG 288

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE------GLYFDSV 244
            +FL  QIR  +  L L+G  K+  + + + L   +    G   PP        L     
Sbjct: 289 YAFLWHQIRCMMAMLFLIGQKKFPVSIIPELLDTSN----GITKPPYEMASEIPLVLFDC 344

Query: 245 EYS 247
            Y 
Sbjct: 345 GYE 347


>gi|170072176|ref|XP_001870114.1| tRNA pseudouridine synthase A [Culex quinquefasciatus]
 gi|167868280|gb|EDS31663.1| tRNA pseudouridine synthase A [Culex quinquefasciatus]
          Length = 431

 Score =  148 bits (375), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 95/260 (36%), Gaps = 26/260 (10%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTDSGVH 56
           +++ Y+G  YFG QR     +I+  +  A+              + +    A RTD GV 
Sbjct: 98  ILMGYSGVNYFGMQRNPGTKTIEEELLVAMLKNEWISDEAFKQPQQIQFQRAARTDKGVS 157

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QV    L        L K L       + I +  +  V K F+++ +   R+Y Y +
Sbjct: 158 AATQVVSIKLPENLDIAGLNKDL------PEQIRVFAVKRVTKGFNSKSNCDARTYTYTL 211

Query: 117 ITRQAPLALEKGRAWLIPKSLD-CENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTIDH 174
            T       E+          D  + ++   +   G  +F  F S        + R I  
Sbjct: 212 PTVAFAAHDEEVSVETYRAPEDRIQKVQETLKLFEGTKNFHNFTSRKEFIDPSVKRFIMS 271

Query: 175 FDVN----SFGNLIEI---RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           F+        G  +E    ++  +SF+  QIR  VG    V  G      + KA +  + 
Sbjct: 272 FECEAPFVPEGTTVEFATIKIKGQSFMLHQIRKMVGLTLAVVRGLTPPETIMKAFE--ET 329

Query: 228 KECGPLAPPEGLYFDSVEYS 247
           +   P AP  GL    + Y 
Sbjct: 330 RYGVPTAPGLGLVLSRIHYE 349


>gi|76803149|ref|YP_331244.1| tRNA pseudouridine synthase A [Natronomonas pharaonis DSM 2160]
 gi|121697999|sp|Q3IMP6|TRUA_NATPD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76559014|emb|CAI50612.1| tRNA-pseudouridine synthase [Natronomonas pharaonis DSM 2160]
          Length = 267

 Score =  148 bits (375), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 65/253 (25%), Positives = 98/253 (38%), Gaps = 32/253 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVH 56
           +R    I Y+G+G+ G+QRQ +G +++ ++ +A+  +      G       AGRTD+GV 
Sbjct: 1   MR-AFRIAYDGTGFRGFQRQPHGETVENALFEALSSLGVAFEDGRPPGYAAAGRTDAGVS 59

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  Q   F+     +P    +ALN  L    ++     + V   FHA   A  R+Y Y +
Sbjct: 60  ARAQTVAFEAPAWLLP----RALNGEL--PASVRAWAAADVGDAFHATHDATARAYRYFL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                P A             D    R A   L G HDF  F           RT+    
Sbjct: 114 Y-APEPSA-------------DTTRARAACARLSGSHDFHNFT---PDDRGTERTL-SMR 155

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC--GPLA 234
           +   G  + +   A  F    +R  V ++  V  G+   + L +AL             A
Sbjct: 156 LRRQGPFLVVDCRAGGFARQLVRRLVAAVAAVARGERPLSFLGRALDDDPLSGADGIAAA 215

Query: 235 PPEGLYFDSVEYS 247
           PPE L    V Y 
Sbjct: 216 PPEPLLLADVVYP 228


>gi|313231689|emb|CBY08802.1| unnamed protein product [Oikopleura dioica]
          Length = 443

 Score =  148 bits (374), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 100/267 (37%), Gaps = 31/267 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------------GEIVVVHGAG 49
           +  ++I Y G  Y G Q       +  +IEK +F                 +        
Sbjct: 82  KVAILISYCGKNYHGLQHNPGDDKV-DTIEKRVFQALVAAKVVYSNVINDRKKCAYQSCS 140

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A+  VA     +  +P  LC+ +NA+L   D I + +   V K F A+     
Sbjct: 141 RTDKGVSAIGNVASL---KCKIPKNLCELVNAHL--PDDIRLTSFEQVTKGFCAKKRCTH 195

Query: 110 RSYLYRIITRQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-S 166
           R+Y Y   T         ++  ++ I      E +R   +  +G   +  F S   Q   
Sbjct: 196 RTYSYYCPTICFGSKEDWDRPSSFRISTE-KLEGVRELLKKYIGTRSYHNFTSGKRQGDE 254

Query: 167 SPIRTIDHFDVN------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           S  R I  F +       +    +E+RVV +SF+  QIR  VG +             E+
Sbjct: 255 SAKRHILDFRIQGDPFICNEWEYVELRVVGQSFMIHQIRKMVGLIIARAGNHCQDDHWER 314

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           A Q     E  P AP  GL    V Y 
Sbjct: 315 AFQRP--FEDVPKAPGNGLVLRQVHYD 339


>gi|18376136|emb|CAD21201.1| related to pseudouridine synthase 3 [Neurospora crassa]
          Length = 669

 Score =  148 bits (374), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 74/344 (21%), Positives = 101/344 (29%), Gaps = 102/344 (29%)

Query: 4   YCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFL-----------VTGEIVVVHGAGR 50
             +   Y G  Y G++ Q      SI+  + KA+             V          GR
Sbjct: 142 IALKFAYLGKNYNGFEYQSSAKMPSIEEELWKALVKSCLIFPERPDEVDFGPWEYSKCGR 201

Query: 51  TDSGVHALRQVAHFDLVRE----------------------------------------- 69
           TD GV A  QV    +                                            
Sbjct: 202 TDRGVSAFGQVIGIRVRSNKPLPKEEPEQTGNEEDDVVMVEAAQQQAKDSEKAAAEVDHQ 261

Query: 70  ---WVPVI----LCKALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT--- 118
              W P+      C+ LN  L     I I+  +  +   F ARFS   R Y Y       
Sbjct: 262 KPEWDPIADEIPYCRVLNRLL--PPDIRIMAWAPDLPPNFSARFSCRERQYRYFFTQPAF 319

Query: 119 RQAPLALEKGRAWLIPKS------LDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIR 170
              P  LE   A    KS      LD + MR AA+   G HDF  F  I    Q ++  R
Sbjct: 320 APMPSTLEPPLASSGHKSGGKQGWLDIDMMRKAAKMFEGVHDFRNFCKIDPGKQITNFSR 379

Query: 171 TIDHFDVNSFGNL-------------------------IEIRVVARSFLHTQIRSFVGSL 205
            +   D+    +L                             V   +FL  QIR  V  L
Sbjct: 380 RVFESDIVEVKDLESDLPYLGLPEFQPPAGSDGPHPKVYYFHVRGSAFLWHQIRHMVAVL 439

Query: 206 KLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
            LVG G    + +++ L  +   RK    +A    L      + 
Sbjct: 440 FLVGQGLEPPSIVQQLLDVEKNPRKPNYVMADEVPLVLWDCIFP 483


>gi|85083865|ref|XP_957207.1| hypothetical protein NCU01784 [Neurospora crassa OR74A]
 gi|28918294|gb|EAA27971.1| conserved hypothetical protein [Neurospora crassa OR74A]
          Length = 608

 Score =  148 bits (374), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 74/344 (21%), Positives = 101/344 (29%), Gaps = 102/344 (29%)

Query: 4   YCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFL-----------VTGEIVVVHGAGR 50
             +   Y G  Y G++ Q      SI+  + KA+             V          GR
Sbjct: 81  IALKFAYLGKNYNGFEYQSSAKMPSIEEELWKALVKSCLIFPERPDEVDFGPWEYSKCGR 140

Query: 51  TDSGVHALRQVAHFDLVRE----------------------------------------- 69
           TD GV A  QV    +                                            
Sbjct: 141 TDRGVSAFGQVIGIRVRSNKPLPKEEPEQTGNEEDDVVMVEAAQQQAKDSEKAAAEVDHQ 200

Query: 70  ---WVPVI----LCKALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT--- 118
              W P+      C+ LN  L     I I+  +  +   F ARFS   R Y Y       
Sbjct: 201 KPEWDPIADEIPYCRVLNRLL--PPDIRIMAWAPDLPPNFSARFSCRERQYRYFFTQPAF 258

Query: 119 RQAPLALEKGRAWLIPKS------LDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIR 170
              P  LE   A    KS      LD + MR AA+   G HDF  F  I    Q ++  R
Sbjct: 259 APMPSTLEPPLASSGHKSGGKQGWLDIDMMRKAAKMFEGVHDFRNFCKIDPGKQITNFSR 318

Query: 171 TIDHFDVNSFGNL-------------------------IEIRVVARSFLHTQIRSFVGSL 205
            +   D+    +L                             V   +FL  QIR  V  L
Sbjct: 319 RVFESDIVEVKDLESDLPYLGLPEFQPPAGSDGPHPKVYYFHVRGSAFLWHQIRHMVAVL 378

Query: 206 KLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
            LVG G    + +++ L  +   RK    +A    L      + 
Sbjct: 379 FLVGQGLEPPSIVQQLLDVEKNPRKPNYVMADEVPLVLWDCIFP 422


>gi|76156463|gb|ABA40375.1| SJCHGC06804 protein [Schistosoma japonicum]
          Length = 334

 Score =  148 bits (374), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 104/262 (39%), Gaps = 26/262 (9%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y+G GY+G QR     +I+G + KA+F             + V    A +TD  V
Sbjct: 50  AILMMYSGWGYYGMQRGPIYPTIEGELSKALFTCGQLVNVTSEEHKKVNFQRASKTDKYV 109

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            AL QV    L   +    L   LN  L     I IL++  V + F +  S   R Y Y 
Sbjct: 110 SALGQVCSLKL---YDDADLLNKLNTAL--PQDIRILDIIRVTRSFSSYNSCTHRVYDYL 164

Query: 116 IIT---RQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIR 170
           + T       L+L     W     +     +    +   G H+F  F S       S  R
Sbjct: 165 LPTFALSSGNLSLSDSTCWTYRVTAEKITKLNNLLERYKGTHNFYNFTSGRLPTDKSCYR 224

Query: 171 TIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            I   +              IR++ +SF+  Q+R  +G +  +  G  T  D+   +  +
Sbjct: 225 HIKSVECIPTFLLGEHEYTVIRIIGQSFMLHQVRKMIGLVLGILRGYAT-EDVFDIVFCK 283

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           +R +  P AP  GL  + V++S
Sbjct: 284 ERVDI-PKAPGLGLMLNQVDFS 304


>gi|301618506|ref|XP_002938660.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Xenopus
           (Silurana) tropicalis]
          Length = 331

 Score =  148 bits (374), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 65/222 (29%), Positives = 102/222 (45%), Gaps = 27/222 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSI---QGSIEKAIFLVTG-EIVVVHGAGRTDSGVHAL 58
           RY +  +Y G+ Y G        S+   Q  +E A   +     V    + RTDSGVHA+
Sbjct: 7   RYLVFFQYYGTKYSGVMETPVTQSVLGVQNYLEMAAQKLRPVGTVKFFISSRTDSGVHAI 66

Query: 59  RQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
              AH D+ R      +   IL +ALN +L+  + I +L    V   FHAR  A+ R+Y+
Sbjct: 67  CNSAHVDIQRANGKPPFTEDILVQALNHHLQ-PEPIRLLKAVRVCDNFHARHKALSRTYV 125

Query: 114 YRIITRQAP---LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSP 168
           YR+    +       E+   W +P SL+   +  A++ L+G H+F+ FRS + +    SP
Sbjct: 126 YRVAAGCSHSELPVFEENLCWAVPGSLNVAAIHEASEMLLGTHNFSAFRSANSENVFKSP 185

Query: 169 IRTIDHFDVN------------SFGNLIEIRVVARSFLHTQI 198
           I+T+   D+                   +    ARSFL+ Q+
Sbjct: 186 IKTLQQADITPSSGILTHHWQYRNLQFWDFTFRARSFLYKQV 227


>gi|68072249|ref|XP_678038.1| tRNA pseudouridine synthase [Plasmodium berghei strain ANKA]
 gi|56498378|emb|CAH98757.1| tRNA pseudouridine synthase, putative [Plasmodium berghei]
          Length = 281

 Score =  148 bits (373), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 98/239 (41%), Gaps = 32/239 (13%)

Query: 17  GWQRQK-NGSSIQGSIEKAIF---LVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP 72
           G   QK N ++++  + + +    L++          RTD GV A        L  ++  
Sbjct: 1   GSAYQKDNNNTVENKLIEKLQQLDLISDSNCSFSRVSRTDKGVSARMNALTIRLKNKYPH 60

Query: 73  VIL-------CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           + +        K LN  L     I I+++  V   F AR + I+R+Y+Y  I        
Sbjct: 61  LSISIIEKIYLKELNKKL---KNIQIIHIQCVPNNFDARLNCIQRTYVYFFIN------- 110

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLI 184
                    K+ +   M  A +  +G H+F+ F       +S IRTI  F++ +   N  
Sbjct: 111 ---------KNYNITKMNEATKIFLGEHNFSNFCKKRKNNTSFIRTIHKFEIKNIDQNFY 161

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD-RKECGPLAPPEGLYFD 242
             ++   SFL+ QIR  V +L LVG  +    D++  L+    + +   +A   GL   
Sbjct: 162 YFKIKGTSFLYNQIRHMVAALFLVGKNQLDGQDIKSMLENNSIKNKNYKIADECGLLLY 220


>gi|116199417|ref|XP_001225520.1| hypothetical protein CHGG_07864 [Chaetomium globosum CBS 148.51]
 gi|88179143|gb|EAQ86611.1| hypothetical protein CHGG_07864 [Chaetomium globosum CBS 148.51]
          Length = 553

 Score =  148 bits (373), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 97/299 (32%), Gaps = 57/299 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAI-----------FLVTGEIVVVHGAGR 50
             + + Y G  Y G++ Q   S  +++  + +A+             V          GR
Sbjct: 110 IALKLAYLGKRYGGFEYQAGVSVSTVEEELWRALAKSCLIWPDDPSRVDFAPWEYSKCGR 169

Query: 51  TDSG----VHALRQVAHFDLVREWVPVI----LCKALNAYLKISDTISILNLSIV-DKQF 101
           TD G    V   R     D  R W PV       + LN  L     I +L  +    + F
Sbjct: 170 TDKGAGVEVERGRGRGEEDGKRAWDPVADEINYPRILNRLL--PPDIRVLAWAPTLPEDF 227

Query: 102 HARFSAIRRSYLYRIIT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
            ARFS   R Y Y          P++++  R       LD + MR AA+   G HDF  F
Sbjct: 228 SARFSCRERQYRYFFTQPAFAPLPISVDPERKKGSEGWLDIDAMRKAAKLFEGVHDFRNF 287

Query: 159 RSIH--CQASSPIRTIDHFDVNSFGN--------------------------LIEIRVVA 190
             +    Q S+  R +   DV    +                          +    V  
Sbjct: 288 CKVDGVKQISNFKRRMFEADVVEVEDAGSALPYLAQQGFKPESLVGGTTYPKVYYFHVRG 347

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE--GLYFDSVEYS 247
            +FL  QIR  V  L LVG G    + +   L  +        A  E   L      + 
Sbjct: 348 SAFLWHQIRHMVAILFLVGQGLEKPSIVTDLLDVEKNPRKPNYAMAEEVPLVLWDCIFP 406


>gi|118782859|ref|XP_312543.3| AGAP002409-PA [Anopheles gambiae str. PEST]
 gi|116129767|gb|EAA08062.3| AGAP002409-PA [Anopheles gambiae str. PEST]
          Length = 451

 Score =  148 bits (373), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 101/261 (38%), Gaps = 28/261 (10%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTDSGVH 56
           +++ Y+G  YFG QR     +I+  + +A+              + +    A RTD GV 
Sbjct: 115 ILLGYSGVNYFGMQRNPGTKTIEEDLLRAMQKREWINDEGFRQPQQIQFQRAARTDKGVS 174

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QV    L          +ALN+ L   + I +  +  V K F+++ +   R+Y Y +
Sbjct: 175 AAMQVVSIKLPDNLD----IEALNSEL--PEDIRVYAVKRVTKGFNSKTNCDARTYTYTL 228

Query: 117 ITRQAPLALEK--GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTID 173
            T       EK   + + +P       +       VG  +F  F S        + R I 
Sbjct: 229 PTIAFAPNEEKVDIQTYRLPAER-LARVNEVLALYVGTKNFHNFTSRKEFLDPSVKRFIM 287

Query: 174 HFDVNS-------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            F+ +              I++  +SF+  QIR  VG    V  G   S  +EKA   QD
Sbjct: 288 SFECDPPFLPEGSTAEFATIKIKGQSFMLHQIRKMVGLTIAVVRGLAESDIIEKAF-GQD 346

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R    P AP  GL    + Y 
Sbjct: 347 R-YGIPTAPGLGLVLSRIHYD 366


>gi|170068141|ref|XP_001868750.1| pseudouridylate synthase [Culex quinquefasciatus]
 gi|167864259|gb|EDS27642.1| pseudouridylate synthase [Culex quinquefasciatus]
          Length = 470

 Score =  148 bits (373), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 95/259 (36%), Gaps = 44/259 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             +   Y G  + G+  Q++  ++I+  +  A+  V      E    H  GRTD GV A 
Sbjct: 76  ILLRFFYLGWDFQGYATQEDSANTIEHHLFNALTRVCLIESRESSNYHRCGRTDKGVSAF 135

Query: 59  RQVA------HFDLVREWVPVILCKALNA----YLKISDTIS-ILNLSIVDKQFHARFSA 107
            QV        F    +  P  L   LN        +   I  +  +   +  + ARF  
Sbjct: 136 HQVVSLDVRSKFPPESQLAPESLQNELNYCQLLNRVLPAEIRCVAWMPTANPNYSARFDC 195

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHCQA 165
             R+Y Y                +    SLD + MR   + LVG HDF       +    
Sbjct: 196 RSRTYRY----------------FFPRGSLDVDAMRKGCEFLVGSHDFRNLCKMDVGNGV 239

Query: 166 SSPIRTIDHFDVN--------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
            +  R + +  +         S  +++   +  ++FL  Q+R  +  L LVG G+   T 
Sbjct: 240 VTFQRNVHYAVIRDSLKDGGDSSYDMLYFELRGKAFLWHQVRCIMAILILVGQGREDPTV 299

Query: 218 LEKALQAQD--RKECGPLA 234
           + + L  +   RK    LA
Sbjct: 300 IRELLDVEKNPRKPQYSLA 318


>gi|307214388|gb|EFN89459.1| tRNA pseudouridine synthase A [Harpegnathos saltator]
          Length = 364

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 58/278 (20%), Positives = 95/278 (34%), Gaps = 46/278 (16%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVHAL 58
           + Y G  Y+G QR     +I+  +  A+                +    A RTD GV A+
Sbjct: 2   LGYLGKNYYGMQRNPGMKTIEEDLVNALLKANLITTEQFENLRTINFQRAARTDKGVSAV 61

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           RQ+    L       I+ +       + D I +  +  V K F+++     R+Y Y I +
Sbjct: 62  RQIVSLKLPENPDKTIINQ------FLPDVIRVFGIKRVTKGFNSKNQCDARTYRYIIPS 115

Query: 119 -------------RQAPLALEK-------GRAWLIPKSLDCENMRI---AAQHLVGRHDF 155
                         +     E+            I   L  E++       +   G H+F
Sbjct: 116 FTFAMEDQSLLKMGEEVDINERIKQISTIDGEPYIDYRLSIESLNRLNSILKLFEGTHNF 175

Query: 156 TTFRSI----HCQASSPIRTIDHFD--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
             F S       +A   I      D  V+     + + V  +SF+  QIR  V ++  V 
Sbjct: 176 HNFTSKTKPLDPRARRYIINFHCVDTFVSKGIEFVVLEVKGQSFMLHQIRKMVATVIAVA 235

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
                   + +A   +  K   P+AP  GL    V Y 
Sbjct: 236 RNIIPEETINEAF--KTVKMEIPIAPSLGLCLCHVHYD 271


>gi|270605639|ref|ZP_06221621.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
 gi|270318160|gb|EFA29385.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
          Length = 131

 Score =  147 bits (372), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 39/106 (36%), Positives = 61/106 (57%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
           M+ A Q L+G HDF++FR+  CQ+ +P R + H +V+  G  I + + A +F+H  +R+ 
Sbjct: 1   MQQAGQCLLGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIGQYIIVDIQANAFVHHMVRNI 60

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           VGSL  VG G      ++  L  ++R+   P A P+GLY   V Y 
Sbjct: 61  VGSLIEVGAGNKPIEWMQWLLDQKNRQLAAPTAKPDGLYLVDVIYP 106


>gi|150400596|ref|YP_001324362.1| tRNA pseudouridine synthase A [Methanococcus aeolicus Nankai-3]
 gi|150013299|gb|ABR55750.1| tRNA pseudouridine synthase A [Methanococcus aeolicus Nankai-3]
          Length = 310

 Score =  147 bits (372), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 89/248 (35%), Gaps = 33/248 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
           Y + I Y+G+   G+Q   +  +++   I  A+         E   +   GRTD+GV AL
Sbjct: 39  YILKIAYDGNN-DGFQSHPHKKNNVCDIIINALLKCGYMDKEETKPLLRGGRTDNGVLAL 97

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
                 +L +E +   +   L         + +L  S + +    ++    R Y Y +  
Sbjct: 98  GNFIIVNLNQEPILSHVYAKLKYT-----GVWVLGYSKISELPEIKY----RHYKYILPN 148

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDV 177
                              +   M   A  L+G H F         +  +P+RTI    +
Sbjct: 149 EGQ----------------NINLMIEGANKLIGTHSFHNLSKRDNTKNKNPLRTIYDIKI 192

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I I +  ++FL   +R  V +L  VG        ++K L   +  E    AP  
Sbjct: 193 KENDFFITIDIFGKNFLWNMVRRIVTALSEVGKENKPLNWIDKLLDI-NHTEGVAPAPAN 251

Query: 238 GLYFDSVE 245
           GL    V+
Sbjct: 252 GLILVDVK 259


>gi|302899152|ref|XP_003047991.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256728923|gb|EEU42278.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 530

 Score =  147 bits (371), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 69/333 (20%), Positives = 93/333 (27%), Gaps = 95/333 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFL-----------VTGEIVVVHGAGR 50
             + + Y G  Y G++ Q   N  SI+  +  A+             V  E       GR
Sbjct: 57  IALKLAYLGKNYGGFEFQAMANAPSIEEELWNALTKACLIFPKDERVVDFECCEYSKCGR 116

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALN------------------------------ 80
           TD GV A  QV    +          + L+                              
Sbjct: 117 TDKGVSAFGQVIGLRVRSNRPLPKKRRRLSEAGDAMVVDEPTGENGEEEDYIETSSFDPI 176

Query: 81  ---------AYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIIT---RQAPLALEK 127
                        +   I IL         F ARFS   R Y Y          P A   
Sbjct: 177 KDELQYPRLLNRVLPPDIRILAWCPSPPPDFSARFSCRERQYRYFFTQPAFTPEPTAGGA 236

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNSFGN--- 182
              W     LD E MR AA+   G HDF  F  I    Q ++ +R I   D+    +   
Sbjct: 237 KNGW-----LDIEAMRDAAKRYEGEHDFRNFCKIDPGKQITNFVRNIFEADIKEVRDVSS 291

Query: 183 -------------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
                                    +   +V   +FL  QIR  VG L LVG        
Sbjct: 292 ALPYLSGSQYAPAGGVVDKDAVHPKVYMFQVRGSAFLWHQIRHMVGVLFLVGQRLEKPEV 351

Query: 218 LEKALQAQDRKECGP---LAPPEGLYFDSVEYS 247
           +   L    +  C P   +A    L      + 
Sbjct: 352 ISTLLDVA-KSPCKPNYVMADEVPLVLWDCIFP 383


>gi|84996449|ref|XP_952946.1| tRNA-pseudouridine synthase I [Theileria annulata strain Ankara]
 gi|65303943|emb|CAI76322.1| tRNA-pseudouridine synthase I, putative [Theileria annulata]
          Length = 480

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 65/351 (18%), Positives = 108/351 (30%), Gaps = 105/351 (29%)

Query: 2   IRYCMIIEYNGSGYFGWQ----------RQKN-----GSSIQGSIEKAIFLVTG------ 40
               +I+ Y+G+ Y G             Q N      +SI   + K I ++ G      
Sbjct: 107 TNLILIVSYDGTFYHGMAGPMIFLKDYGIQVNFDNDKVNSINNELLKTITMLHGYFGNKR 166

Query: 41  -------------------------------------------EIVVVHGAGRTDSGVHA 57
                                                          +  + RTD GVH+
Sbjct: 167 KLKKKNLRELSKKIKSKDEDSTYINGYNDEENTSSPDLLEEYARRFTLITSSRTDRGVHS 226

Query: 58  LRQVAHFDLVREWVPVILCKALNA----------------YLKISDTISILNL-SIVDKQ 100
           +  V+  +LV E      C+ L+                   ++   I + ++ +    +
Sbjct: 227 MGTVSLINLVSEIYLFQACQYLSFDKKFNFDSLEEFQDSLNKRLPSDIRVTSVITPPHDE 286

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWL-----------------IPKSLDCENMR 143
           F+ R   I +SY Y++     P   E+   W                  +      E ++
Sbjct: 287 FNVRHHNIGKSYSYKVDLSPNPSLFERNHYWQIMSDTHFVNTLLRKYRDVKAPFSFEKLK 346

Query: 144 IAAQHLVGRHDFTTFRS-----IHCQASSPIRTIDHFDV--NSFGNLIEIRVVARSFLHT 196
            AA+   G+H+F  FR         +   PI TI   +         +EI V    FL+ 
Sbjct: 347 EAARVFHGKHNFEAFRKNCRGNERDKIIDPICTIHSIEFVNIPQDKKVEIIVNGDRFLYK 406

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +R  V  L L G        +++AL         P AP  GLY   V + 
Sbjct: 407 MVRCIVSHLILAGFNVIKPDQIKRALDNATEIPNIPYAPAHGLYLKKVFFE 457


>gi|159487841|ref|XP_001701931.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158281150|gb|EDP06906.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 287

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 99/297 (33%), Gaps = 71/297 (23%)

Query: 2   IRY-CMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV---------TGEIVVVHGAGR 50
            RY  + + Y G  + G+ RQ N  ++I+G +  A+                +     GR
Sbjct: 10  TRYVALELMYVGWAFQGFARQDNTENTIEGVLFSALRKTKLIPEAAAKPISELAYSRCGR 69

Query: 51  TDSGVHALRQVAHFDLVREWVP-----------------------------VILCKALNA 81
           TD GV AL QV    L     P                                 + +N 
Sbjct: 70  TDRGVSALGQVVALQLRSCARPGGGGLGYHDPSMCGPARESLQCPSWCVQEFDYPRLINK 129

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
            L     + IL  + V   F+AR       ++Y+                    SLD + 
Sbjct: 130 AL--PPEVRILGWTPVPADFNARCGGRAGEWVYQ------------------QHSLDIQA 169

Query: 142 MRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVNSF--------GNLIEIRVVARS 192
           MR AA H +G HDF  F         S  R I  F V             +  + V   +
Sbjct: 170 MRTAAAHFIGEHDFRNFCKPDVATVRSFRRRILSFTVEPVTTSAADAAHQVYALTVRGTA 229

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           FL  Q+R     L +VG G+     + + L  +A  RK    +AP E L   +  + 
Sbjct: 230 FLWHQVRCMAAILLMVGRGQEAPDVVARLLDVEACPRKPQYSMAPEEPLLLYACGFP 286


>gi|289620363|emb|CBI53221.1| unnamed protein product [Sordaria macrospora]
          Length = 603

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 71/337 (21%), Positives = 98/337 (29%), Gaps = 95/337 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFL-----------VTGEIVVVHGAGR 50
             +   Y G  Y G++ Q      SI+  + KA+             V          GR
Sbjct: 81  IALKFAYLGKNYNGFEYQSSAKMPSIEEELWKALVKSCLVFPERPDEVDFGPWEYSKCGR 140

Query: 51  TDSGVHALRQVAHFDLVRE----------------------------------------- 69
           TD GV A  QV    +                                            
Sbjct: 141 TDRGVSAFGQVIGIRVRSNKPLPKEEPEQTGGNGGDDVVMTEPQQQEAEKATDVEHQKPE 200

Query: 70  WVPVI----LCKALNAYLKISDTISILNLSIV-DKQFHARFSAIRRSYLYRIIT---RQA 121
           W P+      C+ LN  L     I I+  +      F ARFS   R Y Y          
Sbjct: 201 WDPIADEVPYCRVLNRLL--PPDIRIMAWAPALPPNFSARFSCRERQYRYFFTQPAFAPM 258

Query: 122 PLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVN 178
           P +LE        +  LD   MR AA+   G HDF  F  I    Q ++  R I   D+ 
Sbjct: 259 PSSLEPLAKKQEKQGWLDIGKMREAAKMFEGVHDFRNFCKIDPGKQITNFSRRIFESDIV 318

Query: 179 SFGNL--------------------------IEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
              ++                              V   +FL  QIR  V  L LVG G 
Sbjct: 319 EVKDVESDLPYLGLPEFQPLAGGSEGSHPKVYYFHVRGSAFLWHQIRHMVAVLFLVGQGL 378

Query: 213 WTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
              + +++ L  +   RK    +A    L      + 
Sbjct: 379 EPPSIVQQLLDVEKNPRKPNYVMADEVPLVLWDCIFP 415


>gi|224118612|ref|XP_002331405.1| predicted protein [Populus trichocarpa]
 gi|222873619|gb|EEF10750.1| predicted protein [Populus trichocarpa]
          Length = 428

 Score =  146 bits (370), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 107/315 (33%), Gaps = 72/315 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-------------VHGA 48
           + + +++ Y+G  + GWQ+Q   +++QG +EK++     E                   A
Sbjct: 105 VTFKIVLSYHGGSFDGWQKQPGLNTVQGLVEKSLGRFVDEKKAQQLKEQCKPLEGCASVA 164

Query: 49  GRTDSGVHALRQVAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL+QV  F   R+   P  +  A+N        + + ++S V + FH  FSA
Sbjct: 165 GRTDKGVSALQQVCSFYTWRKDVKPHEIEDAIND--VAPGKVRVESISEVSRAFHPNFSA 222

Query: 108 IRRSYLYRIITRQAPLAL-------------------EKGRAWLI--------------- 133
             R YLY                              ++     +               
Sbjct: 223 KWRRYLYIFPLNDGENREEIEGEGGIENFSSHENCEKQRNECGELASEENVENSIISDED 282

Query: 134 -------PKSLDCENMRIAAQHLVGR--------HDFTTFRSIHC-------QASSPIRT 171
                  P+S     +    Q L G+         D    R++          A +    
Sbjct: 283 ELQGAKKPRSFSVCRVNQLLQQLEGKLLSYKMFARDTKASRNVGPPTECFLYHARATETR 342

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +   D      ++ + ++A  FL   +R  V +             L K + A  R+   
Sbjct: 343 LPSPDHEKGIRVMCVELIANRFLRKMVRVLVATSVREAAAGAQEDALLKLMDATCRRATA 402

Query: 232 PLAPPEGLYFDSVEY 246
           P APP+GL    V Y
Sbjct: 403 PPAPPDGLCLVDVGY 417


>gi|270006513|gb|EFA02961.1| hypothetical protein TcasGA2_TC030541 [Tribolium castaneum]
          Length = 365

 Score =  146 bits (370), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 95/261 (36%), Gaps = 45/261 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGV 55
             +   Y G  Y G+  Q++  ++  +IE  +F    +  ++        H  GRTD  +
Sbjct: 40  VLLKFLYLGWDYQGYVTQED--TV-NTIEHHVFNALIKTCLIENRSSANYHRCGRTDKDL 96

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            +               +  CK LN  L   + I  +    V+  F ARF    R+Y Y 
Sbjct: 97  RSNG-------DDFESEINYCKILNRVL--PENIQFVAWCPVESAFSARFDCKNRTYKY- 146

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTID 173
                          +    +LD + M+IAA +LVG HDF  F  +          R I 
Sbjct: 147 ---------------FFPKSNLDIDAMKIAANYLVGTHDFRNFCKMDVNNGVVEFKRNIL 191

Query: 174 HFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQD 226
             D++        ++  + +   +FL  QIR  VG L LVG GK     +   L      
Sbjct: 192 SVDISLFQEDERYSIQVLTIKGNAFLWHQIRCIVGILILVGQGKEKPEVVLDLLDITRNP 251

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           RK    +A    L      Y 
Sbjct: 252 RKPDYHMASEIPLNLYDCHYD 272


>gi|332029057|gb|EGI69071.1| tRNA pseudouridine synthase A [Acromyrmex echinatior]
          Length = 398

 Score =  146 bits (369), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 98/283 (34%), Gaps = 49/283 (17%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---VTGEI------VVVHGAGRTDSGV 55
            M++ Y G  Y+G QR     +I+  +  A+     +T E       +    A RTD GV
Sbjct: 46  AMLLGYVGKDYYGMQRNPGMKTIEEDLIIALLKADLITKEQFENTRAINFQRAARTDKGV 105

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A+RQ+    L       ++ +       + D I +  +  V K F+++     R+Y Y 
Sbjct: 106 SAIRQIVSLKLPENSNKTVINQ------FLPDAIRVFGIKRVTKGFNSKNQCDARTYRYV 159

Query: 116 IITRQAPLALE-------------------------KGRAWLIPKSLDCENMRIAAQHLV 150
           I +     ALE                         K            + +    +   
Sbjct: 160 IPS--YAFALEDQSLLKLGEEVDEDERIKQLSIIDGKPYTDYRLSPESLDRLNSILKLFE 217

Query: 151 GRHDFTTF-RSIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGS 204
           G H+F  F   +        R I  F            L  + +  +SF+  QIR  V  
Sbjct: 218 GSHNFHNFTSKVKPLDPRARRYIISFCCTETFVLNDIELAVLEIKGQSFMLHQIRKMVAI 277

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  +     +   +++A +  D+ +  PLAP  GL    V Y 
Sbjct: 278 VIAIARNMISKETIDEAFKTMDKMDL-PLAPSLGLCLCHVHYD 319


>gi|157115880|ref|XP_001658327.1| pseudouridylate synthase [Aedes aegypti]
 gi|108876737|gb|EAT40962.1| pseudouridylate synthase [Aedes aegypti]
          Length = 455

 Score =  146 bits (369), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 101/263 (38%), Gaps = 32/263 (12%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSI-----------EKAIFLVTGEIVVVHGAGRTDSG 54
           +++ Y+G  Y G QR     +I+  +           E+A      + +    A RTD G
Sbjct: 120 IVMGYSGVNYLGMQRNPGTKTIEEELLVAMLKHNWISEEAFNQ--PQQIQFQRAARTDKG 177

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A  QV    L        L K L       + I +  +  V K F+++ +   R+Y Y
Sbjct: 178 VSAATQVVSIKLPDNVDIDALNKDL------PEQIRVFAVKRVTKGFNSKSNCDARTYTY 231

Query: 115 RIITRQAPLALEK--GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRT 171
            + T    L  +K    ++ +P+    + +    +   G  +F  F S       S  R 
Sbjct: 232 TLPTMAFALHEDKVDMESYRVPEER-LKVVEETLKLFEGTKNFHNFTSRKEFIDPSSKRF 290

Query: 172 IDHFDVN----SFGNLIEI---RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           I  F+        G+ +E    ++  +SF+  QIR  VG    V  G      + KA + 
Sbjct: 291 IMSFECEAPFVPEGSTVEFATLKIKGQSFMLHQIRKMVGLTLAVVRGLTPQETIVKAFEE 350

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           Q  +   P AP  GL  + + Y 
Sbjct: 351 Q--RYGVPTAPGLGLVLNRIHYE 371


>gi|257461391|ref|ZP_05626487.1| tRNA pseudouridine synthase A [Campylobacter gracilis RM3268]
 gi|257441114|gb|EEV16261.1| tRNA pseudouridine synthase A [Campylobacter gracilis RM3268]
          Length = 203

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 64/214 (29%), Positives = 91/214 (42%), Gaps = 15/214 (7%)

Query: 34  AIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILN 93
           A+  V G    +  + RTD GVHALRQV+  +    W    L + +N +      I + +
Sbjct: 4   ALGRV-GIFAPLISSSRTDKGVHALRQVSCVECTVHWELPRLKELINRHCA--PYIFVQH 60

Query: 94  LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
           +S V + FH R+ A+ RSY Y +   + P           P+ +D   +  A  + +G H
Sbjct: 61  ISPVPRDFHPRYDAVARSYRYVL-NHERPSPFLSDFCVFYPR-VDLAALNAALANFIGEH 118

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVG-SLKLVGDGK 212
           DF  F        SP+R +      SF NL  I   A  FL  Q+R  V  +LK V  G+
Sbjct: 119 DFREFMKSGSDIKSPVRKLYVARAYSFRNLTLINFKANGFLRAQVRLMVANALKSVQSGR 178

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                      +  R       PP GLY  SV Y
Sbjct: 179 KI---------SFSRALSRIPFPPNGLYLSSVSY 203


>gi|46205610|ref|ZP_00209946.1| COG0101: Pseudouridylate synthase [Magnetospirillum magnetotacticum
           MS-1]
          Length = 193

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 42/162 (25%), Positives = 68/162 (41%), Gaps = 7/162 (4%)

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLV 150
              +     F ARFSA+ R+Y YR+    A    L +       + LD   M  A + L+
Sbjct: 2   HRAAPAPTGFDARFSALHRAYTYRVADDPAQRDPLRREWVLWNRRPLDVAAMDAAVRPLL 61

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN-----LIEIRVVARSFLHTQIRSFVGSL 205
           G  DF +F       ++ IR + H   +   +     L+   V A +F H  +R+ VG+ 
Sbjct: 62  GVRDFASFCKPRP-GATTIRELQHLSWSRPADGPDAGLVVAHVRADAFCHNMVRALVGAS 120

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             VG+G+       + L ++ R     + P  GL  + V Y 
Sbjct: 121 LAVGEGRRDVGWPAELLASRRRDAGAGVVPAHGLVLEEVTYP 162


>gi|196008069|ref|XP_002113900.1| hypothetical protein TRIADDRAFT_57795 [Trichoplax adhaerens]
 gi|190582919|gb|EDV22990.1| hypothetical protein TRIADDRAFT_57795 [Trichoplax adhaerens]
          Length = 385

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 113/260 (43%), Gaps = 23/260 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  +++ + G+GYFG QR +   +I+  +  A+F             + +    A RTD
Sbjct: 46  RKVALLLGFCGAGYFGMQRNRGTKTIEEDLINALFKAGAIPEAAKEHEQKMAFQRASRTD 105

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA  QV  F   + +V   +   +N++L     I +     V K F+++ +   R+Y
Sbjct: 106 KGVHAAAQVVSF---KMFVVDDVIAKINSHL--PREIRVFGHFRVTKGFNSKTACDARTY 160

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRT 171
            Y + T       EK   +++      +++R      VG  +F  F S    +  S  R 
Sbjct: 161 KYVMPTYAFANK-EKKNMYILVIEATIKHVRDILAMYVGTRNFHNFTSKKAYEDDSAKRY 219

Query: 172 IDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           I  FD     V +    + + V  +SF+  QIR  +G +  +  G  T   +EKA + +D
Sbjct: 220 IMQFDCGLPFVRNNLEFVTLTVKGQSFMLHQIRKMIGLMIGIVRGDATIEAMEKAWE-KD 278

Query: 227 RKECGPLAPPEGLYFDSVEY 246
           R +  P AP  GL    + Y
Sbjct: 279 RVDI-PRAPGLGLMLYQLHY 297


>gi|292655987|ref|YP_003535884.1| tRNA pseudouridine synthase A [Haloferax volcanii DS2]
 gi|291370921|gb|ADE03148.1| tRNA pseudouridine synthase A [Haloferax volcanii DS2]
          Length = 283

 Score =  146 bits (368), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 65/253 (25%), Positives = 101/253 (39%), Gaps = 32/253 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVH 56
           +R    + Y+G  Y G+QRQ +  +++ +I  A   +       E      AGRTD+GV 
Sbjct: 1   MR-AFRVAYDGRPYHGFQRQPDVPTVEDAIFDACRALGVCDDDEEPTDYAAAGRTDAGVS 59

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL Q   F+      P    +ALN+ L    T+     +     FHAR    RR Y+Y +
Sbjct: 60  ALAQTVAFECPDWCTP----RALNSEL--PGTVRAWADADAPDDFHARHWPTRREYVYDL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                             +  D +  + A     G HD   FR++       +R ID   
Sbjct: 114 HA--------------PTEGFDDDRAKAAFDACRGDHD---FRNLTPDDHGTVRAIDG-G 155

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLA 234
           +   G+ + +RV A  F    +R  V  ++ VG      + ++ AL     D  E    A
Sbjct: 156 LTRDGDFLLVRVEAGGFARELVRRLVSLVRAVGSDAAPLSKVDDALGPDHLDGPEGIAPA 215

Query: 235 PPEGLYFDSVEYS 247
           PP  L   +V+Y 
Sbjct: 216 PPTPLLLTAVDYP 228


>gi|296423394|ref|XP_002841239.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295637475|emb|CAZ85430.1| unnamed protein product [Tuber melanosporum]
          Length = 483

 Score =  146 bits (368), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 99/308 (32%), Gaps = 71/308 (23%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS----SIQGSIEKAIFL--------VTGEIVVVHG---- 47
             + I Y G  Y G++   N      +I+  I KA+          + GE   V G    
Sbjct: 26  IALRIAYLGGNYTGFEYHANSPNTTNTIEEHIFKALLKARLVPCNGIEGEEETVLGWPGD 85

Query: 48  -------AGRTDSGVHALRQVAHFDLVREWV----------------------------P 72
                   GRTD+GV A  QV    +                                  
Sbjct: 86  EVAEYSKCGRTDTGVSAFGQVIGVRVRSNRPLPKKPTDDVAEEGGEEGKEKTEFDDEKDE 145

Query: 73  VILCKALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
           +   + LN  L     I +L         F ARF+  +R Y Y         +       
Sbjct: 146 LPYPQILNRLL--PKDIRVLAWCPHPPPTFSARFNCQQRHYRYFFTNPAIVPSPNSTV-- 201

Query: 132 LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNSFGN------- 182
               +LD + MR AA+  VG HDF  F  +    Q +   R I H D+            
Sbjct: 202 ---GNLDIDKMREAAKLYVGDHDFRNFCKLDASKQITRFDRVIHHADIVELPQSSPNNNP 258

Query: 183 -LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQD-RKECGPLAPPEGL 239
            +    +   +FL  Q+R  +  L L+  G    + + + L  +++ RK    +A    L
Sbjct: 259 KVYYFELHGSAFLWHQVRHMIAILFLIAQGLEQPSLVTEMLDISKNPRKPMYDIANDRAL 318

Query: 240 YFDSVEYS 247
                 + 
Sbjct: 319 VLWDCIFP 326


>gi|241955317|ref|XP_002420379.1| tRNA pseudouridine synthase, putative [Candida dubliniensis CD36]
 gi|223643721|emb|CAX41457.1| tRNA pseudouridine synthase, putative [Candida dubliniensis CD36]
          Length = 444

 Score =  146 bits (368), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 55/277 (19%), Positives = 85/277 (30%), Gaps = 52/277 (18%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTD 52
           M        Y G  Y G   Q       +++    KA+  V       E V     GRTD
Sbjct: 86  MRFVAFKFAYLGWNYNGLALQGEPTPLPTVEEMFLKALAKVKLIKEPIEEVKFSRCGRTD 145

Query: 53  SGVHALRQVAHFDLVREWVPVI------------LCKALNAYLKISDTISILNLS-IVDK 99
            GV A+ QV   D+                        LNA L     I + ++      
Sbjct: 146 KGVSAMNQVISIDVRSNLSLENQANPEFDDQEIDYISVLNANL--PSDIKVHSICLRPPP 203

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
           +F ARFS +   Y Y                    + L+ + M   A    G HDF  F 
Sbjct: 204 EFDARFSCLSCHYRYI----------------FRKQDLNIDLMNQGANLYQGIHDFRNFC 247

Query: 160 SIH--CQASSPIRTIDHFDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
            +    Q ++ +R I    + +   +     +   +FL  Q+R  V  L  +G    + +
Sbjct: 248 KLDGSKQITNFVREIYQAQILHLHQDYYCFDLKGSAFLWHQVRCMVAILFSIGQELESPS 307

Query: 217 DLEKALQAQDRKECGPLAP----PE--GLYFDSVEYS 247
            +   +         P  P         L     E+ 
Sbjct: 308 IITDLMDMTK----YPTKPQYEMAHDIPLVLYDCEFP 340


>gi|260942163|ref|XP_002615380.1| hypothetical protein CLUG_04262 [Clavispora lusitaniae ATCC 42720]
 gi|238850670|gb|EEQ40134.1| hypothetical protein CLUG_04262 [Clavispora lusitaniae ATCC 42720]
          Length = 447

 Score =  146 bits (368), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 79/245 (32%), Gaps = 43/245 (17%)

Query: 4   YCMIIEYNGSGYFG--WQRQKN-GSSIQGSIEKAIFLV------TGEIVVVHGAGRTDSG 54
                 Y G  Y G  +Q +     +++  I +A+                   GRTD G
Sbjct: 86  VAFRFAYMGWNYNGLNFQNEPTPLPTVEEEILQAMTKAKLVPEADPASCNFSRCGRTDKG 145

Query: 55  VHALRQVAHFDLVREWVPVILCKA------------LNAYLKISDTISILNLS-IVDKQF 101
           V AL QV   D+                        LNA L     I I  +       F
Sbjct: 146 VSALNQVISLDVRSALSKEEHADKEKDVKELPYLTILNALL--PPDIRITAVCLRPPPNF 203

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
           +ARFS   R Y Y                      LD + M+ AA    G HDF  F  I
Sbjct: 204 NARFSCKYRHYKYL----------------FKKTDLDVDLMQEAALKYEGPHDFRNFCKI 247

Query: 162 H--CQASSPIRTIDHFDVNSF-GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
               Q ++  R +    +  F  +     +   +FL  Q+R  V  L  VG    + + +
Sbjct: 248 DGSKQITNHCREVYSARIEHFKDDFYVFDLKGTAFLWHQVRCMVAVLFSVGQKLESPSIV 307

Query: 219 EKALQ 223
           +  L 
Sbjct: 308 DDLLN 312


>gi|270692650|ref|ZP_06222951.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
 gi|270316015|gb|EFA28055.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
          Length = 115

 Score =  146 bits (368), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 39/106 (36%), Positives = 61/106 (57%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSF 201
           M+ A Q L+G HDF++FR+  CQ+ +P R + H +V+  G  I + + A +F+H  +R+ 
Sbjct: 1   MQQAGQCLLGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIGQYIIVDIQANAFVHHMVRNI 60

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           VGSL  VG G      ++  L  ++R+   P A P+GLY   V Y 
Sbjct: 61  VGSLIEVGAGNKPIEWMQWLLDQKNRQLAAPTAKPDGLYLVDVIYP 106


>gi|225718836|gb|ACO15264.1| tRNA pseudouridine synthase 3 [Caligus clemensi]
          Length = 423

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 64/276 (23%), Positives = 100/276 (36%), Gaps = 59/276 (21%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
            +  + I Y G  Y G+  Q++   +I+G +  A+         E    H  GRTD GV 
Sbjct: 60  RKVLLQICYFGWSYHGFAVQEDSPMTIEGHLFNALSRTCLIRSRETSNYHRCGRTDKGVS 119

Query: 57  ALRQVAHFDL-----------------------VREWVPVILCKALNAYLKISDTISILN 93
           A RQV   +L                             +  CK LN+ L     I ++ 
Sbjct: 120 AFRQVVSIELRSNLLEGPGVFDYPECRAHSRPNPTTNEEIDYCKILNSNL--PPDIQVIA 177

Query: 94  LSI-VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
            +   ++ F ARF    R Y Y      A                D   ++ A   L+G 
Sbjct: 178 WAPLTNRDFSARFDCKIREYKYIFPLGAAR---------------DLSRIQEAGAKLLGS 222

Query: 153 HDFTTFRSIHCQAS--SPIRTIDHFDVNSFGN-------LIEIRVVARSFLHTQIRSFVG 203
           HDF  F  +       + IR +    V+   +       L+E+++V  +FL  QIR  V 
Sbjct: 223 HDFRNFCKMDVSNGVLTYIRRMLEVSVSPLESSSTDSYSLVELKIVGNAFLWHQIRCIVT 282

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            L  +G G    + +++ L  +      P  P  GL
Sbjct: 283 VLFHIGQGLEEPSLIDELLDVEKH----PRRPQYGL 314


>gi|47206562|emb|CAF94488.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 181

 Score =  145 bits (367), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 56/177 (31%), Positives = 89/177 (50%), Gaps = 22/177 (12%)

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRI---ITRQAPLAL-EKGRAWLIPK-SLDCENMRIA 145
           + +   V   FHARF A  R+Y+YR+   I R++P+ L E G  W +    LD   M  A
Sbjct: 1   VTHAYCVADNFHARFCAQSRTYVYRVALGICRKSPVPLPEHGFCWNLRDTELDVGGMCEA 60

Query: 146 AQHLVGRHDFTTFRSIHCQA--SSPIRTIDHFDVN-----------SFGNLIEIRVVARS 192
           A  LVG HDF++FR+++      +P++ +D   +                 +E+   +RS
Sbjct: 61  AALLVGVHDFSSFRAVNSDLPFKNPVKRLDAATIQTGVSFAQVHYHRVIPFLELIFTSRS 120

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
           FL+ Q+R   G+L  VG G+ +   L++ L+A+D     P    AP  GL+   V+Y
Sbjct: 121 FLYKQVRRMTGALVAVGQGRLSVAQLKEVLEARD-SLAYPQGLTAPAHGLFLTRVDY 176


>gi|189236260|ref|XP_974416.2| PREDICTED: similar to pseudouridylate synthase [Tribolium
           castaneum]
          Length = 275

 Score =  145 bits (367), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 93/235 (39%), Gaps = 38/235 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGV 55
             +   Y G  Y G+  Q++  ++  +IE  +F    +  ++        H  GRTD GV
Sbjct: 58  VLLKFLYLGWDYQGYVTQED--TV-NTIEHHVFNALIKTCLIENRSSANYHRCGRTDKGV 114

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            +L   ++         +  CK LN  L   + I  +    V+  F ARF    R+Y Y 
Sbjct: 115 ISLDLRSNG--DDFESEINYCKILNRVL--PENIQFVAWCPVESAFSARFDCKNRTYKY- 169

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS--SPIRTID 173
                          +    +LD + M+IAA +LVG HDF  F  +          R I 
Sbjct: 170 ---------------FFPKSNLDIDAMKIAANYLVGTHDFRNFCKMDVNNGVVEFKRNIL 214

Query: 174 HFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             D++        ++  + +   +FL  QIR  VG L LVG GK     +   L 
Sbjct: 215 SVDISLFQEDERYSIQVLTIKGNAFLWHQIRCIVGILILVGQGKEKPEVVLDLLD 269


>gi|91076290|ref|XP_968649.1| PREDICTED: similar to AGAP002409-PA [Tribolium castaneum]
          Length = 588

 Score =  145 bits (367), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 100/264 (37%), Gaps = 28/264 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTD 52
            ++ +++ Y+G+ Y+G QR  N  +I+    KA++             + +    A RTD
Sbjct: 255 RKFAVLLGYSGTNYYGMQRNPNTPTIEEEFFKALYKNNYISEENFTQVQTMQFQRAARTD 314

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A RQV    L  +     + + L       + I +  +  V K F+++     RSY
Sbjct: 315 KGVSAARQVVSLKLREDIDISKINEQL------PEVIRVFGIRRVTKGFNSKVQCDSRSY 368

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFRS----IHCQA 165
            Y + T                  LD      +    Q  +G  +F  F S        A
Sbjct: 369 TYLLPT--VSFTPHDQLMVQKGFRLDDSTLNRINDLLQKYLGTKNFHNFTSKKQATDPSA 426

Query: 166 SSPIRTI--DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
              ++T+  +   V        I++  +SF+  QIR  VG L  V  G  +   L+  L 
Sbjct: 427 KRYMKTLICEKPFVKDDVEFALIKIRGQSFMLHQIRKMVGLLIAVVKGYTSEDTLD--LA 484

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
               K   P AP  GL  D V Y 
Sbjct: 485 FGMDKVNIPKAPGLGLLLDYVHYE 508


>gi|50556320|ref|XP_505568.1| YALI0F18216p [Yarrowia lipolytica]
 gi|49651438|emb|CAG78377.1| YALI0F18216p [Yarrowia lipolytica]
          Length = 443

 Score =  145 bits (367), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 53/249 (21%), Positives = 89/249 (35%), Gaps = 40/249 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAI--FLVTGEIVVVH-----GAGRT 51
            +  +   Y G  Y G   Q       +I+G+I  A+    +  E   +        GRT
Sbjct: 84  RKIAIRFSYLGWNYGGLAVQHEDTPLPTIEGTILSAMQRCRLIPESASLFDLDFSRCGRT 143

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQ 100
           D GV A  QV    +  +  P     A N              +   I I +++  + + 
Sbjct: 144 DRGVSAFSQVIALKVRSKLSPEEQQDAANDNKELNYIHILNQLLPPDIRIYSVALRLPEG 203

Query: 101 FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           F +RFS   R Y Y                +     LD + MR AA+  +G HD+  F  
Sbjct: 204 FDSRFSCEYRHYRY----------------FFHKGDLDIDLMRQAAKLYLGEHDYRNFCK 247

Query: 161 IH--CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
           +    Q +   R +   ++     ++    +  R+FL  Q+R  +  L LVG      + 
Sbjct: 248 VDGSKQLAHHNRVMLEAEIEQLSDDIYYFNLKGRAFLWHQVRCMMAILFLVGQKLEKPSV 307

Query: 218 LEKALQAQD 226
           +   L  + 
Sbjct: 308 ITDLLNPEK 316


>gi|167524395|ref|XP_001746533.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163774803|gb|EDQ88429.1| predicted protein [Monosiga brevicollis MX1]
          Length = 415

 Score =  145 bits (366), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 101/266 (37%), Gaps = 34/266 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           +Y +++ + G+ Y G QR     +I+ ++ +A+ +          T + +      RTD 
Sbjct: 32  KYALLMGFQGTSYAGMQRNIGFETIESTLLRALLVTGCIDKNNYETPQSMHFQRCARTDK 91

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA RQV      R  +       LNA L   D I I       K F+ + +   R Y 
Sbjct: 92  GVHAARQVVAM---RMILTENTVDELNAKL--PDDIRIFGAFRTTKGFNPKNACTGRRYE 146

Query: 114 YRIIT------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           Y + T       + P+       + + +       R   +  +G H F  F +    +  
Sbjct: 147 YLLPTYALMPKEKVPVP-----EYRVDEP-KLTWFRETLKRYIGTHKFHNFTAGKSASDD 200

Query: 168 PIRT-IDHFDV----NSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
             R  I  F V       G   + I+V  +SF+  QIR  +G    +  G      +++ 
Sbjct: 201 SCRRYITDFTVSEPFEREGIEWVRIQVKGQSFILHQIRKMIGLAVAIVRGHVKDDYMDRC 260

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
               D +   P  P  GL+ D V + 
Sbjct: 261 FS--DERVDVPKIPGLGLFLDCVFFD 284


>gi|213513998|ref|NP_001134221.1| tRNA pseudouridine synthase A [Salmo salar]
 gi|209731596|gb|ACI66667.1| tRNA pseudouridine synthase A [Salmo salar]
          Length = 392

 Score =  145 bits (366), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 98/266 (36%), Gaps = 27/266 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY+G QR        +I+  +  A+              + +      
Sbjct: 50  RKVVLLLAYSGKGYYGMQRNAGSSQFKTIEDELVTALIKSGCIPDNHGDDMKKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV    L   W+   + + +N+ L     I +L L  V   F+++ S   
Sbjct: 110 RTDKGVSAAGQVVSLKL---WMIEDVMEKINSNL--PPQIRVLGLKRVTGGFNSKNSCDA 164

Query: 110 RSYLYRIITRQA--PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-AS 166
           R+Y Y + T          K  A    +    + +        G H+F  F S       
Sbjct: 165 RTYSYMLPTVAFSPKDYYTKNYAAFRLEPETLQRVNQLFGSYKGTHNFHNFTSQKAAWDP 224

Query: 167 SPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
           S  R I         V       EI V  +SF+  QIR  +G +  V  G      L+++
Sbjct: 225 SARRYITEMSCGEPFVRGGAEFAEITVRGQSFMMHQIRKMIGLVIAVVKGYSGDEVLKRS 284

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
               + K   P AP  GL  + V + 
Sbjct: 285 W--GEEKVDVPKAPGLGLVLEKVHFD 308


>gi|255710543|ref|XP_002551555.1| KLTH0A02222p [Lachancea thermotolerans]
 gi|238932932|emb|CAR21113.1| KLTH0A02222p [Lachancea thermotolerans]
          Length = 443

 Score =  144 bits (365), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 54/243 (22%), Positives = 87/243 (35%), Gaps = 39/243 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
                 Y G  Y G   QK      +++G+I +A+        +  +       GRTD G
Sbjct: 89  VAFKFAYLGWNYNGLAIQKEPTPLPTVEGTILEAMNACKLVPSMVPQDYNFSRCGRTDKG 148

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLSIVDK-QFHA 103
           V A+ QV    +             N              + D I I  + +     F A
Sbjct: 149 VSAMNQVISLHVRSNLTREEQQDEENDGREIDYIHILNQLLPDDIRISAVCLRPPTNFDA 208

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS   R Y Y                      LD + M  AA+   G HDF  F  +  
Sbjct: 209 RFSCQYRHYRYL----------------FHKDGLDIKKMEEAARMYEGEHDFRNFCKLDG 252

Query: 163 -CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  R I+   + S   ++  + ++  +FL  Q+R  + +L L+G G   +T L+ 
Sbjct: 253 SKQINNYKRNIERSRIISLSEDIYCLDLIGSAFLWHQVRCMMANLFLIGQGLEDTTLLKD 312

Query: 221 ALQ 223
            + 
Sbjct: 313 LMD 315


>gi|270002527|gb|EEZ98974.1| hypothetical protein TcasGA2_TC004829 [Tribolium castaneum]
          Length = 390

 Score =  144 bits (365), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 100/264 (37%), Gaps = 28/264 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTD 52
            ++ +++ Y+G+ Y+G QR  N  +I+    KA++             + +    A RTD
Sbjct: 57  RKFAVLLGYSGTNYYGMQRNPNTPTIEEEFFKALYKNNYISEENFTQVQTMQFQRAARTD 116

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A RQV    L  +     + + L       + I +  +  V K F+++     RSY
Sbjct: 117 KGVSAARQVVSLKLREDIDISKINEQL------PEVIRVFGIRRVTKGFNSKVQCDSRSY 170

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFRS----IHCQA 165
            Y + T                  LD      +    Q  +G  +F  F S        A
Sbjct: 171 TYLLPT--VSFTPHDQLMVQKGFRLDDSTLNRINDLLQKYLGTKNFHNFTSKKQATDPSA 228

Query: 166 SSPIRTI--DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
              ++T+  +   V        I++  +SF+  QIR  VG L  V  G  +   L+  L 
Sbjct: 229 KRYMKTLICEKPFVKDDVEFALIKIRGQSFMLHQIRKMVGLLIAVVKGYTSEDTLD--LA 286

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
               K   P AP  GL  D V Y 
Sbjct: 287 FGMDKVNIPKAPGLGLLLDYVHYE 310


>gi|150865972|ref|XP_001385404.2| pseudouridine synthase [Scheffersomyces stipitis CBS 6054]
 gi|149387228|gb|ABN67375.2| pseudouridine synthase [Scheffersomyces stipitis CBS 6054]
          Length = 465

 Score =  144 bits (365), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 91/280 (32%), Gaps = 52/280 (18%)

Query: 1   MIRY-----CMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVH 46
           M +Y      +   Y G  Y G   Q       +++  + KA+ +       T +     
Sbjct: 83  MNKYNKRFIALKFAYLGWNYNGLAYQSEPTPLPTVEEVVLKALTMSRLITEPTPDKCKFS 142

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLK----------ISDTISILNLS- 95
             GRTD GV A+ QV    +             N + +          +   I +  +  
Sbjct: 143 RCGRTDKGVSAMNQVISLVVRSNLNEEEQLLKENDHKEIKYLSIINALLPPDIRMTAVCL 202

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
               +F ARFS   R Y Y                      LD E M  A    +G HDF
Sbjct: 203 RPPPKFDARFSCDYRHYRYL----------------FKKHDLDIELMNEACIKYIGSHDF 246

Query: 156 TTFRSIH--CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
             F  I    Q ++ +R +    +     +   + +   +FL  Q+R  V  L L+G   
Sbjct: 247 RNFCKIDGSKQITNYVREVYSMKIIHLKDDFYAVDLKGSAFLWHQVRCMVAILFLIGQKL 306

Query: 213 WTSTDLEKA--LQAQDRKECGPLA---PPEGLYFDSVEYS 247
             +T +E    L+    K    +A   P   L      Y 
Sbjct: 307 EATTIIEDLFDLEKYPTKPVYEMANDIP---LVLYDCIYP 343


>gi|119504507|ref|ZP_01626586.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2080]
 gi|119459529|gb|EAW40625.1| tRNA pseudouridine synthase A [marine gamma proteobacterium
           HTCC2080]
          Length = 226

 Score =  144 bits (365), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 42/109 (38%), Positives = 64/109 (58%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
           C  M  A+Q L+G HDF+ FR+  CQA+ P+R I    VN  G+ + + + A +FL+  +
Sbjct: 99  CIAMHNASQILLGEHDFSAFRAAQCQAAHPVRQIFGVSVNRVGDFVILDIEANAFLYHMV 158

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           R+ VGSL++VG G+     +E+ L+ +DR   G  A   GLY  S+ Y 
Sbjct: 159 RNLVGSLQMVGSGQRPPEWIEQLLEGKDRTLGGDTASASGLYLQSITYP 207


>gi|158298322|ref|XP_318500.4| AGAP010807-PA [Anopheles gambiae str. PEST]
 gi|157014345|gb|EAA13705.4| AGAP010807-PA [Anopheles gambiae str. PEST]
          Length = 485

 Score =  144 bits (365), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 95/248 (38%), Gaps = 44/248 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q++   +I+  +  A+  V      E    +  GRTD GV A 
Sbjct: 76  ILLRFYYLGWDYQGFAAQEDSIETIEHHMFAALKKVCLIESRETSNYNRCGRTDKGVSAF 135

Query: 59  RQVAHFDLVREWVPVILCKALNA----------YLKISDTISILNLSI-VDKQFHARFSA 107
            QV   D+  ++ P +   A N              + + I  L     V+  + ARF  
Sbjct: 136 HQVISLDVRSKFAPELQLDANNLTNELDYCAMLNRVLPEEIRCLAWMPMVNPAYSARFDC 195

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHCQA 165
             R+Y Y                +     L+   M  +A++LVG HDF       +    
Sbjct: 196 RSRTYRY----------------FFPRGDLNITAMEESARYLVGAHDFRNLCKMDVGNGV 239

Query: 166 SSPIRTIDHFDV-------NSFG---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
            S +R+ID   +          G   +++ + +  ++FL  Q+R  +  L LVG G+   
Sbjct: 240 VSFVRSIDAISIKPSQRDSERDGSSYDMMYLELQGKAFLWHQVRCIMAVLLLVGQGREKP 299

Query: 216 TDLEKALQ 223
           + ++  L 
Sbjct: 300 SVVKDLLD 307


>gi|294790441|ref|ZP_06755599.1| tRNA pseudouridine synthase A [Scardovia inopinata F0304]
 gi|294458338|gb|EFG26691.1| tRNA pseudouridine synthase A [Scardovia inopinata F0304]
          Length = 382

 Score =  144 bits (365), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 59/220 (26%), Positives = 92/220 (41%), Gaps = 41/220 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT------GEI------------- 42
           +R  +   Y+G+ + GW RQ +  ++QG +E AI  V       G+              
Sbjct: 1   MRLKIDCSYDGTDFHGWARQPDLRTVQGELEAAIAKVLHLWQPAGQTADYPSAFAKALAN 60

Query: 43  --------VVVHGAGRTDSGVHALRQVAHFDLVR--------EWVPVIL--CKALNAYLK 84
                     +  AGRTD+GVHA  QV H DL +           P       AL   L+
Sbjct: 61  QSAPVSFWPHLVVAGRTDTGVHARGQVCHLDLDQDLLGRAQGHLDPARFKPWDALTYRLR 120

Query: 85  --ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ-APLALEKGRAWLIPKSLDCEN 141
             + D +S+  +S   + F ARFSA  R Y+YR+   Q +     +     + +S D + 
Sbjct: 121 RILPDDLSVSAISPAPEGFDARFSASDRVYVYRVADDQTSYDPRLRSFVLNLRRSTDIQI 180

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           M  A   +VG HDF +F + +    + IR + +      G
Sbjct: 181 MNTALAEIVGLHDFGSFATPNP-GGTTIREVKYAHWRRVG 219



 Score = 79.9 bits (196), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              D+   G L+E  ++A +F H  +RS V +   VG GK +       +    R+    
Sbjct: 290 YQIDILESG-LLEFTIIADAFAHNMVRSLVNASLQVGMGKKSLEWFLDKIHNPQREGASG 348

Query: 233 LAPPEGLYFDSVEYS 247
            AP  GL  + V Y 
Sbjct: 349 PAPACGLTLEKVNYP 363


>gi|312385729|gb|EFR30155.1| hypothetical protein AND_00413 [Anopheles darlingi]
          Length = 443

 Score =  144 bits (365), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 63/261 (24%), Positives = 96/261 (36%), Gaps = 27/261 (10%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTDSGVH 56
           +++ Y+G  YFG QR     +I+  + +A+              + +    A RTD GV 
Sbjct: 108 ILLGYSGVDYFGMQRNPGTRTIEEDLLRAMLKQEWINDEGFRQPQQIQFQRAARTDKGVS 167

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A  QV    L           ALN  L     I +  +  V K F+++ +   R+Y Y +
Sbjct: 168 AAVQVVSIKLPDNLD----VAALNGEL--PPQIRVYAVKRVTKGFNSKTNCDARTYTYTL 221

Query: 117 ITRQAPLALEKGR-AWLIPKSLD-CENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTID 173
            T       EK           D  + +       +G  +F  F S        + R I 
Sbjct: 222 PTIAFAANDEKDLDILTYRAPADRLQRVNEVLALYLGTKNFHNFTSRKEFIDPSVKRYIM 281

Query: 174 HFDV-------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            F+         +      IR+  +SF+  QIR  VG    V  G   +  +EKA   Q+
Sbjct: 282 EFECGTPFVPDGTTAEFATIRIKGQSFMLHQIRKMVGLTLAVVRGLSQADIIEKAF-GQE 340

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R    P AP  GL    + Y 
Sbjct: 341 R-YGIPTAPGLGLVLSRIHYD 360


>gi|241713555|ref|XP_002412103.1| pseudouridylate synthase, putative [Ixodes scapularis]
 gi|215505180|gb|EEC14674.1| pseudouridylate synthase, putative [Ixodes scapularis]
          Length = 398

 Score =  144 bits (365), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 102/290 (35%), Gaps = 68/290 (23%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q++  ++++ ++ +A+         E    H  GRTD GV A 
Sbjct: 4   VALRFLYLGWNYDGYVVQEDTANTVEAALFQALQRTRLLDLRETSNYHRCGRTDKGVSAF 63

Query: 59  RQVAHFDLVREWVP-----------------------VILCKALNAYLKISDTISILNLS 95
            QV   DL                             +   K LN  L     I +L  +
Sbjct: 64  SQVISIDLRSNLTEGPEGTAPSARSIHSVISVARSTELDYVKILNGVL--PPDIRVLAWA 121

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
             +  F ARF    R+Y Y +                   +L  + MR AA+ LVG HDF
Sbjct: 122 PAEPSFSARFDCQARTYRYFLP----------------KGNLVVQRMREAAKLLVGEHDF 165

Query: 156 TTFRS--IHCQASSPIRTI---DHFDVNSFGN-------LIEIRVVARSFLHTQIRSFVG 203
                  +    +  +R I   + +D    G+       ++ + +V ++FL  Q+R  V 
Sbjct: 166 RNLCKMDVGNGVTRYVRRILSTELYDGEPEGDGGSSGYQMLCLEIVGQAFLWHQVRCIVA 225

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG------LYFDSVEYS 247
            L LVG G      + K L      E  P  P  G      L     ++ 
Sbjct: 226 ILLLVGQGLEEPEVVSKLLDV----EAHPCKPQYGMASEIPLVLYDCQFE 271


>gi|66805521|ref|XP_636482.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
 gi|60464862|gb|EAL62978.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
          Length = 491

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 95/305 (31%), Gaps = 83/305 (27%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
               + Y G  +FG+  Q  +  +I+  + KA    +     +      +GRTD GV A 
Sbjct: 87  VAFKLSYVGWPFFGFAAQDCSEETIENYLIKAFLKTSLIPDIKTANYFKSGRTDKGVSAY 146

Query: 59  RQVAHFDLVREW------------------------------------------------ 70
            QV    +                                                    
Sbjct: 147 GQVISLYVRSNLKEGEGIIPPKDQSGGPISNRTKSNKTELTKNNDNEKARKGNKKSIEDD 206

Query: 71  VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRA 130
             +   K LN  L     I IL  + V   F+ARFS + R+Y Y                
Sbjct: 207 EELPYIKMLNGVL--PPEIRILAWAPVPFHFNARFSTLSRTYKY---------------- 248

Query: 131 WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN--LIEIRV 188
           +  P  LD   M+ A++  +G H++  F  I     S +R I  FD+    N  L    +
Sbjct: 249 FFNPNGLDLNLMKEASKLYLGEHNYINFCKIDVNVKSFMRVILQFDIEKVENSELYVATI 308

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE------GLYFD 242
              +FL  QIR  +  L L+G  K   + + + L            PP        L   
Sbjct: 309 KGFAFLWHQIRCMMAVLFLIGQKKANISLITQLLD----TNKTITKPPYEMASEVPLVLF 364

Query: 243 SVEYS 247
              Y 
Sbjct: 365 DCGYD 369


>gi|14318522|ref|NP_116655.1| Deg1p [Saccharomyces cerevisiae S288c]
 gi|399356|sp|P31115|PUS3_YEAST RecName: Full=tRNA pseudouridine synthase 3; AltName:
           Full=Depressed growth-rate protein DEG1; AltName:
           Full=tRNA pseudouridylate synthase 3; AltName:
           Full=tRNA-uridine isomerase 3
 gi|836755|dbj|BAA09239.1| depressed growth-rate protein [Saccharomyces cerevisiae]
 gi|51013845|gb|AAT93216.1| YFL001W [Saccharomyces cerevisiae]
 gi|285811895|tpg|DAA12440.1| TPA: Deg1p [Saccharomyces cerevisiae S288c]
          Length = 442

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 83/241 (34%), Gaps = 39/241 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK      +++G+I +A+        +  +       GRTD G
Sbjct: 94  IALRFAYLGWNYNGLAVQKEYTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKG 153

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++             N              + D I I  +       F A
Sbjct: 154 VSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLRPPPNFDA 213

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS + R Y Y I   +               +L+ E M  AA + VG  DF  F  +  
Sbjct: 214 RFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYFVGERDFRNFCKLDG 257

Query: 163 -CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RTI    +           +V  +FL  Q+R  +  L LVG        + +
Sbjct: 258 SKQITNFKRTIISSKILPLSETFYCFDLVGSAFLWHQVRCMMAILFLVGQSLEVPEIVLR 317

Query: 221 A 221
            
Sbjct: 318 L 318


>gi|145355737|ref|XP_001422107.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582347|gb|ABP00424.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 308

 Score =  144 bits (363), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 104/259 (40%), Gaps = 22/259 (8%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
            +   Y G+GY G QR     +I+G +E AI    G           V    A RTD GV
Sbjct: 6   AVTFAYVGAGYAGMQRNPGVRTIEGELEGAIARAGGISDANAGDFAKVQWTRAARTDKGV 65

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A+ QV    +V    P  + + +NA L   +   +  +  V   F+A+    RR Y Y 
Sbjct: 66  SAVGQVVALKMV--LEPSGMVERINAAL--PERFEVFGIDRVTGGFNAKTMCDRRRYEYV 121

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRI--AAQHLVGRHDFTTFR-SIHCQASSPIRTI 172
           I TR     L    A       +    R+    ++  G H+F  +   +    +   R I
Sbjct: 122 IPTRAFDPNLGAEGAAEAFAFTEETRSRVDGVLKNYCGTHNFHNYTVKVKPTDAQAKRYI 181

Query: 173 DHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
             F+ +          +  +VV +SF+  QIR  +G++  V  G+ T  D + AL   + 
Sbjct: 182 ISFECSAPFEVEGEQFVRCQVVGQSFMLHQIRKLIGTMLAVVRGELTEDDQKFALLTHEF 241

Query: 228 KECGPLAPPEGLYFDSVEY 246
               P+AP  GL+     Y
Sbjct: 242 VPT-PMAPELGLFLCECIY 259


>gi|323305104|gb|EGA58854.1| Deg1p [Saccharomyces cerevisiae FostersB]
          Length = 431

 Score =  144 bits (363), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 83/241 (34%), Gaps = 39/241 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK      +++G+I +A+        +  +       GRTD G
Sbjct: 83  IALRFAYLGWNYNGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKG 142

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++             N              + D I I  +       F A
Sbjct: 143 VSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLRPPPNFDA 202

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS + R Y Y I   +               +L+ E M  AA + VG  DF  F  +  
Sbjct: 203 RFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYFVGERDFRNFCKLDG 246

Query: 163 -CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RTI    +           ++  +FL  Q+R  +  L LVG        + +
Sbjct: 247 SKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLR 306

Query: 221 A 221
            
Sbjct: 307 L 307


>gi|190406572|gb|EDV09839.1| tRNA pseudouridine synthase 3 [Saccharomyces cerevisiae RM11-1a]
 gi|256268860|gb|EEU04212.1| Deg1p [Saccharomyces cerevisiae JAY291]
 gi|323309245|gb|EGA62466.1| Deg1p [Saccharomyces cerevisiae FostersO]
          Length = 442

 Score =  144 bits (363), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 83/241 (34%), Gaps = 39/241 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK      +++G+I +A+        +  +       GRTD G
Sbjct: 94  IALRFAYLGWNYNGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKG 153

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++             N              + D I I  +       F A
Sbjct: 154 VSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLRPPPNFDA 213

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS + R Y Y I   +               +L+ E M  AA + VG  DF  F  +  
Sbjct: 214 RFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYFVGERDFRNFCKLDG 257

Query: 163 -CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RTI    +           ++  +FL  Q+R  +  L LVG        + +
Sbjct: 258 SKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLR 317

Query: 221 A 221
            
Sbjct: 318 L 318


>gi|151940762|gb|EDN59149.1| tRNA-pseudouridine synthase [Saccharomyces cerevisiae YJM789]
          Length = 442

 Score =  144 bits (363), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 83/241 (34%), Gaps = 39/241 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK      +++G+I +A+        +  +       GRTD G
Sbjct: 94  IALRFAYLGWNYNGLAVQKEYTPLPTVEGTILEAMNKCKLVPSMVLQDYKFSRCGRTDKG 153

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++             N              + D I I  +       F A
Sbjct: 154 VSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLRPPPNFDA 213

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS + R Y Y I   +               +L+ E M  AA + VG  DF  F  +  
Sbjct: 214 RFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYFVGERDFRNFCKLDG 257

Query: 163 -CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RTI    +           ++  +FL  Q+R  +  L LVG        + +
Sbjct: 258 SKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLR 317

Query: 221 A 221
            
Sbjct: 318 L 318


>gi|297742024|emb|CBI33811.3| unnamed protein product [Vitis vinifera]
          Length = 402

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 64/286 (22%), Positives = 107/286 (37%), Gaps = 47/286 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-------------VHGAGR 50
           + +++ Y+G+ + GWQ+Q   +++QG +E ++     E                V  AGR
Sbjct: 110 FKIVLSYHGASFDGWQKQPGLNTVQGLVEASLGRFVDERKAQQLKEKNLPVEGMVTVAGR 169

Query: 51  TDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GV AL+QV  F   ++ V V  +  A+N        + ++++S V + FH  FSA  
Sbjct: 170 TDKGVTALQQVCSFYTWKKDVKVQDIEDAING--AAPGKLRVISVSEVSRIFHPNFSAKW 227

Query: 110 RSYLYRIITRQAPL--------------ALEKGRAWLIPKSLDCENMRIAAQHLVGR--- 152
           R Y Y                       +  + R    P +     +    + L G+   
Sbjct: 228 RHYFYIFPLNDGDDGEQISENEMDIQKISFNENR--KKPSTFSISRVDQLLRQLEGKLLS 285

Query: 153 -----HDFTTFRSIHC-------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
                 D    R+I          A +    +   D      ++ I +VA  FL   +R 
Sbjct: 286 YKIFARDTKASRNIGPPTECFVFHARATEARLQFSDDGEGTKVMCIELVANRFLRKMVRV 345

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            V +             L K + A  R+   P APP+GL    V +
Sbjct: 346 LVATSIREAAAGAEQDALLKLMDATCRRATAPPAPPDGLCLIDVGF 391


>gi|156537085|ref|XP_001602396.1| PREDICTED: similar to pseudouridylate synthase [Nasonia
           vitripennis]
          Length = 421

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 89/246 (36%), Gaps = 44/246 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q++  S+I+  +  A+       + E    H  GRTD GV A 
Sbjct: 73  IFLKFYYLGWDYQGFAAQEDTTSTIEYYLFAALTKSCLIESRETSNYHRCGRTDKGVSAF 132

Query: 59  RQVAHFDLVREWVPVI---------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
            QV   D+     P            CK LN  L     I   + S    +  ARF    
Sbjct: 133 SQVISLDIRSRLEPEKQDNLSDELHYCKMLNRLL--PKNIRCFSWSPAHPEMSARFDCKF 190

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASS 167
           RSY Y                +    +L+ E M  AA+  VG HDF     +       +
Sbjct: 191 RSYKY----------------FFPRGNLNIEAMDKAAKLTVGSHDFRNLCKMDVANGVVN 234

Query: 168 PIRTIDHFDVN----------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
             R I +  V           S  ++ E+ + + +FL  QIR  +G L LVG  +     
Sbjct: 235 FFRNIVNAQVTCIKREDPEKISGYDMCELSIKSNAFLWHQIRCIMGILLLVGREQEKPEV 294

Query: 218 LEKALQ 223
           +   L 
Sbjct: 295 ITDLLD 300


>gi|259146190|emb|CAY79449.1| Deg1p [Saccharomyces cerevisiae EC1118]
          Length = 442

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 83/241 (34%), Gaps = 39/241 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK      +++G+I +A+        +  +       GRTD G
Sbjct: 94  IALRFAYLGWNYNGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQNYKFSRCGRTDKG 153

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++             N              + D I I  +       F A
Sbjct: 154 VSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLRPPPNFDA 213

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS + R Y Y I   +               +L+ E M  AA + VG  DF  F  +  
Sbjct: 214 RFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYFVGERDFRNFCKLDG 257

Query: 163 -CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RTI    +           ++  +FL  Q+R  +  L LVG        + +
Sbjct: 258 SKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLR 317

Query: 221 A 221
            
Sbjct: 318 L 318


>gi|307177137|gb|EFN66370.1| tRNA pseudouridine synthase 3 [Camponotus floridanus]
          Length = 345

 Score =  143 bits (361), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 63/271 (23%), Positives = 99/271 (36%), Gaps = 45/271 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q+ N  +I+  +  A+       + E    H  GRTD GV + 
Sbjct: 19  ILLKFYYLGWDYHGFTVQEDNNDTIEHHLFTALLKSCCIESRESANYHRCGRTDKGVSSF 78

Query: 59  RQVAHFDLVREWVPVI---------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
            QV   D+     P            CK LN  L     I  +    V   F ARF    
Sbjct: 79  SQVISLDIRSRLEPENQHNLSEELPYCKILNRLL--PTNIRCIAWCPVSPNFSARFDCKY 136

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASS 167
           R+Y Y                +    +LD + M  + ++ +G HDF     +       +
Sbjct: 137 RTYKY----------------FFPKSNLDIDAMDKSVKYAIGDHDFRNICKMDVANGVIN 180

Query: 168 PIRTIDHFDVN---------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
             RT+    V+         +  N+ E+ + +++FL  QIR  +G L LVG  K     +
Sbjct: 181 FKRTVIDAKVSMSNQNVEKITGYNMCELEITSQAFLWHQIRCLMGILLLVGQRKEEPEII 240

Query: 219 EKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            K L  +   +K    +A    L     +Y 
Sbjct: 241 LKLLNIETCPQKPQYNMAHEVPLNLWYCDYE 271


>gi|325115883|emb|CBZ51437.1| hypothetical protein NCLIV_012350 [Neospora caninum Liverpool]
          Length = 475

 Score =  143 bits (361), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 82/229 (35%), Gaps = 38/229 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + + + Y+GS Y G   Q       +++G++  A+        ++          +A + 
Sbjct: 89  FLLKLAYDGSAYSGIAYQGENSAVRTVEGALFDALEK----TCLI-------RDRNAWQP 137

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                    +    +  A+     +   I I+  + V   F ARF    R Y Y      
Sbjct: 138 AKRLFPEENYDYAAVLNAV-----LPGDIRIVASAPVPPGFDARFDCTGRVYKY------ 186

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS 179
                     +   + LD   M  AAQ  VG H+F  F  +   Q  +P RT+  F +  
Sbjct: 187 ----------FFHSEGLDLPRMHRAAQRFVGEHNFRYFCKLDPRQYRNPRRTLTSFAIEP 236

Query: 180 FGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
            G+       +  RSFL  Q+R  + +L  VG G      +   L   +
Sbjct: 237 VGDSACAVATIAGRSFLWHQVRFMMAALLKVGRGTCDEAYIVGLLNRGE 285


>gi|126459314|ref|YP_001055592.1| tRNA pseudouridine synthase ACD [Pyrobaculum calidifontis JCM
           11548]
 gi|166228753|sp|A3MU09|TRUA_PYRCJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|126249035|gb|ABO08126.1| Pseudouridylate synthase [Pyrobaculum calidifontis JCM 11548]
          Length = 257

 Score =  143 bits (361), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 94/248 (37%), Gaps = 36/248 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y   + Y+G+ + G+    N       +E A+  V G   ++    RTD GV A+  
Sbjct: 1   MP-YLYRVAYDGALFHGFTGHSNS------VEAALRRVFGH--LLGRGSRTDPGVSAVGN 51

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                         +   L         +    ++ V + F+ R +  R  YLY      
Sbjct: 52  AVL--APSRLPLGYINSRL------PRGVWTWAVAEVGEGFNPRRARRR-RYLYVAP--- 99

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP-IRTIDHFDVNS 179
                            D E MR  A+   G HDF++F     +  +P + T+D   V  
Sbjct: 100 -------------HWGEDVEAMREVAELFKGTHDFSSFIQFRGERGTPPVTTVDEVGVEV 146

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L+ +  V + F + QIR    ++   G G  +   +E+ L+ + R    P AP EGL
Sbjct: 147 AGRLVYLYFVGKGFRNKQIRKMAWAILAAGRGVVSRRYVEELLE-RPRPGAVPSAPAEGL 205

Query: 240 YFDSVEYS 247
               +EY 
Sbjct: 206 ILLDIEYD 213


>gi|46138645|ref|XP_391013.1| hypothetical protein FG10837.1 [Gibberella zeae PH-1]
          Length = 538

 Score =  143 bits (361), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 71/335 (21%), Positives = 96/335 (28%), Gaps = 94/335 (28%)

Query: 2   IRY-CMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFL-----------VTGEIVVVHG 47
            RY  + + Y G  Y G++ Q   N  SI+  +  A+             V  +      
Sbjct: 60  TRYIALKLAYLGKNYGGFEFQAMANAPSIEEELWNALTKACLIFPEDERIVDFDCCEYSK 119

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKAL---------------NA----------- 81
            GRTD GV A  QV    +          + +               NA           
Sbjct: 120 CGRTDKGVSAFGQVIGLRVRSARPVPKKRRRMSEAGEAMVVDEQSGENAEEEVEDNTPPF 179

Query: 82  -------------YLKISDTISILNLSIV-DKQFHARFSAIRRSYLYRIIT---RQAPLA 124
                           +   I IL         F ARFS   R Y Y          P A
Sbjct: 180 DPIKDELQYPRLLNRVLPPDIRILAWCPSPPPDFSARFSCRERQYRYFFTQPAFTPEPSA 239

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNSFGN 182
                 W     LD E MR AA+   G HDF  F  I    Q ++  RTI   D+    +
Sbjct: 240 GGARNGW-----LDIEAMRDAAKRYEGDHDFRNFCKIDPGKQITNFERTIYEADIEEVQD 294

Query: 183 ----------------------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
                                       +   +V   +FL  QIR  V  L L G    T
Sbjct: 295 VSSALPYLSSPQFAPAEGLPTDDAKYPKVYCFKVRGSAFLWHQIRHMVAVLFLAGQRLET 354

Query: 215 STDLEKALQ-AQDR-KECGPLAPPEGLYFDSVEYS 247
              +   L  A++  K    +A    L      + 
Sbjct: 355 PDVVTTMLDVAKNPCKPNYVMADEVPLVLWDCIFP 389


>gi|169854752|ref|XP_001834048.1| pseudouridine synthase [Coprinopsis cinerea okayama7#130]
 gi|116504845|gb|EAU87740.1| pseudouridine synthase [Coprinopsis cinerea okayama7#130]
          Length = 511

 Score =  143 bits (361), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 62/332 (18%), Positives = 95/332 (28%), Gaps = 102/332 (30%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVT-------GEIVVVHGAGRT 51
            +  +   Y G  Y G   Q +     +++G +  A+            E       GRT
Sbjct: 58  RKIALKFSYAGWDYGGLAYQPDDTPLPTVEGVLFDALSTAHLVDSNAGLEGCGWERCGRT 117

Query: 52  DSGVHALRQVAHFDL-----------------VREWVPVILCKALNAYLKISD------- 87
           D GV   RQ+    +                    + P     A++    + +       
Sbjct: 118 DRGVSGARQIVSVWVRSALRKEELAEADIRPGPVAFPPNSRRAAMDDDDDLPERVDDEPV 177

Query: 88  ---------------------------------TISILNLSIVDKQFHARFSAIRRSYLY 114
                                            TI +   S V   F ARFS   R Y Y
Sbjct: 178 IVNGQDLWKPDTVEPQSRNEHDYVSILNRLLPETIRVSAWSPVPSTFSARFSCNFRHYKY 237

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTI 172
                           +  PK LD   M+ AA  L+G HDF     +    Q +S  R +
Sbjct: 238 ----------------FFTPKGLDIVRMQEAAGRLIGEHDFRNLCKLDPAKQITSFKRKV 281

Query: 173 DHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ------ 225
               +     NL    +   +FL+ Q+R  +  L L+G G  + + +   L         
Sbjct: 282 MSAHIERLNDNLHVFNLTGSAFLYHQVRHIMAILFLIGMGMESPSLVSNLLNVTSDSEVP 341

Query: 226 ----------DRKECGPLAPPEGLYFDSVEYS 247
                     DRK    +A    L      Y 
Sbjct: 342 RADDLPYEIVDRKPEYQMADGLPLMLWDCGYP 373


>gi|296005181|ref|XP_001351959.2| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|225631808|emb|CAD51770.2| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 312

 Score =  143 bits (360), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 52/221 (23%), Positives = 93/221 (42%), Gaps = 25/221 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFL---VTGEIVVVHGAGRTDSGVHAL 58
            + +++ Y G  + G   QK N ++++  + + ++    +      +    RTD GV A 
Sbjct: 6   NFLILLSYFGMEFNGSAYQKDNDNTVENKLLENLYKLELIDNYDTPLSRVSRTDKGVSAR 65

Query: 59  RQVAHFDLVREWVPVILCK----ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
               +  L  ++  V + +     +    K    I I ++  V   F AR + I+R+Y+Y
Sbjct: 66  INGINLRLNIKYENVPIFEIEKKYVKELKKKLKNIHIHDIKHVSNTFDARLNCIQRTYVY 125

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
             I                 K+ + E M+ AA+  +G HDF+         +S  RT+  
Sbjct: 126 FFIN----------------KNYNIEKMKKAAKLFIGEHDFSNCCKKGKNVTSNRRTVLK 169

Query: 175 FDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           FD+ +   +    ++   SFL+ QIR  V  L LVG G   
Sbjct: 170 FDIRNIDKHFYYFKIKGISFLYNQIRHMVAILFLVGKGLLD 210


>gi|221054442|ref|XP_002258360.1| tRNA pseudouridine synthase [Plasmodium knowlesi strain H]
 gi|193808429|emb|CAQ39132.1| tRNA pseudouridine synthase, putative [Plasmodium knowlesi strain
           H]
          Length = 306

 Score =  143 bits (360), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 61/253 (24%), Positives = 100/253 (39%), Gaps = 32/253 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIF---LVTGEIVVVHGAGRTDSGVHAL 58
           ++ +   Y G G+ G   QK N ++++  +   +    L++G         RTD GV A 
Sbjct: 6   KFIIFFSYVGMGFNGSAYQKDNPNTVENRLMDCLHDMNLISGVDQPFSRVSRTDKGVSAR 65

Query: 59  RQVAHFDLVREWVPVIL-------CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
                  L      + L        K +N  L     + ++++  V   F AR + I R+
Sbjct: 66  MNALTIRLKIRHPHMTLQDIQRVYVKEINKKL---KNMQVIDIRSVPNFFDARLNCIHRT 122

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           YLY                + I K+ + + ++   +  VG HDF+ F      ++   RT
Sbjct: 123 YLY----------------FFIDKNYNFDRIKQGCKLFVGEHDFSNFCKKRKNSTCFRRT 166

Query: 172 IDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA-QDRKE 229
           I  F+V     N    ++   SFL+ QIR  V +L  VG G     DL   L      K+
Sbjct: 167 ILKFEVRRMDKNFHYFKIKGTSFLYNQIRHMVAALFQVGTGNLALGDLANMLNNHPSSKK 226

Query: 230 CGPLAPPEGLYFD 242
              +A  +GL   
Sbjct: 227 NFQIANEDGLLLY 239


>gi|294656526|ref|XP_458796.2| DEHA2D07722p [Debaryomyces hansenii CBS767]
 gi|199431537|emb|CAG86940.2| DEHA2D07722p [Debaryomyces hansenii]
          Length = 444

 Score =  143 bits (360), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 79/241 (32%), Gaps = 39/241 (16%)

Query: 4   YCMIIEYNGSGYFG--WQRQKN-GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G  +Q +     +++  I KA+        V          GRTD G
Sbjct: 86  IALRFAYVGWDYNGLNFQYEPTPLPTVEEEILKALAKSKLITQVDPACCNFSRCGRTDKG 145

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   D+    +P     + N              +   I I  +      +F A
Sbjct: 146 VSAMNQVISLDVRSNLIPEDQLSSSNDDKELPYLAILNSLLPTDIRITAVCLRPPPKFDA 205

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS   R Y Y                      LD + M+  A+   G  DF  F  I  
Sbjct: 206 RFSCSYRHYRYI----------------FRKYDLDLDLMQEGAKRYEGVRDFRNFCKIDG 249

Query: 163 -CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  R +   ++     +     +   +FL  Q+R  +  L  VG      + ++ 
Sbjct: 250 SKQITNYKREVLSANIIHLRDDFYIFDLKGSAFLWHQVRCMMAVLFAVGQKLEAPSIIDD 309

Query: 221 A 221
            
Sbjct: 310 L 310


>gi|195122857|ref|XP_002005927.1| GI20747 [Drosophila mojavensis]
 gi|193910995|gb|EDW09862.1| GI20747 [Drosophila mojavensis]
          Length = 500

 Score =  143 bits (360), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 97/266 (36%), Gaps = 46/266 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             M I Y G  Y G+  Q++   +I+G + +A+              H  GRTD  V A 
Sbjct: 103 VLMKITYFGWDYQGFACQEDSADTIEGYLFRALERTCLIESRATSNYHRCGRTDKEVSAF 162

Query: 59  RQVAHFDLVREWVPVILCK--ALNA--------YLKISDTI-SILNLSIVDKQFHARFSA 107
            QV   +L  +  P    K  +LN            +   I  +  + + +  + ARF  
Sbjct: 163 CQVISINLRSKHSPDTQMKPESLNTEIDYCSLLNRVLPKNIQCVSWMPLRNPDYSARFDC 222

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHCQA 165
           I R+Y Y                +     LD ++M+ A Q LV   DF  F    +H   
Sbjct: 223 ISRTYRY----------------YFPKGDLDIDSMQQACQLLVCHGDFRNFCKMDVHNGV 266

Query: 166 SSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           ++ +R + H ++    N            +  + + A +FL  QIR  +  L LVG    
Sbjct: 267 TNYMRNLQHAEIRPCDNTERQLEQNSGYIMYYLEIKANAFLWHQIRCIMAVLLLVGQKNE 326

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGL 239
             + + K L            P  GL
Sbjct: 327 QPSIITKLLDVGSNPCKPQYTPAIGL 352


>gi|219122763|ref|XP_002181709.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406985|gb|EEC46923.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 421

 Score =  142 bits (359), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 67/340 (19%), Positives = 104/340 (30%), Gaps = 97/340 (28%)

Query: 5   CMIIEYNGSGYFGW-------QRQKNG-----------------------SSIQGSIEKA 34
            + + Y+G  ++GW        R+ N                         S+QG I+  
Sbjct: 72  LLHVSYDGRQFYGWSSGNDPKDRESNAARPRYSTRSRRRRRNRGNYDGTVRSVQGEIQYC 131

Query: 35  IFLVTG----EIVVVHGAGRTDSGVHALRQVAHFDL-------------VREWVPVILCK 77
           +  V G    + VVV G  RTD GVHA   +A                            
Sbjct: 132 LSKVYGNIDPQRVVVEGCSRTDKGVHARGMMAQIYCLHETTSPNDDPVVDWSIPGKRQPH 191

Query: 78  ALNA--------------------YLKISDTISILNLSIVDKQ-------------FHAR 104
             NA                       +   ISI+ ++                  FH  
Sbjct: 192 PRNATDTSYFTQLPMNLTKLAFTLNRMLPHDISIMGIAPTPHPHVTGCNPAISALPFHPT 251

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFRSI 161
            S   ++Y Y +         ++   W + +++     +    A Q L G H+F  F+  
Sbjct: 252 LSCRHKTYRYVVSVGTRADPTKRLYVWHLDRAISTFSLDQAEQACQILQGSHNFAAFQGA 311

Query: 162 HCQASSPIR-------------TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
              + + I+              I H           + V    FL+  IR  VG++  V
Sbjct: 312 PRGSDNKIKFTMRNTTCQLISIRIQHQSTWLDTETYVVSVTGDRFLYKMIRFLVGTVVGV 371

Query: 209 GDGKWTSTDLEKALQAQDRKE-CGPLAPPEGLYFDSVEYS 247
           G GK T  ++   L  Q R       APP  L  + VEY 
Sbjct: 372 GTGKLTLDNVAAMLLTQSRNNLQVECAPPHALVLEHVEYD 411


>gi|303288890|ref|XP_003063733.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454801|gb|EEH52106.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 313

 Score =  142 bits (359), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 66/263 (25%), Positives = 100/263 (38%), Gaps = 23/263 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            +  + + Y G GY G QR     +I+  +EKAI    G           V    A RTD
Sbjct: 2   RKVAIFLAYVGKGYQGMQRNPGAVTIEDELEKAIVAAGGISDLNAGDFAKVQWMRAARTD 61

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ Q     +V    P  +   +NA L   +         V   F+A+    RR Y
Sbjct: 62  KGVSAVGQCVSLRMV--IDPPGVIDRVNAAL--PEGFEFFGYERVTGGFNAKTMCDRRRY 117

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDC---ENMRIAAQHLVGRHDFTTFR-SIHCQASSP 168
            Y +  +      +       P   D    + +     + VG H+F  F   +     S 
Sbjct: 118 EYVVPVKAFDPRAKNSDDASPPFEFDETMRQRVNKILGNYVGTHNFHNFTVRVSPDEPSA 177

Query: 169 IRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R I  FD ++         +   VV +SF+  QIR  +G +  V  G W+  D   AL 
Sbjct: 178 MRYIISFDCSAPFVVDGVAFVRCVVVGQSFMLHQIRKLIGMMLGVIRGAWSEEDQLFALN 237

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
            ++     P+AP  GL+     Y
Sbjct: 238 TKE-SVNVPMAPELGLFLCECIY 259


>gi|323337774|gb|EGA79017.1| Deg1p [Saccharomyces cerevisiae Vin13]
          Length = 442

 Score =  142 bits (358), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 83/241 (34%), Gaps = 39/241 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL------VTGEIVVVHGAGRTDSG 54
             +   Y G  Y G   QK      +++G+I +A+        +  +       GRTD G
Sbjct: 94  IALRFAYLGWNYNGLAVQKEFTPLPTVEGTILEAMNKCKLVPSMVLQBYKFSRCGRTDKG 153

Query: 55  VHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTISILNLS-IVDKQFHA 103
           V A+ QV   ++             N              + D I I  +       F A
Sbjct: 154 VSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIRISAVCLRPPPNFDA 213

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH- 162
           RFS + R Y Y I   +               +L+ E M  AA + VG  DF  F  +  
Sbjct: 214 RFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYFVGERDFRNFCKLDG 257

Query: 163 -CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             Q ++  RTI    +           ++  +FL  Q+R  +  L LVG        + +
Sbjct: 258 SKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILFLVGQSLEVPEIVLR 317

Query: 221 A 221
            
Sbjct: 318 L 318


>gi|294461715|gb|ADE76416.1| unknown [Picea sitchensis]
          Length = 448

 Score =  142 bits (358), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 69/315 (21%), Positives = 113/315 (35%), Gaps = 74/315 (23%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-------------VVVHGAGR 50
           + +++ Y+G+ + GWQ+Q   +++QG +EK++     E                V  AGR
Sbjct: 126 FKIVLSYDGNLFDGWQKQPGMNTVQGLVEKSLGKFVDEKKAQELEAKKASVEAAVAVAGR 185

Query: 51  TDSGVHALRQVAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GV A +QV  F   R +     +   +NA       + ++++S V ++FH  FSA  
Sbjct: 186 TDKGVSAFQQVCSFYTWRKDTSLEDIESEINAAAL--GKLKVVSISEVSREFHPNFSAKW 243

Query: 110 RSYLYRIITRQ----------------------------------------APLALEKGR 129
           R YLY +  +                                            A  K +
Sbjct: 244 RRYLYILPLKDGEGNKTVVDGGSPVTYDSLCLADEGGNQSTDMNVINMEAMNISATGKHQ 303

Query: 130 AWLIPKSLDCENMRIAAQHLVGR--------HDFTTFRSIHCQASSPIRTIDHF------ 175
           A + P + + + +    Q L G+         D    RS        +            
Sbjct: 304 ASVKPHNFNVDTVNQLLQQLEGQSLSYRIFARDTQASRSRGPATECFMHHARAAVATLPY 363

Query: 176 ---DVNSFGNLI-EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
              D  S G  +  + +VA  FL   +R  V +         T  +L K + A  R+   
Sbjct: 364 MGQDHTSKGRTVMCVELVANRFLRKMVRVLVATAVREAAAGATPDNLLKLMHATCRRASA 423

Query: 232 PLAPPEGLYFDSVEY 246
           P APPEGL    + Y
Sbjct: 424 PPAPPEGLCLVDIGY 438


>gi|134114618|ref|XP_774017.1| hypothetical protein CNBH0640 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50256647|gb|EAL19370.1| hypothetical protein CNBH0640 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 514

 Score =  142 bits (358), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 64/321 (19%), Positives = 96/321 (29%), Gaps = 90/321 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQ-------KNGSSIQGSIEKAIFLV-------TGEIVVVHGAG 49
             ++I Y+G  Y G   Q           +++  +  A+            E       G
Sbjct: 75  IALLISYHGWPYSGLALQAPATPDGPPVPTVEAELLAALEKTRLIAEGKGWEGCGFGRCG 134

Query: 50  RTDSGVHALRQVAHFDL------------------------------------------- 66
           RTD GV    QV +  +                                           
Sbjct: 135 RTDRGVSGEGQVVNLWVRSSRKRGDGGGELGDGWRDAVEPEVEKMEKTVIVQEDEEKGVK 194

Query: 67  ---------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
                     R+       K LN+ L    +I IL  S +   F +RFS   R Y Y   
Sbjct: 195 EKKSKVIQPPRQPSEFPYPKLLNSVL--PPSIRILAWSPIPASFDSRFSCTYRHYRYAFH 252

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTIDHF 175
           TR  P + E          LD E MR  AQ L+G HD+  F  +    Q  +  R +   
Sbjct: 253 TRPTPTSPE----------LDLELMRQGAQLLLGEHDYRNFCKLDGSKQIENHTRGVLKA 302

Query: 176 DVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                        ++   ++  +FL  Q+R  +  L LVG      + +   L  + R  
Sbjct: 303 WFEGGESQGVGDGMMVFNLIGTAFLWHQVRHIIAVLFLVGAKLEPPSIVSDLLDVK-RFP 361

Query: 230 CGP---LAPPEGLYFDSVEYS 247
             P   +  P  L      Y 
Sbjct: 362 SKPNYTMGHPLPLTLHHCGYP 382


>gi|328876653|gb|EGG25016.1| tRNA pseudouridylate synthase [Dictyostelium fasciculatum]
          Length = 542

 Score =  142 bits (358), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 59/275 (21%), Positives = 103/275 (37%), Gaps = 33/275 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           +    + Y+G+ Y G Q+    S+I+  +EKA F           +   +      RTD 
Sbjct: 117 KIAFCVGYSGTNYCGMQKNWGYSTIEEELEKACFKTGSISPNNFYSQRKIDWIRCARTDK 176

Query: 54  GVHALRQVAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A+R +    L  +      L  A+N++L   + I +  +  V+  FHA+     RSY
Sbjct: 177 GVSAVRNMVSCKLEYDPPTLEELKNAINSHL--PEDIKVFGIKRVNNSFHAKNCVDGRSY 234

Query: 113 LYRIITRQAPLALE---KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSP 168
           LY   T           +   +   ++ +   +       +G H F  + S       S 
Sbjct: 235 LYITPTFAFEPVHATSGRPETYKFDET-ERSRVNSMLAMFLGTHKFHNYTSRKDSGDPSA 293

Query: 169 IRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGD---------GKWT 214
            RT+  F  +          + I ++  SF+  QIR  +G +  V              +
Sbjct: 294 KRTMSLFQCSEPFVMEGIEFVSINIIGGSFMLHQIRKMIGFVMSVMRRGFFWEKNNDTES 353

Query: 215 STDLEKALQA--QDRKECGPLAPPEGLYFDSVEYS 247
              + K + A    R+   P+AP  GL  D+  + 
Sbjct: 354 LDYVRKIITATLCHRQFNLPMAPGTGLMLDACLFD 388


>gi|302023348|ref|ZP_07248559.1| tRNA pseudouridine synthase A [Streptococcus suis 05HAS68]
          Length = 124

 Score =  141 bits (357), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 36/123 (29%), Positives = 55/123 (44%), Gaps = 2/123 (1%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF--DVNSFGNLI 184
           +  A   P  LD   +  A Q LVG HDFT F +        +RTI     + +     +
Sbjct: 1   RHYATFYPYDLDLSLIEEAIQDLVGTHDFTGFTASGTSVEDKVRTIKAASMEYDQRRQFL 60

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
                   FL+ Q+R+ VG+L  +G+G+     +++ L  +DR   GP A   GLY   +
Sbjct: 61  IFTFSGNGFLYKQVRNMVGTLLKIGNGRMPVGQIKRILAEKDRSLAGPTAAGNGLYLKEI 120

Query: 245 EYS 247
            Y 
Sbjct: 121 IYE 123


>gi|70166599|ref|NP_001002019.1| tRNA pseudouridine synthase A, mitochondrial isoform 2 [Homo
           sapiens]
 gi|70166634|ref|NP_001002020.1| tRNA pseudouridine synthase A, mitochondrial isoform 2 [Homo
           sapiens]
 gi|12804097|gb|AAH02901.1| Pseudouridylate synthase 1 [Homo sapiens]
 gi|123989720|gb|ABM83888.1| pseudouridylate synthase 1 [synthetic construct]
 gi|123999259|gb|ABM87208.1| pseudouridylate synthase 1 [synthetic construct]
 gi|158257916|dbj|BAF84931.1| unnamed protein product [Homo sapiens]
 gi|311347139|gb|ADP90495.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347142|gb|ADP90497.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347145|gb|ADP90499.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347148|gb|ADP90501.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347151|gb|ADP90503.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347154|gb|ADP90505.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347157|gb|ADP90507.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347160|gb|ADP90509.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347163|gb|ADP90511.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347166|gb|ADP90513.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347169|gb|ADP90515.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347172|gb|ADP90517.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347175|gb|ADP90519.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347178|gb|ADP90521.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347181|gb|ADP90523.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347184|gb|ADP90525.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347187|gb|ADP90527.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347190|gb|ADP90529.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347193|gb|ADP90531.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347196|gb|ADP90533.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347199|gb|ADP90535.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347202|gb|ADP90537.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347205|gb|ADP90539.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347208|gb|ADP90541.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347211|gb|ADP90543.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347214|gb|ADP90545.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347217|gb|ADP90547.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347220|gb|ADP90549.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347223|gb|ADP90551.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347226|gb|ADP90553.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347229|gb|ADP90555.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347232|gb|ADP90557.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347235|gb|ADP90559.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347238|gb|ADP90561.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347241|gb|ADP90563.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347244|gb|ADP90565.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347247|gb|ADP90567.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347250|gb|ADP90569.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347253|gb|ADP90571.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347256|gb|ADP90573.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
          Length = 399

 Score =  141 bits (357), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 56  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 115

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 116 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 170

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 171 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQD 228

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 229 PSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 288

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 289 SW--GTEKVDVPKAPGLGLVLERVHFE 313


>gi|114647862|ref|XP_001139560.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial [Pan
           troglodytes]
          Length = 427

 Score =  141 bits (357), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 84  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 143

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 144 RTDKGVSAAGQVVSL---KVWLIEDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 198

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 199 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQD 256

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 257 PSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 316

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 317 SW--GTEKVDVPKAPGLGLVLERVHFE 341


>gi|58271292|ref|XP_572802.1| pseudouridylate synthase [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57229061|gb|AAW45495.1| pseudouridylate synthase, putative [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 514

 Score =  141 bits (357), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 64/321 (19%), Positives = 96/321 (29%), Gaps = 90/321 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQ-------KNGSSIQGSIEKAIFLV-------TGEIVVVHGAG 49
             ++I Y+G  Y G   Q           +++  +  A+            E       G
Sbjct: 75  IALLISYHGWPYSGLALQAPATPDGPPVPTVEAELLAALEKTRLIAEGKGWEGCGFGRCG 134

Query: 50  RTDSGVHALRQVAHFDL------------------------------------------- 66
           RTD GV    QV +  +                                           
Sbjct: 135 RTDRGVSGEGQVVNLWVRSSRKRGDGGGELGDGWRDAVEPEVEKMEKTVIVQEDEEKGVK 194

Query: 67  ---------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
                     R+       K LN+ L    +I IL  S +   F +RFS   R Y Y   
Sbjct: 195 EKKSKVIQPPRQPSEFPYPKLLNSVL--PPSIRILAWSPIPASFDSRFSCTYRHYRYAFH 252

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTIDHF 175
           TR  P + E          LD E MR  AQ L+G HD+  F  +    Q  +  R +   
Sbjct: 253 TRPTPTSPE----------LDLELMRQGAQLLLGEHDYRNFCKLDGSKQIENHTRGVLKA 302

Query: 176 DVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                        ++   ++  +FL  Q+R  +  L LVG      + +   L  + R  
Sbjct: 303 WFEGGKSQGVGDGMMVFNLIGTAFLWHQVRHIIAVLFLVGAKLEPPSIVSDLLDVK-RFP 361

Query: 230 CGP---LAPPEGLYFDSVEYS 247
             P   +  P  L      Y 
Sbjct: 362 SKPNYTMGHPLPLTLHHCGYP 382


>gi|324501041|gb|ADY40469.1| tRNA pseudouridine synthase tag-124 [Ascaris suum]
 gi|324504466|gb|ADY41930.1| tRNA pseudouridine synthase tag-124 [Ascaris suum]
          Length = 388

 Score =  141 bits (357), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 68/288 (23%), Positives = 101/288 (35%), Gaps = 69/288 (23%)

Query: 10  YNGSGYFGW-QRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHALRQVA-- 62
           Y G  Y G  Q+Q   ++++  I+ A+       +        +GRTD GV A RQ+A  
Sbjct: 4   YYGWEYEGLVQQQDTVNTVEEVIKDALLRTRLIESWNKCEWIRSGRTDKGVSAFRQIASL 63

Query: 63  ----------HFDLVREWVPVI----------LCKALNAYLKISDTISILNLSIVDKQFH 102
                     H        P              K LN  L     I +L  + V   F+
Sbjct: 64  IVRSSDPEGEHVFWPENADPHSRITPPHSELMYLKMLNGVL--PKNIRVLAWAPVALDFN 121

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           ARFS  +R Y Y         A  +G         D E +R A   L+G HDF     I 
Sbjct: 122 ARFSCTKRVYKY---------AFPRG-------DFDLEAIRKACSLLIGEHDFRNICRID 165

Query: 163 CQAS----SPIRTI------------DHFDVNSFGN------LIEIRVVARSFLHTQIRS 200
              +    S +R +            +  +V+S         L+E  +++  FL  QIR 
Sbjct: 166 LNKARVEMSYVRMVFDASISVVLESGERVEVSSEPEPHSPYSLVEFTMISSGFLWHQIRC 225

Query: 201 FVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEY 246
            +  +  +G G      + + L  +   RK    LAP   L      Y
Sbjct: 226 VMALMYEIGKGNEKPEVISELLDIEKTPRKPAYGLAPSSPLCLFDCSY 273


>gi|307184937|gb|EFN71202.1| tRNA pseudouridine synthase A [Camponotus floridanus]
          Length = 330

 Score =  141 bits (357), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 100/287 (34%), Gaps = 50/287 (17%)

Query: 1   MIRYC-----MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVH 46
           M +       +++ Y G  Y+G QR     +I+  +  A+                +   
Sbjct: 40  MQKIKRKNHAILLGYLGKDYYGMQRNPGMKTIEEDLVTALLKADLITTEHFKNIRSISFQ 99

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
            A RTD GV A+RQ+    L  +    ++ K L       D I I  +  V K F+++  
Sbjct: 100 RAARTDKGVSAIRQIVSLKLPEKPDKTVINKFL------PDVIKIFGIKRVTKGFNSKNQ 153

Query: 107 AIRRSYLYRIIT---RQAPLALEK------------------GRAWLIPK--SLDCENMR 143
              R+Y Y I T       L L K                  G++++  +        + 
Sbjct: 154 CDARTYRYIIPTFAFAPEDLTLLKIGEEINEEERIKQLSTIDGKSYVDYRLSPESLNRLN 213

Query: 144 IAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQ 197
              + + G H+F  F   +        R I  F               + +  +SF+  Q
Sbjct: 214 SILKLMEGTHNFHNFTSKVKPLDPRAQRYIIKFHCVETFISNGMEFAILEIKGQSFMLHQ 273

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           IR  V  +  +     +   + +A +  DR E  P+AP  GL    V
Sbjct: 274 IRKMVAVVVGIARNIISEEIINEAFKTMDRLEI-PIAPSLGLCLCHV 319


>gi|70166645|ref|NP_079491.2| tRNA pseudouridine synthase A, mitochondrial isoform 1 [Homo
           sapiens]
 gi|114152895|sp|Q9Y606|TRUA_HUMAN RecName: Full=tRNA pseudouridine synthase A, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase I; AltName:
           Full=tRNA-uridine isomerase I; Flags: Precursor
 gi|18027830|gb|AAL55876.1|AF318369_1 unknown [Homo sapiens]
 gi|94466373|gb|AAH09505.2| Pseudouridylate synthase 1 [Homo sapiens]
 gi|94466377|gb|AAH19320.2| Pseudouridylate synthase 1 [Homo sapiens]
 gi|193786660|dbj|BAG51983.1| unnamed protein product [Homo sapiens]
 gi|261860288|dbj|BAI46666.1| pseudouridylate synthase 1 [synthetic construct]
 gi|311347138|gb|ADP90494.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347141|gb|ADP90496.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347144|gb|ADP90498.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347147|gb|ADP90500.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347150|gb|ADP90502.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347153|gb|ADP90504.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347156|gb|ADP90506.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347159|gb|ADP90508.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347162|gb|ADP90510.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347165|gb|ADP90512.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347168|gb|ADP90514.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347171|gb|ADP90516.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347174|gb|ADP90518.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347177|gb|ADP90520.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347180|gb|ADP90522.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347183|gb|ADP90524.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347186|gb|ADP90526.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347189|gb|ADP90528.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347192|gb|ADP90530.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347195|gb|ADP90532.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347198|gb|ADP90534.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347201|gb|ADP90536.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347204|gb|ADP90538.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347207|gb|ADP90540.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347210|gb|ADP90542.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347213|gb|ADP90544.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347216|gb|ADP90546.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347219|gb|ADP90548.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347222|gb|ADP90550.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347225|gb|ADP90552.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347228|gb|ADP90554.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347231|gb|ADP90556.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347234|gb|ADP90558.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347237|gb|ADP90560.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347240|gb|ADP90562.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347243|gb|ADP90564.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347246|gb|ADP90566.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347249|gb|ADP90568.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347252|gb|ADP90570.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
 gi|311347255|gb|ADP90572.1| mitochondrial tRNA pseudouridine synthase A [Homo sapiens]
          Length = 427

 Score =  141 bits (357), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 84  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 143

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 144 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 198

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 199 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQD 256

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 257 PSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 316

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 317 SW--GTEKVDVPKAPGLGLVLERVHFE 341


>gi|4455035|gb|AAD21042.1| pseudouridine synthase 1 [Homo sapiens]
          Length = 365

 Score =  141 bits (356), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 22  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 81

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 82  RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 136

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 137 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQD 194

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 195 PSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 254

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 255 SW--GTEKVDVPKAPGLGLVLERVHFE 279


>gi|119618938|gb|EAW98532.1| pseudouridylate synthase 1, isoform CRA_c [Homo sapiens]
          Length = 432

 Score =  141 bits (356), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 89  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 148

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 149 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 203

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 204 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQD 261

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 262 PSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 321

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 322 SW--GTEKVDVPKAPGLGLVLERVHFE 346


>gi|73994983|ref|XP_852307.1| PREDICTED: similar to tRNA pseudouridine synthase A (tRNA-uridine
           isomerase I) (tRNA pseudouridylate synthase I) [Canis
           familiaris]
          Length = 409

 Score =  141 bits (356), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 64/267 (23%), Positives = 101/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 61  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVQSGCIPENHGEDMRKMSFQRCA 120

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 121 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PPHIRILGLKRVTGGFNSKNKCDA 175

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 176 RTYFYMLPT--FAFAHKDHDVQDESYRLSAETLQRVNGLLACYKGTHNFHNFTSQKGPQE 233

Query: 166 SSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +S  R I     +   V        I+V  +SF+  QIR  VG L  +  G    + LE+
Sbjct: 234 ASARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLLVAIVKGYAPESVLER 293

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    D K   P AP  GL  + V + 
Sbjct: 294 SW--GDAKVDVPKAPGLGLVLERVHFE 318


>gi|195055095|ref|XP_001994456.1| GH16145 [Drosophila grimshawi]
 gi|193892219|gb|EDV91085.1| GH16145 [Drosophila grimshawi]
          Length = 395

 Score =  141 bits (356), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 67/263 (25%), Positives = 103/263 (39%), Gaps = 28/263 (10%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 61  AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHNWITEDSFKQVQIASFQRAARTDKGV 120

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E   V   K L       +TI +  +  V K F+A+     R+Y Y 
Sbjct: 121 SAARQVCSIKLPDELDLVAFNKDL------PETIRLFGVERVTKGFNAKEQCNARTYTYT 174

Query: 116 IITRQAPLALE----KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIR 170
           + +       E    + +A         E +    +   G  +F  F S       S  R
Sbjct: 175 LPSIAFAGCNEQQNQQDQATFRLTPALHEQICETLKLYEGTKNFHNFTSKKNFLDPSAKR 234

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            I  F  ++          + ++V  +SF+  QIR  VG    +  G  T   LE+AL  
Sbjct: 235 FIMSFTSSAPFHSPQGIEFVTLQVKGQSFMLHQIRKMVGLAIAIVRGNTTRITLERALTE 294

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
           +  +   P+AP  GL  D+V Y 
Sbjct: 295 E--RLDLPMAPGLGLVLDTVHYE 315


>gi|323454992|gb|EGB10861.1| hypothetical protein AURANDRAFT_62396 [Aureococcus anophagefferens]
          Length = 321

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 95/256 (37%), Gaps = 29/256 (11%)

Query: 19  QRQKN-GSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREW----VP 72
             Q     ++QG +  A+     G  +   GA RTD+GVHA  Q AH DL          
Sbjct: 66  AVQPGRARTVQGELNAALRTRFGGADIPTLGASRTDAGVHARGQCAHADLPVAPLGGAPL 125

Query: 73  VILCKALNAYLKISDTISILNLSIVDKQ----------FHARFSAIRRSYLYRIITRQ-A 121
            +L   +N  L   D   + +L                +HA  +A  + Y YR+  R+ +
Sbjct: 126 ELLEHQINRLL--PDDARVHDLRPAPAPKPWQAREGLPWHAIANAAGKRYAYRLTARRGS 183

Query: 122 PLALEKGRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRS------IHCQASSPIRTIDH 174
              L +     +  +++D   +  A    VG HDF  F +          A S  R+I  
Sbjct: 184 ADPLGRLYRGHVAYRAVDFGRLDDALACFVGEHDFAAFANNAPGVDPSGAARSTTRSIRS 243

Query: 175 FDV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP- 232
             + +  G    +       L+  +R+ VG+   V DG      +   L    R+   P 
Sbjct: 244 ATLLDEGGGDATLTFELDGALYKMVRNVVGAAVAVADGALPRDAIPALLAPGARRADNPA 303

Query: 233 -LAPPEGLYFDSVEYS 247
             AP  GL  + V Y 
Sbjct: 304 KAAPACGLCLEEVYYD 319


>gi|109099290|ref|XP_001113470.1| PREDICTED: tRNA pseudouridine synthase A-like [Macaca mulatta]
          Length = 483

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 140 RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 199

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 200 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 254

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 255 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQE 312

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 313 PSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 372

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 373 SW--GTEKVDVPKAPGLGLVLERVHFE 397


>gi|307212020|gb|EFN87913.1| tRNA pseudouridine synthase 3 [Harpegnathos saltator]
          Length = 368

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 93/245 (37%), Gaps = 43/245 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q++ + +I+  +  A+       + E    H  GRTD GV + 
Sbjct: 19  ILLKLYYLGWNYDGFTVQEDSNATIEHHLFAALTKSCCIESRETSNYHRCGRTDKGVSSF 78

Query: 59  RQVAHFDLVREWVPVI---------LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
            QV   D+  +  P            CK LN  L     I  +    +   F ARF    
Sbjct: 79  CQVISLDIRSKLEPEQQSNLSKELPYCKILNKLL--PTNIRCIAWCPISSDFSARFDCKY 136

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASS 167
           R Y Y                +    +LD + M  A ++++G  DF     +      ++
Sbjct: 137 RKYKY----------------FFPRGNLDIDAMDKAVKYVIGEFDFRNICKMDVANGVTN 180

Query: 168 PIRTI---------DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
             R +            D ++  ++ E+ + +++FL  QIR  +G L LVG  +     +
Sbjct: 181 FKRKVIDAKISMNNQAVDKSTGYDICELEITSQAFLWHQIRCLMGILLLVGKKREEPEII 240

Query: 219 EKALQ 223
            K L 
Sbjct: 241 SKLLD 245


>gi|322709808|gb|EFZ01383.1| putative pseudouridine synthase 3 [Metarhizium anisopliae ARSEF 23]
          Length = 564

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 70/340 (20%), Positives = 99/340 (29%), Gaps = 98/340 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVT-----------GEIVVVHGAGR 50
             + + Y G  Y G++ Q   N  SI+  +  A+                +       GR
Sbjct: 81  IALKLAYLGKNYGGFEFQAMGNQPSIEEELWNALTRACLIFPEDERIVQFDCCEYSKCGR 140

Query: 51  TDSGVHALRQVAHFDLVREWVPVI------------------------------------ 74
           TD GV A  QV    +                                            
Sbjct: 141 TDRGVSAFGQVIGLKVRSNRPLPKKRAETDVAAAEDIALADADPQGVKQAEEEVEAQEED 200

Query: 75  -----------LCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIIT---R 119
                        + LN  L   D I IL         F ARFS   R Y Y        
Sbjct: 201 KPFDDIHDELCYPRILNRLL--PDDIRILAWCPSPPPDFSARFSCRERQYRYFFTQPAFA 258

Query: 120 QAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHF 175
             P +L+   A    K+  LD + MR AA+   G HDF  F  I    Q ++  R I   
Sbjct: 259 PDPTSLDLSGASKPLKAGWLDIDAMRDAAKRYEGEHDFRNFCKIDPAKQITNFHRRIFES 318

Query: 176 DVNS--------------------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           D+                            +  +    V   +FL  QIR  V  L LVG
Sbjct: 319 DIVEVQGAGSVMPYLQTPGFSSPGLEGSGPYPKVYYFHVRGSAFLWHQIRHMVAVLFLVG 378

Query: 210 DGKWTSTDLEKALQ-AQDR-KECGPLAPPEGLYFDSVEYS 247
            G  + T + + L  A++  +    +A    L      + 
Sbjct: 379 QGLESPTVISELLDTAKNPGRPSYVMADEVPLVLWDCIFP 418


>gi|315928911|gb|EFV08168.1| tRNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 186

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 43/191 (22%), Positives = 69/191 (36%), Gaps = 6/191 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHS 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D +         VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAY 175

Query: 181 GNLIEIRVVAR 191
            +       A 
Sbjct: 176 KDFSIFHFKAN 186


>gi|164659606|ref|XP_001730927.1| hypothetical protein MGL_1926 [Malassezia globosa CBS 7966]
 gi|159104825|gb|EDP43713.1| hypothetical protein MGL_1926 [Malassezia globosa CBS 7966]
          Length = 604

 Score =  140 bits (354), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/276 (21%), Positives = 93/276 (33%), Gaps = 56/276 (20%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG----SSIQGSIEKAIFLV-------TGEIVVVHGAGR 50
            +  +   Y+G  Y G   Q        +++ +I +A+          + + V     GR
Sbjct: 80  RKIALRFCYDGGSYSGLAAQMGQMTPLPTVEETIWEALCTARLVDATKSMDDVDWSRCGR 139

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKA----------------------LNAYLKISDT 88
           TD+GV A  QV    +    V     +                       LN  L    T
Sbjct: 140 TDAGVSAAGQVVALWIRSRCVDERPLRYKTGEAAIPLTDTSDEELPYVATLNRLL--PPT 197

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITR-QAPLALEKGRAWLIPKSLDCENMRIAAQ 147
           I I   S V   F ARF  + R Y Y       + L  +          LD + MR AA 
Sbjct: 198 IRIQAWSPVRPTFSARFDCVYRHYKYFFTLGAPSTLVWQPESLSQFSGRLDLDRMRDAAA 257

Query: 148 HLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNS------------------FGNLIEIR 187
            LVG HDF     +    Q ++  R ID   ++                      +  + 
Sbjct: 258 RLVGEHDFRNMCKVDASKQITNFRRRIDGASIDPVCRGWSDRPIPAPDPHSTDEPMYVLN 317

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +   +FL+ Q+R  +  L +VG      + +++ L 
Sbjct: 318 LRGSAFLYHQVRHIMAVLFMVGARLEDPSIVDELLN 353


>gi|256371245|ref|YP_003109069.1| tRNA pseudouridine synthase [Acidimicrobium ferrooxidans DSM 10331]
 gi|256007829|gb|ACU53396.1| tRNA pseudouridine synthase [Acidimicrobium ferrooxidans DSM 10331]
          Length = 294

 Score =  140 bits (354), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 95/249 (38%), Gaps = 9/249 (3%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             +++ Y+G  + G   Q    ++ G++  A+ LV      +  AGRTD+GVHA  Q+  
Sbjct: 7   LLLVVGYDGREFAGAAPQPGVRTVVGALRSALELVLQRPTSLAIAGRTDAGVHARAQLVS 66

Query: 64  FDL-VREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRII--- 117
             L   E   +   + L   L       + + +  ++     AR  A  R YLYR+    
Sbjct: 67  VPLQPGERARLGDVERLCGRLGRLAGRGLWVRSAGVLPGSVDARRVARWRHYLYRLDLGH 126

Query: 118 -TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             R+  + LE          L+ + +  A   L G  D T             R +    
Sbjct: 127 GDRRGRVILEP--TAWACGPLELDVLAGALATLRGDLDATGLCRAGAAGGYRRRVLSTRV 184

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
                + +++ V+  SF H  +R  VG+   V  G+       + +   +R     +APP
Sbjct: 185 WARARDRVDVSVIGVSFCHEFVRRAVGNAVAVAQGRLDGERWREGVDRGERALLATVAPP 244

Query: 237 EGLYFDSVE 245
            GL    V 
Sbjct: 245 WGLSLWRVG 253


>gi|256087148|ref|XP_002579738.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665217|emb|CAZ35977.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 413

 Score =  140 bits (354), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 103/264 (39%), Gaps = 30/264 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y+G GY+G QR     +I+G + KA+F             + V    A +TD  V
Sbjct: 41  AILLMYSGWGYYGMQRCPVFPTIEGELSKALFTCGQLDNLTSEEHKRVHFQRASKTDKSV 100

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            AL QV    L  +     L   LN  L   + I +L++  V + F +  S   R Y Y 
Sbjct: 101 SALGQVCSMQLKEDTD---LLSKLNNSL--PENIRVLDIIRVTRGFSSYSSCTHRIYDYL 155

Query: 116 IIT---RQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRSIH-CQASSP 168
           + T     A  +L     W     L  E +       +   G H+F  F S       S 
Sbjct: 156 LPTFALSPATSSLNDSTCWTYR--LTVEQITQVNRLLEKYKGTHNFYNFTSGRLVTDRSC 213

Query: 169 IRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            R I   +              IR+  +SF+  QIR  +G    V  G  T   +   + 
Sbjct: 214 SRYIISAECMPTFLLGEHQYTIIRIAGQSFMLHQIRKMIGLALAVLRGYAT-EAVFDIVF 272

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           ++ R +  P AP  GL  + V++S
Sbjct: 273 SKARIDI-PKAPGLGLMLNQVDFS 295


>gi|256087146|ref|XP_002579737.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665216|emb|CAZ35976.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 428

 Score =  140 bits (354), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 103/264 (39%), Gaps = 30/264 (11%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y+G GY+G QR     +I+G + KA+F             + V    A +TD  V
Sbjct: 56  AILLMYSGWGYYGMQRCPVFPTIEGELSKALFTCGQLDNLTSEEHKRVHFQRASKTDKSV 115

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            AL QV    L  +     L   LN  L   + I +L++  V + F +  S   R Y Y 
Sbjct: 116 SALGQVCSMQLKEDTD---LLSKLNNSL--PENIRVLDIIRVTRGFSSYSSCTHRIYDYL 170

Query: 116 IIT---RQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRSIH-CQASSP 168
           + T     A  +L     W     L  E +       +   G H+F  F S       S 
Sbjct: 171 LPTFALSPATSSLNDSTCWTYR--LTVEQITQVNRLLEKYKGTHNFYNFTSGRLVTDRSC 228

Query: 169 IRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            R I   +              IR+  +SF+  QIR  +G    V  G  T   +   + 
Sbjct: 229 SRYIISAECMPTFLLGEHQYTIIRIAGQSFMLHQIRKMIGLALAVLRGYAT-EAVFDIVF 287

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
           ++ R +  P AP  GL  + V++S
Sbjct: 288 SKARIDI-PKAPGLGLMLNQVDFS 310


>gi|321261750|ref|XP_003195594.1| pseudouridylate synthase [Cryptococcus gattii WM276]
 gi|317462068|gb|ADV23807.1| pseudouridylate synthase, putative [Cryptococcus gattii WM276]
          Length = 511

 Score =  139 bits (352), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 62/318 (19%), Positives = 95/318 (29%), Gaps = 87/318 (27%)

Query: 4   YCMIIEYNGSGYFGWQRQ-------KNGSSIQGSIEKAIFLV-------TGEIVVVHGAG 49
             ++I Y+G  Y G   Q           +++  +  A+            E       G
Sbjct: 75  IALLISYHGWPYSGLALQAPATPDGPPVPTVEAELLAALEKTRLIAEGKGWEGCGFGRCG 134

Query: 50  RTDSGVHALRQVAHFDL------------------------------------------- 66
           RTD GV    QV +  +                                           
Sbjct: 135 RTDRGVSGEGQVINLWVRSSRRRDDGGGELGDGWRDAAEPEVEKPVVVQEDGEAKGQEKK 194

Query: 67  ------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                  R+       K LN+ L    +I +L  S +   F +RFS   R Y Y   TR 
Sbjct: 195 SKIVQPTRQPSEFPYPKLLNSVL--PPSIRVLAWSPIPSSFDSRFSCTYRHYRYAFHTRP 252

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTIDHFDVN 178
            P + E          LD E M   AQ L+G HD+  F  +    Q  +  R +      
Sbjct: 253 TPTSPE----------LDLELMSQGAQLLLGEHDYRNFCKLDGSKQIENHTRGVLKAWFE 302

Query: 179 S------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                     ++   ++  +FL  Q+R  V  L L+G      + +   L   +R    P
Sbjct: 303 GGESQGVGEGMMVFNLIGTAFLWHQVRHIVAVLFLIGAKLEPPSIVSDLLDV-ERFPSKP 361

Query: 233 ---LAPPEGLYFDSVEYS 247
              +  P  L      Y 
Sbjct: 362 NYTMGHPLPLTLHHCGYP 379


>gi|159479156|ref|XP_001697664.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158274274|gb|EDP00058.1| tRNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 382

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 86/233 (36%), Gaps = 50/233 (21%)

Query: 10  YNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           Y+GS + G+Q Q     ++QG +E+    +      + G+ RTD G HA  QV HFD+  
Sbjct: 29  YDGSEFAGFQFQPGKVRTVQGELERCAKRLFVGCSRMVGSSRTDGGAHAYGQVVHFDVYG 88

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
           E   +     L     +   + +L LS  ++ F + FSA  ++Y+Y+      P  ++  
Sbjct: 89  ERDNLE-SDTLYYNSFLPPDVRVLELSYAEEGFDSHFSACGKTYIYKFAAG-LPDPMQAK 146

Query: 129 RAWLIPK----------------SLDCENMRIAAQHLVGRHDFTTFRSIH---------- 162
             W +                   LD   M  A Q L+GRHDF+ F              
Sbjct: 147 YRWWVYDRWCERSRGKPSKLSDIRLDVGAMCEAGQLLLGRHDFSAFMDAKRPAGLGSAKR 206

Query: 163 --------------CQASSPIRTIDHFDVNS------FGNLIEIRVVARSFLH 195
                           A +  R + H  +         G  + + V    FL+
Sbjct: 207 KNPKLAERGIKPERTSAKNT-RILSHLSITEGVSALSGGQEVTMEVTGNGFLY 258


>gi|322698560|gb|EFY90329.1| putative pseudouridine synthase 3 [Metarhizium acridum CQMa 102]
          Length = 564

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 72/340 (21%), Positives = 101/340 (29%), Gaps = 98/340 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAI---FLVTGEI--------VVVHGAGR 50
             + + Y G  Y G++ Q   N  SI+  +  A+    L+  E               GR
Sbjct: 81  IALKLAYLGKNYGGFEFQAMGNQPSIEEELWNALTRACLIFPEDERIVQFNCCEYSKCGR 140

Query: 51  TDSGVHALRQVAHFDLVREWVPVI------------------------------------ 74
           TD GV A  QV    +                                            
Sbjct: 141 TDRGVSAFGQVIGLKVRSNRPLPKNGSKTDVAAAEDIAMAEAGPQGGKQAEEDVEVQEEE 200

Query: 75  -----------LCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIIT---R 119
                        + LN  L   D I IL         F ARFS   R Y Y        
Sbjct: 201 KPFDDIHDELCYPRILNRLL--PDDIRILAWCPSPPPDFSARFSCRERQYRYFFTQPAFA 258

Query: 120 QAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHF 175
             P +L+   A    K+  LD + MR AA+   G HDF  F  I    Q ++  R I   
Sbjct: 259 PDPASLDLSGASKPLKAGWLDIDAMRDAAKRYEGEHDFRNFCKIDPAKQITNFRRRIFES 318

Query: 176 DVNSFGN--------------------------LIEIRVVARSFLHTQIRSFVGSLKLVG 209
           D+    +                          +    V   +FL  QIR  V  L LVG
Sbjct: 319 DIVEVQDASSVMPYLQTSGFSPPGLQGSGPYPKVYYFHVRGSAFLWHQIRHMVAILFLVG 378

Query: 210 DGKWTSTDLEKALQ-AQDR-KECGPLAPPEGLYFDSVEYS 247
            G  + T + + L  A++  +    +A    L      + 
Sbjct: 379 QGLESPTVVSELLDTAKNPGRPSYVMADEVPLVLWDCIFP 418


>gi|71985046|ref|NP_496062.3| Temporarily Assigned Gene name family member (tag-124)
           [Caenorhabditis elegans]
 gi|1353139|sp|Q09524|TG124_CAEEL RecName: Full=Probable tRNA pseudouridine synthase tag-124;
           AltName: Full=tRNA pseudouridylate synthase; AltName:
           Full=tRNA-uridine isomerase
 gi|3875428|emb|CAA87378.1| C. elegans protein E02H1.3, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 402

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 97/290 (33%), Gaps = 63/290 (21%)

Query: 2   IRYCMIIE--YNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSG 54
            R  + I+  Y G  + G  +Q +  ++++  I +A+                 GRTD G
Sbjct: 28  PRRKIAIQFFYLGWEHDGLVQQPHTQNTVENHIMQALIKTHLIEDWTKCDFSRCGRTDKG 87

Query: 55  VHALRQVAHFDLVREWV------------------------PVILCKALNAYLKISDTIS 90
           V A +Q A   +                              +   K LN  L    TI 
Sbjct: 88  VSAFKQTAAMVVRSLCPGDSGVFWSDSTQEHQKVDYKASGEELPYVKMLNGVL--PKTIR 145

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           +   + V + F+ARF   RR+Y Y                      L+ E MR  A+ LV
Sbjct: 146 VFAWAPVAQTFNARFDCNRRTYKYSFA----------------KADLNLEKMRQGAELLV 189

Query: 151 GRHDFTTFRSIHCQAS----SPIRTIDHFDVNS--------FGNLIEIRVVARSFLHTQI 198
           G HDF+ F  I         S +R +    V            +++E+ V    FL   I
Sbjct: 190 GEHDFSNFCQIDMNEKRLLQSYVRKVYEVKVEQVSTHPENDMYSMVELTVSGSGFLWHMI 249

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
           R  V  L+ +G      + + + L  +    +    LA    L      Y
Sbjct: 250 RYIVTILQEIGRENEQPSLISQLLDLKKYPSRPQYTLASDTPLCLFDCGY 299


>gi|297693488|ref|XP_002824050.1| PREDICTED: tRNA pseudouridine synthase A-like [Pongo abelii]
          Length = 424

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 96/267 (35%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 81  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 140

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 141 RTDKGVSAAGQVVSL---KVWLIDNILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDA 195

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 196 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQE 253

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G      LE+
Sbjct: 254 PSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPECVLER 313

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 314 SW--GTEKVDVPKAPGLGLVLERVHFE 338


>gi|290987319|ref|XP_002676370.1| predicted protein [Naegleria gruberi]
 gi|284089972|gb|EFC43626.1| predicted protein [Naegleria gruberi]
          Length = 477

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 61/287 (21%), Positives = 99/287 (34%), Gaps = 54/287 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIFLVTG---------EIVVVHGA 48
            R  + I Y G+ Y G Q       N  +++ ++ KA+    G           V  H +
Sbjct: 116 RRVAIFIGYLGTNYNGSQTSNFTNPNVKTVEETVFKALCQAGGVSGDNSTDMNKVHFHRS 175

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            RTD GVHA   V    L+ +       + L     + + I       V K F+A+    
Sbjct: 176 SRTDKGVHAASNVLEMKLLMKPGLEEEMRKL-----LPEDIVFYGYKKVSKSFNAKEHCT 230

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLD------------------------CENMRI 144
            R+Y Y +    A     K   W    ++D                         E    
Sbjct: 231 ARTYEYLLP-AFALSPDPKAATWFGQINIDKITKEDVESENLNDIYNYDPTDEQIEKANR 289

Query: 145 AAQHLVGR---HDFTTFRSIHCQASSPIRTIDHFDVNSFGNL-----IEIRVVARSFLHT 196
             ++ VG    H++T          S  R I  F+ +    +     +++ V   SF++ 
Sbjct: 290 VLKNFVGTNSFHNYTQLTKAKPN--SFNRHITKFECSKAFEIDGMKVVKLTVTGSSFIYN 347

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           QIR  VG +  V  G    +D   ++  ++     PLAP  GL    
Sbjct: 348 QIRKMVGFMIAVMRGSLNESDFSTSVD-KEVTANVPLAPANGLLLCE 393


>gi|330793042|ref|XP_003284595.1| hypothetical protein DICPUDRAFT_45589 [Dictyostelium purpureum]
 gi|325085509|gb|EGC38915.1| hypothetical protein DICPUDRAFT_45589 [Dictyostelium purpureum]
          Length = 473

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 100/270 (37%), Gaps = 31/270 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
           +  +++ Y G  Y G Q+     +I+  +E AIF   G           +      RTD 
Sbjct: 69  KVAVLLGYLGKNYAGMQKNPGLRTIEEELEMAIFKAGGILPDNLYFQHKIDWVRCARTDK 128

Query: 54  GVHALRQVAHFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV ALR V    +         + KALN  L   + I +  +  V+  FHA+     RSY
Sbjct: 129 GVSALRNVVSLKMEVGPPELDEMVKALNKLL--PEDIHVFKIMRVNNSFHAKNGVDARSY 186

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDC--ENMRIAAQHLVGRHDFTTFRSIH-CQASSPI 169
           +Y   T          +     K  +   E +     + +G H F  + S       S  
Sbjct: 187 VYVCPTSAFEPKFATNKLVEPFKFTEETRETLNRVLSYYLGNHRFHNYTSRKESNDVSVF 246

Query: 170 RTIDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLV--------GDGKWTS- 215
           R I  F+ +         ++ I V+  SF+  QIR  +G L              K ++ 
Sbjct: 247 RKIIKFECSVPFILEGVEMVSINVIGESFMLHQIRKMIGCLMSFMRKGIFQDAQDKESAF 306

Query: 216 TDLEKALQAQDRKE--CGPLAPPEGLYFDS 243
             + K ++A    +    P+AP  GL  D 
Sbjct: 307 DQIRKYIEATFYHQPLNLPVAPGAGLLLDH 336


>gi|316973638|gb|EFV57202.1| putative tRNA pseudouridine synthase tag-124 [Trichinella spiralis]
          Length = 471

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 60/303 (19%), Positives = 100/303 (33%), Gaps = 61/303 (20%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAI----FLVTGEIVVVHGAGRTDSGVHAL 58
             +++ Y G    G+  Q N  ++++  I KA+     + + E       GRTD  V A 
Sbjct: 39  IALMVAYLGWDLDGFCAQNNSQNTVESKIFKALIETKLIQSLETANYSRCGRTDKTVSAF 98

Query: 59  RQV------------AHFDLVREWVPVI----------------LCKALNAYLKISDTIS 90
            QV                    + P                    K LN+ L     I 
Sbjct: 99  SQVLSLDVRSNQTTGVGVFEPDGYCPNEPKPTSRKTTPKSEELDYAKILNSVL--PQEIR 156

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQ------------APLALEKGRAWLIPKSLD 138
           +L  + V++ F+AR++   R Y Y                     A+    +     ++ 
Sbjct: 157 VLAWAPVERTFNARYNCTSRQYKYFFPKGALNLKVSTVVDFLHFSAIVALFSNFRRGTIC 216

Query: 139 C--ENMRIAAQHLVGRHDFTTFRS---IHCQASSPIRTIDHFDVNSFG-------NLIEI 186
              + M  A++ L+G HDF  F        +  S +RT+                 L   
Sbjct: 217 VYFQLMEQASKRLIGEHDFRNFCKIDMSKNEIQSCVRTVFDVQFTKVNAGGLNSRTLCCF 276

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSV 244
            +VA +FL  QIR  +  L  +G+GK     +E  L  +    K    +     L     
Sbjct: 277 TIVANAFLWHQIRCIMSVLFAIGEGKEQPDVIEWLLNTELCPAKPQYSMVVGWPLVLYGC 336

Query: 245 EYS 247
           +Y 
Sbjct: 337 QYD 339


>gi|74149634|dbj|BAE36440.1| unnamed protein product [Mus musculus]
          Length = 393

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 50  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    + 
Sbjct: 165 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPRE 222

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 223 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 282

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 283 SW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|268529206|ref|XP_002629729.1| C. briggsae CBR-TAG-124 protein [Caenorhabditis briggsae]
 gi|187038647|emb|CAP22290.1| CBR-TAG-124 protein [Caenorhabditis briggsae AF16]
          Length = 401

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 93/290 (32%), Gaps = 63/290 (21%)

Query: 2   IRYCMIIE--YNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGE----IVVVHGAGRTDSG 54
            R  + I+  Y G  + G  +Q N  ++++  + +A+                 GRTD G
Sbjct: 28  PRRKIAIQFFYLGWEHDGLVQQPNTQNTVEHHLMEALIKTHIIEDSIKCDFSRCGRTDKG 87

Query: 55  VHALRQVAHFDLVREWVPVI------------------------LCKALNAYLKISDTIS 90
           V A +Q A F                                    K LN  L    TI 
Sbjct: 88  VSAFKQTAAFLARSTCPDHPNVFWSDSTAEDVKNSYKSKDEELPYIKMLNGVL--PKTIR 145

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           +   + V   F+ARF   RR+Y Y                      LD E MR AA+ L+
Sbjct: 146 VFAWAPVAPTFNARFDCNRRTYKYSFP----------------KAGLDLEKMREAAKLLI 189

Query: 151 GRHDFTTFRSIHCQA----SSPIRTIDHFDVNS--------FGNLIEIRVVARSFLHTQI 198
           G HD++ F  I         S  R I    V            +++E+ V    FL   I
Sbjct: 190 GEHDYSNFCQIDMNKMRLEQSYTRKIYDVTVEQVSTHSENDIYSMVELTVSGSGFLWHMI 249

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQ-AQDRKECGPLAPPE-GLYFDSVEY 246
           R  V  L+ V  G    + +   L  ++           +  L      Y
Sbjct: 250 RYIVTVLQEVARGNEQPSLVSDLLDLSKYPSRPHYTLSSDTPLCLFDCGY 299


>gi|149063709|gb|EDM14032.1| pseudouridine synthase 1, isoform CRA_c [Rattus norvegicus]
          Length = 402

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 99/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 59  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 118

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 119 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 173

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL---VGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++   + L    G H+F  F S    + 
Sbjct: 174 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLGCYKGTHNFHNFTSQKGPRE 231

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 232 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 291

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 292 SW--GEEKVDVPKAPGLGLVLERVHFE 316


>gi|148688059|gb|EDL20006.1| pseudouridine synthase 1, isoform CRA_d [Mus musculus]
          Length = 402

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 59  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 118

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 119 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 173

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    + 
Sbjct: 174 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPRE 231

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 232 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 291

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 292 SW--GEEKVDVPKAPGLGLVLERVHFE 316


>gi|10086461|gb|AAG12521.1|AC015446_2 Putative pseudouridine synthase [Arabidopsis thaliana]
          Length = 442

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/304 (20%), Positives = 95/304 (31%), Gaps = 77/304 (25%)

Query: 3   RY-CMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGV 55
           RY  + I Y G  ++G+  +     SI+  + KA+          +       GRTD GV
Sbjct: 90  RYVALKIMYFGKRFYGFSAEAQMEPSIESEVFKALERTRLLVGDKKDSCYSRCGRTDKGV 149

Query: 56  HALRQVAHFDL-------------------------------------------VREWVP 72
            +  Q  +  L                                             E   
Sbjct: 150 SSTGQFKNQFLIVLMFFQNPVMGAFPNVYKVIALFLRSRLKSPPGDSKAQVNGRTGERPE 209

Query: 73  VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWL 132
               + LN  L   D I ++  S     FHARFS   R Y Y                  
Sbjct: 210 YDYVRVLNRAL--PDDIRVIGWSPAPIDFHARFSCYAREYKYFFW--------------- 252

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVN------SFGNLIE 185
             ++L+   M  A +  +G HDF  F  +         R +  F+V+          L  
Sbjct: 253 -RQNLNLSAMDFAGKKFIGEHDFRNFCKMDVANVHCYTRRVTFFEVSPCQNSHEGDQLCT 311

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDS 243
             +   +FL  QIR  V  L ++G G  +   ++  L  +   RK    LA    L   +
Sbjct: 312 FTMRGSAFLWHQIRCMVAVLFMIGQGVESVDVIDTLLDTKKTPRKPQYLLASEIPLVLRT 371

Query: 244 VEYS 247
            E+ 
Sbjct: 372 CEFE 375


>gi|327283197|ref|XP_003226328.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like
           [Anolis carolinensis]
          Length = 406

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 101/270 (37%), Gaps = 36/270 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-------------IVVVHGA 48
            +  +++ Y+G GY G QR   G+S   +IE  + L   +              +     
Sbjct: 61  RKIVLLVAYSGKGYHGMQRNV-GNSQFKTIEDDLVLALIQSGCIPENHGEDMKKMSFQRC 119

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            RTD GV A  Q+      + W+   + + +N +L     I IL L  V   F+++    
Sbjct: 120 ARTDKGVSAAGQIVSL---KVWLIEDILQKINNHL--PPHIRILGLKRVTGGFNSKNKCD 174

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPK--SLDCENM---RIAAQHLVGRHDFTTFRS-IH 162
            R+Y Y + T     A              L+ E +           G H+F  F S   
Sbjct: 175 ARTYSYMLPT----FAFAHKDCDFQDHTFHLNTETLATVNRLLAGYKGTHNFHNFTSQKG 230

Query: 163 CQASSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
            +  S  R I         V        ++V  +SF+  QIR  +G +  +  G  + + 
Sbjct: 231 PKDPSAKRYIMEMYCEEPFVRQGMEFAVMKVKGQSFMMHQIRKMIGLVIAIVKGYASESI 290

Query: 218 LEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +E++    + K   P AP  GL  + V + 
Sbjct: 291 MEQSW--GEEKVDVPKAPGLGLVLERVHFE 318


>gi|30692743|ref|NP_198390.2| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|27311599|gb|AAO00765.1| putative protein [Arabidopsis thaliana]
 gi|30725698|gb|AAP37871.1| At5g35400 [Arabidopsis thaliana]
 gi|332006580|gb|AED93963.1| tRNA pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 420

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 69/319 (21%), Positives = 108/319 (33%), Gaps = 76/319 (23%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV-------------VVHGA 48
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++     E                V  A
Sbjct: 93  VNFKIVLSYNGASFDGWQKQPDLHTVQGVVEKSLGGFVDERKAQLLKKKCKPLEGRVLVA 152

Query: 49  GRTDSGVHALRQVAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL QV  F   R +  P+ +  A+N     S  + ++++S V + FH  FSA
Sbjct: 153 GRTDKGVSALNQVCSFYTWRKDIEPIAIEDAINK--DASGKLRVVSISKVSRSFHPNFSA 210

Query: 108 IRRSYLYRIITRQAPLALEKG--------------------------------------- 128
             R YLY      A    + G                                       
Sbjct: 211 KWRRYLYIFPLDDAEPLRKSGENHENFIFDENKKKQRNGLLSEEIAEEVIMSEDDELEIE 270

Query: 129 ------RAWLIPKSLDCENMRIAAQHLVGR--------HDFTTFRSIHCQASSPIRTIDH 174
                      P       +    QHL G+         D    R+        +     
Sbjct: 271 ETSNALEVVEKPSDFSVSKVDQLLQHLQGKVLSYKMFARDTKAARNEGPPTECFMYHARA 330

Query: 175 FDVN-------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
            ++            ++ + +VA  FL   +R  V +             L K L+A  R
Sbjct: 331 AEIRLSSSDCVEGRRVMCVELVANRFLRKMVRVLVATSIREAAAGAEDDALLKLLEASCR 390

Query: 228 KECGPLAPPEGLYFDSVEY 246
           +   P AP EGL    V Y
Sbjct: 391 RATAPPAPSEGLCLFDVGY 409


>gi|301605366|ref|XP_002932295.1| PREDICTED: tRNA pseudouridine synthase A-like [Xenopus (Silurana)
           tropicalis]
          Length = 394

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 107/269 (39%), Gaps = 33/269 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ---KNGSSIQGSIEKAI---------FLVTGEIVVVHGAG 49
            ++ +++ Y G GY+G Q      N  +I+ ++  A+         F +  + +      
Sbjct: 69  RKFAIMLAYCGRGYYGMQMDLTRPNFPTIESALISALIQARCIPEMFYMQMKQLKFQRCA 128

Query: 50  RTDSGVHALRQVAHFDL-VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           RTD GV AL Q+    L      P    + +N++L     I I+++  V K F  +    
Sbjct: 129 RTDKGVSALSQLVSVRLLPSCSNP---VEKINSHL--PPEILIIDMKRVTKGFCPKKMCD 183

Query: 109 RRSYLYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC- 163
           +RSY Y + T      AP   +      +P+  D  N+        G H+F  F S    
Sbjct: 184 KRSYSYMVPTFALSCCAPSVPDSNF--RMPRE-DFHNINNLLSFYKGTHNFHNFTSRKAF 240

Query: 164 QASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
           +  S  R +     +           +I +  +SF+  QIR  VG +  +  G   +  L
Sbjct: 241 EDPSSFRHMLDVSCSEPFVFHGTEFAQIHITGQSFMLYQIRKMVGLIIAIAQGIVPADFL 300

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + +Q +  K   P AP  GL  + V + 
Sbjct: 301 PQCMQRE--KINIPPAPGLGLVLERVHFD 327


>gi|149063707|gb|EDM14030.1| pseudouridine synthase 1, isoform CRA_a [Rattus norvegicus]
          Length = 393

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 99/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 50  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL---VGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++   + L    G H+F  F S    + 
Sbjct: 165 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLGCYKGTHNFHNFTSQKGPRE 222

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 223 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 282

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 283 SW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|70906472|ref|NP_001020733.1| tRNA pseudouridine synthase A, mitochondrial isoform 3 [Mus
           musculus]
 gi|4455033|gb|AAD21041.1| pseudouridine synthase 1 [Mus musculus]
 gi|11464734|gb|AAG35308.1| pseudouridine synthase 1 [Mus musculus]
 gi|148688058|gb|EDL20005.1| pseudouridine synthase 1, isoform CRA_c [Mus musculus]
          Length = 393

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 50  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    + 
Sbjct: 165 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPRE 222

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 223 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 282

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 283 SW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|26354378|dbj|BAC40817.1| unnamed protein product [Mus musculus]
          Length = 393

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 50  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 110 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 164

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    + 
Sbjct: 165 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPRE 222

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 223 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 282

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 283 SW--GEEKVDVPKAPGLGLVLERVHFE 307


>gi|40882706|gb|AAR96247.1| putative pseudouridine synthase [Oryza sativa Japonica Group]
 gi|108708473|gb|ABF96268.1| tRNA pseudouridine synthase A family protein [Oryza sativa Japonica
           Group]
          Length = 411

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 86/246 (34%), Gaps = 47/246 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + I Y G  ++G+  + +   +++  I KA+        + +       GRTD GV A
Sbjct: 94  IALKIMYFGQRFYGFASEAHTEPTVESEIFKALERAKLLVGSRKESCYSRCGRTDKGVSA 153

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV    L        L    N                    F ARFS + R Y Y   
Sbjct: 154 TGQVISLFLRSNIKDAKLDVLDNK----------------SGDFLARFSCLGREYKYLFW 197

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFD 176
                              L+   M+ AA   +G HD+  F  +     S+  R I  F+
Sbjct: 198 ----------------KGDLNISEMQKAALKFIGEHDYRNFCKMDAANVSNYRRHITDFN 241

Query: 177 VNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRK 228
           ++++        L  I +   +FL  Q+R  V  L L+G G  T   ++  L      RK
Sbjct: 242 ISAYDQRSNYDELWAITIKGSAFLWHQVRCMVAVLFLIGQGLETPCIVDSLLDITKTPRK 301

Query: 229 ECGPLA 234
               +A
Sbjct: 302 PQYKMA 307


>gi|125544113|gb|EAY90252.1| hypothetical protein OsI_11824 [Oryza sativa Indica Group]
          Length = 403

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 54/246 (21%), Positives = 86/246 (34%), Gaps = 47/246 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + I Y G  ++G+  + +   +++  I KA+        + +       GRTD GV A
Sbjct: 94  IALKIMYFGQRFYGFASEAHTEPTVESEIFKALERAKLLVGSRKESCYSRCGRTDKGVSA 153

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV    L        L    N                    F ARFS + R Y Y   
Sbjct: 154 TGQVISLFLRSNIKDAKLDVLDNK----------------SGDFLARFSCLGREYKYLFW 197

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFD 176
                              L+   M+ AA   +G HD+  F  +     S+  R I  F+
Sbjct: 198 ----------------KGDLNISEMQKAALKFIGEHDYRNFCKMDAANVSNYRRHITDFN 241

Query: 177 VNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRK 228
           ++++        L  I +   +FL  Q+R  V  L L+G G  +   ++  L      RK
Sbjct: 242 ISAYDQRSNYDELWAITIKGSAFLWHQVRCMVAVLFLIGQGLESPCIVDSLLDITKTPRK 301

Query: 229 ECGPLA 234
               +A
Sbjct: 302 PQYKMA 307


>gi|156538138|ref|XP_001608257.1| PREDICTED: similar to pseudouridylate synthase [Nasonia
           vitripennis]
          Length = 437

 Score =  139 bits (350), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 101/285 (35%), Gaps = 48/285 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
            Y M++ Y G  Y+G QR    ++I+  + KA+            T + +    A RTD 
Sbjct: 73  NYAMMLGYCGKNYYGMQRNPGFNTIEEELIKAMLKADLITSEAFETIQNINFQRAARTDK 132

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+RQV    L  +     + + L       + I +  +  V K F+++     R+Y 
Sbjct: 133 GVSAVRQVVSLKLPEDPSKDSINETL------PEDIRVFAIKRVTKGFNSKSQCDARTYS 186

Query: 114 YRIIT--------------RQAPLALEK--------GRAWLIPKSLDC--ENMRIAAQHL 149
           Y + T               +     ++        G+ +   +      E +    + L
Sbjct: 187 YTMPTFALAPENLELFQEMSEYNDVEKRMEQLSTIDGKPFHEYRLPQERKEKLTELLKVL 246

Query: 150 VGRHDFTTF-RSIHCQASSPIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVG 203
            G H+F  F   +        R I  F             I ++V  +SF+  QIR  V 
Sbjct: 247 EGTHNFHNFTSKVLPLDPRAKRYIMSFIAEEPFLVNNMEFITLKVKGQSFMLHQIRKMVA 306

Query: 204 SLKLVGDGKWTSTDLEK-ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +  V        + EK   +    K    +AP  GL  + V Y 
Sbjct: 307 MVIGVIRNIVPREEFEKTVFEQA--KYDITIAPSLGLMLNIVHYD 349


>gi|320165424|gb|EFW42323.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
          Length = 387

 Score =  139 bits (350), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 60/268 (22%), Positives = 110/268 (41%), Gaps = 29/268 (10%)

Query: 3   RYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           R+ + +EY+G+ + G         +  S+   +++AI   T +   V  + RTD+GVHAL
Sbjct: 79  RFLLAVEYDGTAFSGVAASPDEPPDRPSVGSVLDRAIAQATRQDARVTFSSRTDAGVHAL 138

Query: 59  RQVAHF-----------DLVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARF 105
               H               ++W P+ L  A+N + +  +   +S+  +  V +Q HARF
Sbjct: 139 WNTCHVDIEPRTRRGDLMTQQQWTPLALGSAINYFSRGKVPYPMSVRAVCAVPEQVHARF 198

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           +A +R Y+YR++  ++  A      + +  +   E++  A          + F     + 
Sbjct: 199 NATQRVYIYRVVVGESSAASVFDLRYHLTAAPIDESLVQARTT---TRHISQFSVQIDKH 255

Query: 166 SSPIRTIDHF-DVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +     +   D  S   + +   +    FL+ Q+R  VG +  V  GK T  DL     
Sbjct: 256 KTDNPWANSLPDALSKPTVALTFTIRGSGFLYHQVRIMVGHVLSVASGKSTLADLVHL-- 313

Query: 224 AQDRKECGP----LAPPEGLYFDSVEYS 247
            +D  +       + P  GL    V Y 
Sbjct: 314 -RDNPQVIHLHKDMLPAHGLCLKEVCYD 340


>gi|195171697|ref|XP_002026640.1| GL11833 [Drosophila persimilis]
 gi|194111566|gb|EDW33609.1| GL11833 [Drosophila persimilis]
          Length = 421

 Score =  139 bits (350), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 93/264 (35%), Gaps = 46/264 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q++ + +I+  + +A+              H  GRTD  V A 
Sbjct: 104 VLLKLTYFGWDYQGFACQEDSNDTIESHLFRALTRTCLIESRATSNYHRCGRTDKEVSAF 163

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 164 CQVISIDLRSKHTPDTQLEPASLSSEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 221

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
               RSY Y                +     LD E MR A + LVG  DF  F    +H 
Sbjct: 222 DCTSRSYRY----------------YFPKGDLDIEAMREACKLLVGHSDFRNFCKMDVHN 265

Query: 164 QASSPIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
             +  IR +    V        NS  ++  + + A +FL  QIR  +  L LVG  +   
Sbjct: 266 GVTKFIRNLQAARVEPCVEMLNNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQRRELP 325

Query: 216 TDLEKALQAQDRKECGPLAPPEGL 239
             +   L  +         P  GL
Sbjct: 326 RIVSDLLDVETNPCKPQYTPALGL 349


>gi|328780691|ref|XP_624092.3| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like [Apis
           mellifera]
          Length = 389

 Score =  138 bits (349), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 57/283 (20%), Positives = 96/283 (33%), Gaps = 48/283 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSG 54
           + M++ Y G  Y G Q  +   +I+GS+  A+              + +    A RTD G
Sbjct: 49  FVMVLGYLGKNYSGMQINRGIKTIEGSLLSALLKADFITKNEFEDLKEIKFQRAARTDKG 108

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A+RQ+    L        + K L         I + ++  V + F+++     R+Y Y
Sbjct: 109 VSAVRQIVSLQLPNHVNKEDINKHL------PKDIKVFDIKRVTRNFNSKNKCDARTYRY 162

Query: 115 RIIT----RQAPLALE---------------------KGRAWLIPKSLDCENMRIAAQHL 149
            + T     + P  L+                     K        S   + +    +  
Sbjct: 163 VLPTFALASEDPSFLQMDKEEEIDEEKRLEKLSMIDGKPYNEFRLNSDMLDKLNEILKLF 222

Query: 150 VGRHDFTTF-RSIHCQASSPIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVG 203
            G H+F  F   I        R I +F             + + V  +SF+  QIR  V 
Sbjct: 223 EGTHNFHNFTSKIRPMDPRAKRYIVYFRCIETFIANNMEFVVLEVQGQSFMLHQIRKMVS 282

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +  +     T   ++ A   +      P+AP  GL    V Y
Sbjct: 283 LIIGICRNIITIDFVKDAFSLEKVD--IPIAPGLGLSLHFVHY 323


>gi|222625021|gb|EEE59153.1| hypothetical protein OsJ_11064 [Oryza sativa Japonica Group]
          Length = 403

 Score =  138 bits (349), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 86/246 (34%), Gaps = 47/246 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + I Y G  ++G+  + +   +++  I KA+        + +       GRTD GV A
Sbjct: 94  IALKIMYFGQRFYGFASEAHTEPTVESEIFKALERAKLLVGSRKESCYSRCGRTDKGVSA 153

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QV    L        L    N                    F ARFS + R Y Y   
Sbjct: 154 TGQVISLFLRSNIKDAKLDVLDNK----------------SGDFLARFSCLGREYKYLFW 197

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFD 176
                              L+   M+ AA   +G HD+  F  +     S+  R I  F+
Sbjct: 198 ----------------KGDLNISEMQKAALKFIGEHDYRNFCKMDAANVSNYRRHITDFN 241

Query: 177 VNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRK 228
           ++++        L  I +   +FL  Q+R  V  L L+G G  T   ++  L      RK
Sbjct: 242 ISAYDQRSNYDELWAITIKGSAFLWHQVRCMVAVLFLIGQGLETPCIVDSLLDITKTPRK 301

Query: 229 ECGPLA 234
               +A
Sbjct: 302 PQYKMA 307


>gi|125811944|ref|XP_001362058.1| GA15853 [Drosophila pseudoobscura pseudoobscura]
 gi|54637235|gb|EAL26638.1| GA15853 [Drosophila pseudoobscura pseudoobscura]
          Length = 497

 Score =  138 bits (348), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 93/264 (35%), Gaps = 46/264 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q++ + +I+  + +A+              H  GRTD  V A 
Sbjct: 104 VLLKLTYFGWDYQGFACQEDSNDTIESHLFRALTRTCLIESRATSNYHRCGRTDKEVSAF 163

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 164 CQVISIDLRSKHTPDTQLEPASLSSEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 221

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
               RSY Y                +     LD E MR A + LVG  DF  F    +H 
Sbjct: 222 DCTSRSYRY----------------YFPKGDLDIEAMREACKLLVGHSDFRNFCKMDVHN 265

Query: 164 QASSPIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
             +  IR +    V        NS  ++  + + A +FL  QIR  +  L LVG  +   
Sbjct: 266 GVTKFIRNLQAARVEPCVEMLNNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQRRELP 325

Query: 216 TDLEKALQAQDRKECGPLAPPEGL 239
             +   L  +         P  GL
Sbjct: 326 RIVSDLLDVETNPCKPQYTPALGL 349


>gi|70906470|ref|NP_062674.2| tRNA pseudouridine synthase A, mitochondrial isoform 2 [Mus
           musculus]
 gi|114152896|sp|Q9WU56|TRUA_MOUSE RecName: Full=tRNA pseudouridine synthase A, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase I; AltName:
           Full=tRNA-uridine isomerase I; Flags: Precursor
 gi|112180429|gb|AAH34359.2| Pseudouridine synthase 1 [Mus musculus]
 gi|148688056|gb|EDL20003.1| pseudouridine synthase 1, isoform CRA_a [Mus musculus]
          Length = 423

 Score =  138 bits (348), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 80  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 140 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 194

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    + 
Sbjct: 195 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPRE 252

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 253 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 312

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 313 SW--GEEKVDVPKAPGLGLVLERVHFE 337


>gi|50756277|ref|XP_415090.1| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 409

 Score =  138 bits (348), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 57/267 (21%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+              + +      
Sbjct: 64  RKIVLLMAYSGKGYHGMQRNLGSSQFKTIEDDLVSALVRSGCIPENHGEDMKKMSFQRCA 123

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  Q+      +  +   + + +N +L     I IL L  V   F+++     
Sbjct: 124 RTDKGVSAAGQIVSL---KVRLIDDILEKINNHL--PSHIRILGLKRVTGGFNSKNKCDA 178

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L     E +        G H+F  F S    + 
Sbjct: 179 RTYAYMLPT--FAFAHKDHDVQEEAHRLSRETLEKVNSLLARYKGTHNFHNFTSQKGPKD 236

Query: 166 SSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I         V        I+V  +SF+  QIR  +G +  +  G    + +E+
Sbjct: 237 PSARRYIMEMYCGEPFVREGIEFAVIKVKGQSFMMHQIRKMIGLVIAIVKGYAPESIIER 296

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 297 SW--GEEKVDVPKAPGLGLVLERVHFE 321


>gi|195552156|ref|XP_002076382.1| GD15210 [Drosophila simulans]
 gi|194202031|gb|EDX15607.1| GD15210 [Drosophila simulans]
          Length = 498

 Score =  138 bits (348), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 93/264 (35%), Gaps = 46/264 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q++ + +I+ ++ +A+              H  GRTD  V A 
Sbjct: 101 VLLKITYFGWDYQGFACQEDSNDTIESNLFRALTRTCLIESRATSNYHRCGRTDKEVSAF 160

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 161 CQVISIDLRSKHPPESQLDPTSLSSEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 218

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             + RSY Y                +     LD   MR A   LV   DF  F    +H 
Sbjct: 219 DCVSRSYRY----------------YFPKGDLDIAAMRKACDLLVRHADFRNFCKMDVHN 262

Query: 164 QASSPIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
             ++ +R +    V        NS  ++  + + A +FL  QIR  +  L LVG  K   
Sbjct: 263 GVTNYMRNLQSARVEACDENHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKEKP 322

Query: 216 TDLEKALQAQDRKECGPLAPPEGL 239
             +   L  +         P  GL
Sbjct: 323 AVISDLLDVESNPCKPQYTPAIGL 346


>gi|171741245|ref|ZP_02917052.1| hypothetical protein BIFDEN_00320 [Bifidobacterium dentium ATCC
           27678]
 gi|171276859|gb|EDT44520.1| hypothetical protein BIFDEN_00320 [Bifidobacterium dentium ATCC
           27678]
          Length = 219

 Score =  138 bits (348), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 52/201 (25%), Positives = 80/201 (39%), Gaps = 28/201 (13%)

Query: 71  VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGR 129
             V L + L   L   + I+I  ++   + F ARFSA+ R+Y+YRI  R +      +G 
Sbjct: 5   PVVALTRRLQRML--PNDITIHGINEAPQGFDARFSALERTYVYRIADRSSEIDPRMRGF 62

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN------- 182
              +   LD E M  AA   +G HDF +F + +    + IR +                 
Sbjct: 63  VLHVDDDLDLETMNQAAAMTIGLHDFGSFATPNP-GGTTIREVKTAYWRRIPQRPLVDGE 121

Query: 183 ---------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
                          L    +VA +F    +RS V     VG GK +       +    R
Sbjct: 122 MTMGERYRTPSMESGLACFTIVADAFARNMVRSLVNGCVQVGIGKRSLDWFADKMATPLR 181

Query: 228 K-ECGPLAPPEGLYFDSVEYS 247
           +   GP+AP +GL  + +EY 
Sbjct: 182 EGSTGPIAP-QGLTLEHIEYP 201


>gi|70906466|ref|NP_001020734.1| tRNA pseudouridine synthase A, mitochondrial [Rattus norvegicus]
 gi|182676393|sp|Q4KM92|TRUA_RAT RecName: Full=tRNA pseudouridine synthase A, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase I; AltName:
           Full=tRNA-uridine isomerase I; Flags: Precursor
 gi|149063708|gb|EDM14031.1| pseudouridine synthase 1, isoform CRA_b [Rattus norvegicus]
 gi|171847186|gb|AAI61821.1| Pseudouridylate synthase 1 [Rattus norvegicus]
          Length = 423

 Score =  138 bits (348), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 99/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 80  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 140 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 194

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL---VGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++   + L    G H+F  F S    + 
Sbjct: 195 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLGCYKGTHNFHNFTSQKGPRE 252

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 253 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 312

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 313 SW--GEEKVDVPKAPGLGLVLERVHFE 337


>gi|76638649|ref|XP_593895.2| PREDICTED: pseudouridylate synthase 1 isoform 1 [Bos taurus]
 gi|297484682|ref|XP_002694500.1| PREDICTED: pseudouridylate synthase 1 [Bos taurus]
 gi|296478661|gb|DAA20776.1| pseudouridylate synthase 1 [Bos taurus]
          Length = 433

 Score =  138 bits (348), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 99/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 90  RKIVLLMAYSGKGYHGMQRNVGSSKFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 149

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 150 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 204

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRS-IHCQA 165
           R+Y+Y + T     A +   +      L  E +           G H+F  F S      
Sbjct: 205 RTYVYMLPT--FAFAHKDHDSQDETYRLSAETLGRVNRLLACYKGTHNFHNFTSQKGPHE 262

Query: 166 SSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I     +   V        I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 263 PSARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAIVKGYAPESVLER 322

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
                + K   P AP  GL  + V + 
Sbjct: 323 CW--GEAKVDVPKAPGLGLVLERVHFE 347


>gi|149634330|ref|XP_001510884.1| PREDICTED: similar to Pseudouridine synthase 1 [Ornithorhynchus
           anatinus]
          Length = 469

 Score =  138 bits (347), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 106/268 (39%), Gaps = 32/268 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY+G QR        +I+  +  A+              + +      
Sbjct: 100 RKIVLLMAYSGKGYYGMQRHVGSSQFKTIEDDLVSALVQSGCIPENHGDDMKKMSFQRCA 159

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  Q+      + W+   + + +N++L     I IL L  V   F+++ +   
Sbjct: 160 RTDKGVSAAGQIVSL---KVWLIDNILEKINSHL--PSQIRILGLKRVTGGFNSKNNCTA 214

Query: 110 RSYLYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQ 164
           R+Y Y + T     +     ++    L P+ L  E +        G H F  F S    +
Sbjct: 215 RTYFYMLPTLAFAHKDHDPQDETYR-LSPEVL--ERVNRLLACYKGTHHFHNFTSQKGPK 271

Query: 165 ASSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            +S +R I         V        I+V  +SF+  QIR  +G +  +  G    + +E
Sbjct: 272 DASGMRYIMEMYCEEPFVREGMEFAVIKVKGQSFMMHQIRKMIGLVIAIVKGYADQSVME 331

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++    + K   P AP  GL  + V + 
Sbjct: 332 RSW--GEEKVDIPKAPGLGLVLERVHFE 357


>gi|112180395|gb|AAH21446.2| Pseudouridine synthase 1 [Mus musculus]
          Length = 423

 Score =  138 bits (347), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 97/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 80  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   +   +N++L     I IL L  V   F+++     
Sbjct: 140 RTDKGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 194

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    + 
Sbjct: 195 RTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPRE 252

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 253 PSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLER 312

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 313 SW--GEEKVDVPKAPGLGLVLERVHFE 337


>gi|291415803|ref|XP_002724139.1| PREDICTED: pseudouridylate synthase 1-like, partial [Oryctolagus
           cuniculus]
          Length = 391

 Score =  138 bits (347), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 102/268 (38%), Gaps = 32/268 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 57  RKIVLLLAYSGKGYHGMQRNVGSSQFRTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 116

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 117 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 171

Query: 110 RSYLYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQ 164
           R+Y Y + T     +     ++    L  ++L  + +        G H F  F S    +
Sbjct: 172 RTYFYMLPTFAFAHKDRDPQDETYR-LSAETL--QRVNRLLACYQGTHSFHNFTSQKGPR 228

Query: 165 ASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
             S  R I     +   V        IRV  +SF+  QIR  VG +  +  G    + LE
Sbjct: 229 EPSARRYILQMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLE 288

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++    D K   P AP  GL  + V + 
Sbjct: 289 RSW--GDEKVDVPKAPGLGLVLERVHFE 314


>gi|332520423|ref|ZP_08396885.1| Pseudouridine synthase I, TruA, alpha/beta domain [Lacinutrix
           algicola 5H-3-7-4]
 gi|332043776|gb|EGI79971.1| Pseudouridine synthase I, TruA, alpha/beta domain [Lacinutrix
           algicola 5H-3-7-4]
          Length = 227

 Score =  138 bits (347), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 50/222 (22%), Positives = 83/222 (37%), Gaps = 12/222 (5%)

Query: 36  FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNL 94
           F++ G+      +GRTD+ V A        L           K  N  L     I  L +
Sbjct: 8   FILEGKRFKSLASGRTDAMVSAEETAIELFLYEPIEDQKAFLKLFNTNL--PQDIRALEI 65

Query: 95  SIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHD 154
           + VD +F+   +   + Y+Y                  I   LD E M+I A+   G H 
Sbjct: 66  TEVDAKFNIINNPKVKEYIYLFAFGDKFHPFCAPILTTILDDLDVEIMKIGAKLFEGEHY 125

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSF---------GNLIEIRVVARSFLHTQIRSFVGSL 205
             T+           R I   ++                 +RV  + F+  QIR  +G+L
Sbjct: 126 LKTYCYKPSNNGIYTREILTCEIVENTIYTANFFPKKSYLLRVRGKGFMRNQIRLMMGTL 185

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +G GK T  D++ +L+  +  +   +AP  GL   S+++ 
Sbjct: 186 IDLGKGKLTLEDIKASLEPDNTIKMEYIAPASGLILKSLKFD 227


>gi|198429149|ref|XP_002129315.1| PREDICTED: similar to Pseudouridylate synthase 3 [Ciona
           intestinalis]
          Length = 510

 Score =  138 bits (347), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 62/311 (19%), Positives = 99/311 (31%), Gaps = 82/311 (26%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG------SSIQGSIEKAIFLVT---------GEIVVVH 46
            R  + + Y G  Y G+   K+        SI   +E+ +             G ++   
Sbjct: 101 RRIALKVLYLGWDYVGYAFTKSSLAFSKPESISNVVERVLLEALLRQQLITGVGSVLNFD 160

Query: 47  GAGRTDSGVHALRQVAHFDL--------------------------------------VR 68
            AGRTD  V  L QV   ++                                        
Sbjct: 161 RAGRTDRQVSGLSQVVSVNVRSNLNKGHGVWYPKVEGSDNVGNTKPETEYFEDGFPVSDT 220

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
                 L         +   I IL  S V K F  R+    R+Y Y              
Sbjct: 221 TLDDGELPYVSLLNQALPPDIRILAWSPVKKTFSPRYQCRSRTYRY-------------- 266

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA--SSPIRTIDHFDVNSFG----- 181
               +  S+D E M  AAQ  VGRHD   F  +  +    + +RTI+   V  F      
Sbjct: 267 --AFVRGSMDIELMNEAAQKFVGRHDMRNFCKVSSENAYRTYVRTINSIKVEEFNQTNLP 324

Query: 182 --NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP---P 236
             ++    + A S+++ QIR  +  L  +G G+   + +++ L   ++    P      P
Sbjct: 325 ECDICVATISAESYVYKQIRRMMSILGRIGSGEIPPSTIDEMLDV-EKNPKKPSFKSWTP 383

Query: 237 EGLYFDSVEYS 247
             L     E+ 
Sbjct: 384 LNLTLIDAEFD 394


>gi|224071794|ref|XP_002194956.1| PREDICTED: similar to pseudouridylate synthase 1 [Taeniopygia
           guttata]
          Length = 474

 Score =  138 bits (347), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 98/267 (36%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+              + +      
Sbjct: 128 RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVQSGCIPENHGEDMKKMSFQRCA 187

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  Q+      +  +   + + +N +L     I IL L  V   F+++     
Sbjct: 188 RTDKGVSAAGQIVSL---KVRLIDDILEKINNHL--PSHIRILGLKRVTGGFNSKNKCDA 242

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          LD    E +        G H+F  F S    + 
Sbjct: 243 RTYSYMLPT--FAFAHKDHDVQEELFRLDRDTLERVNRLLACYKGTHNFHNFTSQKGPRD 300

Query: 166 SSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I         V        I+V  +SF+  QIR  +G +  +  G    + +E+
Sbjct: 301 PSAKRYIMEMYCGEPFVRENVEFAVIQVRGQSFMMHQIRKMIGLVIAIVKGYAAESIMER 360

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 361 SW--GEEKVDVPKAPGLGLVLEKVHFE 385


>gi|324517253|gb|ADY46767.1| tRNA pseudouridine synthase-like protein 1 [Ascaris suum]
          Length = 315

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 64/291 (21%), Positives = 107/291 (36%), Gaps = 47/291 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHAL 58
            RY + I Y+GS +    +  +G  +   +   +   F   GE +    A RTD GVHAL
Sbjct: 5   RRYLLWISYDGSRFPEMAKGGSGYGVLDFLTTILRSSFPNVGERLKSSAASRTDRGVHAL 64

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTIS---------ILNLSIVDKQFHARFSAIR 109
           R      +  E+  +   K     L   ++I+         IL+   V   F AR +   
Sbjct: 65  RNAIIIQVPLEYGILDQRKD--TLLAEWNSIAEQCKPKALQILDFHTVSPGFSARRNVSY 122

Query: 110 RSYLYRIITRQAPLAL-------------EKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           R Y YR+       A              E+  AW++P   D    + A     G H+  
Sbjct: 123 RCYKYRVCVALTSDAWQRFKEKPSLMHYAERDYAWILPPGFDLYKAQQACSIFKGTHNMA 182

Query: 157 TF-------RSIHCQASSPIRTIDHFDVNSFGN---------LIEIRVVARSFLHTQIRS 200
           +F       R    +  S IR + H  +                +  +++ SFL  Q+R 
Sbjct: 183 SFFKHRERDRRKENEYPSAIRHMRHVAITGGEPRCIDDADHAFYDFSIISTSFLREQVRR 242

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGP----LAPPEGLYFDSVEYS 247
            +G +     G+ +   +E  L+             +AP +GL+ ++V Y 
Sbjct: 243 MIGIIVAHAYGRVSRELIEWLLKNPHPTNFFTRRLLIAPAQGLFLENVVYD 293


>gi|332254114|ref|XP_003276176.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial [Nomascus
           leucogenys]
          Length = 421

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 98/268 (36%), Gaps = 31/268 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQ-RQKN---GSSIQGSIEKAIFL---------VTGEIVVVHGA 48
            +  +++ Y+G GY G Q R        +I+  +  A+                +     
Sbjct: 77  RKIVLLMAYSGKGYHGMQWRNLGSLQAQTIEDDLVSALVRSGCIPENHGEDMRKMSFQRC 136

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++    
Sbjct: 137 ARTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCD 191

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQ 164
            R+Y Y + T     A +          L  E ++          G H+F  F S    Q
Sbjct: 192 ARTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQ 249

Query: 165 ASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
             S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE
Sbjct: 250 EPSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLE 309

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++  ++      P AP  GL  + V + 
Sbjct: 310 RSWGSEKVD--VPKAPGLGLVLERVHFE 335


>gi|194043580|ref|XP_001928625.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial isoform 2
           [Sus scrofa]
 gi|311270525|ref|XP_003132902.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial [Sus
           scrofa]
          Length = 400

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 99/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 57  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 116

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 117 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 171

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E +           G H+F  F S    + 
Sbjct: 172 RTYFYMLPT--FAFAHKDHDVQDETYRLSTETLQRVNRLLACYKGTHNFHNFTSQKGPRE 229

Query: 166 SSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I     +   V        I+V  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 230 PSARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAIIKGYAPESVLER 289

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 290 SW--GEAKVDVPKAPGLGLVLERVHFE 314


>gi|301091109|ref|XP_002895746.1| tRNA pseudouridine synthase [Phytophthora infestans T30-4]
 gi|262096658|gb|EEY54710.1| tRNA pseudouridine synthase [Phytophthora infestans T30-4]
          Length = 470

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 66/301 (21%), Positives = 110/301 (36%), Gaps = 60/301 (19%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            RY + + + G  Y G Q  +   +I+  +E+A+F   G         + +    A RTD
Sbjct: 71  RRYGLWVAFCGKNYCGMQMNEGVKTIEAELERALFEAGGIAESNYGYLQKIGWSRAARTD 130

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA  Q+    L            ++A L   + I ++++  V K F+A+ +  +R+Y
Sbjct: 131 KGVHAAGQLLTAKLHVGDDIAGFMAKVDAAL--PEDIRVMHMVTVTKNFNAKMTCDQRTY 188

Query: 113 LYRII----------------------TRQAPL------------------ALEKGRAWL 132
            Y                         T Q P                    LE  +A+ 
Sbjct: 189 EYLAPTFIFGKRMRSSASKNEEKQAEGTNQWPSNLRDSEEGFDSNVVIDNTTLEAHKAFR 248

Query: 133 IPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS-----FGNLIEI 186
           +   +  E +    +  VG H+F  F   +        R I  F+            + +
Sbjct: 249 LSDEI-LEQLNATLKQYVGTHNFHNFTSKMEPTNPQANRFIISFEAERPFVQNDMEWVRL 307

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           RVV +SFL   IR  +G+   V  G    + +E+A++    K   P AP  GLY     +
Sbjct: 308 RVVGQSFLLHHIRKMIGTAVEVVSGVSDPSTIERAMELT--KMDLPKAPSVGLYLAQAHF 365

Query: 247 S 247
            
Sbjct: 366 E 366


>gi|316969725|gb|EFV53781.1| tRNA pseudouridine synthase A [Trichinella spiralis]
          Length = 380

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 100/260 (38%), Gaps = 62/260 (23%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-----------------TGEIV 43
           M RY     Y GS + G Q Q N  ++QG +E ++                     GE  
Sbjct: 71  MPRYFFNFAYLGSRFSGSQSQPNQLTVQGVLEVSLIKFAYFDCRQNVLAMILLSPLGEEP 130

Query: 44  VVHGAGRTDSGVHALRQVAHFDL--VREWVPVILCKALNAYL-KISDTISILNLSIVDKQ 100
             + + RTD+GVHA    A  DL   R++    L  ALN+ L K+   I I +   V   
Sbjct: 131 RWYFSSRTDAGVHAFMNTATVDLDPERDFDSDYLKSALNSMLTKLDMEIRINSCRRVSGG 190

Query: 101 FHARFSAIRRSYLYRIIT----------------------RQAPLALEKGRAWLIPKSLD 138
           F AR  A+ R YLYR+                          +   +E  RAW +  + +
Sbjct: 191 FCARRHALEREYLYRLAILKPEFESDHHKQTNNTSTTQNAHHSLPLIEHRRAWALSSAFN 250

Query: 139 CENMRIAAQHLVGRHDFTTFRS------IHCQASSPIRTIDHFDV--------------N 178
            E  R AA    G H+F +F +            + ++ I   D+              +
Sbjct: 251 HERFRKAALMFQGSHNFASFMTNSVGNLDRPTGIATVKNISRLDIDFGKALMDSKHEPCS 310

Query: 179 SFGNLIEIRVVARSFLHTQI 198
            F N  ++  V+RSFL+ Q+
Sbjct: 311 DFFNFFDVSFVSRSFLYNQV 330


>gi|321464475|gb|EFX75483.1| hypothetical protein DAPPUDRAFT_323292 [Daphnia pulex]
          Length = 429

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 100/260 (38%), Gaps = 48/260 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q++   +I+  + KA+       + E    H  GRTD GV + 
Sbjct: 69  VLLQVAYVGWDYAGFVVQEHTEKTIEAEVFKALEKTRLLESRETSNYHRCGRTDKGVSSF 128

Query: 59  RQVAHFDLVR--------EWVPVILCKALNA---------YLKISDTISILNLSIVDKQF 101
            Q    DL                  K  N             +   I ++  + +++  
Sbjct: 129 GQAISIDLRSNLSEGKGVFIPDGHQAKVGNTVEIDYVGILNKVLPPEIRMIAWAPINQSL 188

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS- 160
            ARF   +R+Y Y                +    +L+ E MR+A+Q L+G HDF      
Sbjct: 189 SARFDCRQRTYHY----------------YFPKANLNIERMRVASQSLIGEHDFRNLCKM 232

Query: 161 -IHCQASSPIRTIDHFDVNSFGN-------LIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
            +        R I    + +  +       +I ++++ ++FL  Q+R  V  L L+G GK
Sbjct: 233 DVGNGVIKFDRRIMDIQIEAIDDDKANSYSMIRLKLIGQAFLWHQVRCIVAILFLIGQGK 292

Query: 213 WTSTDLEKALQAQDRKECGP 232
             +T +++ L   +R    P
Sbjct: 293 EETTIIQELLNV-ERNPRKP 311


>gi|296213295|ref|XP_002753209.1| PREDICTED: tRNA pseudouridine synthase A [Callithrix jacchus]
          Length = 428

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 96/267 (35%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 85  RKVVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 144

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N +L     I IL L  V   F+++     
Sbjct: 145 RTDKGVSAAGQVVSL---KVWLIDGILEKINRHL--PSHIRILGLKRVTGGFNSKNKCDA 199

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E ++          G H+F  F S    Q 
Sbjct: 200 RTYCYLLPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYEGTHNFHNFTSQKGPQE 257

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I                  IRV  +SF+  QIR  VG +  +  G    + LE+
Sbjct: 258 PSARRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESLLER 317

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +      K   P AP  GL  + V + 
Sbjct: 318 SW--GTEKVDVPKAPGLGLVLERVHFE 342


>gi|156405521|ref|XP_001640780.1| predicted protein [Nematostella vectensis]
 gi|156227916|gb|EDO48717.1| predicted protein [Nematostella vectensis]
          Length = 300

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/258 (22%), Positives = 89/258 (34%), Gaps = 35/258 (13%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDSGV 55
            ++I Y G GY G Q      +I+  +  A+                +      RTD GV
Sbjct: 5   ALLISYCGVGYAGMQINPGVRTIEEQLINALHQAEVITDDAKECLGKMSFQRCARTDKGV 64

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    +        L   +N++L     I I  +    K F  + +   R+Y Y 
Sbjct: 65  SAARQVVSLKISA---LSSLLPKINSFL--PPEIRIFGMIKTTKAFDCKQNCSARTYEYL 119

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDH 174
             T     A  K       K    E +  A  +  G  ++  F S    +  S  R I  
Sbjct: 120 TPT----FAFAKDYVSRTEK---IEEINKALSNYKGTKNYHNFTSGKKFEDPSANRYIIS 172

Query: 175 FDV----NSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           F         G   + + V  +SF+  QIR  +G +  V  G   S+  +          
Sbjct: 173 FKCGKPFERNGREFVVLTVKGQSFVLHQIRKMIGLVIAVVRGVAPSSTFDLI-------- 224

Query: 230 CGPLAPPEGLYFDSVEYS 247
             P AP  GL  D+V + 
Sbjct: 225 DIPKAPALGLVLDTVHFD 242


>gi|119618936|gb|EAW98530.1| pseudouridylate synthase 1, isoform CRA_a [Homo sapiens]
 gi|119618939|gb|EAW98533.1| pseudouridylate synthase 1, isoform CRA_a [Homo sapiens]
          Length = 338

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 94/261 (36%), Gaps = 30/261 (11%)

Query: 8   IEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
           + Y+G GY G QR        +I+  +  A+                +      RTD GV
Sbjct: 1   MAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTDKGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A  QV      + W+   + + +N++L     I IL L  V   F+++     R+Y Y 
Sbjct: 61  SAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNRCDARTYCYL 115

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQASSPIRT 171
           + T     A +          L  E ++          G H+F  F S    Q  S  R 
Sbjct: 116 LPT--FAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQDPSACRY 173

Query: 172 IDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           I                  IRV  +SF+  QIR  VG +  +  G    + LE++     
Sbjct: 174 ILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLERSW--GT 231

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
            K   P AP  GL  + V + 
Sbjct: 232 EKVDVPKAPGLGLVLERVHFE 252


>gi|291227559|ref|XP_002733751.1| PREDICTED: PseudoUridine Synthase family member (pus-1)-like
           [Saccoglossus kowalevskii]
          Length = 320

 Score =  137 bits (345), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 103/258 (39%), Gaps = 25/258 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  +++ Y+G GY G QR K   +I+G + KAI              + +      RTD
Sbjct: 56  RKVVLLLSYSGKGYMGMQRNKGVETIEGDLIKAIVTAGAVPQSHADIPQKMQFQRCARTD 115

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+RQV      +  +     + +N  L    +I ++        F+A+ +   R+Y
Sbjct: 116 KGVSAVRQVVSL---KMMLVDNAVEQINNSL--PPSIRVITYKRTTGGFNAKNTCSHRTY 170

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRT 171
            Y + T        +     +   +  +  +       G H+F  F S       S +R 
Sbjct: 171 SYLMPTFALSSNCNENY--RVTDEVHQKA-QDLLNCYKGTHNFHNFTSGKAFTEQSAMRF 227

Query: 172 IDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           +   +V+          + I ++ +SF+  QIR  +G +  +  G    + L+K  +A  
Sbjct: 228 MRELNVSQAFVRCGLEFVVITIIGQSFMIHQIRKMIGLVIAIIRGVAPKSTLDKCWEAG- 286

Query: 227 RKECGPLAPPEGLYFDSV 244
            K   P AP  GL  ++V
Sbjct: 287 -KMDIPKAPSLGLMLENV 303


>gi|10640247|emb|CAC12061.1| tRNA-pseudouridine synthase I related protein [Thermoplasma
           acidophilum]
          Length = 257

 Score =  137 bits (345), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 94/247 (38%), Gaps = 33/247 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y     Y GS + G+QR     S++ +I   +   +G    +  A RTD  V AL  
Sbjct: 6   MTNYAFKFGYEGSYFTGFQRGNGDHSVEDTIIDTL-KASGFDYAIKAAARTDRYVSALSN 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F L     P  +   +N+ +   D I + + + V   F+ R     ++Y Y I    
Sbjct: 65  V--FSLETGRSPEAVAGLINSRI---DHIYVHSYAEVPDDFNPRH-CTFKTYRYYI---- 114

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                       + + LDC ++ I     +G HDF  F  +   + + +RTI +    + 
Sbjct: 115 ------------LRQDLDCISLDINLGKFIGTHDFRRF--VRADSRNTVRTIINASCKND 160

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ +   ARSFL  QIR+ V  +                    +R     +A  + L 
Sbjct: 161 NGLLYLEFSARSFLWNQIRTMVAFILD----NIGVE--TDPFSTSERY--PRVARAQNLL 212

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 213 LWDIYYD 219


>gi|19922728|ref|NP_611646.1| CG3045 [Drosophila melanogaster]
 gi|7291383|gb|AAF46811.1| CG3045 [Drosophila melanogaster]
 gi|16182987|gb|AAL13605.1| GH14326p [Drosophila melanogaster]
 gi|220945178|gb|ACL85132.1| CG3045-PA [synthetic construct]
 gi|220955082|gb|ACL90084.1| CG3045-PA [synthetic construct]
          Length = 499

 Score =  137 bits (345), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 61/265 (23%), Positives = 93/265 (35%), Gaps = 47/265 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q++ + +I+ ++ +A+              H  GRTD  V A 
Sbjct: 101 VLLKITYFGWDYQGFACQEDSNDTIESNLFRALARTCLIESRATSNYHRCGRTDKEVSAF 160

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 161 CQVISIDLRSKHPPESQLDPTALSSEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 218

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             + R+Y Y                +     LD   MR A   LV   DF  F    +H 
Sbjct: 219 DCVSRTYRY----------------YFPKGDLDIAAMRKACDLLVRHADFRNFCKMDVHN 262

Query: 164 QASSPIRTIDHFDV---------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
             ++ +R +    V         NS  ++  + + A +FL  QIR  +  L LVG  K  
Sbjct: 263 GVTNYMRNLQSARVEACDQTNHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKEN 322

Query: 215 STDLEKALQAQDRKECGPLAPPEGL 239
              +   L  +         P  GL
Sbjct: 323 PGVISDLLDVESNPCKPQYTPAIGL 347


>gi|16082568|ref|NP_394390.1| tRNA pseudouridine synthase A [Thermoplasma acidophilum DSM 1728]
 gi|24212586|sp|Q9HJN5|TRUA_THEAC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 252

 Score =  137 bits (345), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 94/247 (38%), Gaps = 33/247 (13%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y     Y GS + G+QR     S++ +I   +   +G    +  A RTD  V AL  
Sbjct: 1   MTNYAFKFGYEGSYFTGFQRGNGDHSVEDTIIDTL-KASGFDYAIKAAARTDRYVSALSN 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  F L     P  +   +N+ +   D I + + + V   F+ R     ++Y Y I    
Sbjct: 60  V--FSLETGRSPEAVAGLINSRI---DHIYVHSYAEVPDDFNPRH-CTFKTYRYYI---- 109

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                       + + LDC ++ I     +G HDF  F  +   + + +RTI +    + 
Sbjct: 110 ------------LRQDLDCISLDINLGKFIGTHDFRRF--VRADSRNTVRTIINASCKND 155

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             L+ +   ARSFL  QIR+ V  +                    +R     +A  + L 
Sbjct: 156 NGLLYLEFSARSFLWNQIRTMVAFILD----NIGVE--TDPFSTSERY--PRVARAQNLL 207

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 208 LWDIYYD 214


>gi|281340805|gb|EFB16389.1| hypothetical protein PANDA_012338 [Ailuropoda melanoleuca]
          Length = 359

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 100/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 28  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVQSGCIPENHGEDMRKMSFQRCA 87

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 88  RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PPHIRILGLKRVTGGFNSKNKCDA 142

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E +R          G H+F  F S      
Sbjct: 143 RTYFYMLPT--FAFAHKDHDVQDERYRLSAETLRRVNGLLACYRGTHNFHNFTSQKGPHE 200

Query: 166 SSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +S  R I     +   V        I+V  +SF+  QIR  VG +  V  G    + LE+
Sbjct: 201 ASARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAVVKGYAPESVLER 260

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 261 SW--GEAKVDVPKAPGLGLVLERVHFE 285


>gi|194882124|ref|XP_001975163.1| GG20714 [Drosophila erecta]
 gi|190658350|gb|EDV55563.1| GG20714 [Drosophila erecta]
          Length = 497

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 95/264 (35%), Gaps = 46/264 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q++ + +I+ ++ +A+              H  GRTD  V A 
Sbjct: 100 VLLKITYFGWDYQGFACQEDSNDTIESNLFRALSRTCLIDSRANSNYHRCGRTDKEVSAF 159

Query: 59  RQVAHFDLVREWVPV------------ILCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 160 CQVISIDLRSKHSPEFQLDPTALSTEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 217

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             + RSY Y                +     LD   M  A   L    DF  F    +H 
Sbjct: 218 DCVSRSYRY----------------YFPKGDLDIGAMSQACDLLERHADFRNFCKMDVHN 261

Query: 164 QASSPIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
             ++ +R +    V        NS  ++  + + A +FL  QIR  +  L LVG  K + 
Sbjct: 262 GVTNYMRNLQSARVVACDENHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKESP 321

Query: 216 TDLEKALQAQDRKECGPLAPPEGL 239
           T + + L  +        +P  GL
Sbjct: 322 TVISELLDVESNPCKPQYSPAIGL 345


>gi|251823909|ref|NP_001156523.1| tRNA pseudouridine synthase A [Ovis aries]
 gi|238815029|gb|ACR56711.1| pseudouridylate synthase 1 [Ovis aries]
          Length = 400

 Score =  136 bits (344), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 100/274 (36%), Gaps = 44/274 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 57  RKIVLLMAYSGKGYHGMQRNVGSSKFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 116

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 117 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDA 171

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL----------VGRHDFTTFR 159
           R+Y Y + T     A            L  E  R++A+ L           G H+F  F 
Sbjct: 172 RTYFYMLPT----FAF-----AHKDHDLQDETYRLSAETLGRVNRLLACYKGTHNFHNFT 222

Query: 160 S-IHCQASSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S       S  R I     +   V        I+V  +SF+  QIR  VG +  +  G  
Sbjct: 223 SQKGPHEPSARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAIIKGYA 282

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
               LE+     + K   P AP  GL  + V + 
Sbjct: 283 PEGVLERCW--GEAKVDVPKAPGLGLVLERVHFE 314


>gi|301775629|ref|XP_002923235.1| PREDICTED: tRNA pseudouridine synthase A-like [Ailuropoda
           melanoleuca]
          Length = 426

 Score =  136 bits (344), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 100/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 89  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVQSGCIPENHGEDMRKMSFQRCA 148

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 149 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PPHIRILGLKRVTGGFNSKNKCDA 203

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L  E +R          G H+F  F S      
Sbjct: 204 RTYFYMLPT--FAFAHKDHDVQDERYRLSAETLRRVNGLLACYRGTHNFHNFTSQKGPHE 261

Query: 166 SSPIRTI-----DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           +S  R I     +   V        I+V  +SF+  QIR  VG +  V  G    + LE+
Sbjct: 262 ASARRYILDMFCEEPFVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAVVKGYAPESVLER 321

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 322 SW--GEAKVDVPKAPGLGLVLERVHFE 346


>gi|126323933|ref|XP_001378494.1| PREDICTED: similar to Pseudouridine synthase 1 [Monodelphis
           domestica]
          Length = 435

 Score =  136 bits (344), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 99/267 (37%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL------VTGEIVV---VHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+          GE +         
Sbjct: 100 RKIVLLMAYSGKGYHGMQRNLGSSQFKTIEDDLVFALVQSGCIPENHGEDMRKMAFQRCA 159

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  Q+      + W+   + + +N++L     I IL L  V   F+++     
Sbjct: 160 RTDKGVSAAGQIVSL---KVWLIDNILEKINSHL--PSHIRILGLKRVTGSFNSKNRCDA 214

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     A +          L     E +        G H F  F S    + 
Sbjct: 215 RTYFYMLPT--FAFAHKDHDVQDETYRLSSETLEKVNQLLASYKGTHSFHNFTSQKGPKE 272

Query: 166 SSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I         V        I+V  +SF+  QIR  VG +  +  G    + +E+
Sbjct: 273 PSARRYIMEMHCEAPFVREGMEFAVIKVKGQSFMMHQIRKMVGLVIAIMKGYVPESVMER 332

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 333 SW--GEEKVDIPKAPGLGLVLERVHFE 357


>gi|308507857|ref|XP_003116112.1| CRE-PUS-1 protein [Caenorhabditis remanei]
 gi|308251056|gb|EFO95008.1| CRE-PUS-1 protein [Caenorhabditis remanei]
          Length = 438

 Score =  136 bits (343), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 57/267 (21%), Positives = 96/267 (35%), Gaps = 25/267 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---------VHGAGRTDS 53
           +Y M++ Y G  Y+G Q QK+  +I+  + +A+                     A RTD 
Sbjct: 34  KYAMLLGYQGKKYYGMQLQKDLPTIESKLLEAMEKAGWITAAQRDKPFDFFFQRAARTDR 93

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            V A RQ+    L R+        A      + D I +  +      FH +     R+Y 
Sbjct: 94  AVSAARQMCGMQLPRDDDKYQTDGAGVLNNLLPDDIRVFGMRRTINFFHPQKQCDYRTYS 153

Query: 114 YRIIT-RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRT 171
           Y   +   A        A+ +PK      +        G H+F  + +       S  R 
Sbjct: 154 YTCPSFVFAKPTELTNSAFRLPKET-LAEVNDILSIYKGTHNFFNYTAKRAYNDMSSNRY 212

Query: 172 IDHFDVNSFG-----------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           I  F+                  ++I V  +SF+  QIR  VG +  V       + +++
Sbjct: 213 IVSFECKEPFLFRDEFRKEDVEFVQIVVKGQSFVLHQIRKMVGMVITVVRELHLKSAIQR 272

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           + + Q  +   P+AP  GL  +   Y 
Sbjct: 273 SFEGQ--RMDIPMAPGLGLLLERTHYD 297


>gi|268568248|ref|XP_002647980.1| C. briggsae CBR-PUS-1 protein [Caenorhabditis briggsae]
 gi|187040672|emb|CAP20635.1| CBR-PUS-1 protein [Caenorhabditis briggsae AF16]
          Length = 437

 Score =  136 bits (343), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 55/266 (20%), Positives = 92/266 (34%), Gaps = 23/266 (8%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---------VHGAGRTDS 53
           +Y M++ Y G  Y+G Q QK+  +I+  + +A+                     A RTD 
Sbjct: 34  KYAMLLGYQGKKYYGMQLQKDLPTIESKLLEAMEKAGWITAAQREKPFDFFFQRAARTDR 93

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            V A RQ+    L R+     +         + + I +  +      FH +     R+Y 
Sbjct: 94  AVSAARQMCGMQLPRDDEKYKVDGPGILNNLLPNDIRVFGMKRTINFFHPQKQCDYRTYS 153

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTI 172
           Y   T       E   A           +        G H+F  + +       S  R I
Sbjct: 154 YTCPTFVFAKPTELTNAAFRISKETLAEVNDILSIYKGTHNFFNYTAKRAYDDMSSNRYI 213

Query: 173 DHFDVNSFG-----------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
             F+                  I+I V  +SF+  QIR  VG +  V       + ++++
Sbjct: 214 VSFECKEPFLFRDEFRKEDVEFIQIVVKGQSFVLHQIRKMVGMVITVVRELHLKSAIQRS 273

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
            + Q  +   P+AP  GL  +   Y 
Sbjct: 274 FEGQ--RMDIPMAPGLGLLLERTHYD 297


>gi|56693277|ref|NP_001008603.1| tRNA pseudouridine synthase A [Danio rerio]
 gi|56269412|gb|AAH86827.1| Pseudouridine synthase 1 [Danio rerio]
          Length = 376

 Score =  136 bits (343), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/264 (21%), Positives = 100/264 (37%), Gaps = 26/264 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAI---------FLVTGEIVVVHGAGR 50
           +  +++ Y+G GY+G QR        +I+  +  A+              + +    + R
Sbjct: 41  KVALLMAYSGKGYYGMQRNARNSQFKTIEDELVTALVGARCIPEGHAEEMKKMSFQRSAR 100

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GV A+ +V      + W+   + + +NA+L     I +L    V   F+++ +   R
Sbjct: 101 TDKGVSAVGRVVSL---KVWMIENILEKINAHL--PPRIRVLGCKRVTGGFNSKNNCYAR 155

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLD-CENMRIAAQHLVGRHDFTTFRS-IHCQASSP 168
           +Y Y + T                 + D  + +        G H+F  F S    +  S 
Sbjct: 156 TYSYMLPTVAFSPKDYNQEDTSFRLTSDTLQTVNRLFCLYKGTHNFHNFTSQKGHRDPSA 215

Query: 169 IRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           +R I H       +        I V  +SF+  QIR  +G +  V  G      +EK+  
Sbjct: 216 MRYITHMSCGEPFIRKDVEFAVITVRGQSFMMHQIRKMIGLVIAVVKGYVDEGVMEKSW- 274

Query: 224 AQDRKECGPLAPPEGLYFDSVEYS 247
             + K     AP  GL  + V + 
Sbjct: 275 -GEEKVGVSKAPGLGLVLERVHFD 297


>gi|195488597|ref|XP_002092382.1| GE11697 [Drosophila yakuba]
 gi|194178483|gb|EDW92094.1| GE11697 [Drosophila yakuba]
          Length = 497

 Score =  136 bits (342), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 93/264 (35%), Gaps = 46/264 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q++ + +I+ ++ +A+              H  GRTD  V A 
Sbjct: 100 VLLKITYFGWDYQGFACQEDSNDTIEANLFRALTRTCLIESRATSNYHRCGRTDKEVSAF 159

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 160 CQVISIDLRSKHPPESQLDPTAISTEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 217

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             + RSY Y                +     LD   M  A   LV   DF  F    +H 
Sbjct: 218 DCVSRSYRY----------------YFPKGDLDIAAMSKACDLLVRHADFRNFCKMDVHN 261

Query: 164 QASSPIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
             ++ +R +    V        NS  ++  + + A +FL  QIR  +  L LVG  K   
Sbjct: 262 GVTNYMRNLQSARVEACDENHTNSGYDMYYLEIQANAFLWHQIRCIMAVLLLVGQKKENP 321

Query: 216 TDLEKALQAQDRKECGPLAPPEGL 239
             + K L  +         P  GL
Sbjct: 322 AVISKLLDVESNPCKPQYTPAIGL 345


>gi|256087150|ref|XP_002579739.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665218|emb|CAZ35978.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 369

 Score =  136 bits (342), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 100/259 (38%), Gaps = 30/259 (11%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGVHALRQ 60
           Y+G GY+G QR     +I+G + KA+F             + V    A +TD  V AL Q
Sbjct: 2   YSGWGYYGMQRCPVFPTIEGELSKALFTCGQLDNLTSEEHKRVHFQRASKTDKSVSALGQ 61

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-- 118
           V    L  +     L   LN  L   + I +L++  V + F +  S   R Y Y + T  
Sbjct: 62  VCSMQLKEDTD---LLSKLNNSL--PENIRVLDIIRVTRGFSSYSSCTHRIYDYLLPTFA 116

Query: 119 -RQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRSIH-CQASSPIRTID 173
              A  +L     W     L  E +       +   G H+F  F S       S  R I 
Sbjct: 117 LSPATSSLNDSTCWTYR--LTVEQITQVNRLLEKYKGTHNFYNFTSGRLVTDRSCSRYII 174

Query: 174 HFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
             +              IR+  +SF+  QIR  +G    V  G  T   +   + ++ R 
Sbjct: 175 SAECMPTFLLGEHQYTIIRIAGQSFMLHQIRKMIGLALAVLRGYAT-EAVFDIVFSKARI 233

Query: 229 ECGPLAPPEGLYFDSVEYS 247
           +  P AP  GL  + V++S
Sbjct: 234 DI-PKAPGLGLMLNQVDFS 251


>gi|301604562|ref|XP_002931922.1| PREDICTED: tRNA pseudouridine synthase A [Xenopus (Silurana)
           tropicalis]
          Length = 399

 Score =  136 bits (342), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 102/267 (38%), Gaps = 30/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  + +A+ L            + +      
Sbjct: 55  RKVVLLMAYSGKGYHGMQRNVGSSQFKTIEDELVQALVLSGCIPDNHAEDMKKMSFQRCA 114

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A  QV      + W+   + + +N  L     I IL L  V  +F+++ S   
Sbjct: 115 RTDKGVSAAGQVVSL---KIWLIDNVVEKINENL--PSHIRILGLKRVTGRFNSKNSCDA 169

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRS-IHCQA 165
           R+Y Y + T     + +   A      L  E +           G  +F  F S    + 
Sbjct: 170 RTYSYTLPT--FAFSHKDKEAQDENFRLSQETLNRVNELLALYKGTRNFHNFTSQKGPRD 227

Query: 166 SSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I               L  I+V  +SF+  QIR  +G +  V  G   ++ +E+
Sbjct: 228 PSAKRYIMEMHCEPPFQQGGLELAVIKVKGQSFMMHQIRKMIGLVIAVVKGFAPTSIIER 287

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +    + K   P AP  GL  + V + 
Sbjct: 288 SW--GEEKVDIPKAPGLGLVLERVHFE 312


>gi|226468594|emb|CAX69974.1| putative tRNA pseudouridine synthase 3 [Schistosoma japonicum]
          Length = 388

 Score =  136 bits (342), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 92/279 (32%), Gaps = 60/279 (21%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G   Q     ++   +  A+                 GRTD GV  +
Sbjct: 71  IALKLSYLGWQYCGLVPQGCYTLTVMDRLLDALEKAKLIENRSECSFSVCGRTDKGVSGI 130

Query: 59  RQVA-------------------HFDLVREWVPVI---LCKALNAYLKISDTISILNLSI 96
            QV                         R+ VP         LN  L     I +L  S 
Sbjct: 131 CQVVSFVSRSVVAEGVGVIEDSGCRISERQEVPDKEMDFVSILNRNL--PRDIRVLAWSP 188

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           V  +F+ARF   RRSY Y                      LD E+M  A   LVG HDF 
Sbjct: 189 VSPEFNARFDCRRRSYEYYFPES----------------GLDIESMIDAGNRLVGVHDFR 232

Query: 157 TFRSIHCQAS--SPIRTIDHFDVN------SFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
            F +   +    S +R I    +N          L  + V A  FL+ QIR     L +V
Sbjct: 233 NFCASRIEKDTVSFVREIFEVVINVVDSSDHHTKLYCLCVSASGFLYHQIRYIASILFMV 292

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G G  + + ++  L           A P+  Y  + +Y 
Sbjct: 293 GRGYESPSVIDDMLD-----LTKTPAKPQ--YQLAADYP 324


>gi|326774000|ref|ZP_08233282.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
 gi|326636139|gb|EGE37043.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
          Length = 169

 Score =  136 bits (342), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 46/149 (30%), Positives = 70/149 (46%), Gaps = 11/149 (7%)

Query: 109 RRSYLYRIITRQAPLALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
            R Y YRI    AP    +      +P +LD E M  +A+ L+G HDF ++     + ++
Sbjct: 2   SRRYTYRIADAAAPRDPARRATVLWLPDALDVEAMDASARALLGEHDFLSYCKPR-EGAT 60

Query: 168 PIRTIDHFDVNSFG---------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            IRT+                   L+ + VVA +F H+ +RS VG+   VG G+   T  
Sbjct: 61  TIRTLRTLQWRRIEAGPDAGPESGLVTLSVVADAFCHSMVRSLVGAGLAVGQGRKPVTWP 120

Query: 219 EKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + L A+ R+   P+APP GL  + V Y 
Sbjct: 121 RELLDARTRQSAAPVAPPHGLTLEEVTYP 149


>gi|194755854|ref|XP_001960194.1| GF13245 [Drosophila ananassae]
 gi|190621492|gb|EDV37016.1| GF13245 [Drosophila ananassae]
          Length = 492

 Score =  135 bits (341), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 87/248 (35%), Gaps = 46/248 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G   Q++ + +I+  + +A+              H  GRTD  V A 
Sbjct: 100 VLLKVSYFGWDYQGLACQEDSNDTIESHLFRALTRTCLIESRATSNYHRCGRTDKEVSAF 159

Query: 59  RQVAHFDLVREWVPVILCKA------------LNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P     A            LN  L     I  +  + +    + ARF
Sbjct: 160 CQVISIDLRSKHPPESQLDATSISSEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 217

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             + R+Y Y                +     LD   M+ A  HLV   DF  F    +H 
Sbjct: 218 DCVARTYRY----------------YFPKGDLDIPAMQEACNHLVRHADFRNFCKMDVHN 261

Query: 164 QASSPIRTIDHFDVN--------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
             ++  R +    V         S  ++  + + A +FL  QIR  +  L LVG  K   
Sbjct: 262 GVTNYTRNLQSARVEACEETLTDSGYDMYYLEIQANAFLWHQIRCIMAVLILVGQKKEKP 321

Query: 216 TDLEKALQ 223
           + +   L 
Sbjct: 322 SVVTDLLD 329


>gi|300709217|ref|XP_002996775.1| hypothetical protein NCER_100100 [Nosema ceranae BRL01]
 gi|239606099|gb|EEQ83104.1| hypothetical protein NCER_100100 [Nosema ceranae BRL01]
          Length = 313

 Score =  135 bits (341), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/221 (25%), Positives = 90/221 (40%), Gaps = 19/221 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             ++I Y+G  Y G    K+G SI   I+ A+ L T    +V+ AGRTD GV A+  VA 
Sbjct: 39  IALLISYHGEKYRGLAECKDGDSIGNRIKNALLLSTLADHIVY-AGRTDKGVSAIGMVAS 97

Query: 64  FDLVREWVPVILCKALN------------AYLKISDTISILNLSIVDKQFHARFSAIRRS 111
             +            LN                + + I ++  + V+  F ARF+ I+R 
Sbjct: 98  VKIKSLLRENTSRYFLNDDDNHEFNYQAILNNYLPEDIRVIGWAPVEDGFSARFTCIKRK 157

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y Y       P    K     I    D   M    Q ++   +F        +++   RT
Sbjct: 158 YRYYFTN---PFVKIKN---QIRLKYDINKMEEMCQKILTLKNFYNLSKHSDKSARYNRT 211

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +D   +   G+L  + + A+SFLH  +R     L++ G  +
Sbjct: 212 VDICQIIKEGDLYYLDIQAKSFLHNMVRKIFWVLEMAGKDE 252


>gi|195346649|ref|XP_002039870.1| GM15659 [Drosophila sechellia]
 gi|194135219|gb|EDW56735.1| GM15659 [Drosophila sechellia]
          Length = 498

 Score =  135 bits (341), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 93/264 (35%), Gaps = 46/264 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q++ + +I+ ++ +A+              H  GRTD  V A 
Sbjct: 101 VLLKITYFGWDYQGFACQEDSNDTIESNLFRALTRTCLIESRATSNYHRCGRTDKEVSAF 160

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 161 CQVISIDLRSKHPPESQLDPTSLSSEIDYCGLLNRVL--PKNIQCVAWMPLRSSVYSARF 218

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             + RSY Y                +     LD   MR A   LV   DF  F    +H 
Sbjct: 219 DCVSRSYRY----------------FFPKGDLDIAAMRKACDLLVRHADFRNFCKMDVHN 262

Query: 164 QASSPIRTIDHFDV--------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
             ++ +R +    V        NS  ++  + + A +FL  QIR  +  L LVG  K   
Sbjct: 263 GVTNYMRNLQSARVEACDENHTNSGYDMYYLEIRANAFLWHQIRCIMAVLILVGQKKEKP 322

Query: 216 TDLEKALQAQDRKECGPLAPPEGL 239
             +   L  +         P  GL
Sbjct: 323 AIISDLLNVESNPCKPQYTPAIGL 346


>gi|17565126|ref|NP_507242.1| PseudoUridine Synthase family member (pus-1) [Caenorhabditis
           elegans]
 gi|3880517|emb|CAA16518.1| C. elegans protein W06H3.2a, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 415

 Score =  135 bits (340), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 52/266 (19%), Positives = 92/266 (34%), Gaps = 23/266 (8%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV---------VHGAGRTDS 53
           +Y M++ Y G  Y+G Q QK+  +I+  + +A+                     A RTD 
Sbjct: 34  KYAMLLGYQGKKYYGMQLQKDLPTIESKLLEAMETAGWITTAQKEKPFDFFFQRAARTDR 93

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            V A RQ+    L R+        A      +   I +  +      FH +     R+Y 
Sbjct: 94  AVSAARQMCGMQLPRDDAKYQAEGAGILNNILPADIRVFGMRRTTNFFHPQKQCDHRTYS 153

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTI 172
           Y   +       E   +           +       +G H+F  + +       S  R I
Sbjct: 154 YTCPSFVFAKPTELTNSSFRLSPETLAEVNSILSIYLGTHNFFNYTAKRAYDDMSSNRYI 213

Query: 173 DHFDVNSFG-----------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
             F+                  ++I +  +SF+  QIR  VG +  V       + ++++
Sbjct: 214 ISFECKEPFLFRDDFRKEDVEFVQIVIKGQSFVLHQIRKMVGMVITVIRELHLKSSIQRS 273

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
            + Q  +   P+AP  GL  +   Y 
Sbjct: 274 FEGQ--RMDIPMAPGLGLLLERTHYD 297


>gi|302851624|ref|XP_002957335.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
 gi|300257294|gb|EFJ41544.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
          Length = 642

 Score =  135 bits (340), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 92/259 (35%), Gaps = 50/259 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
             + + Y G  Y G+ RQ N    + +IE                 R   GV AL   + 
Sbjct: 111 VALELMYVGWSYQGFARQDNT---ENTIEA------------SSVKRGWGGVVALNLRSV 155

Query: 64  FDLVREWVPVIL----CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
             +     P+ L     + +N  L     + +L  + V + F++        Y+Y     
Sbjct: 156 ARVDEPEAPLELEYDYPRLVNKAL--PPDVRVLGWTAVPENFNS-------RYVY----- 201

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVN 178
             P   E         SLD + MR AA   VG HDF  F         S  R I  F ++
Sbjct: 202 -HPDPPES-----CRYSLDIDAMRAAAARFVGEHDFRNFCKPDVATVRSFRRRILSFTLD 255

Query: 179 SFG--------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRK 228
                       +  I V   +FL  Q+R     L +VG G+     + + L  +A  RK
Sbjct: 256 PVPTSSSDGAHRVFAITVRGTAFLWHQVRCMAAVLLMVGRGQERPEVVSELLDVEAHPRK 315

Query: 229 ECGPLAPPEGLYFDSVEYS 247
               +AP E L   +  +S
Sbjct: 316 PQYSMAPEEPLLLYACGFS 334


>gi|260781560|ref|XP_002585875.1| hypothetical protein BRAFLDRAFT_110975 [Branchiostoma floridae]
 gi|229270936|gb|EEN41886.1| hypothetical protein BRAFLDRAFT_110975 [Branchiostoma floridae]
          Length = 312

 Score =  134 bits (339), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 85/229 (37%), Gaps = 53/229 (23%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+Q Q+   ++I+  + +A+         +    H  GRTD GV A 
Sbjct: 70  VALKVAYLGWSYDGFQSQETTDNTIEARLFEALTKTRLIEKRQSSNYHRCGRTDKGVSAF 129

Query: 59  RQVAHFDLVREWV----------------------PVILCKALNAYLKISDTISILNLSI 96
            QV   DL                            +     LN  L     I +L  + 
Sbjct: 130 GQVISLDLRTNLTDGAGVIPRPEGTANHREGDKTTEIKYVYILNKVL--PPDIRVLAWAP 187

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           VD  F ARFS  +R+Y Y                +    +LD ++M +A Q LVG HDF 
Sbjct: 188 VDPDFSARFSCQQRTYKY----------------FFPKGNLDIQSMHLAGQKLVGEHDFR 231

Query: 157 TFRSIH--CQASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQ 197
            F  +    +  + IR I    V   G       + E +VV  +FL  Q
Sbjct: 232 NFCKMDVANRVVTFIRRIISTHVCVTGEETGGYQMCEFQVVGNAFLWHQ 280


>gi|321464083|gb|EFX75094.1| hypothetical protein DAPPUDRAFT_12957 [Daphnia pulex]
          Length = 319

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/265 (21%), Positives = 98/265 (36%), Gaps = 31/265 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           ++ +++ Y+G  Y G Q      +++G + +A   +         + + V    A RTD 
Sbjct: 4   KFAILLSYSGQNYLGMQFNHGFKTVEGELFQAFMKLEIMDDESFKSPQTVHFQRAARTDK 63

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+RQV    +        L   LN+ L   + I +  +  V   F+++ +   RSY 
Sbjct: 64  GVSAVRQVISLKIRT--PDEDLVNQLNSLL--PNCIKVFAMRKVTGGFNSKIACDSRSYS 119

Query: 114 YRIITRQAPLALEKGRA-----WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
           Y + T     A           + +   +  + +        G  ++  F S    Q  S
Sbjct: 120 YVMPT----FAFTSKEVAPTHGYRVTSKI-LDEVNSLLSVFKGTRNYHNFTSGRPAQDPS 174

Query: 168 PIRTIDHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             R I  F             ++I +  +SF+  QIR  +G    V  G      L+KA 
Sbjct: 175 CKRYITQFSCGDPFMIKEVEFVKITIKGQSFMLHQIRKMIGLTISVMRGFVPREILDKAF 234

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
             +  +   P AP   L  +   Y 
Sbjct: 235 --KMERVNVPTAPSLNLLLEEPHYD 257


>gi|158298879|ref|XP_319023.4| AGAP009903-PA [Anopheles gambiae str. PEST]
 gi|157014098|gb|EAA14028.4| AGAP009903-PA [Anopheles gambiae str. PEST]
          Length = 457

 Score =  134 bits (337), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 94/244 (38%), Gaps = 46/244 (18%)

Query: 50  RTDSGVHALRQVAHFDLVRE----WVPVILCKALNAYLKIS-DTISILNLSIVDKQFHAR 104
           RTD+GVHAL    H DL R     +    + K LN   +    ++ IL+   V   FHAR
Sbjct: 11  RTDTGVHALHNTVHVDLQRPNGKPYDSDRITKTLNRAFEKDGQSLRILSTVRVPASFHAR 70

Query: 105 FSAIRRSYLYRI----------------ITRQAPLALEKGRAWLI-PKSLDCENMRIAAQ 147
             A  R+YLYR+                   +     E  R + +     D       A+
Sbjct: 71  LCAKSRTYLYRLAVLKREYARESGRQQHPHARFIPIEEHDRCYFLGHSEFDINAFASVAR 130

Query: 148 HLVGRHDFTTFRSIHC------QASSPIRTIDHFDVNS---------------FGNLIEI 186
              G HDF TF ++        +A   +R ID   V                 + +  ++
Sbjct: 131 MFEGMHDFRTFMAVAKGNPRQQEAMHSLRRIDQITVERGHTMTAAFNRERTEHYYDFWDV 190

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC---GPLAPPEGLYFDS 243
           R+  RSFL+ Q+R  VG+     +G+ T  D+ + L    +        +AP   LY   
Sbjct: 191 RIRGRSFLYRQVRRMVGAWVAAAEGRITERDIYRMLTVPSQNSWCSNVFVAPAYALYLCH 250

Query: 244 VEYS 247
           VEY 
Sbjct: 251 VEYD 254


>gi|225427081|ref|XP_002275354.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 448

 Score =  134 bits (337), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 107/315 (33%), Gaps = 74/315 (23%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-------------VHGAGR 50
           + +++ Y+G+ + GWQ+Q   +++QG +E ++     E                V  AGR
Sbjct: 125 FKIVLSYHGASFDGWQKQPGLNTVQGLVEASLGRFVDERKAQQLKEKNLPVEGMVTVAGR 184

Query: 51  TDSGVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           TD GV AL+QV  F   ++ V V  +  A+N        + ++++S V + FH  FSA  
Sbjct: 185 TDKGVTALQQVCSFYTWKKDVKVQDIEDAING--AAPGKLRVISVSEVSRIFHPNFSAKW 242

Query: 110 RSYLYRIITRQAPL--------------ALEKGR-------------------------- 129
           R Y Y                       +  +                            
Sbjct: 243 RHYFYIFPLNDGDDGEQISENEMDIQKISFNEKYGEQGSECPAQYNGGENTENLIFDDDG 302

Query: 130 ---AWLIPKSLDCENMRIAAQHLVGR--------HDFTTFRSIHC-------QASSPIRT 171
              +   P +     +    + L G+         D    R+I          A +    
Sbjct: 303 EFESRKKPSTFSISRVDQLLRQLEGKLLSYKIFARDTKASRNIGPPTECFVFHARATEAR 362

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +   D      ++ I +VA  FL   +R  V +             L K + A  R+   
Sbjct: 363 LQFSDDGEGTKVMCIELVANRFLRKMVRVLVATSIREAAAGAEQDALLKLMDATCRRATA 422

Query: 232 PLAPPEGLYFDSVEY 246
           P APP+GL    V +
Sbjct: 423 PPAPPDGLCLIDVGF 437


>gi|312221288|emb|CBY01228.1| similar to pseudouridylate synthase 3 [Leptosphaeria maculans]
          Length = 597

 Score =  134 bits (337), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 67/365 (18%), Positives = 91/365 (24%), Gaps = 121/365 (33%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFL---------------------- 37
             +   Y G  Y G++  KN      +I+  + KA+                        
Sbjct: 72  IALKFAYLGQRYNGFEHHKNNSTPLPTIEEELWKALVKTRLINPIPTQGDATGYSRVDRK 131

Query: 38  -----------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV--------------- 71
                      V  E       GRTD GV A  QV    +                    
Sbjct: 132 TFAAWDREGADVNWEGCEYSKCGRTDRGVSAFGQVIGVRVRSNRPLPKTAKAQDELSASE 191

Query: 72  ---------------PVILCKALN-----------AYLKISDTISILNLSI-VDKQFHAR 104
                          P    K+ N               +   I +          F AR
Sbjct: 192 QAKTSEEPISMADSEPETEGKSFNDLTDELPYIQHLNRVLPPDIRVYAWCPNPPPDFSAR 251

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKS-----------LDCENMRIAAQHLVGRH 153
           FS   R Y Y                +    S           LD E MR   Q L+G H
Sbjct: 252 FSCKERRYKYFFTNPSFAPVPGSSGVYNTHTSSPTATRTREGWLDIEAMRKGCQQLIGLH 311

Query: 154 DFTTFRSIHC--QASSPIRTIDHFD---------------------------VNSFGNLI 184
           DF  F  I    Q S+  R I H D                           V     L 
Sbjct: 312 DFRNFCKIDASKQLSNFQRRIFHADIEEVSPLSIPSFLSHPALQSPWANSPAVEQQPKLY 371

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRKECGPLAPPEGLYFD 242
              +   +FL  Q+RS +  L L+G G    + +   L   A   +    +A    L   
Sbjct: 372 SFTLHGSAFLWHQVRSLIAVLFLIGQGLEPPSLISSLLDISANPTRPKYEMASDAPLVLW 431

Query: 243 SVEYS 247
              + 
Sbjct: 432 DCIFP 436


>gi|290562699|gb|ADD38745.1| tRNA pseudouridine synthase 3 [Lepeophtheirus salmonis]
          Length = 420

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/277 (21%), Positives = 93/277 (33%), Gaps = 60/277 (21%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
            +    I Y G  Y G+  Q++   +I+  + KA+         E    H  GRTD GV 
Sbjct: 58  RKVLFQITYFGWNYHGFTTQEDSCMTIEAHLFKALLTTCLIQSRETSNYHRCGRTDKGVS 117

Query: 57  ALRQVAHFDL---------------------VREWVPVILCKALNAYLKISDTISILNLS 95
           A RQV   D+                           +   K +N+ L     I ++  +
Sbjct: 118 AFRQVISIDVRTNLKEGIGVFDYPDCKADSRPDMPHEIDYIKIINSNL--PPDIQLIAWT 175

Query: 96  IV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHD 154
              +++  ARF   +R+Y Y                           M  A   LVG HD
Sbjct: 176 PAQNRELSARFDCKKRTYKYFFPLGSIKS---------------LSKMNEAGAKLVGSHD 220

Query: 155 FTTFRSIHC------------QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFV 202
           F  F  +                S+ +        +S  +L  ++V   +FL  QIR  V
Sbjct: 221 FRNFCKMDVSNGVLTYIRRMVNVSTSVLEPSKEKESSPYDLCVLKVEGNAFLWHQIRCIV 280

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             L  +G G+     +++ L  +      P  P  GL
Sbjct: 281 TVLFHIGQGREEPELIDELLDIEK----NPCRPQYGL 313


>gi|195429481|ref|XP_002062787.1| GK19511 [Drosophila willistoni]
 gi|194158872|gb|EDW73773.1| GK19511 [Drosophila willistoni]
          Length = 495

 Score =  133 bits (335), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 90/250 (36%), Gaps = 48/250 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q++ + +I+ ++ +A+              H  GRTD  V A 
Sbjct: 109 VLLKVTYFGWDYQGFACQEDSNDTIESNLFRALTRTCLIESRANSNYHRCGRTDKEVSAF 168

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  ++                 C  LN  L     I  +  + +    + ARF
Sbjct: 169 CQVISIDLRSKYPAESQLDPTSLATEIDYCGLLNRVL--PKNIQCVAWMPLRSPVYSARF 226

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             I RSY Y                +     LD E M+ A Q LV   DF  F    +H 
Sbjct: 227 DCIARSYRY----------------YFPKGDLDIEAMQEACQLLVNHADFRNFCKMDVHN 270

Query: 164 QASSPIRTIDHFDVNSFGN----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
             +S +R +    V               +  + + A +FL  QIR  +  L LVG  K 
Sbjct: 271 GVTSFMRNLQAARVQPCEQTRNEKVSGYAMFYLEIKANAFLWHQIRCIMAILLLVGQRKE 330

Query: 214 TSTDLEKALQ 223
            S+ +   L 
Sbjct: 331 KSSIISDLLD 340


>gi|310794568|gb|EFQ30029.1| tRNA pseudouridine synthase A [Glomerella graminicola M1.001]
          Length = 570

 Score =  133 bits (334), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/345 (19%), Positives = 91/345 (26%), Gaps = 110/345 (31%)

Query: 4   YCMIIEYNGSGYFGW--QRQKNGSSIQGSIEKAIFL-----------VTGEIVVVHGAGR 50
             + + Y G  Y G+      +  +I+G +  A+             V  +       GR
Sbjct: 94  IALKLAYLGKRYGGFEYAASASLPTIEGELWNALTKACLIFPEDPDVVNFDCCEYSKCGR 153

Query: 51  TDSGVHALRQVAHFD--------------------------------------------- 65
           TD GV A  QV                                                 
Sbjct: 154 TDRGVSAFGQVIGLRVRSNKPLPKKPEEEAAAAEAEEGDTAMAGTAEEEEKKKRQEQTQK 213

Query: 66  --------LVREWVPVILCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRI 116
                          +   K LN  L   D I I          F ARFS   R Y Y  
Sbjct: 214 QKKKPEKEWDDINDEIQYVKVLNRLL--PDDIRITAWCPSPPPDFSARFSCEERQYRYFF 271

Query: 117 ITRQA----------PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQ 164
                          P  L +G        LD E M  AAQ  VG HDF  F  +    Q
Sbjct: 272 TQPAFTPTAATSDGTPSGLREGY-------LDIEAMNEAAQRFVGDHDFRNFCKVDGSKQ 324

Query: 165 ASSPIRTIDHFDVNSFGN--------------------LIEIRVVARSFLHTQIRSFVGS 204
            ++  R +    V    +                    +    +   +FL  QIR  V  
Sbjct: 325 ITNFERRMFEASVGEVRDVGSALPYLGCSAADGGQLPKVYSFNIRGTAFLWHQIRHMVTI 384

Query: 205 LKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
           L LVG        + + L  +   RK    LA    L   +  + 
Sbjct: 385 LFLVGQRLERPELVTELLDVEKSPRKPNYDLAHETPLVLWNCVFP 429


>gi|159117386|ref|XP_001708913.1| Pseudouridine synthase, putative [Giardia lamblia ATCC 50803]
 gi|157437027|gb|EDO81239.1| Pseudouridine synthase, putative [Giardia lamblia ATCC 50803]
          Length = 351

 Score =  133 bits (334), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 55/275 (20%), Positives = 99/275 (36%), Gaps = 56/275 (20%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           +R  +++ ++G+ + G   Q   GS+++G++ + +          T + + +   GRTD+
Sbjct: 1   MRVALLVAFHGTAFHGNAYQPTGGSTVEGALFEGLQKTGYLKENETIKDIELERTGRTDA 60

Query: 54  GVHALRQVAHFDLVR----------------------EWVPVIL---------CKALNAY 82
           GV A   +    L +                         P  +         C A +  
Sbjct: 61  GVSAECMLYTLQLGKLVPAVPCLPPHNSRVLGALEGLPIEPSSICIHTSGSATCLAFHLN 120

Query: 83  LKISDTISILNLS-IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
             +   I +L LS  + K F AR S + R Y Y +              + +P +L  E 
Sbjct: 121 RVLPSQIRVLGLSTAIPKDFSARHSCVAREYEYILG-------------YNVPPNL-REK 166

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASS-PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
              AAQ  +G + F  F        +   R I   +V    N     V+  +FL+ Q+R 
Sbjct: 167 ANSAAQRFLGSNSFHNFCHHERDHKTVYNRQIYCSEVYEHENACIFHVIGSAFLYHQVRY 226

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
               L  +  G    + +E  L  ++    G   P
Sbjct: 227 MASMLIHIMAGLENESAIEYLL-TKELSISGHSFP 260


>gi|315304909|ref|ZP_07875014.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
 gi|313626716|gb|EFR95744.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
          Length = 127

 Score =  133 bits (334), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 46/117 (39%), Positives = 62/117 (52%), Gaps = 3/117 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY  +I Y+GSG++G+Q Q N  ++Q  IEKA+  +  G+ V V  +GRTD+GVHA  
Sbjct: 8   MTRYKAVISYDGSGFYGYQVQPNTRTVQAEIEKALKKMHKGKSVRVTASGRTDTGVHAKG 67

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           QV HFD           KAL         IS + +      FHARF  + + Y Y I
Sbjct: 68  QVIHFDSELAISAEKFQKALQVM--TPFDISFITVEETPADFHARFGTVGKEYRYII 122


>gi|303317424|ref|XP_003068714.1| pseudouridylate synthase, putative [Coccidioides posadasii C735
           delta SOWgp]
 gi|240108395|gb|EER26569.1| pseudouridylate synthase, putative [Coccidioides posadasii C735
           delta SOWgp]
          Length = 610

 Score =  133 bits (334), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 68/376 (18%), Positives = 99/376 (26%), Gaps = 139/376 (36%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G+    NG      +I+  + KA+                       
Sbjct: 96  IALKFAYLGQRYNGY-EHANGNITPLPTIEEELFKALRKSRLIFPKTVENVDNVDRAGNR 154

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFD-------------------------- 65
                 +  E       GRTD GV A  QV                              
Sbjct: 155 LLRPYSIDWEGCDYSKCGRTDRGVSAFGQVVGVRVRSAKPKKKKDVEPVKTPDIPSSVTP 214

Query: 66  --------------------LVREWVPVILCKALNAYLKISDTISILNLSI-VDKQFHAR 104
                                      +   + LN  L   + I IL         F AR
Sbjct: 215 VESPLGGLDIDVCDLEAEEAWDDIADELPYIQMLNGVL--PEDIRILAWCPHPPPGFDAR 272

Query: 105 FSAIRRSYLYRIIT-----RQAPLALEKG---------RAWLIPKSLDCENMRIAAQHLV 150
           FS   R Y Y            P    K          R       LD + MR  A+  +
Sbjct: 273 FSCRERRYRYFFTQPAFCPTPGPFGFLKRPGDTSGAKMREGW----LDIDAMREGAKRFI 328

Query: 151 GRHDFTTFRSIHC--QASSPIRTIDHFDV------------------NSFGNL------- 183
           G HDF  F  +    Q ++ +R I H D+                    F +L       
Sbjct: 329 GSHDFRNFCKVDASKQITNFVRKISHADIQVLDASKLPPAFLAQQGFQQFEHLGQQERAA 388

Query: 184 ----------IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQD-RKECG 231
                         V   +FL  Q+R  VG L L+G G    + + + L  +++ R+   
Sbjct: 389 SGGHNAALKVYYFSVHGSAFLWHQVRHMVGILFLIGQGLEPPSIVSELLDVSKNPRRPTY 448

Query: 232 PLAPPEGLYFDSVEYS 247
            +A    L      + 
Sbjct: 449 EIASDAPLVLWDCVFP 464


>gi|316970789|gb|EFV54664.1| tRNA pseudouridine synthase A [Trichinella spiralis]
          Length = 390

 Score =  132 bits (333), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 90/266 (33%), Gaps = 37/266 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV---------VVHGAGRTDS 53
           +Y M + Y G  Y G Q   N  +++  I +A+  +    V             A RTD 
Sbjct: 53  KYAMFLAYRGKNYHGMQVNPNVPTVEKYIMEALQKLNLITVDQVVQPSLFKFQRAARTDK 112

Query: 54  GVHALRQVAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GV A +Q+    L             LN             L    K F ++     RSY
Sbjct: 113 GVSATKQICSLLLPTIEGKENDTVNLLN------------GLQRATKSFDSKKWCDYRSY 160

Query: 113 LYRI--ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPI 169
            Y +     +    LE+ +  L  K  D E +       VG H+F  F S       S  
Sbjct: 161 SYTLPSYCFRHQSDLERDKFRLDNK--DIEEINRILMQYVGTHNFYNFTSGKLHKDESCK 218

Query: 170 RTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           R I   +            + + +  +SFL  QIR  +G    +  G       +K  Q 
Sbjct: 219 RFIIRCECGKRFLYNNIEYLTVDIKGQSFLIHQIRKMIGFCISLIRGDLDPCLQQKVWQN 278

Query: 225 QDRKECGPLAPPEGLYFDSV---EYS 247
           +  +   P AP  GL  + V    Y 
Sbjct: 279 E--RIKVPKAPSLGLVLEEVRMPHYE 302


>gi|255609446|ref|XP_002539049.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223509026|gb|EEF23334.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 132

 Score =  132 bits (333), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 52/119 (43%), Positives = 69/119 (57%), Gaps = 2/119 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+G+ + GWQ Q N + +Q +IE AI  V GE V +H AGRTDSGVHAL QV
Sbjct: 16  MKIAIGIEYHGAYFQGWQSQPNAAGVQDAIEHAIKQVGGETVRLHAAGRTDSGVHALMQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           AHF+           +  NA+L     + IL  + V   FHARFSA  RSY Y +   +
Sbjct: 76  AHFETSVVRPLSAWVRGTNAHL--PAWVRILWATEVAADFHARFSARARSYQYVLHNMR 132


>gi|328771895|gb|EGF81934.1| hypothetical protein BATDEDRAFT_87010 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 491

 Score =  132 bits (333), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 98/288 (34%), Gaps = 53/288 (18%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           M +    +++ Y G+GY G Q   +  SI+  + KA+       +      RTD GVHA 
Sbjct: 96  MPKKKVVLLMSYCGTGYQGMQINPDVPSIELDLHKAL--AASGAIAFMRCARTDKGVHAG 153

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV    +        + + +NA L     I +   + V +QFHA+     R Y Y + T
Sbjct: 154 GQVVSLKM--IIQDSDIIERINARL--PPQIRVWGYARVQQQFHAKHHCDSRIYEYILPT 209

Query: 119 ------RQAPLALEKGRAWL----------------IPKSLDCEN--------------- 141
                       L K                     IP+  D E                
Sbjct: 210 SVLKKVDPTYYPLSKIGVAAGVTFENMGRAKMEPIEIPEHTDNEKETIQGYRTNHQELEE 269

Query: 142 MRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNS-----FGNLIEIRVVARSFLH 195
            R      VG H++  F      +  S IR I  F  +          + ++V  +SF+ 
Sbjct: 270 FRAILNEYVGTHNYHNFTIGRKFEDKSSIRYIISFICSEPFQRDNTEWVSLKVKGQSFML 329

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
            QIR  +G   ++         +     +Q R    P AP  GL  + 
Sbjct: 330 HQIRKMIGLAVMMMRTSTPKNLIASTF-SQTRINI-PKAPALGLLLER 375


>gi|242215757|ref|XP_002473691.1| predicted protein [Postia placenta Mad-698-R]
 gi|220727176|gb|EED81103.1| predicted protein [Postia placenta Mad-698-R]
          Length = 495

 Score =  132 bits (333), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 68/327 (20%), Positives = 102/327 (31%), Gaps = 97/327 (29%)

Query: 2   IRYCMIIEYNGSGYFG--WQRQKNG-SSIQGSIEKAIFL------VTG-EIVVVHGAGRT 51
            +  +   YNG+ Y G  +Q+      +++  +  A+         TG E       GRT
Sbjct: 48  RKIALKFTYNGADYSGLEFQKTPTTLPTVEAVLFDALVHTRLIDPATGFEGCGWEKCGRT 107

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKAL----------------------------NA-- 81
           D GV A  QV    +        +  +L                            NA  
Sbjct: 108 DRGVSAAGQVISLWVRSALGQARVRTSLEDANVMDVHPTGLEGDLALMGEWDETPTNAAR 167

Query: 82  ----------------YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                              +  TI ++  S V   F ARFS   R Y Y           
Sbjct: 168 PATPQATNELRYITLLNNVLPPTIRVIAWSPVGPDFSARFSCRYRHYKY----------- 216

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNSFG-- 181
                +  P+ LD   M+ AA  LVG HDF     +    Q ++  R I    +N     
Sbjct: 217 -----FFSPEGLDLAAMQDAADRLVGEHDFRNLCKLDPSKQLTTFARKILSARLNPAQAD 271

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL---QAQDRKECGP--- 232
               L  + ++  +FL+ Q+R  +  L LVG      + ++  L    AQ R    P   
Sbjct: 272 GASTLYVLDLIGTAFLYNQVRHIMAVLFLVGTKLEHPSVIDALLNVDAAQPRAPSRPGEP 331

Query: 233 ------------LAPPEGLYFDSVEYS 247
                       +A P  L      Y 
Sbjct: 332 FPQVIPSKPEYQMADPLPLMLWECAYD 358


>gi|118395831|ref|XP_001030261.1| tRNA pseudouridine synthase family protein [Tetrahymena
           thermophila]
 gi|89284557|gb|EAR82598.1| tRNA pseudouridine synthase family protein [Tetrahymena thermophila
           SB210]
          Length = 297

 Score =  132 bits (333), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 63/251 (25%), Positives = 106/251 (42%), Gaps = 29/251 (11%)

Query: 20  RQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKAL 79
           RQK   +I    ++++     + V +  + RTD GV+A +    F L R+       + +
Sbjct: 22  RQKESININIKNQQSLNNFAKQEVFIKSSSRTDVGVNARKHPVQFVLQRDS-----KRGV 76

Query: 80  NAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRI-----ITRQAPLALEKGRAWLI 133
           N YL+ +   I+I  +  V  +F  R   +++ Y++ I        + PL   K ++W I
Sbjct: 77  NFYLRDAGDQIAINEVYQVPMEFDVRNDCLQKEYVFYIDSQVGYNWENPLLFYK-QSWCI 135

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSIH---CQASSPIRTIDHFDVNSFGNL------- 183
           P  +D + ++ A Q  +GRH+F  F S      Q     + ++ F++  + N        
Sbjct: 136 PDQIDIDRLKQAFQKYLGRHNFYLFTSPEPFQTQFDLFEKELNSFEITHYPNEHFPKIQS 195

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA-------QDRKECGPLAPP 236
           I I V  + FL  Q+R  VG   L    K     L   L         + R      A P
Sbjct: 196 IRISVKGKGFLKYQVRYMVGIAVLYAQKKIDENYLNYLLNPTGFIPQDERRNLIRLKAKP 255

Query: 237 EGLYFDSVEYS 247
           EGL+   V+Y 
Sbjct: 256 EGLFLYDVQYD 266


>gi|198427214|ref|XP_002128771.1| PREDICTED: similar to Pseudouridine synthase 1 [Ciona intestinalis]
          Length = 531

 Score =  132 bits (332), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 57/267 (21%), Positives = 96/267 (35%), Gaps = 32/267 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAI---------FLVTGEIVVVHGAG 49
            +  M+  Y G+ Y G Q  +      +I+G + +A+          +     +    A 
Sbjct: 69  RKVAMLFAYCGANYHGLQMNRGERWIKTIEGDLFQALVDAKVVPSNCVQEPHKMTYKSAS 128

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV    QVA   L    +   +   +N +L   + I ++ +    + F+A+  A  
Sbjct: 129 RTDKGVSTCGQVASLKL---RLNENVVGLINQHL--PEDIVVMAVRRTTQGFNAQLKAEG 183

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRSIHCQAS 166
           R+Y Y + T     A            +  + +   +       G H F  F S      
Sbjct: 184 RTYSYTLPT----FAFADYGTGNTSYKITEDKLLKVKSILYRYKGTHSFHNFTSGKRMGE 239

Query: 167 -SPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I  F+     +      I + +  +SF+  QIR  +G L  + +G        +
Sbjct: 240 MSAQRFIIEFEHGDPFLVQNVEFITLTIKGQSFMLHQIRKMIGLLIAMVNGLAKEQHFIR 299

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           A       E  P AP  GL  + V Y 
Sbjct: 300 AFSEP--LEDIPKAPGTGLVLEKVHYD 324


>gi|315124345|ref|YP_004066349.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|315018067|gb|ADT66160.1| tRNA pseudouridine synthase A [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
          Length = 178

 Score =  132 bits (332), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 42/180 (23%), Positives = 67/180 (37%), Gaps = 6/180 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I  Y+GS + G   Q +   +Q ++  A+  + G +  +  A RTD GVHA   V
Sbjct: 1   MKIKIIFSYDGSAFLGSASQPHKKGVQDALSGALSHL-GIVSPLLMASRTDKGVHASYAV 59

Query: 62  AHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           A  +    +     L K LN +      I I  +  V   F  RF    R Y Y I +  
Sbjct: 60  ASVECGDHFVNLEYLQKQLNKF--SHPFIHIKKIEKVKDDFEVRFDVKSREYRY-IFSHS 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +            PK  D +         VG+ D   F        + +R I      ++
Sbjct: 117 SYSPFMASYVHFYPK-FDLDKANELLGFFVGKKDLKFFCKSGGDNKTTLREIFIARAYAY 175


>gi|67525425|ref|XP_660774.1| hypothetical protein AN3170.2 [Aspergillus nidulans FGSC A4]
 gi|40744565|gb|EAA63741.1| hypothetical protein AN3170.2 [Aspergillus nidulans FGSC A4]
          Length = 625

 Score =  131 bits (331), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 69/359 (19%), Positives = 100/359 (27%), Gaps = 117/359 (32%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAI------------------------ 35
             +   Y G  Y G +   N      +I+  + KA+                        
Sbjct: 128 IALKFAYLGQRYQGLEHANNNPTALPTIEEEMWKALMRTRLIFPTDMGDEDVPDRKAKRK 187

Query: 36  ----FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCK-------------- 77
               F ++ E      AGRTD GV A  QV    +          K              
Sbjct: 188 EIEPFNISWEGCEYSKAGRTDRGVSAFGQVIGLKVRSARPKRKEPKPAQVSNDTAETTRE 247

Query: 78  ------------------ALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT 118
                              LN  L   + I +L       + F AR+S   R Y Y    
Sbjct: 248 TVADEDWDDIADELPYISLLNKAL--PEDIRVLAWCPNPPEDFDARYSCRERHYKYFFTQ 305

Query: 119 ---RQAPLAL----EKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHC--QASS 167
                 P  L     KG A    +   LD + MR AA++  G HDF  F  +    Q  +
Sbjct: 306 PAFSPTPGPLGLLPRKGDAPPKYREGWLDIDAMREAAKYFEGVHDFRNFCKVDTSKQIEN 365

Query: 168 PIRTIDHFDVN-------------------------------------SFGNLIEIRVVA 190
             R I   D+                                          +    +  
Sbjct: 366 FERIIYRADIELLDPRNSPLGYVNRPEFSALNYPDTDSLTQKPAGSVPPGCQVYVFNLQG 425

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
            +FL  Q+R  VG L LVG G  + + + + L      RK    +A    L   +  + 
Sbjct: 426 SAFLWHQVRHMVGILFLVGQGLESPSVVRELLDVTKNPRKPMYEMASDAPLVLWNCVFP 484


>gi|189241446|ref|XP_973048.2| PREDICTED: similar to CG34140 CG34140-PA [Tribolium castaneum]
          Length = 258

 Score =  131 bits (331), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 67/243 (27%), Positives = 96/243 (39%), Gaps = 48/243 (19%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--------SIQGSIEKAIFLVTGE-IVVVHGAGRTDS 53
           RY +   Y G+ + G QRQ  G         ++QG +E A+  +      VV+ + RTDS
Sbjct: 5   RYLLHFSYIGTPFMGAQRQVTGRMPRPDDPSTVQGQLEMALKRLNPTNDPVVYLSSRTDS 64

Query: 54  GVHALRQVAHFDLVR----EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAI 108
           GVHAL    H DL R    E+ P  +   LN Y   ++  I ++    V   FH R +AI
Sbjct: 65  GVHALNSTCHVDLYRSNELEYEPKTITICLNRYFDKNEVPIRVIKTYWVPPDFHCRHTAI 124

Query: 109 RRSYLYRIITRQA------------PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            R+YLYRI   +             P+   +   +    S + + M+ AA+   G HDF 
Sbjct: 125 SRTYLYRIAIAKTGVTEHATILNLLPIEEYQRCLFFYCDSFNIDEMKEAAKVFEGLHDFR 184

Query: 157 TFRSIHCQASSPI--RTIDHFDVN--------------------SFGNLIEIRVVARSFL 194
           TF          I  R +   DV                           +I V A  FL
Sbjct: 185 TFMGRGSHDPDKITRRVVTRVDVCDGRALTYSSFSWPRFASGSAENYQFYDIYVQATGFL 244

Query: 195 HTQ 197
           + Q
Sbjct: 245 YRQ 247


>gi|259485874|tpe|CBF83268.1| TPA: pseudouridylate synthase 3 (AFU_orthologue; AFUA_3G13350)
           [Aspergillus nidulans FGSC A4]
          Length = 664

 Score =  131 bits (331), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 69/359 (19%), Positives = 100/359 (27%), Gaps = 117/359 (32%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAI------------------------ 35
             +   Y G  Y G +   N      +I+  + KA+                        
Sbjct: 167 IALKFAYLGQRYQGLEHANNNPTALPTIEEEMWKALMRTRLIFPTDMGDEDVPDRKAKRK 226

Query: 36  ----FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCK-------------- 77
               F ++ E      AGRTD GV A  QV    +          K              
Sbjct: 227 EIEPFNISWEGCEYSKAGRTDRGVSAFGQVIGLKVRSARPKRKEPKPAQVSNDTAETTRE 286

Query: 78  ------------------ALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT 118
                              LN  L   + I +L       + F AR+S   R Y Y    
Sbjct: 287 TVADEDWDDIADELPYISLLNKAL--PEDIRVLAWCPNPPEDFDARYSCRERHYKYFFTQ 344

Query: 119 ---RQAPLAL----EKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSIHC--QASS 167
                 P  L     KG A    +   LD + MR AA++  G HDF  F  +    Q  +
Sbjct: 345 PAFSPTPGPLGLLPRKGDAPPKYREGWLDIDAMREAAKYFEGVHDFRNFCKVDTSKQIEN 404

Query: 168 PIRTIDHFDVN-------------------------------------SFGNLIEIRVVA 190
             R I   D+                                          +    +  
Sbjct: 405 FERIIYRADIELLDPRNSPLGYVNRPEFSALNYPDTDSLTQKPAGSVPPGCQVYVFNLQG 464

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
            +FL  Q+R  VG L LVG G  + + + + L      RK    +A    L   +  + 
Sbjct: 465 SAFLWHQVRHMVGILFLVGQGLESPSVVRELLDVTKNPRKPMYEMASDAPLVLWNCVFP 523


>gi|320038677|gb|EFW20612.1| pseudouridylate synthase 3 [Coccidioides posadasii str. Silveira]
          Length = 588

 Score =  131 bits (330), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 68/376 (18%), Positives = 100/376 (26%), Gaps = 139/376 (36%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G+    NG      +I+  + KA+                       
Sbjct: 100 IALKFAYLGQRYNGY-EHANGNITPLPTIEEELFKALRKSRLIFPKTVENVDNVDRAGNR 158

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFD-------------------------- 65
                 +  E       GRTD GV A  QV                              
Sbjct: 159 LLRPYSIDWEGCDYSKCGRTDRGVSAFGQVVGVRVRSAKPKKKKDVEPVKTPDIPSSVTP 218

Query: 66  --------------------LVREWVPVILCKALNAYLKISDTISILNLSI-VDKQFHAR 104
                                      +   + LN  L   + I IL         F AR
Sbjct: 219 VESPPGGLDIDVCDLEAEEAWDDIADELPYIQMLNGVL--PEDIRILAWCPHPPPGFDAR 276

Query: 105 FSAIRRSYLYRIIT-----RQAPLALEKG---------RAWLIPKSLDCENMRIAAQHLV 150
           FS   R Y Y            P    K          R       LD + MR  A+  +
Sbjct: 277 FSCRERRYRYFFTQPAFCPTPGPFGFLKRPGDTSGAKMREGW----LDIDAMREGAKRFI 332

Query: 151 GRHDFTTFRSIHC--QASSPIRTIDHFDVN------------------------------ 178
           G HDF  F  +    Q ++ +R I H D+                               
Sbjct: 333 GSHDFRNFCKVDASKQITNFVRKISHADIQVLDASKLPPAFLAQQGFQQFEHPGQQERAA 392

Query: 179 SFGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQD-RKECG 231
           S G+     +    V   +FL  Q+R  VG L L+G G    + + + L  +++ R+   
Sbjct: 393 SGGHNAALKVYYFSVHGSAFLWHQVRHMVGILFLIGQGLEPPSIVSELLDVSKNPRRPTY 452

Query: 232 PLAPPEGLYFDSVEYS 247
            +A    L      + 
Sbjct: 453 EIASDAPLVLWDCVFP 468


>gi|119186911|ref|XP_001244062.1| hypothetical protein CIMG_03503 [Coccidioides immitis RS]
          Length = 537

 Score =  131 bits (330), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 67/376 (17%), Positives = 99/376 (26%), Gaps = 139/376 (36%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G+    NG      +I+  + KA+                       
Sbjct: 100 IALKFAYLGQRYNGY-EHANGNITPLPTIEEELFKALRKSRLIFPKTVENVDNVDRAGNR 158

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFD-------------------------- 65
                 +  E       GRTD GV A  QV                              
Sbjct: 159 LLRPYSIDWEGCDYSKCGRTDRGVSAFGQVVGVRVRSAKPKKKKDVEPVKTPDTPSSVTP 218

Query: 66  --------------------LVREWVPVILCKALNAYLKISDTISILNLSI-VDKQFHAR 104
                                      +   + LN  L   + I IL         F AR
Sbjct: 219 VESPLGGLDIDVSDLEAEEAWDDIADELPYIQMLNGVL--PEDIRILAWCPHPPPGFDAR 276

Query: 105 FSAIRRSYLYRIIT-----RQAPLALEKG---------RAWLIPKSLDCENMRIAAQHLV 150
           FS   R Y Y            P    K          R       LD + MR  A+  +
Sbjct: 277 FSCRERRYRYFFTQPAFCPTPGPFGFLKRPGDTSGAKMREGW----LDIDAMREGAKRFI 332

Query: 151 GRHDFTTFRSIHC--QASSPIRTIDHFDV------------------NSFGN-------- 182
           G HDF  F  +    Q ++ +R I H D+                    F +        
Sbjct: 333 GSHDFRNFCKVDASKQITNFVRKISHADIQVLDASKLPPAFLAQQGFQQFEHPGQQERAA 392

Query: 183 ---------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQD-RKECG 231
                    +    V   +FL  Q+R  VG L L+G G    + + + L  +++ R+   
Sbjct: 393 SGSHNAALKVYYFSVHGSAFLWHQVRHMVGILFLIGQGLEPPSIVSELLDVSKNPRRPTY 452

Query: 232 PLAPPEGLYFDSVEYS 247
            +A    L      + 
Sbjct: 453 EIASDAPLVLWDCVFP 468


>gi|302854296|ref|XP_002958657.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
 gi|300255982|gb|EFJ40260.1| tRNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
          Length = 188

 Score =  131 bits (330), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 75/176 (42%), Gaps = 19/176 (10%)

Query: 7   IIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++ Y+G  + G+Q Q     ++QG +E+    +      + GA RTD G HA  QV HFD
Sbjct: 15  VVAYDGCEFAGFQFQAGKVRTVQGELERGAKRLFHGCSRMVGASRTDGGAHAYGQVVHFD 74

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
           +      +    AL     +   + +L LS  +  F + FS+  ++YLY+      P  L
Sbjct: 75  VYGTRDSLE-SDALYYNSFLPPDVRVLGLSYAEDGFDSHFSSCGKTYLYKFAAG-LPDPL 132

Query: 126 EKGRAWLIPK----------------SLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           +    W +                   LD   M+ AA  L+GRHDF+ F      A
Sbjct: 133 QSKYRWWVYDRWCERSRGKPGKLSDVELDVGLMQQAADMLLGRHDFSAFMDNKRPA 188


>gi|66803188|ref|XP_635437.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
 gi|60463746|gb|EAL61924.1| tRNA pseudouridylate synthase [Dictyostelium discoideum AX4]
          Length = 596

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/284 (21%), Positives = 104/284 (36%), Gaps = 47/284 (16%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
           +  +I+ Y+G+ Y G Q+     +++  +E A+F   G         + V      RTD 
Sbjct: 141 KVAIILGYSGTNYAGMQKNPGLKTVEEELEHALFRTGGISPDNMYYQQKVDWIRCARTDK 200

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A+R V    +     P      +    ++   I++ ++  V+  FHA+ +   RSY+
Sbjct: 201 GVSAIRNVVSLKME-MGPPDFEGMKIALNKELPKDITVFHIMRVNNSFHAKNAVDARSYI 259

Query: 114 YRIITRQAPLALEKGRAWLIPKSLD----------------CENMRIAAQHLVGRHDFTT 157
           Y   T        K    ++ ++ +                   +       +G H F  
Sbjct: 260 YVTPTHVFEPKFSKKNKSIVEEAANGGENNTQPPWKFTSDTLSILNKVLSFYLGNHRFHN 319

Query: 158 FRSIH-CQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKL-VGD 210
           + S       S  R I  F  +         ++ I VV  SF+  QIR  +G L   +  
Sbjct: 320 YTSRKESNDVSVFRKIHSFVCSEPFVLEGVEMVSINVVGESFMLHQIRKMIGCLISFIRK 379

Query: 211 GKWTSTDLEKALQAQDRKECG------------PLAPPEGLYFD 242
           G +   D E   QA D+ +              P+AP  GL  D
Sbjct: 380 GMF--EDCETRDQAFDQIKAYINSTFEHTPLNLPMAPGAGLLLD 421


>gi|159127305|gb|EDP52420.1| pseudouridylate synthase 3 [Aspergillus fumigatus A1163]
          Length = 610

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 69/358 (19%), Positives = 95/358 (26%), Gaps = 119/358 (33%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 116 IALKFAYLGQRYNGL-EHANGNVTPLPTIEEELWKAMRRTRLIFPKNAEAFDDSRGPREL 174

Query: 38  ----VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV---------------------- 71
               ++ E      AGRTD GV A  QV    +                           
Sbjct: 175 KPYAISWEGCDYSKAGRTDRGVSAFGQVIGIRVRSARPKRPDAETTSDVEMTSGGQADDT 234

Query: 72  ----PVILCKALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPL 123
                  +         + D I IL         F ARFS   R Y Y          P 
Sbjct: 235 WDDIADEIPYISILNRVLPDDIRILAWCPNPPPGFDARFSCRERQYKYFFTQPAFSPTPG 294

Query: 124 AL--------EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTI 172
            L        +K  +  + +  LD + MR AA++  G HDF  F  +    Q  +  R I
Sbjct: 295 PLGFAMRGSGDKNASTHLREGWLDIDAMREAARYFEGVHDFRNFCKLDTSKQIENFERII 354

Query: 173 DHFDVN-----------------------------SFGNL--------IEIRVVARSFLH 195
            H D+                                G              +   +FL 
Sbjct: 355 YHADIELLDPKDHPLGYVNQPGFQALQDAPARTSAESGTFTSPAAAKVYVFNLHGSAFLW 414

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL------APPEGLYFDSVEYS 247
            Q+R  V  L LVG G    T +   L    +  C P       AP   L      + 
Sbjct: 415 HQVRHMVSILFLVGQGLEPPTIVRDLLDV-SKNPCKPTYEMASDAP---LVLWDCIFP 468


>gi|70999131|ref|XP_754287.1| pseudouridylate synthase 3 [Aspergillus fumigatus Af293]
 gi|66851924|gb|EAL92249.1| pseudouridylate synthase 3 [Aspergillus fumigatus Af293]
          Length = 610

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 69/358 (19%), Positives = 95/358 (26%), Gaps = 119/358 (33%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 116 IALKFAYLGQRYNGL-EHANGNVTPLPTIEEELWKAMRRTRLIFPKNAEAFDDSRGPREL 174

Query: 38  ----VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV---------------------- 71
               ++ E      AGRTD GV A  QV    +                           
Sbjct: 175 KPYAISWEGCDYSKAGRTDRGVSAFGQVIGIRVRSARPKRPDAETTSDVEMTSGGHADDT 234

Query: 72  ----PVILCKALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPL 123
                  +         + D I IL         F ARFS   R Y Y          P 
Sbjct: 235 WDDIADEIPYISILNRVLPDDIRILAWCPNPPPGFDARFSCRERQYKYFFTQPAFSPTPG 294

Query: 124 AL--------EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTI 172
            L        +K  +  + +  LD + MR AA++  G HDF  F  +    Q  +  R I
Sbjct: 295 PLGFAMRGSGDKNASTHLREGWLDIDAMREAARYFEGVHDFRNFCKLDTSKQIENFERII 354

Query: 173 DHFDVN-----------------------------SFGNL--------IEIRVVARSFLH 195
            H D+                                G              +   +FL 
Sbjct: 355 YHADIELLDPKDHPLGYVNQPGFQALQDAPARTSAESGTFTSPAAAKVYVFNLHGSAFLW 414

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL------APPEGLYFDSVEYS 247
            Q+R  V  L LVG G    T +   L    +  C P       AP   L      + 
Sbjct: 415 HQVRHMVSILFLVGQGLEPPTIVRDLLDV-SKNPCKPTYEMASDAP---LVLWDCIFP 468


>gi|255087382|ref|XP_002505614.1| predicted protein [Micromonas sp. RCC299]
 gi|226520884|gb|ACO66872.1| predicted protein [Micromonas sp. RCC299]
          Length = 294

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 98/256 (38%), Gaps = 28/256 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            +    + Y G GY G+QR     +I+  +E+AI    G           V    A RTD
Sbjct: 5   RKIAAFLAYVGKGYQGFQRNPGARTIEDELERAIVAAGGISADNAGDFTKVQWTRAARTD 64

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ Q     +V    P  + + +NA L   +   I     V   F+A+    RR Y
Sbjct: 65  KGVSAVGQCIALRMV--LDPPGVLERINAAL--PEGFKIFGYKRVTGGFNAKTMCDRRRY 120

Query: 113 LYRIIT---RQAPLALEK-----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHC 163
            Y I T           +      +A++  + L    +     +  G H+F  +   +  
Sbjct: 121 EYVIPTCAFDPRRCLPRREDDKEAKAFVFDEEL-RARVNKILGNYCGTHNFHNYTVRVDP 179

Query: 164 QASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
             ++ +R I  F+            +   VV +SF+  QIR  +G++  V  G     D 
Sbjct: 180 NDAAAMRYIISFECGEPFVIDGVEFVRTTVVGQSFMLHQIRKLIGTMLCVVRGYLAEEDQ 239

Query: 219 EKALQAQDRKECGPLA 234
             AL+ ++     PLA
Sbjct: 240 IFALKTKESCSHEPLA 255


>gi|121706104|ref|XP_001271315.1| pseudouridylate synthase 3 [Aspergillus clavatus NRRL 1]
 gi|119399461|gb|EAW09889.1| pseudouridylate synthase 3 [Aspergillus clavatus NRRL 1]
          Length = 604

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 68/356 (19%), Positives = 98/356 (27%), Gaps = 117/356 (32%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  I KA+                       
Sbjct: 112 IALKFAYLGQRYNGL-EHANGNVTPLPTIEEEIWKAMRRTRLIFPTDAEPFDDSRGPRAL 170

Query: 38  ----VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV---------------------- 71
               ++ E      AGRTD GV A  QV    +                           
Sbjct: 171 KPYSLSWEGCDYSKAGRTDRGVSAFGQVIGIRVRSARPKRPATEVTSDVDMTGLDAPAED 230

Query: 72  -----PVILCKALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAP 122
                   +         + + I IL         F ARFS   R Y Y          P
Sbjct: 231 TWDDIADEIPYISMLNRVLPEDIRILAWCPQPPPGFDARFSCRERQYKYFFTQPAFSPTP 290

Query: 123 LAL--------------EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QAS 166
             L               K R       LD + MR AA+H  G HDF  F  +    Q  
Sbjct: 291 GPLGLALQAVDSANKIPAKYREGW----LDIDAMREAAKHFEGVHDFRNFCKLDTSKQIE 346

Query: 167 SPIRTIDHFDVN---------------------------------SFGNLIEIRVVARSF 193
           +  R I H D+                                  +   +    +   +F
Sbjct: 347 NFERIIYHADIELVDPKHHPLGYVNQPGFQASENSVVGADTVAQATAAQVYVFNLHGSAF 406

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQD-RKECGPLAPPEGLYFDSVEYS 247
           L  Q+R  V  L LVG G  + + + + L  +++ RK    +A    L   +  + 
Sbjct: 407 LWHQVRHMVSILFLVGQGLESPSIVAELLDVSKNPRKPTYEMASDAPLVLWNCIFP 462


>gi|302810046|ref|XP_002986715.1| hypothetical protein SELMODRAFT_124462 [Selaginella moellendorffii]
 gi|300145603|gb|EFJ12278.1| hypothetical protein SELMODRAFT_124462 [Selaginella moellendorffii]
          Length = 318

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 65/263 (24%), Positives = 98/263 (37%), Gaps = 27/263 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--------TGEIVVVHGAGRTD 52
           M +  + + Y G+GY G QR    ++I+G +E+A+           +   +    A RTD
Sbjct: 1   MEKAALFVVYCGAGYKGMQRNPGAATIEGVLEEALVRAGAIGSNGCSRNWLDWKRAARTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
             V AL QV      R ++   L    N +L    +I +L    V   F A+     R Y
Sbjct: 61  KEVSALGQVVS---ARLYLTPDLVHRTNEFL--PGSIRLLGFKRVPDDFSAKKMCASRRY 115

Query: 113 LYRIITRQAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGR-HDFTTFR-SIHCQASSP 168
            Y +       A +      + +    D E         +G  H F  F   +       
Sbjct: 116 EYVLPI----FAFDPRTGDDLEEEFLFDFERFNQILGRFLGTDHSFHNFSWRVRPGDREA 171

Query: 169 IRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            RT+  F             + I V+ARSF+  QIR  VG    V       T + +AL+
Sbjct: 172 RRTVVEFRAADKIWIGGSEFVRIIVLARSFMAYQIRKMVGLAVAVMRDIAPVTTINRALR 231

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           + +     P AP  GL  D   Y
Sbjct: 232 S-EVDVIVPTAPEVGLLLDESFY 253


>gi|13541901|ref|NP_111589.1| tRNA pseudouridine synthase A [Thermoplasma volcanium GSS1]
 gi|24212574|sp|Q979R4|TRUA_THEVO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|14325334|dbj|BAB60238.1| pseudouridylate synthase I [Thermoplasma volcanium GSS1]
          Length = 246

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 98/243 (40%), Gaps = 35/243 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y     Y G  + G+QR     S++ +I KA+ L      ++  A RTD GV AL  V +
Sbjct: 5   YFFKFGYIGYMFTGYQRGNGVKSVEDTIIKALNL--NSPSLIKTAARTDRGVSALSNVFY 62

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
            +  R   P  +   +N+    ++ + + + + V+   + R+    ++Y+Y +       
Sbjct: 63  IETERR--PQDIAGIINSK---NEYVFVHSFAEVEHGRNPRY-CDTKTYMYML------- 109

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                     P   +C+++ + A   +G HDF+ F     +  +P R+ID    +     
Sbjct: 110 ----------PGETECDSLMVTASGFLGFHDFSKFSKKDTR--NPWRSIDEVKCHRESFG 157

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + +   A+SFL  Q+R  +  +      K     +              +APPE L    
Sbjct: 158 VVLEFSAKSFLWNQVRRMLAFILEFRGNKIDPFSVSNIY--------SHIAPPENLILKD 209

Query: 244 VEY 246
           + Y
Sbjct: 210 IVY 212


>gi|330914180|ref|XP_003296528.1| hypothetical protein PTT_06654 [Pyrenophora teres f. teres 0-1]
 gi|311331289|gb|EFQ95392.1| hypothetical protein PTT_06654 [Pyrenophora teres f. teres 0-1]
          Length = 599

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 63/358 (17%), Positives = 95/358 (26%), Gaps = 114/358 (31%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFL---------------------- 37
             +   Y G  Y G++  KN      +I+  + KA+                        
Sbjct: 80  IALKFAYLGQKYNGFEHHKNNTTPLPTIEEELWKALVKTRLITPIPTAGGEKESYERIDR 139

Query: 38  ------------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLK- 84
                       V  +       GRTD GV A  QV    +          ++ N  L+ 
Sbjct: 140 KTFARWDREGADVNWDGCEYSKCGRTDRGVSAFGQVIGVRVRSNKPLPKALQSPNETLET 199

Query: 85  -------------------------------------ISDTISILNLSIVDK-QFHARFS 106
                                                +   I +          F ARFS
Sbjct: 200 NEDENPPSSPASDSNPPPKPFNDLTDELPYIQLLNRVLPPDIRVYAWCPNPPADFSARFS 259

Query: 107 AIRRSYLYRIITRQAPLAL----EKGRAWLIPKS-----LDCENMRIAAQHLVGRHDFTT 157
              R Y Y                   +   P++     LD   M+    HLVG HDF  
Sbjct: 260 CKERRYKYFFTNPCFAPVPGSSGRYNTSSTSPQAMREGWLDINAMKQGCAHLVGLHDFRN 319

Query: 158 FRSIHC--QASSPIRTIDHFDVNSF------------------------GNLIEIRVVAR 191
           F  I    Q ++  R I H D+                             L    +   
Sbjct: 320 FCKIDASKQLTNFQRRIFHADIEEVSPLSVPAFLSHPALSTPGLPASEAPKLYSFTLHGS 379

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           +FL  Q+RS +  L L+G G  +   + K L  +A   +    +A    L      + 
Sbjct: 380 AFLWHQVRSLIAVLFLIGQGLESPDIIPKLLDIEANPTRPKYEMASDAPLVLWDCIFP 437


>gi|300175988|emb|CBK22205.2| unnamed protein product [Blastocystis hominis]
          Length = 399

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 92/270 (34%), Gaps = 55/270 (20%)

Query: 22  KNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHALRQVAHFDLVRE-------- 69
            + +S++ +I  A+  V              GRTD+GV A  QV    L           
Sbjct: 17  ADDNSVESAIFSALKRVHLIDDISKCHYQRCGRTDAGVSAFNQVISLYLRSNLRSGVEFV 76

Query: 70  --WVPVILCKALNA-----------------------YLKISDTISILNLSIVDKQFHAR 104
             + P I   A N                           +  TI I     VD+ F AR
Sbjct: 77  DEFDPSIPYNAPNTSNQPQSAPSSSTPVTEFDYASVLNKVLPPTIRITGWCPVDRSFSAR 136

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC- 163
           +S     +   +   +        R + + ++ D E MR A +   G HDF  F  I   
Sbjct: 137 YSCCGEDWAANLSAGRV------YRYYFLRRNYDVELMRSAVKLFEGEHDFRNFCRIDAV 190

Query: 164 QASSPIRTIDHFDV-------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                 RT+   DV           +++ + +V R+FL  QIR  +  L LV   K   T
Sbjct: 191 NVCDFTRTVFRGDVVEIRKGETPQHDVLAVEIVGRAFLWHQIRCMMSILFLVASKKEKQT 250

Query: 217 DLEKALQAQDRKECGP---LAPPEGLYFDS 243
            +   L    +  C P   LA PE L    
Sbjct: 251 IISDLLDV-SKSPCKPQYHLADPEPLVLYD 279


>gi|325190406|emb|CCA24877.1| tRNA pseudouridine synthase putative [Albugo laibachii Nc14]
          Length = 463

 Score =  130 bits (327), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 72/300 (24%), Positives = 111/300 (37%), Gaps = 60/300 (20%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            RY   + Y G  Y G Q  +  ++I+  +E+A+F   G         + +    A RTD
Sbjct: 72  RRYGFWVAYCGEKYSGMQLNEGVATIEAELERALFQAGGISDANYGFLQKIGWSRAARTD 131

Query: 53  SGVHALRQVAHFDLVREWVPVI---------LCKALNAYLKISDTISILNLSIVDKQFHA 103
            GVHA  Q+    L  +                + +NA L     I ++++  V K F+A
Sbjct: 132 KGVHAAGQLVTAKLSFDSKSSEDRNGEQIKGFIEKINASL--PSDIRVMDMVTVTKNFNA 189

Query: 104 RFSAIRRSYLYRIIT--------RQAPLALEKGRA-WLIPKSLDC--------------- 139
           + S   R+Y Y I T        +     ++  +A  ++PK+ D                
Sbjct: 190 KLSCDYRTYEYLIPTFVFAGRQRKDHKDPVKVTQAEEIVPKTTDLHLDVNHQQAYRMSTE 249

Query: 140 --ENMRIAAQHLVGRHDFTTFRSIHCQASSPI-RTIDHFDV-------NSFGNLIEIRVV 189
             +++        G H F  F S     S    R I  F         NS    I +RV 
Sbjct: 250 QYDDLNRILAKFEGSHTFHNFTSKLLPTSPKCQRYIVSFKADQPFVPSNSAFEWIRLRVK 309

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK--ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +SFL  QIR  +G+   +  G   S  +E+   L   D     P AP  GLY     + 
Sbjct: 310 GQSFLLHQIRKMIGTAVDLCAGAAESNVIERVMLLDKMD----LPKAPSVGLYLSEAHFE 365


>gi|115391499|ref|XP_001213254.1| hypothetical protein ATEG_04076 [Aspergillus terreus NIH2624]
 gi|114194178|gb|EAU35878.1| hypothetical protein ATEG_04076 [Aspergillus terreus NIH2624]
          Length = 613

 Score =  130 bits (327), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 69/366 (18%), Positives = 99/366 (27%), Gaps = 123/366 (33%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 110 IALKFAYLGQRYNGL-EHANGNVTPLPTIEEELWKALRKTRLIFPTGATADDMREFQEPR 168

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV-------------------- 71
                 +  E      AGRTD GV A  QV    +                         
Sbjct: 169 ALKPYALNWEGCEYSKAGRTDRGVSAFGQVVGIRVRSARPKKKAAVADPGADTPMQDGGE 228

Query: 72  ----------------PVILCKALNAYLKISDTISILNLSIVDKQ-FHARFSAIRRSYLY 114
                              L         + + I +L       + F ARFS   R Y Y
Sbjct: 229 GNVTADRSVDDNWDDIADELPYINLLNRVLPEDIRVLAWCPHPPEGFDARFSCRERQYKY 288

Query: 115 RIIT---RQAP-----LALEKGRAWLIPKS----LDCENMRIAAQHLVGRHDFTTFRSIH 162
                     P           +A  +PK     LD E MR AA+  VGRHDF  F  + 
Sbjct: 289 FFTQPAFSPTPGPGGFAPRANDKAGSVPKYREGWLDIEAMREAARMFVGRHDFRNFCKLD 348

Query: 163 C--QASSPIRTIDHFDVN-------------------------------------SFGNL 183
              Q  +  R I H D+                                      +   +
Sbjct: 349 TSKQIENFERIIYHSDIELVDPRSTPLGYVAQPGFTALESPSAEQGSGSLETPVPTASQV 408

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQD-RKECGPLAPPEGLYF 241
               +   +FL  Q+R  V  L LVG G    + + + L  +++ RK    +A    L  
Sbjct: 409 YVFSLQGSAFLWHQVRHMVSVLFLVGQGLEKPSIVSELLDVSKNPRKPSYEMASDAPLVL 468

Query: 242 DSVEYS 247
               + 
Sbjct: 469 WDCIFP 474


>gi|242008043|ref|XP_002424822.1| tRNA pseudouridine synthase, putative [Pediculus humanus corporis]
 gi|212508372|gb|EEB12084.1| tRNA pseudouridine synthase, putative [Pediculus humanus corporis]
          Length = 430

 Score =  130 bits (327), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/254 (22%), Positives = 89/254 (35%), Gaps = 44/254 (17%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFL----VTGEIVVVHGAGRTDSGVHAL 58
             +   Y G    G+  Q+N  ++I+  +  A+         E       GRTD GV A 
Sbjct: 64  IFLKFCYFGWDTSGFVIQENTSNTIEQFMFDALKKCCLIENIETSNYQKCGRTDKGVSAF 123

Query: 59  RQVAHFDLVREWV---------PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
            QV   D+  +            +  C  LN  L     I   + + V     +R     
Sbjct: 124 SQVISLDVRSKLENPNHENAEQEIEYCSMLNRLL--PPFIKCYSWAHVGSDVGSRHDCSE 181

Query: 110 RSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASS 167
           R+Y Y                +    +LD   MR AA+ L+G HDF     +      ++
Sbjct: 182 RTYKY----------------YFPKGNLDINLMREAAKSLLGSHDFRNLCKMDVANGITN 225

Query: 168 PIRTIDHFDV---------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
             R I + D+          S        + ++ FL+ QIRS +  L LVG  K +   +
Sbjct: 226 FNRNIIYADIKPCSFLLEKQSGYQFYIFEIKSKCFLYHQIRSIMSVLLLVGQKKESPDII 285

Query: 219 EKALQAQDRKECGP 232
              L   ++    P
Sbjct: 286 NDLLDI-NKNPAKP 298


>gi|219120809|ref|XP_002185636.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582485|gb|ACI65106.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 293

 Score =  130 bits (327), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 98/290 (33%), Gaps = 52/290 (17%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
            ++ Y G+ Y G+Q      + Q   E A+            +        +GRTD GVH
Sbjct: 1   FLLAYVGTNYGGFQINDGQRTPQAEFELAMLRTRLLLPCNFGSPHKYSWSTSGRTDKGVH 60

Query: 57  ALRQVAHFDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           A  QV    +          +   +N  L   D + +L++    + F A+    R  Y Y
Sbjct: 61  ACAQVVSAKVELLPDQTMAEVRDEMNTVL--PDDVRVLDVVRTTRNFCAKTQRDRVRYQY 118

Query: 115 RIITRQAPLA-----LEKGRAWLIPK--------------------------SLDCENMR 143
            I +     A     L K       +                           +    ++
Sbjct: 119 MIPSFVFADADTLRVLFKDVVGHSNRGQSKAELLLPEELKSIQSALKDFRANPMHIAKLQ 178

Query: 144 IAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS------FGNLIEIRVVARSFLHT 196
            A Q   G H F  F R +    +   R I+ F V            I  +V+ +SFL  
Sbjct: 179 EALQVYEGTHAFHNFSRGVKANEARAARYIERFHVEEPIVFPNGVEWIPTQVLGQSFLLN 238

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           QIR  V     V  G    T++ +AL+ Q       +AP +GL+ +   Y
Sbjct: 239 QIRKMVCMAMDVARGVVPLTNVSRALERQS-DVRINVAPAQGLFLEMSYY 287


>gi|326474345|gb|EGD98354.1| pseudouridylate synthase [Trichophyton tonsurans CBS 112818]
          Length = 614

 Score =  129 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 69/380 (18%), Positives = 97/380 (25%), Gaps = 147/380 (38%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 93  IAIKFAYLGKRYNGL-EHANGNYTEVPTIEEELWKALRKTRLIFPTHKNCTEEFSGKDNS 151

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI----------------- 74
                 +  +       GRTD GV A  QV    +                         
Sbjct: 152 PSRPYEIHWDGCQYSKCGRTDKGVSAFGQVIGIRVRSLRPADPNPSADLKGGDVMDSVVA 211

Query: 75  -------------------------------LCKALNAYLKISDTISILNLSI-VDKQFH 102
                                            + LN  L   + I +L     +   F 
Sbjct: 212 TESGMADKNTQNGVSDTGAAKGWDDIADELPYIQILNGAL--PEDIRVLAWCPHLPPDFD 269

Query: 103 ARFSAIRRSYLYRIITRQAPLA-----------------LEKGRAWLIPKSLDCENMRIA 145
           ARFS  +R Y Y                           L + R       LD E MR A
Sbjct: 270 ARFSCRQRRYRYFFTQPAFCPTPGARGIVRSPELKDDLSLARPREGW----LDIEAMREA 325

Query: 146 AQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN------------------------- 178
           AQ+ VG HDF  F  +    Q ++ +R I   D+                          
Sbjct: 326 AQYFVGSHDFRNFCKVDTSKQITNFVRRILRADIELVDPQRTPLGFVQMPGFEPFENGPR 385

Query: 179 -------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                        + G +    V   +FL  QIR  VG L LVG G    + + + L   
Sbjct: 386 NTGVPESVNDINPAAGKVYSFTVHGTAFLWHQIRHMVGILFLVGQGLEHPSIVPELLDVT 445

Query: 226 D--RKECGPLAPPEGLYFDS 243
              R+    +A    L    
Sbjct: 446 KNPRRPVYEMASDSPLVLWD 465


>gi|219117902|ref|XP_002179737.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408790|gb|EEC48723.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 216

 Score =  129 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 82/232 (35%), Gaps = 33/232 (14%)

Query: 31  IEKAIFLVTGEIVVV--------HGAGRTDSGVHALRQVAHFDL--VREWVPVILCKALN 80
           +EKA+F       +V           GRTD GV A  Q     L   R        K LN
Sbjct: 2   VEKALFRALRTSRLVESRASSGYSRCGRTDKGVSAAGQQTDPPLRQQRALREHAYDKILN 61

Query: 81  AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCE 140
             L   D I +L    V   F ARFSA                       +   ++LD E
Sbjct: 62  NLL--PDDIRVLGWIPVSDDFSARFSATS---------------RTYRYFFRRRRTLDVE 104

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQ-ASSPIRTIDHFDV---NSFGNLIEIRVVARSFLHT 196
            MR     + G HDF  F  +  +   +  R ID  ++        +    +V ++FL  
Sbjct: 105 AMRQGLHRMQGTHDFRNFCKMDVEKVYNFERRIDKAEIVNMERDTGVSYFLIVGQAFLWH 164

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQ-AQDR-KECGPLAPPEGLYFDSVEY 246
           QIR     L  +G G  T   +   L  AQ+  K   PLA  + L      Y
Sbjct: 165 QIRYMASILFAIGQGLETPELVTAMLDIAQNPGKPAYPLADEQPLVLHDCGY 216


>gi|50294374|ref|XP_449598.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49528912|emb|CAG62574.1| unnamed protein product [Candida glabrata]
          Length = 317

 Score =  129 bits (325), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 67/271 (24%), Positives = 96/271 (35%), Gaps = 40/271 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDSGV 55
            +++ Y G+GY G Q      +I   + KA+                     A RTD GV
Sbjct: 2   ALVLGYLGTGYQGIQYNPPAHTIDNELFKALVATNCISQSNSDDFSKSSFSRATRTDKGV 61

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HAL  +    + R  VP  +   LN  L   D I I ++  V K+F+AR  A  R Y Y 
Sbjct: 62  HALTNLVALKMQRYEVPQQVKAELNEIL--PDDIRIWDVVPVKKKFNARVMAGTRHYRYV 119

Query: 116 IITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF--RSIHCQASSP--IR 170
           I T               + +  +  NM       +G H++  F  R     A SP  +R
Sbjct: 120 IPTFLLQCGPHSDLSTSQLARFKNIWNM------FLGTHNYYNFTPRRKDTNADSPQNMR 173

Query: 171 TIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
            +    V+           + I +  +SFL  QIR  V           + T   + L+ 
Sbjct: 174 HMYSIQVSDPFTIAGSTQWLSIAIHGQSFLLHQIRKMVHYALSEYHRSSSDTKSMELLET 233

Query: 225 QDRKEC------------GPLAPPEGLYFDS 243
            D                 PLAP  GLY   
Sbjct: 234 VDPDLTSATALDTPTEQYIPLAPAAGLYLHH 264


>gi|302818082|ref|XP_002990715.1| hypothetical protein SELMODRAFT_132245 [Selaginella moellendorffii]
 gi|300141453|gb|EFJ08164.1| hypothetical protein SELMODRAFT_132245 [Selaginella moellendorffii]
          Length = 318

 Score =  129 bits (325), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 65/263 (24%), Positives = 97/263 (36%), Gaps = 27/263 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV--------TGEIVVVHGAGRTD 52
           M +  + + Y G+GY G QR     +I+G +E+A+           +   +    A RTD
Sbjct: 1   MEKAALFVVYCGAGYKGMQRNPGALTIEGVLEEALGRAGAIGSNGCSRNWLDWKRAARTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
             V AL QV      R ++   L    N +L    +I +L    V   F A+     R Y
Sbjct: 61  KEVSALGQVVS---ARLYLTPDLVHRTNEFL--PGSIQLLGFKRVPDDFSAKKMCDSRRY 115

Query: 113 LYRIITRQAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGR-HDFTTFR-SIHCQASSP 168
            Y +       A +      + +    D E         +G  H F  F   +       
Sbjct: 116 EYVLPV----FAFDPRTGDDLEEEFLFDFERFNQILGRFLGTDHSFHNFSWRVRPGDREA 171

Query: 169 IRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            RT+  F             + I V+ARSF+  QIR  VG    V       T + +AL+
Sbjct: 172 RRTVVEFRAADKIWIGGSEFVRIIVLARSFMAYQIRKMVGLAVAVMRDIAPVTTINRALR 231

Query: 224 AQDRKECGPLAPPEGLYFDSVEY 246
           + +     P AP  GL  D   Y
Sbjct: 232 S-EVDVIVPTAPEVGLLLDESFY 253


>gi|169604989|ref|XP_001795915.1| hypothetical protein SNOG_05510 [Phaeosphaeria nodorum SN15]
 gi|160706683|gb|EAT86574.2| hypothetical protein SNOG_05510 [Phaeosphaeria nodorum SN15]
          Length = 475

 Score =  129 bits (325), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 58/350 (16%), Positives = 92/350 (26%), Gaps = 106/350 (30%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFL---------------------- 37
             +   Y G  Y G++  KN      +I+  + KA+                        
Sbjct: 74  IALKFAYLGQKYNGFEHHKNNSTPLPTIEEELWKALVKTRLINPIPTTGDTADYNKADRK 133

Query: 38  -----------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV--------------- 71
                      V  +       GRTD GV A  QV    +                    
Sbjct: 134 TFATWDREGADVNWDGCEYSKCGRTDRGVSAFGQVIGVRVRSNRPLPKQPAKEPESQENP 193

Query: 72  -------------PVILCKALN-----------AYLKISDTISILNLSI-VDKQFHARFS 106
                        P    K  N               +   I +        + F ARFS
Sbjct: 194 PAAEDELDILDSEPDAATKHFNEVTDELPYIQLLNRVLPPDIRVYAWCPNPPENFSARFS 253

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKS------LDCENMRIAAQHLVGRHDFTTFRS 160
              R Y Y                +  P S      LD   M++A + L+G HDF     
Sbjct: 254 CKERRYKYFFTNPCFAPVPGSAGTYHTPSSPMREGTLDIAAMQLACESLIGLHDFRNMCK 313

Query: 161 IHC--QASSPIRTIDHFDVNS-------------------FGNLIEIRVVARSFLHTQIR 199
           I    Q ++  R I +  +                        +    +   +FL  Q+R
Sbjct: 314 IDASKQLTNFKRRIFYAGIEEVSPLSVPSYLSHGAIAPPDQPKMYAFVLHGSAFLWHQVR 373

Query: 200 SFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           S V  L L+G      + +++ L  +    +    +A    L      + 
Sbjct: 374 SIVAILFLIGQRLEPPSLVQQLLDIETNPTRPKYEMASDAPLVLWDCIFP 423


>gi|327307008|ref|XP_003238195.1| tRNA pseudouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326458451|gb|EGD83904.1| tRNA pseudouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 614

 Score =  129 bits (325), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 69/380 (18%), Positives = 97/380 (25%), Gaps = 147/380 (38%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 93  IAIKFAYLGKRYNGL-EHANGNYTEVPTIEEELWKALRKTRLIFPTHKDCTEEFSGKDNS 151

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI----------------- 74
                 +  +       GRTD GV A  QV    +                         
Sbjct: 152 PSRPYAIHWDGCQYSKCGRTDKGVSAFGQVIGIRVRSLRPAEPNPPVELKGGDVVNSVVA 211

Query: 75  -------------------------------LCKALNAYLKISDTISILNLSI-VDKQFH 102
                                            + LN  L   + I +L     +   F 
Sbjct: 212 TESGMGDKNTQSGVSDTGEAKGWDDIADELPYIQILNGAL--PEDIRVLAWCPHLPPDFD 269

Query: 103 ARFSAIRRSYLYRIITRQAPLA-----------------LEKGRAWLIPKSLDCENMRIA 145
           ARFS  +R Y Y                           L + R       LD E MR A
Sbjct: 270 ARFSCRQRRYRYFFTQPAFCPTPGTRGIVRSPELKDDLSLARPREGW----LDIEAMRKA 325

Query: 146 AQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN------------------------- 178
           AQ+ VG HDF  F  +    Q ++ +R I   D+                          
Sbjct: 326 AQYFVGSHDFRNFCKVDTSKQITNFVRRILRADIELVDPQRTPLGFVQMPGFEPFENGPR 385

Query: 179 -------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                        + G +    V   +FL  QIR  VG L LVG G    + + + L   
Sbjct: 386 NTGVPGSINDINSAAGKVYSFTVHGTAFLWHQIRHMVGILFLVGQGLEHPSIVPELLDVT 445

Query: 226 D--RKECGPLAPPEGLYFDS 243
              R+    +A    L    
Sbjct: 446 KNPRRPVYEMASDSPLVLWD 465


>gi|302656723|ref|XP_003020113.1| hypothetical protein TRV_05887 [Trichophyton verrucosum HKI 0517]
 gi|291183894|gb|EFE39489.1| hypothetical protein TRV_05887 [Trichophyton verrucosum HKI 0517]
          Length = 614

 Score =  129 bits (324), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 69/380 (18%), Positives = 97/380 (25%), Gaps = 147/380 (38%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 93  IAIKFAYLGKRYNGL-EHANGNYTEAPTIEEELWKALRKTHLIFPTHKDCTEEFSGKDNS 151

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI----------------- 74
                 +  +       GRTD GV A  QV    +                         
Sbjct: 152 PSRPYAIHWDGCQYSKCGRTDKGVSAFGQVIGIRVRSLRPADPNPPADLEEGDVMDSDVA 211

Query: 75  -------------------------------LCKALNAYLKISDTISILNLSI-VDKQFH 102
                                            + LN  L   + I +L     +   F 
Sbjct: 212 TESGMGDRNTQSGVSDTGEAKGWDDIADELPYIQILNGAL--PEDIRVLAWCPHLPPDFD 269

Query: 103 ARFSAIRRSYLYRIITRQAPLA-----------------LEKGRAWLIPKSLDCENMRIA 145
           ARFS  +R Y Y                           L + R       LD E MR A
Sbjct: 270 ARFSCRQRRYRYFFTQPAFCPTPGARGIVRSSELKDDLSLARLREGW----LDIEAMREA 325

Query: 146 AQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN------------------------- 178
           AQ+ VG HDF  F  +    Q ++ +R I   D+                          
Sbjct: 326 AQYFVGSHDFRNFCKVDTSKQITNFVRRILRADIELVDPQRTPLGFVQMPGFEPFENGPR 385

Query: 179 -------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                        + G +    V   +FL  QIR  VG L LVG G    + + + L   
Sbjct: 386 NTGVPESIDDINPAAGKVYSFTVHGTAFLWHQIRHMVGILFLVGQGLEHPSIVPELLDVT 445

Query: 226 D--RKECGPLAPPEGLYFDS 243
              R+    +A    L    
Sbjct: 446 KNPRRPVYEMASDSPLVLWD 465


>gi|189193015|ref|XP_001932846.1| pseudouridylate synthase 3 [Pyrenophora tritici-repentis Pt-1C-BFP]
 gi|187978410|gb|EDU45036.1| pseudouridylate synthase 3 [Pyrenophora tritici-repentis Pt-1C-BFP]
          Length = 599

 Score =  128 bits (323), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 66/360 (18%), Positives = 94/360 (26%), Gaps = 118/360 (32%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFL---------------------- 37
             +   Y G  Y G++  KN      +I+  + KA+                        
Sbjct: 80  IALKFAYLGQKYNGFEHHKNNTTPLPTIEEELWKALVKTRLITPIPTAGGETESYERIDR 139

Query: 38  ------------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI----------- 74
                       V  +       GRTD GV A  QV    +                   
Sbjct: 140 KTFARWDREGADVNWDGCEYSKCGRTDRGVSAFGQVIGVRVRSNKPLPKAPQSPEETPET 199

Query: 75  -----------------------------LCKALNAYLKISDTISILNLSIVDK-QFHAR 104
                                          + LN  L     I +          F AR
Sbjct: 200 NEEESPPSSPSSDSKPPPKPFNDLTDELPYIQLLNRVL--PPDIRVYAWCPNPPADFSAR 257

Query: 105 FSAIRRSYLYRIITRQ-APLALEKGRAWLIPKS--------LDCENMRIAAQHLVGRHDF 155
           FS   R Y Y       AP+    GR               LD   M+    HLVG HDF
Sbjct: 258 FSCKERRYKYFFTNPCFAPVPGSSGRYNTSSTPPQAMREGWLDINAMKQGCAHLVGLHDF 317

Query: 156 TTFRSIHC--QASSPIRTIDHFDVNSF------------------------GNLIEIRVV 189
             F  I    Q ++  R I H D+                             L    + 
Sbjct: 318 RNFCKIDASKQLTNFQRRIFHADIEEVSPLSVPAFLSHPALTAPGLPASEAPKLYSFTLH 377

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
             +FL  Q+RS +  L L+G G  +   + + L  +A   +    +A    L      + 
Sbjct: 378 GSAFLWHQVRSLIAVLFLIGQGLESPDIIPQLLDIEANPTRPKYEMASDAPLVLWDCIFP 437


>gi|167967303|ref|ZP_02549580.1| tRNA pseudouridine synthase A [Mycobacterium tuberculosis H37Ra]
          Length = 243

 Score =  128 bits (323), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 40/136 (29%), Positives = 65/136 (47%), Gaps = 2/136 (1%)

Query: 113 LYRIITRQAPL-ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           +YR+ T    +   +       P+ LD + M  A++ L+G HDF  F   H + ++ IR 
Sbjct: 1   MYRLSTAPYGVEPQQARYITAWPRELDLDAMTAASRDLMGLHDFAAFCR-HREGATTIRD 59

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +   D +  G L+   V A +F  + +RS VG+L  VG+ +  +T   + L A  R    
Sbjct: 60  LQRLDWSRAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRSSDF 119

Query: 232 PLAPPEGLYFDSVEYS 247
            +AP  GL    V+Y 
Sbjct: 120 AVAPAHGLTLIQVDYP 135


>gi|195382396|ref|XP_002049916.1| GJ20484 [Drosophila virilis]
 gi|194144713|gb|EDW61109.1| GJ20484 [Drosophila virilis]
          Length = 509

 Score =  128 bits (323), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 58/252 (23%), Positives = 88/252 (34%), Gaps = 50/252 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q++   +I+  + +A+              H  GRTD  V A 
Sbjct: 100 VLIKVMYFGWDYQGFACQEDSMDTIEAYLFRALIRTCLIESRATSNYHRCGRTDKEVSAF 159

Query: 59  RQVAHFDLVREWVPV------------ILCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + + +  + ARF
Sbjct: 160 CQVISIDLRSKHAPDVQMEPEALSSEIDYCSLLNRVL--PKNIQCVSWMPLRNPAYSARF 217

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             I R+Y Y                +     LD E MRIA Q LV   DF  F    +H 
Sbjct: 218 DCISRTYRY----------------YFPKGDLDIEAMRIACQSLVCHGDFRNFCKMDVHN 261

Query: 164 QASSPIRTIDHFDVNSFGN------------LIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
             ++ +R +    +    N            +  + +   +FL  QIR  +  L LVG  
Sbjct: 262 GVTNYMRNLQGAAIKPCDNTDIQMHSNSGYAMYYLEIQGNAFLWHQIRCIMAVLLLVGQK 321

Query: 212 KWTSTDLEKALQ 223
                 + K L 
Sbjct: 322 HEQPCVISKLLD 333


>gi|307211854|gb|EFN87801.1| tRNA pseudouridine synthase A [Harpegnathos saltator]
          Length = 270

 Score =  128 bits (323), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 103/243 (42%), Gaps = 44/243 (18%)

Query: 22  KNGSSIQGSIEKAIFLVTGEIV---VVHGAGRTDSGVHALRQVAHFDLVREW----VPVI 74
           ++G ++QG++E A+  +  +      ++ + RTD+GVHAL    H +L  ++        
Sbjct: 2   RDGDTVQGALEAALLNILPKTTIRPNIYLSSRTDAGVHALCNAGHVELENKYNVLYKDDN 61

Query: 75  LCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-----LALEKG 128
           +   +N Y      TI +L  + V   FHAR S   R+Y+YR +  + P       ++  
Sbjct: 62  IKAFVNRYFNKCGHTIRLLEFTPVTNDFHARGSCKSRTYIYRFMIPKVPGEQRIPLVDAP 121

Query: 129 RAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
             +L+     D + ++   Q  +G  DFTTF S+    S   R I++             
Sbjct: 122 HTYLVKAHDFDVDRVKCGTQLFMGVKDFTTFSSM----SITNRKIEY------------- 164

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP---LAPPEGLYFDSV 244
                     +R  VG+L  +G  K T  D+   LQ        P    AP  GL+  ++
Sbjct: 165 ----------VRRMVGALISLGLRKITEKDINVMLQVPSHHNWNPRASSAPANGLHLVNL 214

Query: 245 EYS 247
           EY 
Sbjct: 215 EYD 217


>gi|168049023|ref|XP_001776964.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162671665|gb|EDQ58213.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 680

 Score =  128 bits (323), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 50/211 (23%), Positives = 75/211 (35%), Gaps = 16/211 (7%)

Query: 46  HGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           H   R      + ++   F              LN  L   + I +L    V   F+ARF
Sbjct: 350 HSGDRVAMARASRKEEEQFARTAYEDEYDYVGILNRAL--PEDIRVLGWCPVPPGFNARF 407

Query: 106 SAIRRSYLYR-IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC- 163
           S + R Y Y  I             A+    ++    M+ A +   G HDFT F  +   
Sbjct: 408 SCMYREYKYFFIDDGLNIDVWTLIYAFNRQYNV----MKFACKQFEGEHDFTNFCKMDAA 463

Query: 164 QASSPIRTIDHFDVNSFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD 217
              + +RTI HFD+           +  + V   +FL  Q+R     L +VG G    T 
Sbjct: 464 NVHNYMRTITHFDIIPSNEKWGGKSVWIMNVKGTAFLWHQVRCMAAVLFMVGAGHEKPTI 523

Query: 218 LEKALQAQD--RKECGPLAPPEGLYFDSVEY 246
           +E+ L  +   RK    +A    L      Y
Sbjct: 524 VEELLDVKKIVRKPQYIMASETPLLLFHCGY 554


>gi|317027085|ref|XP_001400055.2| pseudouridylate synthase 3 [Aspergillus niger CBS 513.88]
          Length = 608

 Score =  128 bits (323), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 67/363 (18%), Positives = 96/363 (26%), Gaps = 122/363 (33%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 109 IALKFAYLGQRYNGL-EHANGNATPLPTIEEEMYKALRKTRLIFPTDTTGDEFVESYAPR 167

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVP------------------- 72
                 +  +      AGRTD GV A  QV    +                         
Sbjct: 168 ETKPYYINWDGCEYSKAGRTDRGVSAFGQVIGIRVRSARPKRDEVVQSDENADTTMQNTD 227

Query: 73  --------------VILCKALNAYLKISDTISILNLSIVDKQ-FHARFSAIRRSYLYRII 117
                           L         + + I +L       + F ARFS   R Y Y   
Sbjct: 228 EANASVDDGWDDIKDELPYVSMLNKVLPEDIRVLAWCPRPPEGFDARFSCGERHYKYFF- 286

Query: 118 TRQAPLALEKGRAWLIPKS------------LDCENMRIAAQHLVGRHDFTTFRSIH--C 163
           T+ A      G +  +P+             LD E MR AA++  G HDF  F  +    
Sbjct: 287 TQPAFSP-TPGASGFVPRDGTGKPPKLREGWLDIEAMRKAAKYFEGTHDFRNFCKLDVTK 345

Query: 164 QASSPIRTIDHFDVN-------------------------------------SFGNLIEI 186
           Q  S  R I   D+                                      +   +   
Sbjct: 346 QIESFYRDIFRADIELLDARTNPLGYVTQPEFQARPASGADESAESSAAPLPTAAQVYVF 405

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSV 244
            +   +FL  Q+R  V  L LVG G    + ++  L      RK    +A    L     
Sbjct: 406 HLEGSAFLWHQVRHMVNVLFLVGQGLEEPSIVQDLLDVTKNPRKPTYEMASDAPLVLWDC 465

Query: 245 EYS 247
            Y 
Sbjct: 466 IYP 468


>gi|297619849|ref|YP_003707954.1| Pseudouridine synthase I, TruA, alpha/beta domain-containing
           protein [Methanococcus voltae A3]
 gi|297378826|gb|ADI36981.1| Pseudouridine synthase I, TruA, alpha/beta domain protein
           [Methanococcus voltae A3]
          Length = 271

 Score =  128 bits (322), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 94/247 (38%), Gaps = 29/247 (11%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHALRQ 60
           Y   + Y+G  Y  +Q Q +  ++   +   +     ++     ++  GRTD GV AL  
Sbjct: 2   YIFKVAYDG-RYS-FQLQPHEKTVCDILTNILVDCGYLSEFKKPLYYGGRTDLGVSALGN 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
              +DL +E +   +      +      I +L    +++  +  +    R Y Y +    
Sbjct: 60  FVIYDLDKEPILTHIYSKCKGF-----GIWVLGYQKINEFPNVEY----RHYRYILPKVD 110

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI-HCQASSPIRTIDHFDVNS 179
           A                D + ++  ++ L+G H F         +   P+RTI    V  
Sbjct: 111 AYGNFH-----------DMDKIKKVSECLIGTHSFHNLSKRDKTKNRDPVRTIYDITVED 159

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECGPLAPP 236
               I + +  +SFL   +R  +G +  VG  + T+ ++E+ +        K   P++  
Sbjct: 160 NEYFITLNIYGKSFLWNMVRKIIGLISNVGISEMTNEEIEEYMDKVFNPSIKVGSPISSA 219

Query: 237 EGLYFDS 243
           EGL    
Sbjct: 220 EGLVLVE 226


>gi|296412959|ref|XP_002836186.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295629994|emb|CAZ80377.1| unnamed protein product [Tuber melanosporum]
          Length = 454

 Score =  128 bits (322), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 94/260 (36%), Gaps = 28/260 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           +  ++I Y G+GY G Q      SI+  + +A               +   +    RTD 
Sbjct: 92  KVAVLIGYCGTGYRGMQLNPPHKSIESDLFEAFVQAGAISKANSDDPKKSSLVRCARTDK 151

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N+YL   + I +  +      F +      R Y 
Sbjct: 152 GVHAAGNVISLKL--IIEDPDITEKINSYL--PEQIRVWGIVRTVGSFSSYHQCDSRRYE 207

Query: 114 YRIITRQAPLALEKGR----AWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASS 167
           Y + +        K       + I PK L  + +R   +   G H+F  F         S
Sbjct: 208 YLVPSHCFIPPHPKSYLAKKTYRISPKRL--QRVREGFRSYEGTHNFHNFTIQKTFNDPS 265

Query: 168 PIRTIDHFDV-----NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
             R I  F+V      +    + +RV  +SF+  QIR  VG + +V         +++  
Sbjct: 266 SKRFIKSFEVLDPIIINNTEWLSLRVHGQSFMMHQIRKMVGMVMMVVRTGCPLERIKE-- 323

Query: 223 QAQDRKECGPLAPPEGLYFD 242
               R    P AP  GL  +
Sbjct: 324 ACGPRVVSIPKAPSLGLLLE 343


>gi|2160170|gb|AAB60733.1| F21M12.19 gene product [Arabidopsis thaliana]
          Length = 250

 Score =  128 bits (321), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 53/201 (26%), Positives = 87/201 (43%), Gaps = 55/201 (27%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            RY + IEY G+ + G Q+Q    ++ G ++                   D+GVHAL  V
Sbjct: 55  QRYLVAIEYIGTRFSGSQQQAKDRTVVGVLQ-------------------DAGVHALSNV 95

Query: 62  AHFDLVR-----------EWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSA-- 107
            H D+ R              P ++ +A+N +L+  D  + ++++  V   +HAR+ A  
Sbjct: 96  CHVDVERISKRKPGEVLPPHEPGVVQRAVNHFLQRKDGDVMVIDVRCVPSNYHARYKAQE 155

Query: 108 ---------------------IRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIA 145
                                    Y YR+++   P   LEK R W +P+ L+   M+ A
Sbjct: 156 RTVLGYDLKVYSLQLEIENLFTHCRYFYRLLSGSDPLSILEKDRCWHVPEELNLRFMQEA 215

Query: 146 AQHLVGRHDFTTFRSIHCQAS 166
            + LVG HDF++FR+  CQ  
Sbjct: 216 CRVLVGSHDFSSFRAAGCQVK 236


>gi|47208274|emb|CAF91572.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 375

 Score =  128 bits (321), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 85/235 (36%), Gaps = 26/235 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAGR 50
           +  +++ Y+G GY+G QR        +I+  +  A+              + +      R
Sbjct: 76  KVALLLAYSGKGYYGMQRNPGSSEFRTIEDDLVAALVKSGCIPENHAEDMKKMSFQRCAR 135

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GV A  QV    L   W+   L + +N +L     I +L +  V + F+++ +   R
Sbjct: 136 TDKGVSAAGQVVSLKL---WLIDDLAEKINQHL--PPQIRVLGVKRVTQGFNSKNNCDAR 190

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL---VGRHDFTTFRSIH-CQAS 166
           +Y Y + T           +      L  E ++   +      G H+F  F S       
Sbjct: 191 TYAYMLPTVAFAPKDSDAASDAASFRLQPETLQRVNRLFALYKGTHNFHNFTSQKAPNDP 250

Query: 167 SPIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           S  R + H                I V  +SF+  QIR  +G +  V  G     
Sbjct: 251 SARRYVTHVCCGEPFMGGDTEFAVITVRGQSFMLHQIRKMIGLVIAVVKGYAREE 305


>gi|296824052|ref|XP_002850540.1| pseudouridylate synthase 3 [Arthroderma otae CBS 113480]
 gi|238838094|gb|EEQ27756.1| pseudouridylate synthase 3 [Arthroderma otae CBS 113480]
          Length = 614

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 76/380 (20%), Positives = 98/380 (25%), Gaps = 147/380 (38%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL----------------VTGEI 42
             +   Y G  Y G     NG      +I+  + KA+                  V    
Sbjct: 93  IALKFAYLGKRYNGL-EHANGNFTEVPTIEEELWKALRKTRLIFPTHKDCIDDFAVPSRP 151

Query: 43  VVVH-------GAGRTDSGVHALRQVAHFD------------------------------ 65
             +H         GRTD GV A  QV                                  
Sbjct: 152 QSIHWDGCQYSKCGRTDKGVSAFGQVIGIRVRSLKPAAPSLAAEGKGKRTTGSAAAAVSE 211

Query: 66  ----------------------LVREWVPVILCKALNAYLKISDTISILNLSI-VDKQFH 102
                                        +   + LN  L   D I +L         F 
Sbjct: 212 PGDENILGSFDVSDKEEAKAPVWDDIADELPYIQILNGAL--PDDIRVLAWCPHPPPDFD 269

Query: 103 ARFSAIRRSYLYRIITRQAPLA-----------------LEKGRAWLIPKSLDCENMRIA 145
           ARFS  +R Y Y         A                 L K R       LD E MR A
Sbjct: 270 ARFSCRQRRYRYFFTQPAFCPAPGARGIVRAPELKQDLSLPKLREGW----LDIEAMREA 325

Query: 146 AQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDV------------------NSFGN--- 182
           AQH VG HDF  F  +    Q ++ +R I   D+                    F N   
Sbjct: 326 AQHFVGSHDFRNFCKVDTSKQITNFVRRILRADIELVDPQKTPLGFVQMPGFEQFDNSPR 385

Query: 183 -----------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                            +    V   +FL  QIR  VG L LVG G    + + + L   
Sbjct: 386 NTGVSESVSDTSPAAAKVYSFTVHGTAFLWHQIRHMVGILFLVGQGLEPPSIVPQLLDVT 445

Query: 226 D--RKECGPLAPPEGLYFDS 243
              R+    +A    L    
Sbjct: 446 KNPRRPVYEMASDSPLVLWD 465


>gi|11464733|gb|AAG35307.1| pseudouridine synthase 1 [Mus musculus]
          Length = 411

 Score =  127 bits (320), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 97/285 (34%), Gaps = 48/285 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 50  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 109

Query: 50  RTDS------------------GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           RTD                   GV A  QV      + W+   +   +N++L     I I
Sbjct: 110 RTDKPLRTSACFCLYTGFLFHWGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRI 164

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQH 148
           L L  V   F+++     R+Y Y + T     A +          L  E ++        
Sbjct: 165 LGLKRVTGGFNSKNKCDARTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLAC 222

Query: 149 LVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFV 202
             G H+F  F S    +  S  R I                  I+V  +SF+  QIR  V
Sbjct: 223 YKGTHNFHNFTSQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMV 282

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G +  +  G    + LE++    + K   P AP  GL  + V + 
Sbjct: 283 GLVVAIVKGYAPESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 325


>gi|260817697|ref|XP_002603722.1| hypothetical protein BRAFLDRAFT_93048 [Branchiostoma floridae]
 gi|229289044|gb|EEN59733.1| hypothetical protein BRAFLDRAFT_93048 [Branchiostoma floridae]
          Length = 352

 Score =  127 bits (320), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 96/261 (36%), Gaps = 22/261 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +   ++ Y+G GY G QR +   +I+  +  A +             + +      RTD
Sbjct: 42  RKVACLLAYSGVGYMGMQRNQGFKTIEEDLLAAFYKAGAIPKDHMDCMQKMHFQRCARTD 101

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  Q+      + ++     + +N  L   ++I ++ +      F ++ +   R+Y
Sbjct: 102 KGVSAAGQIVSL---KMYMIEDAVQKINDCLA--ESIRLIGIKRTTNGFDSKNACDARTY 156

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRT 171
           +Y + T       E+            E +        G H+F  F S    +  S  R 
Sbjct: 157 MYVLPTYSFAPTKEETEQDFRATDDVMEKVNDVLSAYKGTHNFHNFTSGKKFKDPSAKRY 216

Query: 172 IDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           I         V        I +  +SF+  QIR  +G +  +  G    + LE+A Q   
Sbjct: 217 IIESKCLDTFVRDDIEWTVISIKGQSFMIHQIRKMIGMMLAIVRGLAPRSMLERAWQEG- 275

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
            K   P AP  GL  D V + 
Sbjct: 276 -KCDIPKAPGLGLVLDKVHFD 295


>gi|194696534|gb|ACF82351.1| unknown [Zea mays]
          Length = 257

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 46/187 (24%), Positives = 68/187 (36%), Gaps = 27/187 (14%)

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
              +   K LN  L     I +L    V   FHARF+ + R Y Y               
Sbjct: 5   RSEIDYVKVLNRIL--PRDIRVLGWCPVPADFHARFTCLSREYKYLFW------------ 50

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS------FGN 182
                  LD   M+ AA   +G HDF  F  +     S+  R I  F +++         
Sbjct: 51  ----KGDLDILEMQKAASKFIGEHDFRNFCKMDAANVSNYRRHITEFTISACDRRSNNDE 106

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRKECGPLAPPEGLY 240
           L  + +   +FL  Q+R  V  L L+G G  + + ++  L      RK    +AP   L 
Sbjct: 107 LCSMTIKGSAFLWHQVRCMVAVLFLIGQGLESPSVVDSLLDIMKTSRKPQYKMAPELPLI 166

Query: 241 FDSVEYS 247
             S  + 
Sbjct: 167 LQSCLFD 173


>gi|148688057|gb|EDL20004.1| pseudouridine synthase 1, isoform CRA_b [Mus musculus]
          Length = 452

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 97/285 (34%), Gaps = 48/285 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 91  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 150

Query: 50  RTDS------------------GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           RTD                   GV A  QV      + W+   +   +N++L     I I
Sbjct: 151 RTDKPLRTSACFCLYTGFLFHWGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRI 205

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQH 148
           L L  V   F+++     R+Y Y + T     A +          L  E ++        
Sbjct: 206 LGLKRVTGGFNSKNKCDARTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLAC 263

Query: 149 LVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFV 202
             G H+F  F S    +  S  R I                  I+V  +SF+  QIR  V
Sbjct: 264 YKGTHNFHNFTSQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMV 323

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G +  +  G    + LE++    + K   P AP  GL  + V + 
Sbjct: 324 GLVVAIVKGYAPESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 366


>gi|67481869|ref|XP_656284.1| tRNA pseudouridine synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56473473|gb|EAL50898.1| tRNA pseudouridine synthase, putative [Entamoeba histolytica
           HM-1:IMSS]
          Length = 401

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 103/268 (38%), Gaps = 30/268 (11%)

Query: 4   YCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
             +I  Y G GYFG      N  +I+G IE A++             + V      RTD 
Sbjct: 43  VAVIFSYVGRGYFGLMYLNNNPKTIEGEIENAMYKAKCISEDNKHDLKKVGWSRCARTDK 102

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A   +      +  +     + +N++L   +TI I ++  V   F+A+     R+Y 
Sbjct: 103 GVSAANNLISL---KMGLDGNYIERINSFL--PETIRIQDVVKVSHSFNAKTRVDSRTYE 157

Query: 114 YRIIT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----RSIHCQAS 166
           Y   +   ++      +      P+  D +       + V  H+F  +    +     + 
Sbjct: 158 YIFPSYAIQKIDSEHPEINVEYNPQQEDIDYFNSVISNYVKTHNFQNYTFNTKETKADSK 217

Query: 167 SPIRTIDHFD---VNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           S  R I       V   G N+I + +  +SF+  QIR  +G   ++ + +     + + +
Sbjct: 218 SNNRYIISMSAQLVQRNGLNVIAVSIHGQSFMLWQIRRMIGFAIVLTNFRLPIEQMNEIM 277

Query: 223 QAQ----DRKECGPLAPPEGLYFDSVEY 246
           +      + +   P AP  GL+ D   +
Sbjct: 278 KTSFTLINWRSVIPTAPAHGLFLDQCHF 305


>gi|167383737|ref|XP_001736651.1| tRNA pseudouridine synthase A [Entamoeba dispar SAW760]
 gi|165900832|gb|EDR27064.1| tRNA pseudouridine synthase A, putative [Entamoeba dispar SAW760]
          Length = 403

 Score =  126 bits (318), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 103/268 (38%), Gaps = 30/268 (11%)

Query: 4   YCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
             +I  Y G GYFG      N  +I+G IE A++             + V      RTD 
Sbjct: 45  VAVIFSYVGRGYFGLMYLNNNPKTIEGEIENAMYKAKCISEDNKHDLKKVGWSRCARTDK 104

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GV A   +      +  +     + +N++L   +TI I ++  V   F+A+     R+Y 
Sbjct: 105 GVSAANNLISL---KMGLDGNYIERINSFL--PETIRIQDVVKVSHSFNAKTRVDSRTYE 159

Query: 114 YRIIT---RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF----RSIHCQAS 166
           Y   +   ++      +      P+  D +       + V  H+F  +    +     + 
Sbjct: 160 YIFPSYAIQKIDSEHPEINVEYNPQQEDVDYFNSVISNYVKTHNFQNYTFNTKETKADSK 219

Query: 167 SPIRTIDHFD---VNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           S  R I       V   G N+I + +  +SF+  QIR  +G   ++ + +     + + +
Sbjct: 220 SNNRYIISMSAQLVQRNGLNVIAVSIHGQSFMLWQIRRMIGFAIVLTNFRLPIEQMNEIM 279

Query: 223 QAQ----DRKECGPLAPPEGLYFDSVEY 246
           +      + +   P AP  GL+ D   +
Sbjct: 280 KTSFTLINWRSVIPTAPAHGLFLDQCHF 307


>gi|70906468|ref|NP_001020732.1| tRNA pseudouridine synthase A, mitochondrial isoform 1 [Mus
           musculus]
          Length = 441

 Score =  126 bits (318), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 97/285 (34%), Gaps = 48/285 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 80  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDS------------------GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           RTD                   GV A  QV      + W+   +   +N++L     I I
Sbjct: 140 RTDKPLRTSACFCLYTGFLFHWGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRI 194

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI---AAQH 148
           L L  V   F+++     R+Y Y + T     A +          L  E ++        
Sbjct: 195 LGLKRVTGGFNSKNKCDARTYCYMLPT--FAFAHKDRDVQDESYRLSAETLQQVNRLLAC 252

Query: 149 LVGRHDFTTFRS-IHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFV 202
             G H+F  F S    +  S  R I                  I+V  +SF+  QIR  V
Sbjct: 253 YKGTHNFHNFTSQKGPREPSARRYILEMYCEEPFVREGLEFAVIKVKGQSFMMHQIRKMV 312

Query: 203 GSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G +  +  G    + LE++    + K   P AP  GL  + V + 
Sbjct: 313 GLVVAIVKGYAPESVLERSW--GEEKVDVPKAPGLGLVLERVHFE 355


>gi|294949997|ref|XP_002786409.1| tRNA pseudouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
 gi|239900701|gb|EER18205.1| tRNA pseudouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
          Length = 427

 Score =  126 bits (318), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 68/282 (24%), Positives = 102/282 (36%), Gaps = 53/282 (18%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS------SIQGSIEKAIF---------LVTGEIVVVHGAG 49
            + + Y+G G  G Q Q N        +I+G  +KA+          L   + +    A 
Sbjct: 76  LVALGYSGEGLKGMQIQTNEKGEEIHSTIEGIFQKALLATNLSTEEILADKKKLKFSRAA 135

Query: 50  RTDSGVHALRQVAHFDLV------------------REWVPVILCKALNAYLKISDTISI 91
           RTD GVHA   +    L                     +      KALN +L+    + +
Sbjct: 136 RTDKGVHAALNILALALPVTLDKTLPQGEGDATRNVWTFDEKKNVKALNDFLE-PLNMQV 194

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
             +  V  +F AR    RR Y Y +              + +    D   +       VG
Sbjct: 195 FGIQRVSNKFDARKQCERRRYEYLLPE------------FALDGKADAAKLEEVMSQYVG 242

Query: 152 R-HDFTTFR-SIHCQASSPIRTIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSL 205
           +  +F  F   I  +  S  R I               I I++V +SFL  QIR  +G  
Sbjct: 243 KNKNFFNFTAKIPAEDPSAKRHIISITCQPTEIDANTFIRIQLVGQSFLLHQIRKMIGLA 302

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             V  G      +E+ L A++RK    LAP EGL+ D V + 
Sbjct: 303 VEVCRGSAPEGAIEECLAAKERKHI-HLAPAEGLFLDRVYFD 343


>gi|225463117|ref|XP_002264487.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 1520

 Score =  126 bits (318), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 45/185 (24%), Positives = 70/185 (37%), Gaps = 27/185 (14%)

Query: 72   PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
             +   + LN  L     I ++    V   FHARFS + R Y Y                 
Sbjct: 1268 EIDYMRVLNRVL--PKDIRVMGWCPVPIGFHARFSCLSREYKYFFWRG------------ 1313

Query: 132  LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGN------LI 184
                +L+   M  A +  VG HDF  F  +      +  R I  F++    N      L 
Sbjct: 1314 ----NLNILAMESAGKKFVGEHDFRNFCKMDAVNVHNYRRHIISFEIAPTNNRYDGNQLW 1369

Query: 185  EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFD 242
             I++   +FL  Q+R  V  L ++G G  +   ++  L  +   RK    +AP   L  +
Sbjct: 1370 AIKIKGSAFLWHQVRCMVAVLFMIGQGLESPDVVDALLDTERTSRKPQYAMAPEIPLVLE 1429

Query: 243  SVEYS 247
            S E+ 
Sbjct: 1430 SCEFE 1434



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 41/100 (41%), Gaps = 8/100 (8%)

Query: 3   RY-CMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGV 55
           RY  + + Y G  ++G+  + +   +++  I KA+          + +     GRTD GV
Sbjct: 81  RYVALKVMYFGPRFYGFASEAHMDPTVESEIFKALEKTWLAVGDKKELQYSRCGRTDKGV 140

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLS 95
            ++ QV    L      +   +  N+   + +   + +L 
Sbjct: 141 SSVGQVIALFLRSNLKEIG-AREENSKEVVPEEQYVRDLE 179


>gi|238489663|ref|XP_002376069.1| pseudouridylate synthase 3 [Aspergillus flavus NRRL3357]
 gi|220698457|gb|EED54797.1| pseudouridylate synthase 3 [Aspergillus flavus NRRL3357]
          Length = 656

 Score =  126 bits (317), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 68/371 (18%), Positives = 95/371 (25%), Gaps = 132/371 (35%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 150 IALKFAYLGQRYNGL-EHANGNVTPLPTIEEEMWKALRKTRLIFPENGEADGFEDTRGPR 208

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV-------------------- 71
                 +  E      AGRTD GV A  QV    +                         
Sbjct: 209 ELKPYLINWEGCQYSKAGRTDRGVSAFGQVIGLRVRSARPKRDDVAQADPSSDTTMQTGE 268

Query: 72  ----------------PVILCKALNAYLKISDTISILNLSIVDKQ-FHARFSAIRRSYLY 114
                              L         + + I +L       + F ARFS   R Y Y
Sbjct: 269 EASALDDAAQDNWDDIADELPYVSILNRVLPEDIRVLAWCPHPPEGFDARFSCRERHYKY 328

Query: 115 RII-----------------TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
                                 +A  +  K R       LD E MR AA++  G HDF  
Sbjct: 329 FFTQPAFSPTPGPLGFTSRANNKAGDSRAKYREGW----LDIEAMREAAKYFEGVHDFRN 384

Query: 158 FRSIHC--QASSPIRTIDHFDVN------------------------------------- 178
           F  +    Q  +  R I H D+                                      
Sbjct: 385 FCKLDTSKQIENFERVIYHSDIELLDPRSSPLGYVSQPGFQALEDPAAQQTPGSPESPSP 444

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRKECGPLAPP 236
           +   +    +   +FL  Q+R  VG L LVG G    T +   L      RK    +A  
Sbjct: 445 TPSQVYVFNLRGSAFLWHQVRHMVGILFLVGQGLEPPTIVPDLLDITKNPRKPTYEMASD 504

Query: 237 EGLYFDSVEYS 247
             L   +  + 
Sbjct: 505 APLVLWNCVFP 515


>gi|296187337|ref|ZP_06855732.1| tRNA pseudouridine synthase A domain protein [Clostridium
           carboxidivorans P7]
 gi|296047859|gb|EFG87298.1| tRNA pseudouridine synthase A domain protein [Clostridium
           carboxidivorans P7]
          Length = 120

 Score =  126 bits (317), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 42/115 (36%), Positives = 63/115 (54%), Gaps = 7/115 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN-----GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
           M    M+I+Y+GS Y GWQ+Q +      S+IQ  IE  +  +TGE + V G GRTD+GV
Sbjct: 1   MRNLKMLIQYDGSRYKGWQKQNHKDNNSVSTIQDKIESVLSKMTGEDIQVVGCGRTDTGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           HA   VA+F          + K L  Y  + + I + +L    ++FHAR++A  +
Sbjct: 61  HAENYVANFHTDSILTVEDMLKYL--YEFLPEDIVVKSLRDTSERFHARYNAKYK 113


>gi|253744705|gb|EET00865.1| Pseudouridylate synthase, putative [Giardia intestinalis ATCC
           50581]
          Length = 507

 Score =  126 bits (317), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 63/323 (19%), Positives = 95/323 (29%), Gaps = 95/323 (29%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIF-------LVTGEIVVVHGAGRTDSGV 55
             + + Y+G+ Y G  +Q N   +I+  +  A+          T   +    +GRTD GV
Sbjct: 72  IAIQVCYDGTEYAGLAQQSNKEYTIEELLLNALRDAALIPQHATANDIHFERSGRTDRGV 131

Query: 56  HALRQVAHFD--------LVREWVPVILCKALNA-------------------------- 81
            A  QV  F           R           +                           
Sbjct: 132 IAAGQVFSFYARTNNKEITPRPIPAPDPRFYRDRRDGMAPPTKPNDNFDETRGGDTVSVG 191

Query: 82  --------------------YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                                +++ +TI +L  + VD+ F AR S   R Y+Y       
Sbjct: 192 KEPELKQVPQEVEIDYVSAINMRLPETIRVLGWAPVDENFSARHSTSSRRYIYTFGQV-- 249

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVNSF 180
                         SL+ + M  A   LVG HDF            +  R I    +   
Sbjct: 250 -------------GSLNIQRMAEACTTLVGFHDFRNICKPSLDNVKTFERVIFSCQLEID 296

Query: 181 GNLIEIR---------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           G   E                 V   +FL+ Q+R     L  +G      + +   L   
Sbjct: 297 GQPYECEGSRAAVSEDSSLSLVVCGSAFLYHQVRCIASLLLHIGAELEPPSIISDLLDVT 356

Query: 226 DR--KECGPLAPPEGLYFDSVEY 246
               K   P+AP E L F+  EY
Sbjct: 357 RFPGKPDYPIAPGELLIFEKAEY 379


>gi|313223412|emb|CBY40401.1| unnamed protein product [Oikopleura dioica]
          Length = 307

 Score =  126 bits (317), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 89/233 (38%), Gaps = 29/233 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-------------GEIVVVHGAG 49
           +  ++I Y G  Y G Q       +  +IEK +F                 +        
Sbjct: 82  KVAILISYCGKNYHGLQHNPGDDKV-DTIEKRVFQALVAAKVVYSNVINDRKKCAYQSCS 140

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           RTD GV A+  VA     +  +P  LC+ +NA+L   D I + +   V K F A+     
Sbjct: 141 RTDKGVSAIGNVASL---KCKIPKNLCELVNAHL--PDDIRLTSFEQVTKGFCAKKRCTH 195

Query: 110 RSYLYRIITRQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-S 166
           R+Y Y   T         ++  ++ I      E +R   +  +G   +  F S   Q   
Sbjct: 196 RTYSYYCPTICFGSKEDWDRPSSFRISAE-KLEGVRELLKKYIGTRSYHNFTSGKRQGDE 254

Query: 167 SPIRTIDHFDVN------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S  R I  F +       +    +E+RVV +SF+  QIR  VG +       W
Sbjct: 255 SAKRHILDFRIQGDPFICNEWEYVELRVVGQSFMIHQIRKMVGLIIARAGNHW 307


>gi|119490947|ref|XP_001263134.1| pseudouridylate synthase 3 [Neosartorya fischeri NRRL 181]
 gi|119411294|gb|EAW21237.1| pseudouridylate synthase 3 [Neosartorya fischeri NRRL 181]
          Length = 610

 Score =  126 bits (316), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 74/360 (20%), Positives = 99/360 (27%), Gaps = 123/360 (34%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 116 IALKFAYLGQRYNGL-EHANGNVTPLPTIEEELWKAMRRTRLIFPKNAEAFDDSRGPREL 174

Query: 38  ----VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKA--------------- 78
               ++ E      AGRTD GV A  QV    +          +A               
Sbjct: 175 KPYAISWEGCDYSKAGRTDRGVSAFGQVIGIRVRSARPKRPDAEATSDVEMTSGAHADDT 234

Query: 79  -------------LNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQA 121
                        LN  L   D I IL         F ARFS   R Y Y          
Sbjct: 235 WDDIADEIPYISMLNRVL--PDDIRILAWCPNPPPGFDARFSCRERQYKYFFTQPAFSPT 292

Query: 122 PLAL--------EKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIR 170
           P  L        +K  +  + +  LD + MR AA++  G HDF  F  +    Q  +  R
Sbjct: 293 PGPLGFAMRGSGDKNASAQLREGWLDIDAMREAARYFEGVHDFRNFCKLDTSKQIENFER 352

Query: 171 TIDHF-------------DVNSFG------------------------NLIEIRVVARSF 193
            I H               VN  G                         +    +   +F
Sbjct: 353 IIYHAGIELLDPKNHPLGYVNQPGFQALQDAPAGTDAESGTITNSAAAKVYVFNLHGSAF 412

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL------APPEGLYFDSVEYS 247
           L  Q+R  V  L LVG G    T +   L    +  C P       AP   L      + 
Sbjct: 413 LWHQVRHMVSILFLVGQGLEPPTIVRDLLDV-SKNPCKPTYEMASDAP---LVLWDCIFP 468


>gi|195026984|ref|XP_001986382.1| GH21331 [Drosophila grimshawi]
 gi|193902382|gb|EDW01249.1| GH21331 [Drosophila grimshawi]
          Length = 503

 Score =  125 bits (315), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 56/257 (21%), Positives = 89/257 (34%), Gaps = 58/257 (22%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--------HGAGRTDSGV 55
             + + Y G  Y G+  Q++ +    +IE  +F       ++        H  GRTD  V
Sbjct: 99  VLLKVMYFGWDYQGFACQEDSN---ETIEAFLFRALIRTCLIESRATSNYHRCGRTDKEV 155

Query: 56  HALRQVAHFDLVREWVPV------------ILCKALNAYLKISDTI-SILNLSIVDKQFH 102
            A  QV   DL  +  P               C  LN  L     I  +  + + +  + 
Sbjct: 156 SAFCQVISIDLRSKHAPDVQLESDSLATEIDYCSLLNRVL--PKNIQCVSWMPLRNHVYS 213

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-- 160
           ARF  I R+Y Y                +     LD E MR+A   +V   DF  F    
Sbjct: 214 ARFDCISRTYRY----------------YFPKGDLDIEAMRMACDLIVCHGDFRNFCKMD 257

Query: 161 IHCQASSPIRTIDHFDVNSFGN--------------LIEIRVVARSFLHTQIRSFVGSLK 206
           +H   ++ +R +    + +                 +  + + A +FL  QIR  +  L 
Sbjct: 258 VHNGVTNYMRNLQAARIQACEGTAVEVENDLNSGYTMYYLEIQANAFLWHQIRCIMAVLL 317

Query: 207 LVGDGKWTSTDLEKALQ 223
           LVG        + K L 
Sbjct: 318 LVGQKHEEPVIISKLLD 334


>gi|308161029|gb|EFO63491.1| Pseudouridylate synthase, putative [Giardia lamblia P15]
          Length = 515

 Score =  125 bits (314), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 64/319 (20%), Positives = 97/319 (30%), Gaps = 91/319 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLV-------TGEIVVVHGAGRTDSGV 55
             + + Y+G+ Y G  +Q N   +I+  +  A+          T   V    +GRTD GV
Sbjct: 83  IAIQVCYDGTEYAGLAQQPNKEYTIEELLLNALRDAALIPQYATASDVHFERSGRTDRGV 142

Query: 56  HALRQVAHF--------DLVREWVPVILCKALNA-------------------------- 81
            A  QV  F           +           +                           
Sbjct: 143 SAAGQVFSFYARTNNKAMTPQSIPVPDPRFYRDRRDGLTPPAKPNDNVDGDLVNSEKEPE 202

Query: 82  ----------------YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                            +++ +TI +L  + VD+ F AR S   R Y+Y           
Sbjct: 203 LKQVPQEQEIDYVSAINMRLPETIRVLGWAPVDENFSARHSTSSRHYIYTFGQI------ 256

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFGNLI 184
                     SL+   M  A   LVG HDF         +  +  R I    +   G   
Sbjct: 257 ---------GSLNIRRMAEACTKLVGFHDFRNICKPSLDSIKTFERVIFSCYLEIDGQPY 307

Query: 185 EIR---------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR-- 227
           E                 V   +FL+ QIR     L  +G      + +   L  ++   
Sbjct: 308 ECENDRMVIKENSSLSLVVCGSAFLYHQIRCIASLLLHIGAELEPPSLISDLLNIENFPG 367

Query: 228 KECGPLAPPEGLYFDSVEY 246
           K   P+AP E L F+  EY
Sbjct: 368 KPDYPIAPGELLLFEKAEY 386


>gi|317137489|ref|XP_003190065.1| pseudouridylate synthase 3 [Aspergillus oryzae RIB40]
          Length = 617

 Score =  125 bits (314), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 68/371 (18%), Positives = 95/371 (25%), Gaps = 132/371 (35%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 111 IALKFAYLGQRYNGL-EHANGNVTPLPTIEEEMWKALRKTRLIFPENGEADGFEDTRGPR 169

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV-------------------- 71
                 +  E      AGRTD GV A  QV    +                         
Sbjct: 170 ELKPYLINWEGYQYSKAGRTDRGVSAFGQVIGLRVRSARPKRDDVAQADPSSDTTMQTGE 229

Query: 72  ----------------PVILCKALNAYLKISDTISILNLSIVDKQ-FHARFSAIRRSYLY 114
                              L         + + I +L       + F ARFS   R Y Y
Sbjct: 230 EASALDDTAQDNWDDIADELPYVSILNRVLPEDIRVLAWCPHPPEGFDARFSCRERHYKY 289

Query: 115 RII-----------------TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
                                 +A  +  K R       LD E MR AA++  G HDF  
Sbjct: 290 FFTQPAFSPTPGPLGFTSRANNKAGDSRAKYREGW----LDIEAMREAAKYFEGVHDFRN 345

Query: 158 FRSIHC--QASSPIRTIDHFDVN------------------------------------- 178
           F  +    Q  +  R I H D+                                      
Sbjct: 346 FCKLDTSKQIENFERVIYHSDIELLDPRSSPLGYVSQPGFQALEDPAAQQTPGSPESPSP 405

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRKECGPLAPP 236
           +   +    +   +FL  Q+R  VG L LVG G    T +   L      RK    +A  
Sbjct: 406 TPSQVYVFNLRGSAFLWHQVRHMVGILFLVGQGLEPPTIVPDLLDITKNPRKPTYEMASD 465

Query: 237 EGLYFDSVEYS 247
             L   +  + 
Sbjct: 466 APLVLWNCVFP 476


>gi|71021049|ref|XP_760755.1| hypothetical protein UM04608.1 [Ustilago maydis 521]
 gi|46100185|gb|EAK85418.1| hypothetical protein UM04608.1 [Ustilago maydis 521]
          Length = 913

 Score =  124 bits (313), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 60/324 (18%), Positives = 103/324 (31%), Gaps = 94/324 (29%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK--------NGSSIQGSIEKAIFLVTGEIVVV-------H 46
            +  +   Y+G+GY G   Q         +  +++G +  A+         +        
Sbjct: 129 RKIALRFSYDGAGYSGLAAQNTTVPGSGSSLPTVEGVLWDALCTARLVDPALGMDGAGFS 188

Query: 47  GAGRTDSGVHALRQVAHFDLVR----EWVP------------------------VILCKA 78
             GRTD GV A  QV    +      +W                            L + 
Sbjct: 189 RCGRTDRGVSAAGQVVALWVRSKKLNQWPDRLEHQEQFSPLASSLLSKPSPQEWDDLQEK 248

Query: 79  LNAYLK-------------ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
            NA L+             +  +I I   S V   F +RF  + R Y Y        L  
Sbjct: 249 RNAKLEGTELPYVQILNRILPSSIRIQAWSPVRSNFSSRFDCVYRHYKYFFPAGPPRLFY 308

Query: 126 EK--------GRAWLI-------PKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSP 168
            +        G A+ +          LD   MR AA+ L+G HDF     I    Q ++ 
Sbjct: 309 PRSKTINGEDGVAFSVGGGQDAGATRLDIALMRDAARRLLGEHDFRNLCKIDASKQITNY 368

Query: 169 IRTIDHFDVNS---------------------FGNLIEIRVVARSFLHTQIRSFVGSLKL 207
            R ID   ++                        ++  + +   +FL+ Q+R+ +  L L
Sbjct: 369 RRRIDGVSIDRVSSHWPSKNDGVEDDDGGEEGEEHMYVLNLRGTAFLYHQVRNIMAILFL 428

Query: 208 VGDGKWTSTDLEKALQAQDRKECG 231
           VG      + +E+ +  +  +   
Sbjct: 429 VGARLEPPSVIEELMNTESGRIAA 452


>gi|154276726|ref|XP_001539208.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
 gi|150414281|gb|EDN09646.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
          Length = 555

 Score =  124 bits (313), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 63/333 (18%), Positives = 101/333 (30%), Gaps = 90/333 (27%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL---VTGEIVVVHGAGRTDSGV 55
             +   Y G  Y G+    NG      +I+  + KA+     +  + V   G   T+   
Sbjct: 92  IALKFAYLGQRYNGY-EHANGNTTPLPTIEEELWKALRKARLIFPQAVEADGVSSTEPST 150

Query: 56  H----ALRQVA-------------HFDLVREWVPVI--LCKALNAYLKISDTISILNLSI 96
                A                  + +    W  +   L         + + I +L    
Sbjct: 151 ATSTDAYNSGVENLLGGLSLSGSENSETEDSWDDIADELPYITILNRVLPEDIRVLAWCP 210

Query: 97  -VDKQFHARFSAIRRSYLYRIIT---RQAPLAL---EKGRAWLI-------PKS------ 136
                F ARFS   R Y Y          P  L   ++GR           P +      
Sbjct: 211 NPPPDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGREENCLGEGSGAPHNEQFREG 270

Query: 137 -LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN--------------- 178
            LD E MR  A++L+G HDF  F  +    Q ++ +R I H D+                
Sbjct: 271 WLDIEAMRKGAKYLIGSHDFRNFCKVDPSKQITNHVRHIYHADIELLDPKTKPLSYLRQH 330

Query: 179 ----------------SFGN------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
                           S G+      +  I +   +FL  Q+R     L LVG G    +
Sbjct: 331 EFTTFDTENDKAAANGSIGDPSSNLKVYSITIHGSAFLWHQVRHLAAILFLVGQGLEAPS 390

Query: 217 DLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
            + + L  +   R+    +A    L      + 
Sbjct: 391 IIPELLDVEKHPRRPTYEIASDTPLVLWDCIFP 423


>gi|207345339|gb|EDZ72195.1| YGL063Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 330

 Score =  124 bits (313), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 99/311 (31%), Gaps = 79/311 (25%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
           M++ Y GSGY+G Q      +I+G I   +F V           +      A RTD GVH
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDVGAISEENSLAPKKNSFMAAARTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY-- 114
           A+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y  
Sbjct: 61  AMLNLLSLKITLREDTVA---KLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYLI 115

Query: 115 --RIITRQAPLALEKGRAWLIPKS------LD--------------CENMRIAAQHL--- 149
              I+      +L         +        D                 ++  AQ L   
Sbjct: 116 PEFILIGPPRSSLLHRNVGGCYREDGSQEVWDTFLEQTRGRFSGDELCRLQDTAQKLSES 175

Query: 150 -----------------------------------VGRHDFTTFRSIH-CQASSPIRTID 173
                                              VG H+F  F +       S  R I 
Sbjct: 176 DPLVQDYVGLLSGTLSGYCLPPSKLDAFEAAMQEYVGTHNFHNFTTGKLWGDPSAQRHIK 235

Query: 174 HFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              V+      I +R+  +SF+  QIR  V    L    +     +     A  RK   P
Sbjct: 236 KVVVSQASPGWICVRIHGQSFMLHQIRRMVALAVLAARCQLPPNIVRNYFNAGPRKYI-P 294

Query: 233 LAPPEGLYFDS 243
            AP +GL  + 
Sbjct: 295 RAPAQGLLLEG 305


>gi|289742875|gb|ADD20185.1| pseudouridylate synthase [Glossina morsitans morsitans]
          Length = 444

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 58/276 (21%), Positives = 97/276 (35%), Gaps = 52/276 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             +   Y G  Y G+  Q++  ++I+  + KA+              H  GRTD  V A 
Sbjct: 57  VLLKFLYFGWDYQGFACQEDSNNTIEFHLFKALTRTCLIESRSSANYHRCGRTDKKVSAF 116

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTISILNLSIVDKQ-FHARF 105
            QV   DL  ++                 C  +N  L     I  ++   +    F ARF
Sbjct: 117 CQVISIDLRSKFPEKQQFEESCLEKEIDYCGIMNRVL--PKNIRCISWMPIRNHLFSARF 174

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             I R+Y Y                +    +L+   M+ A + L    DF       +H 
Sbjct: 175 DCITRTYRY----------------FFPKGNLNITAMQDACKLLQRHTDFRNLCKMDVHN 218

Query: 164 QASSPIRTIDHFDV----------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
             ++ +R I+  +V          N    +  + + A +FL  QIR  +  L L+G  K 
Sbjct: 219 GVTNYVRHIEAANVRLCPHQNESKNKGYAMHYLEIKANAFLWHQIRCIMTVLLLIGQEKE 278

Query: 214 TSTDLEKALQAQDRKECGP---LAPPEGLYFDSVEY 246
             + + + L   ++  C P    A    L     E+
Sbjct: 279 EPSVINELLNV-EKNPCKPQYTPAMGFPLNLYHCEF 313


>gi|258563566|ref|XP_002582528.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
 gi|237908035|gb|EEP82436.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
          Length = 615

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 65/382 (17%), Positives = 98/382 (25%), Gaps = 146/382 (38%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G+    NG      +I+  + KA+                       
Sbjct: 98  IALKFAYLGQRYNGY-EHANGNITPLPTIEEELWKALRKARLIFPHIVENSENVDESGSR 156

Query: 38  -------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV------------------- 71
                  ++ E       GRTD GV A  QV    +                        
Sbjct: 157 SLSRPYSISWEGCDYSKCGRTDRGVSAFGQVVGVRVRSSRPKKTVEPVATPDTSTSVTPK 216

Query: 72  -------------------------------PVILCKALNAYLKISDTISIL-NLSIVDK 99
                                           +   + LN  L   + I IL        
Sbjct: 217 LISKDVESPFGGLGIDVSELEVEEKWDDVADELPYIQMLNGVL--PEDIRILAWCPRPPP 274

Query: 100 QFHARFSAIRRSYLYRIIT---RQAPLALEKGRAWLIPKS------------LDCENMRI 144
            F ARFS   R Y Y          P  L       + +             LD + MR 
Sbjct: 275 DFDARFSCRERRYRYFFTQPAFCPTPGPL-----GFVKRPGDTPGSKMREGWLDIDAMRE 329

Query: 145 AAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDV------------------NSFGN-- 182
            A+  +G HDF  F  +    Q ++ +R I H D+                    + N  
Sbjct: 330 GAKRYIGSHDFRNFCKVDASKQITNFVRKISHADIQVLDAKNLPPAFLAQQGFQQYENVD 389

Query: 183 ---------------LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQ 225
                          +    V   +FL  Q+R  V  L L+G G    + + + L     
Sbjct: 390 RELRDSSDVQDPALKVYYFSVHGSAFLWHQVRHMVAVLFLIGQGLEPPSIVSQLLDVSTN 449

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
            R+    +A    L      + 
Sbjct: 450 PRRPTYDIASDAPLVLWDCVFP 471


>gi|302686228|ref|XP_003032794.1| hypothetical protein SCHCODRAFT_82025 [Schizophyllum commune H4-8]
 gi|300106488|gb|EFI97891.1| hypothetical protein SCHCODRAFT_82025 [Schizophyllum commune H4-8]
          Length = 561

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 98/293 (33%), Gaps = 58/293 (19%)

Query: 5   CMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSG 54
            ++I + GSGY G Q Q     +I+  +  A   V             V +  A RTD+G
Sbjct: 133 AVLIGFCGSGYNGMQIQKPPAKTIENELFDAFVRVGAVSRDNSDDPVKVGLKRAARTDAG 192

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           VHA   +    L+     V    A     ++   I +   + V   F AR     R Y Y
Sbjct: 193 VHAAGNLVSLKLITAIPGVPDLVA-RVNEELPPQIRMWGFTRVTNSFEARQMCDSRKYTY 251

Query: 115 RII--------------------TRQAPLA------------------LEKGRAWLIPKS 136
                                     AP+                   +++ R W +P  
Sbjct: 252 FFPSYMLIPPKPGTGNHTNLQQFCEDAPVPALDHPFWQGHTEDDPETEMQRKRLWRLPSD 311

Query: 137 LDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFD-----VNSFGNLIEIRVVA 190
              E +R  A+   G H+F  F      Q  S +R +   +     V      I + +  
Sbjct: 312 -KLEALRRTAEKFEGTHNFHNFTVGRTFQDRSCMRYMKKIEIADPVVYGDTEWIAVTLHG 370

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +SF+  QIR  + +L L       ++ +++   A  R    P  P  GL  + 
Sbjct: 371 QSFMLHQIRKMMSALVLSVRNDTPASVMDELYGA--RTSFIPKMPSLGLLLEH 421


>gi|315055729|ref|XP_003177239.1| tRNA pseudouridine synthase 3 [Arthroderma gypseum CBS 118893]
 gi|311339085|gb|EFQ98287.1| tRNA pseudouridine synthase 3 [Arthroderma gypseum CBS 118893]
          Length = 616

 Score =  124 bits (311), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 71/378 (18%), Positives = 98/378 (25%), Gaps = 141/378 (37%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 93  IAIKFAYLGKRYNGL-EHANGNFTEVPTIEEELWKALRKTRLIFPTHKDCTEEFSGKDSS 151

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI----------------- 74
                 +  +       GRTD GV A  QV    +                         
Sbjct: 152 PSRPYSIHWDGCQYSKCGRTDKGVSAFGQVIGIRVRSLRPADSSPPTEANGGDAMDSAVA 211

Query: 75  ---------------------------------LCKALNAYLKISDTISILNLSI-VDKQ 100
                                              + LN  L   + I +L     +   
Sbjct: 212 VELGTGDENRRSGVPGTGEAKAAVWDDIADELPYIQILNGAL--PEDIRVLAWCPHLPAD 269

Query: 101 FHARFSAIRRSYLYRIITRQA-PLALEKGRAWL--------IPKS----LDCENMRIAAQ 147
           F ARFS  +R Y Y        P    +G             P+     LD E MR AAQ
Sbjct: 270 FDARFSCRQRRYRYFFTQPAFCPTPGARGIVRAPELKDDPSSPRPREGWLDIEAMREAAQ 329

Query: 148 HLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN--------------------------- 178
           + VG HDF  F  +    Q ++ +R I   D+                            
Sbjct: 330 YFVGSHDFRNFCKVDTSKQITNFVRRILRADLELVDPQRTPLGFVQMPGFERLENSPRNT 389

Query: 179 ---SFGNLIE--------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD- 226
                 N I           V   +FL  QIR  VG L LVG G    + + + L     
Sbjct: 390 GIPEGPNDINPAASKVYSFTVHGTAFLWHQIRHMVGILFLVGQGLEHPSIVPELLDVTKN 449

Query: 227 -RKECGPLAPPEGLYFDS 243
            R+    +A    L    
Sbjct: 450 PRRPVYEMASDSPLVLWD 467


>gi|156087442|ref|XP_001611128.1| tRNA pseudouridine synthase [Babesia bovis T2Bo]
 gi|154798381|gb|EDO07560.1| tRNA pseudouridine synthase, putative [Babesia bovis]
          Length = 414

 Score =  124 bits (311), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 96/306 (31%), Gaps = 67/306 (21%)

Query: 6   MIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAI---------FLVTGEIVVVHGAGRT 51
           +++ Y G+ Y G+Q Q++       +++  +  A+                + +  A RT
Sbjct: 31  IVLSYIGTNYHGFQIQRDAGDDGIDTVEARVINALVTTDAIHGSHKNNLGKLQLSKASRT 90

Query: 52  DSGVHALRQVAHFDLVREWV---------PVILCKALNAYLKISDTISILNLSIVDKQFH 102
           D GVHA             +            L   LN  L   D I    +  V + F 
Sbjct: 91  DKGVHAACTYIGGRFELSHLSAGEPGISKEQCLVSRLNTVL--PDDIRCFQVLRVTRGFC 148

Query: 103 ARFSAIRRSYLYRII---------------------TRQAPLALEKGRAWLIPKSL---- 137
           AR    +R Y Y I                      T          R  +  K L    
Sbjct: 149 ARSMCSKRMYEYVIPLSLLRYRYVCGEDDNKRTFEKTSNLMNLHMNSRQNIHCKRLSSVA 208

Query: 138 -----------DCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG---- 181
                      D   ++       G HDF  F      +  +  R I    V        
Sbjct: 209 LHEGTTEERDVDMVLLQSILSDYCGSHDFKNFTQRQKVEEKTTQRFIHEIKVEGSESIGI 268

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + + +  +SFL+ QIR  +G    V  G      ++ AL ++      PLAP EGL+ 
Sbjct: 269 NAVRVIITGQSFLYNQIRKMIGLGYAVYLGVAPRCAIKFAL-SKWHAVNTPLAPAEGLFL 327

Query: 242 DSVEYS 247
               + 
Sbjct: 328 HHPYFD 333


>gi|145545961|ref|XP_001458664.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124426485|emb|CAK91267.1| unnamed protein product [Paramecium tetraurelia]
          Length = 351

 Score =  123 bits (310), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 58/285 (20%), Positives = 104/285 (36%), Gaps = 51/285 (17%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIF---LVTGEIVV------VHGAGR 50
            +  +   YNG+ Y G Q QK     +++  + +A+    L+  +              R
Sbjct: 8   QKVLLTFGYNGANYHGLQIQKGVEFETVESKLFQALKDSNLIMEQNANDLSKSGWSRGAR 67

Query: 51  TDSGVHALRQVAHFDLV---------------------REWVPVILCKALNA-YLKISDT 88
           TD GVHAL       L                      R+   V   K LN     + + 
Sbjct: 68  TDKGVHALCNSIAVKLCINKEFFKDEIQQNEEEIVSKLRDKQKVDYSKVLNVINSNLPND 127

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           I + ++ +V + F  R +A  R Y Y      AP+++   +          E +    + 
Sbjct: 128 IKVHSIKLVTQGFDVRKNARYRFYEYI-----APVSIYSDK----KGEEILEKVSNLVKK 178

Query: 149 LVGRHDFTTF-RSIHCQASSPIRTIDHFDVN----SFGNLIEIRVVARSFLHTQIRSFVG 203
            VG H+F  + R +       +R I    V           +  +  +SF++ QIR  +G
Sbjct: 179 FVGTHNFHNYSRGMKYTDPQSMRYILSIQVELFKCQDREFFKFLIHGQSFIYHQIRKMMG 238

Query: 204 SLKLVGDGKWTSTDLEK-ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +  +   +   T ++    + Q R     LAP EGL+ + + + 
Sbjct: 239 IVIQIFQEELPDTFIDNTFFKNQLR---IILAPAEGLFLNRISFE 280


>gi|323337610|gb|EGA78855.1| Pus2p [Saccharomyces cerevisiae Vin13]
          Length = 406

 Score =  123 bits (309), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 99/311 (31%), Gaps = 79/311 (25%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
           M++ Y GSGY+G Q      +I+G I   +F V           +      A RTD GVH
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDVGAISEENSLAPKKNSFMAAARTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY-- 114
           A+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y  
Sbjct: 61  AMLNLLSLKITLREDTVA---KLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYLI 115

Query: 115 --RIITRQAPLALEKGRAWLIPKS------LD--------------CENMRIAAQHL--- 149
              I+      +L         +        D                 ++  AQ L   
Sbjct: 116 PEFILIGPPRSSLLHRNVGGCYREDGSQEVWDTFLEQTRGRFSGDELCRLQDTAQKLSES 175

Query: 150 -----------------------------------VGRHDFTTFRSIH-CQASSPIRTID 173
                                              VG H+F  F +       S  R I 
Sbjct: 176 DPLVQDYVGLLSGTLSGYCLPPSKLDAFEAAMQEYVGTHNFHNFTTGKLWGDPSAQRHIK 235

Query: 174 HFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              V+      I +R+  +SF+  QIR  V    L    +     +     A  RK   P
Sbjct: 236 KVVVSQASPGWICVRIHGQSFMLHQIRRMVALAVLAARCQLPPNIVRNYFNAGPRKYI-P 294

Query: 233 LAPPEGLYFDS 243
            AP +GL  + 
Sbjct: 295 RAPAQGLLLEG 305


>gi|302789057|ref|XP_002976297.1| hypothetical protein SELMODRAFT_105100 [Selaginella moellendorffii]
 gi|300155927|gb|EFJ22557.1| hypothetical protein SELMODRAFT_105100 [Selaginella moellendorffii]
          Length = 175

 Score =  123 bits (309), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 44/164 (26%), Positives = 64/164 (39%), Gaps = 20/164 (12%)

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
              +   I +L    V   FHARFS + R Y Y                + I   L+ + 
Sbjct: 9   NRALPADIRVLGWCPVPPGFHARFSCLYREYKY----------------FFIDDGLNIDA 52

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIR 199
           M+ A+Q L+G HDF  F  +      +  R I  FD+      L  + V   +FL  Q+R
Sbjct: 53  MKQASQRLLGEHDFRNFCKMDADNIHNYTRQILAFDILPIEECLWVMHVRGNAFLWHQVR 112

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYF 241
                L ++G G  T T ++  L      RK    +AP   L  
Sbjct: 113 CMAAVLFMIGRGHETLTIIDDLLDVDKTMRKPQYVMAPELPLVL 156


>gi|123483294|ref|XP_001323995.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
 gi|121906870|gb|EAY11772.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
          Length = 346

 Score =  123 bits (308), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 53/271 (19%), Positives = 99/271 (36%), Gaps = 37/271 (13%)

Query: 3   RYCMI---------IEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGE-------IVV 44
           RY +            Y G+GY G Q  +   +I   + + +    +  E        + 
Sbjct: 23  RYLITKKPACVVIYFRYIGTGYHGLQYNEKVRTIDSDLFEGLEKSGILPEGSYKRRGKIA 82

Query: 45  VHGAGRTDSGVHALRQVAHF--DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFH 102
            + A RTD+GVHA  Q+  F    + +     + + +N  L    TI I++    +  F 
Sbjct: 83  WNEASRTDAGVHACGQLICFKSYEICDMECSQIPELINKNLPSDSTIKIMSCLCTNSPFP 142

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
            +  A  R Y Y +             +   P  LD    +      +G+H+F  + +  
Sbjct: 143 VKDFATHRKYNYLLP--------LHVFSSTDPDHLDYLR-QKICPLFIGQHNFHNYTNGT 193

Query: 163 CQA-SSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
            +      R I  F        +    +   +   SF+  QIR  +  +      + T  
Sbjct: 194 PKTYKGAQRFITDFTFGDVFTINGEEYVLFYIRGISFMLNQIRKMISMVTAASFNQVTPE 253

Query: 217 DLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           ++ ++L  +  +    L P +GL+ D +EY 
Sbjct: 254 EVSRSLTEETCR--IQLLPGDGLFLDQIEYE 282


>gi|270719040|ref|ZP_06223281.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
 gi|270315483|gb|EFA27724.1| tRNA pseudouridine synthase A [Haemophilus influenzae HK1212]
          Length = 96

 Score =  123 bits (308), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 36/98 (36%), Positives = 50/98 (51%), Gaps = 2/98 (2%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
          ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1  MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSCIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62 AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDK 99
           HF+              NA L   D I++     VD 
Sbjct: 61 VHFETNAVRPEKAWAFGTNANL--PDDIAVSWAKQVDD 96


>gi|169838040|ref|ZP_02871228.1| tRNA pseudouridine synthase A [candidate division TM7 single-cell
           isolate TM7a]
          Length = 154

 Score =  123 bits (308), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 44/154 (28%), Positives = 68/154 (44%), Gaps = 4/154 (2%)

Query: 97  VDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
            ++ F+ARF A  R+YLY +   +     E      + + ++ E  +      +G+HDF+
Sbjct: 1   ANENFNARFDAKNRAYLYIMRAEKDITPFESNYITGLKEKVEAEKFQKIMDSFIGKHDFS 60

Query: 157 TFRSIHCQASSPIRTIDHFDV---NSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           +F        +P+R I +        FG N + I +    FL T +R  +GS   V  GK
Sbjct: 61  SFMKKDKAYRNPVREIFYIKCYYDKKFGKNQVNIEICGNGFLKTMVRIMIGSALTVYFGK 120

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                + K L+  D      LAP EGLY   V Y
Sbjct: 121 EKEDYIIKRLKNPDADNKKILAPSEGLYLYKVNY 154


>gi|310821765|ref|YP_003954123.1| tRNA pseudouridylate synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309394837|gb|ADO72296.1| tRNA pseudouridylate synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 252

 Score =  122 bits (307), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 88/230 (38%), Gaps = 18/230 (7%)

Query: 28  QGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISD 87
           Q ++E  +   TG    V  AGRTD GVHA  QV    L     P  L         +  
Sbjct: 2   QSTLEAVL-RSTGVPATVMPAGRTDRGVHARMQVVSLRLEAGDTPEALAAR--LPALLPP 58

Query: 88  TISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW-------LIPKSLDCE 140
            + +  +      FHA++SA  ++Y YR+          +           L  +++  E
Sbjct: 59  DLGVCAVRRPPPSFHAQWSAAGKTYCYRVQLGGRVSETWRPYVLEAAEEPRLAQRAIAPE 118

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIR 199
            +    Q  VG+ DF  F +         RT++   V+   G L EI++   SF   Q+R
Sbjct: 119 RLAELLQGAVGQRDFWAFHASSSPRKP--RTLESATVHELEGGLFEIQLRGDSFARYQVR 176

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP--LAPPEGLYFDSVEYS 247
             VGS  L   G+        AL++    E  P   A   GL    V Y 
Sbjct: 177 YLVGSALLTAAGQLPEAQWRAALES---AEAIPGLRAAAAGLILWEVRYP 223


>gi|330443553|ref|NP_011452.2| Pus2p [Saccharomyces cerevisiae S288c]
 gi|1403093|emb|CAA56699.1| pseudouridine synthase 2 [Saccharomyces cerevisiae]
 gi|329138894|tpg|DAA08039.2| TPA: Pus2p [Saccharomyces cerevisiae S288c]
          Length = 370

 Score =  122 bits (307), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 99/311 (31%), Gaps = 79/311 (25%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
           M++ Y GSGY+G Q      +I+G I   +F V           +      A RTD GVH
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDVGAISEENSLAPKKNSFMAAARTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY-- 114
           A+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y  
Sbjct: 61  AMLNLLSLKITLREDTVA---KLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYLI 115

Query: 115 --RIITRQAPLALEKGRAWLIPKS------LD--------------CENMRIAAQHL--- 149
              I+      +L         +        D                 ++  AQ L   
Sbjct: 116 PEFILIGPPRSSLLHRNVGGCYREDGSQEVWDTFLEQTRGRFSGDELCRLQDTAQKLSES 175

Query: 150 -----------------------------------VGRHDFTTFRSIH-CQASSPIRTID 173
                                              VG H+F  F +       S  R I 
Sbjct: 176 DPLVQDYVGLLSGTLSGYCLSPSKLDAFEAAMQEYVGTHNFHNFTTGKLWGDPSAQRHIK 235

Query: 174 HFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              V+      I +R+  +SF+  QIR  V    L    +     +     A  RK   P
Sbjct: 236 KVVVSQASPGWICVRIHGQSFMLHQIRRMVALAVLAARCQLPPNIVRNYFNAGPRKYI-P 294

Query: 233 LAPPEGLYFDS 243
            AP +GL  + 
Sbjct: 295 RAPAQGLLLEG 305


>gi|151943741|gb|EDN62051.1| pseudouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190407023|gb|EDV10290.1| pseudouridine synthase [Saccharomyces cerevisiae RM11-1a]
 gi|256269708|gb|EEU04978.1| Pus2p [Saccharomyces cerevisiae JAY291]
 gi|259146442|emb|CAY79699.1| Pus2p [Saccharomyces cerevisiae EC1118]
 gi|323333685|gb|EGA75078.1| Pus2p [Saccharomyces cerevisiae AWRI796]
 gi|323348667|gb|EGA82910.1| Pus2p [Saccharomyces cerevisiae Lalvin QA23]
 gi|323354937|gb|EGA86768.1| Pus2p [Saccharomyces cerevisiae VL3]
          Length = 370

 Score =  122 bits (307), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 99/311 (31%), Gaps = 79/311 (25%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
           M++ Y GSGY+G Q      +I+G I   +F V           +      A RTD GVH
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDVGAISEENSLAPKKNSFMAAARTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY-- 114
           A+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y  
Sbjct: 61  AMLNLLSLKITLREDTVA---KLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYLI 115

Query: 115 --RIITRQAPLALEKGRAWLIPKS------LD--------------CENMRIAAQHL--- 149
              I+      +L         +        D                 ++  AQ L   
Sbjct: 116 PEFILIGPPRSSLLHRNVGGCYREDGSQEVWDTFLEQTRGRFSGDELCRLQDTAQKLSES 175

Query: 150 -----------------------------------VGRHDFTTFRSIH-CQASSPIRTID 173
                                              VG H+F  F +       S  R I 
Sbjct: 176 DPLVQDYVGLLSGTLSGYCLPPSKLDAFEAAMQEYVGTHNFHNFTTGKLWGDPSAQRHIK 235

Query: 174 HFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              V+      I +R+  +SF+  QIR  V    L    +     +     A  RK   P
Sbjct: 236 KVVVSQASPGWICVRIHGQSFMLHQIRRMVALAVLAARCQLPPNIVRNYFNAGPRKYI-P 294

Query: 233 LAPPEGLYFDS 243
            AP +GL  + 
Sbjct: 295 RAPAQGLLLEG 305


>gi|323305032|gb|EGA58786.1| Pus2p [Saccharomyces cerevisiae FostersB]
          Length = 370

 Score =  122 bits (306), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 99/311 (31%), Gaps = 79/311 (25%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
           M++ Y GSGY+G Q      +I+G I   +F V           +      A RTD GVH
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDVGAISEENSLAPKKNSFMAAARTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY-- 114
           A+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y  
Sbjct: 61  AMLNLLSLKITLREDTVA---KLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYLI 115

Query: 115 --RIITRQAPLALEKGRAWLIPKS------LD--------------CENMRIAAQHL--- 149
              I+      +L         +        D                 ++  AQ L   
Sbjct: 116 PEFILIGPPRSSLLHRNVGGCYREDGSQEVWDTFLEQTRGRFSGDELCRLQDTAQKLSES 175

Query: 150 -----------------------------------VGRHDFTTFRSIH-CQASSPIRTID 173
                                              VG H+F  F +       S  R I 
Sbjct: 176 DPLVQDYVGLLSGTLSGYCLPPSKLDAFEAAMQDYVGTHNFHNFTTGKLWGDPSAQRHIK 235

Query: 174 HFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              V+      I +R+  +SF+  QIR  V    L    +     +     A  RK   P
Sbjct: 236 KVVVSQASPGWICVRIHGQSFMLHQIRRMVALAVLAARCQLPPNIVRNYFNAGPRKYI-P 294

Query: 233 LAPPEGLYFDS 243
            AP +GL  + 
Sbjct: 295 RAPAQGLLLEG 305


>gi|253742628|gb|EES99427.1| Pseudouridine synthase, putative [Giardia intestinalis ATCC 50581]
          Length = 351

 Score =  122 bits (306), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 54/285 (18%), Positives = 97/285 (34%), Gaps = 59/285 (20%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           ++  ++I +NG+ + G   Q   G +++G++   +  +       T   + +  AGRTD+
Sbjct: 1   MKVALLIAFNGTAFCGNAFQPAGGLTVEGALLDGLQKLGYVKADKTIRDIGLERAGRTDA 60

Query: 54  GVHALRQVAHFDLVREWV-----PVILCKALN--------------------------AY 82
           GV A   +    L R        P+   + +N                            
Sbjct: 61  GVSAECMLYTVCLSRSIPEAPQFPLHNPRTINGLKASPLEPSSIYISAMGPATCLVFHFN 120

Query: 83  LKISDTISILNL-SIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCE- 140
             +   I +L + + + + F  R S   R Y Y +                    LD   
Sbjct: 121 RVLPPQIRVLGVMTALPENFSPRHSCAAREYEYILG---------------YNIPLDLCT 165

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
               AAQ  +G + F  F     +      R +   +V    N+    VV  +FL+ Q+R
Sbjct: 166 KANSAAQRFLGSNSFHNFCHWEKEQELVYNRQVYCSEVYVRENVCIFHVVGSAFLYHQVR 225

Query: 200 SFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFD 242
                L  +  G    + +E  L  +    +   PL P + L F 
Sbjct: 226 YMASMLAHIMAGLERESIIEYLLTTEQLRPRRSFPLLPSQYLTFK 270


>gi|321468438|gb|EFX79423.1| hypothetical protein DAPPUDRAFT_319620 [Daphnia pulex]
          Length = 424

 Score =  122 bits (306), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 85/234 (36%), Gaps = 56/234 (23%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS---------SIQGSIEKAIFLVTGEIVV------- 44
           M RY +   Y+G+ + G QRQ             SIQ  +EK I                
Sbjct: 1   MQRYLIKFSYSGTRFRGLQRQPGEIYNDEIPYRASIQTILEKGILRFLQHKKSATSFEPG 60

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           V  + RTD GVH+   +AH DL        L K +N            N+  V   FHAR
Sbjct: 61  VQFSSRTDQGVHSFCNLAHVDLE-------LLKNVN------------NVEAVPSTFHAR 101

Query: 105 FSAIRRSYLYRIITRQ----APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR- 159
           +S+  R YLYRI            +E  + + I K    +      +   G  DF +F  
Sbjct: 102 YSSYSRHYLYRIGVTPQDVKCHPVIEWRKCYFIEKPFCLDKAIEVCKLFEGTKDFASFCH 161

Query: 160 --SIHCQASSPIRTIDHFDVNSFG--------------NLIEIRVVARSFLHTQ 197
             S        +RTID F +                  +  +  + +RSF++ Q
Sbjct: 162 GISGRPPGYPTVRTIDAFHIKPGRPLFDPLYDPLYSGIDFYDFHIKSRSFMYRQ 215


>gi|226288982|gb|EEH44494.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 574

 Score =  122 bits (306), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 61/339 (17%), Positives = 98/339 (28%), Gaps = 95/339 (28%)

Query: 4   YCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFL---VTGEIVVVHGAGRTDSGVH 56
             +   Y G  Y G++          +I+  + KA+     +  + V   G  + +  V 
Sbjct: 95  IALKFAYLGQRYGGYEHSNGNITPLPTIEEELWKALRKARLIFPQSVEGDGQAQVERAVA 154

Query: 57  ----------ALRQVAHFDL---------------VREWVPVILCKALNAYLKISDTISI 91
                     A R  A   L                 + +   L         + + I +
Sbjct: 155 TPEISSTTPDAYRSGAETPLVGASGCASEESDNEDEWDDIADELPYITILNKVLPEDIRV 214

Query: 92  LNLSIVDK-QFHARFSAIRRSYLYRIIT-----RQAPLALEKGRAWL-------IPKS-- 136
           L         F ARFS   R Y Y            PL   K  +          P +  
Sbjct: 215 LAWCPNPPSDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGSDQKSSGSDSYPSTEL 274

Query: 137 ----LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN------------ 178
               LD E MR  A++L+G HDF  F  I    Q ++ +R I H D+             
Sbjct: 275 REGWLDIEAMREGARYLIGTHDFRNFCKIDPSKQITNHVRHIYHADIELLDPQTKPLSYL 334

Query: 179 ----------------------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
                                       S   +  I +   +FL  Q+R     L L+G 
Sbjct: 335 GQPEFQALEAGNGEVDRNLVTKDSLLSSSNMKIYSITIHGSAFLWHQVRHLAAILFLIGQ 394

Query: 211 GKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           G    + + + L  +   R+    +A    L      + 
Sbjct: 395 GLERPSIIPELLDIEKNPRRPTYEIASDAPLVLWDCIFP 433


>gi|83305357|sp|P53167|PUS2_YEAST RecName: Full=tRNA pseudouridine synthase 2; AltName: Full=tRNA
           pseudouridylate synthase 2; AltName: Full=tRNA-uridine
           isomerase 2
 gi|1322568|emb|CAA96766.1| PUS2 [Saccharomyces cerevisiae]
          Length = 370

 Score =  121 bits (304), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 99/311 (31%), Gaps = 79/311 (25%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
           M++ Y GSGY+G Q      +I+G I   +F V           +      A RTD GVH
Sbjct: 1   MLLGYCGSGYYGMQYNPPHKTIEGEILTKLFDVGAISEENSLAPKKNSFMAAARTDKGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY-- 114
           A+  +    +      V     LNA L     I +  +  V+K+F+AR +   R Y Y  
Sbjct: 61  AMLNLLSLKITLREDTVA---KLNAAL--PPEIRVWGIQPVNKKFNARSACDSRWYQYLI 115

Query: 115 --RIITRQAPLALEKGRAWLIPKS------LD--------------CENMRIAAQHL--- 149
              I+      +L         +        D                 ++  AQ L   
Sbjct: 116 PEFILIGPPRSSLLHRNVGGSYREDGSQEVWDTFLEQTRGRFSGDELCRLQDTAQKLSES 175

Query: 150 -----------------------------------VGRHDFTTFRSIH-CQASSPIRTID 173
                                              VG H+F  F +       S  R I 
Sbjct: 176 DPLVQDYVGLLSGTLSGYCLSPSKLDAFEAAMQEYVGTHNFHNFTTGKLWGDPSAQRHIK 235

Query: 174 HFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
              V+      I +R+  +SF+  QIR  V    L    +     +     A  RK   P
Sbjct: 236 KVVVSQASPGWICVRIHGQSFMLHQIRRMVALAVLAARCQLPPNIVRNYFNAGPRKYI-P 294

Query: 233 LAPPEGLYFDS 243
            AP +GL  + 
Sbjct: 295 RAPAQGLLLEG 305


>gi|308813608|ref|XP_003084110.1| tRNA pseudouridylate synthase (ISS) [Ostreococcus tauri]
 gi|116055993|emb|CAL58526.1| tRNA pseudouridylate synthase (ISS) [Ostreococcus tauri]
          Length = 450

 Score =  121 bits (304), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 92/260 (35%), Gaps = 34/260 (13%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGV 55
            +   Y G+GY G QR     +I+G +E AI    G           V    A RTD GV
Sbjct: 45  ALTFAYVGAGYAGMQRNPGVRTIEGELEGAIARAGGISDANAGDFAKVQWTRAARTDKGV 104

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A+ QV    +V    P  +   +N  L   +   +  +  V              Y Y 
Sbjct: 105 SAVGQVIALKMV--MEPDGMLARINEAL--PERFEVFGIDRVTGG-----------YEYV 149

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL---VGRHDFTTFR-SIHCQASSPIRT 171
           I T      L    A     +   E  R   + L    G H+F  +   +    +   R 
Sbjct: 150 IPTWAFDPNLFVEGAEKEKFTFTEETRRRVERVLGNYCGTHNFHNYTVKVKPTDAQAKRY 209

Query: 172 IDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           I  F+ +          +   VV +SF+  QIR  +G++  V  G     D + A+ +  
Sbjct: 210 ILSFECSQPFEVDGEEFVRCEVVGQSFMLHQIRKLIGTMLAVMRGTLDEDDQKFAILSHQ 269

Query: 227 RKECGPLAPPEGLYFDSVEY 246
                P+AP  GL+     Y
Sbjct: 270 FVPT-PMAPELGLFLCECIY 288


>gi|224000315|ref|XP_002289830.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975038|gb|EED93367.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 323

 Score =  120 bits (302), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 61/308 (19%), Positives = 112/308 (36%), Gaps = 67/308 (21%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTDSGVH 56
           +++ + G+ Y G+Q      ++Q +IE  +F                    + RTD GVH
Sbjct: 1   ILVSFLGTNYSGFQINSTQHTLQAAIELGLFKAGLISPSNFGWPSKYSWSNSARTDKGVH 60

Query: 57  ALRQVAHFD--LVREWVPVILCKALNAYL-----KISDTISILNLSIVDKQFHARFSAIR 109
           A  QV      ++     V +   LNA        + + I +L++  V + F AR +  +
Sbjct: 61  AAAQVVSMKGEMIFHSDTVSIEDQLNAMREKVNEHLPNDIRVLDIERVTRAFCARTNRDK 120

Query: 110 RSYLYR-----------------------IITRQAPL------------------ALEKG 128
             Y Y                        I   ++                     +++ 
Sbjct: 121 VRYQYMVPSFMFSSREEICCAFGNIGETAIEDAKSRAKITPMEASNIVQDAVTDEVMQQA 180

Query: 129 RAWLIPKSLDCENM---RIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFD-----VNS 179
           R  LI   ++ + M   R   +   G H F  + R +    +S  R I  F      V  
Sbjct: 181 RGKLIGYRVNDDQMERLRSGLKVFEGTHTFHNYTRRLGSDNASASRYIISFAPLDPIVVD 240

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I +++V +SFL  QIR  + +   +  G  T   ++++L+   R +   +AP +GL
Sbjct: 241 GTEWIPVQIVGQSFLLNQIRKMISAAVDLARGTVTHEQIQQSLKKGSRMKVN-VAPAQGL 299

Query: 240 YFDSVEYS 247
           + D   + 
Sbjct: 300 FLDRSYFE 307


>gi|257076635|ref|ZP_05570996.1| tRNA pseudouridine synthase A [Ferroplasma acidarmanus fer1]
          Length = 250

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 92/246 (37%), Gaps = 37/246 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           + Y +   Y+G+ + G+QR    +S++ SI K +    G    +  A RTD  V A   V
Sbjct: 1   MYYLIKYGYDGTSFTGFQRGNGENSVEDSIIKILKK-YGIGNNIESAARTDRYVSARGNV 59

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
              D         +   LNA               +   F   +SA+ R           
Sbjct: 60  MLVDTDTNI--GNVMGILNA--------------RIPGMFFYSYSALDRYL-------NP 96

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                K  +++I +++D   +       VG+HDF  F  +  +  + +RTI   + ++  
Sbjct: 97  RHNSMKQYSYIITENIDISRVMETLGEFVGQHDFVNFCKLDSR--NTVRTIKSINYSTRN 154

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
               I +  RSF+  QIRS +    +   GK     LE         +   LA PE L  
Sbjct: 155 GFYIINIQGRSFVWHQIRSMMAFALM---GKKHPFSLE--------NKFTYLASPEPLVL 203

Query: 242 DSVEYS 247
             + Y 
Sbjct: 204 MDISYD 209


>gi|223996591|ref|XP_002287969.1| hypothetical protein THAPSDRAFT_268327 [Thalassiosira pseudonana
           CCMP1335]
 gi|220977085|gb|EED95412.1| hypothetical protein THAPSDRAFT_268327 [Thalassiosira pseudonana
           CCMP1335]
          Length = 369

 Score =  119 bits (299), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 51/281 (18%), Positives = 82/281 (29%), Gaps = 60/281 (21%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I Y+G+                 + K    V    +V+    RTD+GVHA   VA F 
Sbjct: 100 LKIAYDGTH---------------LLAKVYGNVNPNQIVMDSCSRTDAGVHATHLVAQFY 144

Query: 66  LVRE--------WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
                            L   LN  L     + ++  S     FH       ++Y+Y+  
Sbjct: 145 CYSTNLSNDMEVTSLSKLVFVLNRML--PPDVRVMAASPAPFAFHPTLHVRSKTYIYQFA 202

Query: 118 TRQAPLALEKGRAWLIPKSLDCEN-MRIAAQHLVGRHD-FTTFRSIHCQASSPIRTIDHF 175
                  +     W +  S      M           D   +FR +    S     I+  
Sbjct: 203 IGPVHDPIRSQYVWHLDGSSGRAVGMN--GSRFCLERDGGISFRPVDNFMSDSSNAINGL 260

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL------------- 222
                     + +    FL+  +R+ VG++  VG G     D++ AL             
Sbjct: 261 --MESPQSFSVVITGDRFLYKMVRNIVGTIVAVGCGHLEVNDVQMALHTGKWGDNIGAVE 318

Query: 223 QAQDRKECGPL----------------APPEGLYFDSVEYS 247
           + + +                      AP  GL    VEY 
Sbjct: 319 EEESKSSDDFTSSHVKSNSTCIIRRICAPARGLSLHEVEYP 359


>gi|308159447|gb|EFO61978.1| Pseudouridine synthase, putative [Giardia lamblia P15]
          Length = 351

 Score =  119 bits (298), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 98/289 (33%), Gaps = 57/289 (19%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDS 53
           +R  +++ +NG+ + G   Q    S+++ ++ + +  +       T   + +   GRTD+
Sbjct: 1   MRAALLVAFNGAAFRGNAYQPTRDSTVERALFEGLQRIGYLKENETIRDIELERTGRTDA 60

Query: 54  GVHALRQVAHFDLVREWV-----PVILCKALNA--------------------------Y 82
           GV A   +    L +        P    +AL A                           
Sbjct: 61  GVSAECMLYTVRLSKIIPDVPHLPPHNPRALGALEAFPIESSSIYVHTSGIATCLVFHLN 120

Query: 83  LKISDTISILNL-SIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
             +   + +L L + + K F AR S + R Y Y +          +            E 
Sbjct: 121 RVLPSQVRVLGLLTAIPKDFSARHSCVAREYEYIL--GYNIPPHLR------------EK 166

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASS-PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRS 200
              AA+  +G + F  F        +   R I   +V    N+    V+  +FL+ Q+R 
Sbjct: 167 ANSAARRFLGSNSFHNFCHHEKDHKTVYNRQIYCSEVYEHENVCIFHVIGSAFLYHQVRY 226

Query: 201 FVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
               L  +  G    + +E  L  +        PL P + L F    Y 
Sbjct: 227 MASMLVHIMAGLERESAIEYLLTKELSTFGHSLPLVPSQYLTFKCGWYP 275


>gi|159118829|ref|XP_001709633.1| Pseudouridylate synthase, putative [Giardia lamblia ATCC 50803]
 gi|157437750|gb|EDO81959.1| Pseudouridylate synthase, putative [Giardia lamblia ATCC 50803]
          Length = 531

 Score =  118 bits (296), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 63/325 (19%), Positives = 93/325 (28%), Gaps = 97/325 (29%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIF-------LVTGEIVVVHGAGRTDSGV 55
             + + Y+G+ Y G  +Q N   +I+  +  A+              V    +GRTD GV
Sbjct: 93  IAIQVCYDGTEYAGLAQQPNREYTIEELLLNALRGAALIPQHAEASDVHFERSGRTDRGV 152

Query: 56  HALRQVAHFDL----------VREWVPVILCKALNAYLKIS------------------- 86
            A  QV  F +                    +     L                      
Sbjct: 153 SAAGQVFSFYVRTNNKGMGPQPIPAPDPRFYRDRRDGLTPPAKPSDSATDDRGADGDLVN 212

Query: 87  ---------------------------DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                                      +TI +L  + VD+ F AR S   R Y+Y     
Sbjct: 213 AEKEPELKQVPQEQEIDYVSAINMRLPETIRVLGWAPVDENFSARHSTSSRRYVYMFGEV 272

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVN 178
                           SL+   M  A   LVG HDF         +  +  R I    + 
Sbjct: 273 ---------------GSLNIRRMAEACTKLVGFHDFRNICKPSLDSIKTFERVIFSCFLE 317

Query: 179 SFGNLIEIR---------------VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
             G   +                 V   +FL+ QIR     L  +G      + +   L 
Sbjct: 318 IDGQPYDCENDRMAMKENSTLSLVVCGSAFLYHQIRCIASLLLHIGAELEPPSLISDLLN 377

Query: 224 AQDR--KECGPLAPPEGLYFDSVEY 246
            +    K   P+AP E L F+  EY
Sbjct: 378 VEQFPGKPDYPIAPGELLLFERAEY 402


>gi|256087925|ref|XP_002580112.1| pseudouridylate synthase [Schistosoma mansoni]
 gi|238665620|emb|CAZ36351.1| pseudouridylate synthase, putative [Schistosoma mansoni]
          Length = 1304

 Score =  118 bits (296), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 75/227 (33%), Gaps = 49/227 (21%)

Query: 36   FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREW----------------------VPV 73
            F+           GRTD GV  + QV                                 +
Sbjct: 959  FIFDRNECDFSVCGRTDRGVSGMCQVISLVSRSLIARGVGVIEDSGPCISERQDVPDEEM 1018

Query: 74   ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
                ALN  L     I +L  S V   F ARF   +RSY Y                   
Sbjct: 1019 DYVSALNRNL--PRDIRVLAWSPVSPDFSARFMCCKRSYEYYFPES-------------- 1062

Query: 134  PKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS--PIRTIDHFDVNSFGN------LIE 185
               LD ++M  A   LVG HDF  F +   +  +   IR I    V+   +      L  
Sbjct: 1063 --GLDIKSMIDAGNRLVGVHDFRNFCASRIEKDTVTFIREIFEVVVSDVDSCDHHSKLCR 1120

Query: 186  IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
            I + A  FL+ QIR  +  L +VG G  + + ++  L    +    P
Sbjct: 1121 ISISASGFLYHQIRFVMSILFMVGRGYESPSVVDDMLDL-SKTPAKP 1166


>gi|49899182|gb|AAH75766.1| Zgc:56653 protein [Danio rerio]
          Length = 386

 Score =  118 bits (296), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 82/247 (33%), Gaps = 61/247 (24%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G+  Q+N  ++++  + +A+         +    H  GRTD GV A 
Sbjct: 60  VALRLAYLGWQYQGFAVQENTDNTVEARLFEALLKTKLIQDRQTSCYHRCGRTDKGVSAF 119

Query: 59  RQVAHFDLVREW---------------------VPVILCKALNAYLKISDTISILNLSIV 97
            QV   DL                           +   K LN  L     I IL  + V
Sbjct: 120 SQVISIDLRSTQYGGGLGVTVPADVDVKGKTSADELPYVKILNRVL--PQDIRILQWAPV 177

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
           +  F ARF    R+Y Y                +     LD E M  AA+   G HDF  
Sbjct: 178 ESGFSARFDCQSRTYRY----------------YFPRGDLDLELMAEAAKRYEGTHDFRN 221

Query: 158 FRSIHCQASSPIRTIDHFDVN---------------SFGNLIEIRVVARSFLHTQIRSFV 202
              +  +  +P +      V+                     EI +   +F    +++ V
Sbjct: 222 LCKMDVE-KNPRKPQYSMAVDYPLALYDCHFEGVNWRNETEEEIHI-LNTFHQHWVQNAV 279

Query: 203 GSLKLVG 209
            +  L+G
Sbjct: 280 KTQILLG 286


>gi|149756822|ref|XP_001493954.1| PREDICTED: similar to tRNA pseudouridine synthase A (tRNA-uridine
           isomerase I) (tRNA pseudouridylate synthase I) [Equus
           caballus]
          Length = 351

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 89/252 (35%), Gaps = 30/252 (11%)

Query: 17  GWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGVHALRQVAHF 64
           G QR        +I+  +  A+                +      RTD GV A  QV   
Sbjct: 27  GMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTDKGVSAAGQVVSL 86

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
              + W+   + + +N++L     I IL L  V   F+++     R+Y Y + T     A
Sbjct: 87  ---KVWLIDDILEKINSHL--PSHIRILGLKRVTGGFNSKNKCDARTYFYMLPT--FAFA 139

Query: 125 LEKGRAWLIPKSLDCENM---RIAAQHLVGRHDFTTFRS-IHCQASSPIRTI-----DHF 175
            +          L  E +           G H+F  F S    +  S  R I     +  
Sbjct: 140 HKDRDVQDETYRLTAETLQSVNRLLACYKGTHNFHNFTSQKGPREPSAQRYILDMYCEEP 199

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V        I+V  +SF+  QIR  VG +  +  G    + L ++    + K   P AP
Sbjct: 200 FVREGMEFAVIKVKGQSFMTHQIRKMVGLVVAIVKGYAPESVLARSW--GEAKVDVPKAP 257

Query: 236 PEGLYFDSVEYS 247
             GL  + V + 
Sbjct: 258 GLGLVLERVHFE 269


>gi|170086730|ref|XP_001874588.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164649788|gb|EDR14029.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 525

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 53/294 (18%), Positives = 95/294 (32%), Gaps = 56/294 (19%)

Query: 2   IRY-----CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHG 47
            RY      +++ + GSGY G Q   +  +I+G++  A+  V             V +  
Sbjct: 93  PRYPKRQCALLVGFCGSGYSGMQMYGHTRTIEGALFGALVKVGAVSQDNADDPVKVALAR 152

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           A RTD+GVHA   +    ++     +    A     ++   I +         F+AR   
Sbjct: 153 AARTDAGVHAAGNLVSLKMIITVPGIKDLVA-RINEELPPEIRLWGYVRTQNSFNARLVC 211

Query: 108 IRRSYLYRIITRQAPLA-------------------------------LEKGRAWLIPKS 136
             R Y Y   T                                     L + R W   + 
Sbjct: 212 DSRKYTYFFPTYLMIPPKPGTGLHRVLQLPSQPHSFWEGAISDSFQDDLRRKRCWRTGQE 271

Query: 137 LDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNS-----FGNLIEIRVVA 190
              + +R  A+   G H+F  F      +  S  R +   +V+          I +    
Sbjct: 272 -QVQKLRELAKGYEGTHNFHNFTVGREFKERSNHRFMKQIEVSDPVVYGDTEWISVMFHG 330

Query: 191 RSFLHTQIRS-FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +SF+  Q+R   +  L +    + +   +++      R    P  P  GL  + 
Sbjct: 331 QSFMLHQVRRLMMSMLVMTCRTETSPQIIDEL--YGPRNVFVPKMPSLGLLLEH 382


>gi|321265516|ref|XP_003197474.1| pseudouridylate synthase [Cryptococcus gattii WM276]
 gi|317463954|gb|ADV25687.1| Pseudouridylate synthase, putative [Cryptococcus gattii WM276]
          Length = 560

 Score =  116 bits (291), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 59/309 (19%), Positives = 94/309 (30%), Gaps = 71/309 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFL---------VTGEIVVVHGAGRT 51
            R  ++I Y G+GY G Q Q +   +I+G I  A+           V    V +  A RT
Sbjct: 123 RRCAVLIGYCGTGYQGMQIQDHTDRTIEGEIFAALVKAGAVSADNAVDARKVDIARAART 182

Query: 52  DSGVHALRQVAHF--DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           D+GVHA   V                  A      + D I +       K F+AR +A  
Sbjct: 183 DAGVHAAGNVISIKMITEPPLPEGFKNVAEYVNTFLPDQIRMWGWVRTVKSFNARTAADS 242

Query: 110 RSYLYRIIT---------------------------RQAPLAL----------------- 125
           R Y Y + +                            + P +                  
Sbjct: 243 RIYEYLLPSYCLIPPHKDDPLAKHLDISSPDWREIVGEYPCSFADARLPMPTSDEGEVDP 302

Query: 126 ------EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT------ID 173
                 E+ R W + +       R       G H+F  +          ++       + 
Sbjct: 303 KVRGEYERKRKWRVDERT-LNRFRDIIAQYKGTHNFYNYTVGKPFNDRAVKRFMIQLEVK 361

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V      I +++  +SF+  QIR  +    L        + L +    +  K   P 
Sbjct: 362 EPKVYGEIEWISVQIHGQSFMLHQIRKMISMAMLACRTGSPPSLLPETFGPK--KIHIPK 419

Query: 234 APPEGLYFD 242
           APP GL  +
Sbjct: 420 APPLGLLLE 428


>gi|328861209|gb|EGG10313.1| hypothetical protein MELLADRAFT_76951 [Melampsora larici-populina
           98AG31]
          Length = 568

 Score =  116 bits (291), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 64/371 (17%), Positives = 104/371 (28%), Gaps = 135/371 (36%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAI----------------------- 35
            +  + I Y G  + G   Q      ++++G + KA+                       
Sbjct: 87  RKIALQIVYQGWNHGGLAWQPEITPLTTVEGELFKALLSARLVEMSEEFQEEDREEILKT 146

Query: 36  ----FLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILC--------------- 76
                 V  E      AGRTD+GV    QV    +    +   L                
Sbjct: 147 EEWREAVDLEGWEYSRAGRTDAGVSGSGQVVSLWVRSNLLDSKLRQELLDSKQSPPGSFR 206

Query: 77  ------------------KALNA----------------YLKISDTISILNLSIVDKQFH 102
                             K LN+                   + ++I ++  S V  +F 
Sbjct: 207 DPEGFERSTDEENEEVHPKILNSSISNKPQEELPYISILNSLLPESIKVIAWSPVSTEFD 266

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           ARFS   R Y Y                  + +SLD E MR  A+ L+G HDF     + 
Sbjct: 267 ARFSCKGRHYKY----------FFTKFESDLNQSLDIEMMREGAKKLIGEHDFRNLCKLD 316

Query: 163 C--QASSPIRTIDHFDVN---------------------------SFGNLIEIRVVARSF 193
              Q  +  R I   ++N                               +    +   +F
Sbjct: 317 KSKQIENFKREIYSAEINLVDENAIGPEFNKNDGLEGSVGQDGLGEKNQMYVFDLRGSAF 376

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKAL-----------------QAQDRKECGPLAPP 236
           L+ Q+R+ +  L L+G    +   ++  L                 +  DRK    +A  
Sbjct: 377 LYNQVRNIMAILFLIGSRLESPNLIDGLLYTDSSAQKPEGLGLITDEFVDRKPEMAIASE 436

Query: 237 EGLYFDSVEYS 247
             L      Y 
Sbjct: 437 LPLLLWDCIYP 447


>gi|38639411|gb|AAR25833.1| tRNA pseudouridine synthase A [Buchnera aphidicola (Tetraneura
           caerulescens)]
          Length = 107

 Score =  116 bits (290), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 30/93 (32%), Positives = 51/93 (54%)

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT 214
           F+ FR+ +CQ+ +  R I   D+      + I + A +FL+  +R+ VGSL  VG  +  
Sbjct: 1   FSGFRAKNCQSKTAFRKIIRLDIFRKNFFVIIEIEANAFLYKMVRNIVGSLIEVGLKRKN 60

Query: 215 STDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            + ++  L++++RK  GP A   GLY   V+Y 
Sbjct: 61  VSWIDTILKSKNRKLSGPTASANGLYLVYVDYP 93


>gi|330902540|gb|EGH33555.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 231

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 39/116 (33%), Positives = 55/116 (47%), Gaps = 8/116 (6%)

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  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            HFD   E          N  L     +S+    ++        SA  R   +R+ 
Sbjct: 68  VHFDTQAERTLKAWVMGANINL--PHDVSVTWARVMPAS-----SAAGRPSSWRLP 116


>gi|58262434|ref|XP_568627.1| pseudouridylate synthase [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57230801|gb|AAW47110.1| pseudouridylate synthase, putative [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 560

 Score =  115 bits (289), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 97/309 (31%), Gaps = 71/309 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFL---------VTGEIVVVHGAGRT 51
            R  ++I Y G+GY G Q Q +   +I+G +  A+           +    V +  A RT
Sbjct: 123 RRCAVLIGYCGTGYQGMQIQDHTDRTIEGEVFAALVKAGAVSADNAIDARKVDIARAART 182

Query: 52  DSGVHALRQVAHF-DLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           D+GVHA   V     +    +P      A      + D I +       K F+AR +A  
Sbjct: 183 DAGVHAAGNVISIKMITEPPLPEGFKDVAEYVNTFLPDQIRMWGWVRTVKSFNARTAADS 242

Query: 110 RSYLYRIIT---------------------------RQAPLAL----------------- 125
           R Y Y + +                            + P +                  
Sbjct: 243 RIYEYLLPSYCLIPPHKDDSLAKHLDLSSPDWREIVGEGPCSFADARLPMPTSDEGEVDP 302

Query: 126 ------EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT------ID 173
                 E+ R W + +       R       G H+F  +          ++       + 
Sbjct: 303 KVRGEYERKRKWRVDEKT-LGRFRDIIAQYKGTHNFYNYTVGKPFNDRAVKRFMIKLEVK 361

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V      I +++  +SF+  QIR  +    L        + L +    +  K   P 
Sbjct: 362 EPKVYGEIEWISVQIHGQSFMLHQIRKMISMAMLACRTGSPPSLLPETFGPK--KIHIPK 419

Query: 234 APPEGLYFD 242
           APP GL  +
Sbjct: 420 APPLGLLLE 428


>gi|134118796|ref|XP_771901.1| hypothetical protein CNBN0810 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50254505|gb|EAL17254.1| hypothetical protein CNBN0810 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 560

 Score =  115 bits (289), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 97/309 (31%), Gaps = 71/309 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFL---------VTGEIVVVHGAGRT 51
            R  ++I Y G+GY G Q Q +   +I+G +  A+           +    V +  A RT
Sbjct: 123 RRCAVLIGYCGTGYQGMQIQDHTDRTIEGEVFAALVKAGAVSADNAIDARKVDIARAART 182

Query: 52  DSGVHALRQVAHF-DLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIR 109
           D+GVHA   V     +    +P      A      + D I +       K F+AR +A  
Sbjct: 183 DAGVHAAGNVISIKMITEPPLPEGFKDVAEYVNTFLPDQIRMWGWVRTVKSFNARTAADS 242

Query: 110 RSYLYRIIT---------------------------RQAPLAL----------------- 125
           R Y Y + +                            + P +                  
Sbjct: 243 RIYEYLLPSYCLIPPHKDDSLAKHLDLSSPDWREIVGEGPCSFADARLPMPTSDEGEVDP 302

Query: 126 ------EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT------ID 173
                 E+ R W + +       R       G H+F  +          ++       + 
Sbjct: 303 KVRGEYERKRKWRVDEKT-LGRFRDIIAQYKGTHNFYNYTVGKPFNDRAVKRFMIKLEVK 361

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
              V      I +++  +SF+  QIR  +    L        + L +    +  K   P 
Sbjct: 362 EPKVYGEIEWISVQIHGQSFMLHQIRKMISMAMLACRTGSPPSLLPETFGPK--KIHIPK 419

Query: 234 APPEGLYFD 242
           APP GL  +
Sbjct: 420 APPLGLLLE 428


>gi|154418432|ref|XP_001582234.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
 gi|121916468|gb|EAY21248.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
          Length = 345

 Score =  115 bits (289), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 50/260 (19%), Positives = 98/260 (37%), Gaps = 28/260 (10%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDSG 54
             ++  Y G+ Y G Q+  +  +++  + +A+                +    A RTD+G
Sbjct: 29  IILLYRYIGTQYHGLQQNIDTHTVEKELFQALISAGFLSDQANCNLNRIKWSEASRTDAG 88

Query: 55  VHALRQVAHFDLV--REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           VHA  QV  F     +      +   +N  L  +  I I+    + +QF+A+  A  R+Y
Sbjct: 89  VHACAQVLSFKASGLKGICIADIPDLINKQLPRTSDIEIITCITLRRQFYAQKFAESRNY 148

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS-SPIRT 171
            + + T        +   +L    L            +G  ++  F S    ++ S +R 
Sbjct: 149 NFLLPTNAFSSNSIEHLNYLRTSIL---------PLFIGWLNYHNFTSNKSASNPSSMRK 199

Query: 172 IDHFDVN-----SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD 226
           ID F             +   +   SF+  QIR  + ++         + ++++ L  + 
Sbjct: 200 IDVFTFTDPFEVEGVEFVLFTIHGESFMLNQIRKMIATVISASHNYIGAEEVKRCLSEE- 258

Query: 227 RKECGPLAPPEGLYFDSVEY 246
                 + P +GL  D V+Y
Sbjct: 259 -GWSIKMCPGDGLMLDHVDY 277


>gi|326929552|ref|XP_003210926.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like
           [Meleagris gallopavo]
          Length = 596

 Score =  115 bits (288), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 48/217 (22%), Positives = 83/217 (38%), Gaps = 20/217 (9%)

Query: 41  EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
           + +      RTD GV A  Q+      +  +   + + +N +L     I IL L  V   
Sbjct: 173 KKMSFQRCARTDKGVSAAGQIVSL---KVRLIDDILEKINNHL--PSHIRILGLKRVTGG 227

Query: 101 FHARFSAIRRSYLYRIIT----RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT 156
           F+++     R+Y Y + T     +     E+  A+ + +    E +        G H+F 
Sbjct: 228 FNSKNKCDARTYAYMLPTFAFAHKDHDVQEE--AYRLSRET-LEKVNSLLACYKGTHNFH 284

Query: 157 TFRS-IHCQASSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
            F S    +  S  R I         V        I+V  +SF+  QIR  +G +  +  
Sbjct: 285 NFTSQKGPKDPSARRYIMEMYCGEPFVRENIEFAVIKVKGQSFMMHQIRKMIGLVIAIVK 344

Query: 211 GKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           G    + +E++    + K   P AP  GL  + V + 
Sbjct: 345 GYAPESVIERSW--GEEKVDVPKAPGLGLVLERVHFE 379


>gi|237844499|ref|XP_002371547.1| hypothetical protein TGME49_020220 [Toxoplasma gondii ME49]
 gi|211969211|gb|EEB04407.1| hypothetical protein TGME49_020220 [Toxoplasma gondii ME49]
          Length = 370

 Score =  115 bits (288), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 44/148 (29%), Positives = 62/148 (41%), Gaps = 21/148 (14%)

Query: 79  LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD 138
           LNA L     I I+  + V   F ARF    R Y Y                +   + LD
Sbjct: 22  LNAVL--PGDIRIVASAPVSPTFDARFDCTGRVYKY----------------FFHSEGLD 63

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGNLI--EIRVVARSFLH 195
            + M  AAQ  VG H+F  F  +   Q  +P RT+  F V S G+ +     +  RSFL 
Sbjct: 64  LQRMHQAAQRFVGEHNFRYFCKLDPRQYRNPRRTLTSFAVESAGDGVCAVATIAGRSFLW 123

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            Q+R  + +L  VG G    + +   L+
Sbjct: 124 HQVRFMMAALLKVGRGSCDESYIVDLLK 151


>gi|207345658|gb|EDZ72410.1| YFL001Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 315

 Score =  115 bits (288), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 44/195 (22%), Positives = 66/195 (33%), Gaps = 30/195 (15%)

Query: 41  EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTIS 90
           +       GRTD GV A+ QV   ++             N              + D I 
Sbjct: 13  QDYKFSRCGRTDKGVSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIR 72

Query: 91  ILNLS-IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL 149
           I  +       F ARFS + R Y Y I   +               +L+ E M  AA + 
Sbjct: 73  ISAVCLRPPPNFDARFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYF 116

Query: 150 VGRHDFTTFRSIH--CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLK 206
           VG  DF  F  +    Q ++  RTI    +           ++  +FL  Q+R  +  L 
Sbjct: 117 VGERDFRNFCKLDGSKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILF 176

Query: 207 LVGDGKWTSTDLEKA 221
           LVG        + + 
Sbjct: 177 LVGQSLEVPEIVLRL 191


>gi|169849317|ref|XP_001831362.1| pseudouridylate synthase [Coprinopsis cinerea okayama7#130]
 gi|116507630|gb|EAU90525.1| pseudouridylate synthase [Coprinopsis cinerea okayama7#130]
          Length = 568

 Score =  114 bits (287), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 95/298 (31%), Gaps = 68/298 (22%)

Query: 5   CMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
            ++I + GSGY G Q Q   +  +I+G + +A+  V             V +  A RTD+
Sbjct: 137 ALLIGFCGSGYSGMQIQPMDSVKTIEGVLFQALVKVGAVSQDNADDPVKVALARAARTDA 196

Query: 54  GVHALRQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GVHA   V    ++     V  L  A+N  L     I           F+ARF    R Y
Sbjct: 197 GVHAAGNVVSMKMISTIPGVPDLVAAVNEQL--PPEIRFWGFVRTQNSFNARF----RKY 250

Query: 113 LYRII--------------------------TRQAP-LALE--------------KGRAW 131
            Y                             T   P                   + R W
Sbjct: 251 TYFFPSYLLIPPKPGSGLDERLKAFNESLGDTVPRPIHPFWADAPGNSTKEEDLIRKRRW 310

Query: 132 LIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIR-----TIDHFDVNSFGNLIE 185
            +      E +R  A+   G H+F  F      +  S  R     TI+   V      I 
Sbjct: 311 RVDSGP-IERLRETARRYEGTHNFHNFTVGRDFKDRSNFRFMKSITIEDPVVYGETEWIS 369

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +    +SF+  QIR  +  L L          +++    +  +   P  P  GL  + 
Sbjct: 370 VLFHGQSFMLHQIRKMMSGLVLSCRTGAPPEVIDQLYNEE--QVFVPKMPSLGLLLEE 425


>gi|302495964|ref|XP_003009994.1| hypothetical protein ARB_03805 [Arthroderma benhamiae CBS 112371]
 gi|291173519|gb|EFE29349.1| hypothetical protein ARB_03805 [Arthroderma benhamiae CBS 112371]
          Length = 409

 Score =  114 bits (287), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 73/238 (30%), Gaps = 66/238 (27%)

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIITRQAPLA 124
                  +   + LN  L   + I +L     +   F ARFS  +R Y Y          
Sbjct: 29  WDDIADELPYIQILNGAL--PEDIRVLAWCPHLPPDFDARFSCRQRRYRYFFTQPAFCPT 86

Query: 125 -----------------LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QA 165
                            LE+ R       LD E MR AAQ+ VG HDF  F  +    Q 
Sbjct: 87  PGARGIVRSSELKDDLSLERPREGW----LDIEAMREAAQYFVGSHDFRNFCKVDTSKQI 142

Query: 166 SSPIRTIDHFDVN--------------------------------------SFGNLIEIR 187
           ++ +R I   D+                                       + G +    
Sbjct: 143 TNFVRRILRADIELVDPQRTPLGFVQMPGFEPFENGSRNTGVPENINDINPAAGKVYSFT 202

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDS 243
           V   +FL  QIR  VG L LVG G    + + + L      R+    +A    L    
Sbjct: 203 VHGTAFLWHQIRHMVGILFLVGQGLEHPSIVPELLDVTKNPRRPVYEMASDSPLVLWD 260


>gi|67624003|ref|XP_668284.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54659475|gb|EAL38050.1| hypothetical protein Chro.80602 [Cryptosporidium hominis]
          Length = 210

 Score =  114 bits (287), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 70/187 (37%), Gaps = 22/187 (11%)

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK 135
            + LN  L     I ++    V   F ARF    R Y Y       PL  E+ +    PK
Sbjct: 1   MEMLNGVL--PWDIRVIGYCEVRPDFSARFDCEYRLYKYFF-----PLNHERTKISKFPK 53

Query: 136 --SLDCENMRIAAQHLVGRHDFTTFRSIH---CQASSPIRTIDHFDVNSFGNLIEI---R 187
                   M IAA+  +G HD+  F  +     +  + IRTI  FD+N            
Sbjct: 54  IPPEQVPLMDIAAKQFLGTHDYRRFCKMDLKNRKNQTYIRTIYEFDINFVDENRTFAVAT 113

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP----LAPPEGLYFDS 243
           +   +FL  Q+R  +G L  +G  K+    + + L   ++K        +A   GL    
Sbjct: 114 IKGSAFLWHQVRLMMGILFEIGQQKFNPEVITQMLTDVEQKNIAELSFQMATELGLVLWD 173

Query: 244 V---EYS 247
               EY 
Sbjct: 174 CVFKEYD 180


>gi|156040419|ref|XP_001587196.1| hypothetical protein SS1G_12226 [Sclerotinia sclerotiorum 1980]
 gi|154696282|gb|EDN96020.1| hypothetical protein SS1G_12226 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 592

 Score =  114 bits (287), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 47/217 (21%), Positives = 68/217 (31%), Gaps = 42/217 (19%)

Query: 71  VPVILCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIIT---RQAPLALE 126
             +   + LN  L     I IL         F ARFS   R Y Y          P  LE
Sbjct: 222 DEIPYPQVLNRLL--PPDIRILAWCPSPPVDFSARFSCRERRYRYFFTQPAFSPIPSQLE 279

Query: 127 KGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVNSFGN 182
            G +    K   LD E MR AA+   G HDF  F  +    Q ++  R I + ++    +
Sbjct: 280 HGASASKMKDGWLDIEAMREAAKLYEGLHDFRNFCKVDPGKQITNFERRIFYANIEEVKD 339

Query: 183 L------------------------------IEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
                                              +   +FL  Q+R  V  L LVG G 
Sbjct: 340 YTSSLAYVNGDSFLDDSIRSKIDGESKAPKVYTFDLHGSAFLWHQVRHMVAILFLVGQGL 399

Query: 213 WTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEYS 247
              + + + L  +    +    +A    L      + 
Sbjct: 400 EKPSVVSELLDVEKNPGRPAYEMATDTPLVLWDCIFP 436



 Score = 53.7 bits (128), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 29/90 (32%), Gaps = 19/90 (21%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL----------------VTGEIVV 44
             + + Y G  Y G++   +    ++I+  + +A+                  V  E   
Sbjct: 60  IALKLAYLGKRYNGFEHHAHPTPLTTIEEELWQALNKARLIFPQGVNPMAPGEVNWEGCE 119

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVI 74
               GRTD GV A  QV    +        
Sbjct: 120 YSKCGRTDKGVSAFGQVIGIRVRSNRPLAK 149


>gi|323348774|gb|EGA83014.1| Deg1p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 315

 Score =  114 bits (287), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 44/195 (22%), Positives = 66/195 (33%), Gaps = 30/195 (15%)

Query: 41  EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN----------AYLKISDTIS 90
           +       GRTD GV A+ QV   ++             N              + D I 
Sbjct: 13  QNYKFSRCGRTDKGVSAMNQVISLEVRSNLTDEEQRDPTNDSREIPYVHVLNQLLPDDIR 72

Query: 91  ILNLS-IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHL 149
           I  +       F ARFS + R Y Y I   +               +L+ E M  AA + 
Sbjct: 73  ISAVCLRPPPNFDARFSCVHRHYKY-IFNGK---------------NLNIEKMSKAASYF 116

Query: 150 VGRHDFTTFRSIH--CQASSPIRTIDHFDVNSFGN-LIEIRVVARSFLHTQIRSFVGSLK 206
           VG  DF  F  +    Q ++  RTI    +           ++  +FL  Q+R  +  L 
Sbjct: 117 VGERDFRNFCKLDGSKQITNFKRTIISSKILPLSETFYCFDLIGSAFLWHQVRCMMAILF 176

Query: 207 LVGDGKWTSTDLEKA 221
           LVG        + + 
Sbjct: 177 LVGQSLEVPEIVLRL 191


>gi|154320712|ref|XP_001559672.1| hypothetical protein BC1G_01828 [Botryotinia fuckeliana B05.10]
 gi|150853517|gb|EDN28709.1| hypothetical protein BC1G_01828 [Botryotinia fuckeliana B05.10]
          Length = 575

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/225 (21%), Positives = 69/225 (30%), Gaps = 44/225 (19%)

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIIT---R 119
            D       +   + LN  L     I IL         F ARFS   R Y Y        
Sbjct: 215 LDFDHITDEIPYPQVLNRLL--PPDIRILAWCPSPPIDFSARFSCRERRYRYFFTQPAFS 272

Query: 120 QAPLALEKGRAWLIPKS--LDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHF 175
             P  LE G +    K   LD + MR AA+   G HDF  F  +    Q ++  R I + 
Sbjct: 273 PIPSQLEHGTSASKMKDGWLDIDAMREAARLYEGLHDFRNFCKVDPGKQITNFERRIFYA 332

Query: 176 DVNSFGNL------------------------------IEIRVVARSFLHTQIRSFVGSL 205
           ++    +                                   +   +FL  Q+R  V  L
Sbjct: 333 NIEEVDDYTSSLAYVNGGSFLDESVRSKADGEIKAPKIYTFDLHGSAFLWHQVRHMVAIL 392

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPL---APPEGLYFDSVEYS 247
            LVG G    + + + L   ++    P    A    L      + 
Sbjct: 393 FLVGQGLEKPSVVTELLDV-EKNPGRPTYEMATDTPLVLWDCIFP 436



 Score = 54.1 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 19/87 (21%)

Query: 4   YCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFL----------------VTGEIVV 44
             + + Y G  Y G++   +    ++I+  + +A+                  V  E   
Sbjct: 60  IALKLAYLGKRYNGFEHHAHPTPLTTIEEELWQALNKARLIFPQGVNPLAPGEVNWEGCE 119

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWV 71
               GRTD GV A  QV    +     
Sbjct: 120 YSKCGRTDKGVSAFGQVIGIRVRSNRP 146


>gi|325182027|emb|CCA16480.1| tRNA pseudouridine synthase A putative [Albugo laibachii Nc14]
          Length = 209

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 47/201 (23%), Positives = 83/201 (41%), Gaps = 41/201 (20%)

Query: 84  KISDTISILNLSIVDKQFHARFSAIR---RSYLYRIITRQAPLALEKGRAWLIPKSLDCE 140
           ++  TI +  L+ + ++F   F+ IR   + Y+Y I     P       +W + K ++  
Sbjct: 4   RLPSTIRVHCLAPL-EEFVDDFTRIRPRYKRYVYYIQQGARPDLELSKYSWFLRKRIEPT 62

Query: 141 NMRIAAQHLVGRHDFTTFR---SIHCQASSPIRTIDHFDVN------------------- 178
            ++ A   L+G HDF  F     +  +  S  RT+    V                    
Sbjct: 63  RLQQALNFLLGTHDFEPFSQGLGMVLEGKSTTRTLYQASVTLKRNVNFCLDPAVCGSGDT 122

Query: 179 -------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
                        +  + I I +VA  FL   +R  VGSL+L+G+G     ++ + L++Q
Sbjct: 123 VNNQAKLCDMEGKTLTHFICIELVANGFLRHMVRRIVGSLRLIGEGSQHPQEMHRILKSQ 182

Query: 226 DRKECGPLAPPEGLYFDSVEY 246
              E GP AP +GL+   + +
Sbjct: 183 V--EAGPSAPAKGLWLQQIWF 201


>gi|123438137|ref|XP_001309856.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
 gi|121891601|gb|EAX96926.1| tRNA pseudouridine synthase family protein [Trichomonas vaginalis
           G3]
          Length = 365

 Score =  114 bits (285), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 92/265 (34%), Gaps = 37/265 (13%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV-------TGEIVVVHGAGRTDSGVH 56
             +   Y G+ Y G        ++   +++A+  +       T   +    + RTD+GVH
Sbjct: 40  IALCYGYLGTNYHGSSLHDQDKTVTLELQEALVNLGVISPNRTKGALKWSESSRTDTGVH 99

Query: 57  ALRQVAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           A +QVA F L          L + +   L  +  I +         F+A+ SA  R Y Y
Sbjct: 100 AAKQVATFRLVLPEGVKVKDLPRLIQKQLSKNSPIRVWAAVKPGIIFNAQQSASSRRYHY 159

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIA--AQHLVGRHDFTTFRSIHCQA--SSPIR 170
            +                  +++D  N   A      VGRH +  +          + I+
Sbjct: 160 LLPVN-----------TFSSENIDHLNYLRAKICPIFVGRHQYANYTRHITDELLHTSIK 208

Query: 171 TIDHFDVNSFGN-----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           TI  F      +      +   +   SF+  QIR  + ++  V     T  DL+  L   
Sbjct: 209 TISEFTFTDPFDVNGTKYVLFTISGNSFMLNQIRKMIAAVLAVSHHLMTEDDLKDTLTET 268

Query: 226 D---RKECGPLAPPEGLYFDSVEYS 247
                +  G      GL+ D V + 
Sbjct: 269 RWLLPRLIGT-----GLFLDQVFFE 288


>gi|170583043|ref|XP_001896407.1| tRNA pseudouridine synthase family protein [Brugia malayi]
 gi|158596407|gb|EDP34752.1| tRNA pseudouridine synthase family protein [Brugia malayi]
          Length = 234

 Score =  113 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/207 (24%), Positives = 79/207 (38%), Gaps = 48/207 (23%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            R  ++  Y G  Y G   Q+    +++  + KA+         E    + +GRTD GV 
Sbjct: 30  RRIALMFMYFGWEYNGLVEQREIARTVEEEMRKALIKTKLVENWENCSWNRSGRTDKGVS 89

Query: 57  ALRQVAHFDLVREWVP---------------------VILCKALNAYLKISDTISILNLS 95
           A +QVA   +                           +   K LN+ L     I +L  +
Sbjct: 90  AFKQVASVIVRSNEPEGEGVFWPNVAHASSETAMKGELQYVKMLNSTL--PTNIRVLAWA 147

Query: 96  IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
            V + F AR++  +R+Y Y         A  +        + + E MR A Q LVG HDF
Sbjct: 148 PVPRNFSARYNCTQRTYTY---------AFPRT-------NFNIEAMRQACQFLVGEHDF 191

Query: 156 TTFRSIHCQAS----SPIRTIDHFDVN 178
             F  I         + IRTI + D++
Sbjct: 192 RNFCRIDMNKKRVEMNYIRTITYADIS 218


>gi|145606084|ref|XP_370178.2| hypothetical protein MGG_06675 [Magnaporthe oryzae 70-15]
 gi|145013810|gb|EDJ98451.1| hypothetical protein MGG_06675 [Magnaporthe oryzae 70-15]
          Length = 694

 Score =  113 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 60/362 (16%), Positives = 98/362 (27%), Gaps = 120/362 (33%)

Query: 2   IRY-CMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFL--------------VTGEIVV 44
            RY  + + Y G  Y G + Q +G   +I+  + KA+                V  ++  
Sbjct: 165 TRYIALKLAYLGKNYNGLEYQPSGALPAIEEELWKALVKTCLIFPDPERDPSEVDFKVCD 224

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDT------------ISIL 92
               GRTD GV A  QV    +        L K   + +++               +   
Sbjct: 225 YSKCGRTDRGVSAFGQVVALRVKSNKP---LRKKKQSAVQLDQDGSGEAASASTGAVDAA 281

Query: 93  NLSIVDKQ-------------FHARFSAIRRSYLYRIITR------------QAPLA--- 124
              +V +                A + A +     +++                P     
Sbjct: 282 GAQVVPEDSQPGQEDEQEGEEDDAPYPADKEIKYCKMLNAVLPVDIRVLAWCPNPPPGFS 341

Query: 125 -----LEKGRAWLIPKS--------------------------LDCENMRIAAQHLVGRH 153
                 E+   +   +                           LD + MR AA+   G H
Sbjct: 342 ARHSCHERQYRYFFTQPIFSPVPARLDGVMGYKEPGSTHKDGYLDLDAMREAARLFEGEH 401

Query: 154 DFTTFRSIHC--QASSPIRTIDHFDVNSFGN-------------------------LIEI 186
           DF  F  I    Q S+  R I    +                              +   
Sbjct: 402 DFRNFCKIDASKQISNFKRLIREASIVEVPEAASSLPYLDTPDFRPSGEDSQARPKVYYF 461

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSV 244
            V   +FL  QIR  +  L LVG      + + + L  +    K   P+A    L     
Sbjct: 462 HVRGSAFLWHQIRHMIAVLFLVGQRLEKPSIVSELLDIEKYPGKPNYPMASDAPLVLWDC 521

Query: 245 EY 246
            Y
Sbjct: 522 LY 523


>gi|213622913|ref|ZP_03375696.1| tRNA pseudouridine synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. E98-2068]
          Length = 91

 Score =  113 bits (283), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 34/81 (41%), Positives = 45/81 (55%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
          +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11 KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVV 70

Query: 63 HFDLVREWVPVILCKALNAYL 83
          HF+             +NA L
Sbjct: 71 HFETTALRKDAAWTLGVNANL 91


>gi|84997902|ref|XP_953672.1| tRNA pseudouridine synthase [Theileria annulata]
 gi|65304669|emb|CAI72994.1| tRNA pseudouridine synthase, putative [Theileria annulata]
          Length = 478

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 59/343 (17%), Positives = 101/343 (29%), Gaps = 100/343 (29%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTG---------EIVV 44
            +Y +   Y G+GY G+Q+Q            +++G++E  +F +             + 
Sbjct: 69  TKYVIAFGYLGTGYHGYQKQVEYKTGEMDKVKTVEGTLENCLFRIGAINEAFRNMTHKLQ 128

Query: 45  VHGAGRTDSGVHA----LRQVAHFDLVREWV----------------------------- 71
           +    RTD GVHA    L    + ++                                  
Sbjct: 129 MSKCSRTDKGVHAACTYLGGRFNIEMEDVPEDHVPQVNNHSEINNSSKPDTSDNVELQSD 188

Query: 72  -----PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR--QAPLA 124
                     + LNA L   + I    +  V K F AR    +R Y Y I          
Sbjct: 189 GKLSKEEKFVQRLNAAL--PEDIRCFKIQRVTKGFDARSLCSKRKYEYIIPEWLLSKKFV 246

Query: 125 LEKGRAWLIPKSLDC-----------------------------------ENMRIAAQHL 149
           L         ++L+                                      +    +  
Sbjct: 247 LPNEEHEKHFRNLEVIFEENTKTKDIIKLSKLNDTLYEVKGGFEETEIEHSRLYEILKLY 306

Query: 150 VGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGS 204
            G H+F  F      + ++  R I    + S       +++I +V +SFL+ QIR  +  
Sbjct: 307 QGTHNFHNFTVKQKEEINNTSRFIHKISIKSHKIQELEVVKILIVGQSFLYNQIRKMISL 366

Query: 205 LKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
              V  G      +E +L  +       L P EGL      + 
Sbjct: 367 ALQVYLGIAPKNSVEFSLN-KSHFLNINLVPSEGLILHHPYFD 408


>gi|224007493|ref|XP_002292706.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971568|gb|EED89902.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 437

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 101/322 (31%), Gaps = 83/322 (25%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN--------------------GSSIQGSIEKAIFLVTGE- 41
              + + Y G  + GW+ Q++                      S+QG++   +  + G+ 
Sbjct: 120 NLKLTVAYRGLDFCGWEDQRHELYRSDASGAVKQSAVEEEVLPSVQGTLVDILDPLLGKK 179

Query: 42  ---------------------------IVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI 74
                                       + +  AGRTD+GV A+ QV      R  +   
Sbjct: 180 ATHHNDCKHLEQQAKYNPNFQKKTKVMPIEIKVAGRTDTGVSAISQVCRIRTYRTDIGES 239

Query: 75  ------------LCKALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRII-TRQ 120
                       +   +N  ++ + + + I ++  V   FH  F A  R+Y+Y I     
Sbjct: 240 TNNNTGEGLEKFVQNLVNYEMQQLGEGLRIRDVERVKHDFHPTFDASCRAYIYLIDVNDD 299

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTIDHFDVN- 178
           A  A+       I        +    + L G+  D+        +  + + T+ H     
Sbjct: 300 ASDAITPKITRHI-----VPKLNSVLKTLEGKELDYLAMSHGKVKTQTTLCTLLHARAGI 354

Query: 179 ------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTD--LEKALQA 224
                            I I +V   FL   +R  V +      G     D  L   L +
Sbjct: 355 VEWKCNNDSESPKRKQAICIELVGDRFLRRMVRLLVATALREASGADGCDDNALLNILTS 414

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
            DR      APP+GL F    Y
Sbjct: 415 MDRTYRARAAPPDGLIFVGAGY 436


>gi|148683103|gb|EDL15050.1| mCG23338, isoform CRA_a [Mus musculus]
          Length = 130

 Score =  112 bits (282), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 15/124 (12%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-------------NLIE 185
              M+ AAQHL+G HDF+ F+S     ++ +RT+    V+                    
Sbjct: 1   MAAMQEAAQHLLGTHDFSAFQSAGSPVTNTVRTLRRVSVSPGPASPFVLPEGSRRLQFWT 60

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDS 243
           +   ++SFL+ Q+R     L  VG G    T ++  L++QD   K    +AP  GL+  S
Sbjct: 61  LEFESQSFLYRQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAPARGLFLKS 120

Query: 244 VEYS 247
           V Y 
Sbjct: 121 VLYD 124


>gi|66812718|ref|XP_640538.1| tRNA pseudouridine synthase [Dictyostelium discoideum AX4]
 gi|60468568|gb|EAL66571.1| tRNA pseudouridine synthase [Dictyostelium discoideum AX4]
          Length = 504

 Score =  112 bits (281), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 108/319 (33%), Gaps = 91/319 (28%)

Query: 4   YCMIIEYNGSGYF--GWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
             M+  Y+G+GY+  G+Q      SI+  IEK +F             + +    + RTD
Sbjct: 91  VAMVFGYDGTGYYGLGYQVDIKYPSIENLIEKVLFRCGHILPSNVGELKRLKWSHSSRTD 150

Query: 53  SGVHALRQVAHFD------LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
            GVH+L  V            +  +       +N YL    +I + +   V + F AR  
Sbjct: 151 KGVHSLATVISCFLVVDDNTFKNDINQTFIDTINNYL--PSSIRLFSACKVSRSFQARKK 208

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG---RHDFTTFRSIH- 162
            I RSY Y + +                 ++  + M    Q+ +G    H+FT+ R+ + 
Sbjct: 209 GIERSYNYMVPSE-------------YLNNIKIDEMNKILQNFIGINSYHNFTSKRNTYL 255

Query: 163 ------------------------------------------------CQASSPIRTIDH 174
                                                              S+ IR I  
Sbjct: 256 SNNNNKNHEKDEKDEEDGDEEEEEDDEVEVENSNNNNSNYRLNEKLLFRNNSTNIRNIKS 315

Query: 175 FDVN------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           F V             +  ++  SF+  QIR  VG    +  G  T   LE +L++    
Sbjct: 316 FYVENEIIEIKGKGWYKFVIIGESFILYQIRRMVGFFLSIVKGYSTVEALELSLKSP-FS 374

Query: 229 ECGPLAPPEGLYFDSVEYS 247
            C P APP  LY  +V++ 
Sbjct: 375 ICVPTAPPFPLYLFNVKFD 393


>gi|194389944|dbj|BAG60488.1| unnamed protein product [Homo sapiens]
          Length = 142

 Score =  112 bits (281), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 37/121 (30%), Positives = 55/121 (45%), Gaps = 15/121 (12%)

Query: 141 NMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-------------NLIEIR 187
            M+ AAQHL+G HDF+ F+S      SP+RT+    V+                    + 
Sbjct: 3   AMQEAAQHLLGTHDFSAFQSAGSPVPSPVRTLRRVSVSPGQASPLVTPEESRKLRFWNLE 62

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVE 245
             ++SFL+ Q+R     L  VG G      ++  L++QD   K    +AP  GL+  SV 
Sbjct: 63  FESQSFLYRQVRRMTAVLVAVGLGALAPAQVKTILESQDPLGKHQTRVAPAHGLFLKSVL 122

Query: 246 Y 246
           Y
Sbjct: 123 Y 123


>gi|297805092|ref|XP_002870430.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297316266|gb|EFH46689.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 420

 Score =  112 bits (280), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 43/141 (30%), Positives = 69/141 (48%), Gaps = 16/141 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--------FLVTGEIV-----VVHGA 48
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++          +  +        V  A
Sbjct: 93  VNFKIVLSYNGTSFDGWQKQPDLHTVQGVVEKSLGGFVDDRKAQLLKKKCKPLEGRVLVA 152

Query: 49  GRTDSGVHALRQVAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL QV  F   R +  P+ +  A+N     S  + ++++S V + FH  FSA
Sbjct: 153 GRTDKGVSALNQVCSFYTWRKDIEPIAIEDAINK--DASGKLRVVSISKVSRSFHPNFSA 210

Query: 108 IRRSYLYRIITRQAPLALEKG 128
             R YLY      A    E G
Sbjct: 211 KWRRYLYIFPLDDAESLHESG 231



 Score = 61.4 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 20/76 (26%), Positives = 30/76 (39%)

Query: 171 TIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC 230
            +   D      ++ + +VA  FL   +R  V +          +  L K L+A  R+  
Sbjct: 334 RLSCSDCVEGRRVMCVELVANRFLRKMVRVLVATSIREAAAGAENDALLKLLEASCRRAT 393

Query: 231 GPLAPPEGLYFDSVEY 246
            P AP EGL    V Y
Sbjct: 394 APPAPSEGLCLFDVGY 409


>gi|242781979|ref|XP_002479909.1| pseudouridylate synthase 3 [Talaromyces stipitatus ATCC 10500]
 gi|218720056|gb|EED19475.1| pseudouridylate synthase 3 [Talaromyces stipitatus ATCC 10500]
          Length = 621

 Score =  112 bits (280), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 58/277 (20%), Positives = 81/277 (29%), Gaps = 64/277 (23%)

Query: 27  IQGS-IEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKI 85
           +Q   +E +I   T E +           V A               +   + LN  L  
Sbjct: 211 VQQVDVEASIVDSTEENIGS------APSVEANETEVDDGWDDIRDELPYIQILNGVL-- 262

Query: 86  SDTISILNLSI-VDKQFHARFSAIRRSYLYRIITRQAPLA-----LEKGRAWL--IPKS- 136
              I IL         F ARFS   R Y Y                 +  A    I K  
Sbjct: 263 PRDIRILAWCPNPPPDFDARFSCRERQYRYFFTQPAFNPVPGELGFLRSAAHHRGIAKKE 322

Query: 137 -----LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDH--------------- 174
                LD E MR A +  +GRHDF  F  +    Q  +  R I H               
Sbjct: 323 LRDGWLDIEAMREACKQYIGRHDFRNFCRVDTSKQIENFERIIYHASIDLVDPNQHPLGF 382

Query: 175 ------------FDVNSFGN----------LIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
                        D+++ GN          +    +   +FL  Q+R  V  L LVG G 
Sbjct: 383 VGSKEFQPTRNLVDLDNEGNVNEERPSTPLVYTFTLHGSAFLWHQVRHMVAILFLVGQGV 442

Query: 213 WTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
              + + + L      RK    +A    L      + 
Sbjct: 443 EDPSIVSELLDVSKHPRKPTYEMASDAPLVLWDCVFP 479



 Score = 45.2 bits (106), Expect = 0.008,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 32/99 (32%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G+    NG      +I+  I KA+                       
Sbjct: 90  IALKFAYLGQRYNGF-EHANGNITPLPTIEEEIWKALRKTRLIFPTTSSSMELDFNKDDR 148

Query: 38  -----VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV 71
                ++ +       GRTD GV A  QV    +     
Sbjct: 149 ARPFDLSWDGCQYSKCGRTDRGVSAFGQVIGIRVRSARP 187


>gi|242096622|ref|XP_002438801.1| hypothetical protein SORBIDRAFT_10g026490 [Sorghum bicolor]
 gi|241917024|gb|EER90168.1| hypothetical protein SORBIDRAFT_10g026490 [Sorghum bicolor]
          Length = 318

 Score =  112 bits (280), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 89/228 (39%), Gaps = 30/228 (13%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           AGRTD GV AL+QV  F   R+ V    +  A+N      D +  L++S V ++FH  FS
Sbjct: 82  AGRTDKGVTALQQVCSFYTWRKDVKSGDIKDAINE--AAPDKLKPLHVSEVPREFHPNFS 139

Query: 107 AIRRSYLYRIITRQAPLA----------LEKGRAWLIPKSLDCENMRIAAQHLVGR---- 152
           A  R Y+Y     +              LE     + P+S D   +    + L G+    
Sbjct: 140 AKWRRYMYIFPLDEDANLILGEAHSSKILENSEHNIKPQSFDVAKVDKILKTLAGKTLSY 199

Query: 153 ----HDFTTFRSI---------HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
                D    RS+         H +A+       + D      ++ + +VA  FL   +R
Sbjct: 200 KMFARDTQASRSVGPPTECFMFHSRAAVAKLHYANEDYKEGMMVMCVELVANRFLRKMVR 259

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             V +             L   ++A DR+   P APPEGL    V Y 
Sbjct: 260 VLVATAIREAAAGAGDDALLNLMEATDRRATAPPAPPEGLCLIDVGYE 307


>gi|260655352|ref|ZP_05860840.1| tRNA pseudouridine synthase A [Jonquetella anthropi E3_33 E1]
 gi|260629800|gb|EEX47994.1| tRNA pseudouridine synthase A [Jonquetella anthropi E3_33 E1]
          Length = 113

 Score =  111 bits (279), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 31/108 (28%), Positives = 44/108 (40%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
            +      + L GRHDF+ F        +P R +        G L+ + V   +FL   +
Sbjct: 1   MDLFAAGCRLLEGRHDFSAFCRQSEVPENPWRRLYSVRFRRRGPLVVVAVCGDAFLTNMV 60

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           R  +G+L  V  GK +   L   L+   R      APP GL F  V Y
Sbjct: 61  RIMMGNLDDVSRGKRSLDWLAGLLEGGRRSSSAMTAPPSGLTFWRVGY 108


>gi|146084629|ref|XP_001465060.1| tRNA pseudouridine synthase A-like protein [Leishmania infantum
           JPCM5]
 gi|134069156|emb|CAM67303.1| tRNA pseudouridine synthase A-like protein [Leishmania infantum
           JPCM5]
          Length = 525

 Score =  111 bits (279), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 52/201 (25%), Positives = 87/201 (43%), Gaps = 32/201 (15%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKN-------GSSIQG--------------SIEKAI 35
           M RY + ++Y GS + GW    QR +N       G++                  +E+A+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNSKDAAPAGNTTTAAADYGTGSRHFAKVVLEEAL 189

Query: 36  FLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE---WVPVILCKALNAYLKISDTISI 91
            +      V V  A   ++GV   R   H D+  E       IL +A     +    +++
Sbjct: 190 AVALDVPTVSVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRATLWLHQRRQPLAV 249

Query: 92  LNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+     ++ FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + 
Sbjct: 250 LSCHPCRNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLME 309

Query: 151 GRHDFTTFRSIHCQASSPIRT 171
           G HD+  F     + ++ +R 
Sbjct: 310 GTHDYGFF--ADSKMANALRR 328



 Score = 81.0 bits (199), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 31/88 (35%), Positives = 42/88 (47%), Gaps = 9/88 (10%)

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-- 225
            IRT+D  +V    + + I  V +SFL  QIR+ V +LK  G G W   +L+ A Q+   
Sbjct: 414 TIRTLDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVSALKAGGHGLWDDQELQHAFQSGFE 473

Query: 226 ------DRKECGPLAPPEGLYFDSVEYS 247
                  R+   P AP  GL    VEY 
Sbjct: 474 VSRKKFKRERLSP-APAHGLTLWDVEYP 500


>gi|17544142|ref|NP_500962.1| hypothetical protein Y73B6BL.29 [Caenorhabditis elegans]
 gi|15375270|gb|AAK95894.1|AC084197_22 Hypothetical protein Y73B6BL.29 [Caenorhabditis elegans]
          Length = 322

 Score =  111 bits (279), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 56/300 (18%), Positives = 98/300 (32%), Gaps = 54/300 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL-VTGEIVV----------VHGAGR 50
            RY   I Y+GS +    +   G  +   + + I   + G                 + R
Sbjct: 5   RRYLFWIGYDGSKFPEMAKGGTGFGVMDLLNQTISTSIFGSRCEQTPNCSDRLKFSPSSR 64

Query: 51  TDSGVHALRQVAHFDLVREW-----VPVILCKALNAYLKI-----SDTISILNLSIVDKQ 100
           TD+ VHA+R      +  E+      P      + ++          ++ I ++  V   
Sbjct: 65  TDAKVHAIRNSVICQVPLEYAELDKTPETKKAFMTSWKNTIDVANPGSLEIHDVHSVSAG 124

Query: 101 FHARFSAIRRSYLYR------------IITRQAPLAL-EKGRAWLIPKSLDCENMRIAAQ 147
           F  R S   R Y YR            I    +     E+  AW +P       +  A +
Sbjct: 125 FCIRRSVSYRKYTYRMAVCRSWELWESIRQEPSISCFSERDYAWRLPPGFSAHKVLQAGK 184

Query: 148 HLVGRHDFTTFRSIHCQAS-------SPIRTIDHFDVNSFG---------NLIEIRVVAR 191
              G     +F     +         + ++ I H  ++            +   + +VA+
Sbjct: 185 LFEGEQVMGSFFKHTAREKRYEPISPTALKYIFHVGLSKGEAYSMENDIYDYYNVTIVAK 244

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD----RKECGPLAPPEGLYFDSVEYS 247
           SF+  QIR  +  L      +   T +E  L             P+APP+GL+   V Y 
Sbjct: 245 SFVREQIRRMMSCLVNYSYDRIPLTTIEWLLSNPISSNFFDLGIPVAPPQGLFLTDVVYD 304


>gi|331231235|ref|XP_003328281.1| pseudouridine synthase 3 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309307271|gb|EFP83862.1| pseudouridine synthase 3 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 650

 Score =  111 bits (278), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 65/350 (18%), Positives = 105/350 (30%), Gaps = 125/350 (35%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIF---------------------- 36
            +  ++I Y G  + G   Q +    S+++G + +A+                       
Sbjct: 162 RKIALMISYQGELHGGLAWQPDVTRLSTVEGELFRALLVARLVEGAGEFEEQEEEDSERW 221

Query: 37  --LVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREW------------------------ 70
             LV         AGRTD+GV    QV    +  +                         
Sbjct: 222 RGLVDLNKWGYSRAGRTDAGVSGAGQVVSLWVRSQLRSVPAPFGFLPPKKTDSDDGSEEE 281

Query: 71  ------------------VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
                               +     +N+ L   +++ +L  S V   F ARFS   R Y
Sbjct: 282 PRGESAGPKQEQEQEEAEEELQYHTIINSIL--PNSVRVLAWSPVHHDFDARFSCQARHY 339

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIR 170
            Y     ++P A            LD E M  AA  L+G HDF  F  I    Q +   R
Sbjct: 340 KYFFSLYESPQA----------PGLDIEAMNRAADRLIGEHDFRNFCKIDPSKQLAHFRR 389

Query: 171 TIDHFDVN----------------------------------------SFGNLIEIRVVA 190
            I   ++                                             L  + +V 
Sbjct: 390 KILSAEIKPVLDPHHHHLLLLQQQQLSGPSGSSEKHPHPQIYPDALAPETNPLFVLDLVG 449

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEG 238
            +FL+  +R  V  L L+G GK   + +++ L  +  ++      A  EG
Sbjct: 450 TAFLYNMVRHIVSVLFLIGSGKEEISVIDRLLYTEPNEQPSIITTASEEG 499


>gi|308477475|ref|XP_003100951.1| hypothetical protein CRE_16900 [Caenorhabditis remanei]
 gi|308264295|gb|EFP08248.1| hypothetical protein CRE_16900 [Caenorhabditis remanei]
          Length = 322

 Score =  111 bits (278), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 58/300 (19%), Positives = 101/300 (33%), Gaps = 54/300 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-----------GEIVVVHGAGR 50
            RY   I Y+GS +    +   G  +   + + +                E +    + R
Sbjct: 5   RRYLFWIGYDGSKFPEMAKGGTGFGVMDLLNQTVSTSLFGFRNERKPEQHECLKFSPSSR 64

Query: 51  TDSGVHALRQVAHFDLVREW-----VPVILCKALNAYLKI-----SDTISILNLSIVDKQ 100
           TD+ VHA+R      +  E+      P I    +  +          ++ I ++  V   
Sbjct: 65  TDAKVHAIRNSVICQIPLEYSELDKTPEIKADYMKKWKSTIDAANPGSLVIRDVHSVSAG 124

Query: 101 FHARFSAIRRSYLYRI----------ITRQAPLAL---EKGRAWLIPKSLDCENMRIAAQ 147
           F  R S   R Y YR+            RQ P      E+  AW +P     E +  A +
Sbjct: 125 FCIRRSVSYRKYTYRLAVCRSWELWESIRQEPSIACFSERDYAWRLPPGFSPERLLTAGR 184

Query: 148 HLVGRHDFTTFRSIHCQAS-------SPIRTIDHFDVNSFG---------NLIEIRVVAR 191
              G     +F     +         S ++ I H  +++           +   + +VA+
Sbjct: 185 RFEGEQVMGSFFKHTNREKRFEPITPSALKYILHVGLSNGEAYSINNDIYDYYNVTIVAK 244

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD----RKECGPLAPPEGLYFDSVEYS 247
           SF+  QIR  +  L      +     ++  L             P+APP+GL+   V Y 
Sbjct: 245 SFVREQIRRMMSCLVNYSYDRIPLATVDWLLNNPISSNFFDMGIPIAPPQGLFLTDVVYD 304


>gi|156097182|ref|XP_001614624.1| tRNA pseudouridine synthase [Plasmodium vivax SaI-1]
 gi|148803498|gb|EDL44897.1| tRNA pseudouridine synthase, putative [Plasmodium vivax]
          Length = 241

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 39/153 (25%), Positives = 64/153 (41%), Gaps = 18/153 (11%)

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           ++++  V   F AR + I R+YLY                + + K+ + E M+   +  +
Sbjct: 37  VIDMRSVPNFFDARLNCIHRTYLY----------------FFMDKNYNFERMKEGCKLFL 80

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVG 209
           G HDF+ F      ++   RTI  F+V          ++   SFL+ QIR  V +L  +G
Sbjct: 81  GEHDFSNFCKKRKNSTCFRRTILKFEVRRMDKKFHYFKIKGTSFLYNQIRHMVAALFQLG 140

Query: 210 DGKWTSTDLEKALQA-QDRKECGPLAPPEGLYF 241
            G     DL   L     R +   +A  +GL  
Sbjct: 141 TGNLEVEDLANMLNNHPCRDKNFKIADEDGLLL 173


>gi|149024844|gb|EDL81341.1| similar to pseudouridylate synthase-like 1, isoform CRA_b [Rattus
           norvegicus]
          Length = 127

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 36/121 (29%), Positives = 54/121 (44%), Gaps = 15/121 (12%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-------------NLIEIRV 188
           M+ AAQHL+G HDF+ F+S        +RT+    V+                    +  
Sbjct: 1   MQEAAQHLLGTHDFSAFQSAGSPVPHAVRTLRRVSVSPGPASLFVLPQESRRLQFWTLEF 60

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            ++SFL+ Q+R     L  VG G    T ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 61  ESQSFLYRQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAPAHGLFLKSVLY 120

Query: 247 S 247
            
Sbjct: 121 D 121


>gi|268536920|ref|XP_002633595.1| Hypothetical protein CBG05472 [Caenorhabditis briggsae]
 gi|187035020|emb|CAP25947.1| hypothetical protein CBG_05472 [Caenorhabditis briggsae AF16]
          Length = 322

 Score =  111 bits (277), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 100/300 (33%), Gaps = 54/300 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL-----------VTGEIVVVHGAGR 50
            RY   I Y+GS +    +   G  +   + + +                + +    + R
Sbjct: 5   RRYLFWIRYDGSKFPEMAKGGTGFGVMDLLNQTVSQSIFGPRREQHPEQKDKLKFSPSSR 64

Query: 51  TDSGVHALRQVAHFDLVREW-----VPVILCKALNAYLKI-----SDTISILNLSIVDKQ 100
           TD+ VHA+R      +  E+      P    + +  +  I       ++ IL+   V   
Sbjct: 65  TDAKVHAIRSSVICQVPLEFADLDKCPETKIQYMRTWKSIIDAANPGSLEILDAHSVSAG 124

Query: 101 FHARFSAIRRSYLYRIITRQAPLAL-------------EKGRAWLIPKSLDCENMRIAAQ 147
           F  R S   R Y YR+   ++                 E+  AW +P     E +  A +
Sbjct: 125 FCIRRSVSYRKYTYRLAVCRSWDLWDTIRQEPSIACFSERDYAWRLPPGFSPERLLRAGK 184

Query: 148 HLVGRHDFTTF-----RSIHCQASSPIRTIDHFDV-----------NSFGNLIEIRVVAR 191
              G     +F     R    +  SP      F V           N   +   + +VA+
Sbjct: 185 IFEGEQVMGSFFKHTNREKRTEPISPSALKYIFYVGLSNGEAYSVENDIYDYYNVTIVAK 244

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD----RKECGPLAPPEGLYFDSVEYS 247
           SF+  QIR  +  L      +   + +   L+            P+APP+GLY   V Y 
Sbjct: 245 SFVREQIRRMISCLVNYSYDRIPLSTVNWLLKNPISSNFYDMGIPVAPPQGLYLTDVVYD 304


>gi|74216027|dbj|BAE23701.1| unnamed protein product [Mus musculus]
          Length = 347

 Score =  111 bits (277), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 54/255 (21%), Positives = 86/255 (33%), Gaps = 52/255 (20%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            +  +++ Y+G GY G Q                                  GV A  QV
Sbjct: 50  RKIVLLMAYSGKGYHGMQ----------------------------------GVSAAGQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
                 + W+   +   +N++L     I IL L  V   F+++     R+Y Y + T   
Sbjct: 76  VSL---KVWLIDDILDKINSHL--PSHIRILGLKRVTGGFNSKNKCDARTYCYMLPT--F 128

Query: 122 PLALEKGRAWLIPKSLDCENMRI---AAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDV 177
             A +          L  E ++          G H+F  F S    +  S  R I     
Sbjct: 129 AFAHKDRDVQDESYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPREPSARRYILEMYC 188

Query: 178 NSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
                        I+V  +SF+  QIR  VG +  +  G    + LE++    + K   P
Sbjct: 189 EEPFVREGLEFAVIKVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLERSW--GEEKVDVP 246

Query: 233 LAPPEGLYFDSVEYS 247
            AP  GL  + V + 
Sbjct: 247 KAPGLGLVLERVHFE 261


>gi|157868264|ref|XP_001682685.1| tRNA pseudouridine synthase A-like protein [Leishmania major]
 gi|68126140|emb|CAJ07193.1| tRNA pseudouridine synthase A-like protein [Leishmania major strain
           Friedlin]
          Length = 525

 Score =  111 bits (277), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 52/203 (25%), Positives = 88/203 (43%), Gaps = 36/203 (17%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKN-------GSS----------------IQGSIEK 33
           M RY + ++Y GS + GW    QR +N       G++                +   +E+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNNKDAAPVGNTATAAADYGAGSRHFAKV--VLEE 187

Query: 34  AIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE---WVPVILCKALNAYLKISDTI 89
           A+ +      V V  A   ++GV   R   H D+  E       IL +A     +    +
Sbjct: 188 ALGVALDVPTVSVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRATLWLHQRRQPL 247

Query: 90  SILNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           ++L+     ++ FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ 
Sbjct: 248 AVLSCHPCRNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARL 307

Query: 149 LVGRHDFTTFRSIHCQASSPIRT 171
           + G HD+  F     + ++ +R 
Sbjct: 308 MEGTHDYGFF--ADSKMANALRR 328



 Score = 76.8 bits (188), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 31/88 (35%), Positives = 41/88 (46%), Gaps = 9/88 (10%)

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-- 225
            IRT+D  +V    + + I  V +SFL  QIR+ V  LK  G G W   +L+ A Q+   
Sbjct: 414 TIRTLDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVSVLKAGGHGLWDDQELQHAFQSGFE 473

Query: 226 ------DRKECGPLAPPEGLYFDSVEYS 247
                  R+   P AP  GL    VEY 
Sbjct: 474 VSRKKFKRERLSP-APVHGLTLWDVEYP 500


>gi|48477852|ref|YP_023558.1| tRNA pseudouridine synthase A [Picrophilus torridus DSM 9790]
 gi|62901313|sp|Q6L0Y7|TRUA_PICTO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|48430500|gb|AAT43365.1| tRNA pseudouridine synthase A [Picrophilus torridus DSM 9790]
          Length = 251

 Score =  110 bits (276), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 88/246 (35%), Gaps = 38/246 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +   +   Y+G+ + G+ R  + +S++  I   +         +  A RTD  V A   V
Sbjct: 7   MHLLIKYGYDGTKFEGFDRSNSKNSVESVIINVLSEYNITK-NIESAARTDKNVSAAGNV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            +        P  +   LN  +K             +  FH+ +  +  SY+        
Sbjct: 66  FYIKTEER--PEKILGILNGNIK-------------NMFFHSYY--LSNSYI------NP 102

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                K   ++IP  +D   ++      +G HDFT F        +P+RTI+  +   + 
Sbjct: 103 RYNSMKIYKYIIPYRID-SRLKNNIARFLGTHDFTNFSK--NDYRNPVRTINKIEFEEYN 159

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +   +    +SF+  Q+RS +G          +  D         +     LA PE L  
Sbjct: 160 DFTVVNFYGKSFVWHQLRSIIGFAM------HSDEDPFSI-----KYHNRFLAEPEPLIL 208

Query: 242 DSVEYS 247
             + Y 
Sbjct: 209 YDIIYD 214


>gi|71033963|ref|XP_766623.1| tRNA pseudouridine synthase [Theileria parva strain Muguga]
 gi|68353580|gb|EAN34340.1| tRNA pseudouridine synthase, putative [Theileria parva]
          Length = 475

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 59/340 (17%), Positives = 99/340 (29%), Gaps = 97/340 (28%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTG---------EIVV 44
            +Y +   Y G+ Y G+Q+Q            +++G++E  +F +             + 
Sbjct: 69  TKYVISFGYVGTAYHGYQKQVEYKTGEMDKVKTVEGTLENCLFRIGAINEAFRNMTHKLQ 128

Query: 45  VHGAGRTDSGVHA----LRQVAHFDLVREWV----------------------------- 71
           +    RTD GVHA    L    + D+                                  
Sbjct: 129 MSKCSRTDKGVHAACTYLGGRFNIDVEDLSDDVVSQAKNHPSESNGELSNNLESTKDQKL 188

Query: 72  --PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT----------R 119
                    LN+ L   + I    +  V K F AR    +R Y Y I             
Sbjct: 189 SNEDKFVLRLNSVL--PEDIRCFKIQRVTKGFDARTLCSKRKYEYIIPEWILSKKFVVPN 246

Query: 120 QAPLALEKGRAWLIPKSL---------------------------DCENMRIAAQHLVGR 152
           +    L +       ++L                           D + +        G 
Sbjct: 247 EDHENLFRNLELFFEENLKTRDTIKLSKLNESLYEVKGEYEKTEIDHKRLEEILNFYQGT 306

Query: 153 HDFTTFR-SIHCQASSPIRTIDHFDVNSFG----NLIEIRVVARSFLHTQIRSFVGSLKL 207
           H F  F        ++  R I    + S      ++++I +V +SFL+ QIR  +     
Sbjct: 307 HSFHNFTVKQKEDINNSSRFIHKIYIKSDKLQELDVVKILIVGQSFLYNQIRKMISLALQ 366

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           V         LE +L  +       L P EGL      + 
Sbjct: 367 VYLKIAPKNSLEFSLN-KSHILNINLVPSEGLILHHPYFD 405


>gi|157822927|ref|NP_001102169.1| tRNA pseudouridine synthase-like 1 [Rattus norvegicus]
 gi|149024843|gb|EDL81340.1| similar to pseudouridylate synthase-like 1, isoform CRA_a [Rattus
           norvegicus]
          Length = 127

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 36/121 (29%), Positives = 54/121 (44%), Gaps = 15/121 (12%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-------------NLIEIRV 188
           M+ AAQHL+G HDF+ F+S        +RT+    V+                    +  
Sbjct: 1   MQEAAQHLLGTHDFSAFQSAGSPVPHAVRTLRRVSVSPGPASLFVLPQESRRLQFWTLEF 60

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR--KECGPLAPPEGLYFDSVEY 246
            ++SFL+ Q+R     L  VG G    T ++  L++QD   K    +AP  GL+  SV Y
Sbjct: 61  ESQSFLYRQVRRMTAVLVAVGLGILAPTQVKVILESQDPLGKYQARVAPAHGLFLKSVLY 120

Query: 247 S 247
            
Sbjct: 121 D 121


>gi|322498495|emb|CBZ33568.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 525

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 52/203 (25%), Positives = 88/203 (43%), Gaps = 36/203 (17%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKN-------GSS----------------IQGSIEK 33
           M RY + ++Y GS + GW    QR +N       G++                +   +E+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNSKDAAPAGNTATAAADYGTGSRHFAKV--VLEE 187

Query: 34  AIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE---WVPVILCKALNAYLKISDTI 89
           A+ +      V V  A   ++GV   R   H D+  E       IL +A     +    +
Sbjct: 188 ALAVALDVPTVSVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRATLWLHQRRQPL 247

Query: 90  SILNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQH 148
           ++L+     ++ FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ 
Sbjct: 248 AVLSCHPCRNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARL 307

Query: 149 LVGRHDFTTFRSIHCQASSPIRT 171
           + G HD+  F     + ++ +R 
Sbjct: 308 MEGTHDYGFF--ADSKMANALRR 328



 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/88 (35%), Positives = 42/88 (47%), Gaps = 9/88 (10%)

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-- 225
            IRT+D  +V    + + I  V +SFL  QIR+ V +LK  G G W   +L+ A Q+   
Sbjct: 414 TIRTLDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVSALKAGGHGLWDDQELQHAFQSGFE 473

Query: 226 ------DRKECGPLAPPEGLYFDSVEYS 247
                  R+   P AP  GL    VEY 
Sbjct: 474 VSRKKFKRERLSP-APAHGLTLWDVEYP 500


>gi|58699252|ref|ZP_00374050.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58534228|gb|EAL58429.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 100

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 45/101 (44%), Positives = 65/101 (64%), Gaps = 2/101 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EYNGS + GWQ+Q++  +SIQ  IE AIF  +GE + ++  GRTD+GVHAL Q
Sbjct: 1   MRYKITVEYNGSSFSGWQKQQHSANSIQEKIENAIFNFSGEKIALYCGGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQF 101
           VAHFD+ +E     +  A+N +LK S  I      +VD  +
Sbjct: 61  VAHFDMEKECELYRIRNAINYHLK-SIPIVCDEHGVVDTDW 100


>gi|322490513|emb|CBZ25774.1| tRNA pseudouridine synthase A-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 525

 Score =  110 bits (275), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 49/201 (24%), Positives = 86/201 (42%), Gaps = 32/201 (15%)

Query: 1   MIRYCMIIEYNGSGYFGW----QRQKNGSSIQG---------------------SIEKAI 35
           M RY + ++Y GS + GW    QR +NG +                         +E+A+
Sbjct: 130 MTRYRVDVQYQGSDFDGWYKSVQRTRNGKNGASAGSTATAAADYGAGSRHFAKVVLEEAL 189

Query: 36  FLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE--WVPVILCKALNAYLKIS-DTISI 91
            +      V +  A   ++GV   R   H D+  E    P  + +    +L      +++
Sbjct: 190 AVALDVPTVSIVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRTTLWLHQRRQPLAV 249

Query: 92  LNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           L+     ++ FHAR + +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + 
Sbjct: 250 LSCHPCRNQDFHARHNGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLME 309

Query: 151 GRHDFTTFRSIHCQASSPIRT 171
           G HD+  F     + ++ +R 
Sbjct: 310 GTHDYGFF--ADSKMANALRR 328



 Score = 76.8 bits (188), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 32/88 (36%), Positives = 41/88 (46%), Gaps = 9/88 (10%)

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ-- 225
            IRT+D  +V    + I I  V +SFL  QIR+ V  LK  G G W   +L+ A Q+   
Sbjct: 414 TIRTLDKIEVVRQEDEILIWFVGQSFLRHQIRNMVSVLKAGGHGLWDDQELQHAFQSGFE 473

Query: 226 ------DRKECGPLAPPEGLYFDSVEYS 247
                  R+   P AP  GL    VEY 
Sbjct: 474 VSRKKFKRERLSP-APVHGLTLWDVEYP 500


>gi|327351094|gb|EGE79951.1| pseudouridylate synthase 3 [Ajellomyces dermatitidis ATCC 18188]
          Length = 718

 Score =  110 bits (275), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 72/229 (31%), Gaps = 63/229 (27%)

Query: 82  YLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPLAL---EKGRA---- 130
              + + I +L         F ARFS   R Y Y          P  L   ++GR     
Sbjct: 346 NRVLPEDIRVLAWCPNPPPDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGRQEQGS 405

Query: 131 ------WLIPKS----LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN 178
                     +     LD E MR  A++L+G HDF  F  +    Q ++ +R I H D+ 
Sbjct: 406 ERSPNGAHTEQPREGWLDIEAMREGAKYLIGSHDFRNFCKVDPSKQITNHVRHIYHADIE 465

Query: 179 ---------------SFGNL-----------------------IEIRVVARSFLHTQIRS 200
                           FG L                         I +   +FL  Q+R 
Sbjct: 466 LLDPKTKPLSYLGQPGFGPLKSEHDRTTANESTWDTSTSNIKIYTITIHGSAFLWHQVRH 525

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFDSVEYS 247
               L LVG G    + + + L  +   R+    +A    L      + 
Sbjct: 526 LAAILFLVGQGLEPPSIIPELLDVERNPRRPTYEIASDAPLVLWDCVFP 574



 Score = 42.9 bits (100), Expect = 0.046,   Method: Composition-based stats.
 Identities = 21/116 (18%), Positives = 31/116 (26%), Gaps = 42/116 (36%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL---VTGEIVVVHG----- 47
           M    +   Y G  Y G+    NG      +I+  + KA+     +  + V   G     
Sbjct: 164 MRFIALKFAYLGQRYNGY-EHANGNTTPLPTIEEELWKALRKARLIFPQAVEGEGVGSED 222

Query: 48  ----------------------------AGRTDSGVHALRQVAHFDLVREWVPVIL 75
                                        GRTD GV A  QV    +        +
Sbjct: 223 DMGGVNAEQDRGDGRAYKIDWTGCQYSKCGRTDRGVSAFGQVVGIRVRSARPKKRV 278


>gi|239607141|gb|EEQ84128.1| pseudouridylate synthase 3 [Ajellomyces dermatitidis ER-3]
          Length = 664

 Score =  109 bits (274), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 46/229 (20%), Positives = 71/229 (31%), Gaps = 63/229 (27%)

Query: 82  YLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPLAL---EKGRA---- 130
              + + I +L         F ARFS   R Y Y          P  L   ++GR     
Sbjct: 292 NRVLPEDIRVLAWCPNPPPDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGRQEQGS 351

Query: 131 ------WLIPKS----LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN 178
                     +     LD E MR  A++L+G HDF  F  +    Q ++ +R I H D+ 
Sbjct: 352 ERSPNGAHTEQPREGWLDIEAMREGAKYLIGSHDFRNFCKVDPSKQITNHVRHIYHADIE 411

Query: 179 --------------------------------------SFGNLIEIRVVARSFLHTQIRS 200
                                                 S   +  I +   +FL  Q+R 
Sbjct: 412 LLDPKTKPLSYLGQPGFRPLKSEHDRTTANESTWDTSTSNIKIYTITIHGSAFLWHQVRH 471

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFDSVEYS 247
               L LVG G    + + + L  +   R+    +A    L      + 
Sbjct: 472 LAAILFLVGQGLEPPSIIPELLDVERNPRRPTYEIASDAPLVLWDCVFP 520



 Score = 42.9 bits (100), Expect = 0.046,   Method: Composition-based stats.
 Identities = 21/116 (18%), Positives = 31/116 (26%), Gaps = 42/116 (36%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL---VTGEIVVVHG----- 47
           M    +   Y G  Y G+    NG      +I+  + KA+     +  + V   G     
Sbjct: 110 MRFIALKFAYLGQRYNGY-EHANGNTTPLPTIEEELWKALRKARLIFPQAVEGEGVGSED 168

Query: 48  ----------------------------AGRTDSGVHALRQVAHFDLVREWVPVIL 75
                                        GRTD GV A  QV    +        +
Sbjct: 169 DMGGVNAEQDRGDGRAYKIDWTGCQYSKCGRTDRGVSAFGQVVGIRVRSARPKKRV 224


>gi|261201021|ref|XP_002626911.1| pseudouridylate synthase 3 [Ajellomyces dermatitidis SLH14081]
 gi|239593983|gb|EEQ76564.1| pseudouridylate synthase 3 [Ajellomyces dermatitidis SLH14081]
          Length = 718

 Score =  109 bits (274), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 46/229 (20%), Positives = 71/229 (31%), Gaps = 63/229 (27%)

Query: 82  YLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPLAL---EKGRA---- 130
              + + I +L         F ARFS   R Y Y          P  L   ++GR     
Sbjct: 346 NRVLPEDIRVLAWCPNPPPDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGRQEQGS 405

Query: 131 ------WLIPKS----LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN 178
                     +     LD E MR  A++L+G HDF  F  +    Q ++ +R I H D+ 
Sbjct: 406 ERSPNGAHTEQPREGWLDIEAMREGAKYLIGSHDFRNFCKVDPSKQITNHVRHIYHADIE 465

Query: 179 --------------------------------------SFGNLIEIRVVARSFLHTQIRS 200
                                                 S   +  I +   +FL  Q+R 
Sbjct: 466 LLDPKTKPLSYLGQPGFRPLKSEHDRTTANESTWDTSTSNIKIYTITIHGSAFLWHQVRH 525

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFDSVEYS 247
               L LVG G    + + + L  +   R+    +A    L      + 
Sbjct: 526 LAAILFLVGQGLEPPSIIPELLDVERNPRRPTYEIASDAPLVLWDCVFP 574



 Score = 42.9 bits (100), Expect = 0.046,   Method: Composition-based stats.
 Identities = 21/116 (18%), Positives = 31/116 (26%), Gaps = 42/116 (36%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL---VTGEIVVVHG----- 47
           M    +   Y G  Y G+    NG      +I+  + KA+     +  + V   G     
Sbjct: 164 MRFIALKFAYLGQRYNGY-EHANGNTTPLPTIEEELWKALRKARLIFPQAVEGEGVGSED 222

Query: 48  ----------------------------AGRTDSGVHALRQVAHFDLVREWVPVIL 75
                                        GRTD GV A  QV    +        +
Sbjct: 223 DMGGVNAEQDRGDGRAYKIDWTGCQYSKCGRTDRGVSAFGQVVGIRVRSARPKKRV 278


>gi|148693448|gb|EDL25395.1| pseudouridine synthase 3, isoform CRA_a [Mus musculus]
          Length = 361

 Score =  109 bits (274), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 40/166 (24%), Positives = 60/166 (36%), Gaps = 32/166 (19%)

Query: 72  PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
            +     LN  L     I +L  + V+  F ARFS + R+Y Y                +
Sbjct: 38  EIRYTHILNRVL--PADIRVLAWAPVEPSFSARFSCLERTYRY----------------F 79

Query: 132 LIPKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTIDHFDVN----------- 178
                LD   M  AAQ  VG HDF     +       +  RTI    V            
Sbjct: 80  FPRADLDIATMNYAAQKYVGTHDFRNLCKMDVANGVINFQRTILCAQVQLVAQSPGEERR 139

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                L +  V+ ++FL+ Q+R  +  L L+G G      +++ L 
Sbjct: 140 QEPFQLCQFEVIGQAFLYHQVRCMMAILFLIGQGMEKPEIIDELLN 185


>gi|71022667|ref|XP_761563.1| hypothetical protein UM05416.1 [Ustilago maydis 521]
 gi|46101432|gb|EAK86665.1| hypothetical protein UM05416.1 [Ustilago maydis 521]
          Length = 615

 Score =  109 bits (273), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 65/313 (20%), Positives = 93/313 (29%), Gaps = 76/313 (24%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTD 52
            +  +   Y G GY G Q      +I+G I  A            V    V +  A RTD
Sbjct: 121 RKVAVKFGYCGIGYSGLQINPGVKTIEGDIFDAFCTAGAVSSDNAVNPNKVGLQRAARTD 180

Query: 53  SGVHALRQVAHFDLVRE----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            GVHA   +    L+ +         L   +N  L     I I  ++ V   F+AR S  
Sbjct: 181 RGVHAAGNLLSLKLILQPQGLKPGETLVDKVNELL--PPFIRIWGVTRVQNGFNARQSCD 238

Query: 109 RRSYLYRIITR----QAP------------------------------------LALEKG 128
            R Y Y + T       P                                        K 
Sbjct: 239 SRMYEYLLPTYVFIPPKPGSTMHDMLVRIRQQELARLSESEAHVSTTCLDEIIDHPFWKS 298

Query: 129 RAWLIPKSLDCEN-------------MRIAAQHLVGRHDFTT------FRSIHCQASSPI 169
                  S+D                +R      +G H+F        FR   CQ     
Sbjct: 299 HGTTSEFSVDMAAKKQYRLTPAHLAKIRSIFNRFLGSHNFYNFTVGKEFRDRSCQRFMKK 358

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
            TI    +      + I+   +SF+  QIR  +G L L+G        +++      R  
Sbjct: 359 LTISEPKMIQGVEWLSIKFHGQSFMLHQIRKMIGLLVLIGRTGAAERLVDECF-GPARVH 417

Query: 230 CGPLAPPEGLYFD 242
             P AP  GL  +
Sbjct: 418 I-PKAPGLGLLLE 429


>gi|212526856|ref|XP_002143585.1| pseudouridylate synthase 3 [Penicillium marneffei ATCC 18224]
 gi|210072983|gb|EEA27070.1| pseudouridylate synthase 3 [Penicillium marneffei ATCC 18224]
          Length = 630

 Score =  109 bits (273), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 73/242 (30%), Gaps = 67/242 (27%)

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVD-KQFHARFSAIRRSYLYRIITRQAPLA 124
                  +   + LN  L     I IL         F ARFS   R Y Y   T+ A   
Sbjct: 257 WDDIRDELPYIQVLNGVL--PQDIRILAWCPNPGPDFDARFSCRERQYRYFF-TQPAFNP 313

Query: 125 ------LEKGRAWL--IPKS------LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSP 168
                   +  A    I K       LD E MR A +H VGRHDF  F  +    Q  + 
Sbjct: 314 IAGELGFLRSAAHHRGIAKKELRDGWLDIEAMREACKHYVGRHDFRNFCRVDTSKQIENF 373

Query: 169 IRTIDHFDVN--------------------------SFGNLI-----------EIRVVAR 191
            R I    ++                            G+ +              +   
Sbjct: 374 ERIIYRASIDLVDPRTNPLGYVGSKDFQPTRNPVDMPNGSNVNEEQPSTPLVYTFTLHGS 433

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL------APPEGLYFDSVE 245
           +FL  Q+R  V  L LVG G  + + + + L    +  C P       AP   L      
Sbjct: 434 AFLWHQVRHMVAVLFLVGQGVESPSIVPELLDI-SKNPCKPTYEMASDAP---LVLWDCI 489

Query: 246 YS 247
           + 
Sbjct: 490 FP 491



 Score = 45.6 bits (107), Expect = 0.007,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 32/99 (32%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G+    NG      +I+  I KA+                       
Sbjct: 100 IALKFAYLGQRYNGF-EHANGNATPLPTIEEEIWKALRKTRLIFPTTTSPMELSLDRHDR 158

Query: 38  -----VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWV 71
                ++ +       GRTD GV A  QV    +     
Sbjct: 159 TQPFDLSWDGCQYSKCGRTDRGVSAFGQVIGIRVRSARP 197


>gi|295671354|ref|XP_002796224.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb01]
 gi|226284357|gb|EEH39923.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb01]
          Length = 700

 Score =  109 bits (272), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 68/233 (29%), Gaps = 71/233 (30%)

Query: 82  YLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIIT-----RQAPLALEKG------- 128
              + + I +L         F ARFS   R Y Y            PL   K        
Sbjct: 328 NRVLPEDIRVLAWCPNPPSDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGSDQKSS 387

Query: 129 ----------RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFD 176
                     R       LD E MR  A++L+G HDF  F  I    Q ++ +R I H D
Sbjct: 388 VSGSSPITELREGW----LDIEAMREGARYLIGTHDFRNFCKIDPSKQITNHVRHIYHAD 443

Query: 177 VN----------------------SFGNL------------------IEIRVVARSFLHT 196
           +                         G L                    I +   +FL  
Sbjct: 444 IELLDPQTKPLSYLGQPEFQALEARNGELGRNLVSKDSLLSSSNMKIYSITIHGSAFLWH 503

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDSVEYS 247
           Q+R     L L+G G    + + + L  +   R+    +A    L      + 
Sbjct: 504 QVRHLAAILFLIGQGLERPSIIPELLDFEKNPRRPTYEIASDAPLVLWDCIFP 556


>gi|332006581|gb|AED93964.1| tRNA pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 471

 Score =  109 bits (272), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 42/136 (30%), Positives = 66/136 (48%), Gaps = 16/136 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV-------------VVHGA 48
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++     E                V  A
Sbjct: 93  VNFKIVLSYNGASFDGWQKQPDLHTVQGVVEKSLGGFVDERKAQLLKKKCKPLEGRVLVA 152

Query: 49  GRTDSGVHALRQVAHFDLVR-EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           GRTD GV AL QV  F   R +  P+ +  A+N     S  + ++++S V + FH  FSA
Sbjct: 153 GRTDKGVSALNQVCSFYTWRKDIEPIAIEDAINK--DASGKLRVVSISKVSRSFHPNFSA 210

Query: 108 IRRSYLYRIITRQAPL 123
             R YLY      A  
Sbjct: 211 KWRRYLYIFPLDDAEP 226



 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 28/71 (39%)

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D      ++ + +VA  FL   +R  V +             L K L+A  R+   P AP
Sbjct: 390 DCVEGRRVMCVELVANRFLRKMVRVLVATSIREAAAGAEDDALLKLLEASCRRATAPPAP 449

Query: 236 PEGLYFDSVEY 246
            EGL    V Y
Sbjct: 450 SEGLCLFDVGY 460


>gi|290979041|ref|XP_002672243.1| predicted protein [Naegleria gruberi]
 gi|284085818|gb|EFC39499.1| predicted protein [Naegleria gruberi]
          Length = 483

 Score =  108 bits (270), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 62/314 (19%), Positives = 105/314 (33%), Gaps = 71/314 (22%)

Query: 4   YCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTGE-------------- 41
           + +   YNG  + G Q Q         +  +I+  +   ++   GE              
Sbjct: 101 FVISFSYNGIPFNGLQIQNGENLVKHPHLLTIEAVLLDILYGSNGESDFEQDETIIRYTK 160

Query: 42  -----IVVVHGAGRTDSGVHALRQVAHFDLV----------REWVPVILCKALN------ 80
                 + +  A RTD GV A+R      +            ++    LCK LN      
Sbjct: 161 SKNCKDIRLQRACRTDRGVSAVRNAFACVMTLPNTQNHKDTFKFNNEELCKTLNDRINNH 220

Query: 81  ---AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSL 137
                L + D I I N+  V  +F        R YLY +          +          
Sbjct: 221 VRIKNLNLMDQIKIFNIQRVPSRFVLHHWCQFRRYLYVLPLSAL-DLSSRNIITKCNNIF 279

Query: 138 DCE-------NMRIAAQHLVGRHDFTTFR---SIHCQASSP-IRTIDHFDVNSFGNL--I 184
           + E        +     H  G H F  F         +S   ++T+   + N  G+L  +
Sbjct: 280 NLETNEQKCQKLNELLGHFEGIHLFHNFTVDAKPGSDSSRRHVKTLKIIEQNLEGDLPHV 339

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWT-----------STDLEKALQAQDRKECGPL 233
            I +  RSF+  QIR  +G++  +  G                D  + L     +   P+
Sbjct: 340 VIEISGRSFMLHQIRMMIGTVIALMRGMAPNMNTTVQDNTIVNDFFENLFKAQTEVLLPM 399

Query: 234 APPEGLYFDSVEYS 247
           AP EGL+ D++++ 
Sbjct: 400 APSEGLFLDNLDFP 413


>gi|225681814|gb|EEH20098.1| pseudouridylate synthase [Paracoccidioides brasiliensis Pb03]
          Length = 641

 Score =  108 bits (270), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 71/244 (29%), Gaps = 63/244 (25%)

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYRIIT-----RQ 120
             + +   L         + + I +L         F ARFS   R Y Y           
Sbjct: 257 EWDDIADELPYITILNRVLPEDIRVLAWCPNPPSDFDARFSCRERRYRYFFTQPAFSPTP 316

Query: 121 APLALEKGRAWLIPKS-------------LDCENMRIAAQHLVGRHDFTTFRSIHC--QA 165
            PL   K  +                   LD E MR  A++L+G HDF  F  I    Q 
Sbjct: 317 GPLGFLKRGSDQKSSGSDSSPSTELREGWLDIEAMREGARYLIGTHDFRNFCKIDPSKQI 376

Query: 166 SSPIRTIDHFDVN----------------------------------------SFGNLIE 185
           ++ +R I H D+                                         S   +  
Sbjct: 377 TNHVRHIYHADIELLDPQTKPLSYLGQPEFQALEAGNGELDRNLVTKDSLLSSSNMKIYS 436

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--QAQDRKECGPLAPPEGLYFDS 243
           I +   +FL  Q+R     L L+G G    + + + L  +   R+    +A    L    
Sbjct: 437 ITIHGSAFLWHQVRHLAAILFLIGQGLERPSIIPELLDIEKNPRRPTYEIASDAPLVLWD 496

Query: 244 VEYS 247
             + 
Sbjct: 497 CIFP 500


>gi|154335976|ref|XP_001564224.1| tRNA pseudouridine synthase A-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134061258|emb|CAM38282.1| tRNA pseudouridine synthase A-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 525

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 50/191 (26%), Positives = 78/191 (40%), Gaps = 30/191 (15%)

Query: 2   IRYCMIIEYNGSGYFGW----QRQ-------KNGSSIQGS--------------IEKAIF 36
            RY + ++Y GS + GW    QR          G++  G               +E+A+ 
Sbjct: 131 TRYRVDVQYQGSDFDGWYKSVQRTNKKRDAAPAGNTTAGVADYGAGSHHFARVVLEEALA 190

Query: 37  LVTGEI-VVVHGAGRTDSGVHALRQVAHFDLVRE---WVPVILCKALNAYLKISDTISIL 92
           +      V V  A   ++GV   R   H D+  E       IL ++     +    ++IL
Sbjct: 191 VALDVPMVGVVAAVIPETGVSVRRLTCHVDVPSEVELQPRTILQRSTLWLHQRRQPLAIL 250

Query: 93  NLSIVDK-QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG 151
           +        FHAR S +RR Y YRI+ R AP   + G  W + + LD   M+  A+ + G
Sbjct: 251 SCHPCHNQDFHARHSGVRRVYCYRILNRIAPPLFDAGLQWHVDRYLDVPRMQRMARLMEG 310

Query: 152 RHDFTTFRSIH 162
            HD+  F    
Sbjct: 311 THDYGFFADTK 321



 Score = 83.3 bits (205), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 32/87 (36%), Positives = 45/87 (51%), Gaps = 7/87 (8%)

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA--- 224
            +RT+D  +V    + + I  V +SFL  QIR+ VG LK  G G W   +L+ ALQ+   
Sbjct: 414 TVRTVDKIEVVRQEDEVLIWFVGQSFLRHQIRNMVGVLKAGGHGLWDDQELQHALQSGFE 473

Query: 225 ----QDRKECGPLAPPEGLYFDSVEYS 247
               + ++E  P AP  GL    VEY 
Sbjct: 474 VSRKKFKRERLPPAPVHGLTLWDVEYP 500


>gi|225560228|gb|EEH08510.1| pseudouridylate synthase [Ajellomyces capsulatus G186AR]
          Length = 625

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 69/228 (30%), Gaps = 62/228 (27%)

Query: 82  YLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPLAL---EKGR---AW 131
              + + I +L         F ARFS   R Y Y          P  L   ++GR     
Sbjct: 266 NRVLPEDIRVLAWCPNPPPDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGREENCL 325

Query: 132 LI----PKS-------LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN 178
                 P +       LD E MR  A++L+G HDF  F  +    Q ++ +R I H D+ 
Sbjct: 326 WEGSGAPHNEQFREGWLDIEAMREGAKYLIGSHDFRNFCKVDPSKQITNHVRHIYHADIE 385

Query: 179 ------------SFGNLIEIR-------------------------VVARSFLHTQIRSF 201
                                                         +   +FL  Q+R  
Sbjct: 386 LLDPKTKPLSYLRQHEFTTFDTENDKAAANGSIDDPSSNLKVYSITIHGSAFLWHQVRHL 445

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
              L LVG G    + + + L  +   R+    +A    L      + 
Sbjct: 446 AAILFLVGQGLEAPSIIPELLDVEKHPRRPTYEIASDTPLVLWDCIFP 493


>gi|81022386|gb|ABB55198.1| tRNA pseudouridine synthase [Enterococcus faecium]
          Length = 89

 Score =  106 bits (265), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 35/91 (38%), Positives = 48/91 (52%), Gaps = 3/91 (3%)

Query: 1  MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
          M    + IEY+G  Y GWQR   +  +IQG IEK +  +T E + + G+GRTD+G HA  
Sbjct: 1  MRNIKLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMTNEEIEIIGSGRTDAGTHARG 60

Query: 60 QVAHFDLVREWVPVILCKALNAYLKISDTIS 90
          QVA+F    E     +   +N YL     I 
Sbjct: 61 QVANFKTNTEIGLAEMIDFMNRYL--PRDIV 89


>gi|325090241|gb|EGC43551.1| pseudouridylate synthase [Ajellomyces capsulatus H88]
          Length = 626

 Score =  106 bits (264), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 69/228 (30%), Gaps = 62/228 (27%)

Query: 82  YLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPLAL---EKGRAWLI- 133
              + + I +L         F ARFS   R Y Y          P  L   ++GR     
Sbjct: 267 NRVLPEDIRVLAWCPNPPPDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGREENCL 326

Query: 134 ------PKS-------LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN 178
                 P +       LD E MR  A++L+G HDF  F  +    Q ++ +R I H D+ 
Sbjct: 327 GEGSGAPHNEQFREGWLDIEAMREGAKYLIGSHDFRNFCKVDPSKQITNHVRHIYHADIE 386

Query: 179 ------------SFGNLIEIR-------------------------VVARSFLHTQIRSF 201
                                                         +   +FL  Q+R  
Sbjct: 387 LLDPKTKPLSYLRQHEFTTFDTENYKAAANGSIDDPSSNLKVYSITIHGSAFLWHQVRHL 446

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
              L LVG G    + + + L  +   R+    +A    L      + 
Sbjct: 447 AAILFLVGQGLEAPSIIPELLDVEKHPRRPTYEIASDTPLVLWDCIFP 494


>gi|240278982|gb|EER42488.1| pseudouridylate synthase [Ajellomyces capsulatus H143]
          Length = 626

 Score =  106 bits (264), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 69/228 (30%), Gaps = 62/228 (27%)

Query: 82  YLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIIT---RQAPLAL---EKGRAWLI- 133
              + + I +L         F ARFS   R Y Y          P  L   ++GR     
Sbjct: 267 NRVLPEDIRVLAWCPNPPPDFDARFSCRERRYRYFFTQPAFSPTPGPLGFLKRGREENCL 326

Query: 134 ------PKS-------LDCENMRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN 178
                 P +       LD E MR  A++L+G HDF  F  +    Q ++ +R I H D+ 
Sbjct: 327 GEGSGAPHNEQFREGWLDIEAMREGAKYLIGSHDFRNFCKVDPSKQITNHVRHIYHADIE 386

Query: 179 ------------SFGNLIEIR-------------------------VVARSFLHTQIRSF 201
                                                         +   +FL  Q+R  
Sbjct: 387 LLDPKTKPLSYLRQHEFTTFDTENYKAAANGSIDDPSSNLKVYSITIHGSAFLWHQVRHL 446

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQD--RKECGPLAPPEGLYFDSVEYS 247
              L LVG G    + + + L  +   R+    +A    L      + 
Sbjct: 447 AAILFLVGQGLEAPSIIPELLDVEKHPRRPTYEIASDTPLVLWDCIFP 494


>gi|168058399|ref|XP_001781196.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667349|gb|EDQ53981.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 499

 Score =  105 bits (263), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 39/151 (25%), Positives = 61/151 (40%), Gaps = 23/151 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            +  +I+ Y G+ Y G QR     +I+G +E+A+F               V    A RTD
Sbjct: 57  RKVALILAYCGAAYQGMQRNPGAITIEGELEQALFRADAIAECNFGDMRKVDWMRAARTD 116

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ Q+    LV    P  L + +N +L     I +   + V   F+A+    +R Y
Sbjct: 117 KGVSAIGQIVSARLV--IDPPGLVERVNQHL--PKDIRVFGYTRVTSNFNAKQMCDKRRY 172

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
            Y +     P+      A       D E M+
Sbjct: 173 EYLV-----PVFAFNPHAHH-----DRETMQ 193



 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/122 (23%), Positives = 49/122 (40%), Gaps = 7/122 (5%)

Query: 132 LIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDV-----NSFGNLIE 185
            +      E +       VG  ++  F + I  +  S  R I  F             + 
Sbjct: 311 FVFDDAKLERLNEILGKYVGTRNYHNFTARIKPEDPSAKRYIISFTAGKVIEVQGMQFVP 370

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             VV +SF+  QIR  +G+   +  G    + ++ ALQ+++     P+AP  GL+ D   
Sbjct: 371 CTVVGQSFMLHQIRKMIGTAIAIMRGCVPDSIIDFALQSKN-DVNTPMAPELGLFLDECF 429

Query: 246 YS 247
           YS
Sbjct: 430 YS 431


>gi|313223491|emb|CBY41917.1| unnamed protein product [Oikopleura dioica]
          Length = 281

 Score =  105 bits (263), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 49/201 (24%), Positives = 78/201 (38%), Gaps = 38/201 (18%)

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           + GVHA+  V    +        + +               N+++ ++ F A        
Sbjct: 27  EKGVHAVNNVISLFVNSRLSEDEINE---------------NVTVGERNFVA-------- 63

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
               II RQ P  +       I   LD E M+ AA +L+G HDF  F     +  + +R 
Sbjct: 64  ----IINRQLPDDI------WITSGLDVELMKEAASYLIGEHDFRNFSQAQLERQNTVRV 113

Query: 172 IDHFDVNSFGN---LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD-- 226
               D+    N   +    + A  FL+ QIR  +  L LVG+    ST +++ L  +   
Sbjct: 114 CFAADIKQVPNMSSMCVFSIKASGFLYHQIRLTMAILALVGNKLEKSTIVKELLDVEKYP 173

Query: 227 RKECGPLAPPEGLYFDSVEYS 247
           R+     A P+GL     EY 
Sbjct: 174 RRPSYKYANPDGLVLIDCEYE 194


>gi|254168636|ref|ZP_04875479.1| tRNA pseudouridine synthase family [Aciduliprofundum boonei T469]
 gi|197622470|gb|EDY35042.1| tRNA pseudouridine synthase family [Aciduliprofundum boonei T469]
          Length = 225

 Score =  105 bits (262), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 55/215 (25%), Positives = 82/215 (38%), Gaps = 35/215 (16%)

Query: 33  KAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISIL 92
           KA+  +  +   +  A RTD GV AL  V             L   LNA LK      I 
Sbjct: 2   KALESMGIK--NLKSASRTDRGVSALGNVIWIKTD--IDGKELIGRLNANLK-----HIY 52

Query: 93  NLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
             S  +   + R+ A  R Y Y ++                    D + ++ AA    G 
Sbjct: 53  FHSFANLDINPRY-ARIRWYRYHLLDMGQ----------------DMDRLKEAAMIFQGE 95

Query: 153 HDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           HDF  F  +     + +  I   DVN  G++I I    R++L   IR  V +++    GK
Sbjct: 96  HDFRNFTRVR---KNTVIEIKKIDVNKRGSIITIDFYGRNYLWNLIRRIVAAMEAYSLGK 152

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
               ++        RK  G +APPE L    ++Y 
Sbjct: 153 EFGQEIFTI-----RKNFG-IAPPEPLILMDIQYD 181


>gi|325190643|emb|CCA25138.1| ubiquitin fusion degradation protein putative [Albugo laibachii
           Nc14]
          Length = 585

 Score =  105 bits (262), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 102/317 (32%), Gaps = 85/317 (26%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            R  ++  YNGS Y G Q   N  +I+  I KA++ +             +    + RTD
Sbjct: 78  RRVAIVAGYNGSDYHGVQLNPNVPTIEDEIRKAMYHIGALRASNFQDLNKIDWSRSSRTD 137

Query: 53  SGVHALRQVAHFDL---VREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHAR 104
            GVHA   V    L        PV      L +ALN  L     I I +++ V   F+AR
Sbjct: 138 KGVHASTIVFAGKLLLNEDVIDPVTGRVRGLTRALNENL--PPNIRIFSVTRVCNSFNAR 195

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI-------AAQHLVGRHDFTT 157
                R Y Y +     PLA          +      M +       A +   G HDF  
Sbjct: 196 TECALREYEYFL-----PLAFLSASCITENRQKMRGQMNVMVQGFLSALEQYEGIHDFHN 250

Query: 158 FRSIH----------------------------------CQASSPIRTIDHFD------- 176
           +                                         +SP  T   F        
Sbjct: 251 YTRSRSHFYKLHEKKNQKFLERKSAAAHGDTLSDSLGGNSDLTSPFDTASKFRPRLPRHR 310

Query: 177 ---VNSFGNLIE---------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
                  G+LIE         + +  ++FL  QIR  +G          +ST  E +L  
Sbjct: 311 RAVYQCRGSLIEDFYGEPYVKVHITGQAFLLHQIRCMIGGAISFATDAISSTVFEASLYT 370

Query: 225 QDRKECGPLAPPEGLYF 241
            D+    P+AP EGL  
Sbjct: 371 -DQIVRIPIAPAEGLLL 386


>gi|224011898|ref|XP_002294602.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220969622|gb|EED87962.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 394

 Score =  105 bits (262), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 52/202 (25%), Positives = 83/202 (41%), Gaps = 44/202 (21%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQA------PLALEKGRAWLIPKSLDCENM 142
           IS  +++ V   F AR+SA  + Y+Y I +         P    +  AWLI +SLD E M
Sbjct: 191 ISAFSVTPVPLTFDARYSAKWKRYIYYICSGINNGETVQPFVWSR-YAWLIRESLDYEGM 249

Query: 143 RIAAQHLVG-RHDFTTFRSI-HCQASSPIRTID-----------------HFDVNSFGNL 183
             AA+ L G  H++     I   +  +  RT+                   + +    N 
Sbjct: 250 VDAAKMLSGEEHNYEWMCVIQEGELRNTRRTVHLNIETVPVKVNGNDTMVPYFLQQNENS 309

Query: 184 IEIRVVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--------QAQDRK----- 228
           +  +VVA S  FL+  +R  VG L  +G  +   T L++ +         + DR+     
Sbjct: 310 VVYKVVATSDFFLYKMVRRIVGLLVAIGKKQADLTTLKRCIGVYDKYGAASDDREGERMK 369

Query: 229 ---ECGPLAPPEGLYFDSVEYS 247
              +    AP +GL  D +EY 
Sbjct: 370 IPVKLLETAPAKGLCLDHIEYD 391



 Score = 77.6 bits (190), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQV 61
           R+ + + ++G+ Y G+Q Q   ++IQ  IE  +  +     V V G GRTD+GVHA   V
Sbjct: 39  RFAIRLSFDGTTYSGFQSQPYQNTIQDQIEHRLRNLLKRDTVRVIGWGRTDAGVHAKGAV 98

Query: 62  AHFDLVREWVPVILCKA 78
              DL  + V  +L + 
Sbjct: 99  VTVDLWGKEVMELLTRR 115


>gi|224011902|ref|XP_002294604.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220969624|gb|EED87964.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 394

 Score =  105 bits (262), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 52/202 (25%), Positives = 82/202 (40%), Gaps = 44/202 (21%)

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQA------PLALEKGRAWLIPKSLDCENM 142
           IS  +++ V   F AR+SA  + Y+Y I +         P    +  AWLI +SLD E M
Sbjct: 191 ISAFSVTPVPLTFDARYSAKWKRYIYYICSGINNGETVQPFVWSR-YAWLIRESLDYEGM 249

Query: 143 RIAAQHLVG-RHDFTTFRSI-HCQASSPIRTID-----------------HFDVNSFGNL 183
             AA+ L G  H++     I   +  +  RT+                   + +    N 
Sbjct: 250 VDAAKMLSGEEHNYEWMCVIQEGELRNTRRTVHLNIETVPVKVNGNDTMVPYFLQQNENS 309

Query: 184 IEIRVVARS--FLHTQIRSFVGSLKLVGDGKWTSTDLEKAL--------QAQDRK----- 228
           +  +VVA S  FL+  +R  VG L  +G  +   T L++ +         + DR      
Sbjct: 310 VVYKVVATSDFFLYKMVRRIVGLLVAIGKKQADLTTLKRCIGVYDKYGAASDDRDGERMK 369

Query: 229 ---ECGPLAPPEGLYFDSVEYS 247
              +    AP +GL  D +EY 
Sbjct: 370 IPVKLLETAPAKGLCLDHIEYD 391



 Score = 77.6 bits (190), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQV 61
           R+ + + ++G+ Y G+Q Q   ++IQ  IE  +  +     V V G GRTD+GVHA   V
Sbjct: 39  RFAIRLSFDGTTYSGFQSQPYQNTIQDQIEHRLRNLLKRDTVRVIGWGRTDAGVHAKGAV 98

Query: 62  AHFDLVREWVPVILCKA 78
              DL  + V  +L + 
Sbjct: 99  VTVDLWGKEVMELLTRR 115


>gi|221113814|ref|XP_002153998.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 267

 Score =  104 bits (260), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 47/194 (24%), Positives = 67/194 (34%), Gaps = 38/194 (19%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--------VVVHGAGRTDSG 54
           R  +   Y G  Y G   Q+   +   +IE AIF    +               GRTD G
Sbjct: 80  RIALKFLYLGWDYQGLANQE---TTNNTIEDAIFNAMIKAKLIEDRVLCKYSRCGRTDKG 136

Query: 55  VHALRQVAHFDL---------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           V A  QV   ++               +   + LN  L     I +L  + V + F ARF
Sbjct: 137 VSAFGQVIALNVRSNTLVSEEEDTREEISYVRLLNKIL--PPEIRMLAFARVPQDFDARF 194

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
               R Y Y                +   K +D + M  AAQ  VG  DF  F       
Sbjct: 195 DCDTRMYKY----------------FFPAKRMDIKLMDAAAQKFVGEKDFRNFCKFIILT 238

Query: 166 SSPIRTIDHFDVNS 179
            S ++++D F +  
Sbjct: 239 QSWLKSVDLFKIFE 252


>gi|19075416|ref|NP_587916.1| tRNA pseudouridine synthase (predicted) [Schizosaccharomyces pombe
           972h-]
 gi|74676082|sp|O74451|YCG6_SCHPO RecName: Full=Putative tRNA pseudouridine synthase C16C4.06c
 gi|6855456|emb|CAA20745.2| tRNA pseudouridine synthase (predicted) [Schizosaccharomyces pombe]
          Length = 413

 Score =  104 bits (260), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 97/288 (33%), Gaps = 55/288 (19%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVH 56
            ++ Y G+G+ G Q   N  +IQ ++ +A   V         + + + +  A RTD GVH
Sbjct: 41  CVVSYRGTGFAGLQYNANVKTIQDTLFQAFARVGAVVQVNADSPKKIRMCSAARTDKGVH 100

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A+  V    ++       +   +N  L     I +  ++     F        R Y Y +
Sbjct: 101 AIVNVLGLKVLDNQPLPHVVNLVNDIL--PPCIRVWKMARTFNSFSPHTVCDSRVYEYWL 158

Query: 117 ITR----QAPLALEKG-------RAWLIPKSL-------------------------DCE 140
                    P  LE         +A+ I ++L                           +
Sbjct: 159 PVSSLLTPRPCTLEAYVIAKASEKAFPINETLSHLANLSKQDCVANSLSEPFRLSKPKLD 218

Query: 141 NMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDVNS------FGNLIEIRVVARSF 193
            ++ A     G H F ++ +      +S  R +    V++          +++    +SF
Sbjct: 219 FLKHACTMFRGTHRFHSYTTEKGFSDASSRRFLLDVRVDNLHIDKLNRQWVKLIFHGQSF 278

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +  QIR  VG L  +    W +  L        R    P AP E L  
Sbjct: 279 MKHQIRKMVGILIHLTRTGWNAQVLLNTFNNSYRIRI-PRAPAEFLLL 325


>gi|207093371|ref|ZP_03241158.1| tRNA pseudouridine synthase A [Helicobacter pylori HPKX_438_AG0C1]
          Length = 120

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 55/124 (44%), Gaps = 6/124 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSAVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII-TR 119
           V  F   + W    L   L   L     I +  L    K FHARF A +R Y Y +    
Sbjct: 60  VLSFHAPKHWNASKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRVYRYLLTKNL 115

Query: 120 QAPL 123
           + P 
Sbjct: 116 KTPF 119


>gi|72390962|ref|XP_845775.1| pseudouridylate synthase I [Trypanosoma brucei TREU927]
 gi|62175816|gb|AAX69943.1| pseudouridylate synthase I, putative [Trypanosoma brucei]
 gi|70802311|gb|AAZ12216.1| pseudouridylate synthase I, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 618

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 70/353 (19%), Positives = 117/353 (33%), Gaps = 116/353 (32%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y G+ + G Q Q +  +   ++G + +A+             V+GE      + RT
Sbjct: 26  LCVMYCGTAFRGLQLQAHAPTHHTVEGVLIQALKDAGIVDGVQRGRVSGEEHHFARSCRT 85

Query: 52  DSGVHALRQVAHFDLVREWV-----PVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    +    +        L + LNA+L    T+ +  ++ V   F  RF 
Sbjct: 86  DRGVHAVRNLVCLFVPNSKLEAAGGCDRLPQLLNAHL--PSTVRVERVTTVMGDFIPRFC 143

Query: 107 AIRRSYLYRIIT--------------RQAPLALEKGRAW--------LIPKSLD--CENM 142
            + R Y Y I                 + P A+E  R          L P   D     +
Sbjct: 144 CVSRIYRYMIPVYALLSPCSSWNEFYAEFPQAVETLRCRAQGGSFIDLCPNEEDKLLAAL 203

Query: 143 R--------IAAQHLVGRHDFTTFRSIHCQA--------------SSPIRTIDHFDVNS- 179
           R        + A H+VG H F  F +   +               ++ +RT+   ++   
Sbjct: 204 RDVVSRGNGLLAHHVVGTHRFHNFSASPGERYGHGWNRKVVMPNDNTSVRTVMRCEIAPR 263

Query: 180 -----------------------FGN-----------------------LIEIRVVARSF 193
                                   G+                        +  ++  RSF
Sbjct: 264 LFLFPQETIGPTRSEYAKSLKIFEGDTAAEGERVVAVSERTFPETALLPYLLFQIEGRSF 323

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           L   IR  VG +  V  G    + +++ L A +R    PLAP   LY     Y
Sbjct: 324 LFNMIRKIVGLIIAVLRGAR-ESLMQETLSA-ERHALCPLAPGSFLYLFHSFY 374


>gi|302781376|ref|XP_002972462.1| hypothetical protein SELMODRAFT_97541 [Selaginella moellendorffii]
 gi|300159929|gb|EFJ26548.1| hypothetical protein SELMODRAFT_97541 [Selaginella moellendorffii]
          Length = 428

 Score =  103 bits (258), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 69/332 (20%), Positives = 107/332 (32%), Gaps = 101/332 (30%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
              + + Y G+ Y G Q Q+      S++  +E+AI+   G         + V    + R
Sbjct: 3   NVAIWVGYVGTDYKGLQIQRGVAGIHSVENELEEAIYKAGGISEENYRHLDKVRWKRSSR 62

Query: 51  TDSGVHALRQVAHFDLV-------REWVPVILCKALNAYLKISDTISILNLSIVDKQFHA 103
           TD GVH+L  V    L         +   + +  A NAYL     ISI  +  V K F A
Sbjct: 63  TDKGVHSLCTVVTMKLEVAVNSWLNDVDGIKIADAFNAYL--PANISIFGVVPVTKSFDA 120

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFT----- 156
           R S   R+  Y      A + +    +    + +D   ++ R   + L GRH F      
Sbjct: 121 RRSCYSRT--YDYYFPAACIGINNESS---SEDVDQRIQDFRRTLKSLEGRHAFHNYTVR 175

Query: 157 ------------------------------TFRSIHCQASSP----------IRTIDHFD 176
                                         +F+  H +  +P           R     D
Sbjct: 176 RLYRKSQRRGTYSPSRNLIADEESSEDEEPSFKDTHDEQDNPAADIGEERGAGRRAYWLD 235

Query: 177 VNSFG---------------------------NLIEIRVVARSFLHTQIRSFVGSLKLVG 209
            +  G                           +++ IRV   SF+  QIR  VG+   V 
Sbjct: 236 ESEEGKDPVKASHFRNVAKCTCEGPEKLNCPSSVVRIRVTGESFMVHQIRKMVGTAIAVF 295

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   +      +  +   PLAPP GL  
Sbjct: 296 RHVLPEDAIP-VSTCRHARVVLPLAPPHGLVL 326


>gi|19074166|ref|NP_584772.1| PSEUDOURIDYLATE SYNTHASE 2 [Encephalitozoon cuniculi GB-M1]
 gi|19068808|emb|CAD25276.1| PSEUDOURIDYLATE SYNTHASE 2 [Encephalitozoon cuniculi GB-M1]
          Length = 345

 Score =  103 bits (257), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 84/250 (33%), Gaps = 45/250 (18%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           R  +++ Y+GS Y G Q  K+  +++  I + +  +             + +  + RTD 
Sbjct: 4   RVGLLVGYDGSRYHGLQFNKDLDTVEKKIVECLLRMDAISERNAGDPRKIHIKSSSRTDK 63

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   +    +     P  L   L   L   + I + ++  + K       AI R+Y 
Sbjct: 64  GVHAALNLVSVKIELGVSPE-LVSGLRELLSK-EGIHLYDIVRLTKSIVPSKQAISRTYE 121

Query: 114 YRIIT----------------------------RQAPLALEKGRAWLIPKSLDCENMRIA 145
           Y + T                            R  P ++            D       
Sbjct: 122 YIVPTYFLAEGDFSREVEVLSQGDEECRGDRIGRVYPESMIDSVVGYTSSEDDTRVFSTI 181

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRS 200
            Q  VG  DF  F  ++ +  S  R I    V+          ++I +  +SFL  QIR 
Sbjct: 182 LQKYVGTKDFHNFTKLNNEKGST-RYIKSIIVSDTYTDNGVEYVKISITGQSFLLHQIRK 240

Query: 201 FVGSLKLVGD 210
            V    L+  
Sbjct: 241 MVLFAVLLCR 250


>gi|301105176|ref|XP_002901672.1| ubiquitin fusion degradation protein, putative [Phytophthora
           infestans T30-4]
 gi|262100676|gb|EEY58728.1| ubiquitin fusion degradation protein, putative [Phytophthora
           infestans T30-4]
          Length = 840

 Score =  103 bits (257), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 99/318 (31%), Gaps = 96/318 (30%)

Query: 12  GSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVHALRQVA 62
           G+GY G Q   N  +I+  I  AIF               +    + RTD GVHA   V 
Sbjct: 2   GTGYHGLQLNDNVKTIEDDIRNAIFQAGAMRESNFEDLGKIDWARSSRTDKGVHAGCIVF 61

Query: 63  H----FDLVREWVP-----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
                 D   +  P       L +ALNA L   + I + + + V K+F AR + + R Y 
Sbjct: 62  SGKLLIDEENKVDPISGRVHELKEALNASL--PENIRVFSCTRVSKRFSARKNCVLREYE 119

Query: 114 YRIITRQAPLALEKGRAWLIP-KSLD----CENMRIAAQHLVGRHDFTT-------FRSI 161
           Y +     PL+  +G       +  D          A +   G HDF         F  +
Sbjct: 120 YFM-----PLSFLRGSLIGSDGEDFDTDEAVAEFCRALRRYEGVHDFHNFTRSRSYFYKV 174

Query: 162 HCQASSP----------------------------------------------------- 168
             +                                                         
Sbjct: 175 QAKKKHYKAHYRRSVAESDDAGVEDNDEDAEEESGIDDYSEESSQFEDEEELTRKLLPRH 234

Query: 169 IRTIDHFDVNSFGNLI-----EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            R+I     +   +        I +V ++FL  QIR  VG    V     +  + + AL 
Sbjct: 235 RRSIYSCSGSLVPDFCGEPHLRIHIVGQAFLLNQIRCMVGGALAVATKGMSRVEFDAALL 294

Query: 224 AQDRKECGPLAPPEGLYF 241
             +R    P+AP EGL  
Sbjct: 295 T-NRIVRVPIAPAEGLVL 311


>gi|170586438|ref|XP_001897986.1| tRNA pseudouridine synthase family protein [Brugia malayi]
 gi|158594381|gb|EDP32965.1| tRNA pseudouridine synthase family protein [Brugia malayi]
          Length = 225

 Score =  102 bits (256), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 41/169 (24%), Positives = 64/169 (37%), Gaps = 14/169 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSG 54
           Y +++ Y G  Y G Q QK+  +I+G + KA+            +        A RTD  
Sbjct: 29  YALLLAYQGKKYNGMQVQKDFPTIEGELFKAMAKCGYICENDVFSPVRFAFQRAARTDRS 88

Query: 55  VHALRQVAHFDLVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           V A RQ+    L  E     L  A   LN +L   + I +L +    + F A  +  +R+
Sbjct: 89  VSAARQMCSMRLAPENHEYFLKTATDKLNTHL--PEEIRVLGVRRATRSFKAHKNCDKRT 146

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS 160
           Y Y + T     A E   +           +        G H+F  + S
Sbjct: 147 YSYTLPTYAFARADELTTSGFRMSETSIAELNDLLALYKGTHNFFNYTS 195


>gi|323449394|gb|EGB05282.1| hypothetical protein AURANDRAFT_12283 [Aureococcus anophagefferens]
          Length = 239

 Score =  102 bits (256), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 85/236 (36%), Gaps = 35/236 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTG---------EIVVVHGAG 49
            +  +++ Y G+ Y+G Q+Q    +  +I+ ++++A+                +    A 
Sbjct: 6   RKLALLLGYRGANYYGLQKQSKESDLPTIELALQEALNRAGAVHEGNQGDLSKIGWSRAA 65

Query: 50  RTDSGVHALRQVAHFDLV-REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           RTD  V A RQV    L         L + LN  L   D I + +   V K F+ + S  
Sbjct: 66  RTDKRVSAARQVVSAKLEVENDDVPALLERLNGEL--PDDIKVFDAVRVIKGFNCKQSCD 123

Query: 109 RRSYLYRIIT---------RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
           RR Y Y + T           A  A+ +  A         E +R      VG   +  F 
Sbjct: 124 RRHYTYLLPTFLLAPDEAIDAAFDAVAQRLAPHRAAPTLLERLRGFLAAYVGTRKYHNFT 183

Query: 160 -SIHCQASSPIRTIDHF----------DVNSFGNLIEIRVVARSFLHTQIRSFVGS 204
             +     +  R I  F          D       +++ VV +SFL   IR  V  
Sbjct: 184 NKLKPTDMAAQRFIVSFTADDPTYPSGDAADGAEWVKLDVVGQSFLMHMIRKMVAV 239


>gi|3047089|gb|AAC13601.1| contains similarity to pseudouridylate synthases [Arabidopsis
           thaliana]
 gi|10178103|dbj|BAB11490.1| unnamed protein product [Arabidopsis thaliana]
          Length = 364

 Score =  102 bits (256), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 59/299 (19%), Positives = 91/299 (30%), Gaps = 92/299 (30%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV-------------VVHGA 48
           + + +++ YNG+ + GWQ+Q +  ++QG +EK++     E                V  A
Sbjct: 93  VNFKIVLSYNGASFDGWQKQPDLHTVQGVVEKSLGGFVDERKAQLLKKKCKPLEGRVLVA 152

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           GRTD GV AL Q                                    V + FH  FSA 
Sbjct: 153 GRTDKGVSALNQ------------------------------------VSRSFHPNFSAK 176

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC----- 163
            R YLY      A   L K          D    +     L          S        
Sbjct: 177 WRRYLYIFPLDDAE-PLRKSGENHENFIFDENKKKQRNGLLSEEIAEEVIMSEDDELEIE 235

Query: 164 QASSPIRTIDH---FDVNSFGNLIEIRVVAR----------------------SFLHT-- 196
           + S+ +  ++    F V+    L++  +  +                       F++   
Sbjct: 236 ETSNALEVVEKPSDFSVSKVDQLLQ-HLQGKVLSYKMFARDTKAARNEGPPTECFMYHAR 294

Query: 197 ---------QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                     +R  V +             L K L+A  R+   P AP EGL    V Y
Sbjct: 295 AAEIRLSSSMVRVLVATSIREAAAGAEDDALLKLLEASCRRATAPPAPSEGLCLFDVGY 353


>gi|71416935|ref|XP_810423.1| tRNA pseudouridine synthase A-like protein [Trypanosoma cruzi
           strain CL Brener]
 gi|70874950|gb|EAN88572.1| tRNA pseudouridine synthase A-like protein, putative [Trypanosoma
           cruzi]
          Length = 608

 Score =  102 bits (255), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 50/204 (24%), Positives = 79/204 (38%), Gaps = 44/204 (21%)

Query: 2   IRYCMIIEYNGSGYFGW----QRQ-------KNGSSI-----------QG---------- 29
            RY + ++Y GS + GW     RQ        +G ++           Q           
Sbjct: 207 TRYRVDVQYQGSDFDGWWKSTSRQLYRRETLPDG-TVRRVPLTPDTTDQEDSSAKKTMSS 265

Query: 30  ------SIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVREW---VPVILCKAL 79
                  +E+A+ +      V V      + GV   R   HFD+          I+ +A 
Sbjct: 266 RYHARTVLEEALAVALDVHTVKVVAGVIPEVGVSVRRLCCHFDVPSHIELQPRTIIQRAT 325

Query: 80  NAYLKISDTISILNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD 138
               K    +++L+     ++ FHAR S +RR Y+YRI+ R AP   + G  W + + LD
Sbjct: 326 MWLEKRQQPLAVLSCQRCKNQDFHARHSGLRRVYVYRILNRVAPPLFDAGLQWHVDRHLD 385

Query: 139 CENMRIAAQHLVGRHDFTTFRSIH 162
              M+  A+ L G  DF  F    
Sbjct: 386 VPRMQRFAKALEGTKDFGYFADPK 409



 Score = 81.8 bits (201), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 36/104 (34%), Positives = 50/104 (48%), Gaps = 9/104 (8%)

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
           G H    +R+        IRTID  +V    + + I  V +SFL  QIR+ V  LK  G 
Sbjct: 482 GAHSREYYRA--STNLPTIRTIDRLEVVRQDDEVLIWFVGKSFLRHQIRNMVSLLKAAGH 539

Query: 211 GKWTSTDLEKALQA-------QDRKECGPLAPPEGLYFDSVEYS 247
           G W   +L++ALQ+       + ++E  P AP  GL    VEY 
Sbjct: 540 GLWNELELQQALQSGFEPSRRRFKRERFPPAPVYGLTLWDVEYP 583


>gi|207108295|ref|ZP_03242457.1| tRNA pseudouridine synthase A [Helicobacter pylori HPKX_438_CA4C1]
          Length = 122

 Score =  102 bits (254), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 41/117 (35%), Positives = 53/117 (45%), Gaps = 5/117 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  +   I Y+G+ + G+ +Q N   +Q  IE A+    G    V  AGRTD GVHA  Q
Sbjct: 1   MRCFKATIAYDGAYFLGYAKQPNKLGVQDKIESAL-NALGIKSAVIAAGRTDKGVHANNQ 59

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           V  F   + W    L   L   L     I +  L    K FHARF A +R Y Y + 
Sbjct: 60  VLSFHAPKHWNASKLFYYLAPKLAPH--IVLKKLEE--KNFHARFDAQKRVYRYLLT 112


>gi|315304866|ref|ZP_07875006.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
 gi|313626765|gb|EFR95758.1| tRNA pseudouridine synthase A [Listeria ivanovii FSL F6-596]
          Length = 83

 Score =  101 bits (253), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 167 SPIRTIDHFDVNSFGNL-IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
           S +RT+   D     N  + I      FL+  +R   G+L   G G+ +  D+ KAL A+
Sbjct: 1   SKVRTLYSIDFYEEDNETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLAR 60

Query: 226 DR-KECGPLAPPEGLYFDSVEYS 247
           DR K     APP+GLY   V+Y 
Sbjct: 61  DRQKLISKTAPPQGLYLWRVDYE 83


>gi|145529301|ref|XP_001450439.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124418050|emb|CAK83042.1| unnamed protein product [Paramecium tetraurelia]
          Length = 297

 Score =  101 bits (253), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 83/234 (35%), Gaps = 43/234 (18%)

Query: 35  IFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV-----------------REWVPVILCK 77
           +   + + + V    RTD GVHAL  V    L                        +L +
Sbjct: 29  LNADSIKKIGVSRGARTDRGVHALCNVVSLKLQIDQKYCSSMTNNKLVDKWNIDWDLLIQ 88

Query: 78  ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSL 137
            LN+ L     I +  +  V + F+ +  A +R Y Y      +P               
Sbjct: 89  ELNSQL--PSDIKVNAIKHVTQSFNVKHQADQRMYNYI-----SPSFSTVDYV------- 134

Query: 138 DCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS----FGNLIEIRVVARS 192
                +      +G H+F  + S       S  R I  F V +      N ++  ++  S
Sbjct: 135 -----QNICNQYLGTHNFHNYTSKKEYNDPSSKRFIQDFRVQNLNFHNENYLKFTILGNS 189

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           F++ QIR  +G++  +   K   + ++     Q       +AP +GLY   +++
Sbjct: 190 FMYHQIRKIIGTIYQIVQEKKDLSFIQDTFSQQQHSL--YIAPQQGLYLREIKF 241


>gi|4220415|gb|AAD12460.1| Homology to pseudouridine synthetase X02743 [Mycoplasma genitalium]
          Length = 102

 Score =  101 bits (253), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 40/104 (38%), Positives = 59/104 (56%), Gaps = 2/104 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  I+ Y+G  + GW  Q N ++IQG +E++  L+ G  + V G+GRTD GVHA+ Q
Sbjct: 1   MARYLGIVSYDGIYFKGWAIQPNLATIQGLLEQSFSLIIGRKIKVIGSGRTDKGVHAINQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
             H D+  E    +L + +N  L     I +  L +V+  FHAR
Sbjct: 61  TFHVDINGEINLNLLIRKINQ-LIKPHCI-VKTLVLVNDSFHAR 102


>gi|167590068|ref|ZP_02382456.1| tRNA pseudouridine synthase A [Burkholderia ubonensis Bu]
          Length = 77

 Score =  101 bits (252), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 43/77 (55%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
          +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1  MRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFAQTPLHTTVAGRTDTGVHGLGQV 60

Query: 62 AHFDLVREWVPVILCKA 78
           HFD   +       + 
Sbjct: 61 VHFDTELDRADFSWVRG 77


>gi|167537271|ref|XP_001750305.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163771295|gb|EDQ84964.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1025

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/278 (16%), Positives = 71/278 (25%), Gaps = 87/278 (31%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
            +  +   Y G  Y G   Q +   +++  +  A+                 GRTD GV 
Sbjct: 33  RKVALRFAYLGEHYRGLAFQDHQADTVEEHLFNALQRACLIDDRTSCEFSRCGRTDKGVS 92

Query: 57  ALRQVAHFDL--------------------------VREWVPVILCKALNAYLKISDTIS 90
           AL QVA   +                           +    +     LN  L     I 
Sbjct: 93  ALSQVASLYVRTNLEECTSLKPRTEPLPPKKAEAQREKARQEIDYIHVLNRLL--PHDIR 150

Query: 91  ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV 150
           +   + V   F                                                 
Sbjct: 151 VYAWAPVPADF------------------------------------------------- 161

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGD 210
              D  + +  H      + +        + NL  I V   +FL  QIR  V  L L+G 
Sbjct: 162 ---DARSCKKAHNFLRGNMTSATFARNTPYYNLCCITVHGSAFLWHQIRCMVSVLFLIGQ 218

Query: 211 GKWTSTDLEKALQ--AQDRKECGPLAPPEGLYFDSVEY 246
              + + + + L   +   K    +AP   L     EY
Sbjct: 219 QLESPSIVSRLLDVVSLPGKPQYDMAPDLPLVLWDCEY 256


>gi|224007503|ref|XP_002292711.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971573|gb|EED89907.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 162

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 35/146 (23%), Positives = 62/146 (42%), Gaps = 20/146 (13%)

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
              +  +I IL    V  +F ARFS  +R+Y Y                +   ++LD   
Sbjct: 3   NNVLPPSIRILGWCPVSPEFSARFSCGQRTYRY----------------FFPRRNLDLSA 46

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQ---ASSP-IRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           M    Q+++GRHDF     ++C+      P I+  +    +S  ++  + +V ++FL  Q
Sbjct: 47  MAQGLQYMMGRHDFRNLCKMNCEQNEGEHPVIQPTEQSKPSSSRDMCHVEIVGQAFLWHQ 106

Query: 198 IRSFVGSLKLVGDGKWTSTDLEKALQ 223
           IR  +  L  VG    T   +++   
Sbjct: 107 IRCIMSILFYVGRQLETPQIVQQLFD 132


>gi|198426359|ref|XP_002130657.1| PREDICTED: similar to tRNA pseudouridine synthase 3 (tRNA-uridine
           isomerase 3) (tRNA pseudouridylate synthase 3) [Ciona
           intestinalis]
          Length = 557

 Score =  101 bits (251), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 67/178 (37%), Gaps = 28/178 (15%)

Query: 82  YLKISDTISILNLSIVD-KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCE 140
              +   I +L  + V+ ++F AR   + R Y Y                +    + D  
Sbjct: 259 NRVLPAEIKVLAWAPVENEEFSARKHCLGREYRY----------------YFHRGNADIT 302

Query: 141 NMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFGN--------LIEIRVVAR 191
            M  AA+   G HDF  F +       + +R I+HF+++            +   R++  
Sbjct: 303 AMNEAAKLFCGLHDFRNFGKVNVVNCVNYVRRINHFEISFCDEEKGAGPYRMCFARIIGS 362

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKA--LQAQDRKECGPLAPPEGLYFDSVEYS 247
            F++ Q+RS +  L L+G G      + +   ++   +K    L  P  L   +  Y 
Sbjct: 363 GFIYHQVRSMMAVLYLIGVGLEKPEIITELFNIEKHPKKPWFGLVKPHALVLFNSIYP 420



 Score = 57.1 bits (137), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 5/72 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVH 56
            R  + + Y G  Y G Q  +N   +I+  + +A+  V        +     GRTD  V 
Sbjct: 101 RRIALKVAYLGWDYEGLQENENLDDTIERILREALRRVRLVPADRSIYFSRCGRTDKEVS 160

Query: 57  ALRQVAHFDLVR 68
           A  QV    +  
Sbjct: 161 AFSQVIVVKVRS 172


>gi|261329198|emb|CBH12177.1| pseudouridylate synthase I, putative [Trypanosoma brucei gambiense
           DAL972]
          Length = 618

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 70/353 (19%), Positives = 116/353 (32%), Gaps = 116/353 (32%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y G+ + G Q Q +  +   ++G + +A+             V+GE      + RT
Sbjct: 26  LCVMYCGTAFRGLQLQAHAPTHHTVEGVLIQALKDAGIVDGVQRGRVSGEEHHFARSCRT 85

Query: 52  DSGVHALRQVAHFDLVREWV-----PVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    +    +        L + LNA+L    T+ +  ++ V   F  RF 
Sbjct: 86  DRGVHAVRNLVCLFVPNSKLEAAGGCDRLPQLLNAHL--PSTVRVERVTTVMGDFIPRFC 143

Query: 107 AIRRSYLYRIIT--------------RQAPLALEKGRAW--------LIPKSLD--CENM 142
            + R Y Y I                 + P A+E  R          L P   D     +
Sbjct: 144 CVSRIYRYMIPVYALLSPCSSWNEFYAEFPQAVETLRCRAQGGSFIDLCPNEEDKLLAAL 203

Query: 143 R--------IAAQHLVGRHDFTTFRSIHCQA--------------SSPIRTIDHFDVNS- 179
           R        + A H+VG H F  F     +               ++ +RT+   ++   
Sbjct: 204 RDVVSRGNGLLAHHVVGTHRFHNFSVSPGERYGHGWNRKVVMPNDNTSVRTVMRCEIAPR 263

Query: 180 -----------------------FGN-----------------------LIEIRVVARSF 193
                                   G+                        +  ++  RSF
Sbjct: 264 LFLFPQEAIGPTRSEYAKSLKIFEGDTAAEGERVVAVSERTFPETALLPYLLFQIEGRSF 323

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           L   IR  VG +  V  G    + +++ L A +R    PLAP   LY     Y
Sbjct: 324 LFNMIRKIVGLIIAVLRGAR-ESLMQETLSA-ERHALCPLAPDSFLYLFHSFY 374


>gi|261333810|emb|CBH16805.1| tRNA pseudouridine synthase A-like protein,putative [Trypanosoma
           brucei gambiense DAL972]
          Length = 588

 Score =  100 bits (249), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 97/280 (34%), Gaps = 60/280 (21%)

Query: 2   IRYCMIIEYNGSGYFGW----QRQK----------------------------------- 22
            RY + ++Y G+ + GW     RQ                                    
Sbjct: 185 TRYRVDVQYQGNDFDGWWKSTTRQLFRREVGLDGSITRVPVAEPGTIGNAAGASRGETMG 244

Query: 23  ---NGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVREW---VPVIL 75
              +  ++   +E+A+ +      V V      + GV   R   H D+          ++
Sbjct: 245 SRYHARTV---LEEALAVALDVNTVRVVAGVIPEVGVSVRRLCCHVDVPSHIELQPRTVI 301

Query: 76  CKALNAYLKISDTISILNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
            +A     K    ++IL+     ++ FHAR S +RR Y+YRI+ R AP   + G  W + 
Sbjct: 302 QRATMWMEKRQQPLAILSYRRCKNQDFHARHSGLRRVYVYRILNRVAPPLFDAGLQWHVD 361

Query: 135 KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFL 194
           + LD + M+  A+ L G  DF  F     + ++ +R        S G      V   +F 
Sbjct: 362 RHLDVDRMKRFAKALEGTKDFGYF--ADPKMANALRR----AAMSPGGFSTGAVTEENFQ 415

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                   G    V  GK     +EK     DR    P  
Sbjct: 416 PK----ATGESHRVTRGKAPKVTMEKGPSNLDRAAALPTF 451



 Score = 89.1 bits (220), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 33/87 (37%), Positives = 45/87 (51%), Gaps = 7/87 (8%)

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA--- 224
            +RT+D  DV    + + I  V RSFL  QIR+ V  LK  G G W   +L++ALQ+   
Sbjct: 477 TVRTVDRLDVVRQDDEVLIWFVGRSFLRHQIRNMVSVLKAAGHGLWNDLELQQALQSGFE 536

Query: 225 ----QDRKECGPLAPPEGLYFDSVEYS 247
               + ++E  P AP  GL    VEY 
Sbjct: 537 PSRHRFKRERFPTAPAYGLTLWDVEYP 563


>gi|294621110|ref|ZP_06700301.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
 gi|291599346|gb|EFF30372.1| tRNA pseudouridine synthase A [Enterococcus faecium U0317]
          Length = 73

 Score =  100 bits (249), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 35/72 (48%)

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +VN   + +        FL+  IR  VG+L  +G+G+     +   +  +DR   GP A 
Sbjct: 2   EVNETKDELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPTAH 61

Query: 236 PEGLYFDSVEYS 247
           PEGLY   V+Y 
Sbjct: 62  PEGLYLYEVKYE 73


>gi|242223970|ref|XP_002477524.1| predicted protein [Postia placenta Mad-698-R]
 gi|220722803|gb|EED77277.1| predicted protein [Postia placenta Mad-698-R]
          Length = 407

 Score =  100 bits (249), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 55/279 (19%), Positives = 85/279 (30%), Gaps = 62/279 (22%)

Query: 19  QRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Q      +I+G +  A+  V             V +  A RTD+GVHA   V    L+  
Sbjct: 1   QPDPKLRTIEGVLFNALVKVGAVSQDNADDPIKVNLGRAARTDAGVHAAGNVVSMKLITA 60

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY--------------- 114
              V    +     ++   I + N+  V   F+A      R Y Y               
Sbjct: 61  IPGVGDLIS-RVNEELPPEIRLWNVLRVQNSFNA----RTRKYTYFFPSYLMIPPKPGSG 115

Query: 115 ---------------RIITRQAP-----LALEKGRAWLIPKSLDCENMRIAAQHLVGRHD 154
                                AP       L + R + +P     E +R A++   G H+
Sbjct: 116 LFQIAQQNDGNELKHIFWNSPAPEATWQDDLRRKRQYRMPPE-QVEALRAASRKFEGSHN 174

Query: 155 FTTFRS-IHCQASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
           F  F         S +R I   +     V      + +    +SF+  Q R  + +L L 
Sbjct: 175 FHNFTVGRDFGDRSCMRHIKSVEIADPVVYGGTEWVSVLFHGQSFMLHQ-RKMMSALVLA 233

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
                    +E+      R    P  P  GL     EY 
Sbjct: 234 CRTGSPPQTIEEM--YGPRTVFIPKMPALGLLL---EYP 267


>gi|71749392|ref|XP_828035.1| tRNA pseudouridine synthase A-like protein [Trypanosoma brucei
           TREU927]
 gi|70833419|gb|EAN78923.1| tRNA pseudouridine synthase A-like protein [Trypanosoma brucei]
          Length = 579

 Score =  100 bits (249), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 97/280 (34%), Gaps = 60/280 (21%)

Query: 2   IRYCMIIEYNGSGYFGW----QRQK----------------------------------- 22
            RY + ++Y G+ + GW     RQ                                    
Sbjct: 176 TRYRVDVQYQGNDFDGWWKSTTRQLFRREVGLDGSITRVPVAEPGTIGNAAGVSRGETMG 235

Query: 23  ---NGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVREW---VPVIL 75
              +  ++   +E+A+ +      V V      + GV   R   H D+          ++
Sbjct: 236 SRYHARTV---LEEALAVALDVNTVRVVAGVIPEVGVSVRRLCCHVDVPSHIELQPRTVI 292

Query: 76  CKALNAYLKISDTISILNLSIV-DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
            +A     K    ++IL+     ++ FHAR S +RR Y+YRI+ R AP   + G  W + 
Sbjct: 293 QRATMWMEKRQQPLAILSYRRCKNQDFHARHSGLRRVYVYRILNRVAPPLFDAGLQWHVD 352

Query: 135 KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFL 194
           + LD + M+  A+ L G  DF  F     + ++ +R        S G      V   +F 
Sbjct: 353 RHLDVDRMKRFAKTLEGTKDFGYF--ADPKMANALRR----AAMSPGGFSTGAVTEENFQ 406

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                   G    V  GK     +EK     DR    P  
Sbjct: 407 PK----ATGESHRVTRGKAPKVTMEKGPSNLDRAAALPTF 442



 Score = 89.1 bits (220), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 33/87 (37%), Positives = 45/87 (51%), Gaps = 7/87 (8%)

Query: 168 PIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA--- 224
            +RT+D  DV    + + I  V RSFL  QIR+ V  LK  G G W   +L++ALQ+   
Sbjct: 468 TVRTVDRLDVVRQDDEVLIWFVGRSFLRHQIRNMVSVLKAAGHGLWNDLELQQALQSGFE 527

Query: 225 ----QDRKECGPLAPPEGLYFDSVEYS 247
               + ++E  P AP  GL    VEY 
Sbjct: 528 PSRHRFKRERFPTAPAYGLTLWDVEYP 554


>gi|108743218|dbj|BAE95388.1| pseudouridine synthase [Saccharomyces bayanus]
          Length = 202

 Score =   99 bits (248), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 37/153 (24%), Positives = 54/153 (35%), Gaps = 22/153 (14%)

Query: 75  LCKALNAYLKISDTISILNLS-IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
             + LN  L   D I I  +       F ARFS   R Y Y                   
Sbjct: 4   YVQILNQLL--PDDIRISAVCLRPPPGFDARFSCTNRHYKYV----------------FN 45

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTIDHFDVNSFGN-LIEIRVVA 190
            K LD   M  AA + +G +DF  F  +    Q ++  R+I    +    +      +V 
Sbjct: 46  GKHLDITKMSKAASYFLGENDFRNFCKLDGSKQLTNFKRSIVSAKILPVSDTFYCFDLVG 105

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +FL  Q+R  +  L LVG        + + L 
Sbjct: 106 SAFLWHQVRCMMAILFLVGQTHEEPEIVLRLLD 138


>gi|312374395|gb|EFR21957.1| hypothetical protein AND_15974 [Anopheles darlingi]
          Length = 163

 Score =   99 bits (248), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 42/135 (31%), Positives = 66/135 (48%), Gaps = 14/135 (10%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-------Q-KNGSSIQGSIEKAIFLVTG-EIVVVHGAGRT 51
           M RY + + Y G+ + G QR       Q K+  ++QG IE+A+  +       +  + RT
Sbjct: 1   MNRYLINLSYIGTRFRGIQRKIDKAAGQFKDPHTVQGVIEEALLRLRPVNEPTLKLSSRT 60

Query: 52  DSGVHALRQVAHFDLVR----EWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFS 106
           D+GVHAL    H DL R     +    + + +N   +     + I++   V   FHAR S
Sbjct: 61  DTGVHALHNTVHVDLQRPNGKPYDEDRITQTINRACERDGHALRIISTIRVPDTFHARLS 120

Query: 107 AIRRSYLYRIITRQA 121
           A  R+YLYR+   +A
Sbjct: 121 AKSRTYLYRLAVLKA 135


>gi|221057031|ref|XP_002259653.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
 gi|193809725|emb|CAQ40427.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
          Length = 573

 Score = 99.5 bits (247), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 28/118 (23%), Positives = 51/118 (43%), Gaps = 6/118 (5%)

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSI-----HCQASSPIRTIDHFDVNS-FGNLIEIRVV 189
             D E M+  ++  +G+H+F  F          +  +P   I + +++    N+ +  + 
Sbjct: 442 PCDIEKMKECSKLFIGQHNFEFFCGTLKGTEKERKVNPFCNIYYLELHELRSNIYQFVIQ 501

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
              FL+  IR  VG+L  VG G     D++ AL  +   +    AP +GL    V + 
Sbjct: 502 GDRFLYHMIRIIVGTLLQVGVGLLQYQDVQDALHFRKPLKVKLCAPAQGLCLAKVLFP 559



 Score = 83.7 bits (206), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 59/185 (31%), Gaps = 52/185 (28%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN----------------------------GSSIQGSIEK 33
               ++++Y+G+ Y GW   +N                              ++Q +I  
Sbjct: 103 TNILLVVDYDGTNYSGWTGVENCSDIYLRATRNYKNEITGKKKITKGDSKYDTVQNTILN 162

Query: 34  AIFLVTG----------------EIVVVHGAGRTDSGVHALRQVAHFDLVREWVP----- 72
            +  + G                +     G  RTD GVHA   V  +    +  P     
Sbjct: 163 CLLQIHGYGYQVKREEEDMKSNLKAFEFIGVSRTDKGVHAKEYVCQYVSYEKPPPCDGNL 222

Query: 73  VILCKALNAYLKISDTISILNLSIVD-KQFHARFSAIRRSYLYRIITRQAPLALEKGRAW 131
             +  ALN  L     I IL +       F+ RF+ + + Y Y    R     LE+  AW
Sbjct: 223 HKIKMALNGLLN--KDIRILGVLNAPFPDFNVRFNNLGKIYTYNFDIRIPSQPLERNYAW 280

Query: 132 LIPKS 136
            +   
Sbjct: 281 QLYDD 285


>gi|239735631|gb|ACS12725.1| MIP10620p [Drosophila melanogaster]
          Length = 341

 Score = 98.7 bits (245), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 53/213 (24%), Positives = 82/213 (38%), Gaps = 27/213 (12%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGV 55
            +++ Y G+ Y+G QR     +I+  + KA+              +I     A RTD GV
Sbjct: 130 AILLSYCGANYYGMQRNPGMQTIEEELFKAMLKHKWITEDSFEQIQISCFQRAARTDKGV 189

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
            A RQV    L  E       +A NA L     I +  +  V K F+A+     R+Y Y 
Sbjct: 190 SAARQVCSVKLPEELD----LEAFNADL--PQQIRLFGVERVTKGFNAKDQCNARTYTYT 243

Query: 116 IITRQAPLALEK----GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH-------CQ 164
           + T       EK       + I   L  + ++   +   GR   TT  +           
Sbjct: 244 LPTVAFAPFEEKVDDVHDTFRISPEL-LQKVKETLKLYEGRRTSTTSPARKAFWILRPSA 302

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQ 197
           +S P+R   H  V    NL  +R+  R+   T+
Sbjct: 303 SSCPLRAASHSGVPRTSNLSHLRLRVRALCCTR 335


>gi|225459791|ref|XP_002284797.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 558

 Score = 98.4 bits (244), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 34/125 (27%), Positives = 50/125 (40%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +   Y G GY G Q+     +I+G +E+A+F             +      + RTD
Sbjct: 39  RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFFSGAVPEQDRGHPKRFDWARSARTD 98

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P  L + LN+ L     I I     V   F+A+    RR Y
Sbjct: 99  KGVSAVGQVVSGRF--YIDPPGLVERLNSNL--PPQIRIFGFKRVTASFNAKKFCDRRRY 154

Query: 113 LYRII 117
           +Y I 
Sbjct: 155 VYLIP 159



 Score = 69.5 bits (169), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/114 (31%), Positives = 47/114 (41%), Gaps = 7/114 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFD----VNSFG-NLIEIRVVARSF 193
           E       H VG H+F  F   I  +  S  R I  FD    V   G   ++  VV +SF
Sbjct: 366 ERFNRILGHYVGTHNFHNFTTRIKAEDPSAQRFIVSFDGNTIVTVEGIEFVKCEVVGQSF 425

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  QIR  +G    +       + LE AL  +D     P AP  GLY D   +S
Sbjct: 426 MLHQIRKMIGLAVAIMRNVAPESLLETALL-KDVNINVPTAPEVGLYLDECFFS 478


>gi|147780612|emb|CAN69118.1| hypothetical protein VITISV_031845 [Vitis vinifera]
          Length = 559

 Score = 98.4 bits (244), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 34/125 (27%), Positives = 50/125 (40%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +   Y G GY G Q+     +I+G +E+A+F             +      + RTD
Sbjct: 27  RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFFSGAVPEQDRGHPKRFDWARSARTD 86

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P  L + LN+ L     I I     V   F+A+    RR Y
Sbjct: 87  KGVSAVGQVVSGRF--YIDPPGLVERLNSNL--PPQIRIFGFKRVTASFNAKKFCDRRRY 142

Query: 113 LYRII 117
           +Y I 
Sbjct: 143 VYLIP 147



 Score = 69.5 bits (169), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/114 (31%), Positives = 47/114 (41%), Gaps = 7/114 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFD----VNSFG-NLIEIRVVARSF 193
           E       H VG H+F  F   I  +  S  R I  FD    V   G   ++  VV +SF
Sbjct: 367 ERFNRILGHYVGTHNFHNFTTRIKAEDPSAQRFIVSFDGNTIVTVEGIEFVKCEVVGQSF 426

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  QIR  +G    +       + LE AL  +D     P AP  GLY D   +S
Sbjct: 427 MLHQIRKMIGLAVAIMRNVAPESLLETALL-KDVNINVPTAPEVGLYLDECFFS 479


>gi|124506245|ref|XP_001351720.1| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|23504649|emb|CAD51527.1| tRNA pseudouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 681

 Score = 98.0 bits (243), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 30/115 (26%), Positives = 46/115 (40%), Gaps = 6/115 (5%)

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSI-----HCQASSPIRTIDHFDVNS-FGNLIEIRVV 189
             D   ++  A+  +G H+F  FR         +  +   TI   DV     NL +  + 
Sbjct: 550 PCDINKIKECAKLFIGHHNFECFRGTLKGTEKLRKINTFCTIHFLDVYELKNNLYQFVIQ 609

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
              FL+  IR  VG+L  VG G     D+  AL      +    AP +GL  + +
Sbjct: 610 GDRFLYHMIRIIVGTLVQVGVGLLNVEDVRDALHLCKPLKVKLCAPSQGLCLNKI 664



 Score = 73.7 bits (180), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/213 (18%), Positives = 61/213 (28%), Gaps = 80/213 (37%)

Query: 2   IRYCMIIEYNGSGYFGWQ-----------------------RQKNGS-----SIQGSIEK 33
               +I+ Y+G+ Y GW                        RQKN       ++Q +I  
Sbjct: 106 TNLLLIVNYDGTNYNGWTGLENSSEVYLNALQNYKNKKKTERQKNIERKKYSTVQNNILD 165

Query: 34  AIFLVTG--------------------------------------------EIVVVHGAG 49
            I  + G                                            +     G  
Sbjct: 166 CILKLHGYKYIHNNNNNEHICNSYKVGDTDNYNNAHHNDYNQNNVNGIINNKPFEFIGVS 225

Query: 50  RTDSGVHALRQVAHFDLVREWVP-----VILCKALNAYLKISDTISILNLSIVD-KQFHA 103
           RTD GVHA   +  +    +  P       + ++LN+ L     I IL +       F+ 
Sbjct: 226 RTDKGVHAKEYICQYISYEKEPPCDGDMEHIKRSLNSLLN--KDIKILAVLKSPHDHFNI 283

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
           RF    + Y Y +  R     LE+  AW +   
Sbjct: 284 RFHNSGKIYTYNLDIRNPSQPLERNYAWQLYDD 316


>gi|108743226|dbj|BAE95392.1| pseudouridine synthase [Saccharomyces bayanus]
          Length = 215

 Score = 98.0 bits (243), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 38/153 (24%), Positives = 54/153 (35%), Gaps = 22/153 (14%)

Query: 75  LCKALNAYLKISDTISILNLS-IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
             + LN  L   D I I  +       F ARFS  RR Y Y                   
Sbjct: 4   YVQILNQLL--PDDIRISAVCLRPPPGFDARFSCTRRHYKYV----------------FN 45

Query: 134 PKSLDCENMRIAAQHLVGRHDFTTFRSIH--CQASSPIRTIDHFDVNSFGN-LIEIRVVA 190
            + LD   M  AA + +G +DF  F  +    Q +   RTI   ++    +      +V 
Sbjct: 46  GRHLDITKMSKAASYFLGENDFRNFCKLDGSKQLTKFKRTIVSAEILPVSDTFYCFDLVG 105

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
            +FL  Q+R  +  L LVG        +   L 
Sbjct: 106 SAFLWHQVRCMMAILFLVGQTHEEPEIVLCLLD 138


>gi|115750989|ref|XP_001203430.1| PREDICTED: similar to FKSG32, partial [Strongylocentrotus
           purpuratus]
 gi|115923548|ref|XP_794710.2| PREDICTED: similar to FKSG32, partial [Strongylocentrotus
           purpuratus]
          Length = 224

 Score = 98.0 bits (243), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 37/182 (20%), Positives = 59/182 (32%), Gaps = 47/182 (25%)

Query: 4   YCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q++  ++++  + +A+       + +       GRTD GV A 
Sbjct: 65  VALKITYLGWDYHGFVVQEDSNNTVEHHLFEALTKTKLIESRQTSNYSRCGRTDKGVSAF 124

Query: 59  RQVAHFDLVREW--------------------VPVILCKALNAYLKISDTISILNLSIVD 98
            QV   DL                            +   L     +   I ++  +  +
Sbjct: 125 GQVIAIDLRTNLLQGVGVIQRLDGTAHERTGNTTEEINYPLMLNRVLPSEIRVIAWTPAE 184

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
             FHA      R+Y Y                      LD + M  A+Q LVG  DF  F
Sbjct: 185 PSFHA------RTYKYFFPAG----------------DLDTKLMNEASQKLVGTFDFRNF 222

Query: 159 RS 160
             
Sbjct: 223 CK 224


>gi|41615123|ref|NP_963621.1| hypothetical protein NEQ333 [Nanoarchaeum equitans Kin4-M]
 gi|42559722|sp|P60354|TRUA_NANEQ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|40068847|gb|AAR39182.1| NEQ333 [Nanoarchaeum equitans Kin4-M]
          Length = 209

 Score = 98.0 bits (243), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 77/207 (37%), Gaps = 36/207 (17%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            RTD  V A     + ++ +                +   + +L    ++K        +
Sbjct: 25  SRTDKYVSARENYFYGNIPK---------------VLPKNVILLGEEPINK-------VL 62

Query: 109 RRSYLYRI----------ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
            + Y Y +             +    + +     +    + + M+ AA+H +G+ DFT F
Sbjct: 63  SKEYKYFLPKDKAIEQISYLHKVGNIIVRKTKIKVKGLPNLDLMKEAAKHFIGKKDFTNF 122

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
            +I  +A +P+ TI  FD+    +     +V   FL+  +R  +  +  VG   +    +
Sbjct: 123 -TIEREAKNPLCTIIKFDIEERKDYYVFSIVGDRFLYHMVRKIISFIVSVGYKIYPLEYI 181

Query: 219 EKALQAQDRKECGPL-APPEGLYFDSV 244
           +     ++R    P  A P+ L+   +
Sbjct: 182 DLVF--KERLNPKPKDADPKFLWLWKI 206


>gi|326482502|gb|EGE06512.1| pseudouridylate synthase [Trichophyton equinum CBS 127.97]
          Length = 440

 Score = 97.6 bits (242), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 51/275 (18%), Positives = 71/275 (25%), Gaps = 107/275 (38%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-----SSIQGSIEKAIFL--------------------- 37
             +   Y G  Y G     NG      +I+  + KA+                       
Sbjct: 93  IAIKFAYLGKRYNGL-EHANGNYTEVPTIEEELWKALRKTRLIFPTHKNCTEEFSGKDNS 151

Query: 38  ------VTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVI----------------- 74
                 +  +       GRTD GV A  QV    +                         
Sbjct: 152 PSRPYEIHWDGCQYSKCGRTDKGVSAFGQVIGIRVRSLRPADPNPSADLKGGDVMDSVVA 211

Query: 75  -------------------------------LCKALNAYLKISDTISILNLSI-VDKQFH 102
                                            + LN  L   + I +L     +   F 
Sbjct: 212 TESGMADKNTQNGVSDTGAAKGWDDIADELPYIQILNGAL--PEDIRVLAWCPHLPPDFD 269

Query: 103 ARFSAIRRSYLYRIITRQAPLA-----------------LEKGRAWLIPKSLDCENMRIA 145
           ARFS  +R Y Y                           L + R       LD E MR A
Sbjct: 270 ARFSCRQRRYRYFFTQPAFCPTPGARGIVRSPELKDDLSLARPREGW----LDIEAMREA 325

Query: 146 AQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVN 178
           AQ+ VG HDF  F  +    Q ++ +R I   D+ 
Sbjct: 326 AQYFVGSHDFRNFCKVDTSKQITNFVRRILRADIE 360


>gi|167948001|ref|ZP_02535075.1| tRNA pseudouridine synthase A [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 67

 Score = 97.6 bits (242), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 38/65 (58%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +I I V A +FLH  +R+  G L  +G GK   +  E+ LQ +DR++ G  APP GLY  
Sbjct: 1   MIAIEVHANAFLHHMVRNLAGVLMAIGQGKQEVSWAEEILQLRDRRKGGVTAPPHGLYLT 60

Query: 243 SVEYS 247
            V+Y 
Sbjct: 61  KVDYP 65


>gi|70941666|ref|XP_741093.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56519252|emb|CAH76348.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 493

 Score = 97.6 bits (242), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 27/116 (23%), Positives = 46/116 (39%), Gaps = 6/116 (5%)

Query: 138 DCENMRIAAQHLVGRHDFTTFRSI-----HCQASSPIRTIDHFDVNS-FGNLIEIRVVAR 191
           D + ++  ++  +G H+F  FR         +  +    I   D+     NL +  +   
Sbjct: 364 DIDKIKECSKLFIGYHNFECFRGTVKGTEKQRTINTFCNIHFLDIYKVKDNLYQFIIQGD 423

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            FL+  IR  VG+L  VG G     D++ AL           AP +GL    + + 
Sbjct: 424 RFLYHMIRIIVGALIQVGVGILNIQDVKDALYNCKPLRVKLCAPAQGLCLKKILFP 479



 Score = 77.6 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 62/203 (30%), Gaps = 70/203 (34%)

Query: 2   IRYCMIIEYNGSGYFGWQ------------------------------------------ 19
               ++I+Y+G+ Y GW                                           
Sbjct: 30  TNIILVIDYDGTNYNGWTGIENSSPVYLNAVNGFKNVKNSNICKDTVFEQSEDSETSYNS 89

Query: 20  -RQKNGS---SIQGSIEKAIFLVTG----------------EIVVVHGAGRTDSGVHALR 59
            + KN +   +IQ  I   +  + G                +     G  RTD GVHA  
Sbjct: 90  LKNKNENKYNTIQNCILNCLLKIHGYGENPNSIIDQKENDSKPFEFIGVSRTDKGVHAKE 149

Query: 60  QVAHFDLVREWVP-----VILCKALNAYLKISDTISILNLSIVD-KQFHARFSAIRRSYL 113
            V  +   ++  P       +  +LN  L     I +L +       F+ RF  + + Y 
Sbjct: 150 YVCQYISYKKLPPFNGNLEKIKLSLNRLLN--KDIKVLGVFNAPFNSFNVRFHNLGKIYT 207

Query: 114 YRIITRQAPLALEKGRAWLIPKS 136
           Y I  R+    LEK  +W +   
Sbjct: 208 YNIDLRKPSQPLEKNFSWQLYDD 230


>gi|169806638|ref|XP_001828063.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
 gi|161779191|gb|EDQ31215.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
          Length = 347

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 56/294 (19%), Positives = 100/294 (34%), Gaps = 55/294 (18%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGR 50
           M R    +  Y G  Y G Q     ++++  +   +  +         + + + +  A R
Sbjct: 1   MKRKIAFLWGYCGITYSGIQFNNEINTLEKKLIDILCKLQYISEKNAESAQKIKMKSASR 60

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GV A+        + + +   + + L      +  I + N++ V K F    SA  R
Sbjct: 61  TDKGVSAIFN-VTICKINQELTENINQILKNEFSKAGFI-LYNIARVPKTFIPYRSARSR 118

Query: 111 SYLYRIITRQAPLALEKGRAW------------------LIPKSLD-----------CEN 141
            Y Y I        L K  A                       + D            + 
Sbjct: 119 EYKYFIPIG----VLNKNIAKSQIDIMQSSENYNISIEKFKHDTFDWLNKSTSNTQIIDK 174

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHT 196
           +        G HDF  F + + Q  + IR I H   NS         +E+ +   SF+  
Sbjct: 175 LNFILNLFHGNHDFHNFTTQNVQG-TTIRYIKHIYANSIKKINGIEYVEVFLHGDSFIMH 233

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEK---ALQAQDRKECGPLAPPEGLYFDSVEYS 247
           QIR  +     +      +T +E+    + +++     P AP E LY  ++ + 
Sbjct: 234 QIRKMIAFAIFMCRNYDDNTIIEQYYNIIFSKN-NYYIPKAPSEYLYLYNIHFD 286


>gi|217074404|gb|ACJ85562.1| unknown [Medicago truncatula]
          Length = 530

 Score = 96.8 bits (240), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 33/137 (24%), Positives = 49/137 (35%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +   Y G GY G Q+     +I+G +E+A++             +      + RTD
Sbjct: 54  RKVAIFFAYCGVGYQGMQKNPGAKTIEGELEEALYVSGAVPEQDRGLSKRYDWARSARTD 113

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P      LN+ L     I I     V   F A+    RR Y
Sbjct: 114 KGVSAVGQVVSGRF--YIDPPGFVDRLNSNL--PSQIRIFGFKRVTASFSAKKFCDRRRY 169

Query: 113 LYRIITRQAPLALEKGR 129
           +Y I          + R
Sbjct: 170 VYLIPVFALDPCCHRDR 186



 Score = 77.9 bits (191), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/113 (29%), Positives = 47/113 (41%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFD-----VNSFGNLIEIRVVARSF 193
           E      +  VG H+F  F   I  +  S  R I  FD     V      ++  +V +SF
Sbjct: 329 ERFNNILKCYVGTHNFHNFTTRIKPEDPSAKRFIISFDASTTVVVEGMEFVKCEIVGQSF 388

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    +       + +EKALQ +D     P AP  GLY D   +
Sbjct: 389 MLHQIRKMMGLAVAIMRNCAPESLIEKALQ-KDVSITVPTAPEVGLYLDECFF 440


>gi|269862152|ref|XP_002650725.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
 gi|220065712|gb|EED43331.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
          Length = 319

 Score = 96.8 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 72/254 (28%), Gaps = 69/254 (27%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALR 59
            +  + I Y+G  Y G Q+  NG SI   +E A+    +  E   +   GRTD GV A  
Sbjct: 65  RKIALKIAYDGRVYHGVQKDPNGLSIGEVLENALRSTDLYIESNDIVFCGRTDRGVSAAN 124

Query: 60  QVAHFDL-------------------------------------------VREWVPVILC 76
            +    +                                           +++     L 
Sbjct: 125 MIISLKIKSILETYSANPNYHRHIETETYDTYQFNKKEYKRYLLNNSDFEIKKHDAKELP 184

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
             L     +   I +   + V   F AR +  +R Y Y       P  L           
Sbjct: 185 YDLILNKVLPPQIRVKGWAPVPWNFSARHNCCQRRYTYFFTC---PPQLLPKY------- 234

Query: 137 LDCENMRIAAQHLVGRHDFTTFR---SIHCQASSPIRTIDHFDVNSFGNLIE-----IRV 188
                 + A + +    DF  F     +       +  ++   +  + + I+     + +
Sbjct: 235 ------QEAGRIIYKTEDFYNFCTHSKVDANYKFKLSMLEFVSITPYPSQIQKFLCAMNI 288

Query: 189 VARSFLHTQIRSFV 202
            A SF     R   
Sbjct: 289 SAYSFPPNMGRKIF 302


>gi|303389002|ref|XP_003072734.1| pseudouridine synthase 2 [Encephalitozoon intestinalis ATCC 50506]
 gi|303301876|gb|ADM11374.1| pseudouridine synthase 2 [Encephalitozoon intestinalis ATCC 50506]
          Length = 345

 Score = 96.4 bits (239), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 79/245 (32%), Gaps = 47/245 (19%)

Query: 2   IRYC--MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGR 50
           ++    +++ Y+GS Y G Q  K   +++  I   +  +           + V +  + R
Sbjct: 1   MKVRAGLLVGYDGSKYHGLQFNKELDTVEKEIIGCLLEMEVISQRNADDPKKVHIKSSSR 60

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GVHA   +    +  +  P  L   L   L   + I + ++  + K       A+ R
Sbjct: 61  TDKGVHAALNLVSVKIEADITPE-LISGLRTLLSRKE-IHLYDIIRLTKSTIPSKQAVFR 118

Query: 111 SYLYRII----------------------------TRQAPLALEKGRAWLIPKSLDCENM 142
           +Y Y +                             TR  P  +            D    
Sbjct: 119 AYEYIVPTFFLAKGDFDKEVEVLRQKDGECRDGRVTRDYPSDMIDSLVGYTSSEDDLRVF 178

Query: 143 RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQ 197
               Q   G  DF  F  ++ +     R I    V+          + + +  +SFL  Q
Sbjct: 179 EAILQKYTGTKDFHNFTKLNSE-KGTKRYIKSVIVSDPYVNNGIEYVRVSITGQSFLLHQ 237

Query: 198 IRSFV 202
           IR  +
Sbjct: 238 IRKMM 242


>gi|83317781|ref|XP_731310.1| tRNA-pseudouridine synthase I [Plasmodium yoelii yoelii str. 17XNL]
 gi|23491305|gb|EAA22875.1| tRNA-pseudouridine synthase I [Plasmodium yoelii yoelii]
          Length = 497

 Score = 95.7 bits (237), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 28/116 (24%), Positives = 49/116 (42%), Gaps = 6/116 (5%)

Query: 138 DCENMRIAAQHLVGRHDFTTFR-----SIHCQASSPIRTIDHFDVNS-FGNLIEIRVVAR 191
           D + ++  ++  +G H+F  FR     +   +  +    I   D+     NL +  +   
Sbjct: 368 DIDKIKECSKLFIGYHNFECFRGILKGTEKQRTINTFCNIHFLDIYKLKDNLYQFIIQGD 427

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            FL+  IR  VG+L  VG G     D++ AL      +    APP+GL    + + 
Sbjct: 428 RFLYHMIRIIVGTLIQVGVGILNFQDVKDALYNSKPLKVKLCAPPQGLCLKKILFP 483



 Score = 75.2 bits (184), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 33/198 (16%), Positives = 59/198 (29%), Gaps = 65/198 (32%)

Query: 2   IRYCMIIEYNGSGYFGWQ------------------------RQKN-------------- 23
               ++I+Y+G+ Y GW                            N              
Sbjct: 28  TNLILVIDYDGTNYKGWTGIENSSSVYLNAVSGFKNIKRSDNYNANIIEKVEDSDYSFNN 87

Query: 24  ----GSSIQGSIEKAIFLVTG---------------EIVVVHGAGRTDSGVHALRQVAHF 64
                 ++Q  I   +  + G               +     G  RTD GVHA   V  +
Sbjct: 88  LTKKYETVQNCILNCLLKIHGYGENININNYKETNLKPFEFIGVSRTDKGVHAKEYVCQY 147

Query: 65  DLVREWVPV-----ILCKALNAYLKISDTISILNLSIVD-KQFHARFSAIRRSYLYRIIT 118
              ++  P       +  +LN  L     I +L +       F+ R+  + + Y Y +  
Sbjct: 148 ISYKKLPPFNGNLKKIKLSLNRLLN--KDIKVLGIFNAPFNNFNVRYHNLGKIYTYNVDL 205

Query: 119 RQAPLALEKGRAWLIPKS 136
           R+    LE+  +W +   
Sbjct: 206 RKPSQPLERNLSWQLYDD 223


>gi|299469782|emb|CBN76636.1| tRNA Pseudouridine Synthase [Ectocarpus siliculosus]
          Length = 677

 Score = 95.7 bits (237), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 36/126 (28%), Positives = 52/126 (41%), Gaps = 12/126 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           +  ++I Y G+ Y G Q  K   +I+  +E A++L              V    AGRTD 
Sbjct: 192 KVALLISYWGNNYQGLQINKGARTIEAELELALYLAGTISKDNFGNPRKVSWSRAGRTDK 251

Query: 54  GVHALRQVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           GVHA  QV    L           + +N YL   D I  +++    K F +R     R Y
Sbjct: 252 GVHAAAQVISVKLTYLNDGERETVEKINKYL--PDDIRAVDIRRAPKSFDSRTRCSGRRY 309

Query: 113 LYRIIT 118
            Y + T
Sbjct: 310 EYIMPT 315



 Score = 62.9 bits (152), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 25/115 (21%), Positives = 44/115 (38%), Gaps = 8/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDVN-----SFGNLIEIRVVARS 192
            E++R   +  +G  ++  + +      +S  R I  F  +          I + V  +S
Sbjct: 502 LEDLRETLKGFLGTKNYHNYTNHKKATDASCKRLITSFTASDPFEHEGMEWIRLTVGGQS 561

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  V S      G+    D  K+   +       +AP +GLY +   Y 
Sbjct: 562 FIMHQIRKMVASTVDRVRGQSNPEDFTKSFLPEKINLG--IAPSDGLYLERPLYE 614


>gi|326493306|dbj|BAJ85114.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 221

 Score = 95.3 bits (236), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 43/208 (20%), Positives = 69/208 (33%), Gaps = 28/208 (13%)

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
             ++  P  +  ++N      D I  L +S V ++FH  FSA  R YLY     +    +
Sbjct: 5   WRKDIQPGDIKDSINE--AAPDKIKSLVVSEVSREFHPNFSAKWRRYLYIFPLDEDAKPI 62

Query: 126 ---------EKGRAWLIPKSLDCENMRIAAQHLVGR--------HDFTTFRSIHCQAS-- 166
                     +   +   +S D   +    + L G+         D    RS    A   
Sbjct: 63  SGDELSSMILENPEYKASRSFDVAKVDKIIRQLEGKMLSYKIFARDTQASRSDGPAAECF 122

Query: 167 -----SPIRTIDHFD--VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
                + +  +   D        ++ I +VA  FL   +R  V +             L 
Sbjct: 123 MFHSRAAVTKLYSADENCKEGATVMCIELVANRFLRKMVRVLVATTIREAAAGANEDALL 182

Query: 220 KALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + A  R+   P AP EGL    V Y 
Sbjct: 183 NLMDATCRRATAPPAPAEGLCLVDVGYE 210


>gi|302806719|ref|XP_002985091.1| hypothetical protein SELMODRAFT_44317 [Selaginella moellendorffii]
 gi|300147301|gb|EFJ13966.1| hypothetical protein SELMODRAFT_44317 [Selaginella moellendorffii]
          Length = 363

 Score = 95.3 bits (236), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 35/135 (25%), Positives = 54/135 (40%), Gaps = 13/135 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  + + Y+G GY G QR K   +I+G +E+A+F               +    A RTD
Sbjct: 1   RKIAIFVSYSGYGYQGMQRNKGCKTIEGDLEEALFKAGAIAESTFGDPRKIDWARAARTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P    + +N++L     I +L  + V   F A+    RR Y
Sbjct: 61  KGVSAAGQVVSGRF--FVDPPGFVERVNSHL--PKQIRVLGFTRVTGTFSAKNLCDRRRY 116

Query: 113 LYRIITRQAPLALEK 127
            Y +       A  +
Sbjct: 117 EYVLPVFALDPASHR 131



 Score = 68.7 bits (167), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 29/113 (25%), Positives = 45/113 (39%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
             +    Q+ VG   F  F   +  +  S  R I  ++            +   V+ +SF
Sbjct: 193 AKLTKILQNYVGTRYFHNFTCRVKPEDPSTQRYITSYEAGEVFTIQGCKFVRCTVIGQSF 252

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    V  G    T  E+A + +D K   P+AP  GL+ D   Y
Sbjct: 253 MLHQIRKMIGLAVAVMRGDAPETIFERAFR-RDTKIGVPMAPELGLFLDECLY 304


>gi|302809155|ref|XP_002986271.1| hypothetical protein SELMODRAFT_44320 [Selaginella moellendorffii]
 gi|300146130|gb|EFJ12802.1| hypothetical protein SELMODRAFT_44320 [Selaginella moellendorffii]
          Length = 363

 Score = 95.3 bits (236), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 35/135 (25%), Positives = 54/135 (40%), Gaps = 13/135 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  + + Y+G GY G QR K   +I+G +E+A+F               +    A RTD
Sbjct: 1   RKIAIFVSYSGYGYQGMQRNKGCKTIEGDLEEALFKAGAIAESTFGDPRKIDWARAARTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P    + +N++L     I +L  + V   F A+    RR Y
Sbjct: 61  KGVSAAGQVVSGRF--FVDPPGFVERVNSHL--PKQIRVLGFTRVTGTFSAKNLCDRRRY 116

Query: 113 LYRIITRQAPLALEK 127
            Y +       A  +
Sbjct: 117 EYVLPVFALDPASHR 131



 Score = 68.7 bits (167), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 29/113 (25%), Positives = 45/113 (39%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
             +    Q+ VG   F  F   +  +  S  R I  ++            +   V+ +SF
Sbjct: 193 AKLTKILQNYVGTRYFHNFTCRVKPEDPSTQRYITSYEAGEVFTIQGCKFVRCTVIGQSF 252

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    V  G    T  E+A + +D K   P+AP  GL+ D   Y
Sbjct: 253 MLHQIRKMIGLAVAVMRGDAPETIFERAFR-RDTKIGVPMAPELGLFLDECLY 304


>gi|303285768|ref|XP_003062174.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456585|gb|EEH53886.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 554

 Score = 95.3 bits (236), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 59/342 (17%), Positives = 101/342 (29%), Gaps = 99/342 (28%)

Query: 4   YCMIIEYNGSGYFGWQR-----------------------------QKNGSSIQGSIEKA 34
           Y   + Y G  + GW                                    S+  ++++A
Sbjct: 205 YKAAVAYYGPAFAGWAWLPSDGATDALFRAPDDERGGGAGGGGAEWTPGAHSVVATMQRA 264

Query: 35  IFLVT--GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN------------ 80
           +  +    +   +  AGRTD GV AL Q   F  + +  P  +  A+N            
Sbjct: 265 LNPLFAGDKERPIQCAGRTDKGVSALAQTVSFWTLNDLDPAEIVAAVNEGSPAGRAGALR 324

Query: 81  ----------------AYLKISDTI-------SILNLSI-VDKQFHARFSAIRRSYLYRI 116
                              ++   I        + +    V ++FHA F+A  R Y+Y +
Sbjct: 325 VPSFQSPPSTPFNSASDAFQLHPDIRSYGTTLRVTSAPEKVTERFHATFAATWRRYVYIL 384

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTIDHF 175
              +      K         +D   +    + L G+  D T F     Q       +   
Sbjct: 385 PINRIDRIDGKTGDGDESYDVDPSAVDAMLRKLSGKTVDATAFARDTPQGKPSSCRVKVA 444

Query: 176 DV--------------------------NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVG 209
                                       ++   +  + +VA  FL  Q+R  V +     
Sbjct: 445 RAFLSRVPSSVGDGDEEIRDEDETPTNPSTHQPVCVVELVADRFLRKQVRVLVATAAREA 504

Query: 210 DGKWTSTDLEKALQ----AQDRKEC-GPLAPPEGLYFDSVEY 246
           +   TS  L    +    A++R+    P AP  GL F  V Y
Sbjct: 505 NCGATSDVLLALSRAGGSARERRMATAPPAPAVGLVFAGVGY 546


>gi|258574223|ref|XP_002541293.1| hypothetical protein UREG_00807 [Uncinocarpus reesii 1704]
 gi|237901559|gb|EEP75960.1| hypothetical protein UREG_00807 [Uncinocarpus reesii 1704]
          Length = 578

 Score = 94.9 bits (235), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 40/187 (21%), Positives = 63/187 (33%), Gaps = 24/187 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTD 52
            +  +++ Y+G+GY G Q      +I+G I  A+           +  +        RTD
Sbjct: 108 RKVAVLLGYSGTGYHGMQMSTKERTIEGEIFPALVAAGAISKANAMDPKKSSFVRCARTD 167

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        L K +N  L  S  I I  +   +K F        R Y
Sbjct: 168 KGVHAAGNVISLKL--IIEDPDLVKKVNDIL--SPQIRIWGIEPTNKGFSCYQFCDSRIY 223

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T               P +   + ++ AA+      D    R    +  +    I
Sbjct: 224 EYLIPTHCFIPP--------HPSTFLAKKLQEAAEK---EGDLEAHRKRQEEVLTYWEDI 272

Query: 173 DHFDVNS 179
           D+  +  
Sbjct: 273 DNEYIKP 279



 Score = 44.8 bits (105), Expect = 0.011,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 36/103 (34%), Gaps = 8/103 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +  RA+ IP       ++      VG  +F  +      +  S  R I  F ++     
Sbjct: 343 FKAKRAYRIP-PARLARVQEVLDLYVGTRNFHNYTIQKTFRDPSAKRVIKSFKISKDPII 401

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
                 + ++V  +SF+  QIR  V    L+         + +
Sbjct: 402 IGGTEWLSLKVHGQSFMMHQIRKMVAMAALIVRCGSDPQLIAQ 444


>gi|86139957|ref|ZP_01058522.1| tRNA pseudouridine synthase [Roseobacter sp. MED193]
 gi|85823375|gb|EAQ43585.1| tRNA pseudouridine synthase [Roseobacter sp. MED193]
          Length = 113

 Score = 94.9 bits (235), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 41/103 (39%), Positives = 61/103 (59%), Gaps = 4/103 (3%)

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF----GNLI 184
               +P  L    MR  A+HL+G++ FTTFRS  CQA SP++ +D  ++       G  +
Sbjct: 3   HVLRVPPELYVAAMRNGARHLLGKYYFTTFRSRICQAKSPVKALDALEIEEVEGLAGPEL 62

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
              + ARS L+ Q+RS VG+L+ VG G WT  D++ AL+ +DR
Sbjct: 63  RFHLSARSLLYNQVRSIVGTLERVGAGSWTPEDVKTALETRDR 105


>gi|320094550|ref|ZP_08026316.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178
          str. F0338]
 gi|319978465|gb|EFW10042.1| tRNA pseudouridine synthase A [Actinomyces sp. oral taxon 178
          str. F0338]
          Length = 94

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 25/66 (37%), Positives = 38/66 (57%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
          +R  + + Y+G+ + GW  Q    ++QG +E  +  +  + V    AGRTD+GVHA  QV
Sbjct: 16 VRVRIDLAYDGTRFHGWAAQPGLRTVQGELEAVLSTLVRQPVATTVAGRTDAGVHARHQV 75

Query: 62 AHFDLV 67
          AH DL 
Sbjct: 76 AHVDLP 81


>gi|330924858|ref|XP_003300809.1| hypothetical protein PTT_12161 [Pyrenophora teres f. teres 0-1]
 gi|311324870|gb|EFQ91095.1| hypothetical protein PTT_12161 [Pyrenophora teres f. teres 0-1]
          Length = 631

 Score = 94.5 bits (234), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 72/207 (34%), Gaps = 26/207 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTD 52
            +  ++I Y+G+GY G Q      +I+G +  A            V  + V +    RTD
Sbjct: 107 RKVAVMIGYSGTGYKGMQIDNKQKTIEGDLFNAFVAAGAISKANAVDPKKVSLVRCARTD 166

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +N++L   D I +  +      F    +   R Y
Sbjct: 167 KGVHAAGNVVSLKL--IIEDEDIVDKINSHLT--DQIRVWGIQRTVGSFSCYQACDSRWY 222

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T               P S   + +   A+     +D   +R+   + ++    +
Sbjct: 223 EYLIPTHSFLPP--------HPSSFLGKKLEEFAEK---ENDLEGYRARQAEVANFWPEV 271

Query: 173 DHFDVNSFGNLIEIRVV--ARSFLHTQ 197
           +   +    + ++  +    +  L+  
Sbjct: 272 EEKHIKPILDSLDDSIRPLVQEALYNM 298



 Score = 49.4 bits (117), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/111 (20%), Positives = 38/111 (34%), Gaps = 9/111 (8%)

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVARS 192
             ++ A  + +G H +  +         S  R I  F V            + ++V  +S
Sbjct: 420 ARVQAALDNYLGTHRYHNYTVHKKYNDKSAQRYIKSFQVAPKPIIINDTEWLSLKVHGQS 479

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           F+  QIR  VG   L          +E +    +     P AP  GL  + 
Sbjct: 480 FMMHQIRKMVGMAALTVRCGTNPKIMEDSF--GNNVVRIPKAPGLGLLLER 528


>gi|331244832|ref|XP_003335055.1| hypothetical protein PGTG_16662 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
 gi|309314045|gb|EFP90636.1| hypothetical protein PGTG_16662 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
          Length = 547

 Score = 94.5 bits (234), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 58/353 (16%), Positives = 89/353 (25%), Gaps = 123/353 (34%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVHAL 58
           I Y G GY G Q      +I+G++  A                 V +  A RTD+ V A 
Sbjct: 2   IGYYGRGYQGSQINPGTKTIEGTLFNAFVRAGCITQDNSTHPNKVGLQRAARTDANVSAC 61

Query: 59  RQVAHFDLVREWVP--------------------------------VILCKALNAYLKIS 86
             +    L+                                       L K +N +L   
Sbjct: 62  CNLISLKLILNPPEIGQDKRMDQVEEEGQEDALHRSLIEQHSQTSYYPLIKHINRFL--P 119

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA------------LEKGRA---- 130
             + I  +  V   F+ R     R Y Y + T                  L + R     
Sbjct: 120 SDMKIWEIIRVQNSFNPRSFCDSRVYEYSLPTWLFLPPKPGSPLHQRLMKLNQNRIKKTG 179

Query: 131 ---------------WLIPKS----------------------LDCENMRIAAQHLVGRH 153
                          W    S                      +    ++       G H
Sbjct: 180 EEEEDAEKEEDPEANWWNDHSNLLEKDFKSIQAERRGSYRISQMMIARIKSVLDQFRGTH 239

Query: 154 DFTTFRSIHC-QASSPIRTIDHFDVNSFG------------------------NLIEIRV 188
           +F            + +R +  F V+                             I I  
Sbjct: 240 NFHNLTVGKAFTERNAVRIMKDFTVSEPFLVGGSDPTNPKDDDDHQPLENPPTEWISITF 299

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +SF+  QIR  +G L LV   +   + +++      RK   P AP  GL  
Sbjct: 300 HGQSFMLHQIRKMIGLLVLVCRTRTPVSIIKQL--YGPRKVSIPKAPGIGLIL 350


>gi|300175270|emb|CBK20581.2| unnamed protein product [Blastocystis hominis]
          Length = 310

 Score = 94.5 bits (234), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 78/256 (30%), Gaps = 65/256 (25%)

Query: 15  YFGWQRQKNGSSIQGSIEKAIFLVTG-EIVVVH--------GAGRTDSGVHALRQVAHFD 65
           Y G Q      S++  +   +F++   E   V            RTD GV A   V    
Sbjct: 12  YSGMQVNDTRQSVEDKLVDCLFMLDKIEPWNVIKSSKFDWERCSRTDKGVSARSIVVSGK 71

Query: 66  L-------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           L              +  + LN  L   + I + + + V K F+   +   R+Y Y +  
Sbjct: 72  LMDYDDEFDSSMQNQLAVEQLNQLL--PEDIRVFSYTRVSKSFNPHLNTHTRTYSYYL-- 127

Query: 119 RQAPLALEKGRAWLIPKS--------LDCENMRIAAQHLVGRHDFTTFR----------- 159
                 L++ ++     S        +D    + A    +G H    +            
Sbjct: 128 -----PLDQYQSSHYAPSRIIELGVHIDTAKFQKALSVFLGTHSMKNYSGSIQYSLLSCS 182

Query: 160 -------------SIHCQASSPIRTIDHFD--------VNSFGNLIEIRVVARSFLHTQI 198
                        +  C+  S    + HF                + + +   SFL+ QI
Sbjct: 183 CDYFVVIEIRISVNSTCEPCSCYFHLCHFSNHIAATPLTIGNERYLHVLLNGNSFLYHQI 242

Query: 199 RSFVGSLKLVGDGKWT 214
           R  +G    V  G W+
Sbjct: 243 RKMIGGAVAVSCGSWS 258


>gi|2446915|dbj|BAA22474.1| tRNA pseudouridine synthase I [Synechococcus elongatus PCC 6301]
          Length = 81

 Score = 94.5 bits (234), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 33/67 (49%), Positives = 41/67 (61%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  ++I+Y G G+ GWQRQ    S+QG +E AI  V G  V V  AGRTD+GVH   QV
Sbjct: 15 QRIALVIQYLGQGFCGWQRQPRQRSVQGELESAIAAVVGHPVSVQSAGRTDTGVHRAAQV 74

Query: 62 AHFDLVR 68
          AHF+   
Sbjct: 75 AHFETTS 81


>gi|189209550|ref|XP_001941107.1| tRNA pseudouridine synthase 1 [Pyrenophora tritici-repentis
           Pt-1C-BFP]
 gi|187977200|gb|EDU43826.1| tRNA pseudouridine synthase 1 [Pyrenophora tritici-repentis
           Pt-1C-BFP]
          Length = 595

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 72/207 (34%), Gaps = 26/207 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTD 52
            +  ++I Y+G+GY G Q      +I+G +  A            V  + V +    RTD
Sbjct: 98  RKVAVMIGYSGTGYKGMQIDNKQKTIEGDLFNAFVAAGAISKANAVDPKKVSLVRCARTD 157

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +N++L   D I +  +      F    +   R Y
Sbjct: 158 KGVHAAGNVVSLKL--IIEDEDIVDKINSHLT--DQIRVWGIQRTVGSFSCYQACDSRWY 213

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T               P S   + +   A+     +D   +R+   + ++    +
Sbjct: 214 EYLIPTHSFLPP--------HPSSFLGKKLEEFAEK---ENDLEGYRARQAEVANFWPEV 262

Query: 173 DHFDVNSFGNLIEIRVV--ARSFLHTQ 197
           +   +    + ++  +    +  L+  
Sbjct: 263 EEKHIKPILDSLDDSIRPLVQEALYNM 289



 Score = 52.5 bits (125), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 23/111 (20%), Positives = 39/111 (35%), Gaps = 9/111 (8%)

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVARS 192
             ++ A  + +G H +  +         S  R I  F V            + ++V  +S
Sbjct: 411 ARVQAALNNYLGTHRYHNYTVHKKYNDKSAQRYIKSFQVAPKPIIINDTEWLSLKVHGQS 470

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           F+  QIR  VG   L          +E++    +     P AP  GL  + 
Sbjct: 471 FMMHQIRKMVGMAALTVRCGTNPEIMEESF--GNNVVRIPKAPGLGLLLER 519


>gi|18394855|ref|NP_564112.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|9558589|gb|AAF88152.1|AC026234_3 Contains similarity to a pseudouridine synthase 1 from Homo sapiens
           gi|4455035 and contains tRNA pseudoridine synthase
           PF|01416 domain. ESTs gb|T76494, gb|W43440 come from
           this gene [Arabidopsis thaliana]
 gi|14334544|gb|AAK59680.1| unknown protein [Arabidopsis thaliana]
 gi|16323470|gb|AAL15229.1| unknown protein [Arabidopsis thaliana]
 gi|332191845|gb|AEE29966.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 549

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  ++  + G GY G Q+     +I+G +E+A+F                    + RTD
Sbjct: 58  RKVAIVFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPDADRNKPRNYEWARSARTD 117

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P    + LN+ L   D I +     V   F ++    RR Y
Sbjct: 118 KGVSAVGQVVSGRF--YVDPPGFVERLNSKL--PDQIRVFGYKRVAPSFSSKKFCDRRRY 173

Query: 113 LYRII 117
           +Y I 
Sbjct: 174 VYLIP 178



 Score = 65.6 bits (159), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 29/114 (25%), Positives = 51/114 (44%), Gaps = 9/114 (7%)

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFDVNSF-----GNLIEIRVVARS 192
           E       + VG H+F  F +   +A+ P   R I  F+ N+       + ++  VV +S
Sbjct: 319 ERFNRILSYYVGSHNFHNF-TTRTKAADPAANRYILSFNANTVINLDGKDFVKCEVVGQS 377

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           F+  QIR  +G    +       + +E + + +D +   P+AP  GLY D   +
Sbjct: 378 FMLHQIRKMIGLAVAIMRNYAPESLIEASFK-KDVRINVPMAPEVGLYLDECFF 430


>gi|195370371|ref|XP_002045883.1| GM20625 [Drosophila sechellia]
 gi|194121623|gb|EDW43666.1| GM20625 [Drosophila sechellia]
          Length = 248

 Score = 93.7 bits (232), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 45/199 (22%), Positives = 69/199 (34%), Gaps = 38/199 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
             + I Y G  Y G+  Q++ + +I+ ++ +A+              H  GRTD  V A 
Sbjct: 50  VLLKITYFGWDYQGFACQEDSNDTIESNLFRALTRTCLIESRATSNYHRCGRTDKEVSAF 109

Query: 59  RQVAHFDLVREWVPVI------------LCKALNAYLKISDTI-SILNLSIVDKQFHARF 105
            QV   DL  +  P               C  LN  L     I  +  + +    + ARF
Sbjct: 110 CQVISIDLRSKHPPESQLDPTSLSSEIDYCGLLNRVL--PKNIQCVAWMPLRSSVYSARF 167

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS--IHC 163
             + RSY Y                +     LD   MR A   LV   DF  F    +H 
Sbjct: 168 DCVSRSYRY----------------FFPKGDLDIAAMRKACDLLVRHADFRNFCKMDVHN 211

Query: 164 QASSPIRTIDHFDVNSFGN 182
             ++ +R +    V +   
Sbjct: 212 GVTNYMRNLQSARVEACDE 230


>gi|310791388|gb|EFQ26915.1| tRNA pseudouridine synthase A [Glomerella graminicola M1.001]
          Length = 614

 Score = 93.7 bits (232), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 66/199 (33%), Gaps = 24/199 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTD 52
            +  +++ Y+G+GY G Q      +I+G + K      AI        +   +    RTD
Sbjct: 124 RKVAVMVGYSGTGYKGMQINNEEKTIEGDLFKAFVAAGAISKANADDHKKSSLVRCARTD 183

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +NA L   + I +  +   +  F    +   R Y
Sbjct: 184 KGVHAAGNVISLKL--IIEDEDIVDKINANL--PEQIRVWGIQRTNNSFSCYQTCDSRWY 239

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y + T             L P   D    +   +    +  +  F+          R +
Sbjct: 240 EYLLPT----------YCLLPPHP-DSWLWKQLVEVAKEKGYYEEFQKKLADVEGYWREV 288

Query: 173 DHFDVNSFGNLIEIRVVAR 191
           D  D+      ++    A+
Sbjct: 289 DEKDIKPILERLDPETRAK 307



 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/109 (22%), Positives = 38/109 (34%), Gaps = 9/109 (8%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVN------SFGNLIEIRVVARSFL 194
           ++ A     G  +F  +      +  S  R I  F VN           + ++V  +SF+
Sbjct: 402 LQAALSEYCGTINFHNYTVQKSFKDPSAKRHIKSFQVNTQPIQIRDTEWVSLKVHGQSFM 461

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             QIR  VG   LV         + +       +   P AP  GL  + 
Sbjct: 462 MHQIRKMVGMASLVVRCATPLERIRQ--SYGPTRIAIPKAPGLGLLLER 508


>gi|307136307|gb|ADN34131.1| tRNA pseudouridine synthase family protein [Cucumis melo subsp.
           melo]
          Length = 519

 Score = 93.7 bits (232), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 34/137 (24%), Positives = 51/137 (37%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  +   Y G GY G Q+     +I+  +E+A++L            +      + RTD
Sbjct: 55  RKVAIFFAYCGVGYQGMQKNPGAKTIEADLEEALYLAGAVPEQDRGLSKRYDWARSARTD 114

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P      LN+ L  S  I I     V   F+A+    RR Y
Sbjct: 115 KGVSAVGQVVSGRF--YIDPPGFVDRLNSNL--SPQIRIFGYKRVTASFNAKKFCDRRRY 170

Query: 113 LYRIITRQAPLALEKGR 129
           +Y I          + R
Sbjct: 171 VYLIPVFALDPNCHRDR 187



 Score = 73.7 bits (180), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/110 (29%), Positives = 45/110 (40%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFD-----VNSFGNLIEIRVVARSF 193
                  +H VG H+F  F      +  +  R I  FD     V      ++  VV +SF
Sbjct: 325 ARFNRILKHYVGTHNFHNFTTRTKAEDPAARRFIVSFDASTTVVVEGIEFVKCEVVGQSF 384

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  +G    +       + +EKALQ +D     P AP  GLY D 
Sbjct: 385 MLHQIRKMMGLAVAIMRNCAPESLIEKALQ-KDVNINVPTAPEVGLYLDE 433


>gi|325068064|ref|ZP_08126737.1| tRNA pseudouridine synthase A [Actinomyces oris K20]
          Length = 89

 Score = 93.4 bits (231), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 4/87 (4%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
          M R  + + Y+G+ + GW  Q    +++G +  A+ +V  E V +  AGRTD+GVHA  Q
Sbjct: 7  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTSALAIVLREPVRLTVAGRTDAGVHAAAQ 66

Query: 61 VAHFDLVREWVPVILCKALNAYLKISD 87
          V H D+     P           ++ +
Sbjct: 67 VVHLDV----SPEAWAALPGRSERLPE 89


>gi|297850446|ref|XP_002893104.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297338946|gb|EFH69363.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 557

 Score = 93.4 bits (231), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  ++  + G GY G Q+     +I+G +E+A+F                    + RTD
Sbjct: 58  RKVAIVFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPDADRNKPRNYEWARSARTD 117

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P    + LN+ L   D I +     V   F ++    RR Y
Sbjct: 118 KGVSAVGQVVSGRF--YVDPPGFVERLNSKL--PDQIRVFGYKRVAPSFSSKKLCDRRRY 173

Query: 113 LYRII 117
           +Y I 
Sbjct: 174 VYLIP 178



 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 31/114 (27%), Positives = 51/114 (44%), Gaps = 9/114 (7%)

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFDVNSF-----GNLIEIRVVARS 192
           E       + VG H+F  F +   +A+ P   R I  F+ N+       + ++  VV +S
Sbjct: 317 ERFNRILSYYVGSHNFHNF-TTRTKAADPAANRYILSFNANTVINLDGKDFVKCEVVGQS 375

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           F+  QIR  +G    V       + +E A + +D +   P+AP  GLY D   +
Sbjct: 376 FMLHQIRKMIGLAVAVMRNYAPESLIETAFK-KDVRINVPMAPEVGLYLDECFF 428


>gi|414485|gb|AAD12372.1| Homology to pseudouridine synthetase X02743 [Mycoplasma genitalium]
          Length = 116

 Score = 93.4 bits (231), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 29/117 (24%), Positives = 48/117 (41%), Gaps = 3/117 (2%)

Query: 132 LIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-GNLIEIRVVA 190
            + + LD E ++  A   +G+ +F +F S     +  IRTI    +      L+ +    
Sbjct: 1   QLNQQLDLEKLKADATLFLGKKNFLSFSS--SIHTDSIRTISKITIQKETNQLVRLTFFG 58

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             FL +Q+R  V  L  +   K     + K  +   +  C   AP  GLY  +V Y 
Sbjct: 59  SGFLRSQVRMIVACLVNLNTNKMALETVAKLFEHPKKGSCVVKAPSCGLYLKTVVYE 115


>gi|163783824|ref|ZP_02178806.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880914|gb|EDP74436.1| tRNA pseudouridine synthase A [Hydrogenivirga sp. 128-5-R1-1]
          Length = 64

 Score = 93.4 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 27/61 (44%), Positives = 38/61 (62%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + I Y G+ Y GWQRQ    +IQ  IE  + ++    V ++ +GRTD+GVHAL QVA
Sbjct: 4  NYKLTISYLGTNYHGWQRQPKHITIQQVIEDNLKVLVKHPVKLYASGRTDAGVHALGQVA 63

Query: 63 H 63
          +
Sbjct: 64 N 64


>gi|223998991|ref|XP_002289168.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
 gi|220974376|gb|EED92705.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
          Length = 469

 Score = 93.4 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 51/267 (19%), Positives = 78/267 (29%), Gaps = 75/267 (28%)

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D+G +A   +       +W    + +AL+  L     I    +   D+ F AR     ++
Sbjct: 202 DTG-NANDNIQRKTYTDQW---KIRRALSTRLPPDIVIRSTWIWNGDEAFEARQRISCKT 257

Query: 112 YLYRI-----------------------ITRQAPLALEK----GRAWLIPKSLDCENMRI 144
           Y+Y +                       I    P  L +       W  P  LD   +  
Sbjct: 258 YVYHLRFRSLTYCSPSTTNNDDTSQLHPICHAGPHLLRRISDQNNVWSSPWPLDPSLLPT 317

Query: 145 AAQHLVGRHDFTTF--------------RSIHCQASSPIRTIDHFDVNSFGNLIE----- 185
           A Q  VG HDF  F              R+   +  S    +  F V+   +  E     
Sbjct: 318 ACQLFVGVHDFGNFIHKDDRRGGSTRGKRNATDREKSHSIDLFQFTVDLQLDQYEDRSIP 377

Query: 186 ------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL-----QAQDR------- 227
                   + A+ F    +R+ VG +  V  G     D+   L       + R       
Sbjct: 378 PIYDAKFTLKAKGFHRQMVRNLVGFVVDVARGLRLLEDIPMLLTGNAGDEKTRIGDAISS 437

Query: 228 -------KECGPLAPPEGLYFDSVEYS 247
                        AP  GL    VEY 
Sbjct: 438 SIIDASLPSLVNAAPACGLCLAKVEYE 464



 Score = 51.0 bits (121), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 4/52 (7%)

Query: 20  RQKNGS-SIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALRQVAHFDLV 67
           +Q     ++Q  +E A+   TG     + V GAGRTD GVHA  QV  FD+ 
Sbjct: 103 KQNKAPITVQQQLETALHQWTGLSIATLRVRGAGRTDKGVHASGQVVGFDVP 154



 Score = 36.0 bits (82), Expect = 4.4,   Method: Composition-based stats.
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 4  YCMIIEYNGSGYFGWQRQ 21
          + + IEYNG  Y G+QRQ
Sbjct: 17 FVLTIEYNGFAYAGFQRQ 34


>gi|326773999|ref|ZP_08233281.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
 gi|326636138|gb|EGE37042.1| tRNA pseudouridine synthase A [Actinomyces viscosus C505]
          Length = 113

 Score = 93.4 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 28/97 (28%), Positives = 47/97 (48%), Gaps = 4/97 (4%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
          M R  + + Y+G+ + GW  Q    +++G +  A+  V  E V +  AGRTD+GVHA  Q
Sbjct: 7  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTSALATVLREPVRLTVAGRTDAGVHAAAQ 66

Query: 61 VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV 97
          VAH D+     P           ++ +   +  ++ V
Sbjct: 67 VAHLDV----SPEAWAALPGRSQRLPEAALLTRVAGV 99


>gi|308805336|ref|XP_003079980.1| Pseudouridylate synthase (ISS) [Ostreococcus tauri]
 gi|116058437|emb|CAL53626.1| Pseudouridylate synthase (ISS) [Ostreococcus tauri]
          Length = 409

 Score = 93.4 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 90/295 (30%), Gaps = 57/295 (19%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS----------SIQGSIEKAIFLVTGEIVVVHGAGRTDS 53
           +     Y G  + G+    +            S+  S++ A+  +T +      +GRTD 
Sbjct: 114 FAFRCAYRGVAFAGYAWNADVDGEKEWAFGEASVSASLQWALRDITDKGRPTPSSGRTDR 173

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKIS---DTISILNLSIVDKQFHARFSAIRR 110
           GV A      F      V     + L            + +  +  V   FHA FSA RR
Sbjct: 174 GVSAGASCVSFWTRHPEVTSERIERLVNEESAPGKAGVLRVSEIREVPSSFHATFSAFRR 233

Query: 111 SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV---GRHDFTTFRSIHCQASS 167
            Y+Y +   Q     E+         LD   M    Q L    G  D   F        S
Sbjct: 234 RYVYVLPKTQK-FGEERTPCAH----LDGATMNRILQPLAEVDGPIDMHAFARGTPPGRS 288

Query: 168 P----------------------------IRTIDHFDVN-------SFGNLIEIRVVARS 192
                                         R+    D+           +++ I + A  
Sbjct: 289 SEVNFSVARAFDARLPRVALDDPDTHAGIRRSRRDVDITVSDSAAAEDLDVVVIELEADR 348

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDL-EKALQAQDRKECGPLAPPEGLYFDSVEY 246
           FL    R  V +      G  +S D+  +  +A+DR+   P AP  GL      Y
Sbjct: 349 FLRKLARCLVATAAREAAGPPSSDDVLLRIARARDRRLAAPPAPALGLVLAGASY 403


>gi|255539108|ref|XP_002510619.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223551320|gb|EEF52806.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 584

 Score = 93.0 bits (230), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 35/137 (25%), Positives = 52/137 (37%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +   Y G GY G Q+     +I+G +E+A+F             +      + RTD
Sbjct: 54  RKMAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVPEQDRGCPKRYDWARSARTD 113

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P  L   LN+ L     I I     V   F+A+    RR Y
Sbjct: 114 KGVSAVGQVISGRF--YVDPPGLVDRLNSIL--PSQIRIFGYKRVTASFNAKKFCDRRRY 169

Query: 113 LYRIITRQAPLALEKGR 129
           +Y I       +  + R
Sbjct: 170 VYLIPVFALDPSSHRDR 186



 Score = 72.2 bits (176), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 30/113 (26%), Positives = 45/113 (39%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-----SFGNLIEIRVVARSF 193
           E      ++ VG H+F  F      +  S  R I  FD            ++  V+ +SF
Sbjct: 356 EKFNRILKYYVGSHNFHNFTTRTKAEDPSAQRYIISFDARTTVTVEGIEFVKCEVIGQSF 415

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    +       + +  ALQ +D K   P AP  GLY D   +
Sbjct: 416 MLHQIRKMIGLAVAIMRNCAPESLISTALQ-KDVKINVPTAPEVGLYLDECFF 467


>gi|307107300|gb|EFN55543.1| hypothetical protein CHLNCDRAFT_133992 [Chlorella variabilis]
          Length = 593

 Score = 93.0 bits (230), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 32/122 (26%), Positives = 49/122 (40%), Gaps = 10/122 (8%)

Query: 135 KSLDCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVNSFG-------NLIEI 186
           ++LD   M+ AA   +G HDF  F  +   Q ++  R +    V            L+++
Sbjct: 284 EALDVGRMQEAAAFFLGEHDFRNFCKVDVAQVTNFRRRVLDCRVEELPACAWGGRRLLQL 343

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFDSV 244
            +   +FL  Q+R     L +VG G+     +   L  Q   RK    LA  E L   S 
Sbjct: 344 HIRGTAFLWHQVRCMAAVLLMVGRGEEPPGIVATLLDPQQVPRKPQYTLASEEPLLLYSC 403

Query: 245 EY 246
            Y
Sbjct: 404 AY 405



 Score = 88.7 bits (219), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 40/142 (28%), Positives = 55/142 (38%), Gaps = 21/142 (14%)

Query: 2   IRY-CMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFL-------VTGEIVVVHGAGRTD 52
            RY  + + Y G  Y G+ RQ++   +I+G +  A+          + + +     GRTD
Sbjct: 78  QRYVALELLYLGHAYGGFARQEHTEQTIEGHLFAALRTTRLVPAEASWQELRYSRGGRTD 137

Query: 53  SGVHALRQVAHFDL----------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFH 102
            GV AL QV    L              V +     LN  L     I +L  + V   F 
Sbjct: 138 KGVSALGQVVALLLRSAARTGEVQPEADVELDYPSLLNRVL--PQDIRVLGWADVPDDFS 195

Query: 103 ARFSAIRRSYLYRIITRQAPLA 124
           ARFSA  R Y Y I  R     
Sbjct: 196 ARFSAQYREYKYLIAYRPPTPP 217


>gi|164661239|ref|XP_001731742.1| hypothetical protein MGL_1010 [Malassezia globosa CBS 7966]
 gi|159105643|gb|EDP44528.1| hypothetical protein MGL_1010 [Malassezia globosa CBS 7966]
          Length = 226

 Score = 92.6 bits (229), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 38/142 (26%), Positives = 53/142 (37%), Gaps = 17/142 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTD 52
            +  +   Y G+ Y G Q      +I+G I +A            V    V +  A RTD
Sbjct: 77  RKVALFFGYCGTDYSGLQVNPGVKTIEGDIFEAFCRAGAVSKENAVNPNKVQLQRAARTD 136

Query: 53  SGVHALRQVAHFDL----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
            GVHA   +    L            L   +N+ L   D I I  +  V   F+AR S  
Sbjct: 137 RGVHAAGNLLTLKLILDPPNLPPNQTLTTYVNSLL--PDQIRIWGMRRVQSAFNARTSCD 194

Query: 109 RRSYLYRIITRQA--PLALEKG 128
            R Y Y + T     P A+E+ 
Sbjct: 195 SRLYEYLLPTYVFLPPKAMERN 216


>gi|302844654|ref|XP_002953867.1| hypothetical protein VOLCADRAFT_94649 [Volvox carteri f.
           nagariensis]
 gi|300260975|gb|EFJ45191.1| hypothetical protein VOLCADRAFT_94649 [Volvox carteri f.
           nagariensis]
          Length = 709

 Score = 92.6 bits (229), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 44/213 (20%), Positives = 68/213 (31%), Gaps = 49/213 (23%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLV---------TGEIVVVHGA 48
           M R   +  Y+G+GYFG QRQ +     +++  +E+A+                V     
Sbjct: 1   MQRVAFVCGYDGAGYFGLQRQPDNTGRPTVEQELERALVAAGALQARHAGALHKVNWSRT 60

Query: 49  GRTDSGVHALRQVAHFDLVR-------------------------EWVPVILCKALNAYL 83
            RTD GV A   V   D+                                 L   +NA L
Sbjct: 61  SRTDKGVSAAANVVSLDIPSGAAAAAAAANAAGGRGNSGGGGGGAAADLTPLVNLVNAAL 120

Query: 84  KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
                + +   +     F AR +A  R Y Y +       +L           L+ + + 
Sbjct: 121 --PSAVKVWTATRPGPNFEARRAAYGRRYEYLVPVWALDPSLT---------PLELKRLN 169

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPI-RTIDHF 175
           +  +  VG H F  F S        + RTI   
Sbjct: 170 LILEVFVGSHCFHNFTSEPADDPRELRRTIHRA 202



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 20/62 (32%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ-AQDRKECGPLAPPEGLYF 241
            + I  V   FL  QIR  VG    V         +  AL  A+      P APP GL  
Sbjct: 437 YVRIVFVGCGFLMHQIRRMVGLALAVARRTAPPDCMRTALDPARPFLITVPTAPPTGLIM 496

Query: 242 DS 243
           D 
Sbjct: 497 DR 498


>gi|320033682|gb|EFW15629.1| tRNA pseudouridine synthase [Coccidioides posadasii str. Silveira]
          Length = 597

 Score = 92.6 bits (229), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 39/187 (20%), Positives = 62/187 (33%), Gaps = 24/187 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTD 52
            +  +++ Y+G+GY G Q      +I+G I  A+           +  +        RTD
Sbjct: 114 RKVAVLLGYSGTGYHGMQMSAKEKTIEGEIFPALVAAGAISKANAMDPKKSSFVRCARTD 173

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        L   +N  L  S  I I  +   +K F        R Y
Sbjct: 174 KGVHAAGNVISLKL--IIEDPDLVNKVNNIL--SPQIRIWGIEPTNKGFSCYQFCDSRIY 229

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T               P +   + +  AA+      D   ++    +  S    +
Sbjct: 230 EYLIPTHCFLPP--------HPSTFLAKKLLEAAEK---EGDIGDYKKRQEEVLSYWEDV 278

Query: 173 DHFDVNS 179
           DH  +  
Sbjct: 279 DHEYIRP 285



 Score = 51.0 bits (121), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 45/126 (35%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +  +A+ I        ++      +G  +F  +      + +S  R I  F+++     
Sbjct: 362 FKAKKAYRIH-PARLARVQEVLDLYIGTRNFHNYTIQKTFRDASARRVIKSFNISKDPII 420

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    LV         + +      +K   P AP  
Sbjct: 421 IDGTEWLSLKVHGQSFMMHQIRKMVAMAALVVRCGTDPQRITQ--SYGPQKIPIPKAPGL 478

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 479 GLLLER 484


>gi|303312455|ref|XP_003066239.1| tRNA pseudouridine synthase, putative [Coccidioides posadasii C735
           delta SOWgp]
 gi|240105901|gb|EER24094.1| tRNA pseudouridine synthase, putative [Coccidioides posadasii C735
           delta SOWgp]
          Length = 597

 Score = 92.6 bits (229), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 39/187 (20%), Positives = 62/187 (33%), Gaps = 24/187 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTD 52
            +  +++ Y+G+GY G Q      +I+G I  A+           +  +        RTD
Sbjct: 114 RKVAVLLGYSGTGYHGMQMSAKEKTIEGEIFPALVAAGAISKANAMDPKKSSFVRCARTD 173

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        L   +N  L  S  I I  +   +K F        R Y
Sbjct: 174 KGVHAAGNVISLKL--IIEDPDLVNKVNNIL--SPQIRIWGIEPTNKGFSCYQFCDSRIY 229

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T               P +   + +  AA+      D   ++    +  S    +
Sbjct: 230 EYLIPTHCFLPP--------HPSTFLAKKLLEAAEK---EGDIGDYKKRQEEVLSYWEDV 278

Query: 173 DHFDVNS 179
           DH  +  
Sbjct: 279 DHEYIRP 285



 Score = 51.0 bits (121), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 45/126 (35%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +  +A+ I        ++      +G  +F  +      + +S  R I  F+++     
Sbjct: 362 FKAKKAYRIH-PARLARVQEVLDLYIGTRNFHNYTIQKTFRDASARRVIKSFNISKDPII 420

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    LV         + +      +K   P AP  
Sbjct: 421 IDGTEWLSLKVHGQSFMMHQIRKMVAMAALVVRCGTDPQRITQ--SYGPQKIPIPKAPGL 478

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 479 GLLLER 484


>gi|119192942|ref|XP_001247077.1| tRNA pseudouridine synthase 1, putative [Coccidioides immitis RS]
          Length = 597

 Score = 92.6 bits (229), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 39/187 (20%), Positives = 62/187 (33%), Gaps = 24/187 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTD 52
            +  +++ Y+G+GY G Q      +I+G I  A+           +  +        RTD
Sbjct: 114 RKVAVLLGYSGTGYHGMQMSAKEKTIEGEIFPALVAAGAISKANAMDPKKSSFVRCARTD 173

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        L   +N  L  S  I I  +   +K F        R Y
Sbjct: 174 KGVHAAGNVISLKL--IIEDPDLVNKVNNIL--SPQIRIWGIEPTNKGFSCYQFCDSRIY 229

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T               P +   + +  AA+      D   ++    +  S    +
Sbjct: 230 EYLIPTHCFLPP--------HPSTFLAKKLLEAAEK---EGDIGDYKKRQEEVLSYWEDV 278

Query: 173 DHFDVNS 179
           DH  +  
Sbjct: 279 DHEYIRP 285



 Score = 51.0 bits (121), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 45/126 (35%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +  +A+ I        ++      +G  +F  +      + +S  R I  F+++     
Sbjct: 362 FKAKKAYRIH-PARLARVQEVLDLYIGTRNFHNYTIQKTFRDASARRVIKSFNISKDPII 420

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    LV         + +      +K   P AP  
Sbjct: 421 IDGTEWLSLKVHGQSFMMHQIRKMVAMAALVVRCGTDPQRITQ--SYGPQKIPIPKAPGL 478

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 479 GLLLER 484


>gi|50287019|ref|XP_445939.1| hypothetical protein [Candida glabrata CBS 138]
 gi|74637780|sp|Q6FV05|PUS1_CANGA RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|49525245|emb|CAG58858.1| unnamed protein product [Candida glabrata]
          Length = 549

 Score = 92.6 bits (229), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 32/126 (25%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTG---EIVVVHGAGRTD 52
            +  ++I Y G+GY G Q      +I+ ++ K      AI        +      A RTD
Sbjct: 87  RKVAVMIGYCGTGYHGMQYNPPNPTIEAALFKAFVDAGAISKANSNDLKKNNFMRAARTD 146

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        +   +NA L   + I I ++  V+K F  R     R Y
Sbjct: 147 KGVHAGGNLISLKM--IIEDPEIMDKINANL--PEGIRIWDIERVNKAFDCRKMCSSRWY 202

Query: 113 LYRIIT 118
            Y + T
Sbjct: 203 EYLLPT 208



 Score = 58.7 bits (141), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 25/112 (22%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVA 190
               R A    +G H+F  F      +  S IR +    V+       +    + I++  
Sbjct: 306 LNKFRAAMNQYLGAHNFHNFTLGKEFKDPSAIRFMKEIKVSDPFVIGDAKAEWVSIKIHG 365

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +SF+  QIR  +    L+         + +A   Q  K   P AP  GL  +
Sbjct: 366 QSFMLHQIRKMISMATLIARCGTPVERISQAFGPQ--KINIPKAPALGLLLE 415


>gi|297850452|ref|XP_002893107.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297338949|gb|EFH69366.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 571

 Score = 92.2 bits (228), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 31/123 (25%), Positives = 48/123 (39%), Gaps = 13/123 (10%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSG 54
             ++  + G GY G Q+     +I+G +E+A+F                    + RTD G
Sbjct: 60  VAIVFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPEADRNKPRNYEWARSARTDKG 119

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           V A+ QV          P    + LN+ L   D I +     V   F ++    RR Y+Y
Sbjct: 120 VSAVGQVVSGRF--YVDPPGFVERLNSKL--PDQIRVFGYKRVAPSFSSKKLCDRRRYVY 175

Query: 115 RII 117
            I 
Sbjct: 176 LIP 178



 Score = 67.9 bits (165), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/115 (27%), Positives = 51/115 (44%), Gaps = 9/115 (7%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSP--IRTIDHFDVNSF-----GNLIEIRVVAR 191
            E       + VG H+F  F +   +A+ P   R I  F+ N+       + I+  VV +
Sbjct: 330 MERFNRILSYYVGSHNFHNF-TTRTKAADPAANRYILSFNANTVINLDGKDFIKCEVVGQ 388

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           SF+  QIR  +G    V       + +E A + +D +   P+AP  GLY D   +
Sbjct: 389 SFMLHQIRKMIGLAVAVMRNYAPESLIETAFK-KDVRINVPMAPEVGLYLDECFF 442


>gi|168042339|ref|XP_001773646.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162675034|gb|EDQ61534.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 445

 Score = 92.2 bits (228), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 63/196 (32%), Gaps = 43/196 (21%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  M + Y G+ Y G Q Q+      +I+  +E AIF   G           +    + R
Sbjct: 3   KVAMWLGYVGTRYKGLQIQRGPGSAQTIEEELELAIFKAGGMIESNFGNLSKISWTRSSR 62

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  V    +                A N    +S  I +  ++ V + F AR 
Sbjct: 63  TDKGVHSLCTVISMKMEVPEAAWVNDMDGFALADNINFHLSPFIRVFGITPVTRSFRARH 122

Query: 106 SAIRRSYLYR-------IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
               R+Y Y        I     P  +E+               R       G+H +  +
Sbjct: 123 DCCTRTYDYLLPAAILGIHPDTVPSQVEQR----------VTKFRSLLHLFEGKHAYHNY 172

Query: 159 RSIHCQASSPIRTIDH 174
                     IR +  
Sbjct: 173 ---------TIRRLYR 179



 Score = 56.8 bits (136), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 166 SSPIRTIDHFDV---NSFGN--LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           SS  R +  F+     +FG    I I +   SF+  QIR  +G+   V  G      +  
Sbjct: 259 SSHFRKVISFNCGMPETFGEAQFIRISITGSSFMVHQIRKMIGTAIAVFHGLLPGDVIPI 318

Query: 221 ALQAQDRKECGPLAPPEGLYFD 242
           +L    R    PLAPP+GL   
Sbjct: 319 SLARHSR-IVLPLAPPDGLILV 339


>gi|224085970|ref|XP_002307759.1| predicted protein [Populus trichocarpa]
 gi|222857208|gb|EEE94755.1| predicted protein [Populus trichocarpa]
          Length = 426

 Score = 92.2 bits (228), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 35/137 (25%), Positives = 54/137 (39%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  + + Y G GY G Q+     +I+G +E+A+F             +      + RTD
Sbjct: 1   RKIAIFLTYCGVGYQGMQKNPGAKTIEGDLEEALFHAGAVPEHDRGIPKRYDWARSARTD 60

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P  L + L++ L  S  I I     V   F+A+    RR Y
Sbjct: 61  KGVSAVGQVVSGRF--YIDPPGLVERLHSNL--SPQIRIFGYKRVTGSFNAKKFCDRRRY 116

Query: 113 LYRIITRQAPLALEKGR 129
           +Y I          + R
Sbjct: 117 VYLIPVFALNPCSHRDR 133



 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/113 (24%), Positives = 45/113 (39%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-----SFGNLIEIRVVARSF 193
           E       + +G H+F  F      +  S  R I  FD            ++  VV +SF
Sbjct: 247 ERFNRILNYYLGSHNFHNFTTRTKAEDPSAQRYIISFDAKTTVAVEGIEFVKCEVVGQSF 306

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    +     + + ++ ALQ ++     P AP  GLY D   +
Sbjct: 307 MLHQIRKMIGVAVAIMRNCASESLIQTALQ-KNVNINVPTAPEVGLYLDECFF 358


>gi|297842357|ref|XP_002889060.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297334901|gb|EFH65319.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 458

 Score = 91.8 bits (227), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 33/137 (24%), Positives = 52/137 (37%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTD 52
            +  +I  + G GY G Q+     +I+G +E+A+F        + G         + RTD
Sbjct: 22  QKVAIIFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPESIRGKPKLYDFARSARTD 81

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P      LN+ L   + I I     V   F ++    RR Y
Sbjct: 82  KGVSAVGQVVSGRFNV--DPPGFVDRLNSNL--PNQIRIFGYKHVTPSFSSKKFCDRRRY 137

Query: 113 LYRIITRQAPLALEKGR 129
           +Y +          + R
Sbjct: 138 VYLLPVFALDPISHRDR 154



 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/113 (23%), Positives = 46/113 (40%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNS----FG-NLIEIRVVARSF 193
           E         VG ++F  F         +  R I  F  N+     G + I+  V+ +SF
Sbjct: 274 ERFNRILSCYVGSYNFHNFTTRTKADDPAANRQIISFTANTVINLDGIDFIKCEVLGKSF 333

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    +     + + ++ A  ++D     P+AP  GLY D   +
Sbjct: 334 MLHQIRKMMGLAVAIMRNCASESLIQTAF-SKDVNITVPMAPEVGLYLDECFF 385


>gi|326478893|gb|EGE02903.1| tRNA pseudouridine synthase [Trichophyton equinum CBS 127.97]
          Length = 582

 Score = 91.8 bits (227), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 60/187 (32%), Gaps = 26/187 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A            V  +        RTD 
Sbjct: 100 KVIVMLGYSGTGYHGMQLCPTEKTIEGDLFAAFVAANAISKANAVDPKKSSFVRCARTDK 159

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L     I +  +    K F A      R Y 
Sbjct: 160 GVHAAGNVVSLKL--IIEDPDIVQKINEKLN--PQIRVWGIIPATKGFSAYQFCDSRMYE 215

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTI 172
           Y I +               P +   + M   A+    +H D   FR    +  S     
Sbjct: 216 YLIPSHCFLPP--------HPSTFLAQKMVEMAE----KHGDMEAFRERQAEVESYWEET 263

Query: 173 DHFDVNS 179
           D   +  
Sbjct: 264 DKKHIQP 270



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/128 (21%), Positives = 49/128 (38%), Gaps = 14/128 (10%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +    + IP       +  A    VG  +F  +      +  S  R I  F ++     
Sbjct: 343 FKAKNEYRIPPER-LARINAALALYVGTKNFHNYTIQKTFRDPSARRLIKSFKISRDPVV 401

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAP 235
                 + ++V  +SF+  QIR  V  +  LV  G     D+++  ++ Q+ +   P AP
Sbjct: 402 INGTEWLSLKVHGQSFMMHQIRKMVAMVALLVRCG----ADIKRIEESYQNSRIPIPKAP 457

Query: 236 PEGLYFDS 243
             GL  + 
Sbjct: 458 GLGLLLER 465


>gi|326469581|gb|EGD93590.1| tRNA pseudouridine synthase [Trichophyton tonsurans CBS 112818]
          Length = 582

 Score = 91.8 bits (227), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 39/187 (20%), Positives = 61/187 (32%), Gaps = 26/187 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A            V  +        RTD 
Sbjct: 100 KVIVMLGYSGTGYHGMQLCPTEKTIEGDLFAAFVAANAISKANAVDPKKSSFVRCARTDK 159

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L     I +  +    K F A      R Y 
Sbjct: 160 GVHAAGNVVSLKL--IIEDPDIVQKINEKLN--PQIRVWGIIPATKGFSAYQFCDSRMYE 215

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTI 172
           Y I +               P +   + M   A+    +H D   FR    +  S     
Sbjct: 216 YLIPSHCFLPP--------HPSTFLAQKMVEMAE----KHGDMEAFRERQAEVESYWEET 263

Query: 173 DHFDVNS 179
           D   + S
Sbjct: 264 DKKHIQS 270



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/128 (21%), Positives = 49/128 (38%), Gaps = 14/128 (10%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +    + IP       +  A    VG  +F  +      +  S  R I  F ++     
Sbjct: 343 FKAKNEYRIPPER-LARINAALALYVGTKNFHNYTIQKTFRDPSARRLIKSFKISRDPVV 401

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAP 235
                 + ++V  +SF+  QIR  V  +  LV  G     D+++  ++ Q+ +   P AP
Sbjct: 402 INGTEWLSLKVHGQSFMMHQIRKMVAMVALLVRCG----ADIKRIEESYQNSRIPIPKAP 457

Query: 236 PEGLYFDS 243
             GL  + 
Sbjct: 458 GLGLLLER 465


>gi|42572123|ref|NP_974152.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|332197678|gb|AEE35799.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 356

 Score = 91.8 bits (227), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 33/137 (24%), Positives = 53/137 (38%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTD 52
            +  +I  + G GY G Q+     +I+G +E+A+F        + G         + RTD
Sbjct: 22  QKVAIIFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPESIRGKPKLYDFARSARTD 81

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P+     LN+ L   + I I     V   F ++    RR Y
Sbjct: 82  KGVSAVGQVVSGRF--IVDPLGFVNRLNSNL--PNQIRIFGYKHVTPSFSSKKFCDRRRY 137

Query: 113 LYRIITRQAPLALEKGR 129
           +Y +          + R
Sbjct: 138 VYLLPVFALDPISHRDR 154



 Score = 42.5 bits (99), Expect = 0.051,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 6/89 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNS----FG-NLIEIRVVARSF 193
           E         VG ++F  F         +  R I  F  N+     G + I+  V+ +SF
Sbjct: 266 ERFSRILSCYVGSYNFHNFTTRTKADDPTANRQIISFTANTVINLDGIDFIKCEVLGKSF 325

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           +  QIR  +G    +     + + ++ A 
Sbjct: 326 MLHQIRKMMGLAVAIMRNCASESLIQSAF 354


>gi|18411027|ref|NP_565126.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|6573728|gb|AAF17648.1|AC009978_24 T23E18.5 [Arabidopsis thaliana]
 gi|21592498|gb|AAM64448.1| unknown [Arabidopsis thaliana]
 gi|21703099|gb|AAM74492.1| At1g76120/T23E18_5 [Arabidopsis thaliana]
 gi|23308411|gb|AAN18175.1| At1g76120/T23E18_5 [Arabidopsis thaliana]
 gi|332197677|gb|AEE35798.1| pseudouridine synthase-like protein [Arabidopsis thaliana]
          Length = 463

 Score = 91.8 bits (227), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 33/137 (24%), Positives = 53/137 (38%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG---------AGRTD 52
            +  +I  + G GY G Q+     +I+G +E+A+F        + G         + RTD
Sbjct: 22  QKVAIIFAFCGVGYQGMQKNPGAKTIEGELEEALFHAGAVPESIRGKPKLYDFARSARTD 81

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P+     LN+ L   + I I     V   F ++    RR Y
Sbjct: 82  KGVSAVGQVVSGRF--IVDPLGFVNRLNSNL--PNQIRIFGYKHVTPSFSSKKFCDRRRY 137

Query: 113 LYRIITRQAPLALEKGR 129
           +Y +          + R
Sbjct: 138 VYLLPVFALDPISHRDR 154



 Score = 59.8 bits (144), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/113 (23%), Positives = 46/113 (40%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNS----FG-NLIEIRVVARSF 193
           E         VG ++F  F         +  R I  F  N+     G + I+  V+ +SF
Sbjct: 266 ERFSRILSCYVGSYNFHNFTTRTKADDPTANRQIISFTANTVINLDGIDFIKCEVLGKSF 325

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    +     + + ++ A  ++D     P+AP  GLY D   +
Sbjct: 326 MLHQIRKMMGLAVAIMRNCASESLIQSAF-SKDVNITVPMAPEVGLYLDECFF 377


>gi|299470490|emb|CBN78481.1| pseudouridylate synthase, putative [Ectocarpus siliculosus]
          Length = 743

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 66/189 (34%), Gaps = 35/189 (18%)

Query: 2   IRYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIFLVTG---------EIVVVHGA 48
            +  +++ Y G+ + GWQ+    Q N  +++G +E A++               +     
Sbjct: 29  RKVAIVVGYVGTAFHGWQQSTDAQ-NVRTVEGELETALWKAGAIADSNYGDLNKIGWGRT 87

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILC-------KALNAYLKISDTISILNLSIVDKQF 101
            RTD GVHA + VA   L+                  LN  L   D I   ++S V K F
Sbjct: 88  SRTDKGVHASKTVAAAKLLLPQETFTATGMSQYGKDKLNEKL--PDDIRCFSVSKVPKSF 145

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
             R     R Y Y +               L+P        R   +  VG H F  + S 
Sbjct: 146 RGREECTLREYTYYLPRE------------LLPDDEALGKFRELLKLFVGTHSFHNYAST 193

Query: 162 HCQASSPIR 170
             +    +R
Sbjct: 194 KGRQLKEVR 202



 Score = 55.2 bits (132), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I +  ++F++ QIR  +G       G   S  +E AL+    K   PLAP EGL 
Sbjct: 448 DEFVRIDIRGKAFVYNQIRLMIGGALGEARGDLWSGFVEAALKTP-YKLRVPLAPAEGLV 506

Query: 241 FD 242
            +
Sbjct: 507 LE 508


>gi|327303396|ref|XP_003236390.1| tRNA pseudouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326461732|gb|EGD87185.1| tRNA pseudouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 580

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 61/187 (32%), Gaps = 26/187 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A            V  +        RTD 
Sbjct: 100 KVIVMLGYSGTGYHGMQLCPTEKTIEGDLFAAFVAANAISKANAVDPKKSSFVRCARTDK 159

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L  S  I +  +    K F A      R Y 
Sbjct: 160 GVHAAGNVVSLKL--IIEDPDIVQKINEKL--SPQIRVWGIIPATKGFSAYQFCDSRMYE 215

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTI 172
           Y I +               P +   + M   A+    +H D   F+    +  S     
Sbjct: 216 YLIPSHCFLPP--------HPSTFLAQKMDEMAE----KHGDMEAFKERQAEVESYWEET 263

Query: 173 DHFDVNS 179
           D   +  
Sbjct: 264 DKKHIQP 270



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/128 (21%), Positives = 49/128 (38%), Gaps = 14/128 (10%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +    + IP       +  A    VG  +F  +      +  S  R I  F ++     
Sbjct: 341 FKAKNEYRIPPER-LARINAALALYVGTKNFHNYTIQKTFRDPSARRLIKSFKISRDPVV 399

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAP 235
                 + ++V  +SF+  QIR  V  +  LV  G     D+++  ++ Q+ +   P AP
Sbjct: 400 INGTEWLSLKVHGQSFMMHQIRKMVAMVALLVRCG----ADIKRIEESYQNSRIPIPKAP 455

Query: 236 PEGLYFDS 243
             GL  + 
Sbjct: 456 GLGLLLER 463


>gi|300706061|ref|XP_002995341.1| hypothetical protein NCER_101809 [Nosema ceranae BRL01]
 gi|239604377|gb|EEQ81670.1| hypothetical protein NCER_101809 [Nosema ceranae BRL01]
          Length = 344

 Score = 91.0 bits (225), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/265 (19%), Positives = 89/265 (33%), Gaps = 48/265 (18%)

Query: 2   IRYC--MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGR 50
           ++      I Y G+GY G Q   + ++I+ +I + +F               + +  + R
Sbjct: 1   MKIKAGFCIGYIGTGYSGLQLNGDYNTIEKAISECLFSCSAISSQNAKDPSKIHLKSSSR 60

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GVHA   +    +  +   V   K L   L   + I +  +  + K F      I R
Sbjct: 61  TDKGVHAAFNLISCKIECQITDVFFQK-LKECLFSKN-IYLYKILRLTKSFIPTNLTISR 118

Query: 111 SYLYRIITRQ-APLALEKGRAWLIPKSLDCENMRI------------------------- 144
           +Y Y + T   A        + LI K L+ + M                           
Sbjct: 119 TYEYILPTYFLAKSNFSAECSDLIAKDLNRDKMTKREYNEKDIEQIFGYLADKDDIKYFC 178

Query: 145 -AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHTQI 198
                 +G  +F  F ++        R I + +     V      I+I +  +SFL  QI
Sbjct: 179 DIFTKFLGTKNFHNFTTL-SNHKGKQRYIKNIEFSNAYVIDDIEYIKITIEGQSFLLHQI 237

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQ 223
           R  +    L+   K    +     +
Sbjct: 238 RKMIYFSVLLCRYKR--NEFSTIFE 260


>gi|170291222|ref|YP_001738038.1| tRNA pseudouridine synthase [Candidatus Korarchaeum cryptofilum
           OPF8]
 gi|170175302|gb|ACB08355.1| tRNA pseudouridine synthase [Candidatus Korarchaeum cryptofilum
           OPF8]
          Length = 232

 Score = 91.0 bits (225), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 79/240 (32%), Gaps = 64/240 (26%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + I Y G  Y G   Q +  ++  ++ +A+    G    +    RTD GV AL  +A   
Sbjct: 8   LRIAYLGWNYHGVVEQPSLPTVGSALREAMES-QGIRAKLRFTSRTDRGVSALDNIAF-- 64

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSI--VDKQFHARFSAIRRSYLYRIITRQAPL 123
                 P      LN+ L     I++  ++   + K          R+Y Y I       
Sbjct: 65  ---YRGPAPNVSLLNSEL--PKDIAVWAIATGGIPK-------PKARAYCYAI------- 105

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
                    + ++LD       AQ  +G                  + I+  DV S  N 
Sbjct: 106 PFRLSETECVRRALD-----ELAQAGLG------------------KNIERIDVKSGENF 142

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             I +  +SF   +IR  VG    +  G+                    LAPPEGL    
Sbjct: 143 TYIEIYGKSFKKNEIRRIVGRALELHLGR-----------------SIGLAPPEGLVLTE 185


>gi|156095520|ref|XP_001613795.1| tRNA pseudouridine synthase [Plasmodium vivax SaI-1]
 gi|148802669|gb|EDL44068.1| tRNA pseudouridine synthase, putative [Plasmodium vivax]
          Length = 545

 Score = 91.0 bits (225), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 28/118 (23%), Positives = 48/118 (40%), Gaps = 6/118 (5%)

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSI-----HCQASSPIRTIDHFDVNS-FGNLIEIRVV 189
             D E ++   +  +GRH F  FR         +  +P   I   +++    N+ +  + 
Sbjct: 414 PCDVEKIKECCKLFLGRHSFELFRGTLKGTEKQKQVNPFCNISFLELHQLRSNIYQFVIQ 473

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
              FL+  IR  VG+L  VG G  +  D+  AL      +    AP +GL    + + 
Sbjct: 474 GDRFLYHMIRIIVGTLVQVGVGLLSYEDVRDALHFSKPLKVKLCAPAQGLCLTKILFP 531



 Score = 81.8 bits (201), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 41/195 (21%), Positives = 63/195 (32%), Gaps = 51/195 (26%)

Query: 2   IRYCMIIEYNGSGYFGWQ----------------------RQKNGS----SIQGSIEKAI 35
               +I++Y+G+ Y GW                       ++  G     S+Q  I   +
Sbjct: 108 TNLLLIVDYDGTNYSGWTGVENCSDIYLSATRNYKRAATEKKPKGESKCDSVQNVILNCL 167

Query: 36  FLVTG----------------EIVVVHGAGRTDSGVHALRQVAHFDLVREWVP-----VI 74
             + G                +     G  RTD GVHA   V  +       P       
Sbjct: 168 LKIHGYADQWDKHANDVKSNLKAFEFIGVSRTDKGVHAKEYVCQYVSYERPPPCEGNLQK 227

Query: 75  LCKALNAYLKISDTISILNLSIVD-KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLI 133
           +  ALN  L     I IL +       F+ RF+   + Y Y   TR     LE+  AW +
Sbjct: 228 VKMALNGLLNR--DIRILGVLNAPSHDFNVRFNNWGKIYTYNFDTRIPSQPLERNYAWQL 285

Query: 134 PKSLDCE-NMRIAAQ 147
                    +R +A+
Sbjct: 286 YDDPRFAFLLRESAK 300


>gi|218135247|ref|ZP_03464051.1| hypothetical protein BACPEC_03152 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990632|gb|EEC56643.1| hypothetical protein BACPEC_03152 [Bacteroides pectinophilus ATCC
           43243]
          Length = 83

 Score = 90.7 bits (224), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           + FD++  G  I IRV    FL+  +R   G+L   G  + T   +++AL   +R+  GP
Sbjct: 6   EKFDLDR-GREIVIRVSGNGFLYNMVRIIAGTLIDAGCKRRTPLSVKEALDGCNRELAGP 64

Query: 233 LAPPEGLYFDSVE 245
            APP+GL    ++
Sbjct: 65  TAPPQGLTLIEIK 77


>gi|298229126|ref|ZP_06962807.1| tRNA pseudouridine synthase A [Streptococcus pneumoniae str.
          Canada MDR_19F]
          Length = 57

 Score = 90.7 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 28/57 (49%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVH 56
          M RY   I Y+G  + G+QRQ +  S+Q  IEK +  +  G+ + VHGAGRTDSGVH
Sbjct: 1  MTRYKATISYDGYAFAGFQRQPHARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVH 57


>gi|302656568|ref|XP_003020036.1| hypothetical protein TRV_05897 [Trichophyton verrucosum HKI 0517]
 gi|291183816|gb|EFE39412.1| hypothetical protein TRV_05897 [Trichophyton verrucosum HKI 0517]
          Length = 570

 Score = 90.7 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 60/187 (32%), Gaps = 26/187 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A            V  +        RTD 
Sbjct: 100 KVIVMLGYSGTGYHGMQLCPTEKTIEGDLFAAFVAANAISKANAVDPKKSSFVRCARTDK 159

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L     I +  +    K F A      R Y 
Sbjct: 160 GVHAAGNVVSLKL--IIEDPDIVQKINEKLN--PQIRVWGIIPATKGFSAYQFCDSRMYE 215

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTI 172
           Y I +               P +   + M   A+    +H D   F+    +  S     
Sbjct: 216 YLIPSHCFLPP--------HPSTFLAQKMVEMAE----KHGDMEAFKERQAEVESYWEET 263

Query: 173 DHFDVNS 179
           D   +  
Sbjct: 264 DKKHIQP 270



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/114 (21%), Positives = 45/114 (39%), Gaps = 13/114 (11%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVAR 191
              +  A    VG  +F  +      +  S  R I  F ++           + ++V  +
Sbjct: 354 LARINAALALYVGTKNFHNYTIQKTFRDPSARRLIKSFKISRDPVVINGTEWLSLKVHGQ 413

Query: 192 SFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAPPEGLYFDS 243
           SF+  QIR  V  +  LV  G     D+++  ++ Q+ +   P AP  GL  + 
Sbjct: 414 SFMMHQIRKMVAMVALLVRCG----ADIKRIEESYQNSRIPIPKAPGLGLLLER 463


>gi|302509324|ref|XP_003016622.1| hypothetical protein ARB_04913 [Arthroderma benhamiae CBS 112371]
 gi|291180192|gb|EFE35977.1| hypothetical protein ARB_04913 [Arthroderma benhamiae CBS 112371]
          Length = 573

 Score = 90.7 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 60/187 (32%), Gaps = 26/187 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A            V  +        RTD 
Sbjct: 100 KVIVMLGYSGTGYHGMQLCPTEKTIEGDLFAAFVAANAISKANAVDPKKSSFVRCARTDK 159

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L     I +  +    K F A      R Y 
Sbjct: 160 GVHAAGNVVSLKL--IIEDPDIVQKINEKLN--PQIRVWGIIPATKGFSAYQFCDSRMYE 215

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTI 172
           Y I +               P +   + M   A+    +H D   F+    +  S     
Sbjct: 216 YLIPSHCFLPP--------HPSTFLAQKMVEMAE----KHGDMEAFKERQAEVESYWEET 263

Query: 173 DHFDVNS 179
           D   +  
Sbjct: 264 DKKHIQP 270



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/128 (21%), Positives = 49/128 (38%), Gaps = 14/128 (10%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            +    + IP       +  A    VG  +F  +      +  S  R I  F ++     
Sbjct: 344 FKAKNEYRIPPER-LARINAALALYVGTKNFHNYTIQKTFRDPSARRLIKSFKISRDPVV 402

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAP 235
                 + ++V  +SF+  QIR  V  +  LV  G     D+++  ++ Q+ +   P AP
Sbjct: 403 INGTEWLSLKVHGQSFMMHQIRKMVAMVALLVRCG----ADIKRIEESYQNSRIPIPKAP 458

Query: 236 PEGLYFDS 243
             GL  + 
Sbjct: 459 GLGLLLER 466


>gi|326527051|dbj|BAK04467.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 572

 Score = 90.7 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 33/125 (26%), Positives = 47/125 (37%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +I+ Y G+GY G Q+     +I+G +E+A++                    A RTD
Sbjct: 48  RKVAIILAYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRAAPARYEWARAARTD 107

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P      LNA L     I       V   F A+    RR Y
Sbjct: 108 KGVSAAAQVVSGRF--YVDPPGFIDRLNAKLA--PQIRAFGYVRVTNSFSAKKFCDRRRY 163

Query: 113 LYRII 117
           +Y + 
Sbjct: 164 VYLLP 168



 Score = 61.8 bits (149), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 28/110 (25%), Positives = 40/110 (36%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
           E      +H VG  +F  F      +  +  R I  F  NS       + +   VV +SF
Sbjct: 370 EKFNRILKHYVGTRNFHNFTTRTKAEDPAAKRYIISFTANSVVSLDGIDFVRCEVVGQSF 429

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  VG    V         +      +D +   P AP  GL+ D 
Sbjct: 430 MLHQIRKMVGLAVAVMRNC-APESIYDVAFRKDIRLNVPTAPEVGLHLDE 478


>gi|302308519|ref|NP_985445.2| AFL105Cp [Ashbya gossypii ATCC 10895]
 gi|299790670|gb|AAS53269.2| AFL105Cp [Ashbya gossypii ATCC 10895]
          Length = 528

 Score = 90.3 bits (223), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 47/126 (37%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            +  +++ Y G+GY G Q      +I+  + +A               +      A RTD
Sbjct: 67  RKVAVMVGYCGTGYHGMQYNPPNRTIEAELFEAFVKAGAISRANSTDLKKNGFMRAARTD 126

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +N +L     I +  +S V+K F  R     R Y
Sbjct: 127 KGVHAGGNVISLKL--IIEDPAIKDKINEHL--PPGIRVWGISRVNKAFDCRKLCGSRWY 182

Query: 113 LYRIIT 118
            Y + T
Sbjct: 183 EYLLPT 188



 Score = 61.0 bits (147), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 25/129 (19%), Positives = 48/129 (37%), Gaps = 11/129 (8%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG---- 181
             R++ +  +      R A +  +G H+F  +      +  S +R +    V+       
Sbjct: 275 HRRSYRVSSA-KLARFREAMKQYLGPHNFHNYTLGKDFKDPSTVRFMKDITVSDPFVIGE 333

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + I++  +SF+  QIR  +    LV     +   + +      +K   P AP  G
Sbjct: 334 MKTEWVSIKIHGQSFMLHQIRKMISMATLVARCNCSPERIAQ--SYGPQKINIPKAPALG 391

Query: 239 LYFDSVEYS 247
           L  +S  Y 
Sbjct: 392 LLLESPVYE 400


>gi|74693104|sp|Q755C8|PUS1_ASHGO RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
          Length = 528

 Score = 90.3 bits (223), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 47/126 (37%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            +  +++ Y G+GY G Q      +I+  + +A               +      A RTD
Sbjct: 67  RKVAVMVGYCGTGYHGMQYNPPNRTIEAELFEAFVKAGAISRANSTDLKKNGFMRAARTD 126

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +N +L     I +  +S V+K F  R     R Y
Sbjct: 127 KGVHAGGNVISLKL--IIEDPAIKDKINEHL--PPGIRVWGISRVNKAFDCRKLCGSRWY 182

Query: 113 LYRIIT 118
            Y + T
Sbjct: 183 EYLLPT 188



 Score = 62.9 bits (152), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 25/129 (19%), Positives = 48/129 (37%), Gaps = 11/129 (8%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG---- 181
             R++ +  +      R A +  +G H+F  +      +  S +R +    V+       
Sbjct: 275 HRRSYRVSSA-KLARFREAMKQYLGPHNFHNYTLGKDFKDPSTVRFMKDITVSRPFVIGE 333

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + I++  +SF+  QIR  +    LV     +   + +      +K   P AP  G
Sbjct: 334 MKTEWVSIKIHGQSFMLHQIRKMISMATLVARCNCSPERIAQ--SYGPQKINIPKAPALG 391

Query: 239 LYFDSVEYS 247
           L  +S  Y 
Sbjct: 392 LLLESPVYE 400


>gi|218191324|gb|EEC73751.1| hypothetical protein OsI_08404 [Oryza sativa Indica Group]
          Length = 581

 Score = 89.9 bits (222), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 32/125 (25%), Positives = 49/125 (39%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD
Sbjct: 49  RKVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYRAGAVPEADRAAPRRYDWARAARTD 108

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P +    LNA L     I       V   F+A+    RR Y
Sbjct: 109 KGVSAAAQVVSGRF--YVDPPVFTDRLNAQLA--PQIRAFGYVRVTNSFNAKKFCDRRRY 164

Query: 113 LYRII 117
           +Y + 
Sbjct: 165 VYLLP 169



 Score = 68.3 bits (166), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 27/110 (24%), Positives = 38/110 (34%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
           E      +  VG H+F  F      +  +  R I  F  +        + I   VV +SF
Sbjct: 379 ERFNRILKKYVGTHNFHNFTTRTKAEDPAAKRFIISFAADRVVNLDGIDFIRCEVVGQSF 438

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  +G    V         +      +D     P AP  GLY D 
Sbjct: 439 MLHQIRKMIGLAVAVMRNC-APESIYDVAFRKDVNLNVPTAPEVGLYLDE 487


>gi|115447813|ref|NP_001047686.1| Os02g0668400 [Oryza sativa Japonica Group]
 gi|50251324|dbj|BAD28300.1| putative pseudouridine synthase 1 [Oryza sativa Japonica Group]
 gi|50252138|dbj|BAD28134.1| putative pseudouridine synthase 1 [Oryza sativa Japonica Group]
 gi|113537217|dbj|BAF09600.1| Os02g0668400 [Oryza sativa Japonica Group]
          Length = 581

 Score = 89.9 bits (222), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 32/125 (25%), Positives = 49/125 (39%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD
Sbjct: 49  RKVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYRAGAVPEADRAAPRRYDWARAARTD 108

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P +    LNA L     I       V   F+A+    RR Y
Sbjct: 109 KGVSAAAQVVSGRF--YVDPPVFTDRLNAQLA--PQIRAFGYVRVTNSFNAKKFCDRRRY 164

Query: 113 LYRII 117
           +Y + 
Sbjct: 165 VYLLP 169



 Score = 68.3 bits (166), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 27/110 (24%), Positives = 38/110 (34%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
           E      +  VG H+F  F      +  +  R I  F  +        + I   VV +SF
Sbjct: 379 ERFNRILKKYVGTHNFHNFTTRTKAEDPAAKRFIISFAADRVVNLDGIDFIRCEVVGQSF 438

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  +G    V         +      +D     P AP  GLY D 
Sbjct: 439 MLHQIRKMIGLAVAVMRNC-APESIYDVAFRKDVNLNVPTAPEVGLYLDE 487


>gi|315050550|ref|XP_003174649.1| tRNA pseudouridine synthase 1 [Arthroderma gypseum CBS 118893]
 gi|311339964|gb|EFQ99166.1| tRNA pseudouridine synthase 1 [Arthroderma gypseum CBS 118893]
          Length = 582

 Score = 89.9 bits (222), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 60/187 (32%), Gaps = 26/187 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A            V  +        RTD 
Sbjct: 101 KVIVMLGYSGTGYHGMQLCPTEKTIEGDLFAAFVAANAISKANAVDPKKSSFVRCARTDK 160

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L     I +  +    K F A      R Y 
Sbjct: 161 GVHAAGNVVSLKL--IIEDPDVVQKINEKLN--PQIRVWGIIPATKGFSAYQFCDSRMYE 216

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTI 172
           Y I +               P +   + M   A+    +H D   F+    +  S     
Sbjct: 217 YLIPSHCFLPP--------HPSTFLAQKMVEMAE----KHGDMEAFKERQAEVESYWEET 264

Query: 173 DHFDVNS 179
           D   +  
Sbjct: 265 DKKHIQP 271



 Score = 54.4 bits (130), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/128 (21%), Positives = 49/128 (38%), Gaps = 14/128 (10%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
            E    + IP       +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 343 FEAKNEYRIPPER-LARINAALALYVGTKNFHNYTIQKTFRDASARRLIKSFKISRDPVV 401

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAP 235
                 + ++V  +SF+  QIR  V  +  LV  G     D+ +  ++ Q+ +   P AP
Sbjct: 402 INGTEWLSLKVHGQSFMMHQIRKMVAMVALLVRCG----ADINRINESYQNSRIPIPKAP 457

Query: 236 PEGLYFDS 243
             GL  + 
Sbjct: 458 GLGLLLER 465


>gi|320583409|gb|EFW97622.1| tRNA pseudouridine synthase [Pichia angusta DL-1]
          Length = 491

 Score = 89.9 bits (222), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 33/131 (25%), Positives = 45/131 (34%), Gaps = 13/131 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDS 53
           +    + Y G+GY G Q      +I+G +  A               +      A RTD 
Sbjct: 80  KVACYLSYCGTGYHGMQMNPPAKTIEGDLFDAFVKAGAISKNNSNDLKKSSFMRAARTDK 139

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        L + +N+YL   D I       V+K F  R     R Y 
Sbjct: 140 GVHAAGNVISLKL--IIEDPDLVEKINSYL--PDQIRFWGYERVNKSFDCRKVCSSRIYE 195

Query: 114 YRIITRQAPLA 124
           Y + T      
Sbjct: 196 YLMPTYSFLPP 206



 Score = 63.3 bits (153), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/115 (22%), Positives = 45/115 (39%), Gaps = 8/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS-----FGNLIEIRVVARS 192
              +R A +  +G H+F  F +    +  S IR + +  V+          + I++  +S
Sbjct: 296 LNLLRDALKIYLGPHNFHNFTNGKDYKDPSAIRFMKNITVSDPIVVNDQEWVSIKIHGQS 355

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  +    LV         +E+A   +      P AP  GL  +   Y 
Sbjct: 356 FMLHQIRKMIAMATLVVRTGCPLARIEEAFGPEKVN--IPKAPALGLLLEQPVYE 408


>gi|146412075|ref|XP_001482009.1| hypothetical protein PGUG_05772 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 477

 Score = 89.5 bits (221), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 32/127 (25%), Positives = 49/127 (38%), Gaps = 15/127 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRT 51
           +   +I Y G+GY G Q Q   +  +I+G +  A               +      A RT
Sbjct: 30  KVACMIGYCGTGYNGMQIQNNPDVKTIEGDLFDAFVKAGAISPENADDLKKNAFMRAART 89

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D GVHA   V    L        + + +N++L   D I +  +   +K F  R     R 
Sbjct: 90  DKGVHAAGNVISCKL--IIEDQDILQRINSHL--PDQIRVWGIERTNKSFDCRKMCSSRV 145

Query: 112 YLYRIIT 118
           Y Y + T
Sbjct: 146 YEYLLPT 152



 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 8/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVN-----SFGNLIEIRVVARS 192
               R A +   G H+F  F      + +S  R +    V+          + I++  +S
Sbjct: 262 LNLFREAMKLYEGSHNFHNFTIGKPFKDASSRRYMKETTVSNPFIIEGTEWVSIKIHGQS 321

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  +    LV       T ++        K   P AP  GL  ++  Y 
Sbjct: 322 FMLHQIRKMIAMAVLVVRTGCPITRIKDCF--GPTKINIPKAPALGLLLENPVYE 374


>gi|190349084|gb|EDK41674.2| hypothetical protein PGUG_05772 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 477

 Score = 89.5 bits (221), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 32/127 (25%), Positives = 49/127 (38%), Gaps = 15/127 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRT 51
           +   +I Y G+GY G Q Q   +  +I+G +  A               +      A RT
Sbjct: 30  KVACMIGYCGTGYNGMQIQNNPDVKTIEGDLFDAFVKAGAISPENADDLKKNAFMRAART 89

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D GVHA   V    L        + + +N++L   D I +  +   +K F  R     R 
Sbjct: 90  DKGVHAAGNVISCKL--IIEDQDILQRINSHL--PDQIRVWGIERTNKSFDCRKMCSSRV 145

Query: 112 YLYRIIT 118
           Y Y + T
Sbjct: 146 YEYLLPT 152



 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 8/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVN-----SFGNLIEIRVVARS 192
               R A +   G H+F  F      + +S  R +    V+          + I++  +S
Sbjct: 262 LNLFREAMKLYEGSHNFHNFTIGKPFKDASSRRYMKETTVSNPFIIEGTEWVSIKIHGQS 321

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  +    LV       T ++        K   P AP  GL  ++  Y 
Sbjct: 322 FMLHQIRKMIAMAVLVVRTGCPITRIKDCF--GPTKINIPKAPALGLLLENPVYE 374


>gi|169619633|ref|XP_001803229.1| hypothetical protein SNOG_13015 [Phaeosphaeria nodorum SN15]
 gi|111058695|gb|EAT79815.1| hypothetical protein SNOG_13015 [Phaeosphaeria nodorum SN15]
          Length = 621

 Score = 89.5 bits (221), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 62/177 (35%), Gaps = 24/177 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTD 52
            +  ++I Y+G+GY G Q      +I+G +        AI        +   +    RTD
Sbjct: 105 RKVAVMIGYSGTGYKGMQIDNKQKTIEGDLFTAFVAAGAISKANADDPKKSSLVRCARTD 164

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +N++L  S+ I +  +      F    +   R Y
Sbjct: 165 KGVHAAGNVISLKL--IIEEEDIVEKINSHL--SEQIRVWGIQRTTGSFSCYQACDSRWY 220

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
            Y I T           +  + K L+    +          D   +R+   + ++  
Sbjct: 221 EYLIPTHAFLPPHP---SSFLGKKLEEYAEKEG--------DMDAYRARQAEVANFW 266



 Score = 46.4 bits (109), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/113 (20%), Positives = 41/113 (36%), Gaps = 13/113 (11%)

Query: 140 ENMRIAAQHLVGR---HDFTTFRSIHCQASSPIRTIDHFDVNSFG------NLIEIRVVA 190
             ++ A  + +G    H++T  +       S  R I  F V            + ++V  
Sbjct: 410 ARVQAALNNYLGTRKYHNYTVQKKFSD--KSAQRYIKSFKVAPKPIIINDTEWLSLKVHG 467

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +SF+  QIR  VG + L          + ++    +     P AP  GL  + 
Sbjct: 468 QSFMMHQIRKMVGMVALTVRCGSNPDIMIESF--GNTIVRIPKAPGLGLLLER 518


>gi|224061937|ref|XP_002300673.1| predicted protein [Populus trichocarpa]
 gi|222842399|gb|EEE79946.1| predicted protein [Populus trichocarpa]
          Length = 429

 Score = 89.5 bits (221), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 34/137 (24%), Positives = 52/137 (37%), Gaps = 13/137 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  +   Y G GY G Q+     +I+G +E+A+F             +      + RTD
Sbjct: 17  RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHAGAVPEQDRGIPKRYDWARSARTD 76

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A+ QV          P  L + L++ L  S    I     V   F+A+    RR Y
Sbjct: 77  KGVSAVGQVVSGRF--YIDPPGLVERLHSNL--SPQFRIFGYKRVTGSFNAKKFCDRRRY 132

Query: 113 LYRIITRQAPLALEKGR 129
           +Y I          + R
Sbjct: 133 VYLIPVFALDPCSHRDR 149



 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 32/113 (28%), Positives = 47/113 (41%), Gaps = 7/113 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFD----VNSFG-NLIEIRVVARSF 193
           E       + VG H+F  F      +  S  R I  F+    VN  G   ++  VV +SF
Sbjct: 241 ERFNRILGYYVGSHNFHNFTTRTKAEDPSARRYIVSFEAKTTVNVEGIEFVKCEVVGQSF 300

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           +  QIR  +G    +       + ++ ALQ +D     P AP  GLY D   +
Sbjct: 301 MLHQIRKMIGVAVAIMRNCAPESLIQTALQ-KDVNINVPTAPEVGLYLDECFF 352


>gi|269866402|ref|XP_002652261.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
 gi|220062857|gb|EED41795.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
          Length = 268

 Score = 89.5 bits (221), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 58/204 (28%), Gaps = 61/204 (29%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALR 59
            +  + I Y+G  Y G Q+  NG SI   +E A+    +  E   +   GRTD GV A  
Sbjct: 58  RKIALKIAYDGRVYHGVQKDPNGLSIGEVLENALKSTDLYIESNDIVFCGRTDRGVSAAN 117

Query: 60  QVAHFDL-------------------------------------------VREWVPVILC 76
            +    +                                           +++     L 
Sbjct: 118 MIISLKIKSILETYSANPNYHRHIETETYDTYQFNKKEYKRYLLNNSDFEIKKHDAKELP 177

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
             L     +   I +   + V   F AR +  +R Y Y       P  L           
Sbjct: 178 YDLILNKVLPPQIRVKGWAPVPWNFSARHNCCQRRYTYFFTC---PPQLLPKY------- 227

Query: 137 LDCENMRIAAQHLVGRHDFTTFRS 160
                 + A + +    DF  F +
Sbjct: 228 ------QEAGRIIYKTEDFYNFCT 245


>gi|255719542|ref|XP_002556051.1| KLTH0H03894p [Lachancea thermotolerans]
 gi|238942017|emb|CAR30189.1| KLTH0H03894p [Lachancea thermotolerans]
          Length = 546

 Score = 89.5 bits (221), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 31/126 (24%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  ++I Y G+GY G Q      +I+  + +      AI     + +       A RTD
Sbjct: 75  RKVAVMIGYCGTGYHGMQYNPPTPTIEAELFRAFVEAGAISQANSKDLKKSGFMRAARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +N+ L   + I + ++  V+K F  R     R Y
Sbjct: 135 KGVHAGGNVVSLKL--IIEDPDIIAKINSKL--PEGIRVWDIERVNKAFDCRKLCGSRWY 190

Query: 113 LYRIIT 118
            Y + T
Sbjct: 191 EYLLPT 196



 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/129 (24%), Positives = 48/129 (37%), Gaps = 11/129 (8%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDV-------N 178
             RA+ I +S   E  R A +  +G H+F  F      +  S IR +    V        
Sbjct: 283 HRRAYRISESR-LEAFRAAMKQYLGPHNFFNFTLGKEFKDPSAIRFMKEIKVSDPFVIGE 341

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + I++  +SF+  QIR  +    LV         +  A + Q  K   P AP  G
Sbjct: 342 RNTEWVSIKIHGQSFMLHQIRKMISMATLVTRCSCPVDRITDAYKPQ--KINIPKAPALG 399

Query: 239 LYFDSVEYS 247
           L  +   Y 
Sbjct: 400 LLLECPVYE 408


>gi|296812761|ref|XP_002846718.1| tRNA pseudouridylate synthase Lsp1 [Arthroderma otae CBS 113480]
 gi|238841974|gb|EEQ31636.1| tRNA pseudouridylate synthase Lsp1 [Arthroderma otae CBS 113480]
          Length = 576

 Score = 88.7 bits (219), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 60/187 (32%), Gaps = 26/187 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A            +  +        RTD 
Sbjct: 100 KVIVMLGYSGTGYHGMQLCATEKTIEGDLFAAFVAANAISKANAMDPKKSSFVRCARTDK 159

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L     I +  +    K F A      R Y 
Sbjct: 160 GVHAAGNVVSLKL--IIEDPDIVQKINEKLN--PQIRVWGIIPATKGFSAYQFCDSRMYE 215

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH-DFTTFRSIHCQASSPIRTI 172
           Y I +               P +   + M   A+    +H D   F+    +  +     
Sbjct: 216 YLIPSHCFLPP--------HPSTFLAQKMVEMAE----KHGDMEAFKQRQAEVETYWEET 263

Query: 173 DHFDVNS 179
           D   +  
Sbjct: 264 DKKHIQP 270



 Score = 55.2 bits (132), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 30/138 (21%), Positives = 51/138 (36%), Gaps = 15/138 (10%)

Query: 116 IITRQAPLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTID 173
           I  ++  LA  +    + IP       +  A    VG  +F  +      +  S  R I 
Sbjct: 337 IAIKEIRLAYFKAKNEYRIPPER-LARINEALSLYVGTRNFHNYTIQKTFRDPSAKRLIK 395

Query: 174 HFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQAQD 226
            F ++           + ++V  +SF+  QIR  V  +  LV  G     D+ +  ++  
Sbjct: 396 SFKISRDPVVINGTEWLSLKVHGQSFMMHQIRKMVAMVALLVRCG----ADIHRIEESYQ 451

Query: 227 RKECG-PLAPPEGLYFDS 243
           R     P AP  GL  + 
Sbjct: 452 RPRIPIPKAPGLGLLLER 469


>gi|224035593|gb|ACN36872.1| unknown [Zea mays]
          Length = 199

 Score = 88.7 bits (219), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 29/115 (25%), Positives = 47/115 (40%), Gaps = 9/115 (7%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS------FGNLIEIRVVARSFL 194
           M+ AA   +G HDF  F  +     S+  R I  F +++         L  + +   +FL
Sbjct: 1   MQKAASKFIGEHDFRNFCKMDAANVSNYRRHITEFTISACDRRSNNDELCSMTIKGSAFL 60

Query: 195 HTQIRSFVGSLKLVGDGKWTSTDLEKALQ--AQDRKECGPLAPPEGLYFDSVEYS 247
             Q+R  V  L L+G G  + + ++  L      RK    +AP   L   S  + 
Sbjct: 61  WHQVRCMVAVLFLIGQGLESPSVVDSLLDIMKTSRKPQYKMAPELPLILQSCLFD 115


>gi|312217345|emb|CBX97293.1| similar to tRNA pseudouridine synthase [Leptosphaeria maculans]
          Length = 615

 Score = 88.3 bits (218), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 68/197 (34%), Gaps = 24/197 (12%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTD 52
            +  ++I Y+G+GY G Q      +I+G +        AI        +   +    RTD
Sbjct: 108 RKVAVMIGYSGTGYKGMQIDYKQKTIEGDLFNAFVAAGAISKANATDHKKSSLVRCARTD 167

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +N  L  SD I +  +      F    +   R Y
Sbjct: 168 KGVHAAGNVVSLKL--IIEDEDIVQKINDNL--SDQIRVWGIQRTVGSFSCYQACDSRWY 223

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T               P S   + +   A+     +D   +RS   + ++    +
Sbjct: 224 EYLIPTHSFLPP--------HPSSFLGKKLEEYAEK---ENDLEGYRSRQAEVANFWSEV 272

Query: 173 DHFDVNSFGNLIEIRVV 189
           +   +    + ++  + 
Sbjct: 273 EEKHIKPIRDSLDDSIR 289



 Score = 51.8 bits (123), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 9/115 (7%)

Query: 136 SLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRV 188
            +  E ++ A  + +G H +  +         S  R I  F V            + ++V
Sbjct: 398 PIRQERVQAALNNYLGTHKYHNYTVQKKFSDKSAQRYIKSFKVAPKPIIINDTEWLSLKV 457

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
             +SF+  QIR  VG   L          ++++    +     P AP  GL  + 
Sbjct: 458 HGQSFMMHQIRKMVGMAALSVRCGTDPKIIQESF--GNTVVRIPKAPGLGLLLER 510


>gi|289613362|emb|CBI59671.1| unnamed protein product [Sordaria macrospora]
          Length = 634

 Score = 88.3 bits (218), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 38/200 (19%), Positives = 68/200 (34%), Gaps = 28/200 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  ++I Y G+GY G Q      +I+G +  A               +   +    RTD
Sbjct: 126 RKVAVLIGYAGTGYHGIQINHKEKTIEGDLFAAFVKAGAISKANADDPKKSSLVRCARTD 185

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +N++L   D I +  +  V   F    +   R Y
Sbjct: 186 KGVHAAANVLSLKL--IVEDEDIVEKINSHL--PDQIKVWGIQRVTNGFSCYQACDSRWY 241

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDC--ENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            Y          L    A L P+      + +  AA+   G +D   +        +   
Sbjct: 242 EY----------LMPSYALLPPQPQSFLGKKIIDAAKE-KGTYD--EYVDRLDDVKNFWE 288

Query: 171 TIDHFDVNSFGNLIEIRVVA 190
            ++  D+      ++  + A
Sbjct: 289 EVEKNDIQPILEKMDPEIRA 308



 Score = 66.0 bits (160), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 25/112 (22%), Positives = 42/112 (37%), Gaps = 9/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFG------NLIEIRVVAR 191
            E ++ A    +G H+F  +  +      S  R I  F VN           + ++V  +
Sbjct: 417 LEKLQEALNQYLGTHNFHNYTILKSHTDPSARRHIKSFQVNPTPIRINDTEWLSLKVHGQ 476

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           SF+  QIR  V    L+       + + +      R+   P AP  GL  + 
Sbjct: 477 SFMMHQIRKMVAMAVLIVRCGAPMSLINE--SYGPRRISIPKAPGLGLMLER 526


>gi|85091723|ref|XP_959041.1| hypothetical protein NCU07528 [Neurospora crassa OR74A]
 gi|28920438|gb|EAA29805.1| hypothetical protein NCU07528 [Neurospora crassa OR74A]
          Length = 625

 Score = 88.3 bits (218), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 39/200 (19%), Positives = 68/200 (34%), Gaps = 28/200 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  ++I Y G+GY G Q      +I+G +  A               +   +    RTD
Sbjct: 121 RKVAVLIGYAGTGYHGIQINHKEKTIEGDLFAAFVKAGAISKANADDPKKSSLVRCARTD 180

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +N++L   D I +  +  V   F    +   R Y
Sbjct: 181 KGVHAAANVLSLKL--IVEDEDIVDKINSHL--PDQIKVWGIQRVTNGFSCYQACDSRWY 236

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDC--ENMRIAAQHLVGRHDFTTFRSIHCQASSPIR 170
            Y          L    A L P+      + +  AA+   G +D   +R       +   
Sbjct: 237 EY----------LMPSYALLPPQPQSFLGKKIIDAAKE-KGTYDEYMYRL--DDVKNFWE 283

Query: 171 TIDHFDVNSFGNLIEIRVVA 190
            ++  D+      ++  + A
Sbjct: 284 EVEKNDIQPILEKMDPEIRA 303



 Score = 66.4 bits (161), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/157 (19%), Positives = 56/157 (35%), Gaps = 19/157 (12%)

Query: 94  LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
            + V+++F     A+R      +  ++      + R          E ++ A    +G H
Sbjct: 373 AAKVEREFTPVELAVREVKAAYVAAKR------RYRVTAPR----LEKLQEALNQYLGTH 422

Query: 154 DFTTFRSIHCQA-SSPIRTIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLK 206
           +F  +  +      S  R I  F VN           + ++V  +SF+  QIR  V    
Sbjct: 423 NFHNYTILKSHTDPSARRHIKSFQVNPTPIRINDTEWLSLKVHGQSFMMHQIRKMVAMAV 482

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           L+       + + +      R+   P AP  GL  + 
Sbjct: 483 LIVRCGAPMSLVNE--SYGPRRISIPKAPGLGLMLER 517


>gi|159120024|ref|XP_001710229.1| Pseudouridylate synthase 1 [Giardia lamblia ATCC 50803]
 gi|157438347|gb|EDO82555.1| Pseudouridylate synthase 1 [Giardia lamblia ATCC 50803]
          Length = 467

 Score = 88.3 bits (218), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 49/224 (21%), Positives = 78/224 (34%), Gaps = 37/224 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIF---LVTGEIVVVHG---AGRT 51
             + + Y G+ Y G Q Q       +  +++G I  AI    ++ G  +   G     RT
Sbjct: 41  IAVALGYVGTRYSGSQWQAPSATHPDIRTVEGEIYAAIEAAGILYGRDIKSIGWTRCSRT 100

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D  V A   V  F          L +AL  +L     ISI     V  +F A+ +   R+
Sbjct: 101 DRSVSAAMAVFSFFGPGHLD---LVQALQPHL--PKDISIFGTVRVPPKFSAKMACTSRT 155

Query: 112 YLYRI--------ITRQAPLALEKGRAWLIPKSLD-------CENMRIAAQHLVG--RHD 154
           Y Y +           +A    +  +A+     LD        E +R A   L    RHD
Sbjct: 156 YEYMMPLVFLLPSSQEEASEPCQDVQAFFSY--LDSPYSAESTETVREACSRLYTAQRHD 213

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
              F  +  +    IRT      +     +    + + FL   +
Sbjct: 214 ILDFLRLDDELQ-KIRTQVRIRASHDSPAVIFDTMLQPFLQQLV 256


>gi|213401667|ref|XP_002171606.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|211999653|gb|EEB05313.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 453

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 31/130 (23%), Positives = 55/130 (42%), Gaps = 9/130 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSI---EKAIFLVTGEI---VVVHGAGRTDSGV 55
           +R  +++ Y+G+ Y G Q     ++I+  +    +A+ L+       + +  A RTD GV
Sbjct: 41  VRIAVLLGYSGTKYHGIQLNNPHATIERVVLDVFQALGLIRDTDADHISLSRAARTDKGV 100

Query: 56  HALRQVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           HAL  V  F +    +    L   LN  L   + I + ++  V   F+ R     R Y Y
Sbjct: 101 HALGNVVSFLVSNFTFTGKELATRLNEKL--PEDIRVWDVLKVPMSFNPRLCCDSRLYEY 158

Query: 115 RIITRQAPLA 124
            + +      
Sbjct: 159 YLPSFALIPP 168



 Score = 49.4 bits (117), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 6/86 (6%)

Query: 143 RIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFD-----VNSFGNLIEIRVVARSFLHT 196
           + A +  +G H+F  F  +    + S  R I         V      + + +  +SF+  
Sbjct: 278 QKACEEYIGNHNFHNFTVNQDAASRSSWRYIHSIQLGKPFVYKEWEWVPVFLHGQSFMLH 337

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKAL 222
           QIR  +    +V       + + KA 
Sbjct: 338 QIRKMLAHAIMVVRTAAPISCVTKAF 363


>gi|226506356|ref|NP_001150144.1| LOC100283773 [Zea mays]
 gi|195637102|gb|ACG38019.1| tRNA pseudouridine synthase family protein [Zea mays]
          Length = 561

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 33/125 (26%), Positives = 48/125 (38%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD
Sbjct: 52  RKVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRSAPRRYDWARAARTD 111

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P      LNA L     I       V   F+A+    RR Y
Sbjct: 112 KGVSAAAQVVSGRF--YVDPPGFIDRLNAQLA--PQIRAYGYVRVTNSFNAKKFCDRRRY 167

Query: 113 LYRII 117
           LY + 
Sbjct: 168 LYLLP 172



 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 39/110 (35%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
           E      ++ +G H+F  F      +  +  R I  F  +        + +   VV +SF
Sbjct: 346 ERFNRILKYYIGTHNFHNFTTRTKAEDPAAKRFIISFAADRVVSLDGIDFVRCEVVGQSF 405

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  +G    V         +      +D     P AP  GLY D 
Sbjct: 406 MLHQIRKMIGLAVAVIRNC-APESIYDVAFRKDVNLNVPTAPEVGLYLDE 454


>gi|223948195|gb|ACN28181.1| unknown [Zea mays]
          Length = 562

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 33/125 (26%), Positives = 48/125 (38%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD
Sbjct: 52  RKVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRSAPRRYDWARAARTD 111

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P      LNA L     I       V   F+A+    RR Y
Sbjct: 112 KGVSAAAQVVSGRF--YVDPPGFIDRLNAQLA--PQIRAYGYVRVTNSFNAKKFCDRRRY 167

Query: 113 LYRII 117
           LY + 
Sbjct: 168 LYLLP 172



 Score = 67.9 bits (165), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 39/110 (35%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
           E      ++ +G H+F  F      +  +  R I  F  +        + +   VV +SF
Sbjct: 347 ERFNRILKYYIGTHNFHNFTTRTKAEDPAAKRFIISFAADRVVSLDGIDFVRCEVVGQSF 406

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  +G    V         +      +D     P AP  GLY D 
Sbjct: 407 MLHQIRKMIGLAVAVMRNC-APESIYDVAFRKDVNLNVPTAPEVGLYLDE 455


>gi|213401227|ref|XP_002171386.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|211999433|gb|EEB05093.1| tRNA pseudouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 503

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 31/132 (23%), Positives = 49/132 (37%), Gaps = 13/132 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +   ++ Y G+GY G Q      +I+G + +A   V           + V +  A RTD
Sbjct: 44  RKVACLVGYCGTGYHGMQLNPPNKTIEGDLFEAFVKVGAVSSYNADDPKKVALARAARTD 103

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        L + +N  L    TI + ++      F+ R     R Y
Sbjct: 104 KGVHAAGNVITLKL--ILEDENLIQKVNEVL--PPTIRVWDVIRTINSFNPRTYCESRIY 159

Query: 113 LYRIITRQAPLA 124
            Y + +      
Sbjct: 160 EYLLPSYAFAPP 171



 Score = 52.1 bits (124), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 24/106 (22%), Positives = 38/106 (35%), Gaps = 8/106 (7%)

Query: 143 RIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVN-----SFGNLIEIRVVARSFLHT 196
           R A +   G H+F  F         S  R I  F V+          + ++V  +SF+  
Sbjct: 288 REAFKRFEGVHNFHNFTVGQSFHDRSSNRVIKSFTVSDPIIIEGTEWLSLKVHGQSFMLH 347

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           QIR  V  + LV         + +    +  +   P  P  GL  +
Sbjct: 348 QIRKMVALIMLVVRTGCPLGRIGETF--RKPRVNIPRGPGLGLLLE 391


>gi|323346109|gb|EGA80399.1| Pus1p [Saccharomyces cerevisiae Lalvin QA23]
 gi|323351939|gb|EGA84478.1| Pus1p [Saccharomyces cerevisiae VL3]
          Length = 508

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  +++ Y G+GY G Q      +I+ ++ K      AI       +       A RTD
Sbjct: 39  RKVAVMVGYCGTGYHGMQYNPPNPTIESALFKAFVEAGAISKDNSNDLKKNGFMRAARTD 98

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        + + +N  L   + I + ++  V+K F  R     R Y
Sbjct: 99  KGVHAGGNLISLKM--IIEDPDIKQKINEKL--PEGIRVWDIERVNKAFDCRKMCSSRWY 154

Query: 113 LYRIIT 118
            Y + T
Sbjct: 155 EYLLPT 160



 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVA 190
               R +    +G H+F  F      +  S IR +    V+       +    I I++  
Sbjct: 258 LAKFRASTSQYLGAHNFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIGDAQTEWISIKIHG 317

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +SF+  QIR  V    L+         + +A   Q  K   P AP  GL  +
Sbjct: 318 QSFMLHQIRKMVSMATLITRCGCPVERISQAYGQQ--KINIPKAPALGLLLE 367


>gi|323335274|gb|EGA76563.1| Pus1p [Saccharomyces cerevisiae Vin13]
          Length = 545

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  +++ Y G+GY G Q      +I+ ++ K      AI       +       A RTD
Sbjct: 76  RKVAVMVGYCGTGYHGMQYNPPNPTIESALFKAFVEAGAISKDNSNDLKKNGFMRAARTD 135

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        + + +N  L   + I + ++  V+K F  R     R Y
Sbjct: 136 KGVHAGGNLISLKM--IIEDPDIKQKINEKL--PEGIRVWDIERVNKAFDCRKMCSSRWY 191

Query: 113 LYRIIT 118
            Y + T
Sbjct: 192 EYLLPT 197



 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVA 190
               R +    +G H+F  F      +  S IR +    V+       +    I I++  
Sbjct: 295 LAKFRASTSQYLGAHNFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIGDAQTEWISIKIHG 354

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +SF+  QIR  V    L+         + +A   Q  K   P AP  GL  +
Sbjct: 355 QSFMLHQIRKMVSMATLITRCGCPVERISQAYGQQ--KINIPKAPALGLLLE 404


>gi|323302662|gb|EGA56468.1| Pus1p [Saccharomyces cerevisiae FostersB]
          Length = 544

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  +++ Y G+GY G Q      +I+ ++ K      AI       +       A RTD
Sbjct: 75  RKVAVMVGYCGTGYHGMQYNPPNPTIESALFKAFVEAGAISKDNSNDLKKNGFMRAARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        + + +N  L   + I + ++  V+K F  R     R Y
Sbjct: 135 KGVHAGGNLISLKM--IIEDPDIKQKINEKL--PEGIRVWDIERVNKAFDCRKMCSSRWY 190

Query: 113 LYRIIT 118
            Y + T
Sbjct: 191 EYLLPT 196



 Score = 52.1 bits (124), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 45/125 (36%), Gaps = 12/125 (9%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN------ 178
            + R  +    L     R +    +G H+F  F      +  S IR +    V+      
Sbjct: 283 HRRRYRICAAKL--AKFRASTSQYLGAHNFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIG 340

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +    I I++  +SF+  QIR  V    L+         + +A   Q  K   P AP  
Sbjct: 341 DAQTEWISIKIHGQSFMLHQIRKMVSMATLITRCGCPVERISQAYGQQ--KINIPKAPAL 398

Query: 238 GLYFD 242
           GL  +
Sbjct: 399 GLLLE 403


>gi|256272816|gb|EEU07786.1| Pus1p [Saccharomyces cerevisiae JAY291]
          Length = 544

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  +++ Y G+GY G Q      +I+ ++ K      AI       +       A RTD
Sbjct: 75  RKVAVMVGYCGTGYHGMQYNPPNPTIESALFKAFVEAGAISKDNSNDLKKNGFMRAARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        + + +N  L   + I + ++  V+K F  R     R Y
Sbjct: 135 KGVHAGGNLISLKM--IIEDPDIKQKINEKL--PEGIRVWDIERVNKAFDCRKMCSSRWY 190

Query: 113 LYRIIT 118
            Y + T
Sbjct: 191 EYLLPT 196



 Score = 52.1 bits (124), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 45/125 (36%), Gaps = 12/125 (9%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN------ 178
            + R  +    L     R +    +G H+F  F      +  S IR +    V+      
Sbjct: 283 HRRRYRICAAKL--AKFRASTSQYLGAHNFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIG 340

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            +    I I++  +SF+  QIR  V    L+         + +A   Q  K   P AP  
Sbjct: 341 DAQTEWISIKIHGQSFMLHQIRKMVSMATLITRCGCPVERISQAYGQQ--KINIPKAPAL 398

Query: 238 GLYFD 242
           GL  +
Sbjct: 399 GLLLE 403


>gi|207340711|gb|EDZ68976.1| YPL212Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 544

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  +++ Y G+GY G Q      +I+ ++ K      AI       +       A RTD
Sbjct: 75  RKVAVMVGYCGTGYHGMQYNPPNPTIESALFKAFVEAGAISKDNSNDLKKNGFMRAARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        + + +N  L   + I + ++  V+K F  R     R Y
Sbjct: 135 KGVHAGGNLISLKM--IIEDPDIKQKINEKL--PEGIRVWDIERVNKAFDCRKMCSSRWY 190

Query: 113 LYRIIT 118
            Y + T
Sbjct: 191 EYLLPT 196



 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVA 190
               R +    +G H+F  F      +  S IR +    V+       +    I I++  
Sbjct: 294 LAKFRASTSQYLGAHNFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIGDAQTEWISIKIHG 353

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +SF+  QIR  V    L+         + +A   Q  K   P AP  GL  +
Sbjct: 354 QSFMLHQIRKMVSMATLITRCGCPVERISQAYGQQ--KINIPKAPALGLLLE 403


>gi|6325044|ref|NP_015112.1| Pus1p [Saccharomyces cerevisiae S288c]
 gi|3122655|sp|Q12211|PUS1_YEAST RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|1370440|emb|CAA97927.1| PUS1 [Saccharomyces cerevisiae]
 gi|1403091|emb|CAA56698.1| pseudouridine synthase 1 [Saccharomyces cerevisiae]
 gi|151942589|gb|EDN60935.1| tRNA-pseudouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190407751|gb|EDV11016.1| tRNA pseudouridine synthase [Saccharomyces cerevisiae RM11-1a]
 gi|259149945|emb|CAY86748.1| Pus1p [Saccharomyces cerevisiae EC1118]
 gi|285815332|tpg|DAA11224.1| TPA: Pus1p [Saccharomyces cerevisiae S288c]
          Length = 544

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  +++ Y G+GY G Q      +I+ ++ K      AI       +       A RTD
Sbjct: 75  RKVAVMVGYCGTGYHGMQYNPPNPTIESALFKAFVEAGAISKDNSNDLKKNGFMRAARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        + + +N  L   + I + ++  V+K F  R     R Y
Sbjct: 135 KGVHAGGNLISLKM--IIEDPDIKQKINEKL--PEGIRVWDIERVNKAFDCRKMCSSRWY 190

Query: 113 LYRIIT 118
            Y + T
Sbjct: 191 EYLLPT 196



 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVA 190
               R +    +G H+F  F      +  S IR +    V+       +    I I++  
Sbjct: 294 LAKFRASTSQYLGAHNFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIGDAQTEWISIKIHG 353

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +SF+  QIR  V    L+         + +A   Q  K   P AP  GL  +
Sbjct: 354 QSFMLHQIRKMVSMATLITRCGCPVERISQAYGQQ--KINIPKAPALGLLLE 403


>gi|308161589|gb|EFO64028.1| Pseudouridylate synthase 1 [Giardia lamblia P15]
          Length = 467

 Score = 88.0 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/224 (20%), Positives = 75/224 (33%), Gaps = 37/224 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIF---LVTGEIVVVHG---AGRT 51
             + + Y G+ Y G Q Q       +  +++G I  AI    L+ G  +   G     RT
Sbjct: 41  IAVALGYVGTRYSGSQWQAPSATHPDIRTVEGEIYTAIEAAGLLYGRDIKSIGWTRCSRT 100

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D  V A   V  F        V L +       +   ISI     V  +F A+ +   R+
Sbjct: 101 DKSVSAAMAVFSFFGPGHLDLVQLLQP-----HLPKDISIFGTVRVPPKFSAKMACTSRT 155

Query: 112 YLYRI--------ITRQAPLALEKGRAWLIPKSLD-------CENMRIAAQHLVG--RHD 154
           Y Y +           + P   +  +A+     LD        E +R A   L    RHD
Sbjct: 156 YEYMMPLVFLLPSSHDKTPALCQDMQAFFSY--LDSPYSAESTETVREACSRLYTAQRHD 213

Query: 155 FTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
              F  +  +    IR       +     +    + + FL   +
Sbjct: 214 ILDFLRLDDELQE-IRAQARVRASHDSPAVIFDTLLQPFLQQLV 256



 Score = 48.7 bits (115), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 25/62 (40%)

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I +  ++FL  QIR  +G+L  +  G    + L  A Q + +      AP   L      
Sbjct: 314 ITICGQAFLMYQIRRMMGALVAILRGWIPVSFLYFAFQTRTKHLRISTAPSPYLLLKQPN 373

Query: 246 YS 247
           Y 
Sbjct: 374 YE 375


>gi|19075946|ref|NP_588446.1| tRNA pseudouridine synthase Lsp1 [Schizosaccharomyces pombe 972h-]
 gi|74627010|sp|O94396|PUS1_SCHPO RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|4008551|emb|CAA22472.1| tRNA pseudouridine synthase Lsp1 [Schizosaccharomyces pombe]
 gi|6469502|emb|CAB61835.1| pseudouridine synthase [Schizosaccharomyces pombe]
          Length = 534

 Score = 87.6 bits (216), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 31/132 (23%), Positives = 48/132 (36%), Gaps = 13/132 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +   ++ Y GSGY G Q      +I+G +  A               + V +  A RTD
Sbjct: 44  RKVACLVGYCGSGYHGMQLNPPSKTIEGDLFDAFVKAGAVSSYNADDPKKVALARAARTD 103

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        L + +N +L    +I + ++      F+ R     R Y
Sbjct: 104 KGVHAAGNVISLKL--IMEDEKLIEKVNEHL--PPSIRLWDVIRTINSFNPRTYCESRIY 159

Query: 113 LYRIITRQAPLA 124
            Y + T      
Sbjct: 160 EYMVPTYAFVPP 171



 Score = 49.8 bits (118), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 36/107 (33%), Gaps = 8/107 (7%)

Query: 142 MRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNS-----FGNLIEIRVVARSFLH 195
           +R      VG H+F  F         +  R I  F  +          I  +V  +SF+ 
Sbjct: 324 IRETLNQYVGVHNFHNFTVGQAFHQKNSNRVIRSFTASDPFMIGDTEWISCKVHGQSFML 383

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            QIR  +    LV         ++ A   +  K   P  P  GL  +
Sbjct: 384 HQIRKMIALAILVVRTGCPVERIQDAF--KKTKINIPKGPGFGLLLE 428


>gi|322705939|gb|EFY97522.1| tRNA pseudouridine synthase [Metarhizium anisopliae ARSEF 23]
          Length = 612

 Score = 87.6 bits (216), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 54/148 (36%), Gaps = 13/148 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIE------KAIFLVT---GEIVVVHGAGRTD 52
            +  ++I Y+G+GY G Q   +  +I+  +       KAI            +    RTD
Sbjct: 115 RKVAVMIGYSGTGYKGMQVNGDEPTIERDLFRAFIDAKAISKANADDPRKSSLARCARTD 174

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +NA+L   + I I  +   +  F+       R Y
Sbjct: 175 KGVHAAGNVISLKL--IIEDEDIVEKINAHL--PEQIRIWGIQRTNNSFNCYQYCDSRFY 230

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCE 140
            Y + +        +       + L+ E
Sbjct: 231 EYLLPSYCLLPPHPQTYLAKECEKLNKE 258



 Score = 51.8 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/112 (22%), Positives = 40/112 (35%), Gaps = 9/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVAR 191
            + ++       G ++F  F         S  R I  F VN           + ++V  +
Sbjct: 391 LQRLQSVLDKYTGTYNFHNFTIQKTFSDPSARRHIKSFTVNPKPVIIGGTEWLSLKVHGQ 450

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           SF+  QIR  VG   L+         +      Q++K   P AP  GL  + 
Sbjct: 451 SFMMHQIRKMVGLASLMVRCGTALDRVAD--SYQEQKMAIPKAPGLGLLLER 500


>gi|50303379|ref|XP_451631.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|74637053|sp|Q6CWQ8|PUS1_KLULA RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|49640763|emb|CAH02024.1| KLLA0B02244p [Kluyveromyces lactis]
          Length = 553

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 32/126 (25%), Positives = 49/126 (38%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTD 52
            +  ++I Y G+GY G Q      +I+  + +A               +      A RTD
Sbjct: 99  RKVAVMIGYCGTGYHGMQYNPPNDTIEKELFEAFVRAGAISKANSTDLKKNGFQRAARTD 158

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +N  L   D I + ++S V+K F  R     R Y
Sbjct: 159 KGVHAGGNVISLKL--IIEDPEVKEKINNEL--PDQIRVWDISRVNKAFDCRKMCSSRWY 214

Query: 113 LYRIIT 118
            Y + T
Sbjct: 215 EYLLPT 220



 Score = 56.8 bits (136), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/130 (20%), Positives = 44/130 (33%), Gaps = 11/130 (8%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG--- 181
           E  RA+ I K    +  R A +   G  +F  F         S  R +    V+      
Sbjct: 305 EHKRAYRISKER-LDRFRSALKQYEGTFNFHNFTLGKDFNDPSAKRFMKQITVSEPFVIG 363

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + I++  +SF+  QIR  +    L+         + +       K   P AP  
Sbjct: 364 EAKTEWVSIKIHGQSFMLHQIRKMISMATLITRCFSPLERIRQ--AYGQEKINIPKAPAL 421

Query: 238 GLYFDSVEYS 247
           GL  ++  Y 
Sbjct: 422 GLLLEAPVYD 431


>gi|320532726|ref|ZP_08033515.1| hypothetical protein HMPREF9057_01391 [Actinomyces sp. oral taxon
          171 str. F0337]
 gi|320135064|gb|EFW27223.1| hypothetical protein HMPREF9057_01391 [Actinomyces sp. oral taxon
          171 str. F0337]
          Length = 57

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHA 57
          M R  + + Y+G+ + GW  Q    +++G +  A+  V  E V +  AGRTD+GVHA
Sbjct: 1  MPRIRLDLAYDGTFFSGWAAQPGLRTVEGVLTCALATVVREPVRLTVAGRTDAGVHA 57


>gi|312091557|ref|XP_003147023.1| hypothetical protein LOAG_11456 [Loa loa]
 gi|307757811|gb|EFO17045.1| hypothetical protein LOAG_11456 [Loa loa]
          Length = 236

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 33/126 (26%), Positives = 54/126 (42%), Gaps = 14/126 (11%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSG 54
           Y +++ Y G  Y G Q QK+  +++G + KA+           ++        A RTD  
Sbjct: 104 YALLLAYQGKKYNGMQVQKDFPTVEGELFKAMAKCGYISEDDILSPVRFAFQRAARTDRS 163

Query: 55  VHALRQVAHFDLVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           V A RQ+    L  E     L  A   LNA L   + I ++ +    + F A  +  +R+
Sbjct: 164 VSAARQMCSMRLAPENHEYFLKTASDKLNAQL--PEEIRVMGVRRATRSFKAHKNCDKRT 221

Query: 112 YLYRII 117
           Y Y + 
Sbjct: 222 YSYTLP 227


>gi|242776451|ref|XP_002478840.1| tRNA pseudouridine synthase, putative [Talaromyces stipitatus ATCC
           10500]
 gi|218722459|gb|EED21877.1| tRNA pseudouridine synthase, putative [Talaromyces stipitatus ATCC
           10500]
          Length = 580

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 44/204 (21%), Positives = 66/204 (32%), Gaps = 26/204 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  ++I Y+G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 75  KVAVMIGYSGTGYHGMQLSPTEKTIEGDLFAAFVAAGAISKANAADPKKSSLVRCARTDR 134

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + K +N  L  S  I +    IV K F        R Y 
Sbjct: 135 GVHAAGNVVSLKLIVEDPD--IVKKINDNL--SPQIRVWGYEIVTKGFSCYQLCDSRMYE 190

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I T              +P        +   Q      D   F           + ID
Sbjct: 191 YLIPTH-----------CFLPPHPSTHLGKKIVQFAEENEDMEGFLQRQEGVLDFWQNID 239

Query: 174 HFDVNSFGNLI--EIRVVARSFLH 195
              +      +  EIR + +  L+
Sbjct: 240 ESQIKPILEKVPEEIRRLVQRALY 263



 Score = 52.5 bits (125), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 47/125 (37%), Gaps = 10/125 (8%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG--- 181
              RA+ IP+S   + ++ A    VG  +F  +      +  S  R I  F  N      
Sbjct: 347 NAKRAYRIPQSR-LQRVQDALDKYVGTRNFHNYTIQKNFRDPSSKRVIKSFVANKEPIII 405

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + ++V  +SF+  QIR  V  + L+         +E+       +   P AP  G
Sbjct: 406 NGTEWVSLKVHGQSFMMHQIRKMVAMVALIVRCGCDPKIIEE--SYGPTRLSIPKAPGLG 463

Query: 239 LYFDS 243
           L  + 
Sbjct: 464 LLLEH 468


>gi|328350723|emb|CCA37123.1| tRNA pseudouridine synthase A [Pichia pastoris CBS 7435]
          Length = 516

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 31/131 (23%), Positives = 47/131 (35%), Gaps = 13/131 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTG---EIVVVHGAGRTDS 53
           +   +I Y G+GY G Q      +I+G + +      AI        +      A RTD 
Sbjct: 91  KVACLIGYCGTGYHGMQLNPPQKTIEGDLFEAFVESGAISRDNSNDLKKSSFMRAARTDK 150

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    +        + + +N+ L    TI +      +K F  R     R Y 
Sbjct: 151 GVHAAGNVISLKM--IIEDEDILEKINSKL--PPTIRVWGYERTNKNFDCRKMCSSRIYE 206

Query: 114 YRIITRQAPLA 124
           Y + T      
Sbjct: 207 YLMPTFSFLPP 217



 Score = 68.3 bits (166), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 27/115 (23%), Positives = 45/115 (39%), Gaps = 8/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARS 192
            E +  A Q  +G H+F  F    H + +S  R +    V+          + I++  +S
Sbjct: 314 LELVNKAMQMYIGHHNFHNFTLGKHFKDASANRYMKEITVSEPFVIEGTEWVSIKIHGQS 373

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  +    LV         + +A Q+   +   P AP  GL  +   Y 
Sbjct: 374 FMLHQIRKMIAMAALVVRTGCPLGRITEAFQSS--RINIPKAPALGLLLEQPVYE 426


>gi|254566437|ref|XP_002490329.1| tRNA:pseudouridine synthase, introduces pseudouridines at positions
           26-28, 34-36, 65, and 67 of tRNA [Pichia pastoris GS115]
 gi|238030125|emb|CAY68048.1| tRNA:pseudouridine synthase, introduces pseudouridines at positions
           26-28, 34-36, 65, and 67 of tRNA [Pichia pastoris GS115]
          Length = 509

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 31/131 (23%), Positives = 47/131 (35%), Gaps = 13/131 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTG---EIVVVHGAGRTDS 53
           +   +I Y G+GY G Q      +I+G + +      AI        +      A RTD 
Sbjct: 84  KVACLIGYCGTGYHGMQLNPPQKTIEGDLFEAFVESGAISRDNSNDLKKSSFMRAARTDK 143

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    +        + + +N+ L    TI +      +K F  R     R Y 
Sbjct: 144 GVHAAGNVISLKM--IIEDEDILEKINSKL--PPTIRVWGYERTNKNFDCRKMCSSRIYE 199

Query: 114 YRIITRQAPLA 124
           Y + T      
Sbjct: 200 YLMPTFSFLPP 210



 Score = 68.3 bits (166), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 27/115 (23%), Positives = 45/115 (39%), Gaps = 8/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARS 192
            E +  A Q  +G H+F  F    H + +S  R +    V+          + I++  +S
Sbjct: 307 LELVNKAMQMYIGHHNFHNFTLGKHFKDASANRYMKEITVSEPFVIEGTEWVSIKIHGQS 366

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  +    LV         + +A Q+   +   P AP  GL  +   Y 
Sbjct: 367 FMLHQIRKMIAMAALVVRTGCPLGRITEAFQSS--RINIPKAPALGLLLEQPVYE 419


>gi|322695818|gb|EFY87620.1| tRNA pseudouridine synthase [Metarhizium acridum CQMa 102]
          Length = 592

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 53/148 (35%), Gaps = 13/148 (8%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIE------KAIFLVT---GEIVVVHGAGRTD 52
            +  ++I Y+G+GY G Q   +  +I+  +       KAI            +    RTD
Sbjct: 115 RKVAVMIGYSGTGYKGMQVNGDEPTIERDLFRAFIDAKAISKANADDPRKSSLARCARTD 174

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +NA+L   + I I  +   +  F+       R Y
Sbjct: 175 KGVHAAGNVISLKL--IIEDEDIVDKINAHL--PEQIRIWGIQRTNNSFNCYQYCDSRFY 230

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCE 140
            Y + +        +       + L+ E
Sbjct: 231 EYLLPSYCLLPPHPQTYLAKECEKLNKE 258



 Score = 53.3 bits (127), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 40/112 (35%), Gaps = 9/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVAR 191
              ++       G ++F  F         S  R I  F VN           + ++V  +
Sbjct: 380 LRRLQQVLDKYTGTYNFHNFTIQKTFSDPSARRHIKSFTVNPKPIIIGDTEWLSLKVHGQ 439

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           SF+  QIR  VG   L+     T   +      Q++K   P AP  GL  + 
Sbjct: 440 SFMMHQIRKMVGLASLMVRCGTTLDRVGD--SYQEQKMAIPKAPGLGLLLER 489


>gi|156836479|ref|XP_001642300.1| hypothetical protein Kpol_228p5 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156112794|gb|EDO14442.1| hypothetical protein Kpol_228p5 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 562

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  +++ Y G+GY G Q      +I+ ++ K      AI       +       A RTD
Sbjct: 77  RKVAVMVGYCGTGYHGMQYNPPNPTIEDALFKAFVQAGAISKANSNDLKKNGFMRAARTD 136

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    +        + + +N  L   + I + N+  V+K F  R     R Y
Sbjct: 137 KGVHAGGNLISLKM--IIEDPEIKQKINEEL--PNGIKVWNIERVNKAFDCRKMCGSRWY 192

Query: 113 LYRIIT 118
            Y + T
Sbjct: 193 EYLLPT 198



 Score = 54.4 bits (130), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/125 (23%), Positives = 46/125 (36%), Gaps = 12/125 (9%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG--- 181
            + R  +  + L     R A    +G H+F  F      +  S IR +    V+      
Sbjct: 285 HRRRYRISDEKL--TKFRNAMNEYLGAHNFHNFTLGKDFKDPSAIRFMKEIRVSDPFVIG 342

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 I I++  +SF+  QIR  +    LV       + + +A   Q  K   P AP  
Sbjct: 343 AAKTEWISIKIHGQSFMLHQIRKMISMATLVTRCGCPVSRISQAYGPQ--KINIPKAPAL 400

Query: 238 GLYFD 242
           GL  +
Sbjct: 401 GLLLE 405


>gi|212532769|ref|XP_002146541.1| tRNA pseudouridine synthase, putative [Penicillium marneffei ATCC
           18224]
 gi|210071905|gb|EEA25994.1| tRNA pseudouridine synthase, putative [Penicillium marneffei ATCC
           18224]
          Length = 571

 Score = 86.8 bits (214), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/204 (20%), Positives = 67/204 (32%), Gaps = 26/204 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  ++I Y+G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 76  KVAVMIGYSGTGYHGMQLSPTEKTIEGDLFAAFVAAGAISKANAADPKKSSLVRCARTDR 135

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + + +N  L  S  I +     V K F        R Y 
Sbjct: 136 GVHAAGNVVSLKLIVEDPD--IVQKINDNL--SPQIRVWGYETVTKGFSCYQLCDSRMYE 191

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I T              +P        +   Q      D   F +         + ID
Sbjct: 192 YLIPTH-----------CFLPPHPSTHLGKKTVQLAEENEDMEGFLARQEGVLDFWQNID 240

Query: 174 HFDVNSFGNLI--EIRVVARSFLH 195
             ++      +  EIR + +  L+
Sbjct: 241 ENEIKPILEKVPEEIRRLVQRALY 264



 Score = 53.7 bits (128), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/125 (21%), Positives = 47/125 (37%), Gaps = 10/125 (8%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG--- 181
              RA+ IP++   + ++ A    +G  +F  +      +  S  R I  F  N      
Sbjct: 338 NAKRAYRIPQNR-LQRVQDALDKYIGTRNFHNYTIQKTFRDPSSKRIIKSFVANKEPIII 396

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
                + ++V  +SF+  QIR  V  + L+         +E+       K   P AP  G
Sbjct: 397 NGTEWVSLKVHGQSFMMHQIRKMVAMVALIVRCGCDPKIIEE--SYGPTKLSIPKAPGLG 454

Query: 239 LYFDS 243
           L  + 
Sbjct: 455 LLLEH 459


>gi|154300700|ref|XP_001550765.1| hypothetical protein BC1G_10938 [Botryotinia fuckeliana B05.10]
 gi|150856545|gb|EDN31737.1| hypothetical protein BC1G_10938 [Botryotinia fuckeliana B05.10]
          Length = 631

 Score = 86.8 bits (214), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 49/136 (36%), Gaps = 13/136 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDS 53
           +  ++I Y G+GY G Q      +I+G + KA      I        +   +    RTD 
Sbjct: 99  KVAVMIGYAGTGYKGLQINTKEKTIEGDMFKAFVAAGAISKANANDPKKSALIRCARTDK 158

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N++L   D I +  +      F+       R Y 
Sbjct: 159 GVHAAGNVLSLKL--IIEDPKVVENINSHL--PDQIRVWGIERTTGSFNCYQMCDSRWYE 214

Query: 114 YRIITRQAPLALEKGR 129
           Y I T        K  
Sbjct: 215 YLIPTYSFIPPHPKSF 230



 Score = 53.7 bits (128), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 44/110 (40%), Gaps = 9/110 (8%)

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVARS 192
           E ++ A    VG ++F  +  +   + +S  R I  F + +          + ++V  +S
Sbjct: 423 ERVQEALNQYVGTYNFHNYTILKSFKDASSKRHIKSFKIGTQPIIIHDTEWLSLKVHGQS 482

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           F+  QIR  V    LV         +++   A   K   P AP  GL  +
Sbjct: 483 FMMHQIRKMVAMAALVVRCASPMELIKETYTAA--KISIPKAPSLGLLLE 530


>gi|242066426|ref|XP_002454502.1| hypothetical protein SORBIDRAFT_04g032290 [Sorghum bicolor]
 gi|241934333|gb|EES07478.1| hypothetical protein SORBIDRAFT_04g032290 [Sorghum bicolor]
          Length = 567

 Score = 86.4 bits (213), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 33/125 (26%), Positives = 47/125 (37%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTD 52
            +  +++ Y G+GY G Q+     +I+G +E+A++                    A RTD
Sbjct: 52  RKVAILLGYCGAGYQGMQKNPGARTIEGDLEEALYQAGAVPEADRAAPRRYDWARAARTD 111

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GV A  QV          P      LNA L     I       V   F A+    RR Y
Sbjct: 112 KGVSAAAQVVSGRF--YVDPPGFIDRLNAQLAS--QIRAYGYVRVTNSFSAKKFCDRRRY 167

Query: 113 LYRII 117
           LY + 
Sbjct: 168 LYLLP 172



 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 26/110 (23%), Positives = 39/110 (35%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
           E      ++ VG H+F  F      +  +  R I  F  +        + +   VV +SF
Sbjct: 352 ERFNRILKYYVGTHNFHNFTTRTKAEDPAAKRFIISFGADRVVSLDGIDFVRCEVVGQSF 411

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  +G    V         +      +D     P AP  GLY D 
Sbjct: 412 MLHQIRKMIGLAVAVMRNC-APETIYDVAFRKDVNLNVPTAPEVGLYLDE 460


>gi|302803171|ref|XP_002983339.1| hypothetical protein SELMODRAFT_117791 [Selaginella moellendorffii]
 gi|300149024|gb|EFJ15681.1| hypothetical protein SELMODRAFT_117791 [Selaginella moellendorffii]
          Length = 437

 Score = 86.0 bits (212), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 61/328 (18%), Positives = 101/328 (30%), Gaps = 95/328 (28%)

Query: 3   RYCMIIEYNGSGYFG---------WQRQKNGSSIQGSIEKAIFLVTG---------EIVV 44
           +  M I Y G+GY G              + ++I+  ++KAI+   G           V 
Sbjct: 31  KVAMWIGYVGTGYKGNHCSLFLELSALNSSLTAIEADLDKAIYKAGGILDSNYGHHMKVG 90

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVI-------LCKALNAYLKISDTISILNLSIV 97
              + RTD GVH+L  V    +               +   +N +L     I +  +  V
Sbjct: 91  WARSSRTDKGVHSLATVISLKMELPIDAWRDDPGGIEIADRINRHL--PQCIRVFGVVPV 148

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
            K F  R +   RSY Y +      + + +  +    K L  E  R+  +   G H F  
Sbjct: 149 SKTFRPRMACSERSYDYFLP--ALCVGINQRVSTCEIKQL-LEQFRLQLKLFEGEHPFHN 205

Query: 158 FRSIHC------------------------------------------QASSPIRTIDHF 175
           +                                               Q  SP   +   
Sbjct: 206 YTIRRNYGKPKQQDLNWRTRTPIAADNSSSSEEEDEDGDADEPRLRVQQKPSPAYWLQEL 265

Query: 176 D--------------------VNSFGNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKW 213
           D                    +  FG+ + +R  V   SF+  QIR  +G+   V     
Sbjct: 266 DPTDRITSQHYRKIIRCSCGDIEKFGDTLALRVSVTGASFMVHQIRKMIGTAVAVTRKLL 325

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYF 241
               ++ +L  +  +   P+AP EGL  
Sbjct: 326 PPDIIQMSL-CRHSRIVLPIAPCEGLTL 352


>gi|156084710|ref|XP_001609838.1| RNA pseudouridine synthase A 2 [Babesia bovis T2Bo]
 gi|154797090|gb|EDO06270.1| RNA pseudouridine synthase A 2, putative [Babesia bovis]
          Length = 295

 Score = 85.6 bits (211), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 68/237 (28%), Gaps = 85/237 (35%)

Query: 2   IRYCMIIEYNGSGYFGW----------------------QRQKNG-SSIQGSIEKAIFLV 38
               M +EY+G  Y G+                       +QK    SI   I +A+ ++
Sbjct: 54  TNIVMTVEYDGGEYSGFVGPNHFYNEEKAKMLATVVMPRTKQKGVLKSISNEISRAMAII 113

Query: 39  TG-------------------------------------EIVVVHGAGRTDSGVHALRQV 61
            G                                         +  + RTD GVHA    
Sbjct: 114 HGYMPKSRKKKRTNCEPLTTELEENNEDDVHCPDTLPPERRFTLIASSRTDKGVHATETA 173

Query: 62  AHFDLVREWVP-----VILCKALNAYLKISDTISILNLSIVDK-QFHARFSAIRRSYLYR 115
             +    +  P       +   +N  L   D I +  +       FH RF  + + Y Y+
Sbjct: 174 CQYLSFDKEPPYNGDIDAIMDKVNRLL--PDDIRVTAMIHAPTLDFHVRFDNLGKHYTYK 231

Query: 116 IITRQAPLALEKGRAWL-----------------IPKSLDCENMRIAAQHLVGRHDF 155
           +   + P   E+   W                  + +    E+M+  A  + G H+F
Sbjct: 232 VDISETPNIFERKYYWQIMKDSQFRNTLMKKYNDVRQHFSFESMQKGANVIQGTHNF 288


>gi|254583001|ref|XP_002499232.1| ZYRO0E07106p [Zygosaccharomyces rouxii]
 gi|238942806|emb|CAR30977.1| ZYRO0E07106p [Zygosaccharomyces rouxii]
          Length = 537

 Score = 85.6 bits (211), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 48/126 (38%), Gaps = 13/126 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTD 52
            +  ++I Y G+GY G Q      +I+  +        AI       +       A RTD
Sbjct: 75  RKVAVMIGYCGTGYHGMQHNPPNLTIESELFTAFVEAGAISKANSTDLKKNGFMRAARTD 134

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   +    L        + + +N  L   + I + ++  V+K F  R     R Y
Sbjct: 135 KGVHAGGNLISLKL--IIEDPQIKEKINEKL--PEGIRVWDIKRVNKAFDCRKMCSSRWY 190

Query: 113 LYRIIT 118
            Y + T
Sbjct: 191 EYLLPT 196



 Score = 52.5 bits (125), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 10/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-------NLIEIRVVA 190
            +  R   +  +G H+F  F      + SS +R +    V+            + I++  
Sbjct: 294 LKKFRSTMEQYLGAHNFHNFTLGKDFKESSAVRYMKEIKVSEPFVIGDAKTEWVSIKIHG 353

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +SF+  QIR  +    L+      +  + +A   Q  K   P AP  GL  +
Sbjct: 354 QSFMLHQIRKMISMATLMTRCGCPTDRISEAYGPQ--KLNIPKAPALGLLLE 403


>gi|253744083|gb|EET00338.1| Pseudouridylate synthase 1 [Giardia intestinalis ATCC 50581]
          Length = 465

 Score = 85.3 bits (210), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 48/222 (21%), Positives = 79/222 (35%), Gaps = 35/222 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQ------KNGSSIQGSIEKAIF---LVTGEIVVVHG---AGRT 51
             + + Y G+ Y G Q Q       +  +++G +  AI    L+ G  +   G     RT
Sbjct: 41  IAIALGYVGTRYSGSQWQAPSVTHPHICTVEGEVYAAIEAAGLLYGRDIKSIGWTRCSRT 100

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D  V A   V  F          L +AL  +L     ISI     V  +F+A+ +   R+
Sbjct: 101 DKSVSAAMAVFSFFAPINLD---LVQALQPHL--PKDISIFGTVRVPPKFNAKMACTSRT 155

Query: 112 YLYRIITRQAPLALEKGRAWLIPK------SLD-------CENMRIAAQHLVG--RHDFT 156
           Y Y +       + +   A L P        L+        E ++ A   L    RHD  
Sbjct: 156 YEYIMPLAFLLPSSQDKTASLCPDMETFFSYLNSPLSTGGTETIKEACSRLYTAQRHDIL 215

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQI 198
            F  +  +    +R       +S  ++     + + FL   I
Sbjct: 216 DFLQLDDELRE-VRASLCASCDSPADM--FDTILQPFLQKLI 254



 Score = 53.3 bits (127), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 25/62 (40%)

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I +  ++FL  QIR  +G+L  +  G    T L  A Q + +      AP   L      
Sbjct: 312 ITICGQAFLMYQIRRMMGALVAIVRGWIPVTFLYFAFQTRTKHLRMSTAPGHYLLLKQPN 371

Query: 246 YS 247
           Y 
Sbjct: 372 YE 373


>gi|156048366|ref|XP_001590150.1| hypothetical protein SS1G_08914 [Sclerotinia sclerotiorum 1980]
 gi|154693311|gb|EDN93049.1| hypothetical protein SS1G_08914 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 599

 Score = 85.3 bits (210), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 33/136 (24%), Positives = 51/136 (37%), Gaps = 13/136 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDS 53
           +  ++I Y G+GY G Q      +I+G + KA      I        +   +    RTD 
Sbjct: 57  KVAVMIGYAGTGYKGLQINTKEKTIEGDMFKAFVAAGAISKANANDPKKSALVRCARTDK 116

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + + +N++L   D I +  +      F+       R Y 
Sbjct: 117 GVHAAGNVLSLKLITEDP--NVVENINSHL--PDQIRVWGIERTTGSFNCYQMCDSRWYE 172

Query: 114 YRIITRQAPLALEKGR 129
           Y I T        K  
Sbjct: 173 YLIPTYSFIPPHPKSF 188



 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/110 (20%), Positives = 41/110 (37%), Gaps = 9/110 (8%)

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVARS 192
           + ++ A    VG +++  +  +      S  R I  F +            + ++V  +S
Sbjct: 391 QRVQEALNQYVGTYNYHNYTILKNYSDPSSRRHIKSFKIGPKPIIIHDTEWLSLKVHGQS 450

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           F+  QIR  V    LV         +++   A   K   P AP  GL  +
Sbjct: 451 FMMHQIRKMVAMAALVVRCASPMELIKETYTAA--KISIPKAPSLGLLLE 498


>gi|50548607|ref|XP_501773.1| YALI0C12749p [Yarrowia lipolytica]
 gi|74635069|sp|Q6CC39|PUS1_YARLI RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|49647640|emb|CAG82083.1| YALI0C12749p [Yarrowia lipolytica]
          Length = 528

 Score = 85.3 bits (210), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 30/132 (22%), Positives = 49/132 (37%), Gaps = 13/132 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +   +I Y G+GY G Q      +I+G I +A               +      A RTD
Sbjct: 85  RKVACMIGYCGTGYHGMQLNPPQKTIEGDIFQAFVKAGAISQNNADDPKKSAFMRAARTD 144

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    +        + + +N++L   + + +  +S  +K F  R     R Y
Sbjct: 145 KGVHAAGNVISLKM--IIEDENIVEKINSHL--PEQLRVWGVSRTNKAFECRKLCSSRVY 200

Query: 113 LYRIITRQAPLA 124
            Y + T      
Sbjct: 201 EYLMPTYSFLNP 212



 Score = 56.8 bits (136), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/115 (20%), Positives = 39/115 (33%), Gaps = 7/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-----NLIEIRVVARS 192
              +R   +   G H+F  F      +  S +RT+     +          + I++  +S
Sbjct: 308 LAKIREILKIYEGTHNFHNFTLGKAFKDPSAMRTMKSLTCSDPFLIDGTEWVSIKIHGQS 367

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  +  + L          L      + R    P AP  GL  +   Y 
Sbjct: 368 FMLHQIRKMISMVALSVRCNADPQKLIPQTFEKARINI-PKAPALGLLLERPVYD 421


>gi|294655697|ref|XP_002770167.1| DEHA2C04312p [Debaryomyces hansenii CBS767]
 gi|199430534|emb|CAG85917.4| DEHA2C04312p [Debaryomyces hansenii]
          Length = 528

 Score = 84.9 bits (209), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 33/133 (24%), Positives = 48/133 (36%), Gaps = 15/133 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTG---------EIVVVHGAGRT 51
           +   +I Y G+GY G Q Q N    +I+G + +A               +      A RT
Sbjct: 72  KVACMIGYCGTGYNGMQIQNNLDVKTIEGDLFQAFVKAGAISPENADDLKKNGFMRAART 131

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D GVHA   V    L        + + +N  L   D I +  +   +K F  R     R 
Sbjct: 132 DKGVHAAGNVISCKL--IIEDEDILEKINKEL--PDQIRVWGIERTNKSFDCRKMCSSRV 187

Query: 112 YLYRIITRQAPLA 124
           Y Y + T      
Sbjct: 188 YEYLLPTYSFLSP 200



 Score = 62.5 bits (151), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 26/127 (20%), Positives = 47/127 (37%), Gaps = 9/127 (7%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF------RSIHCQASSPIRTIDHFDVNSF 180
           + R++ + K    E  R A +   G H+F  F      +    +    + T+    V   
Sbjct: 299 RRRSYSVSKER-LELFREAMKQYEGSHNFHNFTLGKLYKDPSARRYMKLTTVSDPFVIEG 357

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I++  +SF+  QIR  +    LV       + ++        K   P AP  GL 
Sbjct: 358 TEWVSIKIHGQSFMLHQIRKMISMAVLVIRTGCPISRIQDCF--GPTKINIPKAPALGLL 415

Query: 241 FDSVEYS 247
            ++  Y 
Sbjct: 416 LENPVYE 422


>gi|67539990|ref|XP_663769.1| hypothetical protein AN6165.2 [Aspergillus nidulans FGSC A4]
 gi|40738761|gb|EAA57951.1| hypothetical protein AN6165.2 [Aspergillus nidulans FGSC A4]
 gi|259479643|tpe|CBF70055.1| TPA: tRNA pseudouridine synthase, putative (AFU_orthologue;
           AFUA_2G08460) [Aspergillus nidulans FGSC A4]
          Length = 574

 Score = 84.9 bits (209), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 33/186 (17%), Positives = 66/186 (35%), Gaps = 24/186 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  ++I Y+G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 80  KVAVLIGYSGTGYKGMQLSTTEKTIEGELFTAFVAAGAISKANAADPKKSSLVRCARTDK 139

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   +    L+ E     + + +N +L  S  I +  + + +K F +      R Y 
Sbjct: 140 GVHAAGNIVSLKLIVEDPD--IVQKINDHL--SPQIRVWGILVANKSFSSYQMCDSRIYE 195

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I +              +P   +    +   +      D   +++   + ++    ID
Sbjct: 196 YLIPSH-----------CFLPPHPNTYLGKKLVEIAEKEGDLEAYKARQEEVANYWEDID 244

Query: 174 HFDVNS 179
              +  
Sbjct: 245 ERVIKP 250



 Score = 54.1 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 45/126 (35%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           L+  R + IP +     ++ A    VG  +F  +      +  S  R I  F +N     
Sbjct: 331 LKARREYRIPATR-LARIQQALDKYVGTKNFYNYTIQKQYRDPSAKRHIKSFKLNPEPII 389

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    +V         +       + K   P AP  
Sbjct: 390 IDGTEWLSLKVHGQSFMMHQIRKMVAMATMVVRCGCDPARIND--SYGEFKMAIPKAPGL 447

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 448 GLLLER 453


>gi|323331140|gb|EGA72558.1| Pus1p [Saccharomyces cerevisiae AWRI796]
          Length = 465

 Score = 84.5 bits (208), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 29/120 (24%), Positives = 47/120 (39%), Gaps = 13/120 (10%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVTGEIVV---VHGAGRTDSGVHAL 58
           + Y G+GY G Q      +I+ ++ K      AI       +       A RTD GVHA 
Sbjct: 2   VGYCGTGYHGMQYNPPNPTIESALFKAFVEAGAISKDNSNDLKKNGFMRAARTDKGVHAG 61

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
             +    +        + + +N  L   + I + ++  V+K F  R     R Y Y + T
Sbjct: 62  GNLISLKM--IIEDPDIKQKINEKL--PEGIRVWDIERVNKAFDCRKMCSSRWYEYLLPT 117



 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVA 190
               R +    +G H+F  F      +  S IR +    V+       +    I I++  
Sbjct: 215 LAKFRASTSQYLGAHNFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIGDAQTEWISIKIHG 274

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           +SF+  QIR  V    L+         + +A   Q  K   P AP  GL  +
Sbjct: 275 QSFMLHQIRKMVSMATLITRCGCPVERISQAYGQQ--KINIPKAPALGLLLE 324


>gi|327353057|gb|EGE81914.1| tRNA pseudouridine synthase [Ajellomyces dermatitidis ATCC 18188]
          Length = 610

 Score = 84.5 bits (208), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/181 (21%), Positives = 66/181 (36%), Gaps = 24/181 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDS 53
           +  +++ Y+GSGY G Q      +I+G +  A      I        +   +    RTD 
Sbjct: 122 KVAVMLGYSGSGYKGMQLSPTEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDK 181

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L  S  I +  + I +K F +      R Y 
Sbjct: 182 GVHAAGNVVSLKL--IVEDSDIVQKINEQL--SPQIRVWGIEITNKSFSSYHLCDSRIYE 237

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I T                 SL  + + IA Q     +D   ++    + ++  + +D
Sbjct: 238 YLIPTHCFLPP-------HPSTSLGQKLVEIAEQ----ENDLEGYKQRQAEVATYWKEVD 286

Query: 174 H 174
            
Sbjct: 287 E 287



 Score = 64.5 bits (156), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           L+  RA+ IPK    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 376 LDAKRAYRIPKER-MDRINDALGMYVGTRNFHNYTIQKSFRDASAKRLIKSFKISRDPLI 434

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V  + LV         + +  +  D K   P AP  
Sbjct: 435 INGTEWLSLKVHGQSFMMHQIRKMVAMVALVVRCGCDIQRIPETYE--DHKIAIPKAPGL 492

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 493 GLLLER 498


>gi|239606367|gb|EEQ83354.1| tRNA pseudouridine synthase [Ajellomyces dermatitidis ER-3]
          Length = 596

 Score = 84.5 bits (208), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/181 (21%), Positives = 66/181 (36%), Gaps = 24/181 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDS 53
           +  +++ Y+GSGY G Q      +I+G +  A      I        +   +    RTD 
Sbjct: 122 KVAVMLGYSGSGYKGMQLSPTEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDK 181

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +N  L  S  I +  + I +K F +      R Y 
Sbjct: 182 GVHAAGNVVSLKL--IVEDSDIVQKINEQL--SPQIRVWGIEITNKSFSSYHLCDSRIYE 237

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I T                 SL  + + IA Q     +D   ++    + ++  + +D
Sbjct: 238 YLIPTHCFLPP-------HPSTSLGQKLVEIAEQ----ENDLEGYKQRQAEVATYWKEVD 286

Query: 174 H 174
            
Sbjct: 287 E 287



 Score = 64.5 bits (156), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           L+  RA+ IPK    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 376 LDAKRAYRIPKER-MDRINDALGMYVGTRNFHNYTIQKSFRDASAKRLIKSFKISRDPLI 434

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V  + LV         + +  +  D K   P AP  
Sbjct: 435 INGTEWLSLKVHGQSFMMHQIRKMVAMVALVVRCGCDIQRIPETYE--DHKIAIPKAPGL 492

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 493 GLLLER 498


>gi|322821113|gb|EFZ27528.1| hypothetical protein TCSYLVIO_6263 [Trypanosoma cruzi]
          Length = 602

 Score = 84.5 bits (208), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 32/155 (20%), Positives = 54/155 (34%), Gaps = 24/155 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHG 47
            +  +I  Y G  Y G Q        +++  + +A+                 + +    
Sbjct: 68  RKVAIIFGYVGERYCGLQWNHLPGYPTVEEELLRALHRTGMISKENYEQEKVQQKLNWER 127

Query: 48  AGRTDSGVHALRQVAHFDL--------VREWVPVILCKALNAYLKISDTISILNLSIVDK 99
           A RTD GVHALR V   ++          E+ P    + L     +   I +  +  V +
Sbjct: 128 ASRTDKGVHALRNVISLNVMLPYAKGSTTEYDPQEARRIL--MTVLPHDIVVYEIVPVTR 185

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
            F+A      R+Y Y + T       E  R +  P
Sbjct: 186 SFNAYMLCGARTYEYYLPTFALMSLDEYSRDYFPP 220



 Score = 56.8 bits (136), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 28/60 (46%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++ I +  +SF+  QIR  +G++  +     +   L   L  +  +   P+AP  GL+ 
Sbjct: 464 EVVRIELHGQSFMLNQIRKMIGAVISICAAGLSPQYLRDHLLNKAVRCGVPMAPANGLFL 523


>gi|297723909|ref|NP_001174318.1| Os05g0279300 [Oryza sativa Japonica Group]
 gi|255676206|dbj|BAH93046.1| Os05g0279300 [Oryza sativa Japonica Group]
          Length = 133

 Score = 84.5 bits (208), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---EIVVVHGAGRTDSGVHALR 59
           ++ M+I Y+G+ + GWQ Q +  +IQ SIE A+  +T    + + + GAGRTD+GVHA  
Sbjct: 62  KWRMVIAYDGTKFKGWQYQPSPPTIQCSIENALTRITKLDRKELCLVGAGRTDTGVHAWG 121

Query: 60  QVAHF 64
              H 
Sbjct: 122 GAFHH 126


>gi|224126927|ref|XP_002319961.1| predicted protein [Populus trichocarpa]
 gi|222858337|gb|EEE95884.1| predicted protein [Populus trichocarpa]
          Length = 445

 Score = 84.5 bits (208), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/178 (21%), Positives = 66/178 (37%), Gaps = 28/178 (15%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  + + Y G+ Y G Q+Q +     +I+G +E+AI+   G           +    + R
Sbjct: 33  KVALRVGYVGTDYRGLQKQHDQHSLLTIEGELERAIYEAGGIRESNYGNLNKISWARSSR 92

Query: 51  TDSGVHALRQVAHFDLVREWVPVI-------LCKALNAYLKISDTISILNLSIVDKQFHA 103
           TD GVH+L       +               L K +N+YL   D+I +L++    K F  
Sbjct: 93  TDKGVHSLATTITMKMEIPENAWKDDLYGMVLAKHVNSYL--PDSIRVLSILPAQKSFDP 150

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD--CENMRIAAQHLVGRHDFTTFR 159
           R     R Y Y +     P  +   ++      +D    +         G H F  + 
Sbjct: 151 RRECDIRKYSYLL-----PAEVIGIKSHFSMAEIDDHISDFNNILNAFEGDHPFHNYT 203



 Score = 42.1 bits (98), Expect = 0.072,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +EI +   SF+  QIR  VG+   V         +  +L    R    PLAP E L  
Sbjct: 304 DFVEISIWGESFMLHQIRKMVGTAVAVKRKVLPRDLIMLSLTKFSR-IVLPLAPSEVLIL 362


>gi|242062118|ref|XP_002452348.1| hypothetical protein SORBIDRAFT_04g024105 [Sorghum bicolor]
 gi|241932179|gb|EES05324.1| hypothetical protein SORBIDRAFT_04g024105 [Sorghum bicolor]
          Length = 90

 Score = 84.1 bits (207), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 3/61 (4%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---FLVTGEIVVVHGAGRTDSGVHALR 59
          ++ M+I Y+G+ + GWQ Q +  +IQ  +E A+     +  + + + GAGRTD+GVHA  
Sbjct: 29 KWRMVIAYDGTKFKGWQYQPSIPTIQYFLEDALICITKLDRKKLCLVGAGRTDTGVHAWG 88

Query: 60 Q 60
          Q
Sbjct: 89 Q 89


>gi|261332259|emb|CBH15253.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 573

 Score = 84.1 bits (207), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 55/153 (35%), Gaps = 20/153 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHG 47
            +  +I  Y G  Y G Q     N  +++  + +A+                 + +    
Sbjct: 33  RKVAIIFGYIGERYCGLQWNHLPNYPTVEEELLRALRRADMISEENYAQQKVQQKLNWER 92

Query: 48  AGRTDSGVHALRQVAHFDLVREW-----VPVILCKALNAYLK-ISDTISILNLSIVDKQF 101
           A RTD GVHALR V   +++  +         + +A     + +   I +  +  V + F
Sbjct: 93  ASRTDKGVHALRNVFSLNVMLPYAKDSTSEFDVGEARRLLTEALPSDIVVYEIIPVTRSF 152

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
           +A      R Y Y + T     + E    +  P
Sbjct: 153 NAYMMCGSRKYEYYLPTFAFMNSEEYSNIYFPP 185



 Score = 51.4 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 25/61 (40%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++ I +  +SFL  QIR  +G++  +         L      +  +   P+ P  GL+ 
Sbjct: 435 EVVRIELSGQSFLFNQIRKMIGTVASMCAAGLPPDYLRDHFLNKAVRCGTPMVPANGLFL 494

Query: 242 D 242
            
Sbjct: 495 T 495


>gi|71000998|ref|XP_755180.1| tRNA pseudouridine synthase [Aspergillus fumigatus Af293]
 gi|66852818|gb|EAL93142.1| tRNA pseudouridine synthase, putative [Aspergillus fumigatus Af293]
 gi|159129271|gb|EDP54385.1| tRNA pseudouridine synthase, putative [Aspergillus fumigatus A1163]
          Length = 577

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/186 (18%), Positives = 59/186 (31%), Gaps = 24/186 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  ++I Y G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 80  KVAVLIGYAGTGYHGMQLSDKEKTIEGDLFTAFVAAGAISKANAADPKKSSLVRCARTDK 139

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        L K +N  L     I + ++ + +K F        R Y 
Sbjct: 140 GVHAAGNVVSLKL--IIEDPDLIKKINEKLC--PQIRVWDIQVTNKGFSCYQMCDSRVYE 195

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I +                        R   +      D   +R+   + ++    +D
Sbjct: 196 YLIPSYCFLPPHPSTY-----------LGRKIVELAEKEGDLEAYRARQEEVATYWEDVD 244

Query: 174 HFDVNS 179
           +  +  
Sbjct: 245 NERIKP 250



 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/128 (25%), Positives = 49/128 (38%), Gaps = 16/128 (12%)

Query: 126 EKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           E  RA+ IP   LD   ++      VG ++F  +         S  R I  F V+     
Sbjct: 333 EAKRAYRIPVARLD--RLQATLDKYVGTNNFYNYTIQKTYTDPSAKRFIKSFKVDRNPII 390

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAP 235
                 + ++V  +SF+  QIR  V     LV  G     D ++ + +    K   P AP
Sbjct: 391 INGTEWLSLKVHGQSFMMHQIRKMVAMATMLVRAGC----DPQRIVDSYGPTKIAIPKAP 446

Query: 236 PEGLYFDS 243
             GL  + 
Sbjct: 447 GLGLLLER 454


>gi|260944536|ref|XP_002616566.1| hypothetical protein CLUG_03807 [Clavispora lusitaniae ATCC 42720]
 gi|238850215|gb|EEQ39679.1| hypothetical protein CLUG_03807 [Clavispora lusitaniae ATCC 42720]
          Length = 229

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/124 (27%), Positives = 50/124 (40%), Gaps = 17/124 (13%)

Query: 8   IEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTG----------EIVVVHGAGRTDSGV 55
           I Y G+GY G Q Q   +  +I+  I KA F+  G          +      A RTD GV
Sbjct: 2   IGYCGTGYNGMQIQNNPDVKTIEAEIFKA-FIAAGAVSQENSTDLKKNGFMRAARTDKGV 60

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           HA   V    L        +   +N++L   + I +  +  V++ F  R     R Y Y 
Sbjct: 61  HAAGNVISCKL--ILEDEDIMHKINSHL--PEKIRLWGIERVNRSFDCRKLCSSRVYEYL 116

Query: 116 IITR 119
           + T 
Sbjct: 117 LPTH 120


>gi|255935685|ref|XP_002558869.1| Pc13g04330 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211583489|emb|CAP91502.1| Pc13g04330 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 548

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 48/136 (35%), Gaps = 13/136 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q  +   +I+G +  A+  V           +        RTD 
Sbjct: 84  KVALLMGYSGTGYSGMQLNEQQRTIEGDLFTALVNVGAVSKANAADPKKSSFVRCARTDK 143

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    +        + + +NA L  S  I +    +  K F        R Y 
Sbjct: 144 GVHAAGNVVSLKM--IVEDEDIIQKINAEL--SPQIRVWGYEVTSKSFSCYQMCDSRVYE 199

Query: 114 YRIITRQAPLALEKGR 129
           Y + +           
Sbjct: 200 YLMPSHCLVPPHPSTY 215



 Score = 57.1 bits (137), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 42/126 (33%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFG-- 181
           L   RA+  P S     ++       G  +F  +         S  R I  F VN+    
Sbjct: 300 LTAKRAYRAPASR-IARLQECLNRYEGTKNFHNYTIQKTHKDPSAKRHIKSFKVNTTPII 358

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    +V         + +       +   P AP  
Sbjct: 359 INGTEWLSLKVHGQSFMMHQIRKMVAMATMVVRSGCHPDRITE--TYGPERIAIPKAPGL 416

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 417 GLLLER 422


>gi|71664275|ref|XP_819120.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70884407|gb|EAN97269.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 621

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 32/155 (20%), Positives = 54/155 (34%), Gaps = 24/155 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHG 47
            +  +I  Y G  Y G Q        +++  + +A+                 + +    
Sbjct: 87  RKVAIIFGYVGERYCGLQWNHLPGYPTVEEELLRALHRTGMISKENYEQEKVQQKLNWER 146

Query: 48  AGRTDSGVHALRQVAHFDL--------VREWVPVILCKALNAYLKISDTISILNLSIVDK 99
           A RTD GVHALR V   ++          E+ P    + L     +   I +  +  V +
Sbjct: 147 ASRTDKGVHALRNVISLNVMLPYAKGSTTEYDPQEARRIL--MTVLPHDIVVYEIVPVTR 204

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
            F+A      R+Y Y + T       E  R +  P
Sbjct: 205 SFNAYMLCGARTYEYYLPTFALMSLDEYSRDYFPP 239



 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 15/102 (14%)

Query: 140 ENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIR 199
           E MR   QH+ G  DF++                   V +   ++ I +  +SF+  QIR
Sbjct: 456 EKMREHMQHVYG--DFSSGGVEGS-------------VKTGLEVVRIELHGQSFMLNQIR 500

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +G++  +     +   L   L  +  +   P+AP  GL+ 
Sbjct: 501 KMIGAVISICAAGLSPQYLRDHLLNKAVRCGVPMAPANGLFL 542


>gi|302412567|ref|XP_003004116.1| tRNA pseudouridine synthase [Verticillium albo-atrum VaMs.102]
 gi|261356692|gb|EEY19120.1| tRNA pseudouridine synthase [Verticillium albo-atrum VaMs.102]
          Length = 553

 Score = 83.3 bits (205), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 51/298 (17%), Positives = 80/298 (26%), Gaps = 101/298 (33%)

Query: 3   RY-CMIIEYNGSGYFGWQRQKNGS--SIQGS------------------------IEK-- 33
           RY  + + Y G  Y G++ Q++    +I+ +                        +E+  
Sbjct: 79  RYVALRLAYLGKNYNGFEHQQSAVQATIESALWRLWPGHRPPPPQQQAPAKTAAQLEEEA 138

Query: 34  -----AIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREW-----------VPVILCK 77
                A+     +         +   V A +Q                       +  CK
Sbjct: 139 RKKAEALQEKQKQQQQDGQGDVSMQDVAAEQQQQQQQQPPSPPPAPKPWDPIKDELPYCK 198

Query: 78  ALNAYLKISDTISILNLSI-VDKQFHARFSAIRRSYLYRIITRQAPLALE---------- 126
            LN  L     I IL       + F ARFS   R Y Y         A E          
Sbjct: 199 TLNRLL--PPDIRILAWCPSTPEGFSARFSCTERQYRYYFTQPAFAPAPEGLTPPKGPSQ 256

Query: 127 ---------KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHF 175
                              LD + MR AA+   G HDF  F  +    Q ++ +R +   
Sbjct: 257 PRKKKDAAPPPPPRPKVGYLDIDAMRAAAKKFEGLHDFRNFCKVDGGKQLTNFMRRMFEA 316

Query: 176 DVNSFGN--------------------------------LIEIRVVARSFLHTQIRSF 201
           D+    +                                +  + V   +FL  QIR  
Sbjct: 317 DIVEVDDVASAVPYLSGAAFAQPETAAHGGGGGGGVMPKVYYLHVRGSAFLWHQIRHM 374


>gi|295660198|ref|XP_002790656.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb01]
 gi|226281531|gb|EEH37097.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb01]
          Length = 600

 Score = 83.3 bits (205), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 34/182 (18%), Positives = 62/182 (34%), Gaps = 24/182 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTD 52
            +  +++ Y+GSGY G Q  +   +I+G +  A      I        +   +    RTD
Sbjct: 106 RKVAVLLGYSGSGYHGMQLSQTEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTD 165

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +N +L  S  I +  + + +K F +      R Y
Sbjct: 166 KGVHAAGNVVSLKL--IVEDSNVVQKINNHL--SPQIRVWGIEVTNKSFSSYQLCDSRVY 221

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I T                       +   A+     +D   +     + ++    +
Sbjct: 222 EYLIPTHCFLPPHPSTYLGQ--------KLVEIAEM---ENDLEGYNQRQAEVATYWEKV 270

Query: 173 DH 174
           D 
Sbjct: 271 DE 272



 Score = 65.6 bits (159), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 49/126 (38%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           LE  RA+ IPK    + +  A    VG  +F  +        +S  R I  F ++     
Sbjct: 366 LEAKRAYRIPKER-IDRINDALDLYVGTRNFHNYTIQKSFCEASAKRHIKSFKISRDPVI 424

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V  + +V         + +     D+K   P AP  
Sbjct: 425 INGTEWLSLKVHGQSFMMHQIRKMVAMVAMVVRCGCDIQRIPE--TYGDQKIAIPKAPGL 482

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 483 GLLLER 488


>gi|71413504|ref|XP_808888.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70873184|gb|EAN87037.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 634

 Score = 83.0 bits (204), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 32/155 (20%), Positives = 54/155 (34%), Gaps = 24/155 (15%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHG 47
            +  +I  Y G  Y G Q        +++  + +A+                 + +    
Sbjct: 100 RKVAIIFGYVGERYCGLQWNHLPGYPTVEEELLRALHRTGMISKENYEQEKVQQKLNWER 159

Query: 48  AGRTDSGVHALRQVAHFDL--------VREWVPVILCKALNAYLKISDTISILNLSIVDK 99
           A RTD GVHALR V   ++          E+ P    + L     +   I +  +  V +
Sbjct: 160 ASRTDKGVHALRNVISLNVMLPYAKGSTTEYDPQEARRIL--MTVLPHDIIVYEIVPVTR 217

Query: 100 QFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIP 134
            F+A      R+Y Y + T       E  R +  P
Sbjct: 218 SFNAYMLCGARTYEYYLPTFALMSLDEYSRDYFPP 252



 Score = 56.8 bits (136), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 28/60 (46%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++ I +  +SF+  QIR  +G++  +     +   L   L  +  +   P+AP  GL+ 
Sbjct: 496 EVVRIELHGQSFMLNQIRKMIGAVISICAAGLSPQYLRDHLLNKAVRCGVPMAPANGLFL 555


>gi|302893420|ref|XP_003045591.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256726517|gb|EEU39878.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 616

 Score = 82.6 bits (203), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 30/125 (24%), Positives = 46/125 (36%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTD 52
            +  ++I Y G+GY G Q   N  +I+  + K      AI        +   +    RTD
Sbjct: 114 RKVAVMIGYAGTGYKGMQVNGNEKTIEADLFKAFVAAGAISKANADDPKKSSLVRCARTD 173

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +NA L   + I I  +   +  F    +   R Y
Sbjct: 174 KGVHAAGNVISLKL--IIEDEDIIDKINAEL--PEQIRIWGIQRTNNAFSCYQTCDSRWY 229

Query: 113 LYRII 117
            Y + 
Sbjct: 230 EYLMP 234



 Score = 59.5 bits (143), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 33/152 (21%), Positives = 54/152 (35%), Gaps = 29/152 (19%)

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           +   A + A +R Y  RI T +                   E ++ A     G  +F  +
Sbjct: 380 RDIKAAYVAAKRRY--RISTGR------------------LERLQEALNKYNGTRNFHNY 419

Query: 159 RSIHCQ-ASSPIRTIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                   +S  R I  F VN           + ++V  +SF+  QIR  VG   L+   
Sbjct: 420 TVQKSYFDASAKRHIKSFVVNPKPIIINNTEWLSLKVHGQSFMMHQIRKMVGLASLIVRC 479

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
                 +++    Q++K   P AP  GL  + 
Sbjct: 480 GTPLKRMDE--SYQNQKMAIPKAPGLGLLLER 509


>gi|242040995|ref|XP_002467892.1| hypothetical protein SORBIDRAFT_01g035980 [Sorghum bicolor]
 gi|241921746|gb|EER94890.1| hypothetical protein SORBIDRAFT_01g035980 [Sorghum bicolor]
          Length = 520

 Score = 82.2 bits (202), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/178 (20%), Positives = 66/178 (37%), Gaps = 24/178 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           R  + I Y G+ Y G Q+Q+     S+I+  +E AIF   G         + V    + R
Sbjct: 78  RVVLRIGYIGTEYRGLQKQRELGVDSTIESVLESAIFKSGGILESNYGKLQKVGWERSSR 137

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       E  P  +  A      + D + + ++    + F  R 
Sbjct: 138 TDKGVHSLATMISLKMEIPDRAWEDDPDGIALASFINSNLPDNVRVFSILPAQRSFDVRR 197

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN--MRIAAQHLVGRHDFTTFRSI 161
             + R Y Y +        ++ G +   P+ +           +   G H F  + + 
Sbjct: 198 ECLYREYFYLLPAEVI--GIKDGYS---PEEIQEHLSEFNSILKGFEGNHPFHNYTAR 250



 Score = 49.1 bits (116), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +E+ +   SF+  QIR  VG+   V  G      +E +L    R    P+AP E L  
Sbjct: 362 QFVELTICGVSFMLHQIRKMVGTAVAVKRGLLPKDIIELSLAKFSR-IVLPIAPSEVLIL 420

Query: 242 DS 243
             
Sbjct: 421 KD 422


>gi|241956578|ref|XP_002421009.1| tNA-uridine isomerase, putative; tRNA pseudouridine synthase,
           putative; tRNA pseudouridylate synthase, putative
           [Candida dubliniensis CD36]
 gi|223644352|emb|CAX41165.1| tNA-uridine isomerase, putative [Candida dubliniensis CD36]
          Length = 488

 Score = 82.2 bits (202), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 33/128 (25%), Positives = 46/128 (35%), Gaps = 15/128 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFL---------VTGEIVVVHGAGR 50
            +  +++ Y GSGY G Q Q   N  +I+  I  A+           V  +      A R
Sbjct: 39  RKVAVMLGYCGSGYNGMQVQNDPNVKTIEKDIYDAMTKAGAISLENSVDLKKSGFQRAAR 98

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GVHA   V    +        +   +N  L     I I  +    K F  R     R
Sbjct: 99  TDKGVHAAGNVISLKM--IIEDPNIINKINDLL--PKQIRIWGIQRTTKGFDCRKCCSSR 154

Query: 111 SYLYRIIT 118
            Y Y + T
Sbjct: 155 IYEYLLPT 162



 Score = 55.2 bits (132), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 25/107 (23%), Positives = 40/107 (37%), Gaps = 8/107 (7%)

Query: 143 RIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHF-----DVNSFGNLIEIRVVARSFLHT 196
           R   +   G H+F  F      + +S  R I         V      I I++  +SF+  
Sbjct: 273 REVMKQYEGTHNFHNFTIGKPFKDTSANRFIIKTLISDPFVIEGTEWISIKIHGQSFMLH 332

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           QIR  +    L+      S  +    Q++  K   P AP  GL  ++
Sbjct: 333 QIRKMIAMATLIIRLNLPSNIINNFFQSK--KINIPKAPALGLLLEN 377


>gi|169839443|ref|ZP_02872631.1| tRNA pseudouridine synthase A [candidate division TM7 single-cell
          isolate TM7a]
          Length = 68

 Score = 82.2 bits (202), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 41/65 (63%), Gaps = 2/65 (3%)

Query: 2  IRYCMIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
              +I +Y+GS + G+QRQK  N  ++QG IEK I     + + +  +GRTD GVHA+ 
Sbjct: 4  RNVKIIYQYDGSKFLGFQRQKDNNVKTVQGEIEKVILKTFSQNINMISSGRTDKGVHAME 63

Query: 60 QVAHF 64
          QV++F
Sbjct: 64 QVSNF 68


>gi|116208668|ref|XP_001230143.1| hypothetical protein CHGG_03627 [Chaetomium globosum CBS 148.51]
 gi|88184224|gb|EAQ91692.1| hypothetical protein CHGG_03627 [Chaetomium globosum CBS 148.51]
          Length = 584

 Score = 82.2 bits (202), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 64/199 (32%), Gaps = 26/199 (13%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTD 52
            +  ++I Y G+GY G Q      +I+G +  A               +   +    RTD
Sbjct: 108 RKVAVLIGYAGTGYHGIQINHKEKTIEGDLFSAFVAAGAISKANADDPKKSSLVRCARTD 167

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +N +L   + I I  +      F A  +   R Y
Sbjct: 168 KGVHAAGNVLSLKL--IVEDEDIVTKINEHL--PEQIRIWGIHRTSNGFSAYQACESRWY 223

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV-GRHDFTTFRSIHCQASSPIRT 171
            Y          L    + L P+       RIAA     G +D   +             
Sbjct: 224 EY----------LMPSYSLLPPQPHSFLGKRIAASAKEQGVYD--EYMERLGDVKDFWDE 271

Query: 172 IDHFDVNSFGNLIEIRVVA 190
           ++  D+      ++  V A
Sbjct: 272 VEKNDIEPIFEGLDADVKA 290



 Score = 65.2 bits (158), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 23/112 (20%), Positives = 43/112 (38%), Gaps = 9/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFG------NLIEIRVVAR 191
            E ++ A    +G  ++  +  +     +S +R I  F VN+          + + V  +
Sbjct: 370 IEKLQQALNSYLGTRNYHNYTVMKSHKDASAMRHIKSFQVNTTPITIGDTEWLSLMVHGQ 429

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           SF+  QIR  V    +V       + + +      R+   P AP  GL  + 
Sbjct: 430 SFMMHQIRKMVAMAVMVVRCGAPLSTISE--SYGPRRISIPKAPGLGLMLER 479


>gi|46124417|ref|XP_386762.1| hypothetical protein FG06586.1 [Gibberella zeae PH-1]
          Length = 602

 Score = 81.8 bits (201), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 31/125 (24%), Positives = 46/125 (36%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTD 52
            +  ++I Y G+GY G Q   N  +I+  + K      AI        +   +    RTD
Sbjct: 107 RKVAVMIGYAGTGYKGMQVNGNEKTIEADLFKAFVAAGAISKANADDPKKSSLVRCARTD 166

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        +   +NA L   + I I  L   +  F    +   R Y
Sbjct: 167 KGVHAAGNVISLKL--IIEDEDIVDKINAEL--PEQIRIWGLQRTNNAFSCYQTCDSRWY 222

Query: 113 LYRII 117
            Y + 
Sbjct: 223 EYLMP 227



 Score = 61.0 bits (147), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/152 (21%), Positives = 54/152 (35%), Gaps = 29/152 (19%)

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF 158
           +   A + A +R Y  R+ T +                   E ++ A     G  +F  +
Sbjct: 365 RDIKAAYMAAKRRY--RVSTER------------------LERLQEALNMYNGTRNFHNY 404

Query: 159 RSIHCQ-ASSPIRTIDHFDVNSFG------NLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
                   +S  R I  F VN           + ++V  +SF+  QIR  VG   L+   
Sbjct: 405 TVQKSFFDASAKRHIKSFIVNPKPIIINDTEWLSLKVHGQSFMMHQIRKMVGLASLIVRC 464

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
                 +++    Q++K   P AP  GL  + 
Sbjct: 465 GTPMERIKE--SYQNQKMAIPKAPGLGLLLER 494


>gi|115442996|ref|XP_001218305.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
 gi|114188174|gb|EAU29874.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
          Length = 1199

 Score = 81.8 bits (201), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 31/136 (22%), Positives = 51/136 (37%), Gaps = 13/136 (9%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 80  KVAVLLGYSGTGYKGMQLSDTEKTIEGELFTAFVAAGAISKANAADPKKSSLVRCARTDK 139

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + + +N  L  S  I + ++ + +K F A      R Y 
Sbjct: 140 GVHAAGNVVSLKLIVEDPD--IVQKINEKL--SPQIRVWDILVANKSFSAYQMCDSRIYE 195

Query: 114 YRIITRQAPLALEKGR 129
           Y I T           
Sbjct: 196 YLIPTYCFLPPHPSTY 211



 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/124 (23%), Positives = 47/124 (37%), Gaps = 10/124 (8%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG---- 181
             RA+ IP S     +++A +  VG ++F  +        +S  R I  F ++       
Sbjct: 331 AKRAYRIPSSR-LTRVQVALEKYVGTNNFWNYTIQKTFTDASAKRHIKSFKLDPKPVIIN 389

Query: 182 --NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + ++V  +SF+  QIR  V    LV         +E        K   P AP  GL
Sbjct: 390 GTEWLSLKVHGQSFMMHQIRKMVAMATLVVRCGCDPKRIED--AYGPTKIAIPKAPGLGL 447

Query: 240 YFDS 243
             + 
Sbjct: 448 LLER 451


>gi|171685180|ref|XP_001907531.1| hypothetical protein [Podospora anserina S mat+]
 gi|170942551|emb|CAP68202.1| unnamed protein product [Podospora anserina S mat+]
          Length = 615

 Score = 81.8 bits (201), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 30/125 (24%), Positives = 46/125 (36%), Gaps = 13/125 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTD 52
            +  ++I Y G+GY G Q      +I+G I        AI        +   +    RTD
Sbjct: 120 RKVAVLIGYAGTGYHGIQINHKEKTIEGDIFAAFVAAGAISKANADDPKKSSLVRCARTD 179

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +N++L   + I I  +      F    S   R Y
Sbjct: 180 KGVHAAGNVLSLKL--IVEDEDIVEKINSHL--PEQIRIWGIQRTVNAFSCYQSCDSRWY 235

Query: 113 LYRII 117
            Y + 
Sbjct: 236 EYLMP 240



 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 23/112 (20%), Positives = 45/112 (40%), Gaps = 9/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVAR 191
            E ++ A    +G H++  +  +   + +S  R I  F+ N+          + ++V  +
Sbjct: 401 IERLQQALNLYLGTHNYHNYTVMKSFKDASAKRHIKSFEANTTPIQIGDTEWLSLKVHGQ 460

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           SF+  QIR  V    +V         +++      R+   P AP  GL  + 
Sbjct: 461 SFMMHQIRKMVAMAVMVVRCGAPLDLIKE--SYGPRRISIPKAPGLGLMLER 510


>gi|119480651|ref|XP_001260354.1| tRNA pseudouridine synthase, putative [Neosartorya fischeri NRRL
           181]
 gi|119408508|gb|EAW18457.1| tRNA pseudouridine synthase, putative [Neosartorya fischeri NRRL
           181]
          Length = 577

 Score = 81.4 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/186 (18%), Positives = 61/186 (32%), Gaps = 24/186 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  ++I Y G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 80  KVAVLIGYAGTGYHGMQLSDKEKTIEGDLFTAFVAAGAISKANAADPKKSSLVRCARTDK 139

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     L K +N  L     I + ++ + +K F        R Y 
Sbjct: 140 GVHAAGNVVSLKLIVEDPD--LIKKINEKLC--PQIRVWDIQVTNKGFSCYQMCDSRVYE 195

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I +                        R   +      D   +++   + ++    +D
Sbjct: 196 YLIPSYCFLPPHPSTY-----------LGRKIVELAEKEGDLEAYKARQEEVATYWEDVD 244

Query: 174 HFDVNS 179
           +  +  
Sbjct: 245 NERIKP 250



 Score = 52.5 bits (125), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 30/127 (23%), Positives = 49/127 (38%), Gaps = 14/127 (11%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG--- 181
           E  RA+ IP +   + ++      VG ++F  +         S  R I  F V+      
Sbjct: 333 EAKRAYRIPAAR-LDRLQATLDKYVGTNNFYNYTIQKTYTDPSAKRFIKSFKVDRNPIII 391

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAPP 236
                + ++V  +SF+  QIR  V     LV  G     D ++ + +    K   P AP 
Sbjct: 392 NGTEWLSLKVHGQSFMMHQIRKMVAMATMLVRAGC----DPQRIVDSYGPTKIAIPKAPG 447

Query: 237 EGLYFDS 243
            GL  + 
Sbjct: 448 LGLLLER 454


>gi|255081298|ref|XP_002507871.1| predicted protein [Micromonas sp. RCC299]
 gi|226523147|gb|ACO69129.1| predicted protein [Micromonas sp. RCC299]
          Length = 523

 Score = 81.4 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 55/278 (19%), Positives = 89/278 (32%), Gaps = 57/278 (20%)

Query: 23  NGSSIQGSIEKAIFLV--TGEIVVVHGAGRTDSGVHALRQVAHFDLV--REWVPVILCKA 78
              S+  SI++A+  +  + +  ++H AGRTD GVHA  Q           + P  +  A
Sbjct: 237 GERSVSASIQRALRPLFSSDKERLIHSAGRTDKGVHAAAQCFSVWSNAKDTFTPRNVRDA 296

Query: 79  LNAYLKISDTIS--ILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKS 136
           L A+   +      + ++  V   FHA F A  R Y+Y +  R      E G +     +
Sbjct: 297 LVAHPAHAAGAWRVVGDVEEVSDAFHATFCATWRRYVYILPMRSLGDEEENGLS---NVA 353

Query: 137 LDCENMRIAAQHLVGR-HDFTTFRSIHCQASSPIRTIDHFDVNS---------------- 179
           +D          L G+  D + F             +                       
Sbjct: 354 VDPAATNAMLNALEGKSMDMSAFARATPPGKDSTCFVKVARAFEATVPASKGAERGVGRG 413

Query: 180 -------------------------------FGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
                                             ++ + +VA  FL   +R+ V +    
Sbjct: 414 ARRRKSAGFSEDGGLGVGGGGGGDGGPPNSTMERVLVVELVADRFLRKMVRTLVATAVRE 473

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                    L +  +A +R    P APPEGL F  V Y
Sbjct: 474 AATGARGDVLLRLARAGERAATAPPAPPEGLIFAGVGY 511


>gi|194697948|gb|ACF83058.1| unknown [Zea mays]
          Length = 516

 Score = 81.4 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 31/132 (23%), Positives = 53/132 (40%), Gaps = 17/132 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           R  + I Y G+ Y G Q+Q+     S+I+  +E AIF   G         + +    + R
Sbjct: 78  RVVLRIGYVGTDYRGLQKQQELGVDSTIESVLESAIFKSGGILESNYGKLQKIGWERSSR 137

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       E  P  +  A      + D + + ++    + F  R 
Sbjct: 138 TDKGVHSLATMISLKMEIPDRAWEDDPDGIALASFINSNLPDNVRVFSILPAQRSFDVRR 197

Query: 106 SAIRRSYLYRII 117
             + R Y Y + 
Sbjct: 198 ECLYREYFYLLP 209



 Score = 47.5 bits (112), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +E+ +   SF+  QIR  VG+   V  G      +E +L    R    P+AP E L  
Sbjct: 363 QFVELTICGVSFMLHQIRKMVGTAVTVKRGLLPRDIIELSLAKFSR-IVLPIAPSEVLVL 421

Query: 242 DS 243
             
Sbjct: 422 KD 423


>gi|302417130|ref|XP_003006396.1| tRNA pseudouridine synthase [Verticillium albo-atrum VaMs.102]
 gi|261353998|gb|EEY16426.1| tRNA pseudouridine synthase [Verticillium albo-atrum VaMs.102]
          Length = 439

 Score = 81.4 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 32/140 (22%), Positives = 49/140 (35%), Gaps = 22/140 (15%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRT 51
           M+R         +GY+G Q   +  +I+G + KA      I        +   +    RT
Sbjct: 51  MMR---------TGYYGLQINWDEKTIEGDLFKAFIAAGAISKANADDPKKSSLSRCART 101

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           D GVHA   +    L        +   +NA+L   D I +  L      F A  +   R 
Sbjct: 102 DKGVHAAGNLISLKL--IIEDDDIVDKINAHL--PDQIRVWGLQRTSNSFSAYQACDSRW 157

Query: 112 YLYRIITRQAPLALEKGRAW 131
           Y Y + T     +      W
Sbjct: 158 YEYLLPTYCLLPSHPDSFLW 177



 Score = 45.6 bits (107), Expect = 0.007,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVN------S 179
             RA+ +      + ++ A    VG ++F  +      +  S  R I  F VN       
Sbjct: 299 AKRAYQVTNER-LDQLQAALDQYVGTYNFHNYTIQKSFKDPSAKRHIKSFQVNKTPIQIR 357

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
               + I+V  +SF+  QIR  +    LV
Sbjct: 358 DTQWVSIKVHGQSFMMHQIRKMISMATLV 386


>gi|255553385|ref|XP_002517734.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223543132|gb|EEF44666.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 377

 Score = 81.4 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 38/189 (20%), Positives = 66/189 (34%), Gaps = 27/189 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  + + Y G+ Y G Q+Q++    S+I+  +E AIF   G           +    + R
Sbjct: 55  KVVLRVGYVGTDYRGLQKQEDEHSLSTIEAELECAIFKAGGILDSNYGNLHKIAWARSSR 114

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       +  P  +  A      + D I I ++    K F  R 
Sbjct: 115 TDKGVHSLATMISMKMEIPENAWKEDPNGIALAECVNYYLPDNIRIFSILPSQKSFDPRR 174

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD--CENMRIAAQHLVGR---HDFTTFRS 160
               R Y Y +     P  +   +       +D    +         G    H++T    
Sbjct: 175 ECNLRKYSYLL-----PAEIIGIKGHFTSAEIDNHISDFNDILNAFEGEHPFHNYTIRSK 229

Query: 161 IHCQASSPI 169
              Q  + I
Sbjct: 230 YRKQYPTAI 238


>gi|121698285|ref|XP_001267772.1| tRNA pseudouridine synthase, putative [Aspergillus clavatus NRRL 1]
 gi|119395914|gb|EAW06346.1| tRNA pseudouridine synthase, putative [Aspergillus clavatus NRRL 1]
          Length = 568

 Score = 81.0 bits (199), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/186 (18%), Positives = 60/186 (32%), Gaps = 24/186 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  ++I Y G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 80  KVAVLIGYAGTGYHGMQLSDKEKTIEGDLFAAFVAAGAISKANAADPKKSSLVRCARTDK 139

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + K +N  L     I + ++ + +K F        R Y 
Sbjct: 140 GVHAAGNVVSLKLIVEDPD--IVKKINEQLC--PQIRVWDVQVTNKGFSCYQMCDSRVYE 195

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I +                        R   +      D    ++   + ++    ID
Sbjct: 196 YLIPSYCFLPPHPSTY-----------LGRKIVELAEKEGDLEGLKARQEEVATYWNDID 244

Query: 174 HFDVNS 179
           +  +  
Sbjct: 245 NERIKP 250



 Score = 55.2 bits (132), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 30/127 (23%), Positives = 50/127 (39%), Gaps = 14/127 (11%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFG--- 181
           E  RA+ IP S+  + ++      +G ++F  +         S  R I  F V+      
Sbjct: 322 EAKRAYRIP-SIRLDRLQATLDKYIGTNNFYNYTIQKTHGDPSAKRYIKTFQVDRNSILI 380

Query: 182 ---NLIEIRVVARSFLHTQIRSFVGSL-KLVGDGKWTSTDLEKALQA-QDRKECGPLAPP 236
                + ++V  +SF+  QIR  V     LV  G     D  + +++    K   P AP 
Sbjct: 381 NGTEWLSLKVHGQSFMMHQIRKMVAMATMLVRAG----GDPARIVESYGPTKIAVPKAPG 436

Query: 237 EGLYFDS 243
            GL  + 
Sbjct: 437 LGLLLER 443


>gi|150865014|ref|XP_001384060.2| hypothetical protein PICST_58964 [Scheffersomyces stipitis CBS
           6054]
 gi|149386270|gb|ABN66031.2| predicted protein [Scheffersomyces stipitis CBS 6054]
          Length = 476

 Score = 81.0 bits (199), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 33/128 (25%), Positives = 47/128 (36%), Gaps = 15/128 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFL---------VTGEIVVVHGAGR 50
            +  ++I Y G+GY G Q Q      +I+  + +A            +  +      A R
Sbjct: 80  RKVAVMIGYCGTGYNGMQLQNDPKIPTIERDLYEAFAAAGAVSPENAMDIKKSGFMRAAR 139

Query: 51  TDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           TD GVHA   V    L        +   +N  L   D I I  +  V K F  R     R
Sbjct: 140 TDKGVHAAGNVISLKL--IIEDPEILAKINEKL--PDQIRIWGIQRVTKSFDCRKMCSSR 195

Query: 111 SYLYRIIT 118
            Y Y + T
Sbjct: 196 VYEYLLPT 203



 Score = 62.5 bits (151), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 27/128 (21%), Positives = 46/128 (35%), Gaps = 11/128 (8%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI-------RTIDHFDVNS 179
           + RA+ +      E  R A +   G H+F  F +I      P         T+    +  
Sbjct: 298 RRRAYTVSTER-LELFRQAMKQYEGTHNFHNF-TIGKAFKDPSSKRFMKETTVSDPFIIE 355

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + I++  +SF+  QIR  +    LV       + +     +   K   P AP  GL
Sbjct: 356 GTEWVSIKIHGQSFMLHQIRKMIAMAVLVIRTGCPISRIHDCFSST--KINIPKAPALGL 413

Query: 240 YFDSVEYS 247
             ++  Y 
Sbjct: 414 LLENPVYE 421


>gi|320588025|gb|EFX00500.1| tRNA pseudouridine synthase [Grosmannia clavigera kw1407]
          Length = 899

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 51/259 (19%), Positives = 85/259 (32%), Gaps = 52/259 (20%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTD 52
            +  ++I Y G+GY G Q   +  +I+G +  A               +   +    RTD
Sbjct: 417 RKVAVMIGYAGTGYRGMQINHDEKTIEGDLFAAFVAAGAIAKTNADDPKKSSLVRCARTD 476

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +NA+L     I +  +      F    +   R Y
Sbjct: 477 KGVHAAGNVISLKL--IVEDADVVERINAHL--PPQIRVWGIQRTINSFSCYQACDSRWY 532

Query: 113 LYRIITR----QAPLALEKGRAWLIPKSLDCENMRIAAQHLVG------RH---DFTTF- 158
            Y + +       P +          +  D      AA+  VG       H   D   F 
Sbjct: 533 EYLLPSYALLPPHPDSFLGREMVASARRAD------AAEGAVGGMYDDMVHRLEDVRDFW 586

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL 218
             +     +PI      +V     L+  ++ A  F     R+          G  +  D+
Sbjct: 587 SDVERDVVTPILDGLDAEVRR---LVVEQLHATDF-----RTL---------GHRSLDDI 629

Query: 219 EKALQ--AQDRKECGPLAP 235
           EK ++  A+   E    AP
Sbjct: 630 EKTVEEAAKPAAELTATAP 648



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/113 (22%), Positives = 41/113 (36%), Gaps = 10/113 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVAR 191
              ++ A     G  +F  +      + +S  R I  F VN           + +RV  +
Sbjct: 681 LARLQEALSMYEGTSNFHNYTVQKSFKDASAKRHIKSFVVNPEPIQMRDTQWLSLRVHGQ 740

Query: 192 SFLHTQIRSFVGSLKLVGD-GKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           SF+  QIR  V    ++   G      ++  L    R+   P AP  GL  + 
Sbjct: 741 SFMMHQIRKMVAMAVMLTRCGTAPGPAMK--LSYGPRRISIPRAPGFGLLLER 791


>gi|297745794|emb|CBI15850.3| unnamed protein product [Vitis vinifera]
          Length = 495

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/174 (20%), Positives = 61/174 (35%), Gaps = 20/174 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  M + Y G+ Y G Q Q++    S+I+G +E A+F   G           +    + R
Sbjct: 64  KVVMRVGYVGTNYRGLQMQRDESSLSTIEGELETAVFKAGGIRDSNYGNLHKIGWDRSSR 123

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       +  P  +  A      + + I + ++    + F AR 
Sbjct: 124 TDKGVHSLATMISLKMEIPANAWKEDPNGIALANYVNFHLPNNIKVFSILPSQRSFDARR 183

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
               R Y Y +    A +   K  +                    G H F  + 
Sbjct: 184 ECDLRRYSYLL---PAEIIGIKSNSSASEIDHHIAEFNDILNTFEGEHPFQNYT 234


>gi|225434389|ref|XP_002276856.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 564

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/174 (20%), Positives = 61/174 (35%), Gaps = 20/174 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  M + Y G+ Y G Q Q++    S+I+G +E A+F   G           +    + R
Sbjct: 64  KVVMRVGYVGTNYRGLQMQRDESSLSTIEGELETAVFKAGGIRDSNYGNLHKIGWDRSSR 123

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       +  P  +  A      + + I + ++    + F AR 
Sbjct: 124 TDKGVHSLATMISLKMEIPANAWKEDPNGIALANYVNFHLPNNIKVFSILPSQRSFDARR 183

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
               R Y Y +    A +   K  +                    G H F  + 
Sbjct: 184 ECDLRRYSYLL---PAEIIGIKSNSSASEIDHHIAEFNDILNTFEGEHPFQNYT 234



 Score = 41.7 bits (97), Expect = 0.084,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 165 ASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           ++S  R I +            + +E+ +   SF+  QIR  VG+   V   +    D+ 
Sbjct: 341 SASHFRKIFNCSCGKLEKFLGLDYVELSICGESFMLHQIRKMVGTAIAV-KRELLPRDIL 399

Query: 220 KALQAQDRKECGPLAPPEGLYF 241
                +  +   PLAP E L  
Sbjct: 400 TLSLTKFSRIVLPLAPSEVLIL 421


>gi|147800604|emb|CAN68579.1| hypothetical protein VITISV_034891 [Vitis vinifera]
          Length = 602

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/174 (20%), Positives = 61/174 (35%), Gaps = 20/174 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  M + Y G+ Y G Q Q++    S+I+G +E A+F   G           +    + R
Sbjct: 64  KVVMRVGYVGTNYRGLQMQRDESSLSTIEGELETAVFKAGGIRDSNYGNLHKIGWDRSSR 123

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       +  P  +  A      + + I + ++    + F AR 
Sbjct: 124 TDKGVHSLATMISLKMEIPANAWKEDPNGIALANYVNFHLPNNIKVFSILPSQRSFDARR 183

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
               R Y Y +    A +   K  +                    G H F  + 
Sbjct: 184 ECDLRRYSYLL---PAEIIGIKSNSSASEIDHHIAEFNDILNTFEGEHPFQNYT 234



 Score = 41.7 bits (97), Expect = 0.084,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 165 ASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           ++S  R I +            + +E+ +   SF+  QIR  VG+   V   +    D+ 
Sbjct: 341 SASHFRKIFNCSCGKLEKFLGLDYVELSICGESFMLHQIRKMVGTAIAV-KRELLPRDIL 399

Query: 220 KALQAQDRKECGPLAPPEGLYF 241
                +  +   PLAP E L  
Sbjct: 400 TLSLTKFSRIVLPLAPSEVLIL 421


>gi|325088485|gb|EGC41795.1| tRNA pseudouridine synthase [Ajellomyces capsulatus H88]
          Length = 612

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/181 (19%), Positives = 65/181 (35%), Gaps = 24/181 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDS 53
           +  +++ Y+GSGY G Q  +   +I+G +  A      I        +   +    RTD 
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDK 181

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + + +N +L  S  I +  + I +K F +      R Y 
Sbjct: 182 GVHAAGNVVSLKLIVEDP--NVVQKINGHL--SPQIRVWGIEITNKSFSSYHLCDSRIYE 237

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I +              +P        +   +     +D   ++    + +     +D
Sbjct: 238 YLIPSH-----------CFLPPHPSTHLGQQLVEIAEQENDLEGYQQRQAEVAHYWEEVD 286

Query: 174 H 174
            
Sbjct: 287 E 287



 Score = 60.2 bits (145), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 49/126 (38%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           L+  +A+ IP+    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 378 LDAKKAYRIPRER-MDRINDALGMYVGTRNFHNYTIQKSFRDASAKRHIKSFKISREPLI 436

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    L+         + +     D+K   P AP  
Sbjct: 437 INGTEWLSLKVHGQSFMMHQIRKMVAMAALIVRCGCDIKLVPE--TYGDQKIAIPKAPGL 494

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 495 GLLLER 500


>gi|225559412|gb|EEH07695.1| tRNA pseudouridine synthase [Ajellomyces capsulatus G186AR]
          Length = 612

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/181 (19%), Positives = 65/181 (35%), Gaps = 24/181 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDS 53
           +  +++ Y+GSGY G Q  +   +I+G +  A      I        +   +    RTD 
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDK 181

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + + +N +L  S  I +  + I +K F +      R Y 
Sbjct: 182 GVHAAGNVVSLKLIVEDP--NVVQKINGHL--SPQIRVWGIEITNKSFSSYHLCDSRIYE 237

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I +              +P        +   +     +D   ++    + +     +D
Sbjct: 238 YLIPSH-----------CFLPPHPSTHLGQQLVEIAEQENDLEGYQQRQAEVAHYWEEVD 286

Query: 174 H 174
            
Sbjct: 287 E 287



 Score = 58.7 bits (141), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 48/126 (38%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           L   +A+ IP+    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 378 LGAKKAYRIPRER-MDRINDALGMYVGTRNFHNYTIQKSFRDASAKRHIKSFKISREPLI 436

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    L+         + +     D+K   P AP  
Sbjct: 437 INGTEWLSLKVHGQSFMMHQIRKMVAMAALIVRCGCDIKLVPE--TYGDQKIAIPKAPGL 494

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 495 GLLLER 500


>gi|213584576|ref|ZP_03366402.1| tRNA pseudouridine synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. E98-0664]
          Length = 57

 Score = 80.3 bits (197), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 21/47 (44%), Positives = 29/47 (61%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAG 49
          +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AG
Sbjct: 11 KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAG 57


>gi|118349886|ref|XP_001008224.1| tRNA pseudouridine synthase family protein [Tetrahymena
           thermophila]
 gi|89289991|gb|EAR87979.1| tRNA pseudouridine synthase family protein [Tetrahymena thermophila
           SB210]
          Length = 484

 Score = 79.9 bits (196), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 72/196 (36%), Gaps = 26/196 (13%)

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           +      +  ALN+ L     I  +++  V ++F  R     R Y Y +     PL + +
Sbjct: 230 KHIDIDKIINALNSNL--PADIRCVSIKQVSRKFDIRTHCKYRVYEYLM-----PLFMYQ 282

Query: 128 GRAWLIPKSLDCE-----NMRI---AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               +I  +   E      M+     A    G H++  +     +A  P       D+ +
Sbjct: 283 KYDDIIAGTPMTEEFEQKTMQRVSTLADKFKGTHNYHNYTR-QMKAKDPRCMRYILDMKT 341

Query: 180 F--------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
                       I   +V +SF++ QIR  +G + ++    +    ++ +      +   
Sbjct: 342 ELITNPQNGMKFIRFTLVGQSFVYHQIRKMMGMICMMIQEDYPDNFMDSSFFHNVMRIW- 400

Query: 232 PLAPPEGLYFDSVEYS 247
            LAP  GL+ + + + 
Sbjct: 401 -LAPAHGLFLNRMRFD 415



 Score = 49.8 bits (118), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 11/98 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAI--FLVTGEI-------VVVHGAGRT 51
           +  +   YNG GY G Q QK+ +  +I+ S+ + +    +  E               RT
Sbjct: 12  KVAIFFGYNGKGYHGSQSQKDQNIKTIEKSLFEGLIDSKLISETHMGELKKAGWGRGART 71

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTI 89
           D GVHAL    +  L      ++    L    K  + I
Sbjct: 72  DKGVHALCNGVNVKLAISEEYLMRGSPLRMDDKNPEEI 109


>gi|240282351|gb|EER45854.1| tRNA pseudouridine synthase [Ajellomyces capsulatus H143]
          Length = 612

 Score = 79.9 bits (196), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/181 (19%), Positives = 65/181 (35%), Gaps = 24/181 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDS 53
           +  +++ Y+GSGY G Q  +   +I+G +  A      I        +   +    RTD 
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDK 181

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L+ E     + + +N +L  S  I +  + I +K F +      R Y 
Sbjct: 182 GVHAAGNVVSLKLIVEDP--NVVQKINGHL--SPQIRVWGIEITNKSFSSYHLCDSRIYE 237

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y I +              +P        +   +     +D   ++    + +     +D
Sbjct: 238 YLIPSH-----------CFLPPHPSTHLGQQLVEIAEQENDLEGYQQRQVEVAHYWEEVD 286

Query: 174 H 174
            
Sbjct: 287 E 287



 Score = 60.2 bits (145), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 49/126 (38%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           L+  +A+ IP+    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 378 LDAKKAYRIPRER-MDRINDALGMYVGTRNFHNYTIQKSFRDASAKRHIKSFKISREPLI 436

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    L+         + +     D+K   P AP  
Sbjct: 437 INGTEWLSLKVHGQSFMMHQIRKMVAMAALIVRCGCDIKLVPE--TYGDQKIAIPKAPGL 494

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 495 GLLLER 500


>gi|218192790|gb|EEC75217.1| hypothetical protein OsI_11484 [Oryza sativa Indica Group]
          Length = 722

 Score = 79.9 bits (196), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 31/132 (23%), Positives = 54/132 (40%), Gaps = 17/132 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           R  + + Y G+ Y G Q+Q+     S+I+  +E AIF   G         + V    + R
Sbjct: 73  RVVLRVGYVGTEYRGLQKQRELSADSTIESVLETAIFKAGGILESNYGKLQKVGWERSSR 132

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       E  P  +  +      + D + + ++    + F  R 
Sbjct: 133 TDKGVHSLATMISLKMEIPDRAWENDPDGIALSNFINSNLPDNVRVFSVLPAQRSFDVRR 192

Query: 106 SAIRRSYLYRII 117
             + R YLY + 
Sbjct: 193 ECLYREYLYLLP 204



 Score = 49.1 bits (116), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 41/115 (35%), Gaps = 18/115 (15%)

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
           RA  + +  + + +   A H     D  TF     Q SS I              +E+ +
Sbjct: 528 RARWLHEPDENDRLN--ASHF---RDILTFSCGELQISSGI------------QFVELTI 570

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
              SF+  QIR  VG+   V  G      +  +L    R    P+AP E L    
Sbjct: 571 SGVSFMLHQIRKMVGTSVAVKRGLLPKDIIALSLAKFSR-IVLPIAPSEVLVLRD 624


>gi|125586190|gb|EAZ26854.1| hypothetical protein OsJ_10771 [Oryza sativa Japonica Group]
          Length = 516

 Score = 79.9 bits (196), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 31/132 (23%), Positives = 54/132 (40%), Gaps = 17/132 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           R  + + Y G+ Y G Q+Q+     S+I+  +E AIF   G         + V    + R
Sbjct: 73  RVVLRVGYVGTEYRGLQKQRELSADSTIESVLETAIFKAGGILESNYGKLQKVGWERSSR 132

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       E  P  +  +      + D + + ++    + F  R 
Sbjct: 133 TDKGVHSLATMISLKMEIPDRAWENDPDGIALSNFINSNLPDNVRVFSVLPAQRSFDVRR 192

Query: 106 SAIRRSYLYRII 117
             + R YLY + 
Sbjct: 193 ECLYREYLYLLP 204



 Score = 49.1 bits (116), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 41/115 (35%), Gaps = 18/115 (15%)

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
           RA  + +  + + +   A H     D  TF     Q SS I              +E+ +
Sbjct: 322 RARWLHEPDENDRLN--ASHF---RDILTFSCGELQISSGI------------QFVELTI 364

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
              SF+  QIR  VG+   V  G      +  +L    R    P+AP E L    
Sbjct: 365 SGVSFMLHQIRKMVGTSVAVKRGLLPKDIIALSLAKFSR-IVLPIAPSEVLVLRD 418


>gi|115452911|ref|NP_001050056.1| Os03g0338600 [Oryza sativa Japonica Group]
 gi|108708043|gb|ABF95838.1| tRNA pseudouridine synthase family protein, expressed [Oryza sativa
           Japonica Group]
 gi|113548527|dbj|BAF11970.1| Os03g0338600 [Oryza sativa Japonica Group]
          Length = 516

 Score = 79.9 bits (196), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 31/132 (23%), Positives = 54/132 (40%), Gaps = 17/132 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           R  + + Y G+ Y G Q+Q+     S+I+  +E AIF   G         + V    + R
Sbjct: 73  RVVLRVGYVGTEYRGLQKQRELSADSTIESVLETAIFKAGGILESNYGKLQKVGWERSSR 132

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L  +    +       E  P  +  +      + D + + ++    + F  R 
Sbjct: 133 TDKGVHSLATMISLKMEIPDRAWENDPDGIALSNFINSNLPDNVRVFSVLPAQRSFDVRR 192

Query: 106 SAIRRSYLYRII 117
             + R YLY + 
Sbjct: 193 ECLYREYLYLLP 204



 Score = 49.1 bits (116), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 41/115 (35%), Gaps = 18/115 (15%)

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
           RA  + +  + + +   A H     D  TF     Q SS I              +E+ +
Sbjct: 322 RARWLHEPDENDRLN--ASHF---RDILTFSCGELQISSGI------------QFVELTI 364

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
              SF+  QIR  VG+   V  G      +  +L    R    P+AP E L    
Sbjct: 365 SGVSFMLHQIRKMVGTSVAVKRGLLPKDIIALSLAKFSR-IVLPIAPSEVLVLRD 418


>gi|317498141|ref|ZP_07956443.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894618|gb|EFV16798.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 50

 Score = 79.5 bits (195), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 30/50 (60%)

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            +R   G+L  VG GK    D+ KAL++  R + G  APP+GL+  SVEY
Sbjct: 1   MVRILTGTLVEVGYGKIKPEDITKALESTKRSDAGITAPPQGLFLVSVEY 50


>gi|15227735|ref|NP_180591.1| tRNA pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|3914486|sp|O22928|PUSH_ARATH RecName: Full=Putative tRNA pseudouridine synthase; AltName:
           Full=tRNA pseudouridylate synthase; AltName:
           Full=tRNA-uridine isomerase
 gi|2347206|gb|AAC16945.1| putative pseudouridine synthase [Arabidopsis thaliana]
 gi|330253276|gb|AEC08370.1| putative tRNA pseudouridine synthase [Arabidopsis thaliana]
          Length = 510

 Score = 79.5 bits (195), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 34/190 (17%), Positives = 68/190 (35%), Gaps = 27/190 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  + I Y G+ Y G Q Q++     +I+G +E AI+   G           +    + R
Sbjct: 64  KVVIRIGYVGTDYRGLQIQRDDPSIKTIEGELEVAIYKAGGIRDSNYGDLHKIGWARSSR 123

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L       +       +  P     A      + + I + ++   +++F  R 
Sbjct: 124 TDKGVHSLATSISLKMEIPETAWKDDPQGTVLAKCISKHLPENIRVFSVLPSNRRFDPRR 183

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLD--CENMRIAAQHLVGR---HDFTTFRS 160
               R Y Y +     P+ +   +       +D    +     +   G    H++T    
Sbjct: 184 ECTLRKYSYLL-----PVDVLGIKNSFTSDEIDYHITDFNEILKEFEGEYPFHNYTQRSR 238

Query: 161 IHCQASSPIR 170
              ++   I+
Sbjct: 239 YRRKSEQKIK 248



 Score = 41.4 bits (96), Expect = 0.13,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +EI +   SF+  QIR  +G+   V   +    D+ +    +  +   PLAP E L  
Sbjct: 342 GFVEISIWGESFMLHQIRKMIGTAVAV-KRELLPRDIIRLSLNKFTRIVLPLAPSEVLIL 400


>gi|149236317|ref|XP_001524036.1| tRNA pseudouridine synthase 1 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146452412|gb|EDK46668.1| tRNA pseudouridine synthase 1 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 445

 Score = 79.5 bits (195), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 29/122 (23%), Positives = 43/122 (35%), Gaps = 15/122 (12%)

Query: 8   IEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVH 56
           + Y G+GY G Q Q   N  +I+  +  A+              +        RTD GVH
Sbjct: 2   LGYCGTGYNGLQIQNDPNVKTIERDLYTALHKAGAISLENSLDLKKSGFQRCARTDKGVH 61

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   V    +        + + +N +L     I I  +    K F  R     R Y Y +
Sbjct: 62  AAGNVVSLKM--IIEDPEIKEKINEHL--PQQIRIWGIQRTTKGFDCRKMCSSRVYEYLL 117

Query: 117 IT 118
            T
Sbjct: 118 PT 119



 Score = 58.3 bits (140), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 44/130 (33%), Gaps = 15/130 (11%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG---- 181
             R++ I       + R A Q   G H+F  F      ++    R I    V+       
Sbjct: 223 ARRSYRIS-PTKLAHFRQAMQQYEGTHNFHNFTVGKTYKSPDSSRYIISAKVSEPFVIDD 281

Query: 182 --------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
                     + +++  +SF+  QIR  +    L    K  +  L      +  K   P 
Sbjct: 282 SENSSHATEWVSVKIHGQSFMLHQIRKMICMAALTVRCKLPAEKLLAMCF-KPEKLNIPK 340

Query: 234 APPEGLYFDS 243
           AP  GL  ++
Sbjct: 341 APALGLLLEN 350


>gi|302141694|emb|CBI18897.3| unnamed protein product [Vitis vinifera]
          Length = 419

 Score = 79.5 bits (195), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 43/109 (39%), Gaps = 13/109 (11%)

Query: 18  WQRQKNGSSIQGSIEKAIF---------LVTGEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
            Q+     +I+G +E+A+F             +      + RTD GV A+ QV       
Sbjct: 1   MQKNPGAKTIEGDLEEALFFSGAVPEQDRGHPKRFDWARSARTDKGVSAVGQVVSGRF-- 58

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
              P  L + LN+ L     I I     V   F+A+    RR Y+Y I 
Sbjct: 59  YIDPPGLVERLNSNL--PPQIRIFGFKRVTASFNAKKFCDRRRYVYLIP 105



 Score = 69.5 bits (169), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/114 (31%), Positives = 47/114 (41%), Gaps = 7/114 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFD----VNSFG-NLIEIRVVARSF 193
           E       H VG H+F  F   I  +  S  R I  FD    V   G   ++  VV +SF
Sbjct: 227 ERFNRILGHYVGTHNFHNFTTRIKAEDPSAQRFIVSFDGNTIVTVEGIEFVKCEVVGQSF 286

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +  QIR  +G    +       + LE AL  +D     P AP  GLY D   +S
Sbjct: 287 MLHQIRKMIGLAVAIMRNVAPESLLETALL-KDVNINVPTAPEVGLYLDECFFS 339


>gi|68072745|ref|XP_678286.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56498704|emb|CAH97255.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 438

 Score = 79.1 bits (194), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 59/198 (29%), Gaps = 65/198 (32%)

Query: 2   IRYCMIIEYNGSGYFGWQ------------------------RQKNG------------- 24
               ++I+Y+G+ Y GW                            N              
Sbjct: 87  TNIILVIDYDGTNYKGWTGIENYSSVYLNAIHGFKNVKKSDIYNGNVLEKVDDNDINCNN 146

Query: 25  -----SSIQGSIEKAIFLVTG---------------EIVVVHGAGRTDSGVHALRQVAHF 64
                 ++Q  I   +  + G               +     G  RTD GVHA   V  +
Sbjct: 147 LKKKYETVQNCILNCLLKIHGYGDNPNITNYKENNLKPFEFIGVSRTDKGVHAKEYVCQY 206

Query: 65  DLVREWVP-----VILCKALNAYLKISDTISILNLSIVD-KQFHARFSAIRRSYLYRIIT 118
              +++ P       +  +LN  L     I +L +       F+ R   + + Y Y I  
Sbjct: 207 ISYKKFPPFNGNLEKIKLSLNRLLN--KDIKVLGIFNAPFNNFNVRHHNLGKIYTYNIDF 264

Query: 119 RQAPLALEKGRAWLIPKS 136
           R+    LE+  +W +   
Sbjct: 265 RKPSQPLERNFSWQLYDD 282


>gi|169783932|ref|XP_001826428.1| tRNA pseudouridine synthase [Aspergillus oryzae RIB40]
 gi|83775172|dbj|BAE65295.1| unnamed protein product [Aspergillus oryzae]
          Length = 563

 Score = 79.1 bits (194), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 29/137 (21%), Positives = 48/137 (35%), Gaps = 17/137 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 80  KVAVLLGYSGTGYKGMQLSATEKTIEGDLFAAFVAAGAISKANAADPKKSSLVRCARTDK 139

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +NA+L  S  I +  + +  K F +      R Y 
Sbjct: 140 GVHAAGNVVSLKL--IVEDEDIVQKINAHL--SPQIRVWGILVASKSFSSYQMCDSRIYE 195

Query: 114 Y----RIITRQAPLALE 126
           Y           P    
Sbjct: 196 YLMPSYCFLPPHPSTFL 212



 Score = 52.9 bits (126), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/125 (19%), Positives = 45/125 (36%), Gaps = 12/125 (9%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG---- 181
             R++ IP       ++ A    +G  +F  +      +  S  R I  F V+       
Sbjct: 323 AKRSYRIP-PARVARLQEALDKYLGTKNFYNYTIQKLYKDPSAKRHIKSFKVDPNPIIIN 381

Query: 182 --NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG-PLAPPEG 238
               + ++V  +SF+  QIR  V    L+          ++ + +    +   P AP  G
Sbjct: 382 GTEWLSLKVHGQSFMMHQIRKMVAMATLIVRCGCDP---KRIVDSYGPTKIPIPKAPGLG 438

Query: 239 LYFDS 243
           L  + 
Sbjct: 439 LLLER 443


>gi|238493757|ref|XP_002378115.1| tRNA pseudouridine synthase, putative [Aspergillus flavus NRRL3357]
 gi|317157361|ref|XP_003190833.1| tRNA pseudouridine synthase [Aspergillus oryzae RIB40]
 gi|220696609|gb|EED52951.1| tRNA pseudouridine synthase, putative [Aspergillus flavus NRRL3357]
          Length = 601

 Score = 79.1 bits (194), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 29/137 (21%), Positives = 48/137 (35%), Gaps = 17/137 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI---------FLVTGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q      +I+G +  A               +   +    RTD 
Sbjct: 118 KVAVLLGYSGTGYKGMQLSATEKTIEGDLFAAFVAAGAISKANAADPKKSSLVRCARTDK 177

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   V    L        + + +NA+L  S  I +  + +  K F +      R Y 
Sbjct: 178 GVHAAGNVVSLKL--IVEDEDIVQKINAHL--SPQIRVWGILVASKSFSSYQMCDSRIYE 233

Query: 114 Y----RIITRQAPLALE 126
           Y           P    
Sbjct: 234 YLMPSYCFLPPHPSTFL 250



 Score = 52.9 bits (126), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/125 (19%), Positives = 45/125 (36%), Gaps = 12/125 (9%)

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG---- 181
             R++ IP       ++ A    +G  +F  +      +  S  R I  F V+       
Sbjct: 361 AKRSYRIP-PARVARLQEALDKYLGTKNFYNYTIQKLYKDPSAKRHIKSFKVDPNPIIIN 419

Query: 182 --NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG-PLAPPEG 238
               + ++V  +SF+  QIR  V    L+          ++ + +    +   P AP  G
Sbjct: 420 GTEWLSLKVHGQSFMMHQIRKMVAMATLIVRCGCDP---KRIVDSYGPTKIPIPKAPGLG 476

Query: 239 LYFDS 243
           L  + 
Sbjct: 477 LLLER 481


>gi|255540533|ref|XP_002511331.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223550446|gb|EEF51933.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 178

 Score = 78.7 bits (193), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 28/102 (27%), Positives = 38/102 (37%), Gaps = 10/102 (9%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGA------GRTDSGV 55
            +  +   Y G GY G Q+     +I+G +E+A+F          G        RTD GV
Sbjct: 31  RKIAIFFAYCGVGYQGMQKNPGTKTIEGELEEALFHFDAVPEQDRGCPKRYDWARTDKGV 90

Query: 56  HALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV 97
            A+ QV          P  L   LN+ L     I I     V
Sbjct: 91  SAVGQVISGRF--HIDPPGLVGRLNSIL--PSHIRIFGYKRV 128


>gi|71418252|ref|XP_810793.1| pseudouridylate synthase I [Trypanosoma cruzi strain CL Brener]
 gi|70875381|gb|EAN88942.1| pseudouridylate synthase I, putative [Trypanosoma cruzi]
          Length = 655

 Score = 78.7 bits (193), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 43/204 (21%), Positives = 76/204 (37%), Gaps = 27/204 (13%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y G+GY G Q Q +  +   ++G + +A+             V G++     + RT
Sbjct: 26  LCVMYCGTGYRGLQLQTHAPTHHTVEGVLIQAMKDVGLIEAIERGRVKGDVHHFSRSCRT 85

Query: 52  DSGVHALRQVAHFDLVREWV-----PVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    +  E +        + + LN  L    TI +  ++ +   F  RFS
Sbjct: 86  DRGVHAVRNLVCLFVFTERIEALGGCEKIKEMLNTTL--PLTIRVARVTPLMGNFIPRFS 143

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS 166
             RR Y Y I         +  +++        E +R             +F  +    S
Sbjct: 144 CNRRVYHYLIPAYAFVAPCDYWKSFYEKFPQAAELLRRCYAE------ARSFLDLSPAES 197

Query: 167 SPIRTIDHFDVNSFGNLIEIRVVA 190
            P+       V    +L+   VV 
Sbjct: 198 DPLLAALLAAVTRANDLLLRYVVG 221



 Score = 49.8 bits (118), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +  ++   SFL   IR  VG+L  V  G   +   E    + DR+   PLAP   LY 
Sbjct: 326 FLVFQIEGNSFLFNMIRKIVGTLIAVLRGARETLFAEAV--SPDRRVVCPLAPGPYLYL 382


>gi|257126166|ref|YP_003164280.1| Pseudouridylate synthase-like protein [Leptotrichia buccalis
           C-1013-b]
 gi|257050105|gb|ACV39289.1| Pseudouridylate synthase-like protein [Leptotrichia buccalis
           C-1013-b]
          Length = 340

 Score = 78.7 bits (193), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 81/252 (32%), Gaps = 40/252 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALRQVA 62
           Y   +EY+G  +  +    N  S++    K +     +I   +  AGRTD+ V A   + 
Sbjct: 26  YMFFVEYDGQKFESFDENPNKKSVKSEFRKILENNKIKIFKGIQQAGRTDANVSAKENIL 85

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           + +         L       LKI+  +  L        F      I + Y          
Sbjct: 86  YINSKGIIDFSKLKFLETEGLKINKIVRTL-------PFLEFPQMIEKRY---------- 128

Query: 123 LALEKGRAWLIPKSL---DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                   +  PK L   D E +    + + G+ +F  F S   +     R      V  
Sbjct: 129 ------YIYEYPKKLRKNDEERINQICKKVSGKKNFYEFTSEKGKKLKNHRR--EIFVKY 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLK---LVGDGKWTSTDLE-KALQAQDRKECGPLAP 235
             + +    V   FL  Q+R     +         K T  + E + L  +D+   G    
Sbjct: 181 ENDKLYF--VGDGFLPQQVRIMSNFILNNTKFDIEKLTDENFENRKLGIKDKPLDGKY-- 236

Query: 236 PEGLYFDSVEYS 247
              L    V++S
Sbjct: 237 ---LTLMKVDFS 245


>gi|238883128|gb|EEQ46766.1| tRNA pseudouridine synthase 1 [Candida albicans WO-1]
          Length = 461

 Score = 78.7 bits (193), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 32/122 (26%), Positives = 43/122 (35%), Gaps = 15/122 (12%)

Query: 8   IEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTDSGVH 56
           + Y G+GY G Q Q   N  +I+  I  A+           V  +      A RTD GVH
Sbjct: 2   LGYCGTGYNGMQVQNDPNVKTIEKDIYDAMATAGAISAENAVDLKKSGFQRAARTDKGVH 61

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   V    +        +   +N  L     I I  +    K F  R     R Y Y +
Sbjct: 62  AAGNVISLKM--IIEDPEIINKINDLL--PKQIRIWGIQRTTKGFDCRKCCSSRIYEYLL 117

Query: 117 IT 118
            T
Sbjct: 118 PT 119



 Score = 52.9 bits (126), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 38/107 (35%), Gaps = 8/107 (7%)

Query: 143 RIAAQHLVGRHDFTTFRSIHC-QASSPIR-----TIDHFDVNSFGNLIEIRVVARSFLHT 196
           R   +   G H+F  F      + +S  R      +    V      I I++  +SF+  
Sbjct: 238 REVMKQYEGTHNFHNFTVGKPFKDTSANRFMIKTIVSDPFVIEGTEWISIKIHGQSFMLH 297

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           QIR  +    LV         +    Q+   K   P AP  GL  ++
Sbjct: 298 QIRKMIAMAALVVRLSLPCGIINNFFQST--KINIPKAPALGLLLEN 342


>gi|19113277|ref|NP_596485.1| tRNA pseudouridine synthase Pus2 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74676179|sp|O94295|PUS2_SCHPO RecName: Full=tRNA pseudouridine synthase 2; AltName: Full=tRNA
           pseudouridylate synthase 2; AltName: Full=tRNA-uridine
           isomerase 2
 gi|3850107|emb|CAA21896.1| tRNA pseudouridine synthase Pus2 (predicted) [Schizosaccharomyces
           pombe]
          Length = 451

 Score = 78.3 bits (192), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 39/155 (25%), Positives = 63/155 (40%), Gaps = 17/155 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--------VTGEIVVVHGAGRTDS 53
           +R  +++ Y+G GY G Q      +I+G +   +          +  E + +  A RTD 
Sbjct: 39  VRIIILLGYSGYGYHGIQINNPLKTIEGDVVAVLKKLGYLKTNNIDAEHLCIARAARTDK 98

Query: 54  GVHALRQVAHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           GVH LR +   +L   +     +L   LN  L     I + ++    K F+ R S   R+
Sbjct: 99  GVHTLRNLISLNLFVDKPLDISLLKTELNEALCS--QIRVWSVFPAPKYFNPRISCESRT 156

Query: 112 YLYRIIT----RQAPL-ALEKGRAWLIPKSLDCEN 141
           Y Y I +       P   L K     + + LD E 
Sbjct: 157 YEYLIPSFALLPPKPSCPLFKKMQKNLSRKLDNEL 191



 Score = 52.5 bits (125), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/115 (17%), Positives = 42/115 (36%), Gaps = 7/115 (6%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFD-----VNSFGNLIEIRVVARS 192
            + ++   +   GRH+F  F       + S  R I+        V      I + +   S
Sbjct: 274 LKVLQQLLKKYEGRHNFHNFTVTDDSTSPSNYRFIESVTCGTPFVYENWEWIPVTIKGNS 333

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           F+  QIR  +  + ++      +  ++KA    +       +P   L    +++S
Sbjct: 334 FMLNQIRKMMAHVLMIIRSCAPTGLIDKAFD-PNITMNISKSPGHVLLLKDIKFS 387


>gi|328850113|gb|EGF99282.1| hypothetical protein MELLADRAFT_45767 [Melampsora larici-populina
           98AG31]
          Length = 615

 Score = 77.9 bits (191), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 34/156 (21%), Positives = 51/156 (32%), Gaps = 35/156 (22%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL---------VTGEIVVVHGAGRTD 52
            +  +++ Y G GY G Q      +I+G + KA                 V +  A RTD
Sbjct: 128 RKVAVLLGYYGKGYQGSQVNPGMKTIEGEVFKAFVKAGCVSEDNSAHPNKVGLQRAARTD 187

Query: 53  SGVHALRQVAHFD--------------------LVREWVPVI----LCKALNAYLKISDT 88
           + VHA   +                              P      L K +N++L   + 
Sbjct: 188 ANVHAGCNLICLKLILDPPSLKESSDITAESSETKTCGDPEHHSLPLMKHINSFL--PEE 245

Query: 89  ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           I +  L  V   FHAR     R+Y Y + T      
Sbjct: 246 IRLWGLERVQNSFHARTLCDSRTYEYSLPTYLFLPP 281



 Score = 62.2 bits (150), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/138 (21%), Positives = 52/138 (37%), Gaps = 16/138 (11%)

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHFDV---- 177
             + K  ++ I   +  + ++ + Q   G H+F  F      +  S IR I    V    
Sbjct: 342 SVIHKKSSYRISLPM-LQRLKQSVQKFKGTHNFHNFTVGKEFKDRSAIRIIREMTVSDPF 400

Query: 178 ----NSFGN----LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
                S G+     I ++   +SF+  QIR  +G + L+   +   T + + L    R  
Sbjct: 401 VVGGESEGDPATEWISVKFYGQSFMLHQIRKMIGLIILLCRTRTPCTLIPE-LYGPVRVR 459

Query: 230 CGPLAPPEGLYFDSVEYS 247
             P AP  GL      + 
Sbjct: 460 I-PKAPGLGLILHHPHFD 476


>gi|209876690|ref|XP_002139787.1| tRNA pseudouridine synthase family protein [Cryptosporidium muris
           RN66]
 gi|209555393|gb|EEA05438.1| tRNA pseudouridine synthase family protein [Cryptosporidium muris
           RN66]
          Length = 497

 Score = 77.9 bits (191), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 48/274 (17%), Positives = 75/274 (27%), Gaps = 54/274 (19%)

Query: 26  SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVIL--CKALNAYL 83
           +IQ  + K + L+  + + +    R      A +              +L   K +   L
Sbjct: 173 TIQNYLVKKLNLILPQTIRIFTLIRVSKNFDARKDCFRRQYEYIMPEYVLYPVKFIKQDL 232

Query: 84  KIS-DTISILNLSIVDKQFHARFSAIRRS------YLY--------------------RI 116
                 I+   +        +++   R        Y Y                    RI
Sbjct: 233 YEKLQGIAQSRIIENKNNLKSKYRNKRNRDDLINDYNYCEDEDIDENNNENDQDLKELRI 292

Query: 117 ITRQAPLALEKGRAWLIPKSLDCE-----------------NMRIAAQHLVGRHDFTTFR 159
                   L      L       E                           G H+F  F 
Sbjct: 293 KRYNQHELLRSNNYNLDHYPYIEEICFNRIEEYELNELELERFSKILNQYTGTHNFHNFT 352

Query: 160 SI-HCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           S      +S  R ID  +VN         L++I +  +SFL  QIR  +     +  G  
Sbjct: 353 SRLEYNNASAWRHIDKINVNRLPVKNKLKLLKITIKGQSFLLHQIRKIIALAIEIYRGSA 412

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             + +        RK    LAP +GL  D V Y 
Sbjct: 413 PLSSINLCF--GSRKYSIHLAPSQGLLLDRVYYD 444



 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/105 (27%), Positives = 43/105 (40%), Gaps = 28/105 (26%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGS------SIQGSIEKAI--------FLVTGEIVVV---- 45
           YCM I YNG+ Y+G Q Q N +      +I+  +E+A+             E V +    
Sbjct: 10  YCMAIGYNGTNYYGMQIQSNTNNCKYIETIESKLEEALIKSSMLVIRKSKNEYVNLKEFN 69

Query: 46  ----------HGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN 80
                        GRTD GVH++ Q+  F    +     L + LN
Sbjct: 70  SSSFLTSINWTRVGRTDKGVHSVCQIVSFRGSLKVSDNDLQEELN 114


>gi|297826435|ref|XP_002881100.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297326939|gb|EFH57359.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 507

 Score = 77.9 bits (191), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 32/189 (16%), Positives = 65/189 (34%), Gaps = 25/189 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS---SIQGSIEKAIFLVTG---------EIVVVHGAGR 50
           +  + I Y G+ Y G Q Q++     +I+G +E AI+   G           +    + R
Sbjct: 64  KVVIRIGYVGTDYRGLQIQRDDPSLKTIEGELEVAIYKAGGIRDSNYGDLHKIGWARSSR 123

Query: 51  TDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF 105
           TD GVH+L       +       +  P     A      + + I + ++   +++F  R 
Sbjct: 124 TDKGVHSLATSISLKMEIPETAWKDDPQGTVLAKCISKHLPENIRVFSVLPSNRRFDPRR 183

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPK-SLDCENMRIAAQHLVGR---HDFTTFRSI 161
               R Y Y +        +    ++   +      +         G    H++T     
Sbjct: 184 ECTLRKYSYLLPV----DVIGIKNSFTSDEIDYHITDFNKILNEFEGEYPFHNYTQRSRY 239

Query: 162 HCQASSPIR 170
             ++   I+
Sbjct: 240 RRKSEQKIK 248



 Score = 42.5 bits (99), Expect = 0.054,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 34/94 (36%), Gaps = 11/94 (11%)

Query: 148 HLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKL 207
            L G H    FR    +  + +              +EI +   SF+  QIR  +G+   
Sbjct: 316 KLSGAHFRKVFRCRSGKLENSL----------GFGFVEISIWGESFMLHQIRKMIGTAVA 365

Query: 208 VGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           V   +    D+ +    +  +   PLAP E L  
Sbjct: 366 V-KRELLPRDIIRLSLNKFTRIVLPLAPSEVLIL 398


>gi|307102143|gb|EFN50538.1| hypothetical protein CHLNCDRAFT_138514 [Chlorella variabilis]
          Length = 346

 Score = 77.6 bits (190), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 87/258 (33%), Gaps = 61/258 (23%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
            +  + + Y+G+G  G Q Q++     +I+  +E+AIF   G    +  + R + G    
Sbjct: 42  RKVALFVGYSGTGRRGLQMQRSSAPEETIEDVLEEAIFQAGG----ILPSNRGNLG---- 93

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
                                         + + ++  V K ++AR   IRRSY Y +  
Sbjct: 94  -----------------------------KVRVFSVQRVSKSWNARRECIRRSYSYFVPA 124

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI--RTIDHFD 176
               LAL+ G+            ++ A+    G+             + PI  R     +
Sbjct: 125 SVLGLALDGGKEDQRR----LHLLQHASSK-KGQ--VQVAWKFERDDADPIVRRHFRFIE 177

Query: 177 VNSFG-----------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
               G             I + +   SF+  QIR  VG    V  G      LE +L   
Sbjct: 178 WCRAGTELEVLVPGGQPCIHLSLQGSSFMLHQIRKMVGMAVAVARGNLPLELLEFSLATP 237

Query: 226 DRKECGPLAPPEGLYFDS 243
            R    PLAPP  L    
Sbjct: 238 ARINL-PLAPPSTLMLTG 254


>gi|221508095|gb|EEE33682.1| pseudouridylate synthase, putative [Toxoplasma gondii VEG]
          Length = 904

 Score = 77.2 bits (189), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/119 (27%), Positives = 43/119 (36%), Gaps = 10/119 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVNS------FGNLIEIRV 188
            E +R   +   G H F  F        S      R I    V+         +++ I +
Sbjct: 706 VEKLRAVFKVFEGTHAFQNFTKRGKHKDSSPAAFKRHIHRTAVSQAHLDGVSDDVVVIEL 765

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +SFL  QIR  VG    V  G  T T L  AL+   +      AP EGL   S  Y 
Sbjct: 766 EGQSFLFNQIRKMVGIAVEVCRGTATVTSLTDALRPNRQNVFIHTAPAEGLLLLSPVYD 824



 Score = 40.2 bits (93), Expect = 0.28,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 9/51 (17%)

Query: 25  SSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVHALRQVAHFDL 66
            +++G +E+A+    G         + +    A RTD GVHA   V    L
Sbjct: 281 RTVEGVLEEALLASGGIAPYCLGCLQKLQWSRAARTDRGVHAACNVVSLKL 331



 Score = 39.4 bits (91), Expect = 0.48,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 6/86 (6%)

Query: 32  EKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           E ++   T     +  +G  D     +R+ +   + +    V     LNA L     I  
Sbjct: 409 EASVSAATSNATDLEKSGSRDK----MREKSERLVWQREREVAFLARLNAAL--PPDIRC 462

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRII 117
             +  V K F AR S  RR Y + + 
Sbjct: 463 FAVRRVTKNFDARVSCSRRRYAFLLP 488


>gi|221486308|gb|EEE24569.1| pseudouridylate synthase, putative [Toxoplasma gondii GT1]
          Length = 901

 Score = 77.2 bits (189), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/119 (27%), Positives = 43/119 (36%), Gaps = 10/119 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVNS------FGNLIEIRV 188
            E +R   +   G H F  F        S      R I    V+         +++ I +
Sbjct: 703 VEKLRAVFKVFEGTHAFQNFTKRGKHKDSSPAAFKRHIHRTAVSQAHLDGVSDDVVVIEL 762

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +SFL  QIR  VG    V  G  T T L  AL+   +      AP EGL   S  Y 
Sbjct: 763 EGQSFLFNQIRKMVGIAVEVCRGTATVTSLTDALRPNRQNVFIHTAPAEGLLLLSPVYD 821



 Score = 40.2 bits (93), Expect = 0.28,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 9/51 (17%)

Query: 25  SSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVHALRQVAHFDL 66
            +++G +E+A+    G         + +    A RTD GVHA   V    L
Sbjct: 281 RTVEGVLEEALLASGGIAPCCLGCLQKLQWSRAARTDRGVHAACNVVSLKL 331



 Score = 39.4 bits (91), Expect = 0.48,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 6/86 (6%)

Query: 32  EKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           E ++   T     +  +G  D     +R+ +   + +    V     LNA L     I  
Sbjct: 406 EASVSAATSNATDLEKSGSRDK----MREKSERLVWQREREVAFLARLNAAL--PPDIRC 459

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRII 117
             +  V K F AR S  RR Y + + 
Sbjct: 460 FAVRRVTKNFDARVSCSRRRYAFLLP 485


>gi|237833615|ref|XP_002366105.1| hypothetical protein TGME49_024200 [Toxoplasma gondii ME49]
 gi|211963769|gb|EEA98964.1| hypothetical protein TGME49_024200 [Toxoplasma gondii ME49]
          Length = 904

 Score = 77.2 bits (189), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/119 (27%), Positives = 43/119 (36%), Gaps = 10/119 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVNS------FGNLIEIRV 188
            E +R   +   G H F  F        S      R I    V+         +++ I +
Sbjct: 706 VEKLRAVFKVFEGTHAFQNFTKRGKHKDSSPAAFKRHIHRTAVSQAHLDGVSDDVVVIEL 765

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +SFL  QIR  VG    V  G  T T L  AL+   +      AP EGL   S  Y 
Sbjct: 766 EGQSFLFNQIRKMVGIAVEVCRGTATVTSLTDALRPNRQNVFIHTAPAEGLLLLSPVYD 824



 Score = 40.2 bits (93), Expect = 0.28,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 9/51 (17%)

Query: 25  SSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVHALRQVAHFDL 66
            +++G +E+A+    G         + +    A RTD GVHA   V    L
Sbjct: 281 RTVEGVLEEALLASGGIAPCCLGCLQKLQWSRAARTDRGVHAACNVVSLKL 331



 Score = 39.4 bits (91), Expect = 0.48,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 6/86 (6%)

Query: 32  EKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           E ++   T     +  +G  D     +R+ +   + +    V     LNA L     I  
Sbjct: 409 EASVSAATSNATDLEKSGSRDK----MREKSERLVWQREREVAFLARLNAAL--PPDIRC 462

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRII 117
             +  V K F AR S  RR Y + + 
Sbjct: 463 FAVRRVTKNFDARVSCSRRRYAFLLP 488


>gi|70923191|ref|XP_734642.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56507573|emb|CAH84165.1| hypothetical protein PC300883.00.0 [Plasmodium chabaudi chabaudi]
          Length = 82

 Score = 77.2 bits (189), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 17/94 (18%)

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           + I+R+YLY                + + K+ +   M  AA+  +G HDF+ F       
Sbjct: 2   NCIQRTYLY----------------FFVNKNYNIPRMNEAAKIFLGEHDFSNFCKKRKNT 45

Query: 166 SSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQI 198
            S IRTI  F++     N    ++   SFL+ Q+
Sbjct: 46  ISFIRTIHKFEIKRIDQNFYYFKIKGTSFLYNQV 79


>gi|67608685|ref|XP_666896.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54657966|gb|EAL36665.1| hypothetical protein Chro.80065 [Cryptosporidium hominis]
          Length = 501

 Score = 76.8 bits (188), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/143 (25%), Positives = 56/143 (39%), Gaps = 12/143 (8%)

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTI 172
           YR++  +    L+  R + +    D +  +      +G H F  F S    + S+  R I
Sbjct: 306 YRLVNYKIEDYLDPKRRFSLSDE-DLKRFQSILNEYIGTHSFHNFTSKSSYEDSTSWRHI 364

Query: 173 DHFDVNSFG--------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           +   V            NLI+I +  +SFL  QIR  V     +  G   S  ++     
Sbjct: 365 EEIKVVKVNQNEIKGDINLIKIIIKGQSFLLHQIRKMVALAIEIFRGTAPSNGIQLCFLP 424

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
              K    LAP +GL  D V Y+
Sbjct: 425 D--KFSIHLAPSQGLLLDRVFYN 445



 Score = 64.8 bits (157), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 22/86 (25%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQ-------KNGSSIQGSIEKAIFLV--------------- 38
          M  YCM   Y+GS Y G Q Q       +   +I+G +E  +  +               
Sbjct: 7  MRTYCMSFGYDGSDYHGMQIQMRNNKKVEELRTIEGEMEDCLEKLGMFFVSNEQNDDQGG 66

Query: 39 TGEIVVVHGAGRTDSGVHALRQVAHF 64
            + +     GRTD GVH++ QV  F
Sbjct: 67 LLKKIKWSRVGRTDKGVHSVCQVVSF 92


>gi|269121656|ref|YP_003309833.1| Pseudouridylate synthase-like protein [Sebaldella termitidis ATCC
           33386]
 gi|268615534|gb|ACZ09902.1| Pseudouridylate synthase-like protein [Sebaldella termitidis ATCC
           33386]
          Length = 276

 Score = 76.8 bits (188), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 39/214 (18%), Positives = 74/214 (34%), Gaps = 31/214 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALRQVA 62
           Y   I Y+G+ +  +   K+ +S++G  +K +          +  AGRTD  V A   + 
Sbjct: 14  YLFFIRYDGTKFDSFDENKDKTSVKGEFKKLLDENNISYYKGIQQAGRTDKDVSAEENIL 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           + +  +E          N+ + +     I ++              +R Y+YR    +  
Sbjct: 74  YINTKQELKLENFR---NSSVIL----EIFDIKKTLPYLELPKLIEKRHYIYRYPKDRIK 126

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNSFG 181
            +               E +    + L G+HD + F      +    IR +  +  N   
Sbjct: 127 SS--------------IEEIDKKCRELSGKHDVSAFTTKKGRELKEKIRELAVYYENQ-- 170

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
              E+     SF+  Q+R   G +     GK   
Sbjct: 171 ---ELHFTGSSFMPQQVRIMSGYIL---TGKKQP 198


>gi|255727174|ref|XP_002548513.1| tRNA pseudouridine synthase 1 [Candida tropicalis MYA-3404]
 gi|240134437|gb|EER33992.1| tRNA pseudouridine synthase 1 [Candida tropicalis MYA-3404]
          Length = 427

 Score = 76.8 bits (188), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 29/122 (23%), Positives = 44/122 (36%), Gaps = 15/122 (12%)

Query: 8   IEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVH 56
           + Y G+GY G Q Q   N  +I+  + +A+              +      A RTD GVH
Sbjct: 2   LGYCGTGYNGMQVQNDPNVKTIEKDVYEAMVKAGAISKENSTDLKKSQFQRAARTDKGVH 61

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A   V    +        +   +N  L   + I +  +    K F  R     R Y Y +
Sbjct: 62  AAGNVISLKM--IIEDPEILNKINDNL--PEQIRLWGIQRTTKGFDCRKCCSSRIYEYLL 117

Query: 117 IT 118
            T
Sbjct: 118 PT 119



 Score = 54.1 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/127 (20%), Positives = 45/127 (35%), Gaps = 11/127 (8%)

Query: 128 GRAWLI-PKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFD-----VNSF 180
            R + +    LD    R   +   G H+F  F      + +S  R +         V   
Sbjct: 215 RREYRVSKHKLDH--FRDVMKQYEGTHNFHNFTIGKPFKDTSASRYMISTKMSDPFVIEG 272

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I++  +SF+  QIR  +    +V      S  +      ++ K   P AP  GL 
Sbjct: 273 TEWVSIKIHGQSFMLHQIRKMIAMATMVVRLSLPSKIINNFF--KEDKINIPKAPALGLL 330

Query: 241 FDSVEYS 247
            ++  Y 
Sbjct: 331 LENPVYD 337


>gi|330835922|ref|XP_003292011.1| hypothetical protein DICPUDRAFT_156689 [Dictyostelium purpureum]
 gi|325077781|gb|EGC31472.1| hypothetical protein DICPUDRAFT_156689 [Dictyostelium purpureum]
          Length = 539

 Score = 76.8 bits (188), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 50/301 (16%), Positives = 105/301 (34%), Gaps = 74/301 (24%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEI----------VVVHGAGRT 51
           + +   Y+G+G++G    K+    +I+ +IEKA+F + G I          +    + RT
Sbjct: 129 FALCFGYDGTGFYGLSYNKDLKYKAIENAIEKALF-INGHIAPSNVGDLSRIKWSRSSRT 187

Query: 52  DSGVHALRQVAHFDL-------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           D GVH+L  +    +        RE +     +++N +L   +++ +L+ + + K F AR
Sbjct: 188 DKGVHSLSTLISCFILVDEKTNQREGLSKETIESINKHL--PESVRLLSGTRISKSFRAR 245

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG---RHDFTTFRSI 161
                R+Y Y +  +               + +  ++M     + +G    H++T+ R+ 
Sbjct: 246 RGVCERTYHYMVPKK-------------YLEGISIDHMNEILSNYIGNFSYHNYTSQRNT 292

Query: 162 HCQASS-----------------------PIRTIDHFDVNSFGNLIEIRV------VARS 192
           +    +                        I +     ++        RV        + 
Sbjct: 293 YLAEKNKKQSEDDDDEDEGEDFEEENQPKTILSPTTVTIDRISEKKMFRVNPKNMRTVKK 352

Query: 193 FLHTQIRSFVG------SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           F        +        +  V         L+ ++ +       P APP  LY    E+
Sbjct: 353 FYVESDPILINNQEWFRFVVTVAKKIQPIEALKVSIDSP-FIVSTPTAPPFSLYLYEFEF 411

Query: 247 S 247
            
Sbjct: 412 E 412


>gi|159478785|ref|XP_001697481.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158274360|gb|EDP00143.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 446

 Score = 76.8 bits (188), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 54/293 (18%), Positives = 82/293 (27%), Gaps = 93/293 (31%)

Query: 26  SIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVHALRQVAHFDL---------- 66
           +I+  +EKA+F           +   +    A RTD GVH+L  V    +          
Sbjct: 63  TIEQVLEKALFAAGCISEANFGSFSKIRWSRASRTDKGVHSLGTVMGLRMLVDDAKYVAG 122

Query: 67  -VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +   + L +A+N +L     I +      +K+F AR     R Y Y +         
Sbjct: 123 PDGDCEGLALAEAVNTHL--PPQIRVF---TTNKKFSARHMCEGRVYQYYLP-------- 169

Query: 126 EKGRAWLIPKSLD--------CENMRIAAQHLVGRHDFTTFRS----------------- 160
                 +I    D            R A +   G H F  F                   
Sbjct: 170 ----VSMIDLKCDGSEEDAQRLAKFRDALKCYEGSHPFHNFTKRVTYQPGGSNVQFRPGD 225

Query: 161 -----------------------IHCQASSPIRTIDHFD-------VNSFGNLIEIRVVA 190
                                        +  R I  F        V      + + V  
Sbjct: 226 GVVGRYGPYGRVLLLRWQTEVDPRDRITQTFYRRIYSFTAADPKPMVEGGEPCLLLEVSG 285

Query: 191 RSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +SF+   IR  +G+   V  G  +   L  +L    R    P APP  L    
Sbjct: 286 QSFMLHHIRHMIGAAVAVTLGLISKEVLLGSLTPPAR-VTLPRAPPHTLLLSD 337


>gi|66356668|ref|XP_625512.1| Pus1p-like type II pseudousynthas TruA [Cryptosporidium parvum Iowa
           II]
 gi|46226500|gb|EAK87494.1| Pus1p-like type II pseudousynthas TruA [Cryptosporidium parvum Iowa
           II]
          Length = 501

 Score = 76.4 bits (187), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/143 (25%), Positives = 56/143 (39%), Gaps = 12/143 (8%)

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTI 172
           YR++  +    L+  R + +    D +  +      +G H F  F S    + S+  R I
Sbjct: 306 YRLVNYKIEDYLDPKRRFSLSDE-DLKRFQSILNEYIGTHSFHNFTSKSSYEDSTSWRHI 364

Query: 173 DHFDVNSFG--------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           +   V            NLI+I +  +SFL  QIR  V     +  G   S  ++     
Sbjct: 365 EEIKVVKVSQNEIKGEINLIKIIIKGQSFLLHQIRKMVALAIEIFRGTAPSNGIQLCFLP 424

Query: 225 QDRKECGPLAPPEGLYFDSVEYS 247
              K    LAP +GL  D V Y+
Sbjct: 425 D--KFSIHLAPSQGLLLDRVFYN 445



 Score = 64.5 bits (156), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 22/86 (25%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQ-------KNGSSIQGSIEKAIFLV--------------- 38
          M  YCM   Y+GS Y G Q Q       +   +I+G +E  +  +               
Sbjct: 7  MKTYCMSFGYDGSDYHGMQIQMRNNKKVEELRTIEGEMEDCLEKLGMFFLSNEQNDDQGG 66

Query: 39 TGEIVVVHGAGRTDSGVHALRQVAHF 64
            + +     GRTD GVH++ QV  F
Sbjct: 67 LLKKIKWSRVGRTDKGVHSVCQVVSF 92


>gi|322492588|emb|CBZ27865.1| pseudouridylate synthase-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 696

 Score = 75.2 bits (184), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 32/131 (24%), Positives = 56/131 (42%), Gaps = 21/131 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y+GSG+ G Q Q +  +   ++G + +A+               GE      + RT
Sbjct: 29  LCVLYSGSGFRGLQIQAHAPTCHTVEGVLIQALKDAGIIADVVRGRPAGEHHHFARSCRT 88

Query: 52  DSGVHALRQVAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    + +E    +     +C+ LN  L    T+ + N+  +   F  R  
Sbjct: 89  DRGVHAIRNMVSLFVPKEIFEEVGQTEGICEKLNRQL--PATVRVANVMQLSGSFIPRHC 146

Query: 107 AIRRSYLYRII 117
             RR Y Y + 
Sbjct: 147 CNRRVYRYMLP 157



 Score = 48.7 bits (115), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +  ++   SFL   IR  +GS+  V  G      LE+A  + +R+   PLAP   LY  
Sbjct: 365 FLFFQIEGCSFLLNMIRKIIGSVLAVCRGAREP-ILEEAF-SPERRVTTPLAPGPYLYLA 422

Query: 243 SVEY 246
              Y
Sbjct: 423 QSTY 426


>gi|219116871|ref|XP_002179230.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409121|gb|EEC49053.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 63

 Score = 74.9 bits (183), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 26/63 (41%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 6  MIIEYNGSGYFGWQRQK--NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
          + + Y GS + GWQRQ      S+Q  +E A+    G  V V  AGRTD+GVHAL Q+  
Sbjct: 1  LDLAYFGSDFCGWQRQAQSKKPSVQKIVEDAMQDALGYAVNVRVAGRTDAGVHALGQIGR 60

Query: 64 FDL 66
             
Sbjct: 61 VRT 63


>gi|134080163|emb|CAK46143.1| unnamed protein product [Aspergillus niger]
          Length = 567

 Score = 74.9 bits (183), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 27/130 (20%), Positives = 49/130 (37%), Gaps = 13/130 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q  +   +I+G +  A               +   +    RTD 
Sbjct: 120 KVAVLLGYSGTGYKGMQLSETEKTIEGELFAAFVAAGAISKANATDPKKSSLVRCARTDK 179

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
           GVHA   +    L        + + +N  L     I + ++ + +K F +      R Y 
Sbjct: 180 GVHAAGNIVSLKL--IVEDDDIIQKINEKLSS--QIRVWDILVTNKSFSSYQLCDSRIYE 235

Query: 114 YRIITRQAPL 123
           Y I     P 
Sbjct: 236 YLITHCFLPP 245



 Score = 54.4 bits (130), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 46/126 (36%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFG-- 181
           L+  RA+ IP       ++ A    VG ++F  +      A  S  R I  F +      
Sbjct: 328 LQAKRAYRIPAQR-LARVQEALDKYVGTNNFFNYTIQKTHADPSSKRHIKSFKMAEQPII 386

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    +V         + +   A   K   P AP  
Sbjct: 387 INGTEWLSLKVHGQSFMMHQIRKMVAMAAMVVRCGCDPQRIVETYGAN--KIAIPKAPGL 444

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 445 GLLLER 450


>gi|282934570|ref|ZP_06339821.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
 gi|281301364|gb|EFA93657.1| tRNA pseudouridine synthase A [Lactobacillus jensenii 208-1]
          Length = 38

 Score = 74.9 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 14/38 (36%), Positives = 26/38 (68%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV 38
          M R+ M + Y+G  + G+Q+Q N  ++QG+IE+A+  +
Sbjct: 1  MPRFKMTMAYDGHLFHGFQKQPNQRTVQGTIEEALKKM 38


>gi|71423309|ref|XP_812417.1| pseudouridylate synthase I [Trypanosoma cruzi strain CL Brener]
 gi|70877194|gb|EAN90566.1| pseudouridylate synthase I, putative [Trypanosoma cruzi]
          Length = 655

 Score = 74.5 bits (182), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/161 (22%), Positives = 62/161 (38%), Gaps = 21/161 (13%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y G+GY G Q Q +  +   ++G + +A+             V G++     + RT
Sbjct: 26  LCVMYCGTGYRGLQLQTHAPTHHTVEGVLIQAMKDVGLIEAIERGRVKGDMHHFARSCRT 85

Query: 52  DSGVHALRQVAHFDLVREWV-----PVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D  VHA+R +    +  E +        + + LN  L    TI I  ++ +   F  RFS
Sbjct: 86  DRAVHAVRNLICLFVFTERIEALGGCEKIKEMLNTTL--PLTIRIARVTPLMGNFIPRFS 143

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQ 147
             RR Y Y I         +  + +        E +R    
Sbjct: 144 CNRRVYHYLIPAYAFVAPCDYWKGFYEKFPQAAELLRRCCA 184



 Score = 51.8 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            +  ++   SFL   IR  VG+L  V  G    T   +AL + DR+   PLAP   LY 
Sbjct: 326 FLVFQIEGNSFLFNMIRKIVGTLIAVLRGAR-ETLFAEAL-SPDRRVVCPLAPGPYLYL 382


>gi|322499857|emb|CBZ34930.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 696

 Score = 74.5 bits (182), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/131 (23%), Positives = 54/131 (41%), Gaps = 21/131 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y+GSG+ G Q Q +  +   ++G + +A+               GE      + RT
Sbjct: 29  LCVLYSGSGFRGLQIQAHAPTCHTVEGVLIQALKDAGIIAEVVRGRPAGEHHHFARSCRT 88

Query: 52  DSGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    + +           +C+ LN  L    T+ + N+  +   F  R  
Sbjct: 89  DRGVHAIRNMVSLFVPKEVFEEMGQAEGICEKLNRQL--PSTVRVANVMQLSGSFIPRHC 146

Query: 107 AIRRSYLYRII 117
             RR Y Y + 
Sbjct: 147 CNRRVYRYMLP 157



 Score = 46.7 bits (110), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECGPLAPPEGL 239
            +  ++   SFL   IR  +GS+  V  G       E  L+   + +R+   PLAP   L
Sbjct: 365 FLFFQIEGCSFLLNMIRKIIGSVLAVCRGAR-----ESILEDAFSPERRVTTPLAPGPYL 419

Query: 240 YFDSVEY 246
           Y     Y
Sbjct: 420 YLAQSTY 426


>gi|146089460|ref|XP_001470389.1| pseudouridylate synthase-like protein [Leishmania infantum]
 gi|134070422|emb|CAM68761.1| pseudouridylate synthase-like protein [Leishmania infantum JPCM5]
          Length = 696

 Score = 74.1 bits (181), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/131 (23%), Positives = 54/131 (41%), Gaps = 21/131 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y+GSG+ G Q Q +  +   ++G + +A+               GE      + RT
Sbjct: 29  LCVLYSGSGFRGLQIQAHAPTCHTVEGVLIQALKDAGIVADVVRGRPAGEHHHFARSCRT 88

Query: 52  DSGVHALRQVAHFDLVR-----EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    + +           +C+ LN  L    T+ + N+  +   F  R  
Sbjct: 89  DRGVHAIRNMVSLFVPKEVFEEMGQAEGICEKLNRQL--PSTVRVANVMQLSGSFIPRHC 146

Query: 107 AIRRSYLYRII 117
             RR Y Y + 
Sbjct: 147 CNRRVYRYMLP 157



 Score = 46.7 bits (110), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ---AQDRKECGPLAPPEGL 239
            +  ++   SFL   IR  +GS+  V  G       E  L+   + +R+   PLAP   L
Sbjct: 365 FLFFQIEGCSFLLNMIRKIIGSVLAVCRGAR-----ESILEDAFSPERRVTTPLAPGPYL 419

Query: 240 YFDSVEY 246
           Y     Y
Sbjct: 420 YLAQSTY 426


>gi|281206578|gb|EFA80764.1| hypothetical protein PPL_06350 [Polysphondylium pallidum PN500]
          Length = 624

 Score = 73.3 bits (179), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/181 (19%), Positives = 67/181 (37%), Gaps = 32/181 (17%)

Query: 5   CMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSG 54
            ++  Y G+GY G + Q +G ++++ ++E+A+F             + +    + RTD G
Sbjct: 187 ALLFAYVGTGYHGLEYQISGYNALENTLEQALFKAGLILPSNLGDLDRIRWSRSSRTDKG 246

Query: 55  VHALRQVAHFDLV----REWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           VH+L  +    L       + P     L + +N  L     + IL L+   + F  R   
Sbjct: 247 VHSLSTLLAGCLEIEDGSGYYPEKVAVLIEKINRGL--PPNLRILALAPTSRSFDPRRQC 304

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI-AAQHLVGRHDFTTFRSIHCQAS 166
             R+Y Y +  +             +   L  E +        +G + +  F S      
Sbjct: 305 TSRTYHYVLPKK------------YLGTKLTLEQINESILPLYIGSNSYHNFTSHRRTYK 352

Query: 167 S 167
            
Sbjct: 353 D 353



 Score = 52.5 bits (125), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/90 (26%), Positives = 36/90 (40%), Gaps = 15/90 (16%)

Query: 166 SSPIRTIDHFDVNS--------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDG 211
           S+ +R I+ F V                    +   V   SF+  QIR  +G +  +G+G
Sbjct: 424 STNVRRINSFKVVETSFKTKNVDGGGGGDEEWVRFEVEGASFIQYQIRKMIGFVLAIGNG 483

Query: 212 KWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                 LE AL++       P+APP  LY 
Sbjct: 484 YCDRRMLELALKSP-FSIRSPVAPPNPLYL 512


>gi|114550574|ref|XP_001150260.1| PREDICTED: tRNA pseudouridine synthase-like 1-like [Pan
           troglodytes]
          Length = 102

 Score = 73.3 bits (179), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 2/84 (2%)

Query: 165 ASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
           A +  +T      +       +   ++SFL+ Q+R     L  VG G      ++  L++
Sbjct: 2   ADTAPQTPTGTCFSRKLRFWNLEFESQSFLYRQVRRMTAVLVAVGLGALAPAHVKTILES 61

Query: 225 QDR--KECGPLAPPEGLYFDSVEY 246
           QD   K    +AP  GL+  SV Y
Sbjct: 62  QDPLGKHQTRVAPAHGLFLKSVLY 85


>gi|157870999|ref|XP_001684049.1| pseudouridylate synthase-like protein [Leishmania major]
 gi|68127117|emb|CAJ04679.1| pseudouridylate synthase-like protein [Leishmania major strain
           Friedlin]
          Length = 696

 Score = 72.9 bits (178), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 31/131 (23%), Positives = 54/131 (41%), Gaps = 21/131 (16%)

Query: 6   MIIEYNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRT 51
           + + Y+GSG+ G Q Q +  +   ++G + +A+               GE      + RT
Sbjct: 29  LCVLYSGSGFRGLQIQVHAPTCHTVEGVLIQALKDAGIIADVVRGRPAGEHHHFARSCRT 88

Query: 52  DSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFS 106
           D GVHA+R +    +      +      +C+ LN  L    T+ + N+  +   F  R  
Sbjct: 89  DRGVHAIRNMVSLFVPKEVFEKMGQAEGICEKLNRQL--PATVRVANVMQLSGSFIPRHC 146

Query: 107 AIRRSYLYRII 117
             RR Y Y + 
Sbjct: 147 CNRRVYRYMLP 157



 Score = 43.3 bits (101), Expect = 0.035,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +  ++   SFL   IR  +GS+  V  G    + LE A   + R    PLAP   LY  
Sbjct: 365 FLFFQIEGCSFLLNMIRKIIGSVLAVCRGAR-ESILEDAFSPECR-VTTPLAPGPYLYLA 422

Query: 243 SVEY 246
              Y
Sbjct: 423 QSTY 426


>gi|145348169|ref|XP_001418528.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578757|gb|ABO96821.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 422

 Score = 72.6 bits (177), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 70/251 (27%), Gaps = 62/251 (24%)

Query: 7   IIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDL 66
              Y+G+       +   +S+  +++ A+  V  +      AGRTD GV AL        
Sbjct: 141 DFAYDGT------FEPGCASVSAALQLALRPVLDKTRPTPSAGRTDRGVSALASCVSLWS 194

Query: 67  VRE-WVPVILCKALNAYLKISDT--ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
             +      + + +N          + + ++      FHA F+A  R Y+Y +   Q   
Sbjct: 195 KSDAISAAEIERLVNEDSAPGKAGLLRVSDVRETGSAFHATFAAKSRRYVYCLPKNQ--- 251

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGR-----HDFTTFRSIHCQASSPIRTIDHFDVN 178
           A  + R       LD   +      LV        D   F        S + T       
Sbjct: 252 AFRESRT--PKADLDARIIDRILAALVRECANAPIDMHAFARGTPPGKSSVVTFRVARAF 309

Query: 179 S-------------------------------------------FGNLIEIRVVARSFLH 195
                                                          +I I +VA  FL 
Sbjct: 310 EAKLPSPPGDGADSDNDSKVTAGVRRSKSRNDAHDDTIDITDIDADEVIVIELVADRFLR 369

Query: 196 TQIRSFVGSLK 206
             IR  V +  
Sbjct: 370 KLIRCLVATTI 380


>gi|154339169|ref|XP_001562276.1| pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 689

 Score = 71.8 bits (175), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 31/127 (24%), Positives = 54/127 (42%), Gaps = 21/127 (16%)

Query: 10  YNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRTDSGV 55
           Y+GSG+ G Q Q +  +   ++G + +A+               GE      + RTD GV
Sbjct: 33  YSGSGFRGLQIQVHAPTCHTVEGMLIQALKDTGIIADVVRGRPAGEHHHFARSCRTDRGV 92

Query: 56  HALRQVAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           HA+R +    + +E    +     +C+ LN  L    T+ + ++  +   F  R    RR
Sbjct: 93  HAIRNMVSLFVPKEVFDKVGQSGGICERLNRRL--PATVRVASVMQLSGSFIPRHCCNRR 150

Query: 111 SYLYRII 117
            Y Y + 
Sbjct: 151 VYRYMLP 157



 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +  ++   SFL   IR  +GSL  V  G    + LE+AL + +R+   PLAP   LY  
Sbjct: 365 FLIFQIEGESFLLNMIRKVIGSLLAVCRGAR-ESILEEAL-SPERRVTTPLAPGPYLYLA 422

Query: 243 SVEY 246
              Y
Sbjct: 423 QSTY 426


>gi|322505105|emb|CAM39306.2| pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 689

 Score = 71.8 bits (175), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 31/127 (24%), Positives = 54/127 (42%), Gaps = 21/127 (16%)

Query: 10  YNGSGYFGWQRQKNGSS---IQGSIEKAIF-----------LVTGEIVVVHGAGRTDSGV 55
           Y+GSG+ G Q Q +  +   ++G + +A+               GE      + RTD GV
Sbjct: 33  YSGSGFRGLQIQVHAPTCHTVEGMLIQALKDTGIIADVVRGRPAGEHHHFARSCRTDRGV 92

Query: 56  HALRQVAHFDLVREWVPVI-----LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRR 110
           HA+R +    + +E    +     +C+ LN  L    T+ + ++  +   F  R    RR
Sbjct: 93  HAIRNMVSLFVPKEVFDKVGQSGGICERLNRRL--PATVRVASVMQLSGSFIPRHCCNRR 150

Query: 111 SYLYRII 117
            Y Y + 
Sbjct: 151 VYRYMLP 157



 Score = 50.6 bits (120), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +  ++   SFL   IR  +GSL  V  G    + LE+AL + +R+   PLAP   LY  
Sbjct: 365 FLIFQIEGESFLLNMIRKVIGSLLAVCRGAR-ESILEEAL-SPERRVTTPLAPGPYLYLA 422

Query: 243 SVEY 246
              Y
Sbjct: 423 QSTY 426


>gi|47187449|emb|CAG13480.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 97

 Score = 71.4 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 10/92 (10%)

Query: 3  RYCMIIEYNGSGYFGWQR----QKNGSSIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHA 57
          RY +  +Y G+ Y G  +    Q    S+Q  +E A+  +     V +  + RTD+GVHA
Sbjct: 1  RYLIFFQYIGTKYSGVVKVPPHQLFKKSVQDHLEDALRKLRPLNPVSLSVSSRTDAGVHA 60

Query: 58 LRQVAHFDLVR-----EWVPVILCKALNAYLK 84
          L   AHFDL R      +   IL  ALN +L+
Sbjct: 61 LCNSAHFDLQRRNDKPPFTADILVDALNYHLR 92


>gi|269123330|ref|YP_003305907.1| Pseudouridylate synthase-like protein [Streptobacillus moniliformis
           DSM 12112]
 gi|268314656|gb|ACZ01030.1| Pseudouridylate synthase-like protein [Streptobacillus moniliformis
           DSM 12112]
          Length = 211

 Score = 71.4 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/224 (19%), Positives = 75/224 (33%), Gaps = 42/224 (18%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSI-EKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           Y + I Y G  +  +   K+  +++G + E  +         +  AGRTD+ V A     
Sbjct: 8   YLLEISYKGKKFDCFDEIKDKKTVKGVLKEYILSKGIKIYKGLQQAGRTDARVSAYSNYI 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTIS---ILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           +F   R  + +         L I+  IS   I N+              +R Y+Y     
Sbjct: 68  YFVADRFNIDI---------LDINVDISGLKIKNIIETKNDIVLPDIVEKRIYIY----- 113

Query: 120 QAPLALEKGRAWLIPKSL---DCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTIDHF 175
                         PK     D E +    + + G  DF+ F +    +  +  R +   
Sbjct: 114 ------------FYPKKFLNVDKETILKRCEEISGYRDFSEFTNHKGLKLKNHFRDVKVT 161

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
            V        +     SF+  Q+R   G +     GK  + D +
Sbjct: 162 YVEEK-----LYFEGNSFMPQQVRIMSGYIL---KGKKEAMDPK 197


>gi|320164169|gb|EFW41068.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
          Length = 311

 Score = 71.4 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/202 (15%), Positives = 65/202 (32%), Gaps = 43/202 (21%)

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
             ++   I     + V   F+AR +   R Y Y + T     A    ++      +D   
Sbjct: 12  NEQLPHDIRAHGYARVAGSFNARTACTSRVYSYTLPT----FAFAPYKSMTWDYRIDAAT 67

Query: 142 MRIAAQHL---VGRHDFTTFR-SIHCQASSPIRTIDHFDVN------------------- 178
           ++          G H F  +   +    +  +R +    VN                   
Sbjct: 68  LQKVRDTFAKYTGSHRFHNYTIKVRINDAQAMRVMQSCTVNDPLLTPIDREWLAANPEPV 127

Query: 179 --------------SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA 224
                         +   ++ + +  +SF++ QIR  VG +  +  G+  +  +  +   
Sbjct: 128 SADQPAPEGCPDHLTHLEMVTMVIEGQSFMYNQIRKMVGMVIAIVRGQSETFSIPNSFTL 187

Query: 225 QDRKECGPLAPPEGLYFDSVEY 246
              +   P AP  GL  + V++
Sbjct: 188 P--QMAVPRAPGLGLALERVKF 207


>gi|212723684|ref|NP_001131790.1| hypothetical protein LOC100193161 [Zea mays]
 gi|194692542|gb|ACF80355.1| unknown [Zea mays]
 gi|223946927|gb|ACN27547.1| unknown [Zea mays]
          Length = 173

 Score = 71.0 bits (173), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/131 (21%), Positives = 49/131 (37%), Gaps = 17/131 (12%)

Query: 134 PKSLDCENMRIAAQHLVGR--------HDFTTFRSIHC-------QASSPIRTIDHFDVN 178
           P+S D   +    + L G+         D    RS+          + + +  +   + +
Sbjct: 32  PQSFDVSKVDEILKPLAGKTLSYKMFARDTQASRSVGPPTECFMFHSRAAVAKLHSANED 91

Query: 179 SFGNLIE--IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             G ++   + +VA  FL   +R  V +          +  L   ++A DR+   P APP
Sbjct: 92  HKGGMVVMCVELVANRFLRKMVRVLVATAIREAAAGAGADALLNLMEATDRRATAPPAPP 151

Query: 237 EGLYFDSVEYS 247
           EGL    V Y 
Sbjct: 152 EGLCLVDVGYE 162


>gi|261190138|ref|XP_002621479.1| tRNA pseudouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239591307|gb|EEQ73888.1| tRNA pseudouridine synthase [Ajellomyces dermatitidis SLH14081]
          Length = 605

 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 58/170 (34%), Gaps = 24/170 (14%)

Query: 14  GYFGWQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDSGVHALRQVAHF 64
           GY G  R     +I+G +  A      I        +   +    RTD GVHA   V   
Sbjct: 128 GYSGIYRSPTEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDKGVHAAGNVVSL 187

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
            L        + + +N  L  S  I +  + I +K F +      R Y Y I T      
Sbjct: 188 KL--IVEDSDIVQKINEQL--SPQIRVWGIEITNKSFSSYHLCDSRIYEYLIPTHCFLPP 243

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                      SL  + + IA Q     +D   ++    + ++  + +D 
Sbjct: 244 -------HPSTSLGQKLVEIAEQ----ENDLEGYKQRQAEVATYWKEVDE 282



 Score = 64.5 bits (156), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           L+  RA+ IPK    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 371 LDAKRAYRIPKER-MDRINDALGMYVGTRNFHNYTIQKSFRDASAKRLIKSFKISRDPLI 429

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V  + LV         + +  +  D K   P AP  
Sbjct: 430 INGTEWLSLKVHGQSFMMHQIRKMVAMVALVVRCGCDIQRIPETYE--DHKIAIPKAPGL 487

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 488 GLLLER 493


>gi|116794266|gb|ABK27072.1| unknown [Picea sitchensis]
          Length = 212

 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/115 (25%), Positives = 45/115 (39%), Gaps = 17/115 (14%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN---GSSIQGSIEKAIFLVTG---------EIVVVHGAG 49
            +  M I Y G+ Y G Q Q++     +I+  +EKAI    G           +    + 
Sbjct: 83  RKVAMRIGYVGTNYRGLQIQRDSASTITIEDELEKAILKAGGMLESNYGNLHKLGWRRSS 142

Query: 50  RTDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDK 99
           RTD GVH+L  V    +       E  P  +  A      +   I I ++  V+K
Sbjct: 143 RTDKGVHSLATVIAMKMEIPDGAWEEDPDGIALADVINRHLPYNIRIFSILPVNK 197


>gi|7670391|dbj|BAA95047.1| unnamed protein product [Mus musculus]
          Length = 257

 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 30/147 (20%), Positives = 51/147 (34%), Gaps = 35/147 (23%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 80  RKIVLLMAYSGKGYHGMQRNLGSSQFRTIEDDLVSALVQAGCIPENHGTDMRKMSFQRCA 139

Query: 50  RTDS------------------GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISI 91
           RTD                   GV A  QV      + W+   +   +N++L     I I
Sbjct: 140 RTDKPLRTSACFCLYTGFLFHWGVSAAGQVVSL---KVWLIDDILDKINSHL--PSHIRI 194

Query: 92  LNLSIVDKQFHARFSAIRRSYLYRIIT 118
           L L  V   F+++     R+Y Y + T
Sbjct: 195 LGLKRVTGGFNSKNKCDARTYCYMLPT 221


>gi|170585846|ref|XP_001897693.1| inosine-5'-monophosphate dehydrogenase family protein [Brugia
           malayi]
 gi|158595000|gb|EDP33577.1| inosine-5'-monophosphate dehydrogenase family protein [Brugia
           malayi]
          Length = 721

 Score = 69.9 bits (170), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/169 (20%), Positives = 60/169 (35%), Gaps = 23/169 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           RY +   Y+G+ +          S+   + KA+   T    G  + +  + RTD+GVHA+
Sbjct: 550 RYLLWASYDGARFLSIANGSINHSVLSFL-KALVRDTFPDIGMQLKISPSSRTDAGVHAM 608

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISD-----TISILNLSIVDKQFHARFSAIRRSYL 113
           R      +            L+ +   ++     +  IL+   V K F +R +   R Y 
Sbjct: 609 RNAFIMQIPIRNADESKSNLLHDWNHRANEFVGTSFRILDFHPVSKGFCSRRNVSYRKYK 668

Query: 114 YRII----------TRQAPLAL---EKGRAWLIPKSLDCENMRIAAQHL 149
           YR+             + PL     E+   W +P   D      A    
Sbjct: 669 YRLAIAENEEEWLKNTEQPLLWQFAERPYMWFLPNGFDMRKAADACSLF 717


>gi|300175206|emb|CBK20517.2| unnamed protein product [Blastocystis hominis]
          Length = 282

 Score = 69.5 bits (169), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 49/264 (18%), Positives = 75/264 (28%), Gaps = 50/264 (18%)

Query: 27  IQGSIEKAIFLV---TGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVIL-CKALNAY 82
           +QG  E+ +  +       + V    RT    +A                 L   +    
Sbjct: 15  VQGKEEETVDRINSCLPSDIRVFKILRTTKNFNAKNFCDRRQYEYILPIETLSPFSSTPP 74

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRA------------ 130
           L I + IS      V+ +  A     R      I          + R             
Sbjct: 75  LSIREDISHNWKEFVENE--AYLQKCREHPEESIDNPFEDRPDNRQRVKSLQIAQQLLLN 132

Query: 131 ------------------------WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA- 165
                                   W    SL    +R      VG H+F  +      A 
Sbjct: 133 EASFSTYTEDAQDRSFGGCVVKDEWPAYLSLALSRLRACMSLFVGTHNFHNYTVGKSSAD 192

Query: 166 SSPIRTIDHFDVN---SFGNLIEIRV--VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           SS  R I    V+      + + IRV    +SF+  QIR  +G    V  G+ +   +  
Sbjct: 193 SSAQRHILGISVSDPIRIHDGLYIRVCLEGQSFMLHQIRKMIGIAIEVARGRCSLHTVNS 252

Query: 221 ALQAQDRKECGPLAPPEGLYFDSV 244
           +L         P+AP  GL+   V
Sbjct: 253 SLSRG--TMFTPMAPSTGLFLSMV 274


>gi|308812814|ref|XP_003083714.1| PUSH_ARATH Putative tRNA pseudouridine synthase (ISS) [Ostreococcus
           tauri]
 gi|116055595|emb|CAL58263.1| PUSH_ARATH Putative tRNA pseudouridine synthase (ISS) [Ostreococcus
           tauri]
          Length = 543

 Score = 69.1 bits (168), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 22/177 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQK---NGSSIQGSIEKAIFLVTG-----------EIVVVHGAG 49
             +++ Y G+GY G         G+++   +E A+F   G           + +    + 
Sbjct: 90  VALLLAYVGAGYKGNTHNAQAVRGTTVDDVVEDALFRWGGILLPNYRSKGLQRLKWSRSS 149

Query: 50  RTDSGVHALRQVAHFDL---VREWVPVILCKALNAYL--KISDTISILNLSIVDKQFHAR 104
           RTD GV +L  V           W   +  +A    +   + D +    +    K F AR
Sbjct: 150 RTDKGVSSLCTVVSLRAEIDPEVWTTDVEARATARDITKHLPDDVECFAVYNTPKSFQAR 209

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI 161
              + R+Y Y +    A +    G A              A    +G H F  +   
Sbjct: 210 RECVMRTYEYLL---PARVLGLDGDAMDESGRRRLALFNEALSCFIGSHPFHNYTKR 263



 Score = 58.3 bits (140), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 33/94 (35%), Gaps = 5/94 (5%)

Query: 153 HDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           H+F+       +      T +          + + V   SF+  QIR  + S   V  G 
Sbjct: 358 HNFSA----GSEVERMTITNEDGSTTQSEPFVRVSVRGESFMLYQIRKMIASAVAVSLGH 413

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                L  +L    R    PLAP   LY   VE+
Sbjct: 414 CPLEFLPASLARPCR-AAMPLAPASTLYLYDVEF 446


>gi|145354770|ref|XP_001421649.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144581887|gb|ABO99942.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 556

 Score = 68.7 bits (167), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 59/180 (32%), Gaps = 26/180 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQ---KNGSSIQGSIEKAIFLVTG-----------EIVVVHGAG 49
             +++ Y G GY G         G+++   +E A+F   G           + +    + 
Sbjct: 91  VAIVLAYVGQGYKGNTHNAQAPRGTTVDDVVEDALFAWGGILMPNYRSRGLQRLKWSRSS 150

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYL-------KISDTISILNLSIVDKQFH 102
           RTD GV +L  V          P +  K + A          + + +    +    K F 
Sbjct: 151 RTDKGVSSLCTVVSLRAE--IDPEVWTKDVEARETAREITKHLPEDVECFAVYNTPKSFQ 208

Query: 103 ARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIH 162
           AR   I R+Y Y +    A +   +        +   E    A    VG H F  +    
Sbjct: 209 ARRECIMRTYEYLL---PARVLDLERGVLDASDAERLELFSKALAAFVGAHPFHNYTKRK 265



 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/121 (25%), Positives = 41/121 (33%), Gaps = 8/121 (6%)

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +G  WL     +    +I   H    H+FT              T D     +    I 
Sbjct: 338 RRGTYWLYESDPND---KIGPSHFRRIHNFTA----GADVERMEITNDDGSKTTSEPFIR 390

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           + V   SF+  QIR  + S   V  G      L  +L    R    PLAP   LY   VE
Sbjct: 391 VSVRGESFMLYQIRKMIASAVAVSLGHCPLEFLPASLSRPCR-AAMPLAPASTLYLYDVE 449

Query: 246 Y 246
           +
Sbjct: 450 F 450


>gi|125583196|gb|EAZ24127.1| hypothetical protein OsJ_07867 [Oryza sativa Japonica Group]
          Length = 518

 Score = 68.3 bits (166), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 27/110 (24%), Positives = 38/110 (34%), Gaps = 7/110 (6%)

Query: 140 ENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG-----NLIEIRVVARSF 193
           E      +  VG H+F  F      +  +  R I  F  +        + I   VV +SF
Sbjct: 316 ERFNRILKKYVGTHNFHNFTTRTKAEDPAAKRFIISFAADRVVNLDGIDFIRCEVVGQSF 375

Query: 194 LHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +  QIR  +G    V         +      +D     P AP  GLY D 
Sbjct: 376 MLHQIRKMIGLAVAVMRNC-APESIYDVAFRKDVNLNVPTAPEVGLYLDE 424



 Score = 42.1 bits (98), Expect = 0.068,   Method: Composition-based stats.
 Identities = 28/113 (24%), Positives = 37/113 (32%), Gaps = 20/113 (17%)

Query: 18  WQRQKNGSSIQGSIEK----AI-FLVTGEIVVVHG--------AGRTDSGVHALRQVAHF 64
            Q+     +I+G        A+     G      G        A RTD GV A  QV   
Sbjct: 1   MQKNPGARTIEG---DPGGGALPGRRPGPRPNAPGPAATTGARAARTDKGVSAAAQVVSG 57

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
                  P +    LNA L     I       V   F+A+    RR Y+Y + 
Sbjct: 58  RF--YVDPPVFTDRLNAQLA--PQIRAFGYVRVTNSFNAKKFCDRRRYVYLLP 106


>gi|322494865|emb|CBZ30168.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 700

 Score = 67.9 bits (165), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 55/182 (30%), Gaps = 55/182 (30%)

Query: 6   MIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIF------------LVTGEIVVVHGAGRT 51
           +I  Y G  Y G Q        +++  + KA+F            L   +++    A RT
Sbjct: 60  IIFGYVGECYCGLQWNHLPEYPTVEEVLMKALFETDMISEVNFSNLKVQKLLNFERASRT 119

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNA------------------------------ 81
           D GVHALR V    ++  + P    K L A                              
Sbjct: 120 DKGVHALRNVVSVAVMLPYDPSYTKKHLAALQEHAEGAAAGEVHTADGDVEDDANSAQAA 179

Query: 82  -----------YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRA 130
                         +   I +  +  V + F+A  +   R Y Y + T     A E    
Sbjct: 180 VFSCEEAKRLLNEALPRDIHVYAVVPVTRSFNAYLNCGGRRYEYYLPTFALMTAAEYSET 239

Query: 131 WL 132
           + 
Sbjct: 240 YF 241



 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 176 DVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           DV + G  ++ I +  +SF+  QIR  +G++  V       T +   L  +  +   P+A
Sbjct: 554 DVYAGGIEVVRIELDGQSFMLNQIRKMIGAVVCVAAAGLPETYIRDVLLRKAVRRGIPMA 613

Query: 235 PPEGLYF 241
           P  GL+ 
Sbjct: 614 PANGLFL 620


>gi|302754550|ref|XP_002960699.1| hypothetical protein SELMODRAFT_63437 [Selaginella moellendorffii]
 gi|300171638|gb|EFJ38238.1| hypothetical protein SELMODRAFT_63437 [Selaginella moellendorffii]
          Length = 403

 Score = 67.5 bits (164), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/182 (21%), Positives = 65/182 (35%), Gaps = 30/182 (16%)

Query: 3   RYCMIIEYNGSGYFG---------WQRQKNGSSIQGSIEKAIFLVTG---------EIVV 44
           +  M I Y G+GY G              + ++I+  ++KAI+   G           V 
Sbjct: 4   KVAMWIGYVGTGYKGNHCSLFLELSALNSSLTAIEADLDKAIYKAGGILDSNYGHHMKVG 63

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVI-------LCKALNAYLKISDTISILNLSIV 97
              + RTD GVH+L  V    +               +   +N +L     I +  +  V
Sbjct: 64  WARSSRTDKGVHSLATVISLKMELPIDAWRDDPGGIEIADMINRHL--PQCIRVFGVVPV 121

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
            K F  R +   RSY Y +      + + +  +    K L  E  R+  +   G H F  
Sbjct: 122 SKTFRPRMACSERSYDYFLP--ALCVGINQRVSTCEIKQL-LEQFRLQLKLFEGEHPFHN 178

Query: 158 FR 159
           + 
Sbjct: 179 YT 180



 Score = 48.3 bits (114), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 176 DVNSFGNLIEIRV--VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           D+  FG+ + +RV     SF+  QIR  +G+   V         ++ +L  +  +   P+
Sbjct: 260 DIEKFGDTLALRVSVTGASFMVHQIRKMIGTAVAVTRKLLPPDIIQMSL-CRHSRIVLPI 318

Query: 234 APPEGLYF 241
           AP EGL  
Sbjct: 319 APCEGLTL 326


>gi|255088754|ref|XP_002506299.1| predicted protein [Micromonas sp. RCC299]
 gi|226521571|gb|ACO67557.1| predicted protein [Micromonas sp. RCC299]
          Length = 601

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/195 (21%), Positives = 68/195 (34%), Gaps = 30/195 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQ---KNGSSIQGSIEKAIFLV-----------TGEIVVVHGAG 49
             +++ Y G+GY G         GS++   +E A+F             +   +    + 
Sbjct: 113 VALLMGYVGAGYSGNTTNASLPRGSTVDDVLEDALFDAGCILLSNYRSRSLSRLKWSRSS 172

Query: 50  RTDSGVHALRQVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           RTD GV +L  V    L       E  P     A +    + + + +       K F AR
Sbjct: 173 RTDKGVSSLATVVSARLEVDVGVWENDPEGTRIAADINRHLPNHVRVFGAYSTPKSFQAR 232

Query: 105 FSAIRRSYLYRII--------TRQAPLALEKGRAWLIPKSLDCENM---RIAAQHLVGRH 153
            + +RR+Y Y +           +   AL    A  +  +   E M   R A +   G H
Sbjct: 233 RACVRRTYDYLLPATCLGLNVNGERDAALAWPGAPELADATGEEVMARFRRALRMFEGSH 292

Query: 154 DFTTFRSIHCQASSP 168
            F  +      A +P
Sbjct: 293 YFHNYTRRSAYAPAP 307



 Score = 50.6 bits (120), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 1/66 (1%)

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + V   SF+  QIR  + +      G +    +  +L    R    P+AP   LY
Sbjct: 398 PPFVRVTVNGDSFMLYQIRKMIATAVAAAIGHFPLELIPASLTRPAR-IATPIAPASTLY 456

Query: 241 FDSVEY 246
               E+
Sbjct: 457 LVDAEF 462


>gi|269864426|ref|XP_002651569.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
 gi|220064284|gb|EED42489.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
          Length = 147

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALR 59
            +  + I Y+G  Y G Q+  NG SI   +E A+    +  E   +   GRTD GV A  
Sbjct: 65  RKIALKIAYDGRVYHGVQKDPNGLSIGEVLENALKSTDLYIESNDIVFCGRTDRGVSAAN 124

Query: 60  QVAHFDLVREWV 71
            +    +     
Sbjct: 125 MIISLKIKSILE 136


>gi|66807627|ref|XP_637536.1| hypothetical protein DDB_G0286567 [Dictyostelium discoideum AX4]
 gi|60465972|gb|EAL64039.1| hypothetical protein DDB_G0286567 [Dictyostelium discoideum AX4]
          Length = 615

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 69/185 (37%), Gaps = 35/185 (18%)

Query: 5   CMIIEYNGSGYFGWQRQKNGS--SIQGSIEK--------AIFLVTG-EIVVVHGAGRTDS 53
            +   YNGS Y+G     +    +I+  IEK        A+  +   + + +  + RTD 
Sbjct: 151 ALCFAYNGSKYYGSSYSFDIRFPAIENLIEKSLIRNGHIALENIGNLKRIKLSRSSRTDK 210

Query: 54  GVHALRQVAHFDLVREWVPVILCK--------ALNAYLKISDTISILNLSIVDKQFHARF 105
           GVH++  V    L+ +     L +          N    +   I +++ +   + F AR 
Sbjct: 211 GVHSVSTVISAFLLIDKETERLAQFGTPPQYFIDNINRYLPSDIRLISATKPSRTFRARP 270

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR---HDFTTFRSIH 162
           ++  R Y Y +                  K +  + M     + +G    H++T  R  +
Sbjct: 271 ASKSRVYNYLVPMDHL-------------KDISIDRMNSILSNFIGTSSFHNYTYQRFTY 317

Query: 163 CQASS 167
             +++
Sbjct: 318 LDSNT 322



 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 7/85 (8%)

Query: 169 IRTIDHFDVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
           +RTI +F V                VV  SFL  QIR  +G    V  G      L+ +L
Sbjct: 395 VRTIMNFYVEKETVLFEGKQWYRFVVVGDSFLMYQIRKMMGFFLSVVKGYQNEIGLQLSL 454

Query: 223 QAQDRKECGPLAPPEGLYFDSVEYS 247
           ++     C P++PP  L+   V + 
Sbjct: 455 KSP-FSICSPISPPFPLFLYDVNFP 478


>gi|300123845|emb|CBK25116.2| unnamed protein product [Blastocystis hominis]
          Length = 282

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 49/264 (18%), Positives = 74/264 (28%), Gaps = 50/264 (18%)

Query: 27  IQGSIEKAIFLV---TGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVIL-CKALNAY 82
           +QG  E+ +  +       + V    RT    +A                 L   +    
Sbjct: 15  VQGKEEETVDRINSCLPSDIRVFKILRTTKNFNAKNFCDRRQYEYILPIETLSPFSSTPP 74

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRA------------ 130
           L I + IS      V+ +  A     R      I          + R             
Sbjct: 75  LSIREDISHNWKEFVENE--AYLQKCREHPEESIDNPFEDRPDNRQRVKSLQIAQQLLLN 132

Query: 131 ------------------------WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA- 165
                                   W    SL    +R      VG H+F  +      A 
Sbjct: 133 EASFSTYTEDAQDRSFGGCVAKDEWPAYLSLALSRLRACMSLFVGTHNFHNYTVGKSSAD 192

Query: 166 SSPIRTIDHFDVN---SFGNLIEIRV--VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
           SS  R I    V+      + + IRV    +SF+  QIR  +G    V  G+ +      
Sbjct: 193 SSAQRHILGISVSDPIRIHDGLYIRVCLEGQSFMLHQIRKMIGIAIEVARGRCSLHTANS 252

Query: 221 ALQAQDRKECGPLAPPEGLYFDSV 244
           +L         P+AP  GL+   V
Sbjct: 253 SLSRG--TMFTPMAPSTGLFLSMV 274


>gi|226293711|gb|EEH49131.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 597

 Score = 66.8 bits (162), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           LE  RA+ IPK    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 348 LEAKRAYRIPKER-IDRINDALDLYVGTRNFHNYTIQKSFREASAKRHIKSFKISRDPII 406

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V  + +V         + +     D+K   P AP  
Sbjct: 407 INGTEWLSLKVHGQSFMMHQIRKMVAMVAMVVRCGCDIQRIPE--TYGDQKIAIPKAPGL 464

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 465 GLLLER 470



 Score = 66.4 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 29/135 (21%), Positives = 55/135 (40%), Gaps = 14/135 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTD 52
            +  +++ Y+GSGY G Q  +   +I+G +        AI        +   +    RTD
Sbjct: 134 RKVAVLLGYSGSGYHGMQLSQTEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTD 193

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
            GVHA   V    L        + + +N +L  S  I +  + + +K ++ +  A   +Y
Sbjct: 194 KGVHAAGNVVSLKL--IVEDSDVVQKINNHL--SPQIRVWGIEVTNKSYN-QRQAEVATY 248

Query: 113 LYRIITRQAPLALEK 127
             ++        LE+
Sbjct: 249 WEKVDEEYIKPILER 263


>gi|269861921|ref|XP_002650634.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
 gi|220065855|gb|EED43425.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
          Length = 152

 Score = 66.8 bits (162), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL--VTGEIVVVHGAGRTDSGVHALR 59
            +  + I Y+G  Y G Q+  NG SI   +E A+    +  E   +   GRTD GV A  
Sbjct: 65  RKIALKIAYDGRVYHGVQKDPNGLSIGEVLENALRSTDLYIESNDIVFCGRTDRGVSAAN 124

Query: 60  QVAHFDLVREWV 71
            +    +     
Sbjct: 125 MIISLKIKSILE 136


>gi|331234741|ref|XP_003330029.1| pseudouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309309019|gb|EFP85610.1| pseudouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 252

 Score = 66.4 bits (161), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 27/97 (27%), Positives = 39/97 (40%), Gaps = 12/97 (12%)

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
           + +++ +L    V   F  RFS   R Y Y     ++P A            LD E M+ 
Sbjct: 116 LHNSVRVLAWLPVHHDFDTRFSCQARHYKYFFSLYKSPQA----------PGLDIEAMKW 165

Query: 145 AAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNS 179
           AA  L+G HDF  F  I    Q +   R I   ++  
Sbjct: 166 AAHRLIGEHDFHNFFKIDPSKQLTHFRRKILSAEIKP 202


>gi|312066617|ref|XP_003136355.1| IMP dehydrogenase 1 [Loa loa]
 gi|307768482|gb|EFO27716.1| IMP dehydrogenase 1 [Loa loa]
          Length = 690

 Score = 66.4 bits (161), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 35/169 (20%), Positives = 61/169 (36%), Gaps = 23/169 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHAL 58
           RY +   Y+G+ +          S+   + KA+   T    G+   +  + RTD+GVHA+
Sbjct: 519 RYLLWASYDGARFMAVANGSINHSVLSFL-KALVRGTFPDIGKQFKMSPSSRTDAGVHAI 577

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISD-----TISILNLSIVDKQFHARFSAIRRSYL 113
           R      +    V       L+ +   +      ++ +L+   V K F +R +   R Y 
Sbjct: 578 RNAFIMQIPIGNVDEDKSNLLDDWNHKTKECIGTSLRVLDFHAVSKGFCSRRNVSYRKYK 637

Query: 114 YRII----------TRQAPLAL---EKGRAWLIPKSLDCENMRIAAQHL 149
           YR+             + PL     E+   W +P   D      A    
Sbjct: 638 YRLAIAENEEEWLKNAEQPLLWQFAERPYIWFLPNGFDIRKAADACSLF 686


>gi|322502433|emb|CBZ37516.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 701

 Score = 66.0 bits (160), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 56/182 (30%), Gaps = 55/182 (30%)

Query: 6   MIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHGAGRT 51
           +I  Y G  Y G Q        +++ ++ KA+F                +++    A RT
Sbjct: 60  IIFGYVGECYCGLQWNHLPEYPTVEEALMKALFETDMISEVNFSNVKVQQLLNFERASRT 119

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNA------------------------------ 81
           D GVHALR V    ++  + P    K + A                              
Sbjct: 120 DKGVHALRNVVSVAVMLPYDPSYTKKRVAALQEHAEGAAAGEVYNADGDVEDDANSAQAA 179

Query: 82  -----------YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRA 130
                         +   I +  +  V + F+A  +   R Y Y + T     A E  + 
Sbjct: 180 VFSCDEAKRLLNEALPRDIHVYAVVPVTRSFNAYLNCGGRRYEYYLPTFALMTAAEYTKT 239

Query: 131 WL 132
           + 
Sbjct: 240 YF 241



 Score = 60.2 bits (145), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 176 DVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           DV + G  ++ I +  +SF+  QIR  +G++  +  G    + +   L  +  +   P+A
Sbjct: 555 DVYAGGIEVVRIELDGQSFMLNQIRKMIGAVVCIAAGGLPDSYIRDVLLRKGVRRGIPMA 614

Query: 235 PPEGLYF 241
           P  GL+ 
Sbjct: 615 PANGLFL 621


>gi|146098588|ref|XP_001468420.1| hypothetical protein [Leishmania infantum]
 gi|134072788|emb|CAM71504.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 701

 Score = 66.0 bits (160), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 56/182 (30%), Gaps = 55/182 (30%)

Query: 6   MIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHGAGRT 51
           +I  Y G  Y G Q        +++ ++ KA+F                +++    A RT
Sbjct: 60  IIFGYVGECYCGLQWNHLPEYPTVEEALMKALFETDMISEVNFSNVKVQQLLNFERASRT 119

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNA------------------------------ 81
           D GVHALR V    ++  + P    K + A                              
Sbjct: 120 DKGVHALRNVVSVAVMLPYDPSYTKKRVAALQEHAEGAAAGEVYNADGDVEDDANSAQAA 179

Query: 82  -----------YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRA 130
                         +   I +  +  V + F+A  +   R Y Y + T     A E  + 
Sbjct: 180 VFSCDEAKRLLNEALPRDIHVYAVVPVTRSFNAYLNCGGRRYEYYLPTFALMTAAEYTKT 239

Query: 131 WL 132
           + 
Sbjct: 240 YF 241



 Score = 60.2 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 176 DVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           DV + G  ++ I +  +SF+  QIR  +G++  +  G    + +   L  +  +   P+A
Sbjct: 555 DVYAGGIEVVRIELDGQSFMLNQIRKMIGAVVCIAAGGLPDSYIRDVLLRKGVRRGIPMA 614

Query: 235 PPEGLYF 241
           P  GL+ 
Sbjct: 615 PANGLFL 621


>gi|308448942|ref|XP_003087803.1| hypothetical protein CRE_15245 [Caenorhabditis remanei]
 gi|308252628|gb|EFO96580.1| hypothetical protein CRE_15245 [Caenorhabditis remanei]
          Length = 195

 Score = 66.0 bits (160), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 59/167 (35%), Gaps = 26/167 (15%)

Query: 107 AIRRSYLYRIITRQAPLAL---EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC 163
           A+ RS+      RQ P      E+  AW +P     E +  A +   G     +F     
Sbjct: 11  AVCRSWELWESIRQEPSIACFSERDYAWRLPPGFSPERLLTAGRRFEGEQVMGSFFKHTN 70

Query: 164 QAS-------SPIRTIDHFDVNSFG---------NLIEIRVVARSFLHTQI-R--SFVGS 204
           +         S ++ I H  +++           +   + +VA+SF+  Q+ R    +  
Sbjct: 71  REKRFEPITPSALKYILHVGLSNGEAYSINNDIYDYYNVTIVAKSFVREQVCRFILMMSC 130

Query: 205 LKLVGDGKWTSTDLEKALQAQD----RKECGPLAPPEGLYFDSVEYS 247
           L      +     ++  L             P+APP+GL+   V Y 
Sbjct: 131 LVNYSYDRIPLATVDWLLNNPISSNFFDMGIPIAPPQGLFLTDVVYD 177


>gi|157875459|ref|XP_001686121.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68129195|emb|CAJ07732.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 701

 Score = 66.0 bits (160), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 56/184 (30%), Gaps = 59/184 (32%)

Query: 6   MIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHGAGRT 51
           +I  Y G  Y G Q        +++ ++ KA+F                +++    A RT
Sbjct: 60  IIFGYVGECYCGLQWNHLPEYPTVEEALMKALFETDMISEVNFSNVKVQQLLNFERASRT 119

Query: 52  DSGVHALRQVAHFDLVREWVP--------------------------------------- 72
           D GVHALR V    ++  + P                                       
Sbjct: 120 DKGVHALRNVVSVAVMLPYDPSYTKKRVAVLQEHAEGAAAGEVYNADGDVEDDANSAQTA 179

Query: 73  ----VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
                   + LN  L     I +  +  V + F+A  +   R Y Y + T     A E  
Sbjct: 180 VFSCEEAKRLLNEAL--PRDIHVYAVVPVTRSFNAYLNCGGRRYEYYLPTFALMTAAEYS 237

Query: 129 RAWL 132
           + + 
Sbjct: 238 KTYF 241



 Score = 56.8 bits (136), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/258 (17%), Positives = 75/258 (29%), Gaps = 49/258 (18%)

Query: 21  QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL----RQVAHFDLVREWVPVILC 76
           Q + + +Q ++E+A             A R     +A            L R      + 
Sbjct: 376 QDSDAEVQAALERA------------SAARPCEDNYATHFHDGLFESMILFRSIPADAMR 423

Query: 77  KALNAYLKISDTISILNLSIVDKQFHARFS--AIRRSY---LYRIITR---QAPLALEK- 127
              N  L       + +L    +  H   +     RSY    YR I       P  +   
Sbjct: 424 HVTNYRLPAEQLQHVRHLFHEYEGTHCYHNFTPGGRSYDASCYRFIRSVVVSDPFVVSPE 483

Query: 128 ---------GRAWLIPKSLDC-------ENMRIA-AQHLVG------RHDFTTFRSIHCQ 164
                      +     S D        E M    A  L G       H           
Sbjct: 484 EELLQHSIDSWSLNHFYSPDERVAATYEEWMTEGEAAELQGAAVSVSEHGKLQIPKSADA 543

Query: 165 ASSPIRTIDHFDVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
           A          DV + G  ++ I +  +SF+  QIR  +G++  +       + +   L 
Sbjct: 544 ALRERMRQHIRDVYAGGIEVVRIELDGQSFMLNQIRKMIGAVVCIAAAGLPGSYIRDVLL 603

Query: 224 AQDRKECGPLAPPEGLYF 241
            +  +   P+AP  GL+ 
Sbjct: 604 RKGVRRGIPMAPANGLFL 621


>gi|328871318|gb|EGG19689.1| hypothetical protein DFA_00267 [Dictyostelium fasciculatum]
          Length = 568

 Score = 65.6 bits (159), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 34/174 (19%)

Query: 6   MIIEYNGSGYFG----WQRQKNGSSIQGSIEKAIFL-------VTGEIVVV--HGAGRTD 52
           M+  Y G+GY G       Q +  +++  +E+A+FL         G+   +    + RTD
Sbjct: 134 MLFAYVGTGYHGLEFHMTDQ-DYPTLENCLERALFLSGMILPTNFGDPSRLNWRRSSRTD 192

Query: 53  SGVHALRQVAHFDLV----REWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARF 105
            GVH++  +   +L     R   P  +      +N+ L   D + I+++ +  K F  R 
Sbjct: 193 KGVHSMSTIIKANLEIDRSRMLTPEKIADYVALINSNL--PDALRIISMEMTKKSFDPRR 250

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR 159
             I R+Y Y +  +                +LD E  +I     +G   +  F 
Sbjct: 251 QGIARTYHYVLPKKYLGD----------RYTLD-EINQIILPMFIGNFSYHNFT 293



 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           ++     S    ++  +   SF+  QIR  +G +  + +GK     LE AL +       
Sbjct: 382 LEETFQESGQEWVKFVIEGESFIQYQIRKMMGFVLAITNGKTDLKTLELALHSPFSIHA- 440

Query: 232 PLAPPEGLYF 241
           P+APP  LY 
Sbjct: 441 PIAPPNPLYL 450


>gi|298705212|emb|CBJ28643.1| pseudouridylate synthase 3 [Ectocarpus siliculosus]
          Length = 472

 Score = 65.6 bits (159), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 38/96 (39%), Gaps = 16/96 (16%)

Query: 82  YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN 141
              +   +  L  + V + F ARFS   R+Y Y                + + + +D + 
Sbjct: 379 NRVLPPGVRTLAWAPVTEGFSARFSCSDRTYRY----------------FFMARDMDVKA 422

Query: 142 MRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           M  AA  +VG HDF     I  +  + I  +D+  V
Sbjct: 423 MNEAASKIVGSHDFRNLCKIGTKGHTRIVLVDYMAV 458



 Score = 51.0 bits (121), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 11/77 (14%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV---------HGAGRTDSG 54
             + + Y G GY G+  Q  G+  + +IEK +F       +V            GRTD G
Sbjct: 107 VAVQLMYEGGGYAGFCSQSEGN--EETIEKHLFRALTTTKLVETITTGDNYSRCGRTDRG 164

Query: 55  VHALRQVAHFDLVREWV 71
           V AL  V    +  ++ 
Sbjct: 165 VSALGNVITVSMRSKFP 181


>gi|225678874|gb|EEH17158.1| tRNA pseudouridine synthase [Paracoccidioides brasiliensis Pb03]
          Length = 547

 Score = 65.6 bits (159), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 31/126 (24%), Positives = 51/126 (40%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           LE  RA+ IPK    + +  A    VG  +F  +      + +S  R I  F ++S    
Sbjct: 313 LEAKRAYRIPKER-IDRINDALDLYVGTRNFHNYTIQKSFREASAKRHIKSFKISSDPII 371

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V  + +V         + +     D+K   P AP  
Sbjct: 372 INGTEWLSLKVHGQSFMMHQIRKMVAMVAMVVRCGCDIQRIPE--TYGDQKIAIPKAPGL 429

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 430 GLLLER 435



 Score = 63.3 bits (153), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 53/171 (30%), Gaps = 25/171 (14%)

Query: 18  WQRQKNGSSIQGSIEKA------IFLVT---GEIVVVHGAGRTDSGVHALRQVAHFDLVR 68
           W+ Q    +I+G +  A      I        +   +    RTD GVHA   V    L  
Sbjct: 70  WRSQTE-KTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDKGVHAAGNVVSLKL-- 126

Query: 69  EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKG 128
                 + + +N +L  S  I +  + + +K F +      R Y Y I T          
Sbjct: 127 IVEDSDVVQKINNHL--SPQIRVWGIEVTNKSFSSYQLCDSRVYEYLIPTHCFLPPHPST 184

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                        +   A+     +D   +     + ++    +D   +  
Sbjct: 185 YLGQ--------KLVEIAEM---ENDLEGYNQRQAEVATYWEKVDEEYIKP 224


>gi|325182026|emb|CCA16479.1| tRNA pseudouridine synthase A putative [Albugo laibachii Nc14]
          Length = 97

 Score = 65.2 bits (158), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 4  YCMIIEYNGSGYFGWQRQKNGS-----SIQGSIEKAIFLVT--GEIVVVHGAGRTDSGVH 56
          Y M I Y G+ + GWQRQ   S     S+Q  IE ++       E V V+   RTD+G H
Sbjct: 24 YGMSIAYYGTDFIGWQRQPAASKPGFFSVQQIIEDSLSRALSKSERVNVNAVSRTDAGTH 83

Query: 57 A 57
          A
Sbjct: 84 A 84


>gi|46205445|ref|ZP_00048530.2| COG0223: Methionyl-tRNA formyltransferase [Magnetospirillum
           magnetotacticum MS-1]
          Length = 189

 Score = 65.2 bits (158), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 13/28 (46%), Positives = 21/28 (75%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQ 28
           M RY ++IEY+G+ + GWQRQ +  ++Q
Sbjct: 156 MPRYKLVIEYDGAPFCGWQRQADDPTVQ 183


>gi|255023069|ref|ZP_05295055.1| tRNA pseudouridine synthase A [Listeria monocytogenes FSL J1-208]
          Length = 33

 Score = 65.2 bits (158), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 1  MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK 33
          M RY  II Y+GSG++G+Q Q N  ++Q  IEK
Sbjct: 1  MTRYKAIISYDGSGFYGYQVQPNTRTVQAEIEK 33


>gi|257468648|ref|ZP_05632742.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|317062905|ref|ZP_07927390.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
 gi|313688581|gb|EFS25416.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
          Length = 283

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 72/218 (33%), Gaps = 34/218 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
           Y   I YNG+ +  +       SI+G   + +  +       V  AGRTD+ V A   + 
Sbjct: 14  YMFYISYNGAKFQSFDEMNEKKSIKGKFREVMEKIGFTWAKGVQQAGRTDAKVSANENIL 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +           + +  N           L ++++ K F                    P
Sbjct: 74  YVSSNFNGNIKKIQEDFNKNSDTD-----LKVTMIKKTF---------------PNIVFP 113

Query: 123 LALE-KGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDV 177
             +E +   +  P+ L     E +    + L G +D + F      +    IR     +V
Sbjct: 114 DMIEKREYIYSYPEKLIKNTEEEIEKLCKELSGTYDVSEFTDKKGLELKEHIR-----EV 168

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
                  ++R +  SF+  Q+R   G +     GK   
Sbjct: 169 KITYENGKLRFLGNSFMPKQVRIMSGYIL---TGKKEP 203


>gi|154334040|ref|XP_001563275.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134060287|emb|CAM45698.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 764

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 53/165 (32%), Gaps = 52/165 (31%)

Query: 6   MIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLV------------TGEIVVVHGAGRT 51
           +I  Y G  Y G Q        +++ ++ KA+F                +++    A RT
Sbjct: 126 IIFGYVGECYCGLQWNHLPEYPTVEEALMKALFETDMISEVNFANFKVQQLLNFERASRT 185

Query: 52  DSGVHALRQVAHFDLVREWVPVILCKALNAYLK--------------------------- 84
           D GVHALR V    ++  + P    + L A  +                           
Sbjct: 186 DKGVHALRNVVSVAVMLPYDPAYAKRRLAAMQEHTKGTAAGETHNVDGDSEEDANDAIFS 245

Query: 85  -----------ISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
                      +   + +  +  V + F+A  +   R Y Y + T
Sbjct: 246 CEEAKRLLNKALPRDLHVYGVVPVTRSFNAYLNCGGRRYEYYLPT 290



 Score = 54.4 bits (130), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 176 DVNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           DV + G  ++ I +  +SF+  QIR  +G++  +         +   L  +  +   P+ 
Sbjct: 618 DVYAGGIEVVRIELDGQSFMLNQIRKMIGAVVCIAAAGLPLNHIRDVLLRKGVRRGIPMV 677

Query: 235 PPEGLYF 241
           P  GL+ 
Sbjct: 678 PANGLFL 684


>gi|145609509|ref|XP_367752.2| hypothetical protein MGG_07663 [Magnaporthe oryzae 70-15]
 gi|145016878|gb|EDK01308.1| hypothetical protein MGG_07663 [Magnaporthe oryzae 70-15]
          Length = 720

 Score = 63.7 bits (154), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 43/112 (38%), Gaps = 9/112 (8%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG------NLIEIRVVAR 191
              ++ A    VG H+F  +  +     SS  R I  F VN           + ++V  +
Sbjct: 503 IGKLQAALDKYVGTHNFHNYTILKKFTDSSAKRHIKSFKVNPEPIQIGETEWVSLKVHGQ 562

Query: 192 SFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           SF+  QIR  V    L          + ++ +A+  +   P AP  GL  + 
Sbjct: 563 SFMMHQIRKMVAMAVLTVRCGVPLDRITQSYEAK--RISIPKAPGLGLLLER 612



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 9/88 (10%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTDS 53
           +  ++I Y G+GY G Q      +I+G + +      AI        + V +    RTD 
Sbjct: 113 KVAVLIGYAGTGYKGMQINHFEKTIEGDLFRAFVDAGAISKANASDPKKVSLMRCARTDK 172

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNA 81
           GVHA   V    L+       L    NA
Sbjct: 173 GVHAASNVISLKLIVPLEEKELAGNGNA 200



 Score = 41.4 bits (96), Expect = 0.12,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 2/59 (3%)

Query: 71  VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
               L   +N++L   D I + ++   +  F    +   R Y Y + T           
Sbjct: 286 TMADLVARINSHL--PDQIRVWDILRTNNSFSCYQACDSRWYEYLMPTHALIPPHPDSY 342


>gi|269862295|ref|XP_002650782.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
 gi|220065627|gb|EED43275.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
          Length = 241

 Score = 63.3 bits (153), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 23/143 (16%), Positives = 42/143 (29%), Gaps = 24/143 (16%)

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           ++     L   L     +   I +   + V   F AR +  +R Y Y       P  L  
Sbjct: 52  KKHDAKELPYDLILNKVLPPQIRVKGWAPVPWNFSARHNCCQRRYTYFFTC---PPQLLP 108

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR---SIHCQASSPIRTIDHFDVNSFGN-- 182
                          + A + +    DF  F     +       +  ++   +    +  
Sbjct: 109 KY-------------QEAGRIIYKTEDFYNFCTHSKVDANYKFKLSMLEFVSITPIPSQD 155

Query: 183 ---LIEIRVVARSFLHTQIRSFV 202
              L  + + A SFLH  +R   
Sbjct: 156 TKILCAMNISAYSFLHNMVRKIF 178


>gi|227497211|ref|ZP_03927459.1| conserved hypothetical protein [Actinomyces urogenitalis DSM
          15434]
 gi|226833342|gb|EEH65725.1| conserved hypothetical protein [Actinomyces urogenitalis DSM
          15434]
          Length = 49

 Score = 62.9 bits (152), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 12/41 (29%), Positives = 22/41 (53%)

Query: 3  RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIV 43
          R  + + Y+G+G+ GW  Q    +++G +  A+  V  E V
Sbjct: 9  RLRLDLAYDGAGFKGWAAQPGLRTVEGELTAALATVLREPV 49


>gi|310779345|ref|YP_003967678.1| pseudouridylate synthase-like protein [Ilyobacter polytropus DSM
           2926]
 gi|309748668|gb|ADO83330.1| pseudouridylate synthase-like protein [Ilyobacter polytropus DSM
           2926]
          Length = 292

 Score = 62.9 bits (152), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/214 (16%), Positives = 63/214 (29%), Gaps = 26/214 (12%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
           Y   I Y G  +  +   KN  S++    + +  +       +  AGRTD+ V A   + 
Sbjct: 21  YLFYISYRGGSFDSFDEVKNKKSVKERFREIMNSIGFTWAKGIQQAGRTDAKVSAGENIL 80

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +           +    N        + I  +               R Y YR    +  
Sbjct: 81  YVSSSYSGDMEEIEARFNE--ISKKEMKIKKIQKTLSDLVIPDLVEAREYCYRYPAAKIK 138

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFG 181
                          + E +    + L G +D + F     Q     IR++        G
Sbjct: 139 N--------------NEEKIESLCRELSGTYDVSEFTDFKGQKLKEKIRSV-EISFKDKG 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
               +     SF+  Q+R   G +     G+ T 
Sbjct: 184 ----LWFKGSSFMPKQVRIMSGYIL---TGEKTP 210


>gi|294897084|ref|XP_002775815.1| pseudouridylate synthase, putative [Perkinsus marinus ATCC 50983]
 gi|239882168|gb|EER07631.1| pseudouridylate synthase, putative [Perkinsus marinus ATCC 50983]
          Length = 708

 Score = 62.5 bits (151), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 32/183 (17%), Positives = 62/183 (33%), Gaps = 44/183 (24%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSS----IQGSIEKAIFL--------VTGEIVVVHGAGRTD 52
            +++ +NG+ Y G Q   +       ++  +  A+          V  + +    + RTD
Sbjct: 27  ALVVGFNGTKYRGLQMNADNCDRIDYVESDLLGAMKRAGVVKPDVVRLDEIQWTRSSRTD 86

Query: 53  SGVHALRQVAHFDLVREWVPV---------------ILCKALNAYLKISDTISILNLSIV 97
           +GV A R V    ++    P                 + +A+N  L     I + N   +
Sbjct: 87  AGVSAARIVVSAKILVHEAPEVKGNRQADRVNRTYPEVVEAINKEL--PREIKVFNCMKI 144

Query: 98  DKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTT 157
              F+A+ S   R Y Y +    A                D + ++ A       H++  
Sbjct: 145 CASFNAQKSCNWRHYSYYMPMSLAG---------------DVDKLQEALGKFTNAHNYHN 189

Query: 158 FRS 160
           F +
Sbjct: 190 FTN 192



 Score = 50.6 bits (120), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 163 CQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT-STDLEKA 221
           C ++    T    ++ +    + + V  + FL+ QIR  +G+      G +   + ++ A
Sbjct: 355 CNSAIHSFTATPIEMGNGEKWVRVDVRGQFFLYNQIRLMIGAGIAYARGVFPSISCIQFA 414

Query: 222 LQAQDRKECGPLAPPEGLYFD 242
           +   + K   PLAP  GL   
Sbjct: 415 IDT-NYKFHSPLAPACGLILH 434


>gi|239791165|dbj|BAH72086.1| ACYPI006976 [Acyrthosiphon pisum]
          Length = 157

 Score = 62.2 bits (150), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 37/97 (38%), Gaps = 10/97 (10%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIF----LVTGEIVVVHGAGRTDSGVHAL 58
               I Y G  Y G+  Q  +  +I+  + +A+     + + +    H  GRTD GV + 
Sbjct: 59  VVFKILYLGWDYHGFATQDVSEKTIEYELFRALTICCLIESRQTSNYHRCGRTDKGVSSF 118

Query: 59  RQVAHFDLVREWVPVI---LCKALNAYLKISDTISIL 92
            QV    +            CK LN  L     I ++
Sbjct: 119 SQVISLTVRSNGDDSEELPYCKMLNRLL--PKDIRVV 153


>gi|317033787|ref|XP_001395447.2| tRNA pseudouridine synthase [Aspergillus niger CBS 513.88]
          Length = 517

 Score = 61.8 bits (149), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 23/111 (20%), Positives = 45/111 (40%), Gaps = 13/111 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTDS 53
           +  +++ Y+G+GY G Q  +   +I+G +        AI        +   +    RTD 
Sbjct: 49  KVAVLLGYSGTGYKGMQLSETEKTIEGELFAAFVAAGAISKANATDPKKSSLVRCARTDK 108

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           GVHA   +    L        + + +N  L     I + ++ + +K F + 
Sbjct: 109 GVHAAGNIVSLKL--IVEDDDIIQKINEKLSS--QIRVWDILVTNKSFSSY 155



 Score = 55.2 bits (132), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 29/126 (23%), Positives = 46/126 (36%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA-SSPIRTIDHFDVNSFG-- 181
           L+  RA+ IP       ++ A    VG ++F  +      A  S  R I  F +      
Sbjct: 278 LQAKRAYRIPAQR-LARVQEALDKYVGTNNFFNYTIQKTHADPSSKRHIKSFKMAEQPII 336

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    +V         + +   A   K   P AP  
Sbjct: 337 INGTEWLSLKVHGQSFMMHQIRKMVAMAAMVVRCGCDPQRIVETYGAN--KIAIPKAPGL 394

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 395 GLLLER 400


>gi|170583041|ref|XP_001896406.1| hypothetical protein Bm1_24730 [Brugia malayi]
 gi|158596406|gb|EDP34751.1| hypothetical protein Bm1_24730 [Brugia malayi]
          Length = 189

 Score = 61.8 bits (149), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ--DRKECGPLAPP 236
           +    +++ +  + FL  QIR  +  L  +G G      + + L  +    K    LAP 
Sbjct: 12  THYEFLQLTIKGKGFLWHQIRCIMALLCEIGLGNEKPDIITELLDIRLMPSKPIYGLAPA 71

Query: 237 EGLYFDSVEYS 247
             L      Y 
Sbjct: 72  FPLCLFDCSYE 82


>gi|332262433|ref|XP_003280267.1| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like
           [Nomascus leucogenys]
          Length = 191

 Score = 61.4 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 24/105 (22%), Positives = 41/105 (39%), Gaps = 17/105 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +  +++ Y+G GY G QR        +I+  +  A+                +      
Sbjct: 84  RKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCA 143

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNL 94
           RTD GV A  QV      + W+   + + +N++L     I IL L
Sbjct: 144 RTDKGVSAAGQVVSL---KVWLIDDILEKINSHL--PSHIRILGL 183


>gi|315929089|gb|EFV08321.1| tRNA pseudouridine synthase II [Campylobacter jejuni subsp. jejuni
           305]
          Length = 58

 Score = 61.4 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             A  FL  QIR  V S+  V +GK +  +L++ ++A+ ++    LAPP GLY   + Y
Sbjct: 1   FKANGFLRGQIRLSVASVLKVLEGKMSEKELKEQIEAK-KQYNHFLAPPNGLYLSRICY 58


>gi|68059018|ref|XP_671487.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56487712|emb|CAH95346.1| hypothetical protein PB001270.00.0 [Plasmodium berghei]
          Length = 69

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 25/55 (45%)

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           FL+  IR  VG L  VG G     D++ AL      +    APP+GL    + + 
Sbjct: 1   FLYHMIRIIVGVLIQVGVGILNFQDVKDALYNSKPLKVKLCAPPQGLCLKKILFP 55


>gi|70952835|ref|XP_745558.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56525920|emb|CAH80907.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 507

 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 151 GRHDFTTFRSIHCQASSPIRTIDHFDVNS----FGNLIEIRVVARSFLHTQIRSFVGSLK 206
           G H+F  F   +   ++  R I +FDV++      N I IR++ +SFL  QIR  +    
Sbjct: 366 GYHNFHCFTKNNID-TTTFRYIKYFDVSTVKLYDHNFISIRILGQSFLMHQIRKMITLAV 424

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
                      +  +L  +       L PP+GL   
Sbjct: 425 ETFRNATPKNSIYYSLNTKSYIPIL-LFPPDGLMLV 459



 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSG 54
           +Y + + Y GS Y G Q Q K   +I+  IE+ +  +        G    +  + RTD G
Sbjct: 59  KYGLCVGYIGSRYHGCQGQGKEHMTIENEIERTLTKINAVKNNSKGFNYCLSRSARTDLG 118

Query: 55  VHALRQVAHFDL 66
           VHAL  +  +++
Sbjct: 119 VHALYNLFVYNI 130



 Score = 37.9 bits (87), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 2/52 (3%)

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            R+         LN+ L   + I   ++  V K F AR     R Y Y   T
Sbjct: 197 ERKRKEKKFINLLNSNL--PNDIKCFDIYKVTKSFDARKFCSFRLYEYLFPT 246


>gi|290982091|ref|XP_002673764.1| predicted protein [Naegleria gruberi]
 gi|284087350|gb|EFC41020.1| predicted protein [Naegleria gruberi]
          Length = 495

 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/262 (15%), Positives = 81/262 (30%), Gaps = 66/262 (25%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVP--VILCKALNAYLKISDTISILN---LSIVDKQF 101
            + RTD GVH++  +    +          + +  N +  + D++ + +   +    + F
Sbjct: 42  ASSRTDKGVHSIANIFSCKVPESVKENVDWISELTNRFSNVEDSLRVFHLETIKEDAENF 101

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK----------SLDCEN----MRIAAQ 147
           ++R   + R+Y Y I        + + +  L  K           ++ E     +     
Sbjct: 102 NSRKFGLWRTYEYFIPQYCLKGMISESKMTLYQKLAKKPTVTLPDVNLEAVCKQLNNVFS 161

Query: 148 HLVGRHDFTTFRSIHCQASS---------------------PIRTIDHFDVNSFG----- 181
            + G  +F  F S      S                       RT+       +      
Sbjct: 162 RMEGFKNFQNFTSNTTSNGSSEGGQEDDLDTFQNSDTVGNQYHRTVFQCFAKPYTIGVPN 221

Query: 182 ------------------NLIEIRVVARSFLHTQIRSFVGSLK--LVGDGKWTSTDLEKA 221
                               + I+V A  FL+ QIR  VG     L+   +     ++ A
Sbjct: 222 SKLQQASGLAPISSSDALRGVLIKVTASGFLYHQIRKMVGLAISHLIFPKEINDEFIDIA 281

Query: 222 LQAQDRKECGPLAPPEGLYFDS 243
           + +++     P AP + L    
Sbjct: 282 INSKE-TMFIPTAPGDSLILLH 302


>gi|148238175|ref|NP_001088988.1| pseudouridylate synthase 1 [Xenopus laevis]
 gi|57032536|gb|AAH88978.1| LOC496371 protein [Xenopus laevis]
          Length = 167

 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/103 (24%), Positives = 40/103 (38%), Gaps = 17/103 (16%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFL---------VTGEIVVVHGAG 49
            +   +I Y+G GY G QR        +I+  + +A+ L            + +      
Sbjct: 55  RKVVFLIAYSGKGYHGMQRNVGTSQFKTIEDELVQALVLSECIPDNHAEDMKKMSFQRCA 114

Query: 50  RTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISIL 92
           RTD GV A  QV      + W+   + + +N  L     I IL
Sbjct: 115 RTDKGVSAAGQVVSL---KIWLIDNVVEKINENL--PSHIRIL 152


>gi|302834750|ref|XP_002948937.1| hypothetical protein VOLCADRAFT_104122 [Volvox carteri f.
           nagariensis]
 gi|300265682|gb|EFJ49872.1| hypothetical protein VOLCADRAFT_104122 [Volvox carteri f.
           nagariensis]
          Length = 669

 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/122 (19%), Positives = 51/122 (41%), Gaps = 20/122 (16%)

Query: 1   MIR--YCMIIEYNGSGYFGWQRQKNG---SSIQGSIEKAIFLV---------TGEIVVVH 46
           M++    + + Y G+ + G Q  ++G   S+++  +E+A+F             + V   
Sbjct: 217 MVKRSIALHVGYVGTAFKGLQVNRSGAPDSTVEEVLERAVFEAGLIAESNFGDLKKVKWS 276

Query: 47  GAGRTDSGVHALRQVAHFDL------VREWVPVILCKALNAYLKISDTISILNLSIVDKQ 100
              RTD GVH++  V    +        +  P  L  A +   ++   + + +   V K+
Sbjct: 277 RNSRTDKGVHSVSTVVGLRVLLRGDEGFDLDPEGLEVAADLNTRLPPQVRVFSAQRVQKK 336

Query: 101 FH 102
           F+
Sbjct: 337 FN 338



 Score = 53.3 bits (127), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 31/86 (36%), Gaps = 8/86 (9%)

Query: 169 IRTIDHFDVNSFGNLI-------EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKA 221
            RTI  F  +    L+        +RV   SF+  QIR  +G    V  G      L  +
Sbjct: 463 FRTITSFTADDPAPLVPGGVPCVRLRVRGMSFMLHQIRHMIGGALAVARGSLPLPLLRAS 522

Query: 222 LQAQDRKECGPLAPPEGLYFDSVEYS 247
           L  Q R    P APP  L      + 
Sbjct: 523 LAGQAR-VTVPRAPPHTLILAGCTFP 547


>gi|82595787|ref|XP_725993.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23481212|gb|EAA17558.1| hypothetical protein [Plasmodium yoelii yoelii]
          Length = 1510

 Score = 60.2 bits (145), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 151  GRHDFTTFRSIHCQASSPIRTIDHFDVNS----FGNLIEIRVVARSFLHTQIRSFVGSLK 206
            G H+F  F   +   ++  R I +FD+++      N I IR++ +SFL  QIR  +    
Sbjct: 1369 GYHNFHCFTKNNID-TTTYRYIKYFDISTVKLYDHNFISIRILGQSFLMHQIRKMITLTV 1427

Query: 207  LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +     +   +  +L  ++      L PP+GL  
Sbjct: 1428 EIFRNATSKNSIYYSLNTKNYIPIL-LFPPDGLML 1461



 Score = 55.6 bits (133), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 3    RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSG 54
            +Y + + Y GS Y G Q Q K   +I+  IE+ +  +        G    +  + RTD G
Sbjct: 1069 KYGLCVGYIGSRYHGCQGQGKEYMTIENEIERTLTKINAVKKTSKGFNYCLSRSARTDLG 1128

Query: 55   VHALRQVAHFDLVREW 70
            VHAL  +  +++  + 
Sbjct: 1129 VHALYNLFVYNINIDI 1144


>gi|154274161|ref|XP_001537932.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
 gi|150415540|gb|EDN10893.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
          Length = 634

 Score = 60.2 bits (145), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 49/126 (38%), Gaps = 10/126 (7%)

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFG-- 181
           ++  +A+ IP+    + +  A    VG  +F  +      + +S  R I  F ++     
Sbjct: 320 IDAKKAYRIPRER-LDRINDALGMYVGTRNFHNYTIQKSFRDASAKRHIKSFKISREPLI 378

Query: 182 ----NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + ++V  +SF+  QIR  V    L+         + +     D+K   P AP  
Sbjct: 379 INGTEWLSLKVHGQSFMMHQIRKMVAMTALIVRCGCDIQLVPE--TYGDQKIAIPKAPGL 436

Query: 238 GLYFDS 243
           GL  + 
Sbjct: 437 GLLLER 442



 Score = 53.7 bits (128), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 13/104 (12%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEK------AIFLVT---GEIVVVHGAGRTDS 53
           +  +++ Y+GSGY G Q  +   +I+G +        AI        +   +    RTD 
Sbjct: 122 KVAVMLGYSGSGYKGMQLSETEKTIEGDLFTAFVAAGAISKANATDPKKSSLVRCARTDK 181

Query: 54  GVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV 97
           GVHA   V    L+ E     + + +N +L  S  I      + 
Sbjct: 182 GVHAAGNVVSLKLIVEDP--NVVQKINGHL--SPQIRQRQAEVA 221


>gi|298708456|emb|CBJ30580.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 822

 Score = 60.2 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 64/237 (27%), Gaps = 44/237 (18%)

Query: 55  VHALRQVAHFDLVREWVPVILCKAL--------NAYLKISDTISILNLSIVDKQFHARFS 106
           V A                 + K L        N+     + I +L    V   FHA   
Sbjct: 179 VSATADTICLRAPTTVPQEGIRKWLDDTNAALDNSDGNAREAIRLLGRMAVPSTFHAEIH 238

Query: 107 AIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQ--------HLVGRHD---- 154
           A RR Y Y +         E           +   +    +        H  G HD    
Sbjct: 239 AKRRRYEYLLPAWMLDETAEGPWEGPPRGQENLIPLLRRLRARGLRPFGHCNGEHDGTRR 298

Query: 155 ----FTTFRSIH-CQASSPIRTIDHFDVNSF-----------------GNLIEIRVVARS 192
               +  F +     + S +R +  F                       + + + +   +
Sbjct: 299 RCPLWHNFSASALPHSPSSLRRLFRFYAMEVIQSSPSSSQGGDAGASGADYVCLSINGDA 358

Query: 193 FLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC--GPLAPPEGLYFDSVEYS 247
           F+  Q+R  V        G  ++  +   +    +++    PLAP        V YS
Sbjct: 359 FMSQQVRGMVALAVAGARGLISAEGIAATIDPTRQEDLLPVPLAPAAPCSLAEVGYS 415


>gi|224082524|ref|XP_002306728.1| predicted protein [Populus trichocarpa]
 gi|222856177|gb|EEE93724.1| predicted protein [Populus trichocarpa]
          Length = 162

 Score = 59.8 bits (144), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 21/100 (21%), Positives = 38/100 (38%), Gaps = 7/100 (7%)

Query: 147 QHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
           +  +G HDF          +  ++     D+     L  I++   +FL  Q+   V  L 
Sbjct: 26  KKFMGEHDFRNLCK-----TDAVKCRIVGDMFKGHQLCAIKIKGSAFLLHQVCCMVAVLL 80

Query: 207 LVGDGKWTSTDLEKALQAQ--DRKECGPLAPPEGLYFDSV 244
           ++G G  +   ++  L  +   RK    +AP   L    V
Sbjct: 81  MIGQGLESPDLIDALLDTRRTPRKPQYLMAPEIPLVLLPV 120


>gi|325115129|emb|CBZ50685.1| conserved hypothetical protein [Neospora caninum Liverpool]
          Length = 1140

 Score = 59.8 bits (144), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 53/175 (30%), Gaps = 8/175 (4%)

Query: 57   ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            A                   +     ++ +    I ++ I   QF             R 
Sbjct: 854  AKAMEGLHSFAAFRCEYSGKEKARHLMQDNPFCVIDSIRISPLQFDPWPQPSCGVSSARF 913

Query: 117  ITRQAP--LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT------TFRSIHCQASSP 168
                 P     ++G A       D +            HD           S+  Q S+ 
Sbjct: 914  SEVPVPKGSPGDRGEAHASQDPRDTQREDSEGGATETSHDANERLCHFAGASVLSQGSAV 973

Query: 169  IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
              +    D +     + I VV   FL+  +R  VG+L  V  G+ ++ D+ +AL+
Sbjct: 974  FASPSFTDGHDLPQGLRIDVVGNRFLYKMVRKMVGALVQVALGRLSTEDIRRALE 1028



 Score = 41.0 bits (95), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 19/55 (34%), Gaps = 5/55 (9%)

Query: 42  IVVVHGAGRTDSGVHALR---QVAHFDLVREWVPVILCKALNAYLKISDTISILN 93
            VV+  A RTD GVHA     Q   +              +N  L     + IL 
Sbjct: 506 PVVLRPASRTDRGVHAAGAICQYVSYYHPLHIPLESFVAGVNRRL--PSDVRILA 558



 Score = 36.3 bits (83), Expect = 3.6,   Method: Composition-based stats.
 Identities = 5/32 (15%), Positives = 14/32 (43%), Gaps = 2/32 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQ--KNGSSIQGSI 31
               +++ Y+G+ + GW         ++  S+
Sbjct: 219 TNLLLLVAYDGTDFSGWAANLSPQDRTLVASL 250



 Score = 36.3 bits (83), Expect = 3.7,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 8/51 (15%)

Query: 137 LDCENMRIAAQHLVGRHDFTTFR--------SIHCQASSPIRTIDHFDVNS 179
            D E M+ AA+ + G H F  FR        + H    +P   ID   ++ 
Sbjct: 845 FDLEQMKQAAKAMEGLHSFAAFRCEYSGKEKARHLMQDNPFCVIDSIRISP 895


>gi|328772887|gb|EGF82924.1| hypothetical protein BATDEDRAFT_33866 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 580

 Score = 59.5 bits (143), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 28/122 (22%), Positives = 54/122 (44%), Gaps = 6/122 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-----VVVHGAGRTDSGVH 56
           +R  ++  YNG+G+   +R K   +I+G++   +  +           +  A  T++G H
Sbjct: 23  VRLAILYGYNGTGFDALERTKGEVTIEGTLLAVLASLLSADGKATFTNISRASTTEAGEH 82

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           A +QV  F+      P+IL         +  ++ +  +  V   F AR +   R+Y + I
Sbjct: 83  ASKQVVSFETHAP-TPIILPAVEAVNKLLPSSMRVFRIIPVASDFSARRTCEARTYEFLI 141

Query: 117 IT 118
            T
Sbjct: 142 PT 143



 Score = 46.4 bits (109), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/112 (16%), Positives = 35/112 (31%), Gaps = 16/112 (14%)

Query: 146 AQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVARSFLHTQI 198
                G H++  +       S P   I   +++            + I++ A +F   Q+
Sbjct: 380 LSLFNGTHNWHNY-IPGADQSDPRCYIRIINIDVRDTELHEGMEWVRIKIQAPAFARYQV 438

Query: 199 RSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG---PLAPPEGLYFDSVEYS 247
           R  +  + +V       + +     A          P AP   L  D   Y+
Sbjct: 439 RRMMALVIMVLRTNTPHSVV-----ANSYGFAKMEIPEAPALSLVLDEPHYN 485


>gi|170585848|ref|XP_001897694.1| hypothetical protein [Brugia malayi]
 gi|158595001|gb|EDP33578.1| conserved hypothetical protein [Brugia malayi]
          Length = 140

 Score = 59.1 bits (142), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQD----RKECGPLAPPEG 238
           LIEI V++RSFL +QIR  + ++     G+     L   L   +           APP+G
Sbjct: 45  LIEISVISRSFLRSQIRHMIRTIVEHAYGRLQWERLIWFLNNPNPENFHNSGMVAAPPQG 104

Query: 239 LYFDSVEYS 247
           L+ + V Y 
Sbjct: 105 LFLEDVVYD 113


>gi|221113816|ref|XP_002154062.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 233

 Score = 59.1 bits (142), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 26/149 (17%), Positives = 45/149 (30%), Gaps = 26/149 (17%)

Query: 102 HARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIA-AQHLVGRHDFTTFRS 160
           H  F A  + Y Y       P        +     LD        ++  +   D + F  
Sbjct: 11  HCMFYA-EKHYCYSFDNSMIPF-------FGCGSHLDYLEQNQCYSETFI--LDQSCF-- 58

Query: 161 IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
                      I         ++ E+ +   +FL  Q+R  V  L L+G G      ++ 
Sbjct: 59  -----------IHEMVKKDLVDICEMEITGLAFLWHQVRCMVAVLLLIGLGVEKPEIIDH 107

Query: 221 AL--QAQDRKECGPLAPPEGLYFDSVEYS 247
            L  ++  ++    LA    L      Y 
Sbjct: 108 LLDVESCPKRPQYELASEIPLVLYDCTYD 136


>gi|253582898|ref|ZP_04860116.1| predicted protein [Fusobacterium varium ATCC 27725]
 gi|251835104|gb|EES63647.1| predicted protein [Fusobacterium varium ATCC 27725]
          Length = 283

 Score = 57.9 bits (139), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 69/218 (31%), Gaps = 34/218 (15%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
           Y   I YNG  +  +       S++G  +  +  V       +  AGRTD+ V A   + 
Sbjct: 14  YMFYISYNGQKFQSFDEINGKKSVKGKFKDIMEKVGFTWAKGIQQAGRTDAKVSANENIL 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +           + +  N           L +++V K F                    P
Sbjct: 74  YVSSNFNGDINKIQEKFNKNSDDE-----LKVTMVKKTF---------------PNIIFP 113

Query: 123 LALE-KGRAWLIPKSLD---CENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDV 177
             +E +   +  P+ L     + +    + L G +D + F      +    IR +     
Sbjct: 114 DMIEKREYIYSYPEKLIKNTEKEIEKLCKELSGIYDVSEFTDKKGLELKEHIREV-KITY 172

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
                   +R +  SF+  Q+R   G +     GK   
Sbjct: 173 ERGK----LRFLGSSFMPKQVRIMSGYIL---TGKKEP 203


>gi|170586436|ref|XP_001897985.1| tRNA pseudouridine synthase A [Brugia malayi]
 gi|158594380|gb|EDP32964.1| tRNA pseudouridine synthase A, putative [Brugia malayi]
          Length = 260

 Score = 57.9 bits (139), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 2/99 (2%)

Query: 149 LVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLV 208
            +   D ++ R IH     P + ++          I + +  +SF+  QIR  +G     
Sbjct: 15  FITYEDRSSMRYIHDFKCGPTQLVEDEVRGGMVEFITLYITGQSFMLHQIRKMIGMTVAT 74

Query: 209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             G    T++     ++  +   P AP  GL  D V Y 
Sbjct: 75  FRGLCGKTEVANTFLSE--RMDVPKAPGLGLVLDKVHYE 111


>gi|296004937|ref|XP_002808812.1| pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
 gi|225632204|emb|CAX64089.1| pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
          Length = 556

 Score = 57.9 bits (139), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/117 (19%), Positives = 44/117 (37%), Gaps = 9/117 (7%)

Query: 132 LIPKSLDCENMRIAAQHL---VGRHDFTTFRSIHCQASSPIRTIDHFDVNS----FGNLI 184
              + L+ E +          VG H+F  F        +  R I +FDV++      + +
Sbjct: 367 HFKEDLNEEELNTFFDIFNNYVGYHNFHCFTKKKID-QTTYRFIKYFDVSTVKLFDYHFL 425

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++++ +SFL  QIR  +           +   +   L  ++      L P +GL  
Sbjct: 426 SVKILGQSFLMHQIRKMITLAVETYRKATSINSIYYCLNTKNYIPI-TLFPSDGLML 481



 Score = 57.5 bits (138), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 10/75 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVT---------GEIVVVHGAGRTD 52
           +Y + I Y GS Y G Q Q +N  +I+ ++E+ +  +               +  + RTD
Sbjct: 52  KYALCIGYIGSQYHGCQGQGENCETIENTLERTLLKINAIKKKKFFKNFNFCLSRSARTD 111

Query: 53  SGVHALRQVAHFDLV 67
            GVHAL  +  +++ 
Sbjct: 112 QGVHALFNIFVYNVD 126


>gi|158520883|ref|YP_001528753.1| pseudouridylate synthase-like protein [Desulfococcus oleovorans
           Hxd3]
 gi|158509709|gb|ABW66676.1| Pseudouridylate synthase-like protein [Desulfococcus oleovorans
           Hxd3]
          Length = 148

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 29/57 (50%)

Query: 99  KQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF 155
             F   F AI ++Y Y I++R    A+ +  AW + + L+ + +R A   + G HD 
Sbjct: 16  DFFEPAFQAISKTYRYWIVSRPTSAAIGRQYAWHLSRPLEIKAIRQALPLVTGTHDL 72


>gi|207109637|ref|ZP_03243799.1| tRNA pseudouridine synthase A [Helicobacter pylori HPKX_438_CA4C1]
          Length = 93

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 5/93 (5%)

Query: 158 FRSIHCQASSPIRTIDHFDVNSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           F+      ++P R I +             +  +++  +FL + +R  + +       K 
Sbjct: 2   FKKEGGATTNPKRAIFNAFAYKTFIIGHECVVFKIIGDAFLRSSVRLIIQACVQYSLEKI 61

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           T  ++E  +         P+    GLY   V Y
Sbjct: 62  TLAEIEMQIHNIKATIRTPIM-ANGLYLHRVYY 93


>gi|222630952|gb|EEE63084.1| hypothetical protein OsJ_17892 [Oryza sativa Japonica Group]
          Length = 126

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA---PPEGLYFDSVEYS 247
           V  L  VG        + K + A+DRKE   +A   PP GLY  SV Y 
Sbjct: 49  VALLLQVGREALPPDIVAKIIAARDRKELAKVALSAPPHGLYLMSVNYD 97


>gi|312066615|ref|XP_003136354.1| hypothetical protein LOAG_00766 [Loa loa]
 gi|307768481|gb|EFO27715.1| hypothetical protein LOAG_00766 [Loa loa]
          Length = 141

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 13/96 (13%)

Query: 165 ASSPIRTIDHFDVN----SFGNL-----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTS 215
            +  +R + H  ++     FGN+     I+I V++RSFL +QIR  V S+     G+   
Sbjct: 18  RTPTMRHLLHVGISGGGSRFGNVNGFSVIDINVISRSFLRSQIRHMVRSIVEHAYGRLQR 77

Query: 216 TDLEKALQAQD----RKECGPLAPPEGLYFDSVEYS 247
             L   L   +           APP+GL+ + V Y 
Sbjct: 78  ERLVWLLNNPNPENFHHFGMVAAPPQGLFLEDVVYD 113


>gi|51235381|gb|AAT98576.1| tRNA pseudouridine synthase [Pneumocystis carinii]
          Length = 227

 Score = 57.1 bits (137), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/143 (20%), Positives = 49/143 (34%), Gaps = 28/143 (19%)

Query: 25  SSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVIL 75
            +I+G + +A     G         +   ++ A RTD GVHA   V    L        L
Sbjct: 5   RTIEGDLFRAFVDTGGIAEMNADDPKKSSLNRAARTDRGVHAACNVLSLKL--IIEQPNL 62

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK 135
            + +N  L   +TI +  +S   K F+ R     R Y Y + +            ++ P 
Sbjct: 63  LERINEAL--PETIRVWGISRTLKSFNPRTFCEARIYEYLVPS----------YVFIPPY 110

Query: 136 SLDCENMRIAAQHLVGRHDFTTF 158
                 M   AQ +    +    
Sbjct: 111 P-----MTQLAQRITKHREMINC 128


>gi|221052120|ref|XP_002257636.1| pseudouridylate synthase 1 [Plasmodium knowlesi strain H]
 gi|193807466|emb|CAQ37972.1| pseudouridylate synthase 1, putative [Plasmodium knowlesi strain H]
          Length = 524

 Score = 56.8 bits (136), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 11/76 (14%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVTGEIVVV----------HGAGRT 51
           +Y + I Y GS Y G Q Q K+  +I+  IE+ +  + G                 + RT
Sbjct: 51  KYALCIGYVGSRYHGCQGQGKDCMTIENEIERTLIKMNGVGRRGGCKKDFNFCQSRSART 110

Query: 52  DSGVHALRQVAHFDLV 67
           D GVHAL  V  + + 
Sbjct: 111 DLGVHALYNVFVYQVD 126



 Score = 55.2 bits (132), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 40/102 (39%), Gaps = 6/102 (5%)

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS----FGNLIEIRVVARSFLHTQIR 199
              Q+  G H+F  F        +  R I + DV++      N + ++++ +SFL  QIR
Sbjct: 376 EIVQNYAGYHNFHCFTKNKVD-QTTFRFIKYLDVSTVNLFNYNFVSVKILGQSFLMHQIR 434

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +           +   +   L++ +      L P EGL  
Sbjct: 435 KMLTLSVETFRKATSVNSIYYCLKSGEYVPIS-LFPAEGLML 475



 Score = 38.3 bits (88), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 22/70 (31%), Gaps = 2/70 (2%)

Query: 48  AGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           A  T+   H     +     R+         LN +L   + I    +  V K F AR   
Sbjct: 170 ATSTEVRTHNATTQSTALAERKEKEKKFVHLLNEHL--PEDIRCFGMHRVTKSFDARKFC 227

Query: 108 IRRSYLYRII 117
             R Y Y   
Sbjct: 228 SFRLYEYLFP 237


>gi|68487205|ref|XP_712546.1| hypothetical protein CaO19.10981 [Candida albicans SC5314]
 gi|68487266|ref|XP_712516.1| hypothetical protein CaO19.3477 [Candida albicans SC5314]
 gi|74679680|sp|Q59S63|PUS1_CANAL RecName: Full=tRNA pseudouridine synthase 1; AltName: Full=tRNA
           pseudouridylate synthase 1; AltName: Full=tRNA-uridine
           isomerase 1
 gi|46433909|gb|EAK93335.1| hypothetical protein CaO19.3477 [Candida albicans SC5314]
 gi|46433941|gb|EAK93366.1| hypothetical protein CaO19.10981 [Candida albicans SC5314]
          Length = 450

 Score = 56.8 bits (136), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/74 (27%), Positives = 25/74 (33%), Gaps = 4/74 (5%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
              A RTD GVHA   V    +        +   +N  L     I I  +    K F  R
Sbjct: 41  FQRAARTDKGVHAAGNVISLKM--IIEDPEIINKINDLL--PKQIRIWGIQRATKGFDCR 96

Query: 105 FSAIRRSYLYRIIT 118
                R Y Y + T
Sbjct: 97  KCCSSRIYEYLLPT 110



 Score = 52.9 bits (126), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 38/107 (35%), Gaps = 8/107 (7%)

Query: 143 RIAAQHLVGRHDFTTFRSIHC-QASSPIR-----TIDHFDVNSFGNLIEIRVVARSFLHT 196
           R   +   G H+F  F      + +S  R      +    V      I I++  +SF+  
Sbjct: 227 REVMKQYEGTHNFHNFTVGKPFKDTSANRFMIKTIVSDPFVIEGTEWISIKIHGQSFMLH 286

Query: 197 QIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           QIR  +    LV         +    Q+   K   P AP  GL  ++
Sbjct: 287 QIRKMIAMAALVVRLSLPCGIINNFFQST--KINIPKAPALGLLLEN 331


>gi|119618937|gb|EAW98531.1| pseudouridylate synthase 1, isoform CRA_b [Homo sapiens]
          Length = 162

 Score = 56.4 bits (135), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V        IRV  +SF+  QIR  VG +  +  G    + LE++      K   P AP 
Sbjct: 8   VREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLERSW--GTEKVDVPKAPG 65

Query: 237 EGLYFDSVEYS 247
            GL  + V + 
Sbjct: 66  LGLVLERVHFE 76


>gi|328873726|gb|EGG22093.1| hypothetical protein DFA_01983 [Dictyostelium fasciculatum]
          Length = 604

 Score = 56.4 bits (135), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/179 (20%), Positives = 73/179 (40%), Gaps = 30/179 (16%)

Query: 4   YCMIIEYNGSGYFG--WQRQKNGSSIQGSIEKAIFL-------VTGEIVVV--HGAGRTD 52
             M+  Y G+G+FG  +  ++   +++  +EKA+FL         G++  +    + RTD
Sbjct: 156 VAMLFSYVGTGHFGLEYTYEEKYPALENYLEKALFLSGMILPTNFGDVTRIKWSRSSRTD 215

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYL-----KISDTISILNLSIVDKQFHARFSA 107
            GVH+L  +    ++     +   + + AY+      +  T+ I++++   + F  R   
Sbjct: 216 KGVHSLSTIIGASILINREKIQTKEGVRAYIDQINSYLPPTLHIVSMATTSRSFMPRRQT 275

Query: 108 IRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR---HDFTTFRSIHC 163
             R+Y Y +     P      +  L       E         +G    H+FTT R  + 
Sbjct: 276 SSRTYHYVL-----PKKFLGNQFTL------QEINEKILSLFIGTNSYHNFTTLRKTYS 323



 Score = 51.0 bits (121), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/100 (24%), Positives = 35/100 (35%), Gaps = 14/100 (14%)

Query: 154 DFTTFRSIHCQASSPIRTIDHFDV----------NSFGNLIEIRVVARSFLHTQIRSFVG 203
           D   F   + +     R I  F +                ++  +   SF+  QIR  VG
Sbjct: 404 DEMNFYKTNVKN---CRKIHSFTIGETFLVESNDQQQEEWVKFMIEGESFIQYQIRKMVG 460

Query: 204 SLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
            +  V  G      LE AL+        P+APP+ LY   
Sbjct: 461 FVLAVCHGLVDVKILEIALKGP-FSINSPIAPPDTLYLYD 499


>gi|297601003|ref|NP_001050239.2| Os03g0381100 [Oryza sativa Japonica Group]
 gi|255674546|dbj|BAF12153.2| Os03g0381100 [Oryza sativa Japonica Group]
          Length = 305

 Score = 56.4 bits (135), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 4   YCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV-----TGEIVVVHGAGRTDSGVHA 57
             + I Y G  ++G+  + +   +++  I KA+        + +       GRTD GV A
Sbjct: 94  IALKIMYFGQRFYGFASEAHTEPTVESEIFKALERAKLLVGSRKESCYSRCGRTDKGVSA 153

Query: 58  LRQVAH 63
             Q   
Sbjct: 154 TGQEMQ 159



 Score = 35.6 bits (81), Expect = 5.7,   Method: Composition-based stats.
 Identities = 7/21 (33%), Positives = 11/21 (52%)

Query: 142 MRIAAQHLVGRHDFTTFRSIH 162
           M+ AA   +G HD+  F  + 
Sbjct: 158 MQKAALKFIGEHDYRNFCKMD 178


>gi|94502462|ref|ZP_01308886.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri str. Hc
           (Homalodisca coagulata)]
 gi|94450981|gb|EAT13982.1| tRNA pseudouridine synthase A [Candidatus Sulcia muelleri str. Hc
           (Homalodisca coagulata)]
          Length = 66

 Score = 56.0 bits (134), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 27/66 (40%)

Query: 157 TFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST 216
           +F    C   + I  I +   +   N++  ++ A        R+ VG+L  +G GK T  
Sbjct: 1   SFCKKKCNYKTYICKIFNAKWHIKNNILNFKIEANRNKRKMERTMVGTLIELGIGKITIK 60

Query: 217 DLEKAL 222
           +    L
Sbjct: 61  EFINIL 66


>gi|307105485|gb|EFN53734.1| hypothetical protein CHLNCDRAFT_136316 [Chlorella variabilis]
          Length = 353

 Score = 56.0 bits (134), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 15/86 (17%)

Query: 42  IVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQF 101
            V +  AGRTD GVHAL Q                +ALNA  +    +   + + V + F
Sbjct: 41  TVALAVAGRTDRGVHALGQEV-------------VRALNA--ERPGLLRAWHAAQVPRSF 85

Query: 102 HARFSAIRRSYLYRIITRQAPLALEK 127
           HA F+A  R YLY +  R+      +
Sbjct: 86  HATFAAKWRRYLYLLPLREPENGGMR 111


>gi|260889971|ref|ZP_05901234.1| tRNA pseudouridine synthase A [Leptotrichia hofstadii F0254]
 gi|260860577|gb|EEX75077.1| tRNA pseudouridine synthase A [Leptotrichia hofstadii F0254]
          Length = 168

 Score = 55.6 bits (133), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 54/165 (32%), Gaps = 27/165 (16%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALRQVA 62
           Y   +EY+G  +  +    N  S++    K +     +I   +  AGRTD+ V A   + 
Sbjct: 26  YMFFVEYDGQKFESFDENPNKKSVKSEFRKILENNKIKIFKGIQQAGRTDANVSAKGNIL 85

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           + +         L          ++ + I  ++     F      I + Y          
Sbjct: 86  YINSKEIIDFSKLKF------LETEGMKINKIARTLP-FLEFPQMIEKRY---------- 128

Query: 123 LALEKGRAWLIPKSL---DCENMRIAAQHLVGRHDFTTFRSIHCQ 164
                   +  PK L   D + +      + G+ DF  F S   +
Sbjct: 129 ------YIYEYPKKLRKNDEDRINKICNKVSGKKDFYEFTSEKGK 167


>gi|34782865|gb|AAH13427.2| PUS3 protein [Homo sapiens]
          Length = 253

 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 21/48 (43%)

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
                  L +  V  ++FL+ Q+R  +  L L+G G      +++ L 
Sbjct: 29  RWQEPFQLCQFEVTGQAFLYHQVRCMMAILFLIGQGMEKPEIIDELLN 76


>gi|115684700|ref|XP_001197822.1| PREDICTED: hypothetical protein, partial [Strongylocentrotus
           purpuratus]
          Length = 110

 Score = 55.6 bits (133), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 38/118 (32%), Gaps = 25/118 (21%)

Query: 138 DCENMRIAAQHLVGRHDFTTFRS--IHCQASSPIRTIDHFDVNSFGN------LIEIRVV 189
           + + M  A+Q LVG  DF  F    +       +RTI   ++    +      + E  + 
Sbjct: 2   NEKLMNEASQKLVGTFDFRNFCKMDVGNGVVKFVRTIRSAEIRKLDDSSGGFQMCEFTIG 61

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +FL+ Q    +  L  V              + +  K    +A    L      Y 
Sbjct: 62  GLAFLYHQ---IIDQLLDV--------------ENEPCKPQYAMAADFPLVLYDCAYE 102


>gi|156082175|ref|XP_001608576.1| pseudouridylate synthase 1 [Plasmodium vivax SaI-1]
 gi|148801515|gb|EDL42914.1| pseudouridylate synthase 1, putative [Plasmodium vivax]
          Length = 587

 Score = 55.6 bits (133), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 3   RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVT-----GEIVVV----HGAGRTD 52
           +Y + + Y GS Y G Q Q K+  +I+  IE+ +  +      G           + RTD
Sbjct: 46  KYALCVGYVGSRYHGCQGQGKDCMTIENEIERTLIKMNAVGGGGRRKNFNFCQSRSARTD 105

Query: 53  SGVHALRQVAHFDLV 67
            GVHAL  V  + + 
Sbjct: 106 LGVHALYNVFVYQVD 120



 Score = 55.2 bits (132), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 6/102 (5%)

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS----FGNLIEIRVVARSFLHTQIR 199
              Q   G H+F  F     +  +  R I + +V++      N + ++++ +SFL  QIR
Sbjct: 439 EIVQSYAGYHNFHCFTKSKAE-QTTFRFIKYLEVSTVNLHDHNFVSVQILGQSFLMHQIR 497

Query: 200 SFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +               +   L A +      L P EGL  
Sbjct: 498 KMLTLSVETFRKATCVNSIYYCLNAGEYVPIS-LFPAEGLML 538



 Score = 37.5 bits (86), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
            R        + LN +L   + I   ++  V K F AR     R Y Y   
Sbjct: 179 ERTKKEKKFRQLLNEHL--PEDIRCFDMHRVTKSFDARKFCSFRLYEYLFP 227


>gi|56758144|gb|AAW27212.1| unknown [Schistosoma japonicum]
          Length = 223

 Score = 55.2 bits (132), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 7/87 (8%)

Query: 166 SSPIRTIDHFDVNS-----FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
            S  R I   +              IR++ +SF+  Q+R  +G +  +  G  T  D+  
Sbjct: 21  KSCYRHIKSVECIPTFLLGEHEYTVIRIIGQSFMLHQVRKMIGLVLGILRGYAT-EDVFD 79

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVEYS 247
            +  ++R +  P AP  GL  + V++S
Sbjct: 80  IVFCKERVDI-PKAPGLGLMLNQVDFS 105


>gi|221504231|gb|EEE29906.1| conserved hypothetical protein [Toxoplasma gondii VEG]
          Length = 1512

 Score = 55.2 bits (132), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 21/43 (48%)

Query: 181  GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
               + I  V   FL+  +R  VG+L  V  G+ +  D+  AL+
Sbjct: 1359 PQGLRIDFVGNRFLYKMVRKMVGALVQVALGRLSVDDIRCALE 1401



 Score = 40.2 bits (93), Expect = 0.28,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 5/53 (9%)

Query: 42  IVVVHGAGRTDSGVHALR---QVAHFDLVREWVPVILCKALNAYLKISDTISI 91
            +V+  A RTD GVHA     Q   +              +N  L     + I
Sbjct: 868 PIVLRPASRTDRGVHAAGAICQYVSYYHPLHIPLESFAAGVNRRL--PPDVRI 918



 Score = 39.0 bits (90), Expect = 0.59,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 8/52 (15%)

Query: 136  SLDCENMRIAAQHLVGRHDFTTFR--------SIHCQASSPIRTIDHFDVNS 179
            S D + M+ AA+ L G H F  FR        + H    +P  T++   ++ 
Sbjct: 1217 SFDLDEMKQAAKALEGHHSFAAFRCEYSGKEKARHLHRDNPFCTVESVSISP 1268


>gi|237843965|ref|XP_002371280.1| hypothetical protein, conserved [Toxoplasma gondii ME49]
 gi|211968944|gb|EEB04140.1| hypothetical protein, conserved [Toxoplasma gondii ME49]
 gi|221483763|gb|EEE22075.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 1509

 Score = 55.2 bits (132), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 21/43 (48%)

Query: 181  GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ 223
               + I  V   FL+  +R  VG+L  V  G+ +  D+  AL+
Sbjct: 1356 PQGLRIDFVGNRFLYKMVRKMVGALVQVALGRLSVDDIRCALE 1398



 Score = 40.2 bits (93), Expect = 0.28,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 5/53 (9%)

Query: 42  IVVVHGAGRTDSGVHALR---QVAHFDLVREWVPVILCKALNAYLKISDTISI 91
            +V+  A RTD GVHA     Q   +              +N  L     + I
Sbjct: 865 PIVLRPASRTDRGVHAAGAICQYVSYYHPLHIPLESFAAGVNRRL--PPDVRI 915



 Score = 39.0 bits (90), Expect = 0.59,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 8/52 (15%)

Query: 136  SLDCENMRIAAQHLVGRHDFTTFR--------SIHCQASSPIRTIDHFDVNS 179
            S D + M+ AA+ L G H F  FR        + H    +P  T++   ++ 
Sbjct: 1214 SFDLDEMKQAAKALEGHHSFAAFRCEYSGKEKARHLHRDNPFCTVESVSISP 1265


>gi|115937214|ref|XP_001192125.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 130

 Score = 55.2 bits (132), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 38/118 (32%), Gaps = 25/118 (21%)

Query: 138 DCENMRIAAQHLVGRHDFTTFRS--IHCQASSPIRTIDHFDVNSFGN------LIEIRVV 189
           + + M  A+Q LVG  DF  F    +       +RTI   ++    +      + E  + 
Sbjct: 2   NEKLMNEASQKLVGTFDFRNFCKMDVGNGVVKFVRTIRSAEIRKLDDSSGGFQMCEFTIG 61

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             +FL+ Q    +  L  V              + +  K    +A    L      Y 
Sbjct: 62  GLAFLYHQ---IIDQLLDV--------------ENEPCKPQYAMAADFPLVLYDCAYE 102


>gi|68059255|ref|XP_671610.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56487947|emb|CAH99999.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 332

 Score = 54.4 bits (130), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 3  RYCMIIEYNGSGYFGWQRQ-KNGSSIQGSIEKAIFLVT-------GEIVVVHGAGRTDSG 54
          +Y + + Y GS Y G Q Q K   +I+  IE+ +  +        G    +  + RTD G
Sbjct: 29 KYGLCVGYIGSRYHGCQGQGKEYMTIENEIERILTKINAVKKNSKGFNYCLSRSARTDLG 88

Query: 55 VHALRQVAHF 64
          VHAL  +  +
Sbjct: 89 VHALYNLFVY 98


>gi|312090526|ref|XP_003146648.1| tRNA pseudouridine synthase A [Loa loa]
 gi|307758189|gb|EFO17423.1| tRNA pseudouridine synthase A [Loa loa]
          Length = 238

 Score = 54.4 bits (130), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + V  +SF+  QIR  +G       G    T+LE   +++  +   P AP  GL  
Sbjct: 25  EFISLYVTGQSFMLHQIRKMIGMTVATFRGLCGKTELENTFRSE--RMDVPKAPGLGLVL 82

Query: 242 DSVEYS 247
           D V Y 
Sbjct: 83  DKVHYE 88


>gi|320531321|ref|ZP_08032295.1| hypothetical protein HMPREF9057_00159 [Actinomyces sp. oral taxon
           171 str. F0337]
 gi|320136470|gb|EFW28444.1| hypothetical protein HMPREF9057_00159 [Actinomyces sp. oral taxon
           171 str. F0337]
          Length = 54

 Score = 53.3 bits (127), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 17/34 (50%)

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
             T   + L A+ R+   P+APP GL  + V Y 
Sbjct: 1   PVTWPGELLAARTRQSAAPVAPPHGLTLEEVTYP 34


>gi|323306932|gb|EGA60216.1| Pus1p [Saccharomyces cerevisiae FostersO]
          Length = 361

 Score = 52.9 bits (126), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 52/157 (33%), Gaps = 17/157 (10%)

Query: 94  LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
           +     +F       ++   Y    +Q   A  +       K       R +    +G H
Sbjct: 73  VPPARDEFDINEEXYQKVKKY----KQLENAHRRRYRICAAK---LAKFRASTSQYLGAH 125

Query: 154 DFTTFR-SIHCQASSPIRTIDHFDVN-------SFGNLIEIRVVARSFLHTQIRSFVGSL 205
           +F  F      +  S IR +    V+       +    I I++  +SF+  QIR  V   
Sbjct: 126 NFHNFTLGKDFKEPSAIRFMKDIKVSDPFVIGDAQTEWISIKIHGQSFMLHQIRKMVSMA 185

Query: 206 KLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            L+         + +A   Q  K   P AP  GL  +
Sbjct: 186 TLITRCGCPVERISQAYGQQ--KINIPKAPALGLLLE 220


>gi|296775668|gb|ADH42945.1| hypothetical protein [uncultured SAR11 cluster alpha
           proteobacterium H17925_23J24]
          Length = 52

 Score = 51.8 bits (123), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 19/39 (48%), Positives = 25/39 (64%)

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            VGSLK +G+GKW  +D +KA  ++ R  C P AP  GL
Sbjct: 1   MVGSLKYLGEGKWKLSDFKKAFSSKKRTMCAPPAPAYGL 39


>gi|71746940|ref|XP_822525.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|70832193|gb|EAN77697.1| hypothetical protein, conserved [Trypanosoma brucei]
          Length = 401

 Score = 51.4 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 25/61 (40%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            ++ I +  +SFL  QIR  +G++  +         L      +  +   P+ P  GL+ 
Sbjct: 263 EVVRIELSGQSFLFNQIRKMIGTVASMCAAGLPPDYLRDHFLNKAVRCGTPMVPANGLFL 322

Query: 242 D 242
            
Sbjct: 323 T 323


>gi|326430199|gb|EGD75769.1| hypothetical protein PTSG_07888 [Salpingoeca sp. ATCC 50818]
          Length = 173

 Score = 51.4 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I+V  +SF+  QIR  +G    V  G     D+      +      P  P  GLY 
Sbjct: 2   EWIRIQVKGQSFMLHQIRKMIGMAVAVARGFAVMEDVYSTFNHESVD--VPRIPGLGLYL 59

Query: 242 DSVEYS 247
           DSV + 
Sbjct: 60  DSVFFD 65


>gi|269866935|ref|XP_002652438.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
 gi|220062500|gb|EED41617.1| tRNA pseudouridine synthase A [Enterocytozoon bieneusi H348]
          Length = 107

 Score = 50.2 bits (119), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF 36
           +  + I Y+G  Y G Q+  NG SI   +E A+ 
Sbjct: 65 RKIALKIAYDGRVYHGVQKDPNGLSIGEVLENALR 99


>gi|147812480|emb|CAN72774.1| hypothetical protein VITISV_026284 [Vitis vinifera]
          Length = 812

 Score = 50.2 bits (119), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 5/45 (11%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSI-----EKAIFLVTGE 41
            RY + +EY G+ + G Q+Q N  ++ G++     E  + LV+ +
Sbjct: 674 QRYLVAVEYIGTRFSGSQQQLNCRTVVGALSGVFSELVLCLVSRK 718


>gi|302837035|ref|XP_002950077.1| hypothetical protein VOLCADRAFT_90550 [Volvox carteri f.
           nagariensis]
 gi|300264550|gb|EFJ48745.1| hypothetical protein VOLCADRAFT_90550 [Volvox carteri f.
           nagariensis]
          Length = 738

 Score = 50.2 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 30/84 (35%), Gaps = 8/84 (9%)

Query: 167 SPIRTIDHFDVNSFGNLIE-------IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLE 219
           +  R I HF       L+E       + V  +SF+   IR  +G    V  G      L 
Sbjct: 535 TYYRRIHHFTAADPRPLVEGGTPCLLLEVRGQSFMLHHIRHMIGGAVAVALGLMPKDVLL 594

Query: 220 KALQAQDRKECGPLAPPEGLYFDS 243
            +L+   R    P APP  L    
Sbjct: 595 GSLEPPAR-VAIPRAPPHTLLLAD 617


>gi|255550749|ref|XP_002516423.1| hypothetical protein RCOM_1427170 [Ricinus communis]
 gi|223544458|gb|EEF45978.1| hypothetical protein RCOM_1427170 [Ricinus communis]
          Length = 82

 Score = 50.2 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/35 (37%), Positives = 19/35 (54%)

Query: 2  IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF 36
           +  +   Y G GY G Q+     SI+G +EKA+F
Sbjct: 31 RKIAIFFAYCGVGYQGMQKNPGTKSIEGDLEKALF 65


>gi|303288467|ref|XP_003063522.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226455354|gb|EEH52658.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 419

 Score = 49.4 bits (117), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 1/70 (1%)

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
                 + + V   SF+  QIR  + +   V  G      +   L    R    P+AP  
Sbjct: 213 RPGEPFVRVVVAGDSFVLYQIRKMIATAVGVALGWIPREFIPVTLARPAR-AATPIAPAS 271

Query: 238 GLYFDSVEYS 247
            LY    E+S
Sbjct: 272 TLYLREAEFS 281



 Score = 41.7 bits (97), Expect = 0.084,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 38/101 (37%), Gaps = 9/101 (8%)

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL--EK 127
             P  + + +NA L  +  + +       K F AR +  RR+Y Y +  R   L +  E+
Sbjct: 15  REPGGVVERINAKLPATSGVRVFAAYSAPKSFQARRACARRTYHYLLPARVLGLGVSGER 74

Query: 128 GRAWL------IPKSLDC-ENMRIAAQHLVGRHDFTTFRSI 161
             +W          S D  +  R A +   G H F  +   
Sbjct: 75  EVSWPGAPGGETRSSEDVLDAFRDALRAFEGSHYFHNYTRR 115


>gi|207093446|ref|ZP_03241233.1| tRNA pseudouridine synthase A [Helicobacter pylori HPKX_438_AG0C1]
          Length = 60

 Score = 49.4 bits (117), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            +++  +FL + +R  + +       K T  ++E  +         P+    GLY   V 
Sbjct: 1   FKIIGDAFLRSSVRLIIQACVQYSLEKITLAEIEMQIHNIKATIRTPIM-ANGLYLHRVY 59

Query: 246 Y 246
           Y
Sbjct: 60  Y 60


>gi|108708044|gb|ABF95839.1| tRNA pseudouridine synthase family protein, expressed [Oryza sativa
           Japonica Group]
          Length = 374

 Score = 49.1 bits (116), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 41/115 (35%), Gaps = 18/115 (15%)

Query: 129 RAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRV 188
           RA  + +  + + +   A H     D  TF     Q SS I              +E+ +
Sbjct: 180 RARWLHEPDENDRLN--ASHF---RDILTFSCGELQISSGI------------QFVELTI 222

Query: 189 VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
              SF+  QIR  VG+   V  G      +  +L    R    P+AP E L    
Sbjct: 223 SGVSFMLHQIRKMVGTSVAVKRGLLPKDIIALSLAKFSR-IVLPIAPSEVLVLRD 276


>gi|262038332|ref|ZP_06011713.1| hypothetical protein HMPREF0554_1185 [Leptotrichia goodfellowii
           F0264]
 gi|261747636|gb|EEY35094.1| hypothetical protein HMPREF0554_1185 [Leptotrichia goodfellowii
           F0264]
          Length = 288

 Score = 49.1 bits (116), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 64/205 (31%), Gaps = 56/205 (27%)

Query: 45  VHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHAR 104
           +  AGRTD  V A   + + +  +           N + +I D + I  +          
Sbjct: 51  IQQAGRTDKDVSAKENILYINSKKYIE--------NFHKEI-DGLKIRKIVRTVPFLEFP 101

Query: 105 FSAIRRSYLYRIITRQAPLALEKGRAWLIPKSL---DCENMRIAAQHLVGRHDFTTFRSI 161
               +R Y+Y                   P++L   D E ++   + L G+ +F  + S 
Sbjct: 102 QMVSKRFYIY-----------------EYPQNLIENDEEKIKSNCEKLSGKKNFKKYTSK 144

Query: 162 HCQA-SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEK 220
             +   + IR +       F N  ++      FL  Q+R                     
Sbjct: 145 KGEKLKNHIREVF----VRFENG-KLYFEGDGFLPQQVRIMSNF---------------- 183

Query: 221 ALQAQDRKECGPLAPPEGLYFDSVE 245
            L  + +       P E L  + VE
Sbjct: 184 ILNNKMKSL-----PGEYLTLEKVE 203


>gi|325118855|emb|CBZ54407.1| Pseudouridylate synthase, related [Neospora caninum Liverpool]
          Length = 822

 Score = 48.7 bits (115), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 10/77 (12%)

Query: 139 CENMRIAAQHLVGRHDFTTFRSIHCQASSP----IRTIDHFDVNS------FGNLIEIRV 188
            E +R   +   G H F  F        +      R I    V++        ++I I +
Sbjct: 746 VEKLRAVFKVFEGTHAFQNFTKGGKNKDTSPAAFKRHIHKTSVSTTQMDGVSEDIIVIEL 805

Query: 189 VARSFLHTQIRSFVGSL 205
             +SFL  QIR  V  L
Sbjct: 806 EGQSFLFNQIRKMVAGL 822



 Score = 39.0 bits (90), Expect = 0.63,   Method: Composition-based stats.
 Identities = 14/46 (30%), Positives = 17/46 (36%), Gaps = 2/46 (4%)

Query: 72  PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
                  LNA L     I    +  V K F AR S  RR Y + + 
Sbjct: 448 EAAFLARLNAVL--PPDIRCFAVRRVTKNFDARISCSRRRYAFLLP 491



 Score = 38.7 bits (89), Expect = 0.87,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 9/51 (17%)

Query: 25  SSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVHALRQVAHFDL 66
            +++G +E+++    G         + +    A RTD GVHA   V    L
Sbjct: 303 RTVEGVLEESLLAAGGIAPSHLGCLQKLQWSRAARTDRGVHAACNVISLKL 353


>gi|297606314|ref|NP_001058288.2| Os06g0663100 [Oryza sativa Japonica Group]
 gi|255677299|dbj|BAF20202.2| Os06g0663100 [Oryza sativa Japonica Group]
          Length = 156

 Score = 48.3 bits (114), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 8/28 (28%), Positives = 19/28 (67%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQG 29
           + + +++ Y+G  + GWQ+Q   +++QG
Sbjct: 129 VTFKIVLSYHGGSFDGWQKQPGLNTVQG 156


>gi|124783935|gb|ABN14957.1| tRNA pseudouridine synthase A [Taenia asiatica]
          Length = 123

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 9/64 (14%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGV 55
            +++ Y+G G+ G QR +   +I+G +  A+               ++    A +TD  V
Sbjct: 60  AILVVYSGVGFCGMQRNEGFRTIEGELMMALCNAGYILEEHMKNPSMICFQRASKTDKNV 119

Query: 56  HALR 59
            A  
Sbjct: 120 SAAG 123


>gi|221121945|ref|XP_002160541.1| PREDICTED: similar to tRNA pseudouridine synthase A [Hydra
           magnipapillata]
          Length = 138

 Score = 47.9 bits (113), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKA-LQAQDRKECGPLAPPEGLYFDSVEYS 247
            QIR  +G +  V  G      +EK+ LQA+      P AP  GL    V Y+
Sbjct: 3   HQIRKMIGLVIAVCRGHCPEDTIEKSWLQAK---ADIPKAPGLGLLLCKVFYN 52


>gi|212721194|ref|NP_001132024.1| hypothetical protein LOC100193430 [Zea mays]
 gi|194693226|gb|ACF80697.1| unknown [Zea mays]
          Length = 369

 Score = 47.1 bits (111), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +E+ +   SF+  QIR  VG+   V  G      +E +L    R    P+AP E L  
Sbjct: 216 QFVELTICGVSFMLHQIRKMVGTAVTVKRGLLPRDIIELSLAKFSR-IVLPIAPSEVLVL 274

Query: 242 DS 243
             
Sbjct: 275 KD 276


>gi|207093510|ref|ZP_03241297.1| tRNA pseudouridine synthase A [Helicobacter pylori HPKX_438_AG0C1]
          Length = 75

 Score = 46.4 bits (109), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 124 ALEKGR-AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF-- 180
                  A     SLD   +  A +   G+HDF+ F+      ++P R I +        
Sbjct: 1   PFLAPYIACGDYGSLD--ALNTALKQFTGKHDFSMFKKEGGATTNPKRAIFNAFAYKTFI 58

Query: 181 --GNLIEIRVVARSFLH 195
                +  +++  +FL 
Sbjct: 59  IGHECVVFKIIGDAFLR 75


>gi|224002789|ref|XP_002291066.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220972842|gb|EED91173.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 798

 Score = 46.4 bits (109), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 1/65 (1%)

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKEC-GPLAP 235
           +      +   +    FLH Q R  +G L  +  G   S  +E     +       P AP
Sbjct: 404 IVKNRPFLVFSLTGDVFLHEQARRVIGLLIAICRGVIDSEIIECMFDEEYANLVPAPPAP 463

Query: 236 PEGLY 240
             GL 
Sbjct: 464 SCGLV 468


>gi|320164168|gb|EFW41067.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
          Length = 210

 Score = 45.6 bits (107), Expect = 0.006,   Method: Composition-based stats.
 Identities = 9/36 (25%), Positives = 18/36 (50%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFL 37
            +  M++ + G+ Y G Q   +  +I+G + KA   
Sbjct: 165 RKVAMLVSFVGTRYRGMQYNGDVPTIEGELLKAFAK 200


>gi|226484742|emb|CAX74280.1| putative tRNA pseudouridine synthase 3 [Schistosoma japonicum]
          Length = 171

 Score = 45.2 bits (106), Expect = 0.008,   Method: Composition-based stats.
 Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 5/62 (8%)

Query: 4   YCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHAL 58
             + + Y G  Y G   Q     ++   +  A+                 GRTD GV  +
Sbjct: 71  IALKLSYLGWQYCGLVPQGCYTLTVMDRLLDALEKAKLIENRNECSFSVCGRTDKGVSGI 130

Query: 59  RQ 60
            Q
Sbjct: 131 CQ 132


>gi|302857489|ref|XP_002959885.1| hypothetical protein VOLCADRAFT_101403 [Volvox carteri f.
           nagariensis]
 gi|300254031|gb|EFJ39049.1| hypothetical protein VOLCADRAFT_101403 [Volvox carteri f.
           nagariensis]
          Length = 266

 Score = 44.8 bits (105), Expect = 0.010,   Method: Composition-based stats.
 Identities = 9/30 (30%), Positives = 16/30 (53%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEK 33
           Y + + Y G  + GW  Q    ++QG++E 
Sbjct: 226 YKVTVSYFGPAFEGWAFQPGRRTLQGALEA 255


>gi|290970931|ref|XP_002668312.1| predicted protein [Naegleria gruberi]
 gi|284081639|gb|EFC35568.1| predicted protein [Naegleria gruberi]
          Length = 241

 Score = 42.9 bits (100), Expect = 0.037,   Method: Composition-based stats.
 Identities = 27/132 (20%), Positives = 49/132 (37%), Gaps = 39/132 (29%)

Query: 4   YCMIIEYNGSGYFGWQRQ--------KNGSSIQGSIEKAIFLVTGE-------------- 41
           + +   YNG  + G Q Q         +  +I+  +   ++   GE              
Sbjct: 103 FVISFSYNGIPFNGLQIQNGENLVKHPHLLTIEAVLLDILYGSNGESDFEQDETIIRYTK 162

Query: 42  -----IVVVHGAGRTDSGVHALRQVAHFDL----------VREWVPVILCKALNAYLKIS 86
                 + +  A RTD GV A+R      +            ++    LCK LN   +I+
Sbjct: 163 SKNCKDIRLQRACRTDRGVSAVRNAFACVMTLPNTQNHKDTFKFNNEELCKTLND--RIN 220

Query: 87  DTISILNLSIVD 98
           + + I NL+++D
Sbjct: 221 NHVRIKNLNLMD 232


>gi|237804283|ref|ZP_04591868.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. oryzae
          str. 1_6]
 gi|237805862|ref|ZP_04592566.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. oryzae
          str. 1_6]
 gi|331026270|gb|EGI06326.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. oryzae
          str. 1_6]
 gi|331026970|gb|EGI07025.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. oryzae
          str. 1_6]
          Length = 38

 Score = 41.7 bits (97), Expect = 0.098,   Method: Composition-based stats.
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)

Query: 20 RQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRT 51
          RQ +G  ++Q ++E A+  V    V +  AGRT
Sbjct: 6  RQASGVLTVQETLENALSKVAASPVSLMCAGRT 38


>gi|59634318|gb|AAW88358.1| pseudouridine synthase 1 [Schistosoma japonicum]
          Length = 170

 Score = 41.4 bits (96), Expect = 0.13,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 196 TQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
            Q+R  +G +  +  G  T  D+   +  ++R +  P AP  GL  + V++S
Sbjct: 3   HQVRKMIGLVLGILRGYAT-EDVFDIVFCKERVDI-PKAPGLGLMLNQVDFS 52


>gi|330507838|ref|YP_004384266.1| hypothetical protein MCON_1858 [Methanosaeta concilii GP-6]
 gi|328928646|gb|AEB68448.1| conserved domain protein [Methanosaeta concilii GP-6]
          Length = 54

 Score = 41.0 bits (95), Expect = 0.15,   Method: Composition-based stats.
 Identities = 9/32 (28%), Positives = 13/32 (40%), Gaps = 1/32 (3%)

Query: 216 TDLEKALQAQDRKECGPLAPPEGLYFDSVEYS 247
           +     L+  +R    P AP  GL   +V Y 
Sbjct: 21  SWFSDLLR-PERNHGAPTAPAVGLILMNVGYE 51


>gi|114705223|ref|ZP_01438131.1| hypothetical protein FP2506_09801 [Fulvimarina pelagi HTCC2506]
 gi|114540008|gb|EAU43128.1| hypothetical protein FP2506_09801 [Fulvimarina pelagi HTCC2506]
          Length = 639

 Score = 39.8 bits (92), Expect = 0.31,   Method: Composition-based stats.
 Identities = 28/124 (22%), Positives = 45/124 (36%), Gaps = 26/124 (20%)

Query: 56  HALR---QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           HA R   +     +          ++L         I ++++  V + F A FS   ++Y
Sbjct: 126 HARRGGRRWDEVMVEARRQAENYARSLPVSHGYPPFILVVDVGNVIEVF-ADFSGQGKNY 184

Query: 113 -------LYRIITRQAPL-ALEKGRA--WLIPKSLD------------CENMRIAAQHLV 150
                   YRI        A+++  A  WL P SLD             E +   A+ L 
Sbjct: 185 AHFPDRRSYRITMDDLRDEAIQQRLAAIWLDPHSLDPAKKSAEVTRDIAERLARIAKRLE 244

Query: 151 GRHD 154
           G+HD
Sbjct: 245 GKHD 248


>gi|70928587|ref|XP_736482.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56511054|emb|CAH83189.1| hypothetical protein PC300366.00.0 [Plasmodium chabaudi chabaudi]
          Length = 80

 Score = 39.4 bits (91), Expect = 0.45,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 11/79 (13%)

Query: 17 GWQRQK-NGSSIQGSIEKAIF---LVTGEIVVVHGAGRTDSGVHALRQVAHF-------D 65
          G   QK N ++++  + + +    L++          RTD GV A               
Sbjct: 1  GSAYQKDNNNTVENKLIERLHQLDLISDSNCSFSRVSRTDKGVSARMNALTIRLKIKYPH 60

Query: 66 LVREWVPVILCKALNAYLK 84
          L    +  I  K LN  LK
Sbjct: 61 LSISIIEKIYLKELNKKLK 79


>gi|238024399|ref|YP_002908631.1| Non-ribosomal peptide synthase [Burkholderia glumae BGR1]
 gi|237879064|gb|ACR31396.1| Non-ribosomal peptide synthase [Burkholderia glumae BGR1]
          Length = 1085

 Score = 39.4 bits (91), Expect = 0.49,   Method: Composition-based stats.
 Identities = 10/66 (15%), Positives = 18/66 (27%), Gaps = 4/66 (6%)

Query: 112 YLYRIITRQAPLALEKGR----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           Y YR                   + +   L  + ++ A +  V  HD             
Sbjct: 9   YQYRFWLEWRLAPHSAAYTTALVYRLIGPLRRDALQQALEAFVHEHDEGCRSVFRDDGGD 68

Query: 168 PIRTID 173
           P+R + 
Sbjct: 69  PVRIVH 74


>gi|78068248|gb|ABB18459.1| malate synthase [Rosa pisocarpa]
          Length = 161

 Score = 38.7 bits (89), Expect = 0.68,   Method: Composition-based stats.
 Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 5/91 (5%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-----RHDFTTF 158
            F    R+ +Y++          + R W +P++    +   A   LVG      H++  F
Sbjct: 30  TFHDKARNRVYKLNDHNIAKLFVRPRGWHLPEAHILIDGEPATGCLVGFGLYFYHNYAAF 89

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           R    + S P   +   + +    +      
Sbjct: 90  RRTRGEGSGPFFYLPKMEHSREAKIWNCVFE 120


>gi|312865804|ref|ZP_07726026.1| AMP-binding enzyme [Streptococcus downei F0415]
 gi|311098679|gb|EFQ56901.1| AMP-binding enzyme [Streptococcus downei F0415]
          Length = 5230

 Score = 38.7 bits (89), Expect = 0.80,   Method: Composition-based stats.
 Identities = 25/115 (21%), Positives = 52/115 (45%), Gaps = 5/115 (4%)

Query: 59   RQVAHFDLVREWVPVILCKALNAYLKISD-TISILNLSIVD-KQFHARFSAIRRSYLYRI 116
            +QV   ++     P  L + L A  ++ +    I  ++ V+ ++++    A +R Y   +
Sbjct: 1857 QQVTVAEIFSNTTPEALTELLLAKGQLPETDDQIQKINPVESREYYLTTPAQQRIYTLYM 1916

Query: 117  ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDF--TTFRSIHCQASSPI 169
            +  +  LA     A +I   L+ + ++ A Q L+ RHD   T+F  +  +    I
Sbjct: 1917 MDNKN-LAYNLPSATMITGKLNIDKVKEACQKLIKRHDILRTSFEVVDNEVVQKI 1970


>gi|170698786|ref|ZP_02889849.1| amino acid adenylation domain protein [Burkholderia ambifaria
           IOP40-10]
 gi|170136264|gb|EDT04529.1| amino acid adenylation domain protein [Burkholderia ambifaria
           IOP40-10]
          Length = 1082

 Score = 38.7 bits (89), Expect = 0.81,   Method: Composition-based stats.
 Identities = 11/66 (16%), Positives = 19/66 (28%), Gaps = 4/66 (6%)

Query: 112 YLYRIITRQAPLALEKGR----AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           Y YR                   + +   LD + +R A    V  HD     +     + 
Sbjct: 9   YQYRFWLEWQLNPHSSAYTTALVYRLSGPLDRDALRRALDAFVHEHDEGCRSTFRIDDAR 68

Query: 168 PIRTID 173
            +R + 
Sbjct: 69  VVRDVH 74


>gi|237736444|ref|ZP_04566925.1| predicted protein [Fusobacterium mortiferum ATCC 9817]
 gi|229421486|gb|EEO36533.1| predicted protein [Fusobacterium mortiferum ATCC 9817]
          Length = 199

 Score = 38.7 bits (89), Expect = 0.85,   Method: Composition-based stats.
 Identities = 20/104 (19%), Positives = 37/104 (35%), Gaps = 18/104 (17%)

Query: 126 EKGRAWLIPKSL---DCENMRIAAQHLVGRHDFTTFR-SIHCQASSPIRTIDHFDVNSFG 181
            +   +  PK       E +    + L GR+D + F      +    IR +D    N   
Sbjct: 33  RREYIYEYPKKRVKNSLEEIEKLCRDLSGRYDVSEFTDKKGLELKEHIREVDISFKNGK- 91

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
               +     SF+  Q+R   G +     G+      ++AL+ +
Sbjct: 92  ----LFFSGNSFMPKQVRIMSGYIL---TGR------KEALEGK 122


>gi|219129852|ref|XP_002185093.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403588|gb|EEC43540.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 870

 Score = 38.3 bits (88), Expect = 0.98,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +    +  +     +F+  QIR  V +      G +T +D+ +     D     P+AP  
Sbjct: 517 SREEAIAVLEFRGDNFVAQQIRRIVATALAATHG-YTPSDVFEVATRPDVFTKTPIAPGG 575

Query: 238 GLYF 241
            LY 
Sbjct: 576 RLYL 579


>gi|219113940|ref|XP_002176153.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402894|gb|EEC42860.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 870

 Score = 38.3 bits (88), Expect = 1.0,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +    +  +     +F+  QIR  V +      G +T +D+ +     D     P+AP  
Sbjct: 517 SREEAIAVLEFRGDNFVAQQIRRIVATALAATHG-YTPSDVFEVATRPDVFTKTPIAPGG 575

Query: 238 GLYF 241
            LY 
Sbjct: 576 RLYL 579


>gi|70922772|ref|XP_734499.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56507297|emb|CAH84634.1| hypothetical protein PC301149.00.0 [Plasmodium chabaudi chabaudi]
          Length = 213

 Score = 37.9 bits (87), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 2/52 (3%)

Query: 67  VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            R+         LN+ L   + I   ++  V K F AR     R Y Y   T
Sbjct: 110 ERKRKEKKFINLLNSNL--PNDIKCFDIYKVTKSFDARKFCSFRLYEYLFPT 159


>gi|85375485|ref|YP_459547.1| DegT/DnrJ/EryC1/StrS family protein [Erythrobacter litoralis
           HTCC2594]
 gi|84788568|gb|ABC64750.1| DegT/DnrJ/EryC1/StrS family protein [Erythrobacter litoralis
           HTCC2594]
          Length = 374

 Score = 37.5 bits (86), Expect = 1.6,   Method: Composition-based stats.
 Identities = 33/146 (22%), Positives = 49/146 (33%), Gaps = 26/146 (17%)

Query: 27  IQG----SIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAY 82
           IQG     +E A+    G   VV  A  TD+   AL  +        +VP         Y
Sbjct: 31  IQGPEVKELEAALAKFCGAKRVVTCANGTDALQLALMALDIGPGDAVFVPSF------TY 84

Query: 83  LKISDTISILNLSIV-----DKQFHARFS----AIRRSYL---YR----IITRQAPLALE 126
              ++ I +L    V        F+  F     AI R+     YR    +        ++
Sbjct: 85  TATAEVILLLGARPVFVDSDPDTFNICFDSAEKAIERTKAEGKYRAAALMTVDLFGQPVD 144

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGR 152
             RA  +  + D   +  AAQ   G 
Sbjct: 145 YDRARSLADTHDLAFISDAAQGFGGT 170


>gi|157134892|ref|XP_001656494.1| echinoid [Aedes aegypti]
 gi|108881354|gb|EAT45579.1| echinoid [Aedes aegypti]
          Length = 1033

 Score = 37.1 bits (85), Expect = 2.1,   Method: Composition-based stats.
 Identities = 25/120 (20%), Positives = 39/120 (32%), Gaps = 10/120 (8%)

Query: 111 SYLYRIIT--RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           SY    +      P+A  K      P+      M+      VG  DF+       +    
Sbjct: 255 SYHCHAVNELGHGPMATIKLEVHQPPQF--IGKMQQHMTKRVGDTDFSASCRAKGKPRPT 312

Query: 169 IRTI-DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDR 227
           +R + D  D+ +  N+  I       L   +   V S+  V  GK      +  L   DR
Sbjct: 313 VRWLKDGRDITTDANMYRISTSNNDDLSGMV--IVQSML-VFQGKARPH--KTQLLPSDR 367


>gi|312377644|gb|EFR24427.1| hypothetical protein AND_10993 [Anopheles darlingi]
          Length = 515

 Score = 37.1 bits (85), Expect = 2.1,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 10/100 (10%)

Query: 26  SIQGSIEKAIFLVTGEI---VVVHGAGRTDSGVHALRQVAHFDLV-----REWVPVILCK 77
           S+Q ++E AI    G     ++   +GR D  V  L +   F L       + +P     
Sbjct: 300 SVQETLEAAIAPHFGVPEGQLIFSSSGREDVDVRCLGEGRPFVLEIPNALTDQLPEQDAV 359

Query: 78  ALNAYLKISDTISILNLSIV--DKQFHARFSAIRRSYLYR 115
           A+   ++ S T+SI +L +V      H R +   +   YR
Sbjct: 360 AMEQAVETSGTVSIRDLQLVKRPDLVHIRGNESEKRKFYR 399


>gi|260893437|ref|YP_003239534.1| protein of unknown function DUF72 [Ammonifex degensii KC4]
 gi|260865578|gb|ACX52684.1| protein of unknown function DUF72 [Ammonifex degensii KC4]
          Length = 256

 Score = 36.7 bits (84), Expect = 3.0,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 32/123 (26%), Gaps = 17/123 (13%)

Query: 18  WQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV--IL 75
           WQ      + +  +E    L+ G  V             A R    F     +      L
Sbjct: 113 WQLPPGARAEEEHLESFCRLLKGHPV-----------ASACRHAFEFRHPSWFREEIYAL 161

Query: 76  CKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPK 135
            +  N  L  +D         V   F             R+     P  +    A +I +
Sbjct: 162 LRRFNFALCWADAPRWPRAEEVTADFVYLRFHGHE----RLYASCYPTEILDRWAQVIRQ 217

Query: 136 SLD 138
            LD
Sbjct: 218 QLD 220


>gi|78068268|gb|ABB18469.1| malate synthase [Rosa woodsii]
          Length = 161

 Score = 36.3 bits (83), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 5/91 (5%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-----RHDFTTF 158
            F    R+ +Y++          + R W +P++    +   A   LV       H++  F
Sbjct: 30  TFHDKARNRIYKLNDHNIAKLFVRPRGWHLPEAHILIDGEPATGCLVDFGLYFYHNYAAF 89

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           R    + S P   +   + +    +      
Sbjct: 90  RRTRSEGSGPFFYLPKMEHSREAKIWNCVFE 120


>gi|7378617|emb|CAB83293.1| putative protein [Arabidopsis thaliana]
          Length = 1022

 Score = 36.3 bits (83), Expect = 3.8,   Method: Composition-based stats.
 Identities = 8/67 (11%), Positives = 19/67 (28%), Gaps = 1/67 (1%)

Query: 72  PVILCKALNAYLKISDTISILNLSIVDKQF-HARFSAIRRSYLYRIITRQAPLALEKGRA 130
           P+    +L        ++        D+   H  +  +  +Y   +   + P  L +   
Sbjct: 533 PLHPKHSLQLVSSQPSSVRTRECYCCDEDLAHIFYCCLACNYAMNVACVKKPSVLYRDYT 592

Query: 131 WLIPKSL 137
                 L
Sbjct: 593 RWHEHKL 599


>gi|15242725|ref|NP_195956.1| DC1 domain-containing protein [Arabidopsis thaliana]
 gi|332003208|gb|AED90591.1| DC1 domain-containing protein [Arabidopsis thaliana]
          Length = 1610

 Score = 36.3 bits (83), Expect = 3.8,   Method: Composition-based stats.
 Identities = 8/67 (11%), Positives = 19/67 (28%), Gaps = 1/67 (1%)

Query: 72   PVILCKALNAYLKISDTISILNLSIVDKQF-HARFSAIRRSYLYRIITRQAPLALEKGRA 130
            P+    +L        ++        D+   H  +  +  +Y   +   + P  L +   
Sbjct: 1247 PLHPKHSLQLVSSQPSSVRTRECYCCDEDLAHIFYCCLACNYAMNVACVKKPSVLYRDYT 1306

Query: 131  WLIPKSL 137
                  L
Sbjct: 1307 RWHEHKL 1313


>gi|237736443|ref|ZP_04566924.1| predicted protein [Fusobacterium mortiferum ATCC 9817]
 gi|229421485|gb|EEO36532.1| predicted protein [Fusobacterium mortiferum ATCC 9817]
          Length = 97

 Score = 35.6 bits (81), Expect = 6.3,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 4  YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQVA 62
          Y   I+Y+G+ +  +       +++G  ++ +  +       +   GRTD+ V A   + 
Sbjct: 14 YMFYIKYDGTKFHSFDEIVGKRTVKGRFKELMNEIGFSWAKGIQQGGRTDAKVSATENIL 73

Query: 63 HF 64
          + 
Sbjct: 74 YV 75


>gi|78068160|gb|ABB18415.1| malate synthase [Rosa blanda]
          Length = 161

 Score = 35.6 bits (81), Expect = 6.9,   Method: Composition-based stats.
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 5/91 (5%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-----RHDFTTF 158
            F    R+ +Y++          + R W +P++    +   A   LV       H++  F
Sbjct: 30  TFDDKARNRIYKLNDHNIAKLFVRPRGWHLPEAHILIDGEPATGCLVDFGLYFYHNYAAF 89

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           R    + S P   +   + +    +      
Sbjct: 90  RRTRGEGSGPFFYLPKMEHSREAKIWNCVFE 120


>gi|163881598|gb|ABY48025.1| malate synthase [Rosa woodsii]
          Length = 161

 Score = 35.2 bits (80), Expect = 7.4,   Method: Composition-based stats.
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 5/91 (5%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-----RHDFTTF 158
            F    R+ +Y++          + R W +P++    +   A   LV       H++  F
Sbjct: 30  TFHDKARNRIYKLNDHNIAKLFVRPRGWHLPEAHILIDGEPATGCLVDFGLYFYHNYAAF 89

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           R    + S P   +   + +    +      
Sbjct: 90  RRTRGEGSGPFFYLPKMEHSREAKIWNCVFE 120


>gi|78068150|gb|ABB18410.1| malate synthase [Rosa blanda]
 gi|78068154|gb|ABB18412.1| malate synthase [Rosa blanda]
 gi|78068156|gb|ABB18413.1| malate synthase [Rosa blanda]
 gi|78068158|gb|ABB18414.1| malate synthase [Rosa blanda]
 gi|78068164|gb|ABB18417.1| malate synthase [Rosa blanda]
 gi|78068166|gb|ABB18418.1| malate synthase [Rosa blanda]
 gi|78068168|gb|ABB18419.1| malate synthase [Rosa blanda]
 gi|78068174|gb|ABB18422.1| malate synthase [Rosa blanda]
 gi|78068176|gb|ABB18423.1| malate synthase [Rosa blanda]
 gi|78068178|gb|ABB18424.1| malate synthase [Rosa blanda]
 gi|78068180|gb|ABB18425.1| malate synthase [Rosa blanda]
 gi|78068182|gb|ABB18426.1| malate synthase [Rosa blanda]
 gi|78068186|gb|ABB18428.1| malate synthase [Rosa blanda]
 gi|78068190|gb|ABB18430.1| malate synthase [Rosa blanda]
 gi|78068192|gb|ABB18431.1| malate synthase [Rosa blanda]
 gi|78068194|gb|ABB18432.1| malate synthase [Rosa blanda]
 gi|78068196|gb|ABB18433.1| malate synthase [Rosa blanda]
 gi|78068222|gb|ABB18446.1| malate synthase [Rosa nitida]
 gi|78068256|gb|ABB18463.1| malate synthase [Rosa woodsii]
 gi|78068264|gb|ABB18467.1| malate synthase [Rosa woodsii]
 gi|78068270|gb|ABB18470.1| malate synthase [Rosa woodsii]
 gi|78068272|gb|ABB18471.1| malate synthase [Rosa woodsii]
 gi|78068276|gb|ABB18473.1| malate synthase [Rosa woodsii]
 gi|78068278|gb|ABB18474.1| malate synthase [Rosa woodsii]
 gi|78068280|gb|ABB18475.1| malate synthase [Rosa woodsii]
 gi|163881590|gb|ABY48021.1| malate synthase [Rosa pisocarpa]
 gi|163881592|gb|ABY48022.1| malate synthase [Rosa pisocarpa]
 gi|163881600|gb|ABY48026.1| malate synthase [Rosa woodsii]
 gi|163881602|gb|ABY48027.1| malate synthase [Rosa woodsii]
          Length = 161

 Score = 35.2 bits (80), Expect = 7.5,   Method: Composition-based stats.
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 5/91 (5%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-----RHDFTTF 158
            F    R+ +Y++          + R W +P++    +   A   LV       H++  F
Sbjct: 30  TFHDKARNRIYKLNDHNIAKLFVRPRGWHLPEAHILIDGEPATGCLVDFGLYFYHNYAAF 89

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           R    + S P   +   + +    +      
Sbjct: 90  RRTRGEGSGPFFYLPKMEHSREAKIWNCVFE 120


>gi|72162583|ref|YP_290240.1| hypothetical protein Tfu_2184 [Thermobifida fusca YX]
 gi|71916315|gb|AAZ56217.1| conserved hypothetical protein [Thermobifida fusca YX]
          Length = 288

 Score = 35.2 bits (80), Expect = 7.6,   Method: Composition-based stats.
 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 11/77 (14%)

Query: 30  SIEKAIFLV---------TGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN 80
            +E+A+                  +  AG   +GV +  +     L     P  + + LN
Sbjct: 47  VLERALRRAEVPVAFSAGFSPHPKISYAGAAPTGVASEAEYCELTLAEPMDPERVRERLN 106

Query: 81  AYLKISDTISILNLSIV 97
           A +   D I+IL++   
Sbjct: 107 ATM--PDGIAILDVVPA 121


>gi|78068170|gb|ABB18420.1| malate synthase [Rosa blanda]
 gi|78068172|gb|ABB18421.1| malate synthase [Rosa blanda]
 gi|78068260|gb|ABB18465.1| malate synthase [Rosa woodsii]
 gi|78068262|gb|ABB18466.1| malate synthase [Rosa woodsii]
          Length = 158

 Score = 35.2 bits (80), Expect = 8.3,   Method: Composition-based stats.
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 5/91 (5%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-----RHDFTTF 158
            F    R+ +Y++          + R W +P++    +   A   LV       H++  F
Sbjct: 30  TFHDKARNRIYKLNDHNIAKLFVRPRGWHLPEAHILIDGEPATGCLVDFGLYFYHNYAAF 89

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           R    + S P   +   + +    +      
Sbjct: 90  RRTRGEGSGPFFYLPKMEHSREAKIWNCVFE 120


>gi|163881580|gb|ABY48016.1| malate synthase [Rosa foliolosa]
          Length = 161

 Score = 35.2 bits (80), Expect = 9.1,   Method: Composition-based stats.
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 5/91 (5%)

Query: 104 RFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-----RHDFTTF 158
            F    R+ +Y++          + R W +P++    +   A   LV       H++  F
Sbjct: 30  TFHDKARNRVYKLNDHNIAKLFVRPRGWHLPEAHILIDGEPATSCLVDFGLYFYHNYAAF 89

Query: 159 RSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           R    + S P   +   + +    +      
Sbjct: 90  RRTQGEGSGPFFYLPKMEHSREAKIWNCVFE 120


  Database: nr
    Posted date:  May 22, 2011 12:22 AM
  Number of letters in database: 999,999,966
  Number of sequences in database:  2,987,313
  
  Database: /data/usr2/db/fasta/nr.01
    Posted date:  May 22, 2011 12:30 AM
  Number of letters in database: 999,999,796
  Number of sequences in database:  2,903,041
  
  Database: /data/usr2/db/fasta/nr.02
    Posted date:  May 22, 2011 12:36 AM
  Number of letters in database: 999,999,281
  Number of sequences in database:  2,904,016
  
  Database: /data/usr2/db/fasta/nr.03
    Posted date:  May 22, 2011 12:41 AM
  Number of letters in database: 999,999,960
  Number of sequences in database:  2,935,328
  
  Database: /data/usr2/db/fasta/nr.04
    Posted date:  May 22, 2011 12:46 AM
  Number of letters in database: 842,794,627
  Number of sequences in database:  2,394,679
  
Lambda     K      H
   0.315    0.158    0.504 

Lambda     K      H
   0.267   0.0483    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,066,952,271
Number of Sequences: 14124377
Number of extensions: 210147784
Number of successful extensions: 726109
Number of sequences better than 10.0: 3400
Number of HSP's better than 10.0 without gapping: 5659
Number of HSP's successfully gapped in prelim test: 809
Number of HSP's that attempted gapping in prelim test: 704098
Number of HSP's gapped (non-prelim): 7348
length of query: 247
length of database: 4,842,793,630
effective HSP length: 135
effective length of query: 112
effective length of database: 2,936,002,735
effective search space: 328832306320
effective search space used: 328832306320
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (20.8 bits)
S2: 80 (35.2 bits)